@article {70284, title = {Astrocyte-induced internal state transitions reshape brainwide sensory, integrative, and motor computations}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 05}, abstract = {

Animals rapidly adapt to changing circumstances by shifting how they perceive, integrate, and act. Such flexibility is often attributed to transitions between internal states that exert widespread influence across the brain. Yet the mechanisms that drive state transitions and how they reconfigure brainwide computation remain unclear. Larval zebrafish, when actions are rendered futile by decoupling visual flow feedback from swimming in virtual reality, enter a temporary passive, energy-preserving state. In this state, astrocyte calcium levels are elevated, and swim reinitiation requires greater accumulated visual motion. Using whole-brain, cellular-resolution activity imaging, we observed widespread circuit alterations underlying this disengaged state: neuronal visual responses weakened, visual motion integration over time became dramatically leakier, motor inhibition increased, and motor preparation slowed, together suppressing conversion of sensory evidence into action. Astrocyte calcium rose during futile swimming, tracked the emergence and resolution of these brainwide changes, and was both necessary and sufficient to drive them. Thus, astrocytes orchestrate internal states that profoundly reshape neural computations, most powerfully at intermediate integrative processing stages, to meet changing demands.

}, doi = {10.64898/2026.02.05.704034}, url = {https://www.biorxiv.org/content/early/2026/02/05/2026.02.05.704034}, author = {Lim, Jing-Xuan and Wei, Ziqiang and Narayan, Sujatha and Zhang, Yan and Hasseman, Jeremy P. and Kolb, Ilya and Zheng, Jihong and Sheikhattar, Alireza and Mi, Xuelong and Zheng, Wei and Yang, Xueying and Beriashvili, Mariam and Fleishman, Greg and Wee, Caroline L. and de Zeeuw, Chris and Yu, Guoqiang and Babadi, Behtash and Rubinov, Mikail and Looger, Loren L. and Bergles, Dwight E. and Fitzgerald, James E. and Ahrens, Misha B.} } @article {69864, title = {Abstract 2420: Deep learning enables automated detection of circulating tumor cell-immune cell interactions with prognostic insights in cancer}, journal = {Cancer Research}, volume = {85}, year = {2025}, month = {2025 Apr 21}, pages = {2420-2420}, abstract = {

Circulating tumor cells (CTCs) are critical biomarkers for predicting therapy response and survival in breast cancer patients. Multicellular CTC clusters exhibit enhanced metastatic potential, yet their detection and characterization are constrained by low frequency in blood samples and reliance on labor-intensive manual analysis. Advancing these methods could significantly improve prognostic evaluation and therapeutic strategies.Leveraging FDA-approved CellSearch technology and single-cell sequencing, we analyzed 2, 853 blood specimens, longitudinally collected from 1358 patients with advanced cancer (breast, prostate, etc) and other diseases. Integrating machine learning and deep learning tools, we developed a novel CTCpose platform to automate detection and analysis of CTCs, immune cells, and their interactions. Using artificial intelligence (AI)-driven image analysis, we extracted over 270 cellular and nuclear features including intensity, morphometry, fourier shape, gradient/edge, and haralick of cytokeratin, CD45, and DAPI expression patterns, enabling precise characterization of CTCs, white blood cells (WBCs), CTC clusters, and their interactions with immune cells (WBCs).The CTCpose platform enabled automated identification of CTCs, WBCs, homotypic CTC clusters, heterogenous CTC-WBC clusters, and immune cell clusters, providing comprehensive insights into cell morphology, biomarker expression, and spatial organization. These features correlated with patient survival, disease progression, and treatment response. Our findings highlight the clinical significance of CTC-immune cell interactions and dynamic alterations of CTCs (singles and clusters) and underscore their potential in stratifying patients into distinct risk categories.This study demonstrates the transformative potential of deep learning in overcoming limitations of traditional CTC detection methods and integrating imaging data with large cohorts of patient data. By automating and enhancing the analysis of CTC-immune cell interactions, we present a robust framework for developing predictive models with direct clinical relevance. This work opens avenues for personalized treatment strategies, underscoring the impact of AI in advancing precision oncology.Yuanfei Sun, Joshua R. Squires, Andrew Hoffmann, Youbin Zhang, Allegra Minor, Anmol Singh, David Scholten, Chengsheng Mao, Yuan Luo, Deyu Fang, William J. Gradishar, Massimo Cristofanilli, Carsen Stringer, Huiping Liu. Deep learning enables automated detection of circulating tumor cell-immune cell interactions with prognostic insights in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2420.

}, issn = {0008-5472}, doi = {10.1158/1538-7445.AM2025-2420}, url = {https://doi.org/10.1158/1538-7445.AM2025-2420}, author = {Sun, Yuanfei and Squires, Joshua R. and Hoffmann, Andrew and Zhang, Youbin and Minor, Allegra and Singh, Anmol and Scholten, David and Mao, Chengsheng and Luo, Yuan and Fang, Deyu and Gradishar, William J. and Cristofanilli, Massimo and Stringer, Carsen and Liu, Huiping} } @article {70023, title = {Abstract B049: Deep learning enables identification of cell types and clusters (iCTC) in immune tumor ecosystems for prognostic assessment in cancer}, journal = {Clinical Cancer Research}, volume = {31}, year = {2025}, month = {2025 Jul 10}, pages = {B049-B049}, abstract = {

Spatial multiomic profiling has been transforming the understanding of local tumor ecosystems. Yet, the spatial analyses of tumor-immune interactions at systemic levels, such as in liquid biopsies, are challenging. Within the last 10 years, we have longitudinally collected nearly 3,000 patient blood samples for multiplexing imaging of circulating tumor cells (CTCs) and their interactions with white blood cells (WBCs). Multicellular CTC clusters exhibit enhanced metastatic potential. The detection of CTCs and characterization of tumor immune ecosystems are constrained by (1) low frequency of CTCs in blood samples; (2) specific lineages of immune cells are not recognized by limited channels of current imaging methods, (3) reliance on labor-intensive manual analysis slows down the discovery of biomarkers for predicting therapy response and survival in cancer patients. We hypothesize that an AI-powered platform will accelerate the lineage and spatial characterization of tumor immune ecosystems for prognostic evaluations.

}, issn = {1078-0432}, doi = {10.1158/1557-3265.AIMACHINE-B049}, url = {https://doi.org/10.1158/1557-3265.AIMACHINE-B049}, author = {Squires, Joshua R. and Sun, Yuanfei and Hoffmann, Andrew D. and Zhang, Youbin and Minor, Allegra C. and Singh, Anmol and Scholten, David and Ding, Hannah and Mao, Chengsheng and Platanias, Leonidas C. and Luo, Yuan and Fang, Deyu and Gradishar, William J. and Cristofanilli, Massimo and Stringer, Carsen and Liu, Huiping} } @article {69948, title = {Accelerating neuron reconstruction with PATHFINDER}, journal = {bioRxiv}, year = {2025}, month = {2025 May 21}, abstract = {

Comprehensive mapping of neural connections is essential for understanding brain function. Existing automated methods for connectome reconstruction from high-resolution images of brain tissue introduce errors that require extensive and time-consuming manual correction, a critical bottleneck in the field. To address this, we developed PATHFINDER, an AI system that segments volumetric image data, identifies potential ways to assemble neuron fragments, and evaluates the plausibility of resulting shapes to reconstruct complete neurons. Using a dataset of all axons in an IBEAM-mSEM volume of mouse cortex, we show that PATHFINDER reduces the error rate in axon reconstruction by an order of magnitude over previous state of the art, leading to an improvement in proofreading throughput of up to 84{\texttimes} relative to prior estimates in the context of a whole mouse brain. By drastically reducing the manual effort required for analysis, this advance unlocks the potential for both large-scale connectome mapping and routine investigation of smaller volumes.

}, doi = {10.1101/2025.05.16.654254}, url = {https://www.biorxiv.org/content/early/2025/05/21/2025.05.16.654254}, author = {Januszewski, Micha{\l} and Templier, Thomas and Hayworth, Kenneth Jeffrey and Peale, David and Hess, Harald} } @article {69560, title = {Activity-dependent synapse elimination requires caspase-3 activation}, journal = {eLife}, year = {2025}, month = {2025 Jul 10}, abstract = {

During brain development, synapses are initially formed in excess and are later eliminated in an activity-dependent manner, with weak synapses being preferentially removed. Previous studies identified glia as mediators of synapse removal, but it is unclear how glia specifically target weak synapses. Here we show that, in the developing mouse visual pathway, inhibiting synaptic transmission induces postsynaptic activation of caspase-3. Caspase-3 is essential for synapse elimination driven by both spontaneous and experience-dependent neural activity. Synapse weakening-induced caspase-3 activation determines the specificity of synapse elimination mediated by microglia but not astrocytes. Furthermore, in a mouse model of Alzheimer{\textquoteright}s disease, caspase-3 deficiency protects against synapse loss induced by amyloid-β deposition. Our results reveal caspase-3 activation as a key step in activity-dependent synapse elimination during development and synapse loss in neurodegeneration.

bioRxiv preprint:\ https://doi.org/10.1101/2024.08.02.606316

}, doi = {10.7554/eLife.101779.2}, url = {https://doi.org/10.7554/eLife.101779.2}, author = {Yu, Zhou and Gutu, Andrian and Kim, Namsoo and O{\textquoteright}Shea, Erin K.} } @article {70014, title = {Aggression across sexes from a contextual- and circuit-based perspective.}, journal = {Curr Opin Neurobiol}, volume = {93}, year = {2025}, month = {2025 Jun 26}, pages = {103071}, abstract = {

Often referred to as a {\textquoteright}fight,{\textquoteright} survival involves intense competition over resources. Threat displays and high-intensity attacks are just a few of the aggressive actions exhibited during these contests. Certain motor programs are species-specific, like the vibration of a rattlesnake tail. However, conserved behavioral features are found across species, which appear to be mirrored within the brain. Further parallels have been found across sexes between aggression-promoting contexts and the underlying neuronal circuits. Unraveling the complex web of conserved and variable circuit mechanisms has been considerably advanced by the generation of brain-wiring diagrams in adult female and male Drosophila melanogaster. Here, I will summarize current research, primarily in Drosophila, on how contexts, sensory cues, and internal states regulate aggression across sexes.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2025.103071}, url = {https://doi.org/10.1016/j.conb.2025.103071}, author = {Schretter, Catherine E} } @article {70129, title = {Alternating angle milling suppresses streaking artifacts in FIB-SEM imaging}, journal = {bioRxiv}, year = {2025}, month = {2025 Sep 26}, abstract = {

Focused ion beam scanning electron microscopy (FIB-SEM) (1{\textendash}3) has been used in life sciences to produce large volumetric datasets with high resolution information on ultrastructure of biological organisms. 3D image acquisition is accomplished by serial removal of thin layers of material using focused ion beam (FIB) milling followed by scanning electron microscopy (SEM) imaging.One of the challenges in the standard FIB-SEM imaging protocol is that FIB milling results in characteristic artifacts, known as {\textquotedblleft}streaks{\textquotedblright} or {\textquotedblleft}curtains{\textquotedblright}. These streaks are caused by non-uniform material removal forming long straight trenches parallel to the FIB milling direction. These artifacts get worse along the milling direction and ultimately limit size of the SEM field of view.Various methods have been proposed to mitigate the streaks in acquired images. While these techniques often provide noticeable visual improvement, the underlying problem remains. The structural information in the {\textquotedblleft}streaked{\textquotedblright} areas is lost due to non-uniform material removal during milling and cannot be fully recovered.We propose a simple modification allowing for a significant reduction of milling non-uniformities of streaks. We demonstrate the effectiveness of this approach on various samples.

}, doi = {10.1101/2025.09.25.678572}, url = {https://www.biorxiv.org/content/early/2025/09/26/2025.09.25.678572}, author = {Shtengel, Gleb and Qiu, Wei and Aaron, Jesse and Crowe, Arthur S. and Polilov, Alexey A. and Karkali, Katerina and Bleck, Christopher K.E. and Hess, Harald H.} } @article {69974, title = {Analysis of deep learning for automated recognition of immune cells interacting with CTCs for prognostic assessment in cancer.}, journal = {Journal of Clinical Oncology}, volume = {43}, year = {2025}, month = {2025 May 28}, pages = {e13028-e13028}, abstract = {

e13028Background: Liquid biopsy has emerged as a powerful, minimally invasive tool for predicting treatment response and survival in breast and other advanced cancers. However, the detection and characterization of circulating tumor cells (CTCs) {\textemdash} a key factor in metastatic progression{\textemdash}remain challenging due to their low frequency and reliance on manual, time-intensive validation using only a couple of established methods for immunofluorescence staining, such as CellSearch. Harnessing deep learning for automated CTC detection and characterization of the blood cells interacting with CTCs holds the potential to advance prognostic evaluations and guide more effective therapies significantly. Methods: Leveraging FDA-approved CellSearch technology and sequencing approaches, we analyzed 2,853 blood specimens, longitudinally collected from 1358 patients with advanced cancer (breast, prostate, etc) and additional diseases. We built a novel deep learning platform, CTCpose, which integrates machine learning and AI-driven image analysis to automate the detection and categorization of CTCs, white blood cells (WBCs), and their clustering interactions. We extracted cellular and nuclear features to enable precise evaluation of individual CTCs, WBCs, homotypic CTC clusters, heterotypic CTC{\textendash}WBC clusters, and immune cell aggregates. Results: By employing the CTCpose platform, we achieved fully automated identification of CTCs and immune cells, unraveling the spatial organization and functional characteristics of both homotypic and heterotypic clusters. These highly granular assessments revealed clinically significant correlations with patient survival, disease progression, and therapeutic outcomes. Our data underscore the critical role of CTC{\textendash}immune cell interactions and the dynamic shifts in CTC phenotypes{\textemdash}both as single cells and clusters{\textemdash}in stratifying patients by risk and informing treatment strategies. Conclusions: This work illustrates the transformative power of deep learning in the analysis of liquid biopsy samples. By overcoming the limitations of traditional CTC detection, we have established a robust framework that integrates imaging data with large-scale patient cohorts to deliver predictive models of high clinical relevance. The CTCpose platform not only refines our understanding of CTC{\textendash}immune cell biology but also paves the way for personalized oncology approaches, highlighting the impactful convergence of artificial intelligence and precision medicine.

}, doi = {10.1200/JCO.2025.43.16_suppl.e13028}, url = {https://ascopubs.org/doi/abs/10.1200/JCO.2025.43.16_suppl.e13028}, author = {Liu, Huiping and Squires, Joshua and Sun, Yuanfei and Hoffmann, Andrew Daniel and Zhang, Youbin and Platanias, Leonidas C. and Gradishar, William John and Cristofanilli, Massimo and Stringer, Carsen} } @article {70052, title = {Aurora 2.0: A fluorogenic dye library for expanding the capability of protein-adaptive Differential Scanning Fluorimetry (paDSF).}, journal = {SLAS Discov}, year = {2025}, month = {2025 Aug 8}, pages = {100259}, abstract = {

Differential Scanning Fluorimetry (DSF) is a biophysical assay that is used to estimate protein stability in vitro. In a DSF experiment, the increased fluorescence of a solvatochromatic dye, such as Sypro Orange, is used to detect the unfolding of a protein during heating. However, Sypro Orange is only compatible with a minority of proteins (\< 30\%), limiting the scope of this method. We recently reported that protein-adaptive DSF (paDSF) can partially solve this problem, wherein the protein is initially pre-screened against \~{}300 chemically diverse dyes, termed the Aurora collection. While this approach significantly improves the number of targets amenable to DSF, it still fails to produce protein-dye pairs for some proteins. Here, we report the expansion of the dye collection to Aurora 2.0, which includes a total of 517 structurally diverse molecules and multiple new chemotypes. To assess performance, these dyes were screened against a panel of \~{}100 proteins, which were selected, in part, to represent the most challenging targets (e.g. small size). From this effort, Aurora 2.0 achieved an impressive success rate of 94\%, including producing dyes for some targets that were not matched in the original collection. These findings support the idea that larger, more chemically diverse libraries improve the likelihood of detecting melting transitions across a wider range of proteins. We propose that Aurora 2.0 makes paDSF an increasingly powerful method for studying protein stability, ligand binding and other biophysical properties in high throughput.

}, issn = {2472-5560}, doi = {10.1016/j.slasd.2025.100259}, url = {https://doi.org/10.1016/j.slasd.2025.100259}, author = {Charvat, Annemarie F and Mason-Chalmers, Kayleigh and Grabinska-Rogala, Aneta and Shivakumar, Shloka and Gale-Day, Zachary and Wu, Taiasean and Millbern, Zoe and Grimm, Jonathan and Carroll, Emma C and Nilsson, Peter and Lavis, Luke and Vinueza, Nelson R and Gestwicki, Jason E} } @article {69594, title = {Activity of nested neural circuits drives different courtship songs in Drosophila.}, journal = {Nat Neurosci}, year = {2024}, month = {2024 Aug 28}, abstract = {

Motor systems implement diverse motor programs to pattern behavioral sequences, yet how different motor actions are controlled on a moment-by-moment basis remains unclear. Here, we investigated the neural circuit mechanisms underlying the control of distinct courtship songs in Drosophila. Courting males rapidly alternate between two types of song: pulse and sine. By recording calcium signals in the ventral nerve cord in singing flies, we found that one neural population is active during both songs, whereas an expanded neural population, which includes neurons from the first population, is active during pulse song. Brain recordings showed that this nested activation pattern is present in two descending pathways required for singing. Connectomic analysis reveals that these two descending pathways provide structured input to ventral nerve cord neurons in a manner consistent with their activation patterns. These results suggest that nested premotor circuit activity, directed by distinct descending signals, enables rapid switching between motor actions.

}, issn = {1546-1726}, doi = {10.1038/s41593-024-01738-9}, url = {https://doi.org/10.1038/s41593-024-01738-9}, author = {Shiozaki, Hiroshi M and Wang, Kaiyu and Lillvis, Joshua L and Xu, Min and Dickson, Barry J and Stern, David L} } @article {69424, title = {Adaptive optical third-harmonic generation microscopy for in vivo imaging of tissues}, journal = {bioRxiv}, year = {2024}, month = {2024 May 05}, abstract = {

Third-harmonic generation microscopy is a powerful label-free nonlinear imaging technique, providing essential information about structural characteristics of cells and tissues without requiring external labelling agents. In this work, we integrated a recently developed compact adaptive optics module into a third-harmonic generation microscope, to measure and correct for optical aberrations in complex tissues. Taking advantage of the high sensitivity of the third-harmonic generation process to material interfaces and thin membranes, along with the 1,300-nm excitation wavelength used here, our adaptive optical third-harmonic generation microscope enabled high-resolution in vivo imaging within highly scattering biological model systems. Examples include imaging of myelinated axons and vascular structures within the mouse spinal cord and deep cortical layers of the mouse brain, along with imaging of key anatomical features in the roots of the model plant Brachypodium distachyon. In all instances, aberration correction led to significant enhancements in image quality.

}, doi = {10.1101/2024.05.02.592275}, url = {https://www.biorxiv.org/content/early/2024/05/05/2024.05.02.592275}, author = {Cristina Rodr{\'\i}guez and Daisong Pan and Ryan G. Natan and Manuel A. Mohr and Max Miao and Xiaoke Chen and Trent R. Northen and John P. Vogel and Na Ji} } @article {69482, title = {Aging atlas reveals cell-type-specific effects of pro-longevity strategies.}, journal = {Nat Aging}, year = {2024}, month = {2024 May 30}, abstract = {

Organismal aging involves functional declines in both somatic and reproductive tissues. Multiple strategies have been discovered to extend lifespan across species. However, how age-related molecular changes differ among various tissues and how those lifespan-extending strategies slow tissue aging in distinct manners remain unclear. Here we generated the transcriptomic Cell Atlas of Worm Aging (CAWA, http://mengwanglab.org/atlas ) of wild-type and long-lived strains. We discovered cell-specific, age-related molecular and functional signatures across all somatic and germ cell types. We developed transcriptomic aging clocks for different tissues and quantitatively determined how three different pro-longevity strategies slow tissue aging distinctively. Furthermore, through genome-wide profiling of alternative polyadenylation (APA) events in different tissues, we discovered cell-type-specific APA changes during aging and revealed how these changes are differentially affected by the pro-longevity strategies. Together, this study offers fundamental molecular insights into both somatic and reproductive aging and provides a valuable resource for in-depth understanding of the diversity of pro-longevity mechanisms.

}, issn = {2662-8465}, doi = {10.1038/s43587-024-00631-1}, author = {Gao, Shihong Max and Qi, Yanyan and Zhang, Qinghao and Guan, Youchen and Lee, Yi-Tang and Ding, Lang and Wang, Lihua and Mohammed, Aaron S and Li, Hongjie and Fu, Yusi and Wang, Meng C} } @article {69642, title = {All-optical reporting of inhibitory receptor driving force in the nervous system}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Oct 16}, pages = {8913}, abstract = {

Ionic driving forces provide the net electromotive force for ion movement across receptors, channels, and transporters, and are a fundamental property of all cells. In the nervous system, fast synaptic inhibition is mediated by chloride permeable GABA and glycine receptors, and single-cell intracellular recordings have been the only method for estimating driving forces across these receptors (DF). Here we present a tool for quantifying inhibitory receptor driving force named ORCHID: all-Optical Reporting of CHloride Ion Driving force. We demonstrate ORCHID{\textquoteright}s ability to provide accurate, high-throughput measurements of resting and dynamic DF from genetically targeted cell types over multiple timescales. ORCHID confirms theoretical predictions about the biophysical mechanisms that establish DF, reveals differences in DF between neurons and astrocytes, and affords the first in vivo measurements of intact DF. This work extends our understanding of inhibitory synaptic transmission and demonstrates the potential for all-optical methods to assess ionic driving forces.

}, keywords = {Animals, Astrocytes, Chlorides, Humans, Male, Mice, Neurons, Receptors, GABA-A, Receptors, Glycine, Synaptic Transmission}, issn = {2041-1723}, doi = {10.1038/s41467-024-53074-y}, url = {https://doi.org/10.1038/s41467-024-53074-y}, author = {Selfe, Joshua S and Steyn, Teresa J S and Shorer, Eran F and Burman, Richard J and D{\"u}sterwald, Kira M and Kraitzick, Ariel Z and Abdelfattah, Ahmed S and Schreiter, Eric R and Newey, Sarah E and Akerman, Colin J and Raimondo, Joseph V} } @article {69315, title = {Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity}, journal = {Sci Adv}, volume = {10}, year = {2024}, month = {2024 Oct 18}, pages = {eadq0791}, abstract = {

Starvation triggers bacterial spore formation, a committed differentiation program that transforms a vegetative cell into a dormant spore. Cells in a population enter sporulation nonuniformly to secure against the possibility that favorable growth conditions, which put sporulation-committed cells at a disadvantage, may resume. This heterogeneous behavior is initiated by a passive mechanism: stochastic activation of a master transcriptional regulator. Here, we identify a cell-cell communication pathway containing the proteins ShfA (YabQ) and ShfP (YvnB) that actively promotes phenotypic heterogeneity, wherein Bacillus subtilis cells that start sporulating early use a calcineurin-like phosphoesterase to release glycerol, which simultaneously acts as a signaling molecule and a nutrient to delay nonsporulating cells from entering sporulation. This produced a more diverse population that was better poised to exploit a sudden influx of nutrients compared to those generating heterogeneity via stochastic gene expression alone. Although conflict systems are prevalent among microbes, genetically encoded cooperative behavior in unicellular organisms can evidently also boost inclusive fitness.

}, doi = {10.1126/sciadv.adq0791}, url = {https://doi.org/10.1126/sciadv.adq0791}, author = {Taylor B. Updegrove and Thomas Delerue and V. Anantharaman and Hyomoon Cho and Carissa Chan and Thomas Nipper and Hyoyoung Choo-Wosoba and Lisa Jenkins and Lixia Zhang and Yijun Su and Hari Shroff and Jiji Chen and Carole Bewley and L. Aravind and Kumaran S Ramamurthi} } @article {69371, title = {Amino acid transporter SLC7A5 regulates cell proliferation and secretary cell differentiation and distribution in the mouse intestine}, journal = {Int J Biol Sci}, volume = {20}, year = {2024}, month = {2024 Mar 25}, pages = {2187-2201}, abstract = {

The intestine is critical for not only processing nutrients but also protecting the organism from the environment. These functions are mainly carried out by the epithelium, which is constantly being self-renewed. Many genes and pathways can influence intestinal epithelial cell proliferation. Among them is mTORC1, whose activation increases cell proliferation. Here, we report the first intestinal epithelial cell (IEC)-specific knockout () of an amino acid transporter capable of activating mTORC1. We show that the transporter, SLC7A5, is highly expressed in mouse intestinal crypt and reduces mTORC1 signaling. Surprisingly, adult intestinal crypts have increased cell proliferation but reduced mature Paneth cells. Goblet cells, the other major secretory cell type in the small intestine, are increased in the crypts but reduced in the villi. Analyses with scRNA-seq and electron microscopy have revealed dedifferentiation of Paneth cells in mice, leading to markedly reduced secretory granules with little effect on Paneth cell number. Thus, SLC7A5 likely regulates secretory cell differentiation to affect stem cell niche and indirectly regulate cell proliferation.

}, keywords = {Amino Acid Transport Systems, Animals, Cell Differentiation, Cell Proliferation, Large Neutral Amino Acid-Transporter 1, Mechanistic Target of Rapamycin Complex 1, Mice}, issn = {1449-2288}, doi = {10.7150/ijbs.94297}, author = {Bao, Lingyu and Fu, Liezhen and Su, Yijun and Chen, Zuojia and Peng, Zhaoyi and Sun, Lulu and Gonzalez, Frank J and Wu, Chuan and Zhang, Hongen and Shi, Bingyin and Shi, Yun-Bo} } @article {69668, title = {Analysis methods for large-scale neuronal recordings.}, journal = {Science}, volume = {386}, year = {2024}, month = {2024 Nov 08}, pages = {eadp7429}, abstract = {

Simultaneous recordings from hundreds or thousands of neurons are becoming routine because of innovations in instrumentation, molecular tools, and data processing software. Such recordings can be analyzed with data science methods, but it is not immediately clear what methods to use or how to adapt them for neuroscience applications. We review, categorize, and illustrate diverse analysis methods for neural population recordings and describe how these methods have been used to make progress on longstanding questions in neuroscience. We review a variety of approaches, ranging from the mathematically simple to the complex, from exploratory to hypothesis-driven, and from recently developed to more established methods. We also illustrate some of the common statistical pitfalls in analyzing large-scale neural data.

}, keywords = {Action Potentials, Animals, Humans, Models, Neurological, Neurons, Neurosciences, Software}, issn = {1095-9203}, doi = {10.1126/science.adp7429}, author = {Stringer, Carsen and Pachitariu, Marius} } @article {69455, title = {Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos}, journal = {bioRxiv}, year = {2024}, month = {2024 May 16}, abstract = {

Regulation of transcription during embryogenesis is key to development and differentiation. To study transcript expression throughout Caenorhabditis elegans embryogenesis at single-molecule resolution, we developed a high-throughput single-molecule fluorescence in situ hybridization (smFISH) method that relies on computational methods to developmentally stage embryos and quantify individual mRNA molecules in single embryos. We applied our system to sdc-2, a zygotically transcribed gene essential for hermaphrodite development and dosage compensation. We found that sdc-2 is rapidly activated during early embryogenesis by increasing both the number of mRNAs produced per transcription site and the frequency of sites engaged in transcription. Knockdown of sdc-2 and dpy-27, a subunit of the dosage compensation complex (DCC), increased the number of active transcription sites for the X chromosomal gene dpy-23 but not the autosomal gene mdh-1, suggesting that the DCC reduces the frequency of dpy-23 transcription. The temporal resolution from in silico staging of embryos showed that the deletion of a single DCC recruitment element near the dpy-23 gene causes higher dpy-23 mRNA expression after the start of dosage compensation, which could not be resolved using mRNAseq from mixed-stage embryos. In summary, we have established a computational approach to quantify temporal regulation of transcription throughout C. elegans embryogenesis and demonstrated its potential to provide new insights into developmental gene regulation.

}, doi = {10.1101/2024.05.15.594414}, url = {https://www.biorxiv.org/content/early/2024/05/16/2024.05.15.594414}, author = {Breimann, Laura and Bahry, Ella and Zouinkhi, Marwan and Kolyvanov, Klim and Street, Lena Annika and Preibisch, Stephan and Ercan, Sevin{\c c}} } @article {69713, title = {Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos}, journal = {bioRxiv}, year = {2024}, month = {05/2024}, abstract = {

Regulation of transcription during embryogenesis is key to development and differentiation. To study transcript expression throughout Caenorhabditis elegans embryogenesis at single-molecule resolution, we developed a high-throughput single-molecule fluorescence in situ hybridization (smFISH) method that relies on computational methods to developmentally stage embryos and quantify individual mRNA molecules in single embryos. We applied our system to sdc-2, a zygotically transcribed gene essential for hermaphrodite development and dosage compensation. We found that sdc-2 is rapidly activated during early embryogenesis by increasing both the number of mRNAs produced per transcription site and the frequency of sites engaged in transcription. Knockdown of sdc-2 and dpy-27, a subunit of the dosage compensation complex (DCC), increased the number of active transcription sites for the X chromosomal gene dpy-23 but not the autosomal gene mdh-1, suggesting that the DCC reduces the frequency of dpy-23 transcription. The temporal resolution from in silico staging of embryos showed that the deletion of a single DCC recruitment element near the dpy-23 gene causes higher dpy-23 mRNA expression after the start of dosage compensation, which could not be resolved using mRNAseq from mixed-stage embryos. In summary, we have established a computational approach to quantify temporal regulation of transcription throughout C. elegans embryogenesis and demonstrated its potential to provide new insights into developmental gene regulation.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2024.05.15.594414}, url = {https://www.biorxiv.org/content/early/2024/05/16/2024.05.15.594414}, author = {Breimann, Laura and Bahry, Ella and Zouinkhi, Marwan and Kolyvanov, Klim and Street, Lena Annika and Preibisch, Stephan and Ercan, Sevin{\c c}} } @article {69284, title = {Analysis of meiotic recombination in Drosophila simulans shows heterozygous inversions do not cause an interchromosomal effect}, journal = {Genetics}, year = {2024}, month = {2024 May 19}, abstract = {

Chromosome inversions are of unique importance in the evolution of genomes and species because when heterozygous with a standard arrangement chromosome, they suppress meiotic crossovers within the inversion. In Drosophila species, heterozygous inversions also cause the interchromosomal effect, whereby the presence of a heterozygous inversion induces a dramatic increase in crossover frequencies in the remainder of the genome within a single meiosis. To date, the interchromosomal effect has been studied exclusively in species that also have high frequencies of inversions in wild populations. We took advantage of a recently developed approach for generating inversions in Drosophila simulans, a species that does not have inversions in wild populations, to ask if there is an interchromosomal effect. We used the existing chromosome 3R balancer and generated a new chromosome 2L balancer to assay for the interchromosomal effect genetically and cytologically. We found no evidence of an interchromosomal effect in D. simulans. To gain insight into the underlying mechanistic reasons, we qualitatively analyzed the relationship between meiotic double-strand break formation and synaptonemal complex assembly. We find that the synaptonemal complex is assembled prior to double-strand break formation as in D. melanogaster; however, we show that the synaptonemal complex is assembled prior to localization of the oocyte determination factor Orb, whereas in D. melanogaster, synaptonemal complex formation does not begin until Orb is localized. Together, our data show heterozygous inversions in D. simulans do not induce an interchromosomal effect and that there are differences in the developmental programming of the early stages of meiosis.

}, doi = {10.1093/genetics/iyae084}, author = {Bowen Man and Elizabeth Kim and Alekhya Vadlakonda and David L Stern and Nicole Crown} } @article {69657, title = {Anti-seizure effects of norepinephrine-induced free fatty acid release.}, journal = {Cell Metab}, year = {2024}, month = {2024 Oct 29}, abstract = {

The brain{\textquoteright}s ability to rapidly transition between sleep, quiet wakefulness, and states of high vigilance is remarkable. Cerebral norepinephrine (NE) plays a key role in promoting wakefulness, but how does the brain avoid neuronal hyperexcitability upon arousal? Here, we show that NE exposure results in the generation of free fatty acids (FFAs) within the plasma membrane from both astrocytes and neurons. In turn, FFAs dampen excitability by differentially modulating the activity of astrocytic and neuronal Na, K, ATPase. Direct application of FFA to the occipital cortex in awake, behaving mice dampened visual-evoked potential (VEP). Conversely, blocking FFA production via local application of a lipase inhibitor heightened VEP and triggered seizure-like activity. These results suggest that FFA release is a crucial step in NE signaling that safeguards against hyperexcitability. Targeting lipid-signaling pathways may offer a novel therapeutic approach for seizure prevention.

}, issn = {1932-7420}, doi = {10.1016/j.cmet.2024.10.011}, url = {https://doi.org/10.1016/j.cmet.2024.10.011}, author = {Li, Baoman and Sun, Qian and Ding, Fengfei and Xu, Qiwu and Kang, Ning and Xue, Yang and Ladron-de-Guevara, Antonio and Hirase, Hajime and Weikop, Pia and Gong, Sheng and Nathan, Smith and Nedergaard, Maiken} } @article {69249, title = {Architecture and flexibility of native kinetochores revealed by structural studies utilizing a thermophilic yeast}, journal = { Curr Biol}, volume = {S0960-9822}, year = {2024}, month = {2024 Aug 07}, pages = {00939-4}, abstract = {

Eukaryotic chromosome segregation requires kinetochores, multi-megadalton protein machines that assemble on the centromeres of chromosomes and mediate attachments to dynamic spindle microtubules. Kinetochores are built from numerous complexes, and there has been progress in structural studies on recombinant subassemblies. However, there is limited structural information on native kinetochore architecture. To address this, we purified functional, native kinetochores from the thermophilic yeast Kluyveromyces marxianus and examined them by electron microscopy (EM), cryoelectron tomography (cryo-ET), and atomic force microscopy (AFM). The kinetochores are extremely large, flexible assemblies that exhibit features consistent with prior models. We assigned kinetochore polarity by visualizing their interactions with microtubules and locating the microtubule binder, Ndc80c. This work shows that isolated kinetochores are more dynamic and complex than what might be anticipated based on the known structures of recombinant subassemblies and provides the foundation to study the global architecture and functions of kinetochores at a structural level.

}, doi = {10.1016/j.cub.2024.07.036}, url = {https://doi.org/10.1016/j.cub.2024.07.036}, author = {Daniel J. Barrero and Sithara S. Wijeratne and Xiaowei Zhao and Grace F. Cunningham and Rui Yan and Christian R. Nelson and Yasuhiro Arimura and Hironori Funabiki and Charles L. Asbury and Zhiheng Yu and Radhika Subramanian and Sue Biggins} } @article {69641, title = {Assembloid model to study loop circuits of the human nervous system}, journal = {bioRxiv}, year = {2024}, month = {2024 Oct 14}, abstract = {

Neural circuits connecting the cerebral cortex, the basal ganglia and the thalamus are fundamental networks for sensorimotor processing and their dysfunction has been consistently implicated in neuropsychiatric disorders1-9. These recursive, loop circuits have been investigated in animal models and by clinical neuroimaging, however, direct functional access to developing human neurons forming these networks has been limited. Here, we use human pluripotent stem cells to reconstruct an in vitro cortico-striatal-thalamic-cortical circuit by creating a four-part loop assembloid. More specifically, we generate regionalized neural organoids that resemble the key elements of the cortico-striatal-thalamic-cortical circuit, and functionally integrate them into loop assembloids using custom 3D-printed biocompatible wells. Volumetric and mesoscale calcium imaging, as well as extracellular recordings from individual parts of these assembloids reveal the emergence of synchronized patterns of neuronal activity. In addition, a multi{\textendash}step rabies retrograde tracing approach demonstrate the formation of neuronal connectivity across the network in loop assembloids. Lastly, we apply this system to study heterozygous loss of ASH1L gene associated with autism spectrum disorder and Tourette syndrome and discover aberrant synchronized activity in disease model assembloids. Taken together, this human multi-cellular platform will facilitate functional investigations of the cortico-striatal-thalamic-cortical circuit in the context of early human development and in disease conditions.

}, doi = {10.1101/2024.10.13.617729}, url = {https://doi.org/10.1101/2024.10.13.617729}, author = {Miura, Yuki and Kim, Ji-il and Jurjut, Ovidiu and Kelley, Kevin W. and Yang, Xiao and Chen, Xiaoyu and Thete, Mayuri Vijay and Revah, Omer and Cui, Bianxiao and Pachitariu, Marius and Pasca, Sergiu P.} } @article {69255, title = {Assessing the impact of Brd2 depletion on chromatin compartmentalization}, journal = {bioRxiv}, year = {2024}, month = {2024 Mar 6}, abstract = {

Recent insights into genome organization have emphasized the importance of A/B chromatin compartments. While our previous research showed that Brd2 depletion weakens compartment boundaries and promotes A/B mixing 1, Hinojosa-Gonzalez et al.2 were unable to replicate the findings. In response, we revisited our Micro-C data and successfully replicated the original results using the default parameters in the cooltools software package. We show that, after correcting inconsistencies with the selection and phasing of the compartment profiles, the decrease in B compartment strength persists but the change in compartment identity is to a much lesser extent than originally reported. To further assess the regulatory role of Brd2, we used saddle plots to determine the strength of compartmentalization and observed a consistent decrease of compartment strength especially at B compartments upon Brd2 depletion. This study highlights the importance of selecting appropriate parameters and analytical tools for compartment analysis and carefully interpreting the results.

}, doi = {10.1101/2024.03.02.583085}, url = {https://www.biorxiv.org/content/early/2024/03/06/2024.03.02.583085}, author = {Advait Athreya and Liangqi Xie and Robert Tjian and Bin Zhang and Zhe J. Liu} } @article {69454, title = {Astrocyte Calcium Signaling}, journal = {Cold Spring Harb Perspect Biol}, year = {2024}, month = {2024 May 20}, abstract = {

Astrocytes are predominant glial cells that tile the central nervous system and participate in well-established functional and morphological interactions with neurons, blood vessels, and other glia. These ubiquitous cells display rich intracellular Ca signaling, which has now been studied for over 30 years. In this review, we provide a summary and perspective of recent progress concerning the study of astrocyte intracellular Ca signaling as well as discussion of its potential functions. Progress has occurred in the areas of imaging, silencing, activating, and analyzing astrocyte Ca signals. These insights have collectively permitted exploration of the relationships of astrocyte Ca signals to neural circuit function and behavior in a variety of species. We summarize these aspects along with a framework for mechanistically interpreting behavioral studies to identify directly causal effects. We finish by providing a perspective on new avenues of research concerning astrocyte Ca signaling.

}, issn = {1943-0264}, doi = {10.1101/cshperspect.a041353}, author = {Ahrens, Misha B and Khakh, Baljit S and Poskanzer, Kira E} } @article {68519, title = {ACC neural ensemble dynamics are structured by strategy prevalence}, journal = {eLife}, year = {2023}, month = {2023 Nov 22}, abstract = {

Medial frontal cortical areas are thought to play a critical role in the brain{\textquoteright}s ability to flexibly deploy strategies that are effective in complex settings. Still, the specific circuit computations that underpin this foundational aspect of intelligence remain unclear. Here, by examining neural ensemble activity in rats that sample different strategies in a self-guided search for latent task structure, we demonstrate a robust tracking of individual strategy prevalence in the anterior cingulate cortex (ACC), especially in an area homologous to primate area 32D. Prevalence encoding in the ACC is wide-scale, independent of reward delivery, and persists through a substantial ensemble reorganization that tags ACC representations with contextual content. Our findings argue that ACC ensemble dynamics is structured by a summary statistic of recent behavioral choices, raising the possibility that ACC plays a role in estimating - through statistical learning - which actions promote the occurrence of events in the environment.

}, doi = {10.7554/eLife.84897}, url = {https://doi.org/10.7554/eLife.84897}, author = {Mikhail Proskurin and Maxim Manakov and Alla Y. Karpova} } @article {68967, title = {All-optical reporting of chloride ion driving force in the nervous system}, journal = {bioRxiv}, year = {2023}, month = {2023 Sep 01}, abstract = {

Ionic driving forces provide the net electromotive force for ion movement across membranes and are therefore a fundamental property of all cells. In the nervous system, chloride driving force (DFCl) determines inhibitory signaling, as fast synaptic inhibition is mediated by chloride-permeable GABAA\ and glycine receptors. Here we present a new tool for all-Optical Reporting of CHloride Ion Driving force (ORCHID). We demonstrate ORCHID{\textquoteright}s ability to provide accurate, high-throughput measurements of resting and dynamic DFCl\ from genetically targeted cell types over a range of timescales. ORCHID confirms theoretical predictions about the biophysical mechanisms that establish DFCl, reveals novel differences in DFCl\ between neurons and astrocytes under different network conditions, and affords the first\ in vivo\ measurements of intact DFCl\ in mouse cortical neurons. This work extends our understanding of chloride homeostasis and inhibitory synaptic transmission and establishes a precedent for utilizing all-optical methods to assess ionic driving force.

}, doi = {10.1101/2023.08.30.555464}, url = {https://doi.org/10.1101/2023.08.30.555464}, author = {Joshua S. Selfe and Teresa J. S. Steyn and Eran F. Shorer and Richard J. Burman and Kira M. D{\"u}sterwald and Ahmed S. Abdelfattah and Eric R. Schreiter and Sarah E. Newey and Colin J. Akerman and Joseph V. Raimondo} } @article {69090, title = {All-optical reporting of inhibitory receptor driving force in the nervous system.}, journal = {bioRxiv}, year = {2023}, month = {2023 Nov 20}, abstract = {

Ionic driving forces provide the net electromotive force for ion movement across receptors, channels, and transporters, and are a fundamental property of all cells. In the brain for example, fast synaptic inhibition is mediated by chloride permeable GABAA receptors, and single-cell intracellular recordings have been the only method for estimating driving forces across these receptors (DFGABAA). Here we present a new tool for quantifying inhibitory receptor driving force named ORCHID: all-Optical Reporting of CHloride Ion Driving force. We demonstrate ORCHID{\textquoteright}s ability to provide accurate, high-throughput measurements of resting and dynamic DFGABAA from genetically targeted cell types over multiple timescales. ORCHID confirms theoretical predictions about the biophysical mechanisms that establish DFGABAA, reveals novel differences in DFGABAA between neurons and astrocytes, and affords the first\ in vivo\ measurements of intact DFGABAA. This work extends our understanding of inhibitory synaptic transmission and establishes a precedent for all-optical methods to assess ionic driving forces.

}, doi = {10.1101/2023.08.30.555464}, url = {https://doi.org/10.1101/2023.08.30.555464}, author = {Joshua S. Selfe and Teresa J. S. Steyn and Eran F. Shorer and Richard J. Burman and Kira M. D{\"u}sterwald and Ahmed S. Abdelfattah and Eric R. Schreiter and Sarah E. Newey and Colin J. Akerman and Joseph V. Raimondo} } @article {69137, title = {Anatomically distributed neural representations of instincts in the hypothalamus.}, journal = {bioRxiv}, year = {2023}, month = {2023 Dec 07}, abstract = {

Artificial activation of anatomically localized, genetically defined hypothalamic neuron populations is known to trigger distinct innate behaviors, suggesting a hypothalamic nucleus-centered organization of behavior control. To assess whether the encoding of behavior is similarly anatomically confined, we performed simultaneous neuron recordings across twenty hypothalamic regions in freely moving animals. Here we show that distinct but anatomically distributed neuron ensembles encode the social and fear behavior classes, primarily through mixed selectivity. While behavior class-encoding ensembles were spatially distributed, individual ensembles exhibited strong localization bias. Encoding models identified that behavior actions, but not motion-related variables, explained a large fraction of hypothalamic neuron activity variance. These results identify unexpected complexity in the hypothalamic encoding of instincts and provide a foundation for understanding the role of distributed neural representations in the expression of behaviors driven by hardwired circuits.

}, doi = {10.1101/2023.11.21.568163}, url = {https://doi.org/10.1101/2023.11.21.568163}, author = {Stagkourakis, Stefanos and Spigolon, Giada and Marks, Markus and Feyder, Michael and Kim, Joseph and Perona, Pietro and Pachitariu, Marius and Anderson, David J} } @article {68807, title = {Architecture and dynamics of a desmosome-endoplasmic reticulum complex.}, journal = {Nature Cell Biology}, volume = {25}, year = {2023}, month = {2023 Jun 16}, pages = {823-835}, abstract = {

The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signalling and lipid transfer. Here, using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometre proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization, mobility and expression of ER stress transcripts. These findings indicate that desmosomes and the keratin cytoskeleton regulate the distribution, function and dynamics of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.

}, keywords = {Cytoskeleton, Desmosomes, Endoplasmic Reticulum, Intermediate Filaments, Keratins}, issn = {1476-4679}, doi = {10.1038/s41556-023-01154-4}, author = {Bharathan, Navaneetha Krishnan and Giang, William and Hoffman, Coryn L and Aaron, Jesse S and Khuon, Satya and Chew, Teng-Leong and Preibisch, Stephan and Trautman, Eric T and Heinrich, Larissa and Bogovic, John and Bennett, Davis and Ackerman, David and Park, Woohyun and Petruncio, Alyson and Weigel, Aubrey V and Saalfeld, Stephan and Wayne Vogl, A and Stahley, Sara N and Kowalczyk, Andrew P} } @article {67907, title = {Ascending neurons convey behavioral state to integrative sensory and action selection centers in the brain}, journal = {Nature Neuroscience}, year = {2023}, month = {2023 Mar 31}, abstract = {

Knowledge of one{\textquoteright}s own behavioral state{\textemdash}whether one is walking, grooming, or resting{\textemdash}is critical for contextualizing sensory cues including interpreting visual motion and tracking odor sources. Additionally, awareness of one{\textquoteright}s own posture is important to avoid initiating destabilizing or physically impossible actions. Ascending neurons (ANs), interneurons in the vertebrate spinal cord or insect ventral nerve cord (VNC) that project to the brain, may provide such high-fidelity behavioral state signals. However, little is known about what ANs encode and where they convey signals in any brain. To address this gap, we performed a large-scale functional screen of AN movement encoding, brain targeting, and motor system patterning in the adult fly,\ Drosophila melanogaster. Using a new library of AN sparse driver lines, we measured the functional properties of 247 genetically-identifiable ANs by performing two-photon microscopy recordings of neural activity in tethered, behaving flies. Quantitative, deep network-based neural and behavioral analyses revealed that ANs nearly exclusively encode high-level behaviors{\textemdash}primarily walking as well as resting and grooming{\textemdash}rather than low-level joint or limb movements. ANs that convey self-motion{\textemdash}resting, walking, and responses to gust-like puff stimuli{\textemdash}project to the brain{\textquoteright}s anterior ventrolateral protocerebrum (AVLP), a multimodal, integrative sensory hub, while those that encode discrete actions{\textemdash}eye grooming, turning, and proboscis extension{\textemdash}project to the brain{\textquoteright}s gnathal ganglion (GNG), a locus for action selection. The structure and polarity of AN projections within the VNC are predictive of their functional encoding and imply that ANs participate in motor computations while also relaying state signals to the brain. Illustrative of this are ANs that temporally integrate proboscis extensions over tens-of-seconds, likely through recurrent interconnectivity. Thus, in line with long-held theoretical predictions, ascending populations convey high-level behavioral state signals almost exclusively to brain regions implicated in sensory feature contextualization and action selection.

}, doi = {10.1038/s41593-023-01281-z}, author = {Chin-Lin Chen and Florian Aymanns and Ryo Minegishi and Victor D. V. Matsuda and Nicolas Talabot and Semih G{\"u}nel and Barry J. Dickson and Pavan Ramdya} } @article {68587, title = {Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.}, journal = {Nature Biotechnology}, volume = {41}, year = {2023}, month = {2023 Jan 01}, pages = {44-49}, abstract = {

We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8\% of cell lineages spanning 1 h, as compared to 31.8\% for the competing method. Our approach improves understanding of where and when cell fate decisions are made in developing embryos, tissues, and organs.

}, keywords = {Animals, Blastocyst, Cell Lineage, Embryo, Mammalian, Mice, Microscopy}, issn = {1546-1696}, doi = {10.1038/s41587-022-01427-7}, author = {Malin-Mayor, Caroline and Hirsch, Peter and Guignard, Leo and McDole, Katie and Wan, Yinan and Lemon, William C and Kainmueller, Dagmar and Keller, Philipp J and Preibisch, Stephan and Funke, Jan} } @article {68787, title = {Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 May 18}, pages = {2855}, abstract = {

NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear functions for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We find that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription. Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation. Overall, here we uncover nuclear roles for NDP52 in gene expression and DNA structure regulation.

}, keywords = {Animals, Autophagy, DNA, Mammals, Nuclear Proteins, Nucleic Acid Conformation, RNA Polymerase II}, issn = {2041-1723}, doi = {10.1038/s41467-023-38572-9}, author = {Dos Santos, {\'A}lia and Rollins, Daniel E and Hari-Gupta, Yukti and McArthur, Hannah and Du, Mingxue and Ru, Sabrina Yong Zi and Pidlisna, Kseniia and Stranger, Ane and Lorgat, Faeeza and Lambert, Danielle and Brown, Ian and Howland, Kevin and Aaron, Jesse and Wang, Lin and Ellis, Peter J I and Chew, Teng-Leong and Martin-Fernandez, Marisa and Pyne, Alice L B and Toseland, Christopher P} } @article {68115, title = {Accurate angular integration with only a handful of neurons.}, journal = {bioRxiv}, year = {2022}, month = {2022 May 25}, abstract = {

To flexibly navigate, many animals rely on internal spatial representations that persist when the animal is standing still in darkness, and update accurately by integrating the animal{\textquoteright}s movements in the absence of localizing sensory cues. Theories of mammalian head direction cells have proposed that these dynamics can be realized in a special class of networks that maintain a localized bump of activity via structured recurrent connectivity, and that shift this bump of activity via angular velocity input. Although there are many different variants of these so-called ring attractor networks, they all rely on large numbers of neurons to generate representations that persist in the absence of input and accurately integrate angular velocity input. Surprisingly, in the fly,\ Drosophila melanogaster, a head direction representation is maintained by a much smaller number of neurons whose dynamics and connectivity resemble those of a ring attractor network. These findings challenge our understanding of ring attractors and their putative implementation in neural circuits. Here, we analyzed failures of angular velocity integration that emerge in small attractor networks with only a few computational units. Motivated by the peak performance of the fly head direction system in darkness, we mathematically derived conditions under which small networks, even with as few as 4 neurons, achieve the performance of much larger networks. The resulting description reveals that by appropriately tuning the network connectivity, the network can maintain persistent representations over the continuum of head directions, and it can accurately integrate angular velocity inputs. We then analytically determined how performance degrades as the connectivity deviates from this optimally-tuned setting, and we find a trade-off between network size and the tuning precision needed to achieve persistence and accurate integration. This work shows how even small networks can accurately track an animal{\textquoteright}s movements to guide navigation, and it informs our understanding of the functional capabilities of discrete systems more broadly.

}, doi = {10.1101/2022.05.23.493052}, url = {https://doi.org/10.1101/2022.05.23.493052}, author = {Marcella Noorman and Brad K Hulse and Vivek Jayaraman and Sandro Romani and Ann M Hermundstad} } @article {68045, title = {Actin nano-architecture of phagocytic podosomes}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {2022 Jul 27}, pages = {4363}, abstract = {

Podosomes are actin-enriched adhesion structures important for multiple cellular processes, including migration, bone remodeling, and phagocytosis. Here, we characterized the structure and organization of phagocytic podosomes using interferometric photoactivated localization microscopy (iPALM), a super-resolution microscopy technique capable of 15-20 nm resolution, together with structured illumination microscopy (SIM) and localization-based superresolution microscopy. Phagocytic podosomes were observed during frustrated phagocytosis, a model in which cells attempt to engulf micro-patterned IgG antibodies. For circular patterns, this resulted in regular arrays of podosomes with well-defined geometry. Using persistent homology, we developed a pipeline for semi-automatic identification and measurement of podosome features. These studies revealed an "hourglass" shape of the podosome actin core, a protruding "knob" at the bottom of the core, and two actin networks extending from the core. Additionally, the distributions of paxillin, talin, myosin II, α-actinin, cortactin, and microtubules relative to actin were characterized.

}, doi = {10.1101/2022.05.04.490675}, author = {J. Cody Herron and Shiqiong Hu and Takashi Watanabe and Ana T. Nogueira and Bei Liu and Megan Kern and Jesse Aaron and Aaron Taylor and Michael Pablo and Teng-Leong Chew and Timothy C. Elston and Klaus M. Hahn} } @article {68023, title = {Allosteric interactions prime androgen receptor dimerization and activation.}, journal = {Molecular Cell}, volume = {82}, year = {2022}, month = {2022 Jun 02}, pages = {2021-31}, abstract = {

The androgen receptor (AR) is a nuclear receptor that governs gene expression programs required for prostate development and male phenotype maintenance. Advanced prostate cancers display AR hyperactivation and transcriptome expansion, in part, through AR amplification and interaction with oncoprotein cofactors. Despite its biological importance, how AR domains and cofactors cooperate to bind DNA has remained elusive. Using single-particle cryo-electron microscopy, we isolated three conformations of AR bound to DNA, showing that AR forms a non-obligate dimer, with the buried dimer interface utilized by ancestral steroid receptors repurposed to facilitate cooperative DNA binding. We identify novel allosteric surfaces which are compromised in androgen insensitivity syndrome and reinforced by AR{\textquoteright}s oncoprotein cofactor, ERG, and by DNA-binding motifs. Finally, we present evidence that this plastic dimer interface may have been adopted for transactivation at the expense of DNA binding. Our work highlights how fine-tuning AR{\textquoteright}s cooperative interactions translate to consequences in development and disease.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2022.03.035}, author = {Wasmuth, Elizabeth V and Broeck, Arnaud Vanden and LaClair, Justin R and Hoover, Elizabeth A and Lawrence, Kayla E and Paknejad, Navid and Pappas, Kyrie and Matthies, Doreen and Wang, Biran and Feng, Weiran and Watson, Philip A and Zinder, John C and Karthaus, Wouter R and de la Cruz, M Jason and Hite, Richard K and Manova-Todorova, Katia and Yu, Zhiheng and Weintraub, Susan T and Klinge, Sebastian and Sawyers, Charles L} } @article {68193, title = {Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle}, journal = {bioRxiv}, year = {2022}, month = {2022 Jul 08}, abstract = {

The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.

}, doi = {10.1101/2022.07.07.499185}, url = {https://doi.org/10.1101/2022.07.07.499185}, author = {Navaneetha Krishnan Bharathan and William Giang and Jesse S. Aaron and Satya Khuon and Teng-Leong Chew and Stephan Preibisch and Eric T. Trautman and Larissa Heinrich and John Bogovic and Davis Bennett and David Ackerman and Woohyun Park and Alyson Petruncio and Aubrey V. Weigel and Stephan Saalfeld and COSEM Project Team and A. Wayne Vogl and Sara N. Stahley and Andrew P. Kowalczyk} } @article {68313, title = {Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.}, journal = {Nature Biotechnology}, year = {2022}, month = {2022 Sep 05}, abstract = {

We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8\% of cell lineages spanning 1 h, as compared to 31.8\% for the competing method. Our approach improves understanding of where and when cell fate decisions are made in developing embryos, tissues, and organs.

}, issn = {1546-1696}, doi = {10.1038/s41587-022-01427-7}, author = {Malin-Mayor, Caroline and Hirsch, Peter and Guignard, Leo and McDole, Katie and Wan, Yinan and Lemon, William C and Kainmueller, Dagmar and Keller, Philipp J and Preibisch, Stephan and Funke, Jan} } @article {65319, title = {Accurate localization of linear probe electrodes across multiple brains.}, journal = {eNeuro}, volume = {8}, year = {2021}, month = {2021 Nov 12}, pages = {ENEURO.0241-21.2021}, author = {Liu, Liu D. and Chen, Susu and Economo, Michael N. and Li, Nuo and Svoboda, Karel} } @article {66018, title = {An Acquired and Endogenous Glycocalyx Forms a Bidirectional {\textquotedblleft}Don{\textquoteright}t Eat{\textquotedblright} and {\textquotedblleft}Don{\textquoteright}t Eat Me{\textquotedblright} Barrier to Phagocytosis}, journal = {Current Biology}, volume = {31}, year = {2021}, month = {Jan-01-2021}, pages = {77 - 89.e5}, abstract = {

Macrophages continuously survey their environment in search of pathogens or apoptotic corpses or debris. Targets intended for clearance expose ligands that initiate their phagocytosis ("eat me" signals), while others avoid phagocytosis by displaying inhibitory ligands ("don{\textquoteright}t eat me" signals). We report that such ligands can be obscured by the glycosaminoglycans and glycoproteins that coat pathogenic as well as malignant phagocytic targets. In addition, a reciprocal barrier of self-synthesized or acquired glycocalyx components on the macrophage surface shrouds phagocytic receptors, curtailing their ability to engage particles. The coating layers of macrophages and their targets hinder phagocytosis by both steric and electrostatic means. Their removal by enzymatic means is shown to markedly enhance phagocytic efficiency. In particular, we show that the removal of mucins, which are overexpressed in cancer cells, facilitates their clearance. These results shed light on the physical barriers that modulate phagocytosis, which have been heretofore underappreciated.

}, issn = {09609822}, doi = {10.1016/j.cub.2020.09.082}, url = {https://www.sciencedirect.com/science/article/pii/S0960982220314950?via\%3Dihub}, author = {Imbert, Paul R.C. and Saric, Amra and Pedram, Kayvon and Bertozzi, Carolyn R. and Grinstein, Sergio and Freeman, Spencer A.} } @article {67177, title = {Actin cables and comet tails organize mitochondrial networks in mitosis.}, journal = {Nature}, volume = {591}, year = {2021}, month = {2021 Mar 03}, pages = {659-664}, abstract = {

Symmetric cell division requires the even partitioning of genetic information and cytoplasmic contents between daughter cells. Whereas the mechanisms coordinating the segregation of the genome are well known, the processes that ensure organelle segregation between daughter cells remain less well understood. Here we identify multiple actin assemblies with distinct but complementary roles in mitochondrial organization and inheritance in mitosis. First, we find a dense meshwork of subcortical actin cables assembled throughout the mitotic cytoplasm. This network scaffolds the endoplasmic reticulum and organizes three-dimensional mitochondrial positioning to ensure the equal segregation of mitochondrial mass at cytokinesis. Second, we identify a dynamic wave of actin filaments reversibly assembling on the surface of mitochondria during mitosis. Mitochondria sampled by this wave are enveloped within actin clouds that can spontaneously break symmetry to form elongated comet tails. Mitochondrial comet tails promote randomly directed bursts of movement that shuffle mitochondrial position within the mother cell to randomize inheritance of healthy and damaged mitochondria between daughter cells. Thus, parallel mechanisms mediated by the actin cytoskeleton ensure both equal and random inheritance of mitochondria in symmetrically dividing cells.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-03309-5}, author = {Moore, Andrew S and Coscia, Stephen M and Simpson, Cory L and Ortega, Fabian E and Wait, Eric C and Heddleston, John M and Nirschl, Jeffrey J and Obara, Christopher J and Guedes-Dias, Pedro and Boecker, C Alexander and Chew, Teng-Leong and Theriot, Julie A and Lippincott-Schwartz, Jennifer and Holzbaur, Erika L F} } @article {67304, title = {Activity-dependent Golgi satellite formation in dendrites reshapes the neuronal surface glycoproteome}, journal = {bioRxiv}, year = {2021}, month = {05/2021}, abstract = {

Activity-driven changes in the neuronal surface glycoproteome are known to occur with synapse formation, plasticity and related diseases, but their mechanistic basis and significance are unclear. Here, we observed that N-glycans on surface glycoproteins of dendrites shift from immature to mature forms containing sialic acid in response to increased neuronal excitation. In exploring the basis of these N-glycosylation alterations, we discovered they result from the growth and proliferation of Golgi satellites scattered throughout the dendrite. Golgi satellites that formed with neuronal excitation were in close association with ER exit sites and early endosomes and contained glycosylation machinery without the Golgi structural protein, GM130. They functioned as distal glycosylation stations in dendrites, terminally modifying sugars either on newly synthesized glycoproteins passing through the secretory pathway, or on surface glycoproteins taken up from the endocytic pathway. These activities led to major changes in the dendritic surface of excited neurons, impacting binding and uptake of lectins, as well as causing functional changes in neurotransmitter receptors such as nicotinic acetylcholine receptors. Neural activity thus boosts the activity of the dendrite{\textquoteright}s satellite micro-secretory system by redistributing Golgi enzymes involved in glycan modifications into peripheral Golgi satellites. This remodeling of the neuronal surface has potential significance for synaptic plasticity, addiction and disease.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.04.06.438745}, url = {https://doi.org/10.1101/2021.04.06.438745}, author = {Govind, Anitha P. and Jeyifous, Okunola and Russell, Theron A. and Yi, Zola and Weigel, Aubrey V. and Ramaprasad, Abhijit and Newell, Luke and Ramos, William and Valbuena, Fernando M. and Casler, Jason C. and Yan, Jing-Zhi and Glick, Benjamin S. and Swanson, Geoffrey T. and Lippincott-Schwartz, Jennifer and Green, William N.} } @article {67733, title = {Activity-dependent Golgi satellite formation in dendrites reshapes the neuronal surface glycoproteome.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Sep 21}, abstract = {

Activity-driven changes in the neuronal surface glycoproteome are known to occur with synapse formation, plasticity and related diseases, but their mechanistic basis and significance are unclear. Here, we observed that -glycans on surface glycoproteins of dendrites shift from immature to mature forms containing sialic acid in response to increased neuronal activation. In exploring the basis of these -glycosylation alterations, we discovered they result from the growth and proliferation of Golgi satellites scattered throughout the dendrite. Golgi satellites that formed during neuronal excitation were in close association with ER exit sites and early endosomes and contained glycosylation machinery without the Golgi structural protein, GM130. They functioned as distal glycosylation stations in dendrites, terminally modifying sugars either on newly synthesized glycoproteins passing through the secretory pathway, or on surface glycoproteins taken up from the endocytic pathway. These activities led to major changes in the dendritic surface of excited neurons, impacting binding and uptake of lectins, as well as causing functional changes in neurotransmitter receptors such as nicotinic acetylcholine receptors. Neural activity thus boosts the activity of the dendrite{\textquoteright}s satellite micro-secretory system by redistributing Golgi enzymes involved in glycan modifications into peripheral Golgi satellites. This remodeling of the neuronal surface has potential significance for synaptic plasticity, addiction and disease.

}, issn = {2050-084X}, doi = {10.7554/eLife.68910}, author = {Govind, Anitha P and Jeyifous, Okunola and Russell, Theron A and Yi, Zola and Weigel, Aubrey V and Ramaprasad, Abhijit and Newell, Luke and Ramos, William and Valbuena, Fernando M and Casler, Jason C and Yan, Jing-Zhi and Glick, Benjamin S and Swanson, Geoffrey T and Lippincott-Schwartz, Jennifer and Green, William N} } @article {67180, title = {Acupuncture modulates immunity in sepsis: Toward a science-based protocol.}, journal = {Autonomic Neuroscience}, volume = {232}, year = {2021}, month = {2021 Feb 27}, pages = {102793}, abstract = {

Sepsis is a serious medical condition in which immune dysfunction plays a key role. Previous treatments focused on chemotherapy to control immune function; however, a recognized effective compound or treatment has yet to be developed. Recent advances indicate that a neuromodulation approach with nerve stimulation allows developing a therapeutic strategy to control inflammation and improve organ functions in sepsis. As a quick, non-invasive technique of peripheral nerve stimulation, acupuncture has emerged as a promising therapy to provide significant advantages for immunomodulation in acute inflammation. Acupuncture obtains its regulatory effect by activating the somatic-autonomic-immune reflexes, including the somatic-sympathetic-splenic reflex, the somatic-sympathetic-adrenal reflex, the somatic-vagal-splenic reflex and the somatic-vagal-adrenal reflex, which produces a systemic effect. The peripheral nerve stimulation also induces local reflexes such as the somatic-sympathetic-lung-reflex, which then produces local effects. These mechanisms offer scientific guidance to design acupuncture protocols for immunomodulation and inflammation control, leading to an evidence-based comprehensive therapy recommendation.

}, issn = {1872-7484}, doi = {10.1016/j.autneu.2021.102793}, author = {Pan, Wei-Xing and Fan, Arthur Yin and Chen, Shaozong and Alemi, Sarah Faggert} } @article {65895, title = {An adaptive optics module for deep tissue multiphoton imaging in vivo}, journal = {Nature Methods}, year = {2021}, month = {2021 Oct 04}, pages = {1259-64}, abstract = {

Understanding complex biological systems requires visualizing structures and processes deep within living organisms. We developed a compact adaptive optics module and incorporated it into two- and three-photon fluorescence microscopes, to measure and correct tissue-induced aberrations. We resolved synaptic structures in deep cortical and subcortical areas of the mouse brain, and demonstrated high-resolution imaging of neuronal structures and somatosensory-evoked calcium responses in the mouse spinal cord at unprecedented depths\ in vivo.

}, doi = {10.1038/s41592-021-01279-0}, author = {Cristina Rodr{\'\i}guez and Anderson Chen and Jos{\'e} A. Rivera and Manuel A. Mohr and Yajie liang and Wenzhi Sun and Daniel E. Milkie and Thomas G. Bifano and Xiaoke Chen and Na Ji} } @article {67763, title = {An adaptive optics module for deep tissue multiphoton imaging in vivo.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Oct 01}, pages = {1259-1264}, abstract = {

Understanding complex biological systems requires visualizing structures and processes deep within living organisms. We developed a compact adaptive optics module and incorporated it into two- and three-photon fluorescence microscopes, to measure and correct tissue-induced aberrations. We resolved synaptic structures in deep cortical and subcortical areas of the mouse brain, and demonstrated high-resolution imaging of neuronal structures and somatosensory-evoked calcium responses in the mouse spinal cord at great depths in vivo.

}, issn = {1548-7105}, doi = {10.1038/s41592-021-01279-0}, author = {Rodriguez, Cristina and Chen, Anderson and Rivera, Jos{\'e} A and Mohr, Manuel A and Liang, Yajie and Natan, Ryan G and Sun, Wenzhi and Milkie, Daniel E and Bifano, Thomas G and Chen, Xiaoke and Ji, Na} } @article {67298, title = {Adhesion-mediated mechanosignaling forces mitohormesis.}, journal = {Cell Metabolism}, volume = {33}, year = {2021}, month = {2021 July 6}, pages = {1322}, abstract = {

Mitochondria control eukaryotic cell fate by producing the energy needed to support life and the signals required to execute programed cell death. The biochemical milieu is known to affect mitochondrial function and contribute to the dysfunctional mitochondrial phenotypes implicated in cancer and the morbidities of aging. However, the physical characteristics of the extracellular matrix are also altered in cancerous and aging tissues. Here, we demonstrate that cells sense the physical properties of the extracellular matrix and activate a mitochondrial stress response that adaptively tunes mitochondrial function via solute carrier family 9 member A1-dependent ion exchange and heat shock factor 1-dependent transcription. Overall, our data indicate that adhesion-mediated mechanosignaling may play an unappreciated role in the altered mitochondrial functions observed in aging and cancer.

}, issn = {1932-7420}, doi = {10.1016/j.cmet.2021.04.017}, author = {Tharp, Kevin M and Higuchi-Sanabria, Ryo and Timblin, Greg A and Ford, Breanna and Garzon-Coral, Carlos and Schneider, Catherine and Muncie, Jonathon M and Stashko, Connor and Daniele, Joseph R and Moore, Andrew S and Frankino, Phillip A and Homentcovschi, Stefan and Manoli, Sagar S and Shao, Hao and Richards, Alicia L and Chen, Kuei-Ho and Hoeve, Johanna Ten and Ku, Gregory M and Hellerstein, Marc and Nomura, Daniel K and Saijo, Karou and Gestwicki, Jason and Dunn, Alexander R and Krogan, Nevan J and Swaney, Danielle L and Dillin, Andrew and Weaver, Valerie M} } @article {67302, title = {Advances in Confocal Microscopy and Selected Applications.}, journal = {Methods in Molecular Biology}, volume = {2304}, year = {2021}, month = {2021 May 28}, pages = {1-35}, abstract = {

Over the last 30 years, confocal microscopy has emerged as a primary tool for biological investigation across many disciplines. The simplicity of use and widespread accessibility of confocal microscopy ensure that it will have a prominent place in biological imaging for many years to come, even with the recent advances in light sheet and field synthesis microscopy. Since these more advanced technologies still require significant expertise to effectively implement and carry through to analysis, confocal microscopy-based approaches still remain the easiest way for biologists with minimal imaging experience to address fundamental questions about how their systems are arranged through space and time. In this review, we discuss a number of advanced applications of confocal microscopy for probing the spatiotemporal dynamics of biological systems.

}, issn = {1940-6029}, doi = {10.1007/978-1-0716-1402-0_1}, author = {Reilly, W Matt and Obara, Christopher J} } @article {67299, title = {Algorithms underlying flexible phototaxis in larval zebrafish.}, journal = {Journal of Experimental Biology}, volume = {224}, year = {2021}, month = {2021 May 15}, abstract = {

To thrive, organisms must maintain physiological and environmental variables in suitable ranges. Given that these variables undergo constant fluctuations over varying time scales, how do biological control systems maintain control over these values? We explored this question in the context of phototactic behavior in larval zebrafish. We demonstrate that larval zebrafish use phototaxis to maintain environmental luminance at a set point, that the value of this set point fluctuates on a time scale of seconds when environmental luminance changes, and that it is determined by calculating the mean input across both sides of the visual field. These results expand on previous studies of flexible phototaxis in larval zebrafish; they suggest that larval zebrafish exert homeostatic control over the luminance of their surroundings, and that feedback from the surroundings drives allostatic changes to the luminance set point. As such, we describe a novel behavioral algorithm with which larval zebrafish exert control over a sensory variable.

}, issn = {1477-9145}, doi = {10.1242/jeb.238386}, author = {Chen, Alex B and Deb, Diptodip and Bahl, Armin and Engert, Florian} } @article {67314, title = {Alpha-1 adrenergic receptor antagonists to prevent hyperinflammation and death from lower respiratory tract infection.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Jun 11}, abstract = {

In severe viral pneumonia, including Coronavirus disease 2019 (COVID-19), the viral replication phase is often followed by hyperinflammation, which can lead to acute respiratory distress syndrome, multi-organ failure, and death. We previously demonstrated that alpha-1 adrenergic receptor (⍺-AR) antagonists can prevent hyperinflammation and death in mice. Here, we conducted retrospective analyses in two cohorts of patients with acute respiratory distress (ARD, n = 18,547) and three cohorts with pneumonia (n = 400,907). Federated across two ARD cohorts, we find that patients exposed to ⍺-AR antagonists, as compared to unexposed patients, had a 34\% relative risk reduction for mechanical ventilation and death (OR = 0.70, p = 0.021). We replicated these methods on three pneumonia cohorts, all with similar effects on both outcomes. All results were robust to sensitivity analyses. These results highlight the urgent need for prospective trials testing whether prophylactic use of ⍺-AR antagonists ameliorates lower respiratory tract infection-associated hyperinflammation and death, as observed in COVID-19.

}, issn = {2050-084X}, doi = {10.7554/eLife.61700}, author = {Koenecke, Allison and Powell, Michael and Xiong, Ruoxuan and Shen, Zhu and Fischer, Nicole and Huq, Sakibul and Khalafallah, Adham M and Trevisan, Marco and Sparen, P{\"a}r and Carrero, Juan J and Nishimura, Akihiko and Caffo, Brian and Stuart, Elizabeth A and Bai, Renyuan and Staedtke, Verena and Thomas, David L and Papadopoulos, Nickolas and Kinzler, Ken W and Vogelstein, Bert and Zhou, Shibin and Bettegowda, Chetan and Konig, Maximilian F and Mensh, Brett D and Vogelstein, Joshua T and Athey, Susan} } @article {67235, title = {The anterior cingulate cortex directs exploration of alternative strategies.}, journal = {Neuron}, volume = {109}, year = {2021}, month = {2021 Jun 2}, pages = {1876-87}, abstract = {

The ability to adjust one{\textquoteright}s behavioral strategy in complex environments is at the core of cognition. Doing so efficiently requires monitoring the reliability of the ongoing strategy and, when appropriate, switching away from it to evaluate alternatives. Studies in humans and non-human primates have uncovered signals in the anterior cingulate cortex (ACC) that reflect the pressure to switch away from the ongoing strategy, whereas other ACC signals relate to the pursuit of alternatives. However, whether these signals underlie computations that actually underpin strategy switching or merely reflect tracking of related variables remains unclear. Here we provide causal evidence that the rodent ACC actively arbitrates between persisting with the ongoing behavioral strategy and temporarily switching away to re-evaluate alternatives. Furthermore, by individually perturbing distinct output pathways, we establish that the two associated computations-determining whether to switch strategy and committing to the pursuit of a specific alternative-are segregated in the ACC microcircuitry.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2021.03.028}, author = {Tervo, D Gowanlock R and Kuleshova, Elena and Manakov, Maxim and Proskurin, Mikhail and Karlsson, Mattias and Lustig, Andy and Behnam, Reza and Karpova, Alla Y} } @article {68475, title = {Arnold tongues in oscillator systems with nonuniform spatial driving.}, journal = {Phys Rev E}, volume = {103}, year = {2021}, month = {04/2021}, pages = {042211}, abstract = {

Nonlinear oscillator systems are ubiquitous in biology and physics, and their control is a practical problem in many experimental systems. Here we study this problem in the context of the two models of spatially coupled oscillators: the complex Ginzburg-Landau equation (CGLE) and a generalization of the CGLE in which oscillators are coupled through an external medium (emCGLE). We focus on external control drives that vary in both space and time. We find that the spatial distribution of the drive signal controls the frequency ranges over which oscillators synchronize to the drive and that boundary conditions strongly influence synchronization to external drives for the CGLE. Our calculations also show that the emCGLE has a low density regime in which a broad range of frequencies can be synchronized for low drive amplitudes. We study the bifurcation structure of these models and find that they are very similar to results for the driven Kuramoto model, a system with no spatial structure. We conclude by discussing qualitative implications of our results for controlling coupled oscillator systems such as the social amoebae Dictyostelium and populations of Belousov Zhabotinsky (BZ) catalytic particles using spatially structured external drives.

}, issn = {2470-0053}, doi = {10.1103/PhysRevE.103.042211}, author = {Golden, Alexander and Sgro, Allyson E and Mehta, Pankaj} } @article {66903, title = {The art of lineage tracing: From worm to human.}, journal = {Progress in Neurobiology}, volume = {199}, year = {2021}, month = {2021 Apr}, pages = {101966}, abstract = {

Reconstructing the genealogy of every cell that makes up an organism remains a long-standing challenge in developmental biology. Besides its relevance for understanding the mechanisms underlying normal and pathological development, resolving the lineage origin of cell types will be crucial to create these types on-demand. Multiple strategies have been deployed towards the problem of lineage tracing, ranging from direct observation to sophisticated genetic approaches. Here we discuss the achievements and limitations of past and current technology. Finally, we speculate about the future of lineage tracing and how to reach the next milestones in the field.

}, issn = {1873-5118}, doi = {10.1016/j.pneurobio.2020.101966}, author = {Garcia-Marques, Jorge and Isabel Espinosa Medina and Lee, Tzumin} } @article {67231, title = {Attractor dynamics gate cortical information flow during decision-making.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jun 1}, pages = {843-50}, abstract = {

Decisions are held in memory until enacted, which makes them potentially vulnerable to distracting sensory input. Gating of information flow from sensory to motor areas could protect memory from interference during decision-making, but the underlying network mechanisms are not understood. Here, we trained mice to detect optogenetic stimulation of the somatosensory cortex, with a delay separating sensation and action. During the delay, distracting stimuli lost influence on behavior over time, even though distractor-evoked neural activity percolated through the cortex without attenuation. Instead, choice-encoding activity in the motor cortex became progressively less sensitive to the impact of distractors. Reverse engineering of neural networks trained to reproduce motor cortex activity revealed that the reduction in sensitivity to distractors was caused by a growing separation in the neural activity space between attractors that encode alternative decisions. Our results show that communication between brain regions can be gated via attractor dynamics, which control the degree of commitment to an action.

}, issn = {1546-1726}, doi = {10.1038/s41593-021-00840-6}, author = {Finkelstein, Arseny and Fontolan, Lorenzo and Economo, Michael N and Li, Nuo and Romani, Sandro and Svoboda, Karel} } @article {65832, title = {Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Jul 1}, pages = {771-4}, abstract = {

The study of neural circuits requires the reconstruction of neurons and the identification of synaptic connections between them. To scale the reconstruction to the size of whole-brain datasets, semi-automatic methods are needed to solve those tasks. Here, we present an automatic method for synaptic partner identification in insect brains, which uses convolutional neural networks to identify post-synaptic sites and their pre-synaptic partners. The networks can be trained from human generated point annotations alone and requires only simple post-processing to obtain final predictions. We used our method to extract 244 million putative synaptic partners in the fifty-teravoxel full adult fly brain (FAFB) electron microscopy (EM) dataset and evaluated its accuracy on 146,643 synapses from 702 neurons with a total cable length of 312 mm in four different brain regions. The predicted synaptic connections can be used together with a neuron segmentation to infer a connectivity graph with high accuracy: 96\% of edges between connected neurons are correctly classified as weakly connected (less than five synapses) and strongly connected (at least five synapses). Our synaptic partner predictions for the FAFB dataset are publicly available, together with a query library allowing automatic retrieval of up- and downstream neurons.

}, doi = {10.1038/s41592-021-01183-7}, author = {Buhmann, Julia and Sheridan, Arlo and Gerhard, Stephan and Krause, Renate and Nguyen, Tri and Heinrich, Larissa and Schlegel, Philipp and Lee, Wei-Chung Allen and Wilson, Rachel and Saalfeld, Stephan and Jefferis, Gregory and Bock, Davi and Turaga, Srinivas and Cook, Matthew and Funke, Jan} } @article {68841, title = {Accelerated EM Connectome Reconstruction using 3D Visualization and Segmentation Graphs}, journal = {bioRxiv}, year = {2020}, month = {2020 Jan 17}, abstract = {

Recent advances in automatic image segmentation and synapse prediction in electron microscopy (EM) datasets of the brain enable more efficient reconstruction of neural connectivity. In these datasets, a single neuron can span thousands of images containing complex tree-like arbors with thousands of synapses. While image segmentation algorithms excel within narrow fields of views, the algorithms sometimes struggle to correctly segment large neurons, which require large context given their size and complexity. Conversely, humans are comparatively good at reasoning with large objects. In this paper, we introduce several semi-automated strategies that combine 3D visualization and machine guidance to accelerate connectome reconstruction. In particular, we introduce a strategy to quickly correct a segmentation through merging and\ cleaving, or splitting a segment along supervoxel boundaries, with both operations driven by affinity scores in the underlying segmentation. We deploy these algorithms as streamlined workflows in a tool called\ Neu3\ and demonstrate superior performance compared to prior work, thus enabling efficient reconstruction of much larger datasets. The insights into proofreading from our work clarify the trade-offs to consider when tuning the parameters of image segmentation algorithms.

}, doi = {10.1101/2020.01.17.909572}, url = {https://doi.org/10.1101/2020.01.17.909572}, author = {Philip M. Hubbard and Stuart Berg and Ting Zhao and Donald J. Olbris and Lowell Umayam and Jeremy Maitin-Shepard and Michal Januszewski and William T. Katz and Erika R. Neace and Stephen M. Plaza} } @article {65276, title = {Accurate measurement of fast endocytic recycling kinetics in real time.}, journal = {Journal of Cell Science}, volume = {133}, year = {2020}, month = {2020 Jan 22}, abstract = {

The fast turnover of membrane components through endocytosis and recycling allows precise control of the composition of the plasma membrane. Endocytic recycling can be rapid with some molecules returning to the plasma membrane with a \<5 minutes. Existing methods to study these trafficking pathways utilize chemical, radioactive, or fluorescent labeling of cell surface receptors in pulse-chase experiments, which require tedious washing steps and manual collection of samples. Here, we introduce a live-cell endocytic recycling assay, based on a newly designed cell-impermeable, fluorogenic ligand for HaloTag: {\textquoteright}Janelia Fluor 635i{\textquoteright} (JFi; i=impermeant) which allows real-time detection of membrane receptor recycling at steady state. We used this method to study the effect of iron depletion on transferrin receptor (TfR) recycling using the chelator desferrioxamine. We found this perturbation significantly increases the TfR recycling rate. The high temporal resolution and simplicity of this assay provides a clear advantage over extant methods and makes it ideal for large scale cellular imaging studies. This assay can be adapted to examine other cellular kinetic parameters such as protein turnover and biosynthetic trafficking.

}, issn = {1477-9137}, doi = {10.1242/jcs.231225}, author = {Jonker, Caspar T H and Deo, Claire and Zager, Patrick J and Tkachuk, Ariana N and Weinstein, Alan M and Rodriguez-Boulan, Enrique and Lavis, Luke D and Schreiner, Ryan} } @article {65678, title = {Actin chromobody imaging reveals sub-organellar actin dynamics.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Sep 01}, pages = {917-21}, abstract = {

The actin cytoskeleton plays multiple critical roles in cells, from cell migration to organelle dynamics. The small and transient actin structures regulating organelle dynamics are challenging to detect with fluorescence microscopy, making it difficult to determine whether actin filaments are directly associated with specific membranes. To address these limitations, we developed fluorescent-protein-tagged actin nanobodies, termed {\textquoteright}actin chromobodies{\textquoteright} (ACs), targeted to organelle membranes to enable high-resolution imaging of sub-organellar actin dynamics.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0926-5}, author = {Schiavon, Cara R and Zhang, Tong and Zhao, Bing and Moore, Andrew S and Wales, Pauline and Andrade, Leonardo R and Wu, Melissa and Sung, Tsung-Chang and Dayn, Yelena and Feng, Jasmine W and Quintero, Omar A and Shadel, Gerald S and Grosse, Robert and Manor, Uri} } @article {65313, title = {The anatomy and physiology of claustrum-cortex interactions.}, journal = {Annual Review of Neuroscience}, volume = {43}, year = {2020}, month = {2020 Jul 1}, pages = {231-47}, abstract = {

The claustrum is one of the most widely connected regions of the forebrain, yet its function has remained obscure, largely due to the experimentally challenging nature of targeting this small, thin, and elongated brain area. However, recent advances in molecular techniques have enabled the anatomy and physiology of the claustrum to be studied with the spatiotemporal and cell type-specific precision required to eventually converge on what this area does. Here we review early anatomical and electrophysiological results from cats and primates, as well as recent work in the rodent, identifying the connectivity, cell types, and physiological circuit mechanisms underlying the communication between the claustrum and the cortex. The emerging picture is one in which the rodent claustrum is closely tied to frontal/limbic regions and plays a role in processes, such as attention, that are associated with these areas. Expected final online publication date for the , Volume 43 is July 8, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-092519-101637}, author = {Jackson, Jesse and Smith, Jared B and Lee, Albert K} } @article {65615, title = {Arousal modulates retinal output.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Aug 01}, pages = {487}, abstract = {

At various stages of the visual system, visual responses are modulated by arousal. Here, we find that in mice this modulation operates as early as in the first synapse from the retina and even in retinal axons. To measure retinal activity in the awake, intact brain, we imaged the synaptic boutons of retinal axons in the superior colliculus. Their activity depended not only on vision but also on running speed and pupil size, regardless of retinal illumination. Arousal typically reduced their visual responses and selectivity for direction and orientation. Recordings from retinal axons in the optic tract revealed that arousal modulates the firing of some retinal ganglion cells. Arousal had similar effects postsynaptically in colliculus neurons, independent of activity in the other main source of visual inputs to the colliculus, the primary visual cortex. These results indicate that arousal modulates activity at every stage of the mouse visual system.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.04.026}, author = {Schr{\"o}der, Sylvia and Steinmetz, Nicholas A and Krumin, Michael and Pachitariu, Marius and Rizzi, Matteo and Lagnado, Leon and Harris, Kenneth D and Carandini, Matteo} } @article {69335, title = {An arousal-gated visual circuit controls pursuit during Drosophila courtship}, journal = {bioRxiv}, year = {2020}, month = {2020 Aug 31}, abstract = {

Long-lasting internal states, like hunger, aggression, and sexual arousal, pattern ongoing behavior by defining how the sensory world is translated to specific actions that subserve the needs of an animal. Yet how enduring internal states shape sensory processing or behavior has remained unclear. In Drosophila, male flies will perform a lengthy and elaborate courtship ritual, triggered by activation of sexually-dimorphic P1 neurons, in which they faithfully follow and sing to a female. Here, by recording from males as they actively court a fictive {\textquoteleft}female{\textquoteright} in a virtual environment, we gain insight into how the salience of female visual cues is transformed by a male{\textquoteright}s internal arousal state to give rise to persistent courtship pursuit. We reveal that the gain of LCt0a visual projection neurons is strongly increased during courtship, enhancing their sensitivity to moving targets. A simple network model based on the LCt0a circuit accurately predicts a male{\textquoteright}s tracking of a female over hundreds of seconds, underscoring that LCt0a visual signals, once released by P1-mediated arousal, become coupled to motor pathways to deterministically control his visual pursuit. Furthermore, we find that P1 neuron activity correlates with fluctuations in the intensity of a male{\textquoteright}s pursuit, and that their acute activation is sufficient to boost the gain of the LCt0 pathways. Together, these results reveal how alterations in a male{\textquoteright}s internal arousal state can dynamically modulate the propagation of visual signals through a high-fidelity visuomotor circuit to guide his moment-to-moment performance of courtship.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2020.08.31.275883}, url = {https://www.biorxiv.org/content/early/2020/08/31/2020.08.31.275883}, author = {Tom Hindmarsh Sten and Rufei Li and Adriane Otopalik and Vanessa Ruta} } @article {65857, title = {The art of lineage tracing: from worm to human.}, journal = {Progress in Neurobiology}, year = {2020}, month = {2020 Nov 26}, pages = {101966}, abstract = {

Reconstructing the genealogy of every cell that makes up an organism remains a long-standing challenge in developmental biology. Besides its relevance for understanding the mechanisms underlying normal and pathological development, resolving the lineage origin of cell types will be crucial to create these types on-demand. Multiple strategies have been deployed towards the problem of lineage tracing, ranging from direct observation to sophisticated genetic approaches. Here we discuss the achievements and limitations of past and current technology. Finally, we speculate about the future of lineage tracing and how to reach the next milestones in the field.

}, issn = {1873-5118}, doi = {10.1016/j.pneurobio.2020.101966}, author = {Garcia-Marques, Jorge and Isabel Espinosa Medina and Lee, Tzumin} } @article {65240, title = {Aurora B functions at the apical surface after specialized cytokinesis during morphogenesis in C. elegans.}, journal = {Development}, volume = {147}, year = {2020}, month = {2020 Jan}, pages = {1-16}, abstract = {

While cytokinesis has been intensely studied, the way it is executed during development is not well understood, despite a long-standing appreciation that various aspects of cytokinesis vary across cell and tissue types. To address this, we investigated cytokinesis during the invariant embryonic divisions and found several reproducibly altered parameters at different stages. During early divisions, furrow ingression asymmetry and midbody inheritance is consistent, suggesting specific regulation of these events. During morphogenesis, we found several unexpected alterations to cytokinesis including apical midbody migration in polarizing epithelial cells of the gut, pharynx and sensory neurons. Aurora B kinase, which is essential for several aspects of cytokinesis, remains apically localized in each of these tissues after internalization of midbody ring components. Aurora B inactivation disrupts cytokinesis and causes defects in apical structures, even if inactivated post-mitotically. Therefore, cytokinesis is implemented in a specialized way during epithelial polarization and Aurora B has a new role in the formation of the apical surface.

}, issn = {1477-9129}, doi = {10.1242/dev.181099}, author = {Bai, Xiaofei and Melesse, Michael and Sorensen Turpin, Christopher G and Sloan, Dillon and Chen, Chin-Yi and Wang, Wen-Cheng and Lee, Po-Yi and Simmons, James R and Nebenfuehr, Benjamin and Mitchell, Diana and Klebanow, Lindsey R and Mattson, Nicholas and Betzig, Eric and Chen, Bi-Chang and Cheerambathur, Dhanya and Bembenek, Joshua N} } @article {64784, title = {An actin-based protrusion originating from a podosome-enriched region initiates macrophage fusion.}, journal = {Molecular Biology of the Cell}, volume = {30}, year = {2019}, month = {2019 Aug 1}, pages = {2254-67}, abstract = {

Macrophage fusion resulting in the formation of multinucleated giant cells occurs in a variety of chronic inflammatory diseases, yet the mechanism responsible for initiating macrophage fusion is unknown. Here, we used live cell imaging to show that actin-based protrusions at the leading edge initiate macrophage fusion. Phase contrast video microscopy demonstrated that in the majority of events, short protrusions (3 {\textpm} 1 μm) between two closely apposed cells initiated fusion, but occasionally we observed long protrusions (16 {\textpm} 7 μm). Using macrophages isolated from LifeAct mice and imaging with lattice light sheet microscopy, we further found that fusion-competent actin-based protrusions formed at sites enriched in podosomes. Inducing fusion in mixed populations of GFP- and mRFP-LifeAct macrophages showed rapid spatial overlap between GFP and RFP signal at the site of fusion. Cytochalasin B strongly reduced fusion and when rare fusion events occurred, protrusions were not observed. Fusion of macrophages deficient in Wiskott-Aldrich syndrome protein and Cdc42, key molecules involved in the formation of actin-based protrusions and podosomes, was also impaired both in vitro and in vivo. Finally, inhibiting the activity of the Arp2/3 complex decreased fusion and podosome formation. Together these data indicate that an actin-based protrusion formed at the leading edge macrophage fusion.

}, doi = {10.1101/538314}, author = {Faust, James J and Balabiyev, Arnat and Heddleston, John M and Podolnikova, Nataly P and Baluch, Debra Page and Chew, Teng-Leong and Ugarova, Tatiana P} } @article {64890, title = {Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians.}, journal = {PLoS Genetics}, volume = {15}, year = {2019}, month = {2019 Apr 25}, pages = {e1008092}, abstract = {

Human leukocyte antigen (HLA) is a key genetic factor conferring risk of systemic lupus erythematosus (SLE), but precise independent localization of HLA effects is extremely challenging. As a result, the contribution of specific HLA alleles and amino-acid residues to the overall risk of SLE and to risk of specific autoantibodies are far from completely understood. Here, we dissected (a) overall SLE association signals across HLA, (b) HLA-peptide interaction, and (c) residue-autoantibody association. Classical alleles, SNPs, and amino-acid residues of eight HLA genes were imputed across 4,915 SLE cases and 13,513 controls from Eastern Asia. We performed association followed by conditional analysis across HLA, assessing both overall SLE risk and risk of autoantibody production. DR15 alleles HLA-DRB1*15:01 (P = 1.4x10-27, odds ratio (OR) = 1.57) and HLA-DQB1*06:02 (P = 7.4x10-23, OR = 1.55) formed the most significant haplotype (OR = 2.33). Conditioned protein-residue signals were stronger than allele signals and mapped predominantly to HLA-DRB1 residue 13 (P = 2.2x10-75) and its proxy position 11 (P = 1.1x10-67), followed by HLA-DRB1-37 (P = 4.5x10-24). After conditioning on HLA-DRB1, novel associations at HLA-A-70 (P = 1.4x10-8), HLA-DPB1-35 (P = 9.0x10-16), HLA-DQB1-37 (P = 2.7x10-14), and HLA-B-9 (P = 6.5x10-15) emerged. Together, these seven residues increased the proportion of explained heritability due to HLA to 2.6\%. Risk residues for both overall disease and hallmark autoantibodies (i.e., nRNP: DRB1-11, P = 2.0x10-14; DRB1-13, P = 2.9x10-13; DRB1-30, P = 3.9x10-14) localized to the peptide-binding groove of HLA-DRB1. Enrichment for specific amino-acid characteristics in the peptide-binding groove correlated with overall SLE risk and with autoantibody presence. Risk residues were in primarily negatively charged side-chains, in contrast with rheumatoid arthritis. We identified novel SLE signals in HLA Class I loci (HLA-A, HLA-B), and localized primary Class II signals to five residues in HLA-DRB1, HLA-DPB1, and HLA-DQB1. These findings provide insights about the mechanisms by which the risk residues interact with each other to produce autoantibodies and are involved in SLE pathophysiology.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1008092}, author = {Molineros, Julio E and Looger, Loren L and Kim, Kwangwoo and Okada, Yukinori and Terao, Chikashi and Sun, Celi and Zhou, Xu-Jie and Raj, Prithvi and Kochi, Yuta and Suzuki, Akari and Akizuki, Shuji and Nakabo, Shuichiro and Bang, So-Young and Lee, Hye-Soon and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung-Cheol and Lee, Shin-Seok and Zuo, Xiaoxia and Yamamoto, Kazuhiko and Li, Quan-Zhen and Shen, Nan and Porter, Lauren L and Harley, John B and Chua, Kek Heng and Zhang, Hong and Wakeland, Edward K and Tsao, Betty P and Bae, Sang-Cheol and Nath, Swapan K} } @article {65059, title = {Analysis of phosphatidylinositol transfer at ER-PM junctions in receptor-stimulated live cells.}, journal = {Methods in Molecular Biology}, volume = {1949}, year = {2019}, month = {2019 Feb 23}, pages = {1-11}, abstract = {

Phosphatidylinositol (PI) is an inositol-containing phospholipid synthesized in the endoplasmic reticulum (ER). PI is a precursor lipid for PI 4,5-bisphosphate (PI(4,5)P) in the plasma membrane (PM) important for Ca signaling in response to extracellular stimuli. Thus, ER-to-PM PI transfer becomes essential for cells to maintain PI(4,5)P homeostasis during receptor stimulation. In this chapter, we discuss two live-cell imaging protocols to analyze ER-to-PM PI transfer at ER-PM junctions, where the two membrane compartments make close appositions accommodating PI transfer. First, we describe how to monitor PI(4,5)P replenishment following receptor stimulation, as a readout of PI transfer, using a PI(4,5)P biosensor and total internal reflection fluorescence\ microscopy. The second protocol directly visualizes PI transfer proteins that accumulate at ER-PM junctions and mediate PI(4,5)P replenishment with PI in the ER in stimulated cells. These methods provide spatial and temporal analysis of ER-to-PM PI transfer during receptor stimulation and can be adapted to other research questions related to this topic.

}, keywords = {Biological Transport, Biosensing Techniques, Cell Membrane, Endoplasmic Reticulum, Hela Cells, Humans, Image Processing, Computer-Assisted, Microscopy, Phosphatidylinositol 4,5-Diphosphate, Phosphatidylinositols}, issn = {1940-6029}, doi = {10.1007/978-1-4939-9136-5_1}, author = {Chang, Chi-Lun and Liou, Jen} } @article {68818, title = {Associative conditioning remaps odor representations and modifies inhibition in a higher olfactory brain area.}, journal = {Nat Neurosci}, volume = {22}, year = {2019}, month = {11/2019}, pages = {1844-1856}, abstract = {

Intelligent behavior involves associations between high-dimensional sensory representations and behaviorally relevant qualities such as valence. Learning of associations involves plasticity of excitatory connectivity, but it remains poorly understood how information flow is reorganized in networks and how inhibition contributes to this process. We trained adult zebrafish in an appetitive odor discrimination task and analyzed odor representations in a specific compartment of the posterior zone of the dorsal telencephalon (Dp), the homolog of mammalian olfactory cortex. Associative conditioning enhanced responses with a preference for the positively conditioned odor. Moreover, conditioning systematically remapped odor representations along an axis in coding space that represented attractiveness (valence). Interindividual variations in this mapping predicted variations in behavioral odor preference. Photoinhibition of interneurons resulted in specific modifications of odor representations that mirrored effects of conditioning and reduced experience-dependent, interindividual variations in odor-valence mapping. These results reveal an individualized odor-to-valence map that is shaped by inhibition and reorganized during learning.

}, keywords = {Animals, Animals, Genetically Modified, Association Learning, Brain Mapping, Discrimination Learning, Female, Individuality, Male, Neural Inhibition, Odorants, Olfactory Cortex, Olfactory Perception, Zebrafish}, issn = {1546-1726}, doi = {10.1038/s41593-019-0495-z}, author = {Frank, Thomas and M{\"o}nig, Nila R and Satou, Chie and Higashijima, Shin-Ichi and Friedrich, Rainer W} } @article {65180, title = {Asymmetric ON-OFF processing of visual motion cancels variability induced by the structure of natural scenes.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Oct 15}, abstract = {

Animals detect motion using a variety of visual cues that reflect regularities in the natural world. Experiments in animals across phyla have shown that motion percepts incorporate both pairwise and triplet spatiotemporal correlations that could theoretically benefit motion computation. However, it remains unclear how visual systems assemble these cues to build accurate motion estimates. Here we used systematic behavioral measurements of fruit fly motion perception to show how flies combine local pairwise and triplet correlations to reduce variability in motion estimates across natural scenes. By generating synthetic images with statistics controlled by maximum entropy distributions, we show that the triplet correlations are useful only when images have light-dark asymmetries that mimic natural ones. This suggests that asymmetric ON-OFF processing is tuned to the particular statistics of natural scenes. Since all animals encounter the world{\textquoteright}s light-dark asymmetries, many visual systems are likely to use asymmetric ON-OFF processing to improve motion estimation.

}, issn = {2050-084X}, doi = {10.7554/eLife.47579}, author = {Chen, Juyue and Mandel, Holly B and Fitzgerald, James E and Clark, Damon A} } @article {64847, title = {Attachment of the blastoderm to the vitelline envelope affects gastrulation of insects.}, journal = {Nature}, year = {2019}, month = {2019 Mar 27}, abstract = {

During gastrulation, physical forces reshape the simple embryonic tissue to form the complex body plans of multicellular organisms. These forces often cause large-scale asymmetric movements of the embryonic tissue. In many embryos, the gastrulating tissue is surrounded by a rigid protective shell. Although it is well-recognized that gastrulation movements depend on forces that are generated by tissue-intrinsic contractility,\ it is not known whether interactions between the tissue and the protective shell provide additional forces that affect gastrulation. Here we show that a particular part of the blastoderm tissue of the red flour beetle (Tribolium castaneum) tightly adheres in a temporally coordinated manner to the vitelline envelope that surrounds the embryo. This attachment generates an additional force that counteracts tissue-intrinsic contractile forces to create asymmetric tissue movements. This localized attachment depends on an αPS2 integrin (inflated), and the knockdown of this integrin leads to a gastrulation phenotype that is consistent with complete loss of attachment. Furthermore, analysis of another integrin (the αPS3 integrin, scab) in the fruit fly (Drosophila melanogaster) suggests that gastrulation in this organism also relies on adhesion between the blastoderm and the vitelline envelope. Our findings reveal a conserved mechanism through which the spatiotemporal pattern of tissue adhesion to the vitelline envelope provides controllable, counteracting forces that shape gastrulation movements in insects.

}, doi = {10.1038/s41586-019-1044-3}, author = {Muenster, Stefan and Jain, Akanksha and Mietke, Alexander and Pavlopoulos, Anastasios and Grill, Stephan W and Tomancak, Pavel} } @article {64942, title = {Augmin accumulation on long-lived microtubules drives amplification and kinetochore-directed growth.}, journal = {Journal of Cell Biology}, volume = {218}, year = {2019}, month = {2019 Jul 01}, pages = {2150-68}, abstract = {

Dividing cells reorganize their microtubule cytoskeleton into a bipolar spindle, which moves one set of sister chromatids to each nascent daughter cell. Early spindle assembly models postulated that spindle pole-derived microtubules search the cytoplasmic space until they randomly encounter a kinetochore to form a stable attachment. More recent work uncovered several additional, centrosome-independent microtubule generation pathways, but the contributions of each pathway to spindle assembly have remained unclear. Here, we combined live microscopy and mathematical modeling to show that most microtubules nucleate at noncentrosomal regions in dividing human cells. Using a live-cell probe that selectively labels aged microtubule lattices, we demonstrate that the distribution of growing microtubule plus ends can be almost entirely explained by Augmin-dependent amplification of long-lived microtubule lattices. By ultrafast 3D lattice light-sheet microscopy, we observed that this mechanism results in a strong directional bias of microtubule growth toward individual kinetochores. Our systematic quantification of spindle dynamics reveals highly coordinated microtubule growth during kinetochore fiber assembly.

}, issn = {1540-8140}, doi = {10.1083/jcb.201805044}, author = {David, Ana F and Roudot, Philippe and Legant, Wesley R and Betzig, Eric and Danuser, Gaudenz and Gerlich, Daniel W} } @article {65001, title = {Automated reconstruction of a serial-section EM drosophila brain with flood-filling networks and local realignment.}, journal = {bioRxiv}, year = {2019}, month = {2019 Apr 11}, abstract = {

Reconstruction of neural circuitry at single-synapse resolution is an attractive target for improving understanding of the nervous system in health and disease. Serial section transmission electron microscopy (ssTEM) is among the most prolific imaging methods employed in pursuit of such reconstructions. We demonstrate how Flood-Filling Networks (FFNs) can be used to computationally segment a forty-teravoxel whole-brain\ Drosophila\ ssTEM volume. To compensate for data irregularities and imperfect global alignment, FFNs were combined with procedures that locally re-align serial sections and dynamically adjust image content. The proposed approach produced a largely merger-free segmentation of the entire ssTEM\ Drosophila\ brain, which we make freely available. As compared to manual tracing using an efficient skeletonization strategy, the segmentation enabled circuit reconstruction and analysis workflows that were an order of magnitude faster.

}, doi = {10.1101/605634}, author = {Peter H. Li and Larry F. Lindsey and Micha{\l} Januszewski and Zhihao Zheng and Alexander Shakeel Bates and Istv{\'a}n Taisz and Mike Tyka and Matthew Nichols and Feng Li and Eric Perlman and Jeremy Maitin-Shepard and Tim Blakely and Laramie Leavitt and Gregory S.X.E. Jefferis and Davi Bock and Viren Jain} } @article {65090, title = {An automatic behavior recognition system classifies animal behaviors using movements and their temporal context.}, journal = {Journal of Neuroscience Methods}, volume = {326}, year = {2019}, month = {2019 Aug 12}, pages = {108352}, abstract = {

Animals can perform complex and purposeful behaviors by executing simpler movements in flexible sequences. It is particularly challenging to analyze behavior sequences when they are highly variable, as is the case in language production, certain types of birdsong and, as in our experiments, flies grooming. High sequence variability necessitates rigorous quantification of large amounts of data to identify organizational principles and temporal structure of such behavior. To cope with large amounts of data, and minimize human effort and subjective bias, researchers often use automatic behavior recognition software. Our standard grooming assay involves coating flies in dust and videotaping them as they groom to remove it. The flies move freely and so perform the same movements in various orientations. As the dust is removed, their appearance changes. These conditions make it difficult to rely on precise body alignment and anatomical landmarks such as eyes or legs and thus present challenges to existing behavior classification software. Human observers use speed, location, and shape of the movements as the diagnostic features of particular grooming actions. We applied this intuition to design a new automatic behavior recognition system (ABRS) based on spatiotemporal features in the video data, heavily weighted for temporal dynamics and invariant to the animal{\textquoteright}s position and orientation in the scene. We use these spatiotemporal features in two steps of supervised classification that reflect two time-scales at which the behavior is structured. As a proof of principle, we show results from quantification and analysis of a large data set of stimulus-induced fly grooming behaviors that would have been difficult to assess in a smaller dataset of human-annotated ethograms. While we developed and validated this approach to analyze fly grooming behavior, we propose that the strategy of combining alignment-invariant features and multi-timescale analysis may be generally useful for movement-based classification of behavior from video data.

}, issn = {01650270}, doi = {10.1016/j.jneumeth.2019.108352}, author = {Ravbar, Primoz and Branson, Kristin and Simpson, Jie H.} } @article {49023, title = {Aberrant calcium signaling in astrocytes inhibits neuronal excitability in a human Down syndrome stem cell model.}, journal = {Cell Reports}, volume = {24}, year = {2018}, month = {2018 Jul 10}, pages = {355-65}, abstract = {

Down syndrome (DS) is a genetic disorder that causes cognitive impairment. The staggering effects associated with an extra copy of human chromosome 21 (HSA21) complicates mechanistic understanding of DS pathophysiology. We examined the neuron-astrocyte interplay in a fully recapitulated HSA21 trisomy cellular model differentiated from DS-patient-derived induced pluripotent stem cells (iPSCs). By combining calcium imaging with genetic approaches, we discovered the functional defects of DS astroglia and their effects on neuronal excitability. Compared with control isogenic astroglia, DS astroglia exhibited more-frequent spontaneous calcium fluctuations, which reduced the excitability of co-cultured neurons. Furthermore, suppressed neuronal activity could be rescued by abolishing astrocytic spontaneous calcium activity either chemically by blocking adenosine-mediated signaling or genetically by knockdown of inositol triphosphate (IP3) receptors or S100B, a calcium binding protein coded on HSA21. Our results suggest a mechanism by which DS alters the function of astrocytes, which subsequently disturbs neuronal excitability.

}, doi = {10.1101/247585}, author = {Tian, Lin and Or, Grace and Wang, Yinxue and Shi, Guilai and Wang, Yizhi and Sun, Junqing and Papadopoulos, Stelios and Broussard, Gerard and Unger, Elizabeth and Deng, Wenbin and Weick, Jason and Bhattacharyya, Anita and Chen, Chao-Yin and Yu, Guoqiang and Looger, Loren L} } @article {67283, title = {An Accumulation-of-Evidence Task Using Visual Pulses for Mice Navigating in Virtual Reality}, journal = {Frontiers in Behavioral Neuroscience}, volume = {12}, year = {2018}, month = {Jun-03-2018}, abstract = {

The gradual accumulation of sensory evidence is a crucial component of perceptual decision making, but its neural mechanisms are still poorly understood. Given the wide availability of genetic and optical tools for mice, they can be useful model organisms for the study of these phenomena; however, behavioral tools are largely lacking. Here, we describe a new evidence-accumulation task for head-fixed mice navigating in a virtual reality (VR) environment. As they navigate down the stem of a virtual T-maze, they see brief pulses of visual evidence on either side, and retrieve a reward on the arm with the highest number of pulses. The pulses occur randomly with Poisson statistics, yielding a diverse yet well-controlled stimulus set, making the data conducive to a variety of computational approaches. A large number of mice of different genotypes were able to learn and consistently perform the task, at levels similar to rats in analogous tasks. They are sensitive to side differences of a single pulse, and their memory of the cues is stable over time. Moreover, using non-parametric as well as modeling approaches, we show that the mice indeed accumulate evidence: they use multiple pulses of evidence from throughout the cue region of the maze to make their decision, albeit with a small overweighting of earlier cues, and their performance is affected by the magnitude but not the duration of evidence. Additionally, analysis of the mice{\textquoteright}s running patterns revealed that trajectories are fairly stereotyped yet modulated by the amount of sensory evidence, suggesting that the navigational component of this task may provide a continuous readout correlated to the underlying cognitive variables. Our task, which can be readily integrated with state-of-the-art techniques, is thus a valuable tool to study the circuit mechanisms and dynamics underlying perceptual decision making, particularly under more complex behavioral contexts.

}, doi = {10.3389/fnbeh.2018.00036}, url = {http://journal.frontiersin.org/article/10.3389/fnbeh.2018.00036/full}, author = {Pinto, Lucas and Koay, Sue A. and Engelhard, Ben and Yoon, Alice M. and Deverett, Ben and Thiberge, Stephan Y. and Witten, Ilana B. and Tank, David W. and Brody, Carlos D.} } @article {49128, title = {Accurate and sensitive quantification of protein-DNA binding affinity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Apr 02}, pages = {E3692-701}, abstract = {

Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes.

}, issn = {1091-6490}, doi = {10.1073/pnas.1714376115}, author = {Rastogi, Chaitanya and Rube, H Tomas and Kribelbauer, Judith F and Crocker, Justin and Loker, Ryan E and Martini, Gabriella D and Laptenko, Oleg and Freed-Pastor, William A and Prives, Carol and Stern, David L and Mann, Richard S and Bussemaker, Harmen J} } @article {49341, title = {The actin cytoskeletal architecture of estrogen receptor positive breast cancer cells suppresses invasion.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Jul 30}, pages = {2980}, abstract = {

Estrogen promotes growth of estrogen receptor-positive (ER+) breast tumors. However, epidemiological studies examining the prognostic characteristics of breast cancer in postmenopausal women receiving hormone replacement therapy reveal a significant decrease in tumor dissemination, suggesting that estrogen has potential protective effects against cancer cell invasion. Here, we show that estrogen suppresses invasion of ER+ breast cancer cells by increasing transcription of the Ena/VASP protein, EVL, which promotes the generation of suppressive cortical actin bundles that inhibit motility dynamics, and is crucial for the ER-mediated suppression of invasion in vitro and in vivo. Interestingly, despite its benefits in suppressing tumor growth, anti-estrogenic endocrine therapy decreases EVL expression and increases local invasion in patients. Our results highlight the dichotomous effects of estrogen on tumor progression and suggest that, in contrast to its established role in promoting growth of ER+ tumors, estrogen has a significant role in suppressing invasion through actin cytoskeletal remodeling.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-05367-2}, author = {Padilla-Rodriguez, Marco and Parker, Sara S and Adams, Deanna G and Westerling, Thomas and Puleo, Julieann I and Watson, Adam W and Hill, Samantha M and Noon, Muhammad and Gaudin, Rapha{\"e}l and Aaron, Jesse and Tong, Daoqin and Roe, Denise J and Knudsen, Beatrice and Mouneimne, Ghassan} } @article {49477, title = {Active dendritic integration and mixed neocortical network representations during an adaptive sensing behavior.}, journal = {Nature Neuroscience}, volume = {21}, year = {2018}, month = {2018 Oct 22}, pages = {1583-90}, abstract = {

Animals strategically scan the environment to form an accurate perception of their surroundings. Here we investigated the neuronal representations that mediate this behavior. Ca imaging and selective optogenetic manipulation during an active sensing task reveals that layer 5 pyramidal neurons in the vibrissae cortex produce a diverse and distributed representation that is required for mice to adapt their whisking motor strategy to changing sensory cues. The optogenetic perturbation degraded single-neuron selectivity and network population encoding through a selective inhibition of active dendritic integration. Together the data indicate that active dendritic integration in pyramidal neurons produces a nonlinearly mixed network representation of joint sensorimotor parameters that is used to transform sensory information into motor commands during adaptive behavior. The prevalence of the layer 5 cortical circuit motif suggests that this is a general circuit computation.

}, issn = {1546-1726}, doi = {10.1038/s41593-018-0254-6}, author = {Ranganathan, Gayathri N and Apostolides, Pierre F and Harnett, Mark T and Xu, Ning-long and Druckmann, Shaul and Magee, Jeffrey C} } @article {49311, title = {Adaptive coding for dynamic sensory inference.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jul 10}, abstract = {

Behavior relies on the ability of sensory systems to infer properties of the environment from incoming stimuli. The accuracy of inference depends on the fidelity with which behaviorally relevant properties of stimuli are encoded in neural responses. High-fidelity encodings can be metabolically costly, but low-fidelity encodings can cause errors in inference. Here, we discuss general principles that underlie the tradeoff between encoding cost and inference error. We then derive adaptive encoding schemes that dynamically navigate this tradeoff. These optimal encodings tend to increase the fidelity of the neural representation following a change in the stimulus distribution, and reduce fidelity for stimuli that originate from a known distribution. We predict dynamical signatures of such encoding schemes and demonstrate how known phenomena, such as burst coding and firing rate adaptation, can be understood as hallmarks of optimal coding for accurate inference.

}, issn = {2050-084X}, doi = {10.7554/eLife.32055}, author = {M{\l}ynarski, Wiktor F and Hermundstad, Ann M} } @article {49031, title = {Adaptive optical microscopy for neurobiology.}, journal = {Current Opinion in Neurobiology}, volume = {50}, year = {2018}, month = {2018 Jun}, pages = {83-91}, abstract = {

Highlights:

With the ability to correct for the aberrations introduced by biological specimens, adaptive optics{\textemdash}a method originally developed for astronomical telescopes{\textemdash}has been applied to optical microscopy to recover diffraction-limited imaging performance deep within living tissue. In particular, this technology has been used to improve image quality and provide a more accurate characterization of both structure and function of neurons in a variety of living organisms. Among its many highlights, adaptive optical microscopy has made it possible to image large volumes with diffraction-limited resolution in zebrafish larval brains, to resolve dendritic spines over 600μm deep in the mouse brain, and to more accurately characterize the orientation tuning properties of thalamic boutons in the primary visual cortex of awake mice.

}, doi = {10.1016/j.conb.2018.01.011}, author = {Rodriguez, Cristina and Ji, Na} } @article {49572, title = {Allatostatin-C/AstC-R2 is a novel pathway to modulate the circadian activity pattern in Drosophila.}, journal = {Current Biology : CB}, volume = {29}, year = {2018}, month = {2018 Dec 04}, pages = {13-22}, abstract = {

Seven neuropeptides are expressed within the Drosophila brain circadian network. Our previous mRNA profiling suggested that Allatostatin-C (AstC) is an eighth neuropeptide and specifically expressed in dorsal clock neurons (DN1s). Our results here show that AstC is, indeed, expressed in DN1s, where it oscillates. AstC is also expressed in two less well-characterized circadian neuronal clusters, the DN3s and lateral-posterior neurons (LPNs). Behavioral experiments indicate that clock-neuron-derived AstC is required to mediate evening locomotor activity under short (winter-like) and long (summer-like) photoperiods. The AstC-Receptor 2 (AstC-R2) is expressed in LNds, the clock neurons that drive evening locomotor activity, and AstC-R2 is required in these neurons to modulate the same short photoperiod evening phenotype. Ex\ vivo calcium imaging indicates that AstC directly inhibits a single LNd. The results suggest that a novel AstC/AstC-R2 signaling pathway, from dorsal circadian neurons to an LNd, regulates the evening phase in Drosophila.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2018.11.005}, author = {D{\'\i}az, Madelen M and Schlichting, Matthias and Abruzzi, Katharine C and Long, Xi and Rosbash, Michael} } @article {49533, title = {Analysis of discrete local variability and structural covariance in macromolecular assemblies using Cryo-EM and focused classification.}, journal = {Ultramicroscopy}, volume = {203}, year = {2018}, month = {2018 Nov 29}, pages = {170}, abstract = {

Single-particle electron cryo-microscopy and computational image classification can be used to analyze structural variability in macromolecules and their assemblies. In some cases, a particle may contain different regions that each display a range of distinct conformations. We have developed strategies, implemented within the Frealign and\ cisTEM image processing packages, to focus classify on specific regions of a particle and detect potential covariance. The strategies are based on masking the region of interest using either a 2-D mask applied to reference projections and particle images, or a 3-D mask applied to the 3-D volume. We show that focused classification approaches can be used to study structural covariance, a concept that is likely to gain more importance as datasets grow in size, allowing the distinction of more structural states and smaller differences between states. Finally, we apply the approaches to an experimental dataset containing the HIV-1 Transactivation Response (TAR) element RNA fused into the large bacterial ribosomal subunit to deconvolve structural mobility within localized regions of interest, and to a dataset containing assembly intermediates of the large subunit to measure structural covariance.

}, doi = {10.1016/j.ultramic.2018.11.016}, author = {Zhang, Cheng and Cantara, William and Jeon, Youngmin and Musier-Forsyth, Karin and Grigorieff, Nikolaus and Lyumkis, Dmitry} } @article {49180, title = {Analysis of global and site-specific radiation damage in cryo-EM.}, journal = {Structure (London, England : 1993)}, volume = {26}, year = {2018}, month = {2018 Apr 18}, pages = {759-66}, abstract = {

Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the\ diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data.

}, issn = {1878-4186}, doi = {10.1016/j.str.2018.03.021}, author = {Hattne, Johan and Shi, Dan and Glynn, Calina and Zee, Chih-Te and Gallagher-Jones, Marcus and Martynowycz, Michael W and Rodriguez, Jose A and Gonen, Tamir} } @inbook {49508, title = {Analysis of image similarity and relationship.}, booktitle = {Basic Confocal Microscopy}, year = {2018}, pages = {309-33}, publisher = {Springer}, organization = {Springer}, abstract = {

The ability of fluorescence microscopy to simultaneously image multiple specific molecules of interest has allowed biologists to infer macromolecular organization and colocalization in fixed and live samples. However, a number of factors could\ affect these analyses, and colocalization is a misnomer. We propose that\ image similarity coefficient\ as a better and more descriptive term. In this chapter we will discuss many of the factors involved with determining image similarity including our perception of color in images. In addition, the correct use of several commonly accepted methods such as Pearson{\textquoteright}s correlation coefficient, Manders{\textquoteright} overlap coefficient, and Spearman{\textquoteright}s ranked correlation coefficient is discussed.

}, issn = {978-3-319-97453-8}, doi = {10.1007/978-3-319-97454-5_11}, author = {Aaron, Jesse S and Chew, Teng-Leong} } @article {49493, title = {Analysis tools for large connectomes.}, journal = {Frontiers in Neural Circuits}, volume = {12}, year = {2018}, month = {2018}, pages = {85}, abstract = {

New reconstruction techniques are generating connectomes of unprecedented size. These must be analyzed to generate human comprehensible results. The analyses being used fall into three general categories. The first is interactive tools used during reconstruction, to help guide the effort, look for possible errors, identify potential cell classes, and answer other preliminary questions. The second type of analysis is support for formal documents such as papers and theses. Scientific norms here require that the data be archived and accessible, and the analysis reproducible. In contrast to some other "omic" fields such as genomics, where a few specific analyses dominate usage, connectomics is rapidly evolving and the analyses used are often specific to the connectome being analyzed. These analyses are typically performed in a variety of conventional programming language, such as Matlab, R, Python, or C++, and read the connectomic data either from a file or through database queries, neither of which are standardized. In the short term we see no alternative to the use of specific analyses, so the best that can be done is to publish the analysis code, and the interface by which it reads connectomic data. A similar situation exists for archiving connectome data. Each group independently makes their data available, but there is no standardized format and long-term accessibility is neither enforced nor funded. In the long term, as connectomics becomes more common, a natural evolution would be a central facility for storing and querying connectomic data, playing a role similar to the National Center for Biotechnology Information for genomes. The final form of analysis is the import of connectome data into downstream tools such as neural simulation or machine learning. In this process, there are two main problems that need to be addressed. First, the reconstructed circuits contain huge amounts of detail, which must be intelligently reduced to a form the downstream tools can use. Second, much of the data needed for these downstream operations must be obtained by other methods (such as genetic or optical) and must be merged with the extracted connectome.

}, issn = {1662-5110}, doi = {10.3389/fncir.2018.00085}, author = {Scheffer, Louis K} } @article {49531, title = {Analyzing image segmentation for connectomics.}, journal = {Frontiers in Neural Circuits}, volume = {12}, year = {2018}, month = {2018}, pages = {102}, abstract = {

Automatic image segmentation is critical to scale up electron microscope (EM) connectome reconstruction. To this end, segmentation competitions, such as CREMI and SNEMI, exist to help researchers evaluate segmentation algorithms with the goal of improving them. Because generating ground truth is time-consuming, these competitions often fail to capture the challenges in segmenting larger datasets required in connectomics. More generally, the common metrics for EM image segmentation do not emphasize impact on downstream analysis and are often not very useful for isolating problem areas in the segmentation. For example, they do not capture connectivity information and often over-rate the quality of a segmentation as we demonstrate later. To address these issues, we introduce a novel strategy to enable evaluation of segmentation at large scales both in a supervised setting, where ground truth is available, or an unsupervised setting. To achieve this, we first introduce new metrics more closely aligned with the use of segmentation in downstream analysis and reconstruction. In particular, these include synapse connectivity and completeness metrics that provide both meaningful and intuitive interpretations of segmentation quality as it relates to the preservation of neuron connectivity. Also, we propose measures of segmentation correctness and completeness with respect to the percentage of "orphan" fragments and the concentrations of self-loops formed by segmentation failures, which are helpful in analysis and can be computed without ground truth. The introduction of new metrics intended to be used for practical applications involving large datasets necessitates a scalable software ecosystem, which is a critical contribution of this paper. To this end, we introduce a scalable, flexible software framework that enables integration of several different metrics and provides mechanisms to evaluate and debug differences between segmentations. We also introduce visualization software to help users to consume the various metrics collected. We evaluate our framework on two relatively large public groundtruth datasets providing novel insights on example segmentations.

}, issn = {1662-5110}, doi = {10.3389/fncir.2018.00102}, author = {Plaza, Stephen M and Funke, Jan} } @article {49383, title = {Anterolateral motor cortex connects with a medial subdivision of ventromedial thalamus through cell-type-specific circuits, forming an excitatory thalamo-cortico-thalamic loop via layer 1 apical tuft dendrites of layer 5B pyramidal tract type neurons.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {38}, year = {2018}, month = {2018 Aug 24}, pages = {8787-97}, abstract = {

The anterolateral motor cortex (ALM) and ventromedial (VM) thalamus are functionally linked to support persistent activity during motor planning. We analyzed the underlying synaptic interconnections using optogenetics and electrophysiology in mice (♀/♂). In cortex, thalamocortical (TC) axons from VM excited VM-projecting pyramidal-tract (PT) neurons in layer 5B of ALM. These axons also strongly excited layer 2/3 neurons (which strongly excite PT neurons, as previously shown) but not VM-projecting corticothalamic (CT) neurons in layer 6. The strongest connections in the VM{\textrightarrow}PT circuit were localized to apical-tuft dendrites of PT neurons, in layer 1. These tuft inputs were selectively augmented after blocking hyperpolarization-activated cyclic nucleotide-gated (HCN) channels. In thalamus, axons from ALM PT neurons excited ALM-projecting VM neurons, located medially in VM. These axons provided weak input to neurons in mediodorsal nucleus, and little or no input either to neurons in the GABAergic reticular thalamic nucleus or to neurons in VM projecting to primary motor cortex (M1). Conversely, M1 PT axons excited M1- but not ALM-projecting VM neurons. Our findings indicate, first, a set of cell-type-specific connections forming an excitatory thalamo-cortico-thalamic (T-C-T) loop for ALM<->VM communication and a circuit-level substrate for supporting reverberant activity in this system. Second, a key feature of this loop is the prominent involvement of layer 1 synapses onto apical dendrites, a subcellular compartment with distinct signaling properties, including HCN-mediated gain control. Third, the segregation of the ALM<->VM loop from M1-related circuits of VM adds cellular-level support for the concept of parallel pathway organization in the motor system.Anterolateral motor cortex (ALM), a higher-order motor area in the mouse, and ventromedial thalamus (VM) are anatomically and functionally linked, but their synaptic interconnections at the cellular level are unknown. Our results show that ALM pyramidal tract neurons monosynaptically excite ALM-projecting thalamocortical neurons in a medial subdivision of VM, and vice versa. The thalamo-cortico-thalamic loop formed by these recurrent connections constitutes a circuit-level substrate for supporting reverberant activity in this system.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1333-18.2018}, author = {Guo, KuangHua and Yamawaki, Naoki and Svoboda, Karel and Shepherd, Gordon M G} } @article {49316, title = {Apical and basal matrix remodeling control epithelial morphogenesis.}, journal = {Developmental Cell}, volume = {46}, year = {2018}, month = {2018 Jul 02}, pages = {23-39.e5}, abstract = {

Epithelial tissues can elongate in two dimensions by polarized cell intercalation, oriented cell division, or cell shape change, owing to local or global actomyosin contractile forces acting in the plane of the tissue. In addition, epithelia can undergo morphogenetic change in three dimensions. We show that elongation of the wings and legs of Drosophila involves a columnar-to-cuboidal cell shape change that reduces cell height and expands cell width. Remodeling of the apical extracellular matrix by the Stubble protease and basal matrix by MMP1/2 proteases induces wing and leg elongation. Matrix remodeling does not occur in the haltere, a limb that fails to elongate. Limb elongation is made anisotropic by planar polarized Myosin-II, which drives convergent extension along the proximal-distal axis. Subsequently, Myosin-II relocalizes to lateral membranes to accelerate columnar-to-cuboidal transition and isotropic tissue expansion. Thus, matrix remodeling induces dynamic changes in actomyosin contractility\ to drive epithelial morphogenesis in three dimensions.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2018.06.006}, author = {Diaz-de-la-Loza, Maria-Del-Carmen and Ray, Robert P and Ganguly, Poulami S and Alt, Silvanus and Davis, John R and Hoppe, Andreas and Tapon, Nic and Salbreux, Guillaume and Thompson, Barry J} } @article {49123, title = {Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes.}, journal = {Nature}, volume = {556}, year = {2018}, month = {2018 Mar 28}, pages = {64-9}, abstract = {

Nutrients, such as amino acids and glucose, signal through the Rag GTPases to activate mTORC1. The GATOR1 protein complex-comprising DEPDC5, NPRL2 and NPRL3-regulates the Rag GTPases as a GTPase-activating protein (GAP) for RAGA; loss of GATOR1 desensitizes mTORC1 signalling to nutrient starvation. GATOR1 components have no sequence homology to other proteins, so the function of GATOR1 at the molecular level is currently unknown. Here we used cryo-electron microscopy to solve structures of GATOR1 and GATOR1-Rag GTPases complexes. GATOR1 adopts an extended architecture with a cavity in the middle; NPRL2 links DEPDC5 and NPRL3, and DEPDC5 contacts the Rag GTPase heterodimer. Biochemical analyses reveal that our GATOR1-Rag GTPases structure is inhibitory, and that at least two binding modes must exist between the Rag GTPases and GATOR1. Direct interaction of DEPDC5 with RAGA inhibits GATOR1-mediated stimulation of GTP hydrolysis by RAGA, whereas weaker interactions between the NPRL2-NPRL3 heterodimer and RAGA execute GAP activity. These data reveal the structure of a component of the nutrient-sensing mTORC1 pathway and a non-canonical interaction between a GAP and its substrate GTPase.

}, issn = {1476-4687}, doi = {10.1038/nature26158}, author = {Shen, Kuang and Huang, Rick K and Brignole, Edward J and Condon, Kendall J and Valenstein, Max L and Chantranupong, Lynne and Bomaliyamu, Aimaiti and Choe, Abigail and Hong, Chuan and Yu, Zhiheng and Sabatini, David M} } @article {49475, title = {Astrocytes integrate and drive action potential firing in inhibitory subnetworks.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Oct 18}, pages = {4336}, abstract = {

Many brain functions depend on the ability of neural networks to temporally integrate transient inputs to produce sustained discharges. This can occur through cell-autonomous mechanisms in individual neurons and through reverberating activity in recurrently connected neural networks. We report a third mechanism involving temporal integration of neural activity by a network of astrocytes. Previously, we showed that some types of interneurons can generate long-lasting trains of action potentials (barrage firing) following repeated depolarizing stimuli. Here we show that calcium signaling in an astrocytic network correlates with barrage firing; that active depolarization of astrocyte networks by chemical or optogenetic stimulation enhances; and that chelating internal calcium, inhibiting release from internal stores, or inhibiting GABA transporters or metabotropic glutamate receptors inhibits barrage firing. Thus, networks of astrocytes influence the spatiotemporal dynamics of neural networks by directly integrating neural activity and driving barrages of action potentials in some populations of inhibitory interneurons.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-06338-3}, author = {Deemyad, Tara and L{\"u}thi, Joel and Spruston, Nelson} } @article {49223, title = {Atomic resolution cryo-EM structure of β-galactosidase.}, journal = {Structure (London, England : 1993)}, volume = {26}, year = {2018}, month = {2018 Apr 30}, pages = {848}, abstract = {

The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam. These advances enable determination of a cryo-EM density map for β-galactosidase bound to the inhibitor phenylethyl β-D-thiogalactopyranoside where the ordered regions are resolved at a level of detail seen in X-ray maps at \~{} 1.5\ {\r A} resolution. Using this density map in conjunction with constrained molecular dynamics simulations provides a measure of the local flexibility of the non-covalently bound inhibitor and offers further opportunities for structure-guided inhibitor design.

}, issn = {1878-4186}, doi = {10.1016/j.str.2018.04.004}, author = {Bartesaghi, Alberto and Aguerrebere, Cecilia and Falconieri, Veronica and Banerjee, Soojay and Earl, Lesley A and Zhu, Xing and Grigorieff, Nikolaus and Milne, Jacqueline L S and Sapiro, Guillermo and Wu, Xiongwu and Subramaniam, Sriram} } @article {49117, title = {Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2.}, journal = {Nature Structural \& Molecular Biology}, year = {2018}, month = {2018 Mar 12}, abstract = {

Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a challenge of amyloid research. Here, we detail the wide range of polymorphs formed by a segment of human TAR DNA-binding protein 43 (TDP-43) as a model for the polymorphic capabilities of pathological amyloid aggregation. Using X-ray diffraction, microelectron diffraction (MicroED) and single-particle cryo-EM, we show that theDLIIKGISVHIsegment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These associations include seven distinct interfaces displaying five different symmetry classes of steric zippers. Additionally, we find that this segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the molecular level how amyloid proteins can form diverse fibril structures.

}, issn = {1545-9985}, doi = {10.1038/s41594-018-0045-5}, author = {Guenther, Elizabeth L and Ge, Peng and Trinh, Hamilton and Sawaya, Michael R and Cascio, Duilio and Boyer, David R and Gonen, Tamir and Zhou, Z Hong and Eisenberg, David S} } @article {48218, title = {Actin dynamics and competition for myosin monomer govern the sequential amplification of myosin filaments.}, journal = {Nature Cell Biology}, volume = {19}, year = {2017}, month = {2017 Jan 23}, pages = {85-93}, abstract = {

The cellular mechanisms governing non-muscle myosin II (NM2) filament assembly are largely unknown. Using EGFP-NM2A knock-in fibroblasts and multiple super-resolution imaging modalities, we characterized and quantified the sequential amplification of NM2 filaments within lamellae, wherein filaments emanating from single nucleation events continuously partition, forming filament clusters that populate large-scale actomyosin structures deeper in the cell. Individual partitioning events coincide spatially and temporally with the movements of diverging actin fibres, suppression of which inhibits partitioning. These and other data indicate that NM2A filaments are partitioned by the dynamic movements of actin fibres to which they are bound. Finally, we showed that partition frequency and filament growth rate in the lamella depend on MLCK, and that MLCK is competing with centrally active ROCK for a limiting pool of monomer with which to drive lamellar filament assembly. Together, our results provide new insights into the mechanism and spatio-temporal regulation of NM2 filament assembly in cells.

}, issn = {1476-4679}, doi = {10.1038/ncb3463}, author = {Beach, Jordan R and Bruun, Kyle S and Shao, Lin and Li, Dong and Swider, Zac and Remmert, Kirsten and Zhang, Yingfan and Conti, Mary A and Adelstein, Robert S and Rusan, Nasser M and Betzig, Eric and Hammer, John A} } @article {48843, title = {Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Sep 26}, abstract = {

Leukocytes and other amoeboid cells change shape as they move, forming highly dynamic, actin-filled pseudopods. Although we understand much about the architecture and dynamics of thin lamellipodia made by slow-moving cells on flat surfaces, conventional light microscopy lacks the spatial and temporal resolution required to track complex pseudopods of cells moving in three dimensions. We therefore employed lattice light sheet microscopy to perform three-dimensional, time-lapse imaging of neutrophil-like HL-60 cells crawling through collagen matrices. To analyze three-dimensional pseudopods we: (i) developed fluorescent probe combinations that distinguish cortical actin from dynamic, pseudopod-forming actin networks, and (ii) adapted molecular visualization tools from structural biology to render and analyze complex cell surfaces. Surprisingly, three-dimensional pseudopods turn out to be composed of thin (\<0.75 {\textmu}m), flat sheets that sometimes interleave to form rosettes. Their laminar nature is not templated by an external surface, but likely reflects a linear arrangement of regulatory molecules. Although we find that Arp2/3-dependent pseudopods are dispensable for three-dimensional locomotion, their elimination dramatically decreases the frequency of cell turning, and pseudopod dynamics increase when cells change direction, highlighting the important role pseudopods play in pathfinding.

}, issn = {2050-084X}, doi = {10.7554/eLife.26990}, author = {Fritz-Laylin, Lillian K and Riel-Mehan, Megan and Chen, Bi-Chang and Lord, Samuel J and Goddard, Thomas D and Ferrin, Thomas E and Nicholson-Dykstra, Susan M and Higgs, Henry and Johnson, Graham T and Betzig, Eric and Mullins, R Dyche} } @article {48373, title = {Adaptive optical fluorescence microscopy.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Mar 31}, pages = {374-380}, abstract = {

The past quarter century has witnessed rapid developments of fluorescence microscopy techniques that enable structural and functional imaging of biological specimens at unprecedented depth and resolution. The performance of these methods in multicellular organisms, however, is degraded by sample-induced optical aberrations. Here I review recent work on incorporating adaptive optics, a technology originally applied in astronomical telescopes to combat atmospheric aberrations, to improve image quality of fluorescence microscopy for biological imaging.

}, issn = {1548-7105}, doi = {10.1038/nmeth.4218}, author = {Ji, Na} } @article {48714, title = {Adaptive optical versus spherical aberration corrections for in vivo brain imaging.}, journal = {Biomedical Optics Express}, volume = {8}, year = {2017}, month = {2017 Aug}, pages = {3891-902}, abstract = {

Adjusting the objective correction collar is a widely used approach to correct spherical aberrations (SA) in optical microscopy. In this work, we characterized and compared its performance with adaptive optics in the context of\ in vivo\ brain imaging with two-photon fluorescence microscopy. We found that the presence of sample tilt had a deleterious effect on the performance of SA-only correction. At large tilt angles, adjusting the correction collar even worsened image quality. In contrast, adaptive optical correction always recovered optimal imaging performance regardless of sample tilt. The extent of improvement with adaptive optics was dependent on object size, with smaller objects having larger relative gains in signal intensity and image sharpness. These observations translate into a superior performance of adaptive optics for structural and functional brain imaging applications\ in vivo, as we confirmed experimentally.

}, doi = {10.1364/BOE.8.003891} } @article {49082, title = {Advances in neural engineering for rehabilitation.}, journal = {Behavioural Neurology}, volume = {2017}, year = {2017}, month = {2017}, pages = {9240921}, issn = {1875-8584}, doi = {10.1155/2017/9240921}, author = {Hu, Xiaoling and Zhao, Ting and Yao, Jun and Kuang, Yu and Yang, Yuan} } @article {48449, title = {An Amidase_3 domain-containing N-acetylmuramyl-L-alanine amidase is required for mycobacterial cell division.}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {2017 Apr 25}, pages = {1140}, abstract = {

Mycobacteria possess a multi-layered cell wall that requires extensive remodelling during cell division. We investigated the role of an amidase_3 domain-containing N-acetylmuramyl-L-alanine amidase, a peptidoglycan remodelling enzyme implicated in cell division. We demonstrated that deletion of MSMEG_6281 (Ami1) in Mycobacterium smegmatis resulted in the formation of cellular chains, illustrative of cells that were unable to complete division. Suprisingly, viability in the Δami1 mutant was maintained through atypical lateral branching, the products of which proceeded to form viable daughter cells. We showed that these lateral buds resulted from mislocalization of DivIVA, a major determinant in facilitating polar elongation in mycobacterial cells. Failure of Δami1 mutant cells to separate also led to dysregulation of FtsZ ring bundling. Loss of Ami1 resulted in defects in septal peptidoglycan turnover with release of excess cell wall material from the septum or newly born cell poles. We noted signficant accumulation of 3-3 crosslinked muropeptides in the Δami1 mutant. We further demonstrated that deletion of ami1 leads to increased cell wall permeability and enhanced susceptiblity to cell wall targeting antibiotics. Collectively, these data provide novel insight on cell division in actinobacteria and highlights a new class of potential drug targets for mycobacterial diseases.

}, issn = {2045-2322}, doi = {10.1038/s41598-017-01184-7}, author = {Senzani, Sibusiso and Li, Dong and Bhaskar, Ashima and Ealand, Christopher and Chang, James and Rimal, Binayak and Liu, Chengyin and Joon Kim, Sung and Dhar, Neeraj and Kana, Bavesh} } @article {48415, title = {AMPK and vacuole-associated Atg14p orchestrate {\textmu}-lipophagy for energy production and long-term survival under glucose starvation.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Apr 10}, pages = {e21690}, abstract = {

Dietary restriction increases the longevity of many organisms but the cell signaling and organellar mechanisms underlying this capability are unclear. We demonstrate that to permit long-term survival in response to sudden glucose depletion, yeast cells activate lipid-droplet (LD) consumption through micro-lipophagy ({\textmu}-lipophagy), in which fat is metabolized as an alternative energy source. AMP-activated protein kinase (AMPK) activation triggered this pathway, which required Atg14p. More gradual glucose starvation, amino acid deprivation or rapamycin did not trigger {\textmu}-lipophagy and failed to provide the needed substitute energy source for long-term survival. During acute glucose restriction, activated AMPK was stabilized from degradation and interacted with Atg14p. This prompted Atg14p redistribution from ER exit sites onto liquid-ordered vacuole membrane domains, initiating {\textmu}-lipophagy. Our findings that activated AMPK and Atg14p are required to orchestrate {\textmu}-lipophagy for energy production in starved cells is relevant for studies on aging and evolutionary survival strategies of different organisms.

}, issn = {2050-084X}, doi = {10.7554/eLife.21690}, author = {Seo, Arnold Young and Lau, Pick-Wei and Feliciano, Daniel and Sengupta, Prabuddha and Le Gros, Mark A and Cinquin, Bertrand and Larabell, Carolyn A and Lippincott-Schwartz, Jennifer} } @article {48507, title = {Angular velocity integration in a fly heading circuit.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 May 22}, abstract = {

Many animals maintain an internal representation of their heading as they move through their surroundings. Such a compass representation was recently discovered in a neural population in the Drosophila melanogaster central complex, a brain region implicated in spatial navigation. Here, we use two-photon calcium imaging and electrophysiology in head-fixed walking flies to identify a different neural population that conjunctively encodes heading and angular velocity, and is excited selectively by turns in either the clockwise or counterclockwise direction. We show how these mirror-symmetric turn responses combine with the neurons{\textquoteright} connectivity to the compass neurons to create an elegant mechanism for updating the fly{\textquoteright}s heading representation when the animal turns in darkness. This mechanism, which employs recurrent loops with an angular shift, bears a resemblance to those proposed in theoretical models for rodent head direction cells. Our results provide a striking example of structure matching function for a broadly relevant computation.

}, issn = {2050-084X}, doi = {10.7554/eLife.23496}, author = {Turner-Evans, Daniel and Wegener, Stephanie and Rouault, Herv{\'e} and Franconville, Romain and Wolff, Tanya and Seelig, Johannes D and Druckmann, Shaul and Jayaraman, Vivek} } @article {67220, title = {Anisotropic EM Segmentation by 3D Affinity Learning and Agglomeration}, journal = {CoRR}, volume = {abs/1707.08935}, year = {2017}, abstract = {

The field of connectomics has recently produced neuron wiring diagrams from relatively large brain regions from multiple animals. Most of these neural reconstructions were computed from isotropic (e.g., FIBSEM) or near isotropic (e.g., SBEM) data. In spite of the remarkable progress on algorithms in recent years, automatic dense reconstruction from anisotropic data remains a challenge for the connectomics community. One significant hurdle in the segmentation of anisotropic data is the difficulty in generating a suitable initial over-segmentation. In this study, we present a segmentation method for anisotropic EM data that agglomerates a 3D over-segmentation computed from the 3D affinity prediction. A 3D U-net is trained to predict 3D affinities by the MALIS approach. Experiments on multiple datasets demonstrates the strength and robustness of the proposed method for anisotropic EM segmentation.

}, url = {https://arxiv.org/abs/1707.08935v2}, author = {Toufiq Parag and Fabian Tschopp and William Grisaitis and Srinivas C. Turaga and Xuewen Zhang and Brian Matejek and Lee Kamentsky and Jeff W. Lichtman and Hanspeter Pfister} } @article {65893, title = {Antibodies to biotin enable large-scale detection of biotinylation sites on proteins}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {Jan-12-2017}, pages = {1167 - 1170}, abstract = {

Although purification of biotinylated molecules is highly efficient, identifying specific sites of biotinylation remains challenging. We show that anti-biotin antibodies enable unprecedented enrichment of biotinylated peptides from complex peptide mixtures. Live-cell proximity labeling using APEX peroxidase followed by anti-biotin enrichment and mass spectrometry yielded over 1,600 biotinylation sites on hundreds of proteins, an increase of more than 30-fold in the number of biotinylation sites identified compared to streptavidin-based enrichment of proteins.

}, issn = {1548-7091}, doi = {10.1038/nmeth.4465}, url = {http://www.nature.com/articles/nmeth.4465http://www.nature.com/doifinder/10.1038/nmeth.4465http://www.nature.com/articles/nmeth.4465.pdfhttp://www.nature.com/articles/nmeth.4465.pdfhttp://www.nature.com/articles/nmeth.4465}, author = {Udeshi, Namrata D and Pedram, Kayvon and Svinkina, Tanya and Fereshetian, Shaunt and Myers, Samuel A and Aygun, Ozan and Krug, Karsten and Clauser, Karl and Ryan, Dominic and Ast, Tslil and Mootha, Vamsi K and Ting, Alice Y and Carr, Steven A} } @article {48534, title = {Applying systems-level spectral imaging and analysis to reveal the organelle interactome.}, journal = {Nature}, year = {2017}, month = {2017 May 24}, abstract = {

The organization of the eukaryotic cell into discrete membrane-bound organelles allows for the separation of incompatible biochemical processes, but the activities of these organelles must be coordinated. For example, lipid metabolism is distributed between the endoplasmic reticulum for lipid synthesis, lipid droplets for storage and transport, mitochondria and peroxisomes for β-oxidation, and lysosomes for lipid hydrolysis and recycling. It is increasingly recognized that organelle contacts have a vital role in diverse cellular functions. However, the spatial and temporal organization of organelles within the cell remains poorly characterized, as fluorescence imaging approaches are limited in the number of different labels that can be distinguished in a single image. Here we present a systems-level analysis of the organelle interactome using a multispectral image acquisition method that overcomes the challenge of spectral overlap in the fluorescent protein palette. We used confocal and lattice light sheet instrumentation and an imaging informatics pipeline of five steps to achieve mapping of organelle numbers, volumes, speeds, positions and dynamic inter-organelle contacts in live cells from a monkey fibroblast cell line. We describe the frequency and locality of two-, three-, four- and five-way interactions among six different membrane-bound organelles (endoplasmic reticulum, Golgi, lysosome, peroxisome, mitochondria and lipid droplet) and show how these relationships change over time. We demonstrate that each organelle has a characteristic distribution and dispersion pattern in three-dimensional space and that there is a reproducible pattern of contacts among the six organelles, that is affected by microtubule and cell nutrient status. These live-cell confocal and lattice light sheet spectral imaging approaches are applicable to any cell system expressing multiple fluorescent probes, whether in normal conditions or when cells are exposed to disturbances such as drugs, pathogens or stress. This methodology thus offers a powerful descriptive tool and can be used to develop hypotheses about cellular organization and dynamics.

}, issn = {1476-4687}, doi = {10.1038/nature22369}, author = {Valm, Alex M and Cohen, Sarah and Legant, Wesley R and Melunis, Justin and Hershberg, Uri and Wait, Eric and Cohen, Andrew R and Davidson, Michael W and Betzig, Eric and Lippincott-Schwartz, Jennifer} } @article {48156, title = {Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jan 03}, abstract = {

hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β-cells, leading us to determine the structure and cytotoxicity of protein segments composing the amyloid spine of hIAPP. Using the cryoEM method MicroED, we discover that one segment, 19-29 S20G, forms pairs of β-sheets mated by a dry interface that share structural features with and are similarly cytotoxic to full-length hIAPP fibrils. In contrast, a second segment, 15-25 WT, forms non-toxic labile β-sheets. These segments possess different structures and cytotoxic effects, however, both can seed full-length hIAPP, and cause hIAPP to take on the cytotoxic and structural features of that segment. These results suggest that protein segment structures represent polymorphs of their parent protein and that segment 19-29 S20G may serve as a model for the toxic spine of hIAPP.

}, issn = {2050-084X}, doi = {10.7554/eLife.19273}, author = {Krotee, Pascal and Rodriguez, Jose A and Sawaya, Michael R and Cascio, Duilio and Reyes, Francis E and Shi, Dan and Hattne, Johan and Nannenga, Brent L and Oskarsson, Marie E and Philipp, Stephan and Griner, Sarah and Jiang, Lin and Glabe, Charles G and Westermark, Gunilla T and Gonen, Tamir and Eisenberg, David S} } @article {48265, title = {Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Feb 13}, pages = {399-402}, abstract = {

Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.

}, issn = {1548-7105}, doi = {10.1038/nmeth.4178}, author = {de la Cruz, M Jason and Hattne, Johan and Shi, Dan and Seidler, Paul and Rodriguez, Jose and Reyes, Francis E and Sawaya, Michael R and Cascio, Duilio and Weiss, Simon C and Kim, Sun Kyung and Hinck, Cynthia S and Hinck, Andrew P and Calero, Guillermo and Eisenberg, David and Gonen, Tamir} } @article {48266, title = {Axonal Endoplasmic Reticulum Ca(2+) Content Controls Release Probability in CNS Nerve Terminals.}, journal = {Neuron}, volume = {93}, year = {2017}, month = {2017 Jan 30}, pages = {867-81}, abstract = {

Although the endoplasmic reticulum (ER) extends throughout axons and axonal ER dysfunction is implicated in numerous neurological diseases, its role at nerve terminals is poorly understood. We developed novel genetically encoded ER-targeted low-affinity Ca(2+) indicators optimized for examining axonal ER Ca(2+). Our experiments revealed that presynaptic function is tightly controlled by ER Ca(2+) content. We found that neuronal activity drives net Ca(2+) uptake into presynaptic ER although this activity does not contribute significantly to shaping cytosolic Ca(2+) except during prolonged repetitive firing. In contrast, we found that axonal ER acts as an actuator of plasma membrane (PM) function: [Ca(2+)]ER controls STIM1 activation in presynaptic terminals, which results in the local modulation of presynaptic function, impacting activity-driven Ca(2+) entry and release probability. These experiments reveal a critical role of presynaptic ER in the control of neurotransmitter release and will help frame future investigations into the molecular basis of ER-driven neuronal disease states.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.01.010}, author = {de Juan-Sanz, Jaime and Holt, Graham T and Schreiter, Eric R and de Juan, Fernando and Kim, Douglas S and Ryan, Timothy A} } @article {47875, title = {Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, year = {2016}, month = {2016 Oct 04}, pages = {11232-6}, abstract = {

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.

}, issn = {1091-6490}, doi = {10.1073/pnas.1606287113}, author = {Sawaya, Michael R and Rodriguez, Jose and Cascio, Duilio and Collazo, Michael J and Shi, Dan and Reyes, Francis E and Hattne, Johan and Gonen, Tamir and Eisenberg, David S} } @article {47711, title = {Accurate design of megadalton-scale two-component icosahedral protein complexes.}, journal = {Science (New York, N.Y.)}, volume = {353}, year = {2016}, month = {2016 Jul 22}, pages = {389-94}, abstract = {

Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallography show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of molecular cargo through charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.

}, issn = {1095-9203}, doi = {10.1126/science.aaf8818}, author = {Bale, Jacob B and Gonen, Shane and Liu, Yuxi and Sheffler, William and Ellis, Daniel and Thomas, Chantz and Cascio, Duilio and Yeates, Todd O and Gonen, Tamir and King, Neil P and Baker, David} } @article {47509, title = {Activation of NMDA receptors and the mechanism of inhibition by ifenprodil.}, journal = {Nature}, volume = {534}, year = {2016}, month = {2016 Jun 2}, pages = {63-8}, abstract = {

The physiology of N-methyl-d-aspartate (NMDA) receptors is fundamental to brain development and function. NMDA receptors are ionotropic glutamate receptors that function as heterotetramers composed mainly of GluN1 and GluN2 subunits. Activation of NMDA receptors requires binding of neurotransmitter agonists to a ligand-binding domain (LBD) and structural rearrangement of an amino-terminal domain (ATD). Recent crystal structures of GluN1-GluN2B NMDA receptors bound to agonists and an allosteric inhibitor, ifenprodil, represent the allosterically inhibited state. However, how the ATD and LBD move to activate the NMDA receptor ion channel remains unclear. Here we applied X-ray crystallography, single-particle electron cryomicroscopy and electrophysiology to rat NMDA receptors to show that, in the absence of ifenprodil, the bi-lobed structure of GluN2 ATD adopts an open conformation accompanied by rearrangement of the GluN1-GluN2 ATD heterodimeric interface, altering subunit orientation in the ATD and LBD and forming an active receptor conformation that gates the ion channel.

}, issn = {1476-4687}, doi = {10.1038/nature17679}, author = {Tajima, Nami and Karakas, Erkan and Grant, Timothy and Simorowski, Noriko and Diaz-Avalos, Ruben and Grigorieff, Nikolaus and Furukawa, Hiro} } @article {48468, title = {Active dendritic properties and local inhibitory input enable selectivity for object motion in mouse superior colliculus neurons.}, journal = {The Journal of Neuroscience : the Official Journal of the Society for Neuroscience}, volume = {36}, year = {2016}, month = {2016 Aug 31}, pages = {9111-23}, abstract = {

UNLABELLED: Neurons respond to specific features of sensory stimuli. In the visual system, for example, some neurons respond to motion of small but not large objects, whereas other neurons prefer motion of the entire visual field. Separate neurons respond equally to local and global motion but selectively to additional features of visual stimuli. How and where does response selectivity emerge? Here, we show that wide-field (WF) cells in retino-recipient layers of the mouse superior colliculus (SC) respond selectively to small moving objects. Moreover, we identify two mechanisms that contribute to this selectivity. First, we show that input restricted to a small portion of the broad dendritic arbor of WF cells is sufficient to trigger dendritic spikes that reliably propagate to the soma/axon. In vivo whole-cell recordings reveal that nearly every action potential evoked by visual stimuli has characteristics of spikes initiated in dendrites. Second, inhibitory input from a different class of SC neuron, horizontal cells, constrains the range of stimuli to which WF cells respond. Horizontal cells respond preferentially to the sudden appearance or rapid movement of large stimuli. Optogenetic reduction of their activity reduces movement selectivity and broadens size tuning in WF cells by increasing the relative strength of responses to stimuli that appear suddenly or cover a large region of space. Therefore, strongly propagating dendritic spikes enable small stimuli to drive spike output in WF cells and local inhibition helps restrict responses to stimuli that are both small and moving.

SIGNIFICANCE STATEMENT: How do neurons respond selectively to some sensory stimuli but not others? In the visual system, a particularly relevant stimulus feature is object motion, which often reveals other animals. Here, we show how specific cells in the superior colliculus, one synapse downstream of the retina, respond selectively to object motion. These wide-field (WF) cells respond strongly to small objects that move slowly anywhere through a large region of space, but not to stationary objects or full-field motion. Action potential initiation in dendrites enables small stimuli to trigger visual responses and inhibitory input from cells that prefer large, suddenly appearing, or quickly moving stimuli restricts responses of WF cells to objects that are small and moving.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0645-16.2016}, author = {Gale, Samuel D and Murphy, Gabe J} } @article {47260, title = {Adaptive and background-aware GAL4 expression enhancement of co-registered confocal microscopy images.}, journal = {Neuroinformatics}, volume = {14}, year = {2016}, month = {2016 Jan 7}, pages = {221-33}, abstract = {

GAL4 gene expression imaging using confocal microscopy is a common and powerful technique used to study the nervous system of a model organism such as Drosophila melanogaster. Recent research projects focused on high throughput screenings of thousands of different driver lines, resulting in large image databases. The amount of data generated makes manual assessment tedious or even impossible. The first and most important step in any automatic image processing and data extraction pipeline is to enhance areas with relevant signal. However, data acquired via high throughput imaging tends to be less then ideal for this task, often showing high amounts of background signal. Furthermore, neuronal structures and in particular thin and elongated projections with a weak staining signal are easily lost. In this paper we present a method for enhancing the relevant signal by utilizing a Hessian-based filter to augment thin and weak tube-like structures in the image. To get optimal results, we present a novel adaptive background-aware enhancement filter parametrized with the local background intensity, which is estimated based on a common background model. We also integrate recent research on adaptive image enhancement into our approach, allowing us to propose an effective solution for known problems present in confocal microscopy images. We provide an evaluation based on annotated image data and compare our results against current state-of-the-art algorithms. The results show that our algorithm clearly outperforms the existing solutions.

}, issn = {1559-0089}, doi = {10.1007/s12021-015-9289-y}, author = {Trapp, Martin and Schulze, Florian and Novikov, Alexey A and Tirian, Laszlo and J Dickson, Barry and B{\"u}hler, Katja} } @article {47987, title = {Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms.}, journal = {Nature Biotechnology}, volume = {34}, year = {2016}, month = {2016 Oct 31}, pages = {1267-78}, abstract = {

Optimal image quality in light-sheet microscopy requires a perfect overlap between the illuminating light sheet and the focal plane of the detection objective. However, mismatches between the light-sheet and detection planes are common owing to the spatiotemporally varying optical properties of living specimens. Here we present the AutoPilot framework, an automated method for spatiotemporally adaptive imaging that integrates (i) a multi-view light-sheet microscope capable of digitally translating and rotating light-sheet and detection planes in three dimensions and (ii) a computational method that continuously optimizes spatial resolution across the specimen volume in real time. We demonstrate long-term adaptive imaging of entire developing zebrafish (Danio rerio) and Drosophila melanogaster embryos and perform adaptive whole-brain functional imaging in larval zebrafish. Our method improves spatial resolution and signal strength two to five-fold, recovers cellular and sub-cellular structures in many regions that are not resolved by non-adaptive imaging, adapts to spatiotemporal dynamics of genetically encoded fluorescent markers and robustly optimizes imaging performance during large-scale morphogenetic changes in living organisms.

}, issn = {1546-1696}, doi = {10.1038/nbt.3708}, author = {Royer, Lo{\"\i}c A and Lemon, William C and Chhetri, Raghav K and Wan, Yinan and Coleman, Michael and Myers, Eugene W and Keller, Philipp J} } @article {47894, title = {Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.}, journal = {Nature neuroscience}, volume = {19}, year = {2016}, month = {2016 Feb}, pages = {335-46}, abstract = {

Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. We constructed a cellular taxonomy of one cortical region, primary visual cortex, in adult mice on the basis of single-cell RNA sequencing. We identified 49 transcriptomic cell types, including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types. We also analyzed cell type-specific mRNA processing and characterized genetic access to these transcriptomic types by many transgenic Cre lines. Finally, we found that some of our transcriptomic cell types displayed specific and differential electrophysiological and axon projection properties, thereby confirming that the single-cell transcriptomic signatures can be associated with specific cellular properties.

}, keywords = {Animals, Cell Line, Cerebral Cortex, Classification, gamma-Aminobutyric Acid, Gene Library, Genetic Markers, Glutamic Acid, Interneurons, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, Neurons, RNA, Sequence Analysis, RNA, Transcriptome, Visual Cortex}, issn = {1546-1726}, doi = {10.1038/nn.4216}, author = {Tasic, Bosiljka and Menon, Vilas and Nguyen, Thuc Nghi and Kim, Tae Kyung and Jarsky, Tim and Yao, Zizhen and Levi, Boaz and Gray, Lucas T and Sorensen, Staci A and Dolbeare, Tim and Bertagnolli, Darren and Goldy, Jeff and Shapovalova, Nadiya and Parry, Sheana and Lee, Changkyu and Smith, Kimberly and Bernard, Amy and Madisen, Linda and Sunkin, Susan M and Hawrylycz, Michael and Koch, Christof and Zeng, Hongkui} } @article {48068, title = {All-optical functional synaptic connectivity mapping in acute brain slices using CaMPARI.}, journal = {The Journal of Physiology}, volume = {595}, year = {2016}, month = {2017 Mar 01}, pages = {1465-77}, abstract = {

The calcium-modulated photoactivatable ratiometric integrator CaMPARI (Fosque et\ al., 2015) facilitates the study of neural circuits by permanently marking cells active during user-specified temporal windows. Permanent marking enables measurement of signals from large swathes of tissue and easy correlation of activity with other structural or functional labels. One potential application of CaMPARI is labeling neurons postsynaptic to specific populations targeted for optogenetic stimulation, giving rise to all-optical functional connectivity mapping. Here, we characterized the response of CaMPARI to several common types of neuronal calcium signals in mouse acute cortical brain slices. Our experiments show that CaMPARI is effectively converted by both action potentials and sub-threshold synaptic inputs, and that conversion level is correlated to synaptic strength. Importantly, we found that conversion rate can be tuned: it is linearly related to light intensity. At low photoconversion light levels CaMPARI offers a wide dynamic range due to slower conversion rate; at high light levels conversion is more rapid and more sensitive to activity. Finally, we employed CaMPARI and optogenetics for functional circuit mapping in ex vivo acute brain slices, which preserve in vivo-like connectivity of axon terminals. With a single light source, we stimulated channelrhodopsin-2-expressing long-range posteromedial (POm) thalamic axon terminals in cortex and induced CaMPARI conversion in recipient cortical neurons. We found that POm stimulation triggers robust photoconversion of layer 5 cortical neurons and weaker conversion of layer 2/3 neurons. Thus, CaMPARI enables network-wide, tunable, all-optical functional circuit mapping that captures supra- and sub-threshold depolarization. This article is protected by copyright. All rights reserved.

}, issn = {1469-7793}, doi = {10.1113/JP273116}, author = {Zolnik, Timothy A and Sha, Fern and Johenning, Friedrich and Schreiter, Eric R and Looger, Loren L and Larkum, Matthew E and Sachdev, Robert N S} } @article {47994, title = {AMPK activation prevents and reverses drug-induced mitochondrial and hepatocyte injury by promoting mitochondrial fusion and function.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016 Oct 31}, pages = {e0165638}, abstract = {

Mitochondrial damage is the major factor underlying drug-induced liver disease but whether conditions that thwart mitochondrial injury can prevent or reverse drug-induced liver damage is unclear. A key molecule regulating mitochondria quality control is AMP activated kinase (AMPK). When activated, AMPK causes mitochondria to elongate/fuse and proliferate, with mitochondria now producing more ATP and less reactive oxygen species. Autophagy is also triggered, a process capable of removing damaged/defective mitochondria. To explore whether AMPK activation could potentially prevent or reverse the effects of drug-induced mitochondrial and hepatocellular damage, we added an AMPK activator to collagen sandwich cultures of rat and human hepatocytes exposed to the hepatotoxic drugs, acetaminophen or diclofenac. In the absence of AMPK activation, the drugs caused hepatocytes to lose polarized morphology and have significantly decreased ATP levels and viability. At the subcellular level, mitochondria underwent fragmentation and had decreased membrane potential due to decreased expression of the mitochondrial fusion proteins Mfn1, 2 and/or Opa1. Adding AICAR, a specific AMPK activator, at the time of drug exposure prevented and reversed these effects. The mitochondria became highly fused and ATP production increased, and hepatocytes maintained polarized morphology. In exploring the mechanism responsible for this preventive and reversal effect, we found that AMPK activation prevented drug-mediated decreases in Mfn1, 2 and Opa1. AMPK activation also stimulated autophagy/mitophagy, most significantly in acetaminophen-treated cells. These results suggest that activation of AMPK prevents/reverses drug-induced mitochondrial and hepatocellular damage through regulation of mitochondrial fusion and autophagy, making it a potentially valuable approach for treatment of drug-induced liver injury.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0165638}, author = {Kang, Sun Woo Sophie and Haydar, Ghada and Taniane, Caitlin and Farrell, Geoffrey and Arias, Irwin M and Lippincott-Schwartz, Jennifer and Fu, Dong} } @article {47421, title = {Astrocytic glutamate transport regulates a Drosophila CNS synapse that lacks astrocyte ensheathment.}, journal = {The Journal of Comparative Neurology}, volume = {524}, year = {2016}, month = {2016 Apr 12}, pages = {1979-98}, abstract = {

Anatomical, molecular, and physiological interactions between astrocytes and neuronal synapses regulate information processing in the brain. The fruit fly Drosophila melanogaster has become a valuable experimental system for genetic manipulation of the nervous system and has enormous potential for elucidating mechanisms that mediate neuron-glia interactions. Here, we show the first electrophysiological recordings from Drosophila astrocytes and characterize their spatial and physiological relationship with particular synapses. Astrocyte intrinsic properties were found to be strongly analogous to those of vertebrate astrocytes, including a passive current-voltage relationship, low membrane resistance, high capacitance, and dye-coupling to local astrocytes. Responses to optogenetic stimulation of glutamatergic pre-motor neurons were correlated directly with anatomy using serial electron microscopy reconstructions of homologous identified neurons and surrounding astrocytic processes. Robust bidirectional communication was present: neuronal activation triggered astrocytic glutamate transport via Eaat1, and blocking Eaat1 extended glutamatergic interneuron-evoked inhibitory post-synaptic currents in motor neurons. The neuronal synapses were always located within a micron of an astrocytic process, but none were ensheathed by those processes. Thus, fly astrocytes can modulate fast synaptic transmission via neurotransmitter transport within these anatomical parameters. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.24016}, author = {MacNamee, Sarah E and Liu, Kendra E and Gerhard, Stephan and Tran, Cathy T and Fetter, Richard D and Cardona, Albert and Tolbert, Leslie P and Oland, Lynne A} } @article {47730, title = {Atomic resolution structure determination by the cryo-EM method MicroED.}, journal = {Protein Science : a Publication of the Protein Society}, volume = {26}, year = {2016}, month = {2016 Jul 25}, pages = {8-15}, abstract = {

The electron cryo-microscopy (cryoEM) method MicroED has been rapidly developing. In this review we highlight some of the key steps in MicroED from crystal analysis to structure determination. We compare and contrast MicroED and the latest X-ray based diffraction method the X-ray free electron laser (XFEL). Strengths and shortcomings of both MicroED and XFEL are discussed. Finally, all current MicroED structures are tabulated with a view to the future. This article is protected by copyright. All rights reserved.

}, issn = {1469-896X}, doi = {10.1002/pro.2989}, author = {Liu, Shian and Hattne, Johan and Reyes, Francis E and Sanchez-Martinez, Silvia and de la Cruz, M Jason and Shi, D and Gonen, T} } @article {48163, title = {Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos.}, journal = {Development (Cambridge, England)}, volume = {143}, year = {2016}, month = {2016 Feb 01}, pages = {540-6}, abstract = {

Analysis of differential gene expression is crucial for the study of cell fate and behavior during embryonic development. However, automated methods for the sensitive detection and quantification of RNAs at cellular resolution in embryos are lacking. With the advent of single-molecule fluorescence in situ hybridization (smFISH), gene expression can be analyzed at single-molecule resolution. However, the limited availability of protocols for smFISH in embryos and the lack of efficient image analysis pipelines have hampered quantification at the (sub)cellular level in complex samples such as tissues and embryos. Here, we present a protocol for smFISH on zebrafish embryo sections in combination with an image analysis pipeline for automated transcript detection and cell segmentation. We use this strategy to quantify gene expression differences between different cell types and identify differences in subcellular transcript localization between genes. The combination of our smFISH protocol and custom-made, freely available, analysis pipeline will enable researchers to fully exploit the benefits of quantitative transcript analysis at cellular and subcellular resolution in tissues and embryos.

}, keywords = {Animals, Automation, Cell Membrane, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, In Situ Hybridization, Fluorescence, RNA, RNA, Messenger, Subcellular Fractions, Transcription, Genetic, Zebrafish}, issn = {1477-9129}, doi = {10.1242/dev.128918}, author = {Stapel, L Carine and Lombardot, Benoit and Broaddus, Coleman and Kainmueller, Dagmar and Jug, Florian and Myers, Eugene W and Vastenhouw, Nadine L} } @article {47300, title = {Axonal filtering allows reliable output during dendritic plateau-driven complex spiking in CA1 neurons.}, journal = {Neuron}, volume = {89}, year = {2016}, month = {2016 Feb 17}, pages = {770-783}, abstract = {

In CA1 pyramidal neurons, correlated inputs trigger dendritic plateau potentials that drive neuronal plasticity and firing rate modulation. Given the strong electrotonic coupling between soma and axon, the \>25\ mV depolarization associated with the plateau could propagate through the axon to influence action potential initiation, propagation, and neurotransmitter release. We examined this issue in brain slices, awake mice, and a computational model. Despite profoundly inactivating somatic and proximal axon Na(+) channels, plateaus evoked action potentials that recovered to full amplitude in the distal axon (\>150\ μm) and triggered neurotransmitter release similar to regular spiking. This effect was due to strong attenuation of plateau depolarizations by axonal K(+) channels, allowing full axon repolarization and Na(+) channel deinactivation. High-pass filtering of dendritic plateaus by axonal K(+) channels should thus enable accurate transmission of gain-modulated firing rates, allowing neuronal firing to be efficiently read out by downstream regions as a simple rate code.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.12.040}, author = {Apostolides, Pierre F and Milstein, Aaron D and Grienberger, Christine and Bittner, Katie C and Magee, Jeffrey C} } @article {46774, title = {Actin depletion initiates events leading to granule secretion at the immunological synapse.}, journal = {Immunity}, volume = {42}, year = {2015}, month = {2015 May 19}, pages = {864-76}, abstract = {

Cytotoxic T lymphocytes (CTLs) use polarized secretion to rapidly destroy virally infected and tumor cells. To understand the temporal relationships between key events leading to secretion, we used high-resolution 4D imaging. CTLs approached targets with actin-rich projections at the leading edge, creating an initially actin-enriched contact with rearward-flowing actin. Within 1\ min, cortical actin reduced across the synapse, T\ cell receptors (TCRs) clustered centrally to form the central supramolecular activation cluster (cSMAC), and centrosome polarization began. Granules clustered around the moving centrosome within 2.5\ min and reached the synapse after 6\ min. TCR-bearing intracellular vesicles were delivered to the cSMAC as the centrosome docked. We found that the centrosome and granules were delivered to an area of membrane with reduced cortical actin density and phospholipid PIP2. These data resolve the temporal order of events during synapse maturation in 4D and reveal a critical role for actin depletion in regulating secretion.

}, issn = {1097-4180}, doi = {10.1016/j.immuni.2015.04.013}, author = {Ritter, Alex T and Asano, Yukako and Stinchcombe, Jane C and Dieckmann, N M G and Chen, Bi-Chang and Gawden-Bone, C and van Engelenburg, Schuyler and Legant, Wesley and Gao, Liang and Davidson, Michael W and Betzig, Eric and Lippincott-Schwartz, Jennifer and Griffiths, Gillian M} } @article {46366, title = {Adenotrophic viviparity in tsetse flies: potential for population control and as an insect model for lactation.}, journal = {Annual Review of Entomology}, volume = {60}, year = {2015}, month = {2015 Jan 7}, pages = {351-71}, abstract = {

Tsetse flies (Glossina spp.), vectors of African trypanosomes, are distinguished by their specialized reproductive biology, defined by adenotrophic viviparity (maternal nourishment of progeny by glandular secretions followed by live birth). This trait has evolved infrequently among insects and requires unique reproductive mechanisms. A key event in Glossina reproduction involves the transition between periods of lactation and nonlactation (dry periods). Increased lipolysis, nutrient transfer to the milk gland, and milk-specific protein production characterize lactation, which terminates at the birth of the progeny and is followed by a period of involution. The dry stage coincides with embryogenesis of the progeny, during which lipid reserves accumulate in preparation for the next round of lactation. The obligate bacterial symbiont Wigglesworthia glossinidia is critical to tsetse reproduction and likely provides B vitamins required for metabolic processes underlying lactation and/or progeny development. Here we describe findings that utilized transcriptomics, physiological assays, and RNA interference-based functional analysis to understand different components of adenotrophic viviparity in tsetse flies.

}, issn = {1545-4487}, doi = {10.1146/annurev-ento-010814-020834}, author = {Benoit, Joshua B and Attardo, Geoffrey M and Baumann, Aaron A and Michalkova, Veronika and Aksoy, Serap} } @article {46525, title = {Age-dependent changes in intrinsic neuronal excitability in subiculum after status epilepticus.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015 Mar 16}, pages = {e0119411}, abstract = {

Kainic acid-induced status epilepticus (KA-SE) in mature rats results in the development of spontaneous recurrent seizures and a pattern of cell death resembling hippocampal sclerosis in patients with temporal lobe epilepsy. In contrast, KA-SE in young animals before postnatal day (P) 18 is less likely to cause cell death or epilepsy. To investigate whether changes in neuronal excitability occur in the subiculum after KA-SE, we examined the age-dependent effects of SE on the bursting neurons of subiculum, the major output region of the hippocampus. Patch-clamp recordings were used to monitor bursting in pyramidal neurons in the subiculum of rat hippocampal slices. Neurons were studied either one or 2-3 weeks following injection of KA or saline (control) in immature (P15) or more mature (P30) rats, which differ in their sensitivity to KA as well as the long-term sequelae of the KA-SE. A significantly greater proportion of subicular pyramidal neurons from P15 rats were strong-bursting neurons and showed increased frequency-dependent bursting compared to P30 animals. Frequency-dependent burst firing was enhanced in P30, but not in P15 rats following KA-SE. The enhancement of bursting induced by KA-SE in more mature rats suggests that the frequency-dependent limitation of repetitive burst firing, which normally occurs in the subiculum, is compromised following SE. These changes could facilitate the initiation of spontaneous recurrent seizures or their spread from the hippocampus to other parts of the brain.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0119411}, author = {Chung, Sungkwon and Spruston, Nelson and Koh, Sookyong} } @article {68446, title = {Ankyrin Repeats Convey Force to Gate the NOMPC Mechanotransduction Channel.}, journal = {Cell}, volume = {162}, year = {2015}, month = {09/2015}, pages = {1391-403}, abstract = {

How metazoan mechanotransduction channels sense mechanical stimuli is not well understood. The NOMPC channel in the transient receptor potential (TRP) family, a mechanotransduction channel for Drosophila touch sensation and hearing, contains 29 Ankyrin repeats (ARs) that associate with microtubules. These ARs have been postulated to act as a tether that conveys force to the channel. Here, we report that these N-terminal ARs form a cytoplasmic domain essential for NOMPC mechanogating in vitro, mechanosensitivity of touch receptor neurons in vivo, and touch-induced behaviors of Drosophila larvae. Duplicating the ARs elongates the filaments that tether NOMPC to microtubules in mechanosensory neurons. Moreover, microtubule association is required for NOMPC mechanogating. Importantly, transferring the NOMPC ARs to mechanoinsensitive voltage-gated potassium channels confers mechanosensitivity to the chimeric channels. These experiments strongly support a tether mechanism of mechanogating for the NOMPC channel, providing insights into the basis of mechanosensitivity of mechanotransduction channels.

}, keywords = {Animals, Drosophila, Drosophila Proteins, Kv1.2 Potassium Channel, Larva, Mechanotransduction, Cellular, Microtubules, Protein Structure, Tertiary, Touch, Transient Receptor Potential Channels}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.08.024}, author = {Zhang, Wei and Cheng, Li E and Kittelmann, Maike and Li, Jiefu and Petkovic, Maja and Cheng, Tong and Jin, Peng and Guo, Zhenhao and G{\"o}pfert, Martin C and Jan, Lily Yeh and Jan, Yuh Nung} } @article {46505, title = {Applying superresolution localization-based microscopy to neurons.}, journal = {Synapse}, volume = {69}, year = {2015}, month = {2015 May}, pages = {283-94}, abstract = {

Proper brain function requires the precise localization of proteins and signaling molecules on a nanometer scale. The examination of molecular organization at this scale has been difficult in part because it is beyond the reach of conventional, diffraction-limited light microscopy. The recently developed method of superresolution, localization-based fluorescent microscopy (LBM), such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), has demonstrated a resolving power at a 10 nm scale and is poised to become a vital tool in modern neuroscience research. Indeed, LBM has revealed previously unknown cellular architectures and organizational principles in neurons. Here, we discuss the principles of LBM, its current applications in neuroscience, and the challenges that must be met before its full potential is achieved. We also present the unpublished results of our own experiments to establish a sample preparation procedure for applying LBM to study brain tissue. Synapse, 69:283-294, 2015. {\textcopyright} 2015 Wiley Periodicals, Inc.

}, issn = {1098-2396}, doi = {10.1002/syn.21806}, author = {Zhong, Haining} } @article {47147, title = {Applying the brakes: when to stop eating.}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Nov 4}, pages = {440-1}, abstract = {

The nucleus accumbens regulates consummatory behaviors, such as eating. In this issue of Neuron, O{\textquoteright}Connor et\ al. (2015) identify dopamine receptor 1-expressing neurons that project to the lateral hypothalamus as mediating rapid control over feeding behavior.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.10.034}, author = {Betley, J Nicholas and Sternson, Scott M} } @article {65782, title = {Artificial metalloenzymes derived from three-helix bundles.}, journal = {Current Opinion in Chemical Biology}, volume = {25C}, year = {2015}, month = {01/2015}, pages = {65 {\textendash} 70}, abstract = {

Three-helix bundles and coiled-coil motifs are well-established de novo designed scaffolds that have been investigated for their metal-binding and catalytic properties. Satisfaction of the primary coordination sphere for a given metal is sufficient to introduce catalytic activity and a given structure may catalyze different reactions dependent on the identity of the incorporated metal. Here we describe recent contributions in the de novo design of metalloenzymes based on three-helix bundles and coiled-coil motifs, focusing on non-heme systems for hydrolytic and redox chemistry.

}, doi = {10.1016/j.cbpa.2014.12.034}, author = {Tebo, Alison G and Pecoraro, Vincent L} } @article {46530, title = {Asymmetric formation of coated pits on dorsal and ventral surfaces at the leading edge of motile cells and on protrusions of immobile cells.}, journal = {Molecular Biology of the Cell}, volume = {26}, year = {2015}, month = {2015 Apr 7}, pages = {2044-53}, abstract = {

Clathrin/AP2-coated vesicles are the principal endocytic carriers originating at the plasma membrane. In experiments reported here, we have used spinning disk confocal and lattice light sheet microscopy to study the assembly dynamics of coated pits on the dorsal and ventral membranes of migrating U373 glioblastoma cells stably expressing AP2-EGFP and on lateral protrusions from immobile SUM159 breast carcinoma cells, gene edited to express AP2-EGFP. On U373 cells, coated pits initiated on the dorsal membrane at the front of the lamellipodium, as well as at the approximate boundary between the lamellipodium and lamella, and continued to grow as they were swept back toward the cell body; coated pits were absent from the corresponding ventral membrane. We observed a similar dorsal/ventral asymmetry on membrane protrusions from SUM159 cells. Stationary-coated pits formed and budded on the remainder of the dorsal and ventral surfaces of both types of cells. These observations support a previously proposed model that invokes net membrane deposition at the leading edge due to an imbalance between the endocytic and exocytic membrane flow at the front of a migrating cell.

}, issn = {1939-4586}, doi = {10.1091/mbc.E15-01-0055}, author = {Kural, Comert and Akatay, Ahmet Ata and Gaudin, Rapha{\"e}l and Chen, Bi-Chang and Legant, Wesley R and Betzig, Eric and Kirchhausen, Tom} } @article {47086, title = {Automated cerebellar lobule segmentation with application to cerebellar structural analysis in cerebellar disease.}, journal = {NeuroImage}, volume = {127}, year = {2015}, month = {2015 Sep 23}, pages = {435-44}, abstract = {

The cerebellum plays an important role in both motor control and cognitive function. Cerebellar function is topographically organized and diseases that affect specific parts of the cerebellum are associated with specific patterns of symptoms. Accordingly, delineation and quantification of cerebellar sub-regions from magnetic resonance images are important in the study of cerebellar atrophy and associated functional losses. This paper describes an automated cerebellar lobule segmentation method based on a graph cut segmentation framework. Results from multi-atlas labeling and tissue classification contribute to the region terms in the graph cut energy function and boundary classification contributes to the boundary term in the energy function. A cerebellar parcellation is achieved by minimizing the energy function using the α-expansion technique. The proposed method was evaluated using a leave-one-out cross-validation on 15 subjects including both healthy controls and patients with cerebellar diseases. Based on reported Dice coefficients, the proposed method outperforms two state-of-the-art methods. The proposed method was then applied to 2(j) 77 subjects to study the region-specific cerebellar structural differences in three spinocerebellar ataxia (SCA) genetic subtypes. Quantitative analysis of the lobule volumes show distinct patterns of volume changes associated with different SCA subtypes consistent with known patterns of atrophy in these genetic subtypes.

}, issn = {1095-9572}, doi = {10.1016/j.neuroimage.2015.09.032}, author = {Yang, Zhen and Ye, Chuyang and Bogovic, John A and Carass, Aaron and Jedynak, Bruno M and Ying, Sarah H and Prince, Jerry L} } @article {46974, title = {Automatic adaptation to fast input changes in a time-invariant neural circuit.}, journal = {PLoS Computational Biology}, volume = {11}, year = {2015}, month = {2015 Aug 6}, pages = {e1004315}, doi = {10.1371/journal.pcbi.1004315}, author = {Bharioke, Arjun and Chklovskii, Dmitri B} } @article {47885, title = {Automatic estimation and correction of anisotropic magnification distortion in electron microscopes.}, journal = {Journal of Structural Biology}, volume = {192}, year = {2015}, month = {2015 Nov}, pages = {204-8}, abstract = {

We demonstrate a significant anisotropic magnification distortion, found on an FEI Titan Krios microscope and affecting magnifications commonly used for data acquisition on a Gatan K2 Summit detector. We describe a program (mag_distortion_estimate) to automatically estimate anisotropic magnification distortion from a set of images of a standard gold shadowed diffraction grating. We also describe a program (mag_distortion_correct) to correct for the estimated distortion in collected images. We demonstrate that the distortion present on the Titan Krios microscope limits the resolution of a set of rotavirus VP6 images to \~{}7 {\r A}, which increases to \~{}3 {\r A} following estimation and correction of the distortion. We also use a 70S ribosome sample to demonstrate that in addition to affecting resolution, magnification distortion can also interfere with the classification of heterogeneous data.

}, keywords = {Anisotropy, Cryoelectron Microscopy, Gold, Image Enhancement}, issn = {1095-8657}, doi = {10.1016/j.jsb.2015.08.006}, author = {Grant, Timothy and Grigorieff, Nikolaus} } @article {45043, title = {Abdominal-B neurons control Drosophila virgin female receptivity.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 Jul 21}, pages = {1584-95}, abstract = {

BACKGROUND: Female sexual receptivity offers an excellent model for complex behavioral decisions. The female must parse her own reproductive state, the external environment, and male sensory cues to decide whether to copulate. In the\ fly Drosophila melanogaster, virgin female receptivity has received relatively little attention, and its neural circuitry and individual behavioral components remain unmapped. Using a genome-wide neuronal RNAi screen, we identify a subpopulation of neurons responsible for pausing, a novel behavioral aspect of virgin female receptivity characterized in this study.

RESULTS: We show that Abdominal-B (Abd-B), a homeobox transcription factor, is required in developing neurons for high levels of virgin female receptivity. Silencing adult Abd-B neurons significantly decreased receptivity. We characterize two components of receptivity that are elicited in sexually mature females by male courtship: pausing and vaginal plate opening. Silencing Abd-B neurons decreased pausing but did not affect vaginal plate opening, demonstrating that these two components of female sexual behavior are functionally separable. Synthetic activation of Abd-B neurons increased pausing, but male courtship song alone was not sufficient to elicit this behavior.

CONCLUSIONS: Our results provide an entry point to the neural circuit controlling virgin female receptivity. The female integrates multiple sensory cues from the male to execute discrete motor programs prior to copulation. Abd-B neurons control pausing, a key aspect of female sexual receptivity, in response to male courtship.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.06.011}, author = {Bussell, Jennifer J and Yapici, Nilay and Zhang, Stephen X and Dickson, Barry J and Vosshall, Leslie B} } @article {45102, title = {Accessing the third dimension in localization-based super-resolution microscopy.}, journal = {Physical Chemistry Chemical Physics}, volume = {16}, year = {2014}, month = {2014 Jul 16}, pages = {16340-8}, abstract = {

Only a few years after its inception, localization-based super-resolution microscopy has become widely employed in biological studies. Yet, it is primarily used in two-dimensional imaging and accessing the organization of cellular structures at the nanoscale in three dimensions (3D) still poses important challenges. Here, we review optical and computational techniques that enable the 3D localization of individual emitters and the reconstruction of 3D super-resolution images. These techniques are grouped into three main categories: PSF engineering, multiple plane imaging and interferometric approaches. We provide an overview of their technical implementation as well as commentary on their applicability. Finally, we discuss future trends in 3D localization-based super-resolution microscopy.

}, issn = {1463-9084}, doi = {10.1039/c4cp01380h}, author = {Hajj, Bassam and El Beheiry, Mohamed and Izeddin, Ignacio and Darzacq, Xavier and Dahan, Maxime} } @article {45180, title = {Accurate design of co-assembling multi-component protein nanomaterials.}, journal = {Nature}, volume = {510}, year = {2014}, month = {2014 Jun 5}, pages = {103-8}, abstract = {

The self-assembly of proteins into highly ordered nanoscale architectures is a hallmark of biological systems. The sophisticated functions of these molecular machines have inspired the development of methods to engineer self-assembling protein nanostructures; however, the design of multi-component protein nanomaterials with high accuracy remains an outstanding challenge. Here we report a computational method for designing protein nanomaterials in which multiple copies of two distinct subunits co-assemble into a specific architecture. We use the method to design five 24-subunit cage-like protein nanomaterials in two distinct symmetric architectures and experimentally demonstrate that their structures are in close agreement with the computational design models. The accuracy of the method and the number and variety of two-component materials that it makes accessible suggest a route to the construction of functional protein nanomaterials tailored to specific applications.

}, keywords = {Computer Simulation, Crystallography, X-Ray, Drug Design, Models, Molecular, Nanostructures, Protein Subunits, Proteins}, issn = {1476-4687}, doi = {10.1038/nature13404}, author = {King, Neil P and Bale, Jacob B and Sheffler, William and McNamara, Dan E and Gonen, Shane and Gonen, Tamir and Yeates, Todd O and Baker, David} } @article {48164, title = {Active graph matching for automatic joint segmentation and annotation of C. elegans.}, journal = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {17}, year = {2014}, month = {2014}, pages = {81-8}, abstract = {

In this work we present a novel technique we term active graph matching, which integrates the popular active shape model into a sparse graph matching problem. This way we are able to combine the benefits of a global, statistical deformation model with the benefits of a local deformation model in form of a second-order random field. We present a new iterative energy minimization technique which achieves empirically good results. This enables us to exceed state-of-the art results for the task of annotating nuclei in 3D microscopic images of C. elegans. Furthermore with the help of the generalized Hough transform we are able to jointly segment and annotate a large set of nuclei in a fully automatic fashion for the first time.

}, keywords = {Algorithms, Animals, Caenorhabditis elegans, Cell Nucleus, Image Enhancement, Image Interpretation, Computer-Assisted, Microscopy, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique}, author = {Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene} } @article {46049, title = {Adaptation to background light enables contrast coding at rod bipolar cell synapses.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Jan 22}, pages = {388-401}, abstract = {

Rod photoreceptors contribute to vision over an \~{} 6-log-unit range of light intensities. The wide dynamic range of rod vision is thought to depend upon light intensity-dependent switching between two parallel pathways linking rods to ganglion cells: a rod {\textrightarrow} rod bipolar (RB) cell pathway that operates at dim backgrounds and a rod {\textrightarrow} cone {\textrightarrow} cone bipolar cell pathway that operates at brighter backgrounds. We evaluated this conventional model of rod vision by recording rod-mediated light responses from ganglion and AII amacrine cells and by recording RB-mediated synaptic currents from AII amacrine cells in mouse retina. Contrary to the conventional model, we found that the RB pathway functioned at backgrounds sufficient to activate the rod {\textrightarrow} cone pathway. As background light intensity increased, the RB{\textquoteright}s role changed from encoding the absorption of single photons to encoding contrast modulations around mean luminance. This transition is explained by the intrinsic dynamics of transmission from RB synapses.

}, keywords = {2-Amino-5-phosphonovalerate, Adaptation, Ocular, Animals, Biophysics, Computer Simulation, Excitatory Amino Acid Antagonists, Glucosamine 6-Phosphate N-Acetyltransferase, Green Fluorescent Proteins, In Vitro Techniques, Light, Mice, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, Models, Neurological, Patch-Clamp Techniques, Quinoxalines, Retinal Bipolar Cells, Retinal Rod Photoreceptor Cells, Synapses, Visual Pathways}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.10.054}, author = {Ke, Jiang-Bin and Wang, Yanbin V and Borghuis, Bart G and Cembrowski, Mark S and Riecke, Hermann and Kath, William L and Demb, Jonathan B and Singer, Joshua H} } @article {45717, title = {Agouti-related protein neuron circuits that regulate appetite.}, journal = {Neuroendocrinology}, volume = {507}, year = {2014}, month = {2014 Nov 6}, pages = {238-42}, abstract = {

New tools for mapping and manipulating molecularly defined neural circuits have improved understanding of how the central nervous system regulates appetite. Studies focused on AGRP neurons, a starvation-sensitive hypothalamic population, have identified multiple circuit elements that can elicit or suppress feeding behavior. Distinct axon projections of this neuron population point to different circuits that regulate long-term appetite, short-term feeding, or visceral malaise-mediated anorexia. Here, we review recent studies examining these neural circuits that control food intake. {\textcopyright} 2014 S. Karger AG, Basel.

}, issn = {1423-0194}, doi = {10.1159/000369072}, author = {Sternson, Scott M and Atasoy, Deniz} } @article {6935, title = {Allelic heterogeneity in NCF2 associated with systemic lupus erythematosus (SLE) susceptibility across four ethnic populations.}, journal = {Human Molecular Genetics}, volume = {23}, year = {2014}, month = {2014 Mar 15}, pages = {1656-68}, abstract = {

Recent reports have associated NCF2, encoding a core component of the multi-protein NADPH oxidase (NADPHO), with systemic lupus erythematosus (SLE) susceptibility in individuals of European ancestry. To identify ethnicity-specific and -robust variants within NCF2, we assessed 145 SNPs in and around the NCF2 gene in 5325 cases and 21 866 controls of European-American (EA), African-American (AA), Hispanic (HS) and Korean (KR) ancestry. Subsequent imputation, conditional, haplotype and bioinformatic analyses identified seven potentially functional SLE-predisposing variants. Association with non-synonymous rs17849502, previously reported in EA, was detected in EA, HS and AA (P(EA) = 1.01 {\texttimes} 10(-54), PHS = 3.68 {\texttimes} 10(-10), P(AA) = 0.03); synonymous rs17849501 was similarly significant. These SNPs were monomorphic in KR. Novel associations were detected with coding variants at rs35937854 in AA (PAA = 1.49 {\texttimes} 10(-9)), and rs13306575 in HS and KR (P(HS) = 7.04 {\texttimes} 10(-7), P(KR) = 3.30 {\texttimes} 10(-3)). In KR, a 3-SNP haplotype was significantly associated (P = 4.20 {\texttimes} 10(-7)), implying that SLE predisposing variants were tagged. Significant SNP-SNP interaction (P = 0.02) was detected between rs13306575 and rs17849502 in HS, and a dramatically increased risk (OR = 6.55) with a risk allele at each locus. Molecular modeling predicts that these non-synonymous mutations could disrupt NADPHO complex assembly. The risk allele of rs17849501, located in a conserved transcriptional regulatory region, increased reporter gene activity, suggesting in vivo enhancer function. Our results not only establish allelic heterogeneity within NCF2 associated with SLE, but also emphasize the utility of multi-ethnic cohorts to identify predisposing variants explaining additional phenotypic variance ({\textquoteright}missing heritability{\textquoteright}) of complex diseases like SLE.

}, issn = {1460-2083}, doi = {10.1093/hmg/ddt532}, author = {Kim-Howard, Xana and Sun, Celi and Molineros, Julio E and Maiti, Amit K and Chandru, Hema and Adler, Adam and Wiley, Graham B and Kaufman, Kenneth M and Kottyan, Leah and Guthridge, Joel M and Rasmussen, Astrid and Kelly, Jennifer and S{\'a}nchez, Elena and Raj, Prithvi and Li, Quan-Zhen and Bang, So-Young and Lee, Hye-Soon and Kim, Tae-Hwan and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung Cheol and Lee, Shin-Seok and Han, Bok-Ghee and Olsen, Nancy J and Karp, David R and Moser, Kathy and Pons-Estel, Bernardo A and Wakeland, Edward K and James, Judith A and Harley, John B and Bae, Sang-Cheol and Gaffney, Patrick M and Alarc{\'o}n-Riquelme, Marta and Looger, Loren L and Nath, Swapan K} } @article {6932, title = {Amphotericin forms an extramembranous and fungicidal sterol sponge.}, journal = {Nature Chemical Biology}, volume = {10}, year = {2014}, month = {2014 Mar 30}, pages = {400-6}, abstract = {

For over 50 years, amphotericin has remained the powerful but highly toxic last line of defense in treating life-threatening fungal infections in humans with minimal development of microbial resistance. Understanding how this small molecule kills yeast is thus critical for guiding development of derivatives with an improved therapeutic index and other resistance-refractory antimicrobial agents. In the widely accepted ion channel model for its mechanism of cytocidal action, amphotericin forms aggregates inside lipid bilayers that permeabilize and kill cells. In contrast, we report that amphotericin exists primarily in the form of large, extramembranous aggregates that kill yeast by extracting ergosterol from lipid bilayers. These findings reveal that extraction of a polyfunctional lipid underlies the resistance-refractory antimicrobial action of amphotericin and suggests a roadmap for separating its cytocidal and membrane-permeabilizing activities. This new mechanistic understanding is also guiding development of what are to our knowledge the first derivatives of amphotericin that kill yeast but not human cells.

}, issn = {1552-4469}, doi = {10.1038/nchembio.1496}, author = {Anderson, Thomas M and Clay, Mary C and Cioffi, Alexander G and Diaz, Katrina A and Hisao, Grant S and Tuttle, Marcus D and Nieuwkoop, Andrew J and Comellas, Gemma and Maryum, Nashrah and Wang, Shu and Uno, Brice E and Wildeman, Erin L and Gonen, Tamir and Rienstra, Chad M and Burke, Martin D} } @article {45787, title = {Anesthetized- and awake-patched whole-cell recordings in freely moving rats using UV-cured collar-based electrode stabilization.}, journal = {Nature Protocols}, volume = {9}, year = {2014}, month = {2014 Nov 06}, pages = {2784-95}, abstract = {

Intracellular recording allows precise measurement and manipulation of individual neurons, but it requires stable mechanical contact between the electrode and the cell membrane, and thus it has remained challenging to perform in behaving animals. Whole-cell recordings in freely moving animals can be obtained by rigidly fixing ({\textquoteright}anchoring{\textquoteright}) the pipette electrode to the head; however, previous anchoring procedures were slow and often caused substantial pipette movement, resulting in loss of the recording or of recording quality. We describe a UV-transparent collar and UV-cured adhesive technique that rapidly (within 15 s) anchors pipettes in place with virtually no movement, thus substantially improving the reliability, yield and quality of freely moving whole-cell recordings. Recordings are first obtained from anesthetized or awake head-fixed rats. UV light cures the thin adhesive layers linking pipette to collar to head. Then, the animals are rapidly and smoothly released for recording during unrestrained behavior. The anesthetized-patched version can be completed in \~{}4-7 h (excluding histology) and the awake-patched version requires \~{}1-4 h per day for \~{}2 weeks. These advances should greatly facilitate studies of neuronal integration and plasticity in identified cells during natural behaviors.

}, issn = {1750-2799}, doi = {10.1038/nprot.2014.190}, author = {Lee, Doyun and Shtengel, Gleb and Osborne, Jason E and Lee, Albert K} } @article {6937, title = {Annotating functional RNAs in genomes using infernal.}, journal = {Methods in Molecular Biology}, volume = {1097}, year = {2014}, month = {2014}, pages = {163-97}, abstract = {

Many different types of functional non-coding RNAs participate in a wide range of important cellular functions but the large majority of these RNAs are not routinely annotated in published genomes. Several programs have been developed for identifying RNAs, including specific tools tailored to a particular RNA family as well as more general ones designed to work for any family. Many of these tools utilize covariance models (CMs), statistical models of the conserved sequence, and structure of an RNA family. In this chapter, as an illustrative example, the Infernal software package and CMs from the Rfam database are used to identify RNAs in the genome of the archaeon Methanobrevibacter ruminantium, uncovering some additional RNAs not present in the genome{\textquoteright}s initial annotation. Analysis of the results and comparison with family-specific methods demonstrate some important strengths and weaknesses of this general approach.

}, issn = {1940-6029}, doi = {10.1007/978-1-62703-709-9_9}, author = {Nawrocki, Eric P} } @article {46226, title = {Annotating synapses in large EM datasets.}, journal = {arXiv}, year = {2014}, month = {2014 Sep 5}, pages = {arXiv:1409.1801 [q-bio.QM]}, abstract = {

Reconstructing neuronal circuits at the level of synapses is a central problem in neuroscience and becoming a focus of the emerging field of connectomics. To date, electron microscopy (EM) is the most proven technique for identifying and quantifying synaptic connections. As advances in EM make acquiring larger datasets possible, subsequent manual synapse identification ({\em i.e.}, proofreading) for deciphering a connectome becomes a major time bottleneck. Here we introduce a large-scale, high-throughput, and semi-automated methodology to efficiently identify synapses. We successfully applied our methodology to the Drosophila medulla optic lobe, annotating many more synapses than previous connectome efforts. Our approaches are extensible and will make the often complicated process of synapse identification accessible to a wider-community of potential proofreaders.

}, url = {http://arxiv.org/abs/1409.1801}, author = {Plaza, Stephen M and Parag, Toufiq and Huang, Gary and Olbris, Donald J. and Saunders, Mathew A. and Rivlin, Patricia K.} } @article {45048, title = {Ascending SAG neurons control sexual receptivity of Drosophila females.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Jul 2}, pages = {135-48}, abstract = {

Mating induces pronounced changes in female reproductive behavior, typically including a dramatic reduction in sexual receptivity. In Drosophila, postmating behavioral changes are triggered by sex peptide (SP), a male seminal fluid peptide that acts via a\ receptor (SPR) expressed in sensory neurons (SPSNs) of the female reproductive tract. Here, we identify second-order neurons that mediate the behavioral changes induced by SP. These SAG neurons receive synaptic input from SPSNs in the abdominal ganglion and project to the dorsal protocerebrum. Silencing SAG neurons renders virgin females unreceptive, whereas activating them increases the receptivity of females that have already mated. Physiological experiments demonstrate that SP downregulates the excitability of the SPSNs, and hence their input onto SAG neurons. These data thus provide a physiological correlate of mating status in the female central nervous system and a key entry point into the brain circuits that control sexual receptivity.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.05.017}, author = {Feng, Kai and Palfreyman, Mark T and H{\"a}semeyer, Martin and Talsma, Aaron and Dickson, Barry J} } @article {45788, title = {Assembling cell ensembles.}, journal = {Cell}, volume = {157}, year = {2014}, month = {2014 Jun 19}, pages = {1502-4}, abstract = {

The way the hippocampus processes information and encodes memories in the form of "cell assemblies" is likely determined in part by how its circuits are wired up during development. In this issue, Xu et\ al. now provide new insight into how neurons arising from a single common precursor migrate to their final destination and form functionally synchronous ensembles.

}, keywords = {Animals, Hippocampus}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.05.032}, author = {Spruston, Nelson} } @article {45418, title = {Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience.}, journal = {Development}, volume = {141}, year = {2014}, month = {2014 Jun}, pages = {2524-32}, abstract = {

A major limitation in understanding embryonic development is the lack of cell type-specific markers. Existing gene expression and marker atlases provide valuable tools, but they typically have one or more limitations: a lack of single-cell resolution; an inability to register multiple expression patterns to determine their precise relationship; an inability to be upgraded by users; an inability to compare novel patterns with the database patterns; and a lack of three-dimensional images. Here, we develop new {\textquoteright}atlas-builder{\textquoteright} software that overcomes each of these limitations. A newly generated atlas is three-dimensional, allows the precise registration of an infinite number of cell type-specific markers, is searchable and is open-ended. Our software can be used to create an atlas of any tissue in any organism that contains stereotyped cell positions. We used the software to generate an {\textquoteright}eNeuro{\textquoteright} atlas of the Drosophila embryonic CNS containing eight transcription factors that mark the major CNS cell types (motor neurons, glia, neurosecretory cells and interneurons). We found neuronal, but not glial, nuclei occupied stereotyped locations. We added 75 new Gal4 markers to the atlas to identify over 50\% of all interneurons in the ventral CNS, and these lines allowed functional access to those interneurons for the first time. We expect the atlas-builder software to benefit a large proportion of the developmental biology community, and the eNeuro atlas to serve as a publicly accessible hub for integrating neuronal attributes - cell lineage, gene expression patterns, axon/dendrite projections, neurotransmitters--and linking them to individual neurons.

}, keywords = {Animals, Axons, Cell Lineage, Central Nervous System, Computational Biology, Databases, Genetic, Dendrites, Drosophila melanogaster, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Developmental, Genetic Markers, Interneurons, Mice, Neurons, Neurotransmitter Agents, Rats, Software}, issn = {1477-9129}, doi = {10.1242/dev.108720}, author = {Heckscher, Ellie S and Long, Fuhui and Layden, Michael J and Chuang, Chein-Hui and Manning, Laurina and Richart, Jourdain and Pearson, Joseph C and Crews, Stephen T and Peng, Hanchuan and Myers, Eugene and Doe, Chris Q} } @article {6880, title = {Automated detection of synapses in serial section transmission electron microscopy image stacks.}, journal = {PloS one}, volume = {9}, year = {2014}, month = {2014}, pages = {e87351}, abstract = {We describe a method for fully automated detection of chemical synapses in serial electron microscopy images with highly anisotropic axial and lateral resolution, such as images taken on transmission electron microscopes. Our pipeline starts from classification of the pixels based on 3D pixel features, which is followed by segmentation with an Ising model MRF and another classification step, based on object-level features. Classifiers are learned on sparse user labels; a fully annotated data subvolume is not required for training. The algorithm was validated on a set of 238 synapses in 20 serial 7197{\texttimes}7351 pixel images (4.5{\texttimes}4.5{\texttimes}45 nm resolution) of mouse visual cortex, manually labeled by three independent human annotators and additionally re-verified by an expert neuroscientist. The error rate of the algorithm (12\% false negative, 7\% false positive detections) is better than state-of-the-art, even though, unlike the state-of-the-art method, our algorithm does not require a prior segmentation of the image volume into cells. The software is based on the ilastik learning and segmentation toolkit and the vigra image processing library and is freely available on our website, along with the test data and gold standard annotations (http://www.ilastik.org/synapse-detection/sstem).}, issn = {1932-6203}, doi = {10.1371/journal.pone.0087351}, author = {Kreshuk, Anna and Koethe, Ullrich and Pax, Elizabeth and Bock, Davi D and Hamprecht, Fred A} } @article {45098, title = {Automated image-based tracking and its application in ecology.}, journal = {Trends in Ecology and Evolution}, volume = {29}, year = {2014}, month = {2014 Jul}, pages = {417-428}, abstract = {

The behavior of individuals determines the strength and outcome of ecological interactions, which drive population, community, and ecosystem organization. Bio-logging, such as telemetry and animal-borne imaging, provides essential individual viewpoints, tracks, and life histories, but requires capture of individuals and is often impractical to scale. Recent developments in automated image-based tracking offers opportunities to remotely quantify and understand individual behavior at scales and resolutions not previously possible, providing an essential supplement to other tracking methodologies in ecology. Automated image-based tracking should continue to advance the field of ecology by enabling better understanding of the linkages between individual and higher-level ecological processes, via high-throughput quantitative analysis of complex ecological patterns and processes across scales, including analysis of environmental drivers.

}, issn = {1872-8383}, doi = {10.1016/j.tree.2014.05.004}, author = {Dell, Anthony I and Bender, John A and Branson, Kristin and Couzin, Iain D and de Polavieja, Gonzalo G and Noldus, Lucas P J J and P{\'e}rez-Escudero, Alfonso and Perona, Pietro and Straw, Andrew D and Wikelski, Martin and Brose, Ulrich} } @article {46227, title = {Automatic neuron type identification by neurite localization in the Drosophila medulla.}, journal = {arXiv}, year = {2014}, month = {2014 Sep 5}, pages = {arXiv:1409.1892 [q-bio.NC]}, abstract = {

Mapping the connectivity of neurons in the brain (i.e., connectomics) is a challenging problem due to both the number of connections in even the smallest organisms and the nanometer resolution required to resolve them. Because of this, previous connectomes contain only hundreds of neurons, such as in the C.elegans connectome. Recent technological advances will unlock the mysteries of increasingly large connectomes (or partial connectomes). However, the value of these maps is limited by our ability to reason with this data and understand any underlying motifs. To aid connectome analysis, we introduce algorithms to cluster similarly-shaped neurons, where 3D neuronal shapes are represented as skeletons. In particular, we propose a novel location-sensitive clustering algorithm. We show clustering results on neurons reconstructed from the Drosophila medulla that show high-accuracy.

}, author = {Plaza, Stephen M and Zhao, Ting} } @article {47642, title = {Accelerating 3B single-molecule super-resolution microscopy with cloud computing.}, journal = {Nature methods}, volume = {10}, year = {2013}, month = {2013 Feb}, pages = {96-7}, keywords = {Computational Biology, Computers, Fluorescent Dyes, Microscopy, Fluorescence, Nanotechnology}, issn = {1548-7105}, doi = {10.1038/nmeth.2335}, author = {Hu, Ying S and Nan, Xiaolin and Sengupta, Prabuddha and Lippincott-Schwartz, Jennifer and Cang, Hu} } @article {6534, title = {Addiction.}, journal = {Current Opinion in Neurobiology}, volume = {23}, year = {2013}, month = {2013 Aug}, pages = {463-6}, abstract = {

Drug addiction and obesity share the core feature that those afflicted by the disorders express a desire to limit drug or food consumption yet persist despite negative consequences. Emerging evidence suggests that the compulsivity that defines these disorders may arise, to some degree at least, from common underlying neurobiological mechanisms. In particular, both disorders are associated with diminished striatal dopamine D2 receptor (D2R) availability, likely reflecting their decreased maturation and surface expression. In striatum, D2Rs are expressed by approximately half of the principal medium spiny projection neurons (MSNs), the striatopallidal neurons of the so-called {\textquoteright}indirect{\textquoteright} pathway. D2Rs are also expressed presynaptically on dopamine terminals and on cholinergic interneurons. This heterogeneity of D2R expression has hindered attempts, largely using traditional pharmacological approaches, to understand their contribution to compulsive drug or food intake. The emergence of genetic technologies to target discrete populations of neurons, coupled to optogenetic and chemicogenetic tools to manipulate their activity, have provided a means to dissect striatopallidal and cholinergic contributions to compulsivity. Here, we review recent evidence supporting an important role for striatal D2R signaling in compulsive drug use and food intake. We pay particular attention to striatopallidal projection neurons and their role in compulsive responding for food and drugs. Finally, we identify opportunities for future obesity research using known mechanisms of addiction as a heuristic, and leveraging new tools to manipulate activity of specific populations of striatal neurons to understand their contributions to addiction and obesity.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2013.07.003}, author = {Everitt, Barry J and Heberlein, Ulrike} } @article {6127, title = {Admixture mapping in lupus identifies multiple functional variants within IFIH1 associated with apoptosis, inflammation, and autoantibody production.}, journal = {PLoS Genetics}, volume = {9}, year = {2013}, month = {2013 Feb 18}, pages = {e1003222}, abstract = {

Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease with a strong genetic component. African-Americans (AA) are at increased risk of SLE, but the genetic basis of this risk is largely unknown. To identify causal variants in SLE loci in AA, we performed admixture mapping followed by fine mapping in AA and European-Americans (EA). Through genome-wide admixture mapping in AA, we identified a strong SLE susceptibility locus at 2q22-24 (LOD=6.28), and the admixture signal is associated with the European ancestry (ancestry risk ratio \ 1.5). Large-scale genotypic analysis on 19,726 individuals of African and European ancestry revealed three independently associated variants in the IFIH1 gene: an intronic variant, rs13023380 [P(meta) = 5.20{\texttimes}10(-14); odds ratio, 95\% confidence interval = 0.82 (0.78-0.87)], and two missense variants, rs1990760 (Ala946Thr) [P(meta) = 3.08{\texttimes}10(-7); 0.88 (0.84-0.93)] and rs10930046 (Arg460His) [P(dom) = 1.16{\texttimes}10(-8); 0.70 (0.62-0.79)]. Both missense variants produced dramatic phenotypic changes in apoptosis and inflammation-related gene expression. We experimentally validated function of the intronic SNP by DNA electrophoresis, protein identification, and in vitro protein binding assays. DNA carrying the intronic risk allele rs13023380 showed reduced binding efficiency to a cellular protein complex including nucleolin and lupus autoantigen Ku70/80, and showed reduced transcriptional activity in vivo. Thus, in SLE patients, genetic susceptibility could create a biochemical imbalance that dysregulates nucleolin, Ku70/80, or other nucleic acid regulatory proteins. This could promote antibody hypermutation and auto-antibody generation, further destabilizing the cellular network. Together with molecular modeling, our results establish a distinct role for IFIH1 in apoptosis, inflammation, and autoantibody production, and explain the molecular basis of these three risk alleles for SLE pathogenesis.

}, keywords = {African Americans, Alleles, Antigens, Apoptosis, Autoantibodies, Chromosome Mapping, DEAD-box RNA Helicases, DNA-Binding Proteins, European Continental Ancestry Group, Genetic Predisposition to Disease, Genome, Haplotypes, Human, Humans, Inflammation, Lupus Erythematosus, Nuclear, Polymorphism, Protein Binding, Single Nucleotide, Systemic}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1003222}, author = {Molineros, Julio E and Maiti, Amit K and Sun, Celi and Looger, Loren L and Han, Shizhong and Kim-Howard, Xana and Glenn, Stuart and Adler, Adam and Kelly, Jennifer A and Niewold, Timothy B and Gilkeson, Gary S and Brown, Elizabeth E and Alarc{\'o}n, Graciela S and Edberg, Jeffrey C and Petri, Michelle and Ramsey-Goldman, Rosalind and Reveille, John D and Vil{\'a}, Luis M and Freedman, Barry I and Tsao, Betty P and Criswell, Lindsey A and Jacob, Chaim O and Moore, Jason H and Vyse, Timothy J and Langefeld, Carl L and Guthridge, Joel M and Gaffney, Patrick M and Moser, Kathy L and Scofield, R Hal and Alarc{\'o}n-Riquelme, Marta E and Williams, Scott M and Merrill, Joan T and James, Judith A and Kaufman, Kenneth M and Kimberly, Robert P and Harley, John B and Nath, Swapan K} } @article {6252, title = {Allosteric mechanism of water-channel gating by Ca(2+)-calmodulin.}, journal = {Nature Structural \& Molecular Biology}, volume = {20}, year = {2013}, month = {2013 Jul 28}, pages = {1085-92}, abstract = {

Calmodulin (CaM) is a universal regulatory protein that communicates the presence of calcium to its molecular targets and correspondingly modulates their function. This key signaling protein is important for controlling the activity of hundreds of membrane channels and transporters. However, understanding of the structural mechanisms driving CaM regulation of full-length membrane proteins has remained elusive. In this study, we determined the pseudoatomic structure of full-length mammalian aquaporin-0 (AQP0, Bos taurus) in complex with CaM, using EM to elucidate how this signaling protein modulates water-channel function. Molecular dynamics and functional mutation studies reveal how CaM binding inhibits AQP0 water permeability by allosterically closing the cytoplasmic gate of AQP0. Our mechanistic model provides new insight, only possible in the context of the fully assembled channel, into how CaM regulates multimeric channels by facilitating cooperativity between adjacent subunits.

}, issn = {1545-9985}, doi = {10.1038/nsmb.2630}, author = {Reichow, Steve L and Clemens, Daniel M and Freites, J Alfredo and N{\'e}meth-Cahalan, Karin L and Heyden, Matthias and Tobias, Douglas J and Hall, James E and Gonen, Tamir} } @article {45724, title = {Aphids evolved novel secreted proteins for symbiosis with bacterial endosymbiont.}, journal = {Proc Biol Sci}, volume = {280}, year = {2013}, month = {2013 Jan 7}, pages = {20121952}, abstract = {

Aphids evolved novel cells, called bacteriocytes, that differentiate specifically to harbour the obligatory mutualistic endosymbiotic bacteria Buchnera aphidicola. The genome of the host aphid Acyrthosiphon pisum contains many orphan genes that display no similarity with genes found in other sequenced organisms, prompting us to hypothesize that some of these orphan genes are related to lineage-specific traits, such as symbiosis. We conducted deep sequencing of bacteriocytes mRNA followed by whole mount in situ hybridizations of over-represented transcripts encoding aphid-specific orphan proteins. We identified a novel class of genes that encode small proteins with signal peptides, which are often cysteine-rich, that are over-represented in bacteriocytes. These genes are first expressed at a developmental time point coincident with the incorporation of symbionts strictly in the cells that contribute to the bacteriocyte and this bacteriocyte-specific expression is maintained throughout the aphid{\textquoteright}s life. The expression pattern suggests that recently evolved secretion proteins act within bacteriocytes, perhaps to mediate the symbiosis with beneficial bacterial partners, which is reminiscent of the evolution of novel cysteine-rich secreted proteins of leguminous plants that regulate nitrogen-fixing endosymbionts.

}, keywords = {Amino Acid Sequence, Animals, Aphids, Buchnera, DNA, Complementary, Evolution, Molecular, High-Throughput Nucleotide Sequencing, In Situ Hybridization, Insect Proteins, Protein Sorting Signals, RNA, Messenger, Sequence Alignment, Sequence Analysis, RNA, Symbiosis}, issn = {1471-2954}, doi = {10.1098/rspb.2012.1952}, author = {Shigenobu, Shuji and Stern, David L} } @article {6101, title = {APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, year = {2013}, month = {2013 Jun 1}, pages = {1448-54}, abstract = {Tracing of neuron morphology is an essential technique in computational neuroscience. However, despite a number of existing methods, few open-source techniques are completely or sufficiently automated and at the same time are able to generate robust results for real 3D microscopy images.}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btt170}, author = {Xiao, Hang and Peng, Hanchuan} } @article {6452, title = {ASI regulates satiety quiescence in C. elegans.}, journal = {The Journal of Neuroscience : The Official Journal of the Society for Neuroscience}, volume = {33}, year = {2013}, month = {2013 Jun 5}, pages = {9716-24}, abstract = {

In Caenorhabditis elegans, satiety quiescence mimics behavioral aspects of satiety and postprandial sleep in mammals. On the basis of calcium-imaging, genetics, and behavioral studies, here we report that a pair of amphid neurons, ASI, is activated by nutrition and regulates worms{\textquoteright} behavioral states specifically promoting satiety quiescence; ASI inhibits the switch from quiescence to dwelling (a browsing state) and accelerates the switch from dwelling to quiescence. The canonical TGFβ pathway, whose ligand is released from ASI, regulates satiety quiescence. The mutants of a ligand, a receptor and SMADs in the TGFβ pathway all eat more and show less quiescence than wild-type. The TGFβ receptor in downstream neurons RIM and RIC is sufficient for worms to exhibit satiety quiescence, suggesting neuronal connection from ASI to RIM and RIC is essential for feeding regulation through the TGFβ pathway. ASI also regulates satiety quiescence partly through cGMP signaling; restoring cGMP signaling in ASI rescues the satiety quiescence defect of cGMP signaling mutants. From these results, we propose that TGFβ and cGMP pathways in ASI connect nutritional status to promotion of satiety quiescence, a sleep-like behavioral state.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cyclic GMP, Eating, Genetically Modified, Motor Activity, Protein Kinases, Satiation, Sensory Receptor Cells, Transforming Growth Factor beta}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4493-12.2013}, author = {Gallagher, Thomas and Kim, Jeongho and Oldenbroek, Marieke and Kerr, Rex and You, Young-Jai} } @article {6174, title = {Automated alignment of imperfect EM images for neural reconstruction.}, journal = {arXiv}, year = {2013}, month = {2013 Apr-22}, pages = {arXiv:1304.6034 [q-bio.QM]}, abstract = {

The most established method of reconstructing neural circuits from animals involves slicing tissue very thin, then taking mosaics of electron microscope (EM) images. To trace neurons across different images and through different sections, these images must be accurately aligned, both with the others in the same section and to the sections above and below. Unfortunately, sectioning and imaging are not ideal processes - some of the problems that make alignment difficult include lens distortion, tissue shrinkage during imaging, tears and folds in the sectioned tissue, and dust and other artifacts. In addition the data sets are large (hundreds of thousands of images) and each image must be aligned with many neighbors, so the process must be automated and reliable. This paper discusses methods of dealing with these problems, with numeric results describing the accuracy of the resulting alignments.

}, url = {http://arxiv.org/abs/1304.6034}, author = {Scheffer, L. K. and Karsh, Bill and Vitaladevun, S.} } @article {45850, title = {Automated long-term tracking and social behavioural phenotyping of animal colonies within a semi-natural environment.}, journal = {Nature Communications}, volume = {4}, year = {2013}, month = {2013}, pages = {2018}, abstract = {

Social behaviour has a key role in animal survival across species, ranging from insects to primates and humans. However, the biological mechanisms driving natural interactions between multiple animals, over long-term periods, are poorly studied and remain elusive. Rigorous and objective quantification of behavioural parameters within a group poses a major challenge as it requires simultaneous monitoring of the positions of several individuals and comprehensive consideration of many complex factors. Automatic tracking and phenotyping of interacting animals could thus overcome the limitations of manual tracking methods. Here we report a broadly applicable system that automatically tracks the locations of multiple, uniquely identified animals, such as mice, within a semi-natural setting. The system combines video and radio frequency identified tracking data to obtain detailed behavioural profiles of both individuals and groups. We demonstrate the usefulness of these data in characterizing individual phenotypes, interactions between pairs and the collective social organization of groups.

}, keywords = {Animals, Automation, Behavior, Animal, Crosses, Genetic, Data Collection, Environment, Female, Hierarchy, Social, Locomotion, Male, Mice, Mice, Inbred C57BL, Phenotype, Radio Frequency Identification Device, Social Behavior, Time Factors, Video Recording}, issn = {2041-1723}, doi = {10.1038/ncomms3018}, author = {Weissbrod, Aharon and Shapiro, Alexander and Vasserman, Genadiy and Edry, Liat and Dayan, Molly and Yitzhaky, Assif and Hertzberg, Libi and Feinerman, Ofer and Kimchi, Tali} } @article {6148, title = {Automated multi-day tracking of marked mice for the analysis of social behaviour.}, journal = {Journal of Neuroscience Methods}, volume = {219}, year = {2013}, month = {2013 Sep 30}, pages = {10-19}, abstract = {

A quantitative description of animal social behaviour is informative for behavioural biologists and clinicians developing drugs to treat social disorders. Social interaction in a group of animals has been difficult to measure because behaviour develops over long periods of time and requires tedious manual scoring, which is subjective and often non-reproducible. Computer-vision systems with the ability to measure complex social behaviour automatically would have a transformative impact on biology. Here, we present a method for tracking group-housed mice individually as they freely interact over multiple days. Each mouse is bleach-marked with a unique fur pattern. The patterns are automatically learned by the tracking software and used to infer identities. Trajectories are analysed to measure behaviour as it develops over days, beyond the range of acute experiments. We demonstrate how our system may be used to study the development of place preferences, associations and social relationships by tracking four mice continuously for five days. Our system enables accurate and reproducible characterisation of wild-type mouse social behaviour and paves the way for high-throughput long-term observation of the effects of genetic, pharmacological and environmental manipulations.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2013.05.013}, author = {Ohayon, Shay and Avni, Ofer and Taylor, Adam L and Perona, Pietro and Roian Egnor, S E} } @article {6268, title = {Aβ induces astrocytic glutamate release, extrasynaptic NMDA receptor activation, and synaptic loss.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, year = {2013}, month = {2013 Jul 2}, pages = {E2518-27}, abstract = {

Synaptic loss is the cardinal feature linking neuropathology to cognitive decline in Alzheimer{\textquoteright}s disease (AD). However, the mechanism of synaptic damage remains incompletely understood. Here, using FRET-based glutamate sensor imaging, we show that amyloid-β peptide (Aβ) engages α7 nicotinic acetylcholine receptors to induce release of astrocytic glutamate, which in turn activates extrasynaptic NMDA receptors (eNMDARs) on neurons. In hippocampal autapses, this eNMDAR activity is followed by reduction in evoked and miniature excitatory postsynaptic currents (mEPSCs). Decreased mEPSC frequency may reflect early synaptic injury because of concurrent eNMDAR-mediated NO production, tau phosphorylation, and caspase-3 activation, each of which is implicated in spine loss. In hippocampal slices, oligomeric Aβ induces eNMDAR-mediated synaptic depression. In AD-transgenic mice compared with wild type, whole-cell recordings revealed excessive tonic eNMDAR activity accompanied by eNMDAR-sensitive loss of mEPSCs. Importantly, the improved NMDAR antagonist NitroMemantine, which selectively inhibits extrasynaptic over physiological synaptic NMDAR activity, protects synapses from Aβ-induced damage both in vitro and in vivo.

}, issn = {1091-6490}, doi = {10.1073/pnas.1306832110}, author = {Talantova, Maria and Sanz-Blasco, Sara and Zhang, Xiaofei and Xia, Peng and Akhtar, Mohd Waseem and Okamoto, Shu-ichi and Dziewczapolski, Gustavo and Nakamura, Tomohiro and Cao, Gang and Pratt, Alexander E and Kang, Yeon-Joo and Tu, Shichun and Molokanova, Elena and McKercher, Scott R and Hires, Samuel Andrew and Sason, Hagit and Stouffer, David G and Buczynski, Matthew W and Solomon, James P and Michael, Sarah and Powers, Evan T and Kelly, Jeffery W and Roberts, Amanda and Tong, Gary and Fang-Newmeyer, Traci and Parker, James and Holland, Emily A and Zhang, Dongxian and Nakanishi, Nobuki and Chen, H-S Vincent and Wolosker, Herman and Wang, Yuqiang and Parsons, Loren H and Ambasudhan, Rajesh and Masliah, Eliezer and Heinemann, Stephen F and Pi{\~n}a-Crespo, Juan C and Lipton, Stuart A} } @article {6490, title = {Activity dynamics and behavioral correlates of CA3 and CA1 hippocampal pyramidal neurons.}, journal = {Hippocampus}, volume = {22}, year = {2012}, month = {2012 Aug}, pages = {1659-80}, abstract = {

The CA3 and CA1 pyramidal neurons are the major principal cell types of the hippocampus proper. The strongly recurrent collateral system of CA3 cells and the largely parallel-organized CA1 neurons suggest that these regions perform distinct computations. However, a comprehensive comparison between CA1 and CA3 pyramidal cells in terms of firing properties, network dynamics, and behavioral correlations is sparse in the intact animal. We performed large-scale recordings in the dorsal hippocampus of rats to quantify the similarities and differences between CA1 (n \> 3,600) and CA3 (n \> 2,200) pyramidal cells during sleep and exploration in multiple environments. CA1 and CA3 neurons differed significantly in firing rates, spike burst propensity, spike entrainment by the theta rhythm, and other aspects of spiking dynamics in a brain state-dependent manner. A smaller proportion of CA3 than CA1 cells displayed prominent place fields, but place fields of CA3 neurons were more compact, more stable, and carried more spatial information per spike than those of CA1 pyramidal cells. Several other features of the two cell types were specific to the testing environment. CA3 neurons showed less pronounced phase precession and a weaker position versus spike-phase relationship than CA1 cells. Our findings suggest that these distinct activity dynamics of CA1 and CA3 pyramidal cells support their distinct computational roles.

}, keywords = {Action Potentials, Animal, Animals, Behavior, CA1 Region, CA3 Region, Electroencephalography, Hippocampal, Long-Evans, Male, Maze Learning, Nonparametric, Pyramidal Cells, Rats, Statistics, Theta Rhythm}, issn = {1098-1063}, doi = {10.1002/hipo.22002}, author = {Mizuseki, Kenji and Royer, S{\'e}bastien and Diba, Kamran and Buzs{\'a}ki, Gy{\"o}rgy} } @article {5162, title = {Activity in motor-sensory projections reveals distributed coding in somatosensation.}, journal = {Nature}, volume = {489}, year = {2012}, month = {2012 Sep 13}, pages = {299-303}, abstract = {

Cortical-feedback projections to primary sensory areas terminate most heavily in layer 1 (L1) of the neocortex, where they make synapses with tuft dendrites of pyramidal neurons. L1 input is thought to provide {\textquoteleft}contextual{\textquoteright} information, but the signals transmitted by L1 feedback remain uncharacterized. In the rodent somatosensory system, the spatially diffuse feedback projection from vibrissal motor cortex (vM1) to vibrissal somatosensory cortex (vS1, also known as the barrel cortex) may allow whisker touch to be interpreted in the context of whisker position to compute object location. When mice palpate objects with their whiskers to localize object features, whisker touch excites vS1 and later vM1 in a somatotopic manner. Here we use axonal calcium imaging to track activity in vM1{\textendash}\>vS1 afferents in L1 of the barrel cortex while mice performed whisker-dependent object localization. Spatially intermingled individual axons represent whisker movements, touch and other behavioural features. In a subpopulation of axons, activity depends on object location and persists for seconds after touch. Neurons in the barrel cortex thus have information to integrate movements and touches of multiple whiskers over time, key components of object identification and navigation by active touch.

}, issn = {1476-4687}, doi = {10.1038/nature11321}, author = {Petreanu, Leopoldo and Gutnisky, Diego A and Huber, Daniel and Xu, Ning-long and O{\textquoteright}Connor, Dan H and Tian, Lin and Looger, Loren and Svoboda, Karel} } @article {46604, title = {Acute ethanol responses in Drosophila are sexually dimorphic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Dec 18}, pages = {21087-92}, abstract = {

In mammalian and insect models of ethanol intoxication, low doses of ethanol stimulate locomotor activity whereas high doses induce sedation. Sex differences in acute ethanol responses, which occur in humans, have not been characterized in Drosophila. In this study, we find that male flies show increased ethanol hyperactivity and greater resistance to ethanol sedation compared with females. We show that the sex determination gene transformer (tra) acts in the developing nervous system, likely through regulation of fruitless (fru), to at least partially mediate the sexual dimorphism in ethanol sedation. Although pharmacokinetic differences may contribute to the increased sedation sensitivity of females, neuronal tra expression regulates ethanol sedation independently of ethanol pharmacokinetics. We also show that acute activation of fru-expressing neurons affects ethanol sedation, further supporting a role for fru in regulating this behavior. Thus, we have characterized previously undescribed sex differences in behavioral responses to ethanol, and implicated fru in mediating a subset of these differences.

}, keywords = {Alcoholic Intoxication, Animals, Central Nervous System Stimulants, Crosses, Genetic, Disease Models, Animal, Drosophila melanogaster, Ethanol, Female, Gene Expression Regulation, Male, Models, Statistical, Neurons, Sex Characteristics, Sex Factors}, issn = {1091-6490}, doi = {10.1073/pnas.1218850110}, author = {Devineni, Anita V and Heberlein, Ulrike} } @proceedings {46790, title = {Advanced Programming with ImgLib2}, year = {2012}, month = {2012 Oct 24}, address = {Mondorf-les-Bains, Luxembourg}, author = {Pietzsch, Tobias and Preibisch, Stephan and Tomancak, Pavel and Saalfeld, Stephan} } @article {4922, title = {AKAP2 anchors PKA with aquaporin-0 to support ocular lens transparency.}, journal = {EMBO Molecular Medicine}, volume = {4}, year = {2012}, month = {2012 Jan}, pages = {15-26}, abstract = {

A decline in ocular lens transparency known as cataract afflicts 90\% of individuals by the age 70. Chronic deterioration of lens tissue occurs as a pathophysiological consequence of defective water and nutrient circulation through channel and transporter proteins. A key component is the aquaporin-0 (AQP0) water channel whose permeability is tightly regulated in healthy lenses. Using a variety of cellular and biochemical approaches we have discovered that products of the A-kinase anchoring protein 2 gene (AKAP2/AKAP-KL) form a stable complex with AQP0 to sequester protein kinase A (PKA) with the channel. This permits PKA phosphorylation of serine 235 within a calmodulin (CaM)-binding domain of AQP0. The additional negative charge introduced by phosphoserine 235 perturbs electrostatic interactions between AQP0 and CaM to favour water influx through the channel. In isolated mouse lenses, displacement of PKA from the AKAP2-AQP0 channel complex promotes cortical cataracts as characterized by severe opacities and cellular damage. Thus, anchored PKA modulation of AQP0 is a homeostatic mechanism that must be physically intact to preserve lens transparency.

}, keywords = {A Kinase Anchor Proteins, Animals, Aquaporins, Calmodulin, Cataract, Crystalline, Cyclic AMP-Dependent Protein Kinases, Eye Proteins, Inbred C57BL, Lens, Membrane Proteins, Mice, Phosphopeptides, Phosphorylation, Protein Binding, Sheep, Static Electricity, Water}, issn = {1757-4684}, doi = {10.1002/emmm.201100184}, author = {Gold, Matthew G and Reichow, Steve L and O{\textquoteright}Neill, Susan E and Weisbrod, Chad R and Langeberg, Lorene K and Bruce, James E and Gonen, Tamir and Scott, John D} } @article {5200, title = {Automated tracking of whiskers in videos of head fixed rodents.}, journal = {PLoS Computational Biology}, volume = {8}, year = {2012}, month = {2012 Jul}, pages = {e1002591}, abstract = {

We have developed software for fully automated tracking of vibrissae (whiskers) in high-speed videos (\>500 Hz) of head-fixed, behaving rodents trimmed to a single row of whiskers. Performance was assessed against a manually curated dataset consisting of 1.32 million video frames comprising 4.5 million whisker traces. The current implementation detects whiskers with a recall of 99.998\% and identifies individual whiskers with 99.997\% accuracy. The average processing rate for these images was 8 Mpx/s/cpu (2.6 GHz Intel Core2, 2 GB RAM). This translates to 35 processed frames per second for a 640 px{\texttimes}352 px video of 4 whiskers. The speed and accuracy achieved enables quantitative behavioral studies where the analysis of millions of video frames is required. We used the software to analyze the evolving whisking strategies as mice learned a whisker-based detection task over the course of 6 days (8148 trials, 25 million frames) and measure the forces at the sensory follicle that most underlie haptic perception.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002591}, author = {Clack, Nathan G and O{\textquoteright}Connor, Daniel H and Huber, Daniel and Petreanu, Leopoldo and Hires, Andrew and Peron, Simon and Svoboda, Karel and Myers, Eugene W} } @article {48166, title = {Automatic detection and classification of teeth in CT data.}, journal = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {15}, year = {2012}, month = {2012}, pages = {609-16}, abstract = {

We propose a fully automatic method for tooth detection and classification in CT or cone-beam CT image data. First we compute an accurate segmentation of the maxilla bone. Based on this segmentation, our method computes a complete and optimal separation of the row of teeth into 16 subregions and classifies the resulting regions as existing or missing teeth. This serves as a prerequisite for further individual tooth segmentation. We show the robustness of our approach by providing extensive validation on 43 clinical head CT scans.

}, keywords = {Algorithms, Artifacts, Bone and Bones, Humans, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Maxilla, Models, Statistical, Pattern Recognition, Automated, Radiographic Image Interpretation, Computer-Assisted, Reproducibility of Results, Tomography, X-Ray Computed, Tooth}, author = {Duy, Nguyen The and Lamecker, Hans and Kainmueller, Dagmar and Zachow, Stefan} } @article {46614, title = {Abnormal behavior in mice mutant for the Disc1 binding partner, Dixdc1.}, journal = {Translational Psychiatry}, volume = {1}, year = {2011}, month = {2011}, pages = {e43}, abstract = {

Disrupted-in-Schizophrenia-1 (DISC1) is a genetic susceptibility locus for major mental illness, including schizophrenia and depression. The Disc1 protein was recently shown to interact with the Wnt signaling protein, DIX domain containing 1 (Dixdc1). Both proteins participate in neural progenitor proliferation dependent on Wnt signaling, and in neural migration independently of Wnt signaling. Interestingly, their effect on neural progenitor proliferation is additive. By analogy to Disc1, mutations in Dixdc1 may lead to abnormal behavior in mice, and to schizophrenia or depression in humans. To explore this hypothesis further, we generated mice mutant at the Dixdc1 locus and analyzed their behavior. Dixdc1(-/-) mice had normal prepulse inhibition, but displayed decreased spontaneous locomotor activity, abnormal behavior in the elevated plus maze and deficits in startle reactivity. Our results suggest that Dixdc1(-/-) mice will be a useful tool to elucidate molecular pathophysiology involving Disc1 in major mental illnesses.

}, keywords = {Animals, Behavior, Animal, Epistasis, Genetic, Humans, Intracellular Signaling Peptides and Proteins, Male, Mice, Mice, 129 Strain, Mice, Mutant Strains, Mice, Transgenic, Microfilament Proteins, Nerve Tissue Proteins}, issn = {2158-3188}, doi = {10.1038/tp.2011.41}, author = {Kivim{\"a}e, S and Martin, P-M and Kapfhamer, D and Ruan, Y and Heberlein, U and Rubenstein, J L R and Cheyette, B N R} } @article {5271, title = {Accelerated profile HMM searches.}, journal = {PLoS Computational Biology}, volume = {7}, year = {2011}, month = {2011 Oct}, pages = {e1002195}, abstract = {

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the "multiple segment Viterbi" (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call "sparse rescaling". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.

}, keywords = {Algorithms, Computational Biology, Databases, Information Storage and Retrieval, Markov Chains, Protein, Sequence Alignment, Software}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002195}, author = {Eddy, Sean R.} } @article {6331, title = {An adaptation of the Wiener filter suitable for analyzing images of isolated single particles.}, journal = {Journal of Structural Biology}, volume = {176}, year = {2011}, month = {2011 Oct}, pages = {60-74}, abstract = {

The Wiener filter is a standard means of optimizing the signal in sums of aligned, noisy images obtained by electron cryo-microscopy (cryo-EM). However, estimation of the resolution-dependent ("spectral") signal-to-noise ratio (SSNR) from the input data has remained problematic, and error reduction due to specific application of the SSNR term within a Wiener filter has not been reported. Here we describe an adjustment to the Wiener filter for optimal summation of images of isolated particles surrounded by large regions of featureless background, as is typically the case in single-particle cryo-EM applications. We show that the density within the particle area can be optimized, in the least-squares sense, by scaling the SSNR term found in the conventional Wiener filter by a factor that reflects the fraction of the image field occupied by the particle. We also give related expressions that allow the SSNR to be computed for application in this new filter, by incorporating a masking step into a Fourier Ring Correlation (FRC), a standard resolution measure. Furthermore, we show that this masked FRC estimation scheme substantially improves on the accuracy of conventional SSNR estimation methods. We demonstrate the validity of our new approach in numeric tests with simulated data corresponding to realistic cryo-EM imaging conditions. This variation of the Wiener filter and accompanying derivation should prove useful for a variety of single-particle cryo-EM applications, including 3D reconstruction.

}, keywords = {Algorithms, Computer-Assisted, Cryoelectron Microscopy, Fourier Analysis, Image Processing, Models, Molecular, Protein Conformation, Signal-To-Noise Ratio}, issn = {1095-8657}, doi = {10.1016/j.jsb.2011.06.010}, author = {Sindelar, Charles V and Grigorieff, Nikolaus} } @article {2181, title = {Adeno-associated viral vectors for mapping, monitoring, and manipulating neural circuits.}, journal = {Human Gene Therapy}, volume = {22}, year = {2011}, month = {2011 Feb 14}, pages = {669-77}, abstract = {

Understanding the structure and function of neural circuits are central questions in neuroscience research. To address these questions, new genetically encoded tools have been developed for mapping, monitoring, and manipulating neurons. Essential to implementation of these tools is their selective delivery to defined neuronal populations in the brain. This has been facilitated by recent improvements in cell type-specific transgene expression using recombinant adeno-associated viral vectors. Here, we highlight these developments and discuss areas for improvement that could further expand capabilities for neural circuit analysis.

}, issn = {1557-7422}, doi = {10.1089/hum.2010.204}, author = {Sternson, Scott and Betley, J Nicholas} } @article {4935, title = {Advances in structural and functional analysis of membrane proteins by electron crystallography.}, journal = {Structure}, volume = {19}, year = {2011}, month = {2011 Oct 12}, pages = {1381-93}, abstract = {

Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography.

}, keywords = {Aquaporin 1, Archaea, Automatic Data Processing, Bacteriorhodopsins, Cell Membrane, Computer-Assisted, Cryoelectron Microscopy, Crystallography, Detergents, Dialysis, Humans, Image Processing, Lipid Bilayers, Membrane Proteins, Membrane Transport Proteins, Protein Conformation, Static Electricity}, issn = {1878-4186}, doi = {10.1016/j.str.2011.09.001}, author = {Wisedchaisri, Goragot and Reichow, Steve L and Gonen, Tamir} } @article {4497, title = {Advances in the chemistry of small molecule fluorescent probes.}, journal = {Current Opinion in Chemical Biology}, volume = {15}, year = {2011}, month = {2011 Dec}, pages = {752-9}, abstract = {

Small molecule fluorophores are essential tools for chemical biology. A benefit of synthetic dyes is the ability to employ chemical approaches to control the properties and direct the position of the fluorophore. Applying modern synthetic organic chemistry strategies enables efficient tailoring of the chemical structure to obtain probes for specific biological experiments. Chemistry can also be used to activate fluorophores; new fluorogenic enzyme substrates and photoactivatable compounds with improved properties have been prepared that facilitate advanced imaging experiments with low background fluorescence. Finally, chemical reactions in live cells can be used to direct the spatial distribution of the fluorophore, allowing labeling of defined cellular regions with synthetic dyes.

}, issn = {1879-0402}, doi = {10.1016/j.cbpa.2011.10.013}, author = {Wysocki, Laura M and Lavis, Luke D} } @article {3309, title = {AGRP neurons are sufficient to orchestrate feeding behavior rapidly and without training.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Mar}, pages = {351-5}, abstract = {

Two intermingled hypothalamic neuron populations specified by expression of agouti-related peptide (AGRP) or pro-opiomelanocortin (POMC) positively and negatively influence feeding behavior, respectively, possibly by reciprocally regulating downstream melanocortin receptors. However, the sufficiency of these neurons to control behavior and the relationship of their activity to the magnitude and dynamics of feeding are unknown. To measure this, we used channelrhodopsin-2 for cell type-specific photostimulation. Activation of only 800 AGRP neurons in mice evoked voracious feeding within minutes. The behavioral response increased with photoexcitable neuron number, photostimulation frequency and stimulus duration. Conversely, POMC neuron stimulation reduced food intake and body weight, which required melanocortin receptor signaling. However, AGRP neuron-mediated feeding was not dependent on suppressing this melanocortin pathway, indicating that AGRP neurons directly engage feeding circuits. Furthermore, feeding was evoked selectively over drinking without training or prior photostimulus exposure, which suggests that AGRP neurons serve a dedicated role coordinating this complex behavior.

}, keywords = {Agouti-Related Protein, Animal, Animals, Behavior, Classical, Conditioning, Eating, Feeding Behavior, Hypothalamus, Melanocortins, Mice, Neurons, Photic Stimulation, Pro-Opiomelanocortin, Recombinant Fusion Proteins, Rhodopsin}, issn = {1546-1726}, doi = {10.1038/nn.2739}, author = {Aponte, Yexica and Atasoy, Deniz and Sternson, Scott M} } @article {5483, title = {Alk is a transcriptional target of LMO4 and ERα that promotes cocaine sensitization and reward.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {31}, year = {2011}, month = {2011 Oct 5}, pages = {14134-41}, abstract = {

Previously, we showed that the mouse LIM-domain only 4 (Lmo4) gene, which encodes a protein containing two zinc-finger LIM domains that interact with various DNA-binding transcription factors, attenuates behavioral sensitivity to repeated cocaine administration. Here we show that transcription of anaplastic lymphoma kinase (Alk) is repressed by LMO4 in the striatum and that Alk promotes the development of cocaine sensitization and conditioned place preference, a measure of cocaine reward. Since LMO4 is known to interact with estrogen receptor α (ERα) at the promoters of target genes, we investigated whether Alk expression might be controlled by a similar mechanism. We found that LMO4 and ERα are associated with the Alk promoter by chromatin immunoprecipitation and that Alk is an estrogen-responsive gene in the striatum. Moreover, we show that ERα knock-out mice exhibit enhanced cocaine sensitization and conditioned place preference and an increase in Alk expression in the nucleus accumbens. These data define a novel regulatory network involved in behavioral responses to cocaine. Interestingly, sex differences in several behavioral responses to cocaine in humans and rodents have been described, and estrogen is thought to mediate some of these differences. Our data suggest that estrogen regulation of Alk may be one mechanism responsible for sexually dimorphic responses to cocaine.

}, keywords = {Adaptor Proteins, Animals, Cells, Cocaine, Cultured, Estrogen Receptor alpha, Gene Targeting, Genetic, HEK293 Cells, Humans, Inbred C57BL, Knockout, LIM Domain Proteins, Male, Mice, Motor Activity, Newborn, Receptor Protein-Tyrosine Kinases, Reward, Signal Transducing, Transcription}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3415-11.2011}, author = {Lasek, Amy W and Gesch, Julie and Giorgetti, Francesco and Kharazia, Viktor and Heberlein, Ulrike} } @article {4310, title = {Anisotropic path searching for automatic neuron reconstruction.}, journal = {Medical Image Analysis}, volume = {15}, year = {2011}, month = {2011 Oct}, pages = {680-9}, abstract = {

Full reconstruction of neuron morphology is of fundamental interest for the analysis and understanding of their functioning. We have developed a novel method capable of automatically tracing neurons in three-dimensional microscopy data. In contrast to template-based methods, the proposed approach makes no assumptions about the shape or appearance of neurite structure. Instead, an efficient seeding approach is applied to capture complex neuronal structures and the tracing problem is solved by computing the optimal reconstruction with a weighted graph. The optimality is determined by the cost function designed for the path between each pair of seeds and by topological constraints defining the component interrelations and completeness. In addition, an automated neuron comparison method is introduced for performance evaluation and structure analysis. The proposed algorithm is computationally efficient and has been validated using different types of microscopy data sets including Drosophila{\textquoteright}s projection neurons and fly neurons with presynaptic sites. In all cases, the approach yielded promising results.

}, issn = {1361-8423}, doi = {10.1016/j.media.2011.05.013}, author = {Xie, Jun and Zhao, Ting and Lee, Tzumin and Myers, Eugene and Peng, Hanchuan} } @article {4523, title = {Arouser reveals a role for synapse number in the regulation of ethanol sensitivity.}, journal = {Neuron}, volume = {70}, year = {2011}, month = {2011 Jun 9}, pages = {979-90}, abstract = {

A reduced sensitivity to the sedating effects of alcohol is a characteristic associated with alcohol use disorders (AUDs). A genetic screen for ethanol sedation mutants in Drosophila identified arouser (aru), which functions in developing neurons to reduce ethanol sensitivity. Genetic evidence suggests that aru regulates ethanol sensitivity through its activation by Egfr/Erk signaling and its inhibition by PI3K/Akt signaling. The aru mutant also has an increased number of synaptic terminals in the larva and adult fly. Both the increased ethanol sensitivity and synapse number of the aru mutant are restored upon adult social isolation, suggesting a causal relationship between synapse number and ethanol sensitivity. We thus show that a developmental abnormality affecting synapse number and ethanol sensitivity is not permanent and can be reversed by manipulating the environment of the adult fly.

}, keywords = {Adaptor Proteins, Animal, Animals, Arabidopsis Proteins, Behavior, Brain, Central Nervous System Depressants, Developmental, Drosophila, Drosophila Proteins, Epidermal Growth Factor, Ethanol, Gene Expression Regulation, Genetically Modified, Green Fluorescent Proteins, Invertebrate Peptide, Larva, Mutation, Neuromuscular Junction, Neurons, Phosphatidylinositol 3-Kinases, Receptor, Receptors, Reflex, RNA Interference, Signal Transducing, Signal Transduction, Social Isolation, Synapses}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.03.030}, author = {Eddison, Mark and Guarnieri, Douglas J and Cheng, Ling and Liu, Che-Hsiung and Moffat, Kevin G and Davis, Graeme and Heberlein, Ulrike} } @article {46345, title = {Associative learning between odorants and mechanosensory punishment in larval Drosophila.}, journal = {Journal of Expiremental Biology}, volume = {214}, year = {2011}, month = {2011 Dec 1}, pages = {3897-905}, abstract = {

We tested whether Drosophila larvae can associate odours with a mechanosensory disturbance as a punishment, using substrate vibration conveyed by a loudspeaker (buzz:). One odour (A) was presented with the buzz, while another odour (B) was presented without the buzz (A/B training). Then, animals were offered the choice between A and B. After reciprocal training (A/B), a second experimental group was tested in the same way. We found that larvae show conditioned escape from the previously punished odour. We further report an increase of associative performance scores with the number of punishments, and an increase according to the number of training cycles. Within the range tested (between 50 and 200 Hz), however, the pitch of the buzz does not apparently impact associative success. Last, but not least, we characterized odour-buzz memories with regard to the conditions under which they are behaviourally expressed--or not. In accordance with what has previously been found for associative learning between odours and bad taste (such as high concentration salt or quinine), we report that conditioned escape after odour-buzz learning is disabled if escape is not warranted, i.e. if no punishment to escape from is present during testing. Together with the already established paradigms for the association of odour and bad taste, the present assay offers the prospect of analysing how a relatively simple brain orchestrates memory and behaviour with regard to different kinds of {\textquoteright}bad{\textquoteright} events.

}, keywords = {Animals, Association Learning, Behavior, Animal, Conditioning (Psychology), Drosophila melanogaster, Larva, Mechanotransduction, Cellular, Memory, Odors, Punishment, Sound}, issn = {1477-9145}, doi = {10.1242/jeb.060533}, author = {Eschbach, Claire and Cano, Carmen and Haberkern, Hannah and Schraut, Karla and Guan, Chonglin and Triphan, Tilman and Gerber, Bertram} } @article {6335, title = {Atomic model of an infectious rotavirus particle.}, journal = {The EMBO Journal}, volume = {30}, year = {2011}, month = {2011 Jan 19}, pages = {408-16}, abstract = {

Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling enveloped-virus fusion: membrane distortion linked to conformational changes in a viral protein. Evidence for such a mechanism comes from crystallographic analyses of fragments of VP4, the rotavirus-penetration protein, and infectivity analyses of structure-based VP4 mutants. We describe here the structure of an infectious rotavirus particle determined by electron cryomicroscopy (cryoEM) and single-particle analysis at about 4.3 {\r A} resolution. The cryoEM image reconstruction permits a nearly complete trace of the VP4 polypeptide chain, including the positions of most side chains. It shows how the two subfragments of VP4 (VP8(*) and VP5(*)) retain their association after proteolytic cleavage, reveals multiple structural roles for the β-barrel domain of VP5(*), and specifies interactions of VP4 with other capsid proteins. The virion model allows us to integrate structural and functional information into a coherent mechanism for rotavirus entry.

}, keywords = {Capsid Proteins, Cell Membrane, Cryoelectron Microscopy, Crystallography, Models, Molecular, Protein Structure, Rotavirus, Secondary, Virion, Virus Internalization}, issn = {1460-2075}, doi = {10.1038/emboj.2010.322}, author = {Settembre, Ethan C and Chen, James Z and Dormitzer, Philip R and Grigorieff, Nikolaus and Harrison, Stephen C} } @article {5375, title = {Automated high speed stitching of large 3D microscopic images.}, journal = {2011 8TH IEEE International Symposium on Biomedical Imaging: From Nano to Macro}, year = {2011}, month = {2011 Mar 30}, pages = {238-41}, abstract = {

High-resolution microscopic imaging of biological samples often produces multiple 3D image tiles to cover a large field of view of specimen. Usually each tile has a large size, in the range of hundreds of megabytes to several gigabytes. For many of our image data sets, existing software tools are often unable to stitch those 3D tiles into a panoramic view, thus impede further data analysis. We propose a simple, but accurate, robust, and automatic method to stitch a group of image tiles without a priori adjacency information of them. We first use a multiscale strategy to register a pair of 3D image tiles rapidly, achieving about 8~10 times faster speed and 10 times less memory requirement compared to previous methods. Then we design a minimum-spanning-tree based method to determine the optimal adjacency of tiles. We have successfully stitched large image stacks of model animals including C. elegans, fruit fly, dragonfly, and mouse, which could not be stitched by several existing methods.

}, issn = {1945-7928}, doi = {10.1109/isbi.2011.5872396}, author = {Yu, Yang and Peng, Hanchuan} } @article {2700, title = {Automated reconstruction of neuronal morphology based on local geometrical and global structural models.}, journal = {Neuroinformatics}, volume = {9}, year = {2011}, month = {2011 May 6}, pages = {247-61}, abstract = {

Digital reconstruction of neurons from microscope images is an important and challenging problem in neuroscience. In this paper, we propose a model-based method to tackle this problem. We first formulate a model structure, then develop an algorithm for computing it by carefully taking into account morphological characteristics of neurons, as well as the image properties under typical imaging protocols. The method has been tested on the data sets used in the DIADEM competition and produced promising results for four out of the five data sets.

}, issn = {1559-0089}, doi = {10.1007/s12021-011-9120-3}, author = {Zhao, Ting and Xie, Jun and Amat, Fernando and Clack, Nathan and Ahammad, Parvez and Peng, Hanchuan and Long, Fuhui and Myers, Eugene} } @conference {2721, title = {Automatic 3D neuron tracing using all-paths pruning.}, booktitle = {Conference on Intelligent Systems for Molecular Biology}, year = {2011}, month = {2011}, address = {Vienna}, abstract = {

Motivation: Digital reconstruction, or tracing, of 3D neuron structures is critical toward reverse engineering the wiring and functions of a brain. However, despite a number of existing studies, this task is still challenging, especially when a 3D microscopic image has low signal-to-noise ratio (SNR) and fragmented neuron segments. Published work can handle these hard situations only by introducing global prior information, such as where a neurite segment starts and terminates. However, manual incorporation of such global information can be very time consuming. Thus, a completely automatic approach for these hard situations is highly desirable.

Results: We have developed an automatic graph algorithm, called the all-path pruning (APP), to trace the 3D structure of a neuron. To avoid potential mis-tracing of some parts of a neuron, an APP first produces an initial over-reconstruction, by tracing the optimal geodesic shortest path from the seed location to every possible destination voxel/pixel location in the image. Since the initial reconstruction contains all the possible paths and thus could contain redundant structural components (SC), we simplify the entire reconstruction without compromising its connectedness by pruning the redundant structural elements, using a new maximal-covering minimal-redundant (MCMR) subgraph algorithm. We show that MCMR has a linear computational complexity and will converge. We examined the performance of our method using challenging 3D neuronal image datasets of model organisms (e.g. fruit fly).

}, author = {Long, Fuhui and Peng, Hanchuan and Myers, Eugene} } @article {6385, title = {Acousto-optic laser scanning for multi-site photo-stimulation of single neurons in vitro.}, journal = {Journal of Neural Engineering}, volume = {7}, year = {2010}, month = {2010 Aug}, pages = {045002}, abstract = {

To study the complex synaptic interactions underpinning dendritic information processing in single neurons, experimenters require methods to mimic presynaptic neurotransmitter release at multiple sites with no physiological damage. We show that laser scanning systems built around large-aperture acousto-optic deflectors and high numerical aperture objective lenses provide the sub-millisecond, sub-micron precision necessary to achieve physiological, exogenous synaptic stimulation. Our laser scanning systems can produce the sophisticated spatio-temporal patterns of synaptic input that are necessary to investigate single-neuron dendritic physiology.

}, keywords = {Acoustic Stimulation, Acoustics, Action Potentials, Animals, Cells, Confocal, Cultured, Equipment Design, Equipment Failure Analysis, Hippocampus, Light, Microscopy, Neurons, Photic Stimulation, Rats, Reproducibility of Results, Sensitivity and Specificity, Sprague-Dawley}, issn = {1741-2552}, doi = {10.1088/1741-2560/7/4/045002}, author = {Losavio, Bradley E and Iyer, Vijay and Patel, Saumil and Saggau, Peter} } @article {2075, title = {Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues. (With commentary)}, journal = {Nature Methods}, volume = {7}, year = {2010}, month = {2010 Feb}, pages = {141-7}, abstract = {

Biological specimens are rife with optical inhomogeneities that seriously degrade imaging performance under all but the most ideal conditions. Measuring and then correcting for these inhomogeneities is the province of adaptive optics. Here we introduce an approach to adaptive optics in microscopy wherein the rear pupil of an objective lens is segmented into subregions, and light is directed individually to each subregion to measure, by image shift, the deflection faced by each group of rays as they emerge from the objective and travel through the specimen toward the focus. Applying our method to two-photon microscopy, we could recover near-diffraction-limited performance from a variety of biological and nonbiological samples exhibiting aberrations large or small and smoothly varying or abruptly changing. In particular, results from fixed mouse cortical slices illustrate our ability to improve signal and resolution to depths of 400 microm.

Commentary: Introduces a new, zonal approach to adaptive optics (AO) in microscopy suitable for highly inhomogeneous and/or scattering samples such as living tissue. The method is unique in its ability to handle large amplitude aberrations (\>20 wavelengths), including spatially complex aberrations involving high order modes beyond the ability of most AO actuators to correct. As befitting a technique designed for in vivo fluorescence imaging, it is also photon efficient.
Although used here in conjunction with two photon microscopy to demonstrate correction deep into scattering tissue, the same principle of pupil segmentation might be profitably adapted to other point-scanning or widefield methods. For example, plane illumination microscopy of multicellular specimens is often beset by substantial aberrations, and all far-field superresolution methods are exquisitely sensitive to aberrations.

}, keywords = {Artifacts, Computer-Aided Design, Equipment Design, Equipment Failure Analysis, Fluorescence, Image Enhancement, Lenses, Lighting, Microscopy, Multiphoton, Reproducibility of Results, Sensitivity and Specificity}, issn = {1548-7105}, doi = {10.1038/nmeth.1411}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20037592}, author = {Ji, Na and Milkie, Daniel E and Betzig, Eric} } @article {4019, title = {Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues.}, journal = {Nature Methods}, volume = {7}, year = {2010}, month = {2010 Feb}, pages = {141-7}, abstract = {

Biological specimens are rife with optical inhomogeneities that seriously degrade imaging performance under all but the most ideal conditions. Measuring and then correcting for these inhomogeneities is the province of adaptive optics. Here we introduce an approach to adaptive optics in microscopy wherein the rear pupil of an objective lens is segmented into subregions, and light is directed individually to each subregion to measure, by image shift, the deflection faced by each group of rays as they emerge from the objective and travel through the specimen toward the focus. Applying our method to two-photon microscopy, we could recover near-diffraction-limited performance from a variety of biological and nonbiological samples exhibiting aberrations large or small and smoothly varying or abruptly changing. In particular, results from fixed mouse cortical slices illustrate our ability to improve signal and resolution to depths of 400 microm.

}, keywords = {Artifacts, Computer-Aided Design, Equipment Design, Equipment Failure Analysis, Fluorescence, Image Enhancement, Lenses, Lighting, Microscopy, Multiphoton, Reproducibility of Results, Sensitivity and Specificity}, issn = {1548-7105}, doi = {10.1038/nmeth.1411}, author = {Ji, Na and Milkie, Daniel E and Betzig, Eric} } @article {46615, title = {Addiction-like behavior in Drosophila.}, journal = {Communicative \& Integrative Biology}, volume = {3}, year = {2010}, month = {2010 Jul}, pages = {357-9}, abstract = {

Alcohol abuse is a pervasive problem known to be influenced by genetic factors, yet our understanding of the mechanisms underlying alcohol addiction is far from complete. Drosophila melanogaster has been established as a model for studying the molecular mechanisms that mediate the acute and chronic effects of alcohol. However, the Drosophila model has not yet been extended to include more complex alcohol-related behaviors such as self-administration. We recently established a paradigm to characterize ethanol consumption and preference in flies. We demonstrated that flies prefer to consume ethanol-containing food over regular food, and this preference exhibits several features of alcohol addiction: flies increase ethanol consumption over time, they consume ethanol to pharmacologically relevant concentrations, they will overcome an aversive stimulus in order to consume ethanol, and they exhibit relapse after a period of ethanol deprivation. Thus, ethanol preference in flies provides a new model for studying important aspects of addiction and their underlying mechanisms. One mutant that displayed decreased ethanol preference, krasavietz, may represent a first step toward uncovering those mechanisms.

}, issn = {1942-0889}, author = {Devineni, Anita V and Heberlein, Ulrike} } @article {6337, title = {Adenomatous polyposis coli protein nucleates actin assembly and synergizes with the formin mDia1.}, journal = {The Journal of Cell Biology}, volume = {189}, year = {2010}, month = {2010 Jun 28}, pages = {1087-96}, abstract = {

The tumor suppressor protein adenomatous polyposis coli (APC) regulates cell protrusion and cell migration, processes that require the coordinated regulation of actin and microtubule dynamics. APC localizes in vivo to microtubule plus ends and actin-rich cortical protrusions, and has well-documented direct effects on microtubule dynamics. However, its potential effects on actin dynamics have remained elusive. Here, we show that the C-terminal "basic" domain of APC (APC-B) potently nucleates the formation of actin filaments in vitro and stimulates actin assembly in cells. Nucleation is achieved by a mechanism involving APC-B dimerization and recruitment of multiple actin monomers. Further, APC-B nucleation activity is synergistic with its in vivo binding partner, the formin mDia1. Together, APC-B and mDia1 overcome a dual cellular barrier to actin assembly imposed by profilin and capping protein. These observations define a new function for APC and support an emerging view of collaboration between distinct actin assembly-promoting factors with complementary activities.

}, keywords = {Actin Capping Proteins, Actins, Adenomatous Polyposis Coli Protein, Animals, Carrier Proteins, Fetal Proteins, Mice, Microfilament Proteins, NIH 3T3 Cells, Nuclear Proteins, Profilins, Protein Multimerization, Protein Transport}, issn = {1540-8140}, doi = {10.1083/jcb.201001016}, author = {Okada, Kyoko and Bartolini, Francesca and Deaconescu, Alexandra M and Moseley, James B and Dogic, Zvonimir and Grigorieff, Nikolaus and Gundersen, Gregg G and Goode, Bruce L} } @article {1450, title = {Alignment of cryo-electron tomography datasets.}, journal = {Methods in Enzymology}, volume = {482}, year = {2010}, month = {2010}, pages = {343-67}, abstract = {

Data acquisition of cryo-electron tomography (CET) samples described in previous chapters involves relatively imprecise mechanical motions: the tilt series has shifts, rotations, and several other distortions between projections. Alignment is the procedure of correcting for these effects in each image and requires the estimation of a projection model that describes how points from the sample in three-dimensions are projected to generate two-dimensional images. This estimation is enabled by finding corresponding common features between images. This chapter reviews several software packages that perform alignment and reconstruction tasks completely automatically (or with minimal user intervention) in two main scenarios: using gold fiducial markers as high contrast features or using relevant biological structures present in the image (marker-free). In particular, we emphasize the key decision points in the process that users should focus on in order to obtain high-resolution reconstructions.

}, keywords = {Computer-Assisted, Cryoelectron Microscopy, Electron Microscope Tomography, Image Processing}, issn = {1557-7988}, doi = {10.1016/S0076-6879(10)82014-2}, author = {Amat, Fernando and Casta{\~n}o-Diez, Daniel and Lawrence, Albert and Moussavi, Farshid and Winkler, Hanspeter and Horowitz, Mark} } @article {47682, title = {Analysis of mitochondrial dynamics and functions using imaging approaches.}, journal = {Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]}, volume = {Chapter 4}, year = {2010}, month = {2010 Mar}, pages = {Unit 4.25.1-21}, abstract = {

Mitochondria are organelles that have been primarily known as the powerhouse of the cell. However, recent advances in the field have revealed that mitochondria are also involved in many other cellular activities like lipid modifications, redox balance, calcium balance, and even controlled cell death. These multifunctional organelles are motile and highly dynamic in shapes and forms; the dynamism is brought about by the mitochondria{\textquoteright}s ability to undergo fission and fusion with each other. Therefore, it is very important to be able to image mitochondrial shape changes to relate to the variety of cellular functions these organelles have to accomplish. The protocols described here will enable researchers to perform steady-state and time-lapse imaging of mitochondria in live cells by using confocal microscopy. High-resolution three-dimensional imaging of mitochondria will not only be helpful in understanding mitochondrial structure in detail but it also could be used to analyze their structural relationships with other organelles in the cell. FRAP (fluorescence recovery after photobleaching) studies can be performed to understand mitochondrial dynamics or dynamics of any mitochondrial molecule within the organelle. The microirradiation assay can be performed to study functional continuity between mitochondria. A protocol for measuring mitochondrial potential has also been included in this unit. In conclusion, the protocols described here will aid the understanding of mitochondrial structure-function relationship.

}, keywords = {Cell Survival, Electricity, Fluorescence Recovery After Photobleaching, Humans, Imaging, Three-Dimensional, Membrane Potential, Mitochondrial, Microtubules, Mitochondria, Nocodazole, Staining and Labeling, Time Factors}, issn = {1934-2616}, doi = {10.1002/0471143030.cb0425s46}, author = {Mitra, Kasturi and Lippincott-Schwartz, Jennifer} } @article {1452, title = {Analysis of the intact surface layer of Caulobacter crescentus by cryo-electron tomography.}, journal = {Journal of Bacteriology}, volume = {192}, year = {2010}, month = {2010 Nov}, pages = {5855-65}, abstract = {

The surface layers (S layers) of those bacteria and archaea that elaborate these crystalline structures have been studied for 40 years. However, most structural analysis has been based on electron microscopy of negatively stained S-layer fragments separated from cells, which can introduce staining artifacts and allow rearrangement of structures prone to self-assemble. We present a quantitative analysis of the structure and organization of the S layer on intact growing cells of the Gram-negative bacterium Caulobacter crescentus using cryo-electron tomography (CET) and statistical image processing. Instead of the expected long-range order, we observed different regions with hexagonally organized subunits exhibiting short-range order and a broad distribution of periodicities. Also, areas of stacked double layers were found, and these increased in extent when the S-layer protein (RsaA) expression level was elevated by addition of multiple rsaA copies. Finally, we combined high-resolution amino acid residue-specific Nanogold labeling and subtomogram averaging of CET volumes to improve our understanding of the correlation between the linear protein sequence and the structure at the 2-nm level of resolution that is presently available. The results support the view that the U-shaped RsaA monomer predicted from negative-stain tomography proceeds from the N terminus at one vertex, corresponding to the axis of 3-fold symmetry, to the C terminus at the opposite vertex, which forms the prominent 6-fold symmetry axis. Such information will help future efforts to analyze subunit interactions and guide selection of internal sites for display of heterologous protein segments.

}, keywords = {Amino Acids, Bacterial Proteins, Caulobacter crescentus, Computer-Assisted, Cryoelectron Microscopy, Electron Microscope Tomography, Image Processing, Membrane Glycoproteins, Metal Nanoparticles, Staining and Labeling}, issn = {1098-5530}, doi = {10.1128/JB.00747-10}, author = {Amat, Fernando and Comolli, Luis R and Nomellini, John F and Moussavi, Farshid and Downing, Kenneth H and Smit, John and Horowitz, Mark} } @article {5369, title = {Anatomic analysis of Gal4 expression patterns of the Rubin line collection: the central complex.}, journal = {Journal of Neurogenetics}, volume = {24}, year = {2010}, month = {2010}, pages = {71-2}, chapter = {71}, author = {Jenett, A and Wolff, T and Nern, A. and Pfeiffer, B D and Ngo, T. and Murphy, C. and Long, F. and Peng, H. and Rubin, G M} } @article {1415, title = {Anatomy of a songbird basal ganglia circuit essential for vocal learning and plasticity.}, journal = {Journal of Chemical Neuroanatomy}, volume = {39}, year = {2010}, month = {2010 Mar}, pages = {124-31}, abstract = {

Vocal learning in songbirds requires an anatomically discrete and functionally dedicated circuit called the anterior forebrain pathway (AFP). The AFP is homologous to cortico-basal ganglia-thalamo-cortical loops in mammals. The basal ganglia portion of this pathway, Area X, shares many features characteristic of the mammalian striatum and pallidum, including cell types and connectivity. The AFP also deviates from mammalian basal ganglia circuits in fundamental ways. In addition, the microcircuitry, role of neuromodulators, and function of Area X are still unclear. Elucidating the mechanisms by which both mammalian-like and unique features of the AFP contribute to vocal learning may help lead to a broad understanding of the sensorimotor functions of basal ganglia circuits.

}, keywords = {Animal, Animals, Basal Ganglia, Birds, Brain, Catecholamines, Globus Pallidus, Learning, Neural Pathways, Neuronal Plasticity, Neurons, Thalamus, Vocalization}, issn = {1873-6300}, doi = {10.1016/j.jchemneu.2009.07.003}, author = {Gale, Samuel D and Perkel, David J} } @article {2686, title = {Appetitive and aversive visual learning in freely moving Drosophila.}, journal = {Frontiers in Behavioral Neuroscience}, volume = {4}, year = {2010}, month = {2010 Mar 9}, pages = {10}, abstract = {

To compare appetitive and aversive visual memories of the fruit fly Drosophila melanogaster, we developed a new paradigm for classical conditioning. Adult flies are trained en masse to differentially associate one of two visual conditioned stimuli (CS) (blue and green light as CS) with an appetitive or aversive chemical substance (unconditioned stimulus or US). In a test phase, flies are given a choice between the paired and the unpaired visual stimuli. Associative memory is measured based on altered visual preference in the test. If a group of flies has, for example, received a sugar reward with green light in the training, they show a significantly higher preference for the green stimulus during the test than another group of flies having received the same reward with blue light. We demonstrate critical parameters for the formation of visual appetitive memory, such as training repetition, order of reinforcement, starvation, and individual conditioning. Furthermore, we show that formic acid can act as an aversive chemical reinforcer, yielding weak, yet significant, aversive memory. These results provide a basis for future investigations into the cellular and molecular mechanisms underlying visual memory and perception in Drosophila.

}, issn = {1662-5153}, doi = {10.3389/fnbeh.2010.00010}, author = {Schnaitmann, Christopher and Vogt, Katrin and Triphan, Tilman and Tanimoto, Hiromu} } @article {1160, title = {Approaches toward super-resolution fluorescence imaging of mitochondrial proteins using PALM.}, journal = {Methods}, volume = {51}, year = {2010}, month = {2010 Aug}, pages = {458-63}, abstract = {

Mitochondria are difficult targets for microscopy because of their small size and highly compartmentalized, membranous interior. Super-resolution fluorescence microscopy methods have recently been developed that exceed the historical limits of optical imaging. Here we outline considerations and techniques in preparing to image the relative location of mitochondrial proteins using photoactivated localization microscopy (PALM). PALM and similar methods have the capacity to dramatically increase our ability to image proteins within mitochondria, and to expand our knowledge of the location of macromolecules beyond the current limits of immunoEM.

}, keywords = {Animals, Cryoultramicrotomy, Fluorescence, Freeze Substitution, Genetic, Luminescent Proteins, Mice, Microscopy, Mitochondria, Mitochondrial Proteins, NIH 3T3 Cells, Plastic Embedding, Promoter Regions, Recombinant Fusion Proteins, Transfection}, issn = {1095-9130}, doi = {10.1016/j.ymeth.2010.01.001}, author = {Brown, Timothy A and Fetter, Richard D and Tkachuk, Ariana N and Clayton, David A} } @article {5690, title = {As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets.}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010 Jun 15}, pages = {i57-63}, abstract = {

Tiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections.

}, keywords = {Animals, Databases, Drosophila, Electron, Factual, Imaging, Microscopy, Three-Dimensional, Transmission}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btq219}, author = {Saalfeld, Stephan and Cardona, Albert and Hartenstein, Volker and Tomancak, Pavel.} } @article {2327, title = {Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos.}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010 Jun 15}, pages = {i13-20}, abstract = {

The centrosome is a dynamic structure in animal cells that serves as a microtubule organizing center during mitosis and also regulates cell-cycle progression and sets polarity cues. Automated and reliable tracking of centrosomes is essential for genetic screens that study the process of centrosome assembly and maturation in the nematode Caenorhabditis elegans.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell Division, Cell Lineage, Centrosome, Embryo, Fluorescence, Microscopy, Mitotic Spindle Apparatus, Nonmammalian}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btq190}, author = {Jaensch, Steffen and Decker, Markus and Hyman, Anthony A and Myers, Eugene W} } @article {2698, title = {Automatic neuron tracing in volumetric microscopy images with anisotropic path searching.}, journal = {Medical Image Computing and Computer-Assisted Intervention: MICCAI International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {13}, year = {2010}, month = {2010}, pages = {472-9}, abstract = {

Full reconstruction of neuron morphology is of fundamental interest for the analysis and understanding of neuron function. We have developed a novel method capable of tracing neurons in three-dimensional microscopy data automatically. In contrast to template-based methods, the proposed approach makes no assumptions on the shape or appearance of neuron{\textquoteright}s body. Instead, an efficient seeding approach is applied to find significant pixels almost certainly within complex neuronal structures and the tracing problem is solved by computing an graph tree structure connecting these seeds. In addition, an automated neuron comparison method is introduced for performance evaluation and structure analysis. The proposed algorithm is computationally efficient. Experiments on different types of data show promising results.

}, keywords = {Algorithms, Animals, Anisotropy, Artificial Intelligence, Automated, Cells, Computer-Assisted, Cultured, Humans, Image Enhancement, Image Interpretation, Imaging, Microscopy, Neurons, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity, Three-Dimensional}, author = {Xie, Jun and Zhao, Ting and Lee, Tzumin and Myers, Eugene and Peng, Hanchuan} } @article {2183, title = {Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model.}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010 Jun 15}, pages = {i38-46}, abstract = {

Digital reconstruction of 3D neuron structures is an important step toward reverse engineering the wiring and functions of a brain. However, despite a number of existing studies, this task is still challenging, especially when a 3D microscopic image has low single-to-noise ratio and discontinued segments of neurite patterns.

}, keywords = {Animals, Caenorhabditis elegans, Computer-Assisted, Drosophila, Image Processing, Imaging, Mice, Neurons, Three-Dimensional}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btq212}, author = {Peng, Hanchuan and Ruan, Zongcai and Atasoy, Deniz and Sternson, Scott} } @article {2783, title = {Axial CID and high pressure resonance CID in a miniature ion trap mass spectrometer using a discontinuous atmospheric pressure interface.}, journal = {Journal of the American Society for Mass Spectrometry}, volume = {21}, year = {2010}, month = {2010 Feb}, pages = {209-14}, abstract = {

Axial collision induced dissociation (CID) and high-pressure resonance CID were implemented and compared with normal low-pressure resonance CID in a miniature ion trap mass spectrometer to obtain more complete fragmentation spectra. Axial CID was realized simply by applying a potential to the discontinuous atmospheric pressure interface (DAPI) capillary without performing parent ion isolation before dissociation. High-pressure resonance CID employed a double-introduction pulse scan function, by means of which precursor ions isolated at low-pressure (\<10(-3) torr) were dissociated at high-pressure (0.1 torr-1 torr) with higher excitation energy, so that tandem MS of isolated precursor ions was achieved and extensive fragmentation was obtained. A simple peptide (Leu-enkephalin) and dye molecule (rhodamine B) ionized by ESI were used to investigate both methods and compare them with normal low-pressure resonance CID.

}, issn = {1879-1123}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Li, Guangtao and Cooks, R Graham} } @article {6343, title = {Abeta(1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils.}, journal = {Journal of Molecular Biology}, volume = {386}, year = {2009}, month = {2009 Feb 27}, pages = {869-77}, abstract = {

Amyloid fibrils characterize a diverse group of human diseases that includes Alzheimer{\textquoteright}s disease, Creutzfeldt-Jakob and type II diabetes. Alzheimer{\textquoteright}s amyloid fibrils consist of amyloid-beta (Abeta) peptide and occur in a range of structurally different fibril morphologies. The structural characteristics of 12 single Abeta(1-40) amyloid fibrils, all formed under the same solution conditions, were determined by electron cryo-microscopy and three-dimensional reconstruction. The majority of analyzed fibrils form a range of morphologies that show almost continuously altering structural properties. The observed fibril polymorphism implies that amyloid formation can lead, for the same polypeptide sequence, to many different patterns of inter- or intra-residue interactions. This property differs significantly from native, monomeric protein folding reactions that produce, for one protein sequence, only one ordered conformation and only one set of inter-residue interactions.

}, keywords = {Amyloid beta-Peptides, Cryoelectron Microscopy, Humans, Imaging, Peptide Fragments, Protein Binding, Protein Structure, Quaternary, Three-Dimensional}, issn = {1089-8638}, doi = {10.1016/j.jmb.2008.11.005}, author = {Meinhardt, Jessica and Sachse, Carsten and Hortschansky, Peter and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus} } @article {2165, title = {Accelerating feature based registration using the Johnson-Lindenstrauss Lemma.}, journal = {Medical Image Computing and Computer-Assisted Intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {12}, year = {2009}, month = {2009}, pages = {632-9}, abstract = {

We introduce an efficient search strategy to substantially accelerate feature based registration. Previous feature based registration algorithms often use truncated search strategies in order to achieve small computation times. Our new accelerated search strategy is based on the realization that the search for corresponding features can be dramatically accelerated by utilizing Johnson-Lindenstrauss dimension reduction. Order of magnitude calculations for the search strategy we propose here indicate that the algorithm proposed is more than a million times faster than previously utilized naive search strategies, and this advantage in speed is directly translated into an advantage in accuracy as the fast speed enables more comparisons to be made in the same amount of time. We describe the accelerated scheme together with a full complexity analysis. The registration algorithm was applied to large transmission electron microscopy (TEM) images of neural ultrastructure. Our experiments demonstrate that our algorithm enables alignment of TEM images with increased accuracy and efficiency compared to previous algorithms.

}, keywords = {Algorithms, Animals, Artificial Intelligence, Automated, Computer-Assisted, Electron, Ferrets, Geniculate Bodies, Image Enhancement, Image Interpretation, Imaging, Microscopy, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Three-Dimensional}, author = {Akselrod-Ballin, Ayelet and Bock, Davi and Reid, R Clay and Warfield, Simon K} } @article {3924, title = {Activity correlation imaging: visualizing function and structure of neuronal populations.}, journal = {Biophysical Journal}, volume = {96}, year = {2009}, month = {2009 May 6}, pages = {3801-9}, abstract = {

For the analysis of neuronal networks it is an important yet unresolved task to relate the neurons{\textquoteright} activities to their morphology. Here we introduce activity correlation imaging to simultaneously visualize the activity and morphology of populations of neurons. To this end we first stain the network{\textquoteright}s neurons using a membrane-permeable [Ca(2+)] indicator (e.g., Fluo-4/AM) and record their activities. We then exploit the recorded temporal activity patterns as a means of intrinsic contrast to visualize individual neurons{\textquoteright} dendritic morphology. The result is a high-contrast, multicolor visualization of the neuronal network. Taking the Xenopus olfactory bulb as an example we show the activities of the mitral/tufted cells of the olfactory bulb as well as their projections into the olfactory glomeruli. This method, yielding both functional and structural information of neuronal populations, will open up unprecedented possibilities for the investigation of neuronal networks.

}, keywords = {Aniline Compounds, Animals, Calcium, Computer Simulation, Confocal, Dendrites, Fura-2, Microscopy, Neurons, Olfactory Bulb, Patch-Clamp Techniques, Time Factors, Video Recording, Xanthenes, Xenopus laevis}, issn = {1542-0086}, doi = {10.1016/j.bpj.2008.12.3962}, author = {Junek, Stephan and Chen, Tsai-Wen and Alevra, Mihai and Schild, Detlev} } @proceedings {3295, title = {Algebraic approach to recovering topological information in distributed camera networks.}, year = {2009}, month = {2009 Apr 13}, abstract = {

Camera networks are widely used for tasks such as surveillance, monitoring and tracking. In order to accomplish these tasks, knowledge of localization information such as camera locations and other geometric constraints about the environment (e.g. walls, rooms, and building layout) are typically considered to be essential. However, this information is not always required for many tasks such as estimating the topology of camera network coverage, or coordinate-free object tracking and navigation. In this paper, we propose a simplicial representation (called CN- complex) that can be constructed from discrete local observations from cameras, and utilize this novel representation to recover the topological information of the network coverage. We prove that our representation captures the correct topological information from network coverage for 2.5-D layouts, and demonstrate their utility in simulations as well as a real-world experimental set-up. Our proposed approach is particularly useful in the context of ad-hoc camera networks in indoor/outdoor urban environments with distributed but limited computational power and energy.

}, author = {Ahammad, Parvez and Lobaton, E and Sastry, S} } @article {2697, title = {Analysis of cell fate from single-cell gene expression profiles in C. elegans.}, journal = {Cell}, volume = {139}, year = {2009}, month = {2009 Oct 30}, pages = {623-33}, abstract = {

The C. elegans cell lineage provides a unique opportunity to look at how cell lineage affects patterns of gene expression. We developed an automatic cell lineage analyzer that converts high-resolution images of worms into a data table showing fluorescence expression with single-cell resolution. We generated expression profiles of 93 genes in 363 specific cells from L1 stage larvae and found that cells with identical fates can be formed by different gene regulatory pathways. Molecular signatures identified repeating cell fate modules within the cell lineage and enabled the generation of a molecular differentiation map that reveals points in the cell lineage when developmental fates of daughter cells begin to diverge. These results demonstrate insights that become possible using computational approaches to analyze quantitative expression from many genes in parallel using a digital gene expression atlas.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell Differentiation, Cell Lineage, Gene Expression Profiling}, issn = {1097-4172}, doi = {10.1016/j.cell.2009.08.044}, author = {Liu, Xiao and Long, Fuhui and Peng, Hanchuan and Aerni, Sarah J and Jiang, Min and S{\'a}nchez-Blanco, Adolfo and Murray, John I and Preston, Elicia and Mericle, Barbara and Batzoglou, Serafim and Myers, Eugene W and Kim, Stuart K} } @article {2792, title = {[Analysis on acupuncture literature in Science Citation Index (SCI) periodicals in 2007].}, journal = {Zhongguo Zhen Jiu = Chinese Acupuncture \& Moxibustion}, volume = {29}, year = {2009}, month = {2009 Jun}, pages = {504-7}, abstract = {

To grasp the international developing tendency of acupuncture research and provide some references for promoting acupuncture and moxibustion internationalization process, the articles about acupuncture in Science Citation Index (SCI) periodicals in 2007 were retrieved by adopting the retrieval tactics on line in combination with database searching. Results indicate that 257 articles about acupuncture had been retrived from the SCI Web databases. These articles were published in 125 journals respectively, most of which were Euramerican journals. Among these journals, the impact factor of the Journal of the American Medical Association (JAMA), 25. 547, is the highest one. It is shown that the impact factors of the SCI periodicals, in which acupuncture articles embodied are increased, the quality of these articles are improved obviously and the types of the articles are various in 2007, but there is obvious difference in the results of these studies due to the difference of experimental methods, the subjects of these experiments and acupuncture manipulations. Therefore, standardization of many problems arising from the researches on acupuncture is extremely imminent.

}, keywords = {Acupuncture, Acupuncture Therapy, Journal Impact Factor, Periodicals as Topic, Publications, Reference Standards}, issn = {0255-2930}, doi = {10.1364/AO.50.001792}, author = {Gao, Liang and Tian, Li-xin and Guo, Yi} } @article {48169, title = {An articulated statistical shape model for accurate hip joint segmentation.}, journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, volume = {2009}, year = {2009}, month = {2009}, pages = {6345-51}, abstract = {

In this paper we propose a framework for fully automatic, robust and accurate segmentation of the human pelvis and proximal femur in CT data. We propose a composite statistical shape model of femur and pelvis with a flexible hip joint, for which we extend the common definition of statistical shape models as well as the common strategy for their adaptation. We do not analyze the joint flexibility statistically, but model it explicitly by rotational parameters describing the bent in a ball-and-socket joint. A leave-one-out evaluation on 50 CT volumes shows that image driven adaptation of our composite shape model robustly produces accurate segmentations of both proximal femur and pelvis. As a second contribution, we evaluate a fine grain multi-object segmentation method based on graph optimization. It relies on accurate initializations of femur and pelvis, which our composite shape model can generate. Simultaneous optimization of both femur and pelvis yields more accurate results than separate optimizations of each structure. Shape model adaptation and graph based optimization are embedded in a fully automatic framework.

}, keywords = {Algorithms, Artificial Intelligence, Computer Simulation, Hip Joint, Imaging, Three-Dimensional, Models, Anatomic, Models, Statistical, Pattern Recognition, Automated, Radiographic Image Enhancement, Radiographic Image Interpretation, Computer-Assisted, Reproducibility of Results, Sensitivity and Specificity, Tomography, X-Ray Computed}, issn = {1557-170X}, doi = {10.1109/IEMBS.2009.5333269}, author = {Kainmueller, Dagmar and Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian} } @article {2678, title = {Automated monitoring and analysis of social behavior in Drosophila.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Apr}, pages = {297-303}, abstract = {

We introduce a method based on machine vision for automatically measuring aggression and courtship in Drosophila melanogaster. The genetic and neural circuit bases of these innate social behaviors are poorly understood. High-throughput behavioral screening in this genetically tractable model organism is a potentially powerful approach, but it is currently very laborious. Our system monitors interacting pairs of flies and computes their location, orientation and wing posture. These features are used for detecting behaviors exhibited during aggression and courtship. Among these, wing threat, lunging and tussling are specific to aggression; circling, wing extension (courtship {\textquoteright}song{\textquoteright}) and copulation are specific to courtship; locomotion and chasing are common to both. Ethograms may be constructed automatically from these measurements, saving considerable time and effort. This technology should enable large-scale screens for genes and neural circuits controlling courtship and aggression.

}, keywords = {Animal, Animals, Artificial Intelligence, Automated, Behavior, Computer-Assisted, Drosophila melanogaster, Humans, Image Interpretation, Monitoring, Movement, Pattern Recognition, Physiologic, Posture, Social Behavior}, issn = {1548-7105}, doi = {10.1038/nmeth.1310}, author = {Dankert, Heiko and Wang, Liming and Hoopfer, Eric D and Anderson, David J and Perona, Pietro} } @article {48176, title = {Automatic Extraction of Anatomical Landmarks From Medical Image Data: An Evaluation of Different Methods}, year = {2009}, abstract = {

This work presents three different methods for automatic detection of anatomical landmarks in CT data, namely for the left and right anterior superior iliac spines and the pubic symphysis. The methods exhibit different degrees of generality in terms of portability to other anatomical landmarks and require a different amount of training data. The srst method is problem-specisc and is based on the convex hull of the pelvis. Method two is a more generic approach based on a statistical shape model including the landmarks of interest for every training shape. With our third method we present the most generic approach, where only a small set of training landmarks is required. Those landmarks are transferred to the patient specisc geometry based on Mean Value Coordinates (MVCs). The methods work on surfaces of the pelvis that need to be extracted beforehand. We perform this geometry reconstruction with our previously introduced fully automatic segmentation framework for the pelvic bones. With a focus on the accuracy of our novel MVC-based approach, we evaluate and compare our methods on 100 clinical CT datasets, for which gold standard landmarks were desned manually by multiple observers.

}, author = {Kainmueller, Dagmar and Hans-Christian Hege and Heiko Seim and Markus Heller and Stefan Zachow} } @article {48174, title = {Automatic extraction of mandibular nerve and bone from cone-beam CT data.}, journal = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {12}, year = {2009}, month = {2009}, pages = {76-83}, abstract = {

The exact localization of the mandibular nerve with respect to the bone is important for applications in dental implantology and maxillofacial surgery. Cone beam computed tomography (CBCT), often also called digital volume tomography (DVT), is increasingly utilized in maxillofacial or dental imaging. Compared to conventional CT, however, soft tissue discrimination is worse due to a reduced dose. Thus, small structures like the alveolar nerves are even harder recognizable within the image data. We show that it is nonetheless possible to accurately reconstruct the 3D bone surface and the course of the nerve in a fully automatic fashion, with a method that is based on a combined statistical shape model of the nerve and the bone and a Dijkstra-based optimization procedure. Our method has been validated on 106 clinical datasets: the average reconstruction error for the bone is 0.5 +/- 0.1 mm, and the nerve can be detected with an average error of 1.0 +/- 0.6 mm.

}, keywords = {Algorithms, Artificial Intelligence, Cone-Beam Computed Tomography, Humans, Mandible, Mandibular Nerve, Pattern Recognition, Automated, Radiographic Image Enhancement, Radiographic Image Interpretation, Computer-Assisted, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique}, author = {Kainmueller, Dagmar and Lamecker, Hans and Seim, Heiko and Zinser, Max and Zachow, Stefan} } @article {1495, title = {Automatic tracking of Escherichia coli in phase-contrast microscopy video.}, journal = {IEEE Transactions on Bio-Medical Engineering}, volume = {56}, year = {2009}, month = {2009 Feb}, pages = {390-9}, abstract = {

In this paper, we present an automatic method for estimating the trajectories of Escherichia coli bacteria from in vivo phase-contrast microscopy. To address the low-contrast boundaries in cellular images, an adaptive kernel-based technique is applied to detect cells in each frame. In addition to intensity features, region homogeneity measure and class uncertainty are also applied in this detection technique. To track cells with complex motion, a novel matching gain measure is introduced to cope with the challenges, particularly the presence of low-contrast boundary, the variations of appearance, and the frequent overlapping and occlusion. For multicell tracking over time, an optimal matching strategy is introduced to improve the handling of cell collision and broken trajectories. The results of successful tracking of Escherichia coli from various phase-contrast sequences are reported and compared with manually determined trajectories, as well as those obtained from existing tracking schemes. The stability of the algorithm with different parameter values is also analyzed and discussed.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Chemotaxis, Computer-Assisted, Entropy, Escherichia coli, Image Processing, Microscopy, Pattern Recognition, Phase-Contrast, Video}, issn = {1558-2531}, doi = {10.1109/TBME.2008.2005956}, author = {Xie, Jun and Khan, Shahid and Shah, Mubarak} } @article {4276, title = {Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs.}, journal = {Journal of Neuroscience Methods}, volume = {176}, year = {2009}, month = {2009 Jan 30}, pages = {276-89}, abstract = {

We describe an approach for automation of the process of reconstruction of neural tissue from serial section transmission electron micrographs. Such reconstructions require 3D segmentation of individual neuronal processes (axons and dendrites) performed in densely packed neuropil. We first detect neuronal cell profiles in each image in a stack of serial micrographs with multi-scale ridge detector. Short breaks in detected boundaries are interpolated using anisotropic contour completion formulated in fuzzy-logic framework. Detected profiles from adjacent sections are linked together based on cues such as shape similarity and image texture. Thus obtained 3D segmentation is validated by human operators in computer-guided proofreading process. Our approach makes possible reconstructions of neural tissue at final rate of about 5 microm3/manh, as determined primarily by the speed of proofreading. To date we have applied this approach to reconstruct few blocks of neural tissue from different regions of rat brain totaling over 1000microm3, and used these to evaluate reconstruction speed, quality, error rates, and presence of ambiguous locations in neuropil ssTEM imaging data.

}, keywords = {Animals, Automation, Axons, Electron, Imaging, Microscopy, Neurons, Three-Dimensional, Transmission}, issn = {0165-0270}, doi = {10.1016/j.jneumeth.2008.09.006}, author = {Mishchenko, Yuriy} } @conference {6530, title = {Action recognition using ballistic dynamics.}, booktitle = {2008 IEEE Conference on Computer Vision and Pattern Recognition}, volume = {2008}, year = {2008}, month = {2008 Jun}, pages = {1-8}, publisher = {IEEE}, organization = {IEEE}, address = {Anchorage, AK}, abstract = {

We present a Bayesian framework for action recognition through ballistic dynamics. Psycho-kinesiological studies indicate that ballistic movements form the natural units for human movement planning. The framework leads to an efficient and robust algorithm for temporally segmenting videos into atomic movements. Individual movements are annotated with person-centric morphological labels called ballistic verbs. This is tested on a dataset of interactive movements, achieving high recognition rates. The approach is also applied on a gesture recognition task, improving a previously reported recognition rate from 84\% to 92\%. Consideration of ballistic dynamics enhances the performance of the popular Motion History Image feature. We also illustrate the approach{\textquoteright}s general utility on real-world videos. Experiments indicate that the method is robust to view, style and appearance variations.

}, isbn = {978-1-4244-2242-5}, issn = {1063-6919}, doi = {10.1109/CVPR.2008.4587806}, author = {Vitadalevuni, Shiv N. and Kellokumpu, Vili and Davis, Larry S.} } @article {4020, title = {Advances in the speed and resolution of light microscopy.}, journal = {Current Opinion in Neurobiology}, volume = {18}, year = {2008}, month = {2008 Dec}, pages = {605-16}, abstract = {

Neurobiological processes occur on spatiotemporal scales spanning many orders of magnitude. Greater understanding of these processes therefore demands improvements in the tools used in their study. Here we review recent efforts to enhance the speed and resolution of one such tool, fluorescence microscopy, with an eye toward its application to neurobiological problems. On the speed front, improvements in beam scanning technology, signal generation rates, and photodamage mediation are bringing us closer to the goal of real-time functional imaging of extended neural networks. With regard to resolution, emerging methods of adaptive optics may lead to diffraction-limited imaging or much deeper imaging in optically inhomogeneous tissues, and super-resolution techniques may prove a powerful adjunct to electron microscopic methods for nanometric neural circuit reconstruction.

}, keywords = {Animals, Electron, Fluorescence, Humans, Microscopy, Nerve Net, Neurology, Photobleaching, Photons}, issn = {1873-6882}, doi = {10.1016/j.conb.2009.03.009}, author = {Ji, Na and Shroff, Hari and Zhong, Haining and Betzig, Eric} } @article {2077, title = {Advances in the speed and resolution of light microscopy. (With commentary)}, journal = {Current Opinion in Neurobiology}, volume = {18}, year = {2008}, month = {2008 Dec}, pages = {605-16}, abstract = {

Neurobiological processes occur on spatiotemporal scales spanning many orders of magnitude. Greater understanding of these processes therefore demands improvements in the tools used in their study. Here we review recent efforts to enhance the speed and resolution of one such tool, fluorescence microscopy, with an eye toward its application to neurobiological problems. On the speed front, improvements in beam scanning technology, signal generation rates, and photodamage mediation are bringing us closer to the goal of real-time functional imaging of extended neural networks. With regard to resolution, emerging methods of adaptive optics may lead to diffraction-limited imaging or much deeper imaging in optically inhomogeneous tissues, and super-resolution techniques may prove a powerful adjunct to electron microscopic methods for nanometric neural circuit reconstruction.

Commentary: A brief review of recent trends in microscopy. The section {\textquotedblleft}Caveats regarding the application of superresolution microscopy{\textquotedblright} was written in an effort to inject a dose of reality and caution into the unquestioning enthusiasm in the academic community for all things superresolution, covering the topics of labeling density and specificity, sample preparation artifacts, speed vs. resolution vs. photodamage, and the implications of signal-to-background for Nyquist vs. Rayleigh definitions of resolution.

}, keywords = {Animals, Electron, Fluorescence, Humans, Microscopy, Nerve Net, Neurology, Photobleaching, Photons}, issn = {1873-6882}, doi = {10.1016/j.conb.2009.03.009}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19375302}, author = {Ji, Na and Shroff, Hari and Zhong, Haining and Betzig, Eric} } @article {3917, title = {Altered synaptic and non-synaptic properties of CA1 pyramidal neurons in Kv4.2 knockout mice.}, journal = {The Journal of Physiology}, volume = {586}, year = {2008}, month = {2008 Aug 15}, pages = {3881-92}, abstract = {

Back-propagating action potentials (bAPs) travelling from the soma to the dendrites of neurons are involved in various aspects of synaptic plasticity. The distance-dependent increase in Kv4.2-mediated A-type K(+) current along the apical dendrites of CA1 pyramidal cells (CA1 PCs) is responsible for the attenuation of bAP amplitude with distance from the soma. Genetic deletion of Kv4.2 reduced dendritic A-type K(+) current and increased the bAP amplitude in distal dendrites. Our previous studies revealed that the amplitude of unitary Schaffer collateral inputs increases with distance from the soma along the apical dendrites of CA1 PCs. We tested the hypothesis that the weight of distal synapses is dependent on dendritic Kv4.2 channels. We compared the amplitude and kinetics of mEPSCs at different locations on the main apical trunk of CA1 PCs from wild-type (WT) and Kv4.2 knockout (KO) mice. While wild-type mice showed normal distance-dependent scaling, it was missing in the Kv4.2 KO mice. We also tested whether there was an increase in inhibition in the Kv4.2 knockout, induced in an attempt to compensate for a non-specific increase in neuronal excitability (after-polarization duration and burst firing probability were increased in KO). Indeed, we found that the magnitude of the tonic GABA current increased in Kv4.2 KO mice by 53\% and the amplitude of mIPSCs increased by 25\%, as recorded at the soma. Our results suggest important roles for the dendritic K(+) channels in distance-dependent adjustment of synaptic strength as well as a primary role for tonic inhibition in the regulation of global synaptic strength and membrane excitability.

}, keywords = {Action Potentials, Animals, Dendrites, Knockout, Mice, Neural Conduction, Neuronal Plasticity, Pyramidal Cells, Shal Potassium Channels, Synapses, Synaptic Transmission}, issn = {1469-7793}, doi = {10.1113/jphysiol.2008.154336}, author = {Andr{\'a}sfalvy, B K and Makara, J K and Johnston, D and J.C. Magee} } @article {2689, title = {Analysis of a spatial orientation memory in Drosophila.}, journal = {Nature}, volume = {453}, year = {2008}, month = {2008 Jun 26}, pages = {1244-7}, abstract = {

Flexible goal-driven orientation requires that the position of a target be stored, especially in case the target moves out of sight. The capability to retain, recall and integrate such positional information into guiding behaviour has been summarized under the term spatial working memory. This kind of memory contains specific details of the presence that are not necessarily part of a long-term memory. Neurophysiological studies in primates indicate that sustained activity of neurons encodes the sensory information even though the object is no longer present. Furthermore they suggest that dopamine transmits the respective input to the prefrontal cortex, and simultaneous suppression by GABA spatially restricts this neuronal activity. Here we show that Drosophila melanogaster possesses a similar spatial memory during locomotion. Using a new detour setup, we show that flies can remember the position of an object for several seconds after it has been removed from their environment. In this setup, flies are temporarily lured away from the direction towards their hidden target, yet they are thereafter able to aim for their former target. Furthermore, we find that the GABAergic (stainable with antibodies against GABA) ring neurons of the ellipsoid body in the central brain are necessary and their plasticity is sufficient for a functional spatial orientation memory in flies. We also find that the protein kinase S6KII (ignorant) is required in a distinct subset of ring neurons to display this memory. Conditional expression of S6KII in these neurons only in adults can restore the loss of the orientation memory of the ignorant mutant. The S6KII signalling pathway therefore seems to be acutely required in the ring neurons for spatial orientation memory in flies.

}, keywords = {90-kDa, Animals, Drosophila melanogaster, gamma-Aminobutyric Acid, Locomotion, Memory, Models, Neurological, Neurons, Orientation, Ribosomal Protein S6 Kinases, Signal Transduction, Space Perception}, issn = {1476-4687}, doi = {10.1038/nature07003}, author = {Neuser, Kirsa and Triphan, Tilman and Mronz, Markus and Poeck, Burkhard and Strauss, Roland} } @article {45737, title = {Aphids.}, journal = {Curr Biol}, volume = {18}, year = {2008}, month = {2008 Jun 24}, pages = {R504-5}, abstract = {

Mammalian herbivores profoundly influence plant-dwelling insects [1]. Most studies have focused on the indirect effect of herbivory on insect populations via damage to the host plant [2,3]. Many insects, however, are in danger of being inadvertently ingested during herbivore feeding. Here, we report that pea aphids (Acyrthosiphon pisum) are able to sense the elevated heat and humidity of the breath of an approaching herbivore and thus salvage most of the colony by simultaneously dropping off the plant in large numbers immediately before the plant is eaten. Dropping entails the risk of losing the host plant and becoming desiccated or preyed upon on the ground [4,5], yet pea aphids may sporadically drop when threatened by insect enemies [6]. The immediate mass dropping, however, is an adaptation to the potential destructive impact of mammalian herbivory on the entire aphid colony. The combination of heat and humidity serves as a reliable cue to impending mammalian herbivory, enabling the aphids to avoid unnecessary dropping. No defensive behavior against incidental predation by herbivores has ever been demonstrated. The pea aphids{\textquoteright} highly adaptive escape behavior uniquely demonstrates the strength of the selective pressure large mammalian herbivores impose on insect herbivores.

}, keywords = {Animals, Aphids, Female, Genome, Insect, Insect Vectors, Male, Peas, Plant Diseases, Plant Tumors, Styrax}, issn = {0960-9822}, doi = {10.1016/j.cub.2008.03.034}, author = {Stern, David L} } @proceedings {46794, title = {Automatic landmark correspondence detection for ImageJ.}, year = {2008}, month = {2008 Nov 7}, address = {Luxembourg}, abstract = {

Landmark correspondences can be used for various tasks in image processing such as image alignment, reconstruction of panoramic photographs, object recognition and simultaneous localization and mapping for mobile robots. The computer vision community knows several techniques for extracting and pairwise associating such landmarks using distinctive invariant local image features. Two very successful methods are the Scale Invariant Feature Transform (SIFT)1 and Multi-Scale Oriented Patches (MOPS).2
We implemented these methods in the Java programming language3 for seamless use in ImageJ.4 We use it for fully automatic registration of gigantic serial section Transmission Electron Microscopy (TEM) mosaics. Using automatically detected landmark correspondences, the registration of large image mosaics simplifies to globally minimizing the displacement of corresponding points.
We present here an introduction to automatic landmark correspondence detection and demonstrate our implementation for ImageJ. We demonstrate the application of the plug-in on diverse image data.

}, author = {Saalfeld, Stephan and Tomancak, Pavel} } @conference {2719, title = {Automatic recognition of cells (ARC) for 3D images of C. elegans.}, booktitle = {Proceedings of the 2008 Conference on Computational Molecular Biology (RECOMB) (Singapore, 2008)}, year = {2008}, month = {2008 Apr 2}, abstract = {

The development of high-resolution microscopy makes possible the high-throughput screening of cellular information, such as gene expression at single cell resolution. One of the critical enabling techniques yet to be developed is the automatic recognition or annotation of specific cells in a 3D image stack. In this paper, we present a novel graph-based algorithm, ARC, that determines cell identities in a 3D confocal image of C. elegans based on their highly stereotyped arrangement. This is an essential step in our work on gene expression analysis of C. elegans at the resolution of single cells. Our ARC method integrates both the absolute and relative spatial locations of cells in a C. elegans body. It uses a marker-guided, spatially-constrained, two-stage bipartite matching to find the optimal match between cells in a subject image and cells in 15 template images that have been manually annotated and vetted. We applied ARC to the recognition of cells in 3D confocal images of the first larval stage (L1) of C. elegans hermaphrodites, and achieved an average accuracy of 94.91\%.

}, author = {Long, Fuhui and Peng, Hanchuan and Liu, X and Kim, Stuart K and Myers, Eugene} } @article {48177, title = {Automatic Segmentation of the Pelvic Bones from CT Data Based on a Statistical Shape Model}, year = {2008}, abstract = {

We present an algorithm for automatic segmentation of the human pelvic bones from CT datasets that is based on the application of a statistical shape model. The proposed method is divided into three steps: 1) The averaged shape of the pelvis model is initially placed within the CT data using the Generalized Hough Transform, 2) the statistical shape model is then adapted to the image data by a transformation and variation of its shape modes, and 3) a final free-form deformation step based on optimal graph searching is applied to overcome the restrictive character of the statistical shape representation. We thoroughly evaluated the method on 50 manually segmented CT datasets by performing a leave-one-out study. The Generalized Hough Transform proved to be a reliable method for an automatic initial placement of the shape model within the CT data. Compared to the manual gold standard segmentations, our automatic segmentation approach produced an average surface distance of 1.2 {\textpm} 0.3mm after the adaptation of the statistical shape model, which could be reduced to 0.7{\textpm}0.3mm using a final free-form deformation step. Together with an average segmentation time of less than 5 minutes, the results of our study indicate that our method meets the requirements of clinical routine.

}, doi = {10.2312/VCBM/VCBM08/093-100}, author = {Kainmueller, Dagmar and Seim, Heiko and Heller, Markus and Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian} } @article {1496, title = {Automatic tracking of Escherichia coli bacteria.}, journal = {Medical Image Computing and Computer-Assisted Intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {11}, year = {2008}, month = {2008 Sep 6}, pages = {824-32}, abstract = {

In this paper, we present an automatic method for estimating the trajectories of Escherichia coli bacteria from in vivo phase-contrast microscopy videos. To address the low-contrast boundaries in cellular images, an adaptive kernel-based technique is applied to detect cells in sequence of frames. Then a novel matching gain measure is introduced to cope with the challenges such as dramatic changes of cells{\textquoteright} appearance and serious overlapping and occlusion. For multiple cell tracking, an optimal matching strategy is proposed to improve the handling of cell collision and broken trajectories. The results of successful tracking of Escherichia coli from various phase-contrast sequences are reported and compared with manually-determined trajectories, as well as those obtained from existing tracking methods. The stability of the algorithm with different parameter values is also analyzed and discussed.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Cell Movement, Cluster Analysis, Computer-Assisted, Escherichia coli, Image Enhancement, Image Interpretation, Microscopy, Pattern Recognition, Phase-Contrast, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Video}, author = {Xie, Jun and Khan, Shahid and Shah, Mubarak} } @article {1114, title = {Absence of the Thorpe-Ingold Eet by gem-diphenyl groups in ring-closing enyne metathesis.}, journal = {Tetrahedron Letters}, volume = {48}, year = {2007}, month = {2007 Nov 5}, pages = {7961-4}, abstract = {

In tandem ring-closing metathesis of alkynyl silaketals containing two different tethered olefins, the gem-dimethyl group showed the expected Thorpe-Ingold effect, thereby giving good level of group selectivity. Unexpectedly, however, the corresponding gem-diphenyl group did not show any Thorpe-Ingold effect for the ring closure reaction.

}, issn = {0040-4039}, doi = {10.1016/j.tetlet.2007.09.063}, author = {Kim, Yi Jin and Grimm, Jonathan B and Lee, Daesung} } @article {2167, title = {Alignment of large image series using cubic B-splines tessellation: application to transmission electron microscopy data.}, journal = {Medical Image Computing and Computer-Assisted Intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, volume = {10}, year = {2007}, month = {2007}, pages = {710-7}, abstract = {

3D reconstruction from serial 2D microscopy images depends on non-linear alignment of serial sections. For some structures, such as the neuronal circuitry of the brain, very large images at very high resolution are necessary to permit reconstruction. These very large images prevent the direct use of classical registration methods. We propose in this work a method to deal with the non-linear alignment of arbitrarily large 2D images using the finite support properties of cubic B-splines. After initial affine alignment, each large image is split into a grid of smaller overlapping sub-images, which are individually registered using cubic B-splines transformations. Inside the overlapping regions between neighboring sub-images, the coefficients of the knots controlling the B-splines deformations are blended, to create a virtual large grid of knots for the whole image. The sub-images are resampled individually, using the new coefficients, and assembled together into a final large aligned image. We evaluated the method on a series of large transmission electron microscopy images and our results indicate significant improvements compared to both manual and affine alignment.

}, keywords = {Algorithms, Artificial Intelligence, Automated, Computer-Assisted, Electron, Image Enhancement, Image Interpretation, Imaging, Microscopy, Pattern Recognition, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Three-Dimensional, Transmission}, author = {Dauguet, Julien and Bock, Davi and Reid, R Clay and Warfield, Simon K} } @article {2810, title = {Ambient mass spectrometry with a handheld mass spectrometer at high pressure.}, journal = {Analytical Chemistry}, volume = {79}, year = {2007}, month = {2007 Oct 15}, pages = {7734-9}, abstract = {

The first coupling of atmospheric pressure ionization methods, electrospray ionization (ESI) and desorption electrospray ionization (DESI), to a miniature hand-held mass spectrometer is reported. The instrument employs a rectilinear ion trap (RIT) mass analyzer and is battery-operated, hand-portable, and rugged (total system: 10 kg, 0.014 m(3), 75 W power consumption). The mass spectrometer was fitted with an atmospheric inlet, consisting of a 10 cm x 127 microm inner diameter stainless steel capillary tube which was used to introduce gas into the vacuum chamber at 13 mL/min. The operating pressure was 15 mTorr. Ions, generated by the atmospheric pressure ion source, were directed by the inlet along the axis of the ion trap, entering through an aperture in the dc-biased end plate, which was also operated as an ion gate. ESI and DESI sources were used to generate ions; ESI-MS analysis of an aqueous mixture of drugs yielded detection limits in the low parts-per-billion range. Signal response was linear over more than 3 orders of magnitude. Tandem mass spectrometry experiments were used to identify components of this mixture. ESI was also applied to the analysis of peptides and in this case multiply charged species were observed for compounds of molecular weight up to 1200 Da. Cocaine samples deposited or already present on different surfaces, including currency, were rapidly analyzed in situ by DESI. A geometry-independent version of the DESI ion source was also coupled to the miniature mass spectrometer. These results demonstrate that atmospheric pressure ionization can be implemented on simple portable mass spectrometry systems.

}, keywords = {Alkylation, Calibration, Mass Spectrometry, Molecular Structure, Molecular Weight, Pressure, Proteins, Temperature}, issn = {0003-2700}, doi = {10.1364/AO.50.001792}, author = {Keil, Adam and Talaty, Nari and Janfelt, Christian and Noll, Robert J and Gao, Liang and Ouyang, Zheng and Cooks, R Graham} } @article {2126, title = {Associative pairing enhances action potential back-propagation in radial oblique branches of CA1 pyramidal neurons.}, journal = {The Journal of Physiology}, volume = {580}, year = {2007}, month = {2007 May 1}, pages = {787-800}, abstract = {

Back-propagating action potentials (bAPs) are involved in associative synaptic plasticity and the modulation of dendritic excitability. We have used high-speed confocal and two-photon imaging to measure calcium and voltage signals associated with action potential propagation into oblique branches of CA1 pyramidal neurons in adult hippocampal slices. The spatial profile of the bAP-associated Ca(2+) influx was biphasic, with an initial increase in the proximity of the branch point followed by a progressive decrease. Voltage imaging in the branches showed that bAP amplitude was initially constant and then steadily declined with distance from the soma. To determine the role of transient K(+) channels in this profile, we used external Ba(2+) (150 microm) as a channel blocker, after characterizing its effect on A-type K(+) channels in the apical trunk. Bath application of Ba(2+) significantly reduced the A-type K(+) current in outside-out patches and nearly eliminated the distance-dependent decrease in bAP amplitude and its associated Ca(2+) signal. Finally, small amplitude bAPs at more distal oblique branch locations could be boosted by simultaneous branch depolarization, such that the paired Ca(2+) signal became nearly the same for proximal and distal oblique dendrites. These data suggest that dendritic K(+) channels regulate the amplitude of bAPs to create a dendritic Ca(2+) signal whose magnitude is inversely related to the electrotonic distance from the soma when bAPs are not associated with a significant amount of localized synaptic input. This distance-dependent Ca(2+) signal from bAPs, however, can be amplified and a strong associative signal is produced once the proper correlation between synaptic activation and AP output is achieved. We hypothesize that these two signals may be involved in the regulation of the expression and activity of dendritic voltage- and ligand-gated ion channels.

}, keywords = {Action Potentials, Animals, Barium, Calcium, Dendrites, Hippocampus, Knockout, Male, Mice, Neuronal Plasticity, Potassium Channel Blockers, Potassium Channels, Pyramidal Cells, Rats, Sprague-Dawley, Synapses}, issn = {0022-3751}, doi = {10.1002/cbic.201000254}, author = {Gasparini, Sonia and Losonczy, Attila and Chen, Xixi and Johnston, Daniel and Magee, Jeffrey C} } @article {2154, title = {Automatic image analysis for gene expression patterns of fly embryos.}, journal = {BMC Cell Biology}, volume = {8}, year = {2007}, month = {2007 Jul 10}, pages = {S7}, abstract = {

Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a D. melanogaster embryo delivers the detailed spatio-temporal pattern of expression of the gene. Many biological problems such as the detection of co-expressed genes, co-regulated genes, and transcription factor binding motifs rely heavily on the analyses of these image patterns. The increasing availability of ISH image data motivates the development of automated computational approaches to the analysis of gene expression patterns.

}, keywords = {Algorithms, Animals, Computational Biology, Computer-Assisted, Drosophila, Embryo, Gene Expression Profiling, Genes, Image Processing, In Situ Hybridization, Insect, Nonmammalian, Reproducibility of Results, Software Design}, issn = {1471-2121}, doi = {10.1007/s12021-010-9090-x}, author = {Peng, Hanchuan and Long, Fuhui and Zhou, Jie and Leung, Garmay and Eisen, Michael B and Myers, Eugene W} } @article {2156, title = {Automatic recognition and annotation of gene expression patterns of fly embryos.}, journal = {Bioinformatics}, volume = {23}, year = {2007}, month = {2007 Mar 1}, pages = {589-96}, abstract = {

Gene expression patterns obtained by in situ mRNA hybridization provide important information about different genes during Drosophila embryogenesis. So far, annotations of these images are done by manually assigning a subset of anatomy ontology terms to an image. This time-consuming process depends heavily on the consistency of experts.

}, keywords = {Algorithms, Animals, Computational Biology, Drosophila, Embryo, Gene Expression, In Situ Hybridization, Messenger, Nonmammalian, RNA}, issn = {1367-4811}, doi = {10.1007/s12021-010-9090-x}, author = {Zhou, Jie and Peng, Hanchuan} } @article {2718, title = {Automatic segmentation of nuclei in 3D microscopy images of C. elegans.}, journal = {2007 4TH IEEE International Symposium on Biomedical Imaging: Macro to Nano, VOLS 1-3}, year = {2007}, month = {2007 Apr 12-15}, pages = {536-9}, abstract = {

Automatic segmentation of nuclei in 3D microscopy images is essential for many biological studies including high throughput analysis of gene expression level, morphology, and phenotypes in single cell level. The complexity and variability of the microscopy images present many difficulties to the traditional image segmentation methods. In this paper, we present a new method based on 3D watershed algorithm to segment such images. By using both the intensity information of the image and the geometry information of the appropriately detected foreground mask, our method is robust to intensity fluctuation within nuclei and at the same time sensitive to the intensity and geometrical cues between nuclei. Besides, the method can automatically correct potential segmentation errors by using several post-processing steps. We tested this algorithm on the 3D confocal images of C.elegans, an organism that has been widely used in biological studies. Our results show that the algorithm can segment nuclei in high accuracy despite the non-uniform background, tightly clustered nuclei with different sizes and shapes, fluctuated intensities, and hollow-shaped staining patterns in the images.

}, author = {Long, Fuhui and Peng, Hanchuan and Myers, Eugene} } @article {2407, title = {An ARC/Mediator subunit required for SREBP control of cholesterol and lipid homeostasis.}, journal = {Nature}, volume = {442}, year = {2006}, month = {2006 Aug 10}, pages = {700-4}, abstract = {

The sterol regulatory element binding protein (SREBP) family of transcription activators are critical regulators of cholesterol and fatty acid homeostasis. We previously demonstrated that human SREBPs bind the CREB-binding protein (CBP)/p300 acetyltransferase KIX domain and recruit activator-recruited co-factor (ARC)/Mediator co-activator complexes through unknown mechanisms. Here we show that SREBPs use the evolutionarily conserved ARC105 (also called MED15) subunit to activate target genes. Structural analysis of the SREBP-binding domain in ARC105 by NMR revealed a three-helix bundle with marked similarity to the CBP/p300 KIX domain. In contrast to SREBPs, the CREB and c-Myb activators do not bind the ARC105 KIX domain, although they interact with the CBP KIX domain, revealing a surprising specificity among structurally related activator-binding domains. The Caenorhabditis elegans SREBP homologue SBP-1 promotes fatty acid homeostasis by regulating the expression of lipogenic enzymes. We found that, like SBP-1, the C. elegans ARC105 homologue MDT-15 is required for fatty acid homeostasis, and show that both SBP-1 and MDT-15 control transcription of genes governing desaturation of stearic acid to oleic acid. Notably, dietary addition of oleic acid significantly rescued various defects of nematodes targeted with RNA interference against sbp-1 and mdt-15, including impaired intestinal fat storage, infertility, decreased size and slow locomotion, suggesting that regulation of oleic acid levels represents a physiologically critical function of SBP-1 and MDT-15. Taken together, our findings demonstrate that ARC105 is a key effector of SREBP-dependent gene regulation and control of lipid homeostasis in metazoans.

}, keywords = {Amino Acid Sequence, Animals, Biomolecular, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cholesterol, Homeostasis, Humans, Lipid Metabolism, Mediator Complex, Mice, Models, Molecular, Molecular Sequence Data, Nuclear Magnetic Resonance, Protein Binding, Protein Structure, Sterol Regulatory Element Binding Proteins, Tertiary, Transcription Factors, Transcriptional Activation}, issn = {1476-4687}, doi = {10.1073/pnas.1100640108}, author = {Yang, Fajun and Vought, Bryan W and Satterlee, John S and Walker, Amy K and Jim Sun, Z-Y and Watts, Jennifer L and DeBeaumont, Rosalie and Saito, R Mako and Hyberts, Sven G and Yang, Shaosong and Macol, Christine and Iyer, Lakshmanan and Tjian, Robert and van den Heuvel, Sander and Hart, Anne C and Wagner, Gerhard and N{\"a}{\"a}r, Anders M} } @article {1734, title = {Atomic and molecular parity nonconservation and sum frequency generation solutions to the ozma problem.}, journal = {The Journal of Physical Chemistry}, volume = {110}, year = {2006}, month = {2006 Sep 28}, pages = {18744-7}, abstract = {

Two Ozma problems are defined. Parity nonconservation is necessary for their solutions. Both problems may be solved by beta decay or atomic optical activity. Atomic and molecular sum frequency generation is chosen, as it supplies rich methods of effecting "gedanken" solutions to the Ozma problems. A new method of measuring a parameter manifesting molecular parity violations is advanced.

}, issn = {1520-6106}, doi = {10.1021/jp055038i}, author = {Ji, Na and Harris, Robert A} } @article {1566, title = {Antibody humanization and affinity maturation using phage display.}, journal = {Phage Display in Biotechnology and Drug Discovery}, year = {2005}, month = {2005}, pages = {493-528}, author = {Marvin, Jonathan S and Lowman, Henry B} } @article {2318, title = {Antipsychotic drugs elevate mRNA levels of presynaptic proteins in the frontal cortex of the rat.}, journal = {Biological Psychiatry}, volume = {57}, year = {2005}, month = {2005 May 1}, pages = {1041-51}, abstract = {

Molecular adaptations are believed to contribute to the mechanism of action of antipsychotic drugs (APDs). We attempted to establish common gene regulation patterns induced by chronic treatment with APDs.

}, keywords = {Animals, Antipsychotic Agents, Cluster Analysis, Corpus Striatum, Frontal Lobe, Gene Expression, Male, Messenger, Microtubules, Oligonucleotide Array Sequence Analysis, Presynaptic Terminals, Rats, Reverse Transcriptase Polymerase Chain Reaction, RNA, Sprague-Dawley, Synaptic Vesicles}, issn = {0006-3223}, doi = {10.3389/fnana.2010.00147}, author = {MacDonald, Matthew L and Eaton, Molly E and Dudman, Joshua T and Konradi, Christine} } @article {1292, title = {Ataxin-3 suppresses polyglutamine neurodegeneration in Drosophila by a ubiquitin-associated mechanism.}, journal = {Molecular Cell}, volume = {18}, year = {2005}, month = {2005 Apr 1}, pages = {37-48}, abstract = {

Two central issues in polyglutamine-induced neurodegeneration are the influence of the normal function of the disease protein and modulation by protein quality control pathways. By using Drosophila, we now directly link host protein function and disease pathogenesis to ubiquitin pathways in the polyglutamine disease spinocerebellar ataxia type 3 (SCA3). Normal human ataxin-3{\textendash}a polyubiquitin binding protein with ubiquitin protease activity{\textendash}is a striking suppressor of polyglutamine neurodegeneration in vivo. This suppressor activity requires ubiquitin-associated activities of the protein and is dependent upon proteasome function. Our results highlight the critical importance of host protein function in SCA3 disease and a potential therapeutic role of ataxin-3 activity for polyglutamine disorders.

}, keywords = {Animals, Drosophila melanogaster, Genetic, Genetically Modified, Humans, Machado-Joseph Disease, Mutagenesis, Nerve Degeneration, Nerve Tissue Proteins, Nuclear Proteins, Peptides, Polymorphism, Repressor Proteins, Site-Directed, Ubiquitin}, issn = {1097-2765}, doi = {10.1016/j.molcel.2005.02.030}, author = {Warrick, John M and Morabito, Lance M and Bilen, Julide and Gordesky-Gold, Beth and Faust, Lynn Z and Paulson, Henry L and Bonini, Nancy M} } @article {45956, title = {Aquaporin-0 membrane junctions form upon proteolytic cleavage.}, journal = {Journal of Molecular Biology}, volume = {342}, year = {2004}, month = {2004 Sep 24}, pages = {1337-45}, abstract = {

Aquaporin-0 (AQP0), previously known as major intrinsic protein (MIP), is the only water pore protein expressed in lens fiber cells. AQP0 is highly specific to lens fiber cells and constitutes the most abundant intrinsic membrane protein in these cells. The protein is initially expressed as a full-length protein in young fiber cells in the lens cortex, but becomes increasingly cleaved in the lens core region. Reconstitution of AQP0 isolated from the core of sheep lenses containing a proportion of truncated protein, produced double-layered two-dimensional (2D) crystals, which displayed the same dimensions as the thin 11 nm lens fiber cell junctions, which are prominent in the lens core. In contrast reconstitution of full-length AQP0 isolated from the lens cortex reproducibly yielded single-layered 2D crystals. We present electron diffraction patterns and projection maps of both crystal types. We show that cleavage of the intracellular C terminus enhances the adhesive properties of the extracellular surface of AQP0, indicating a conformational change in the molecule. This change of function of AQP0 from a water pore in the cortex to an adhesion molecule in the lens core constitutes another manifestation of the gene sharing concept originally proposed on the basis of the dual function of crystallins.

}, keywords = {Amino Acid Sequence, Animals, Aquaporins, Biopolymers, Eye Proteins, Hydrolysis, Membrane Glycoproteins, Microscopy, Electron, Molecular Sequence Data, Sheep}, issn = {0022-2836}, doi = {10.1016/j.jmb.2004.07.076}, author = {Gonen, Tamir and Cheng, Yifan and Kistler, Joerg and Walz, Thomas} } @article {45955, title = {Aquaporin-0 membrane junctions reveal the structure of a closed water pore.}, journal = {Nature}, volume = {429}, year = {2004}, month = {2004 May 13}, pages = {193-7}, abstract = {

The lens-specific water pore aquaporin-0 (AQP0) is the only aquaporin known to form membrane junctions in vivo. We show here that AQP0 from the lens core, containing some carboxy-terminally cleaved AQP0, forms double-layered crystals that recapitulate in vivo junctions. We present the structure of the AQP0 membrane junction as determined by electron crystallography. The junction is formed by three localized interactions between AQP0 molecules in adjoining membranes, mainly mediated by proline residues conserved in AQP0s from different species but not present in most other aquaporins. Whereas all previously determined aquaporin structures show the pore in an open conformation, the water pore is closed in AQP0 junctions. The water pathway in AQP0 also contains an additional pore constriction, not seen in other known aquaporin structures, which may be responsible for pore gating.

}, keywords = {Animals, Aquaporins, Biological Transport, Cell Membrane, Cell Membrane Permeability, Cryoelectron Microscopy, Crystallization, Electric Conductivity, Eye Proteins, Hydrogen-Ion Concentration, Lens, Crystalline, Membrane Glycoproteins, Models, Molecular, Molecular Sequence Data, Protein Conformation, Sheep, Water}, issn = {1476-4687}, doi = {10.1038/nature02503}, author = {Gonen, Tamir and Sliz, Piotr and Kistler, Joerg and Cheng, Yifan and Walz, Thomas} } @article {2682, title = {Axon pruning during Drosophila metamorphosis: evidence for local degeneration and requirement of the ubiquitin-proteasome system.}, journal = {Neuron}, volume = {38}, year = {2003}, month = {2003 Jun 19}, pages = {871-85}, abstract = {

Axon pruning is widely used for the refinement of neural circuits in both vertebrates and invertebrates, and may also contribute to the pathogenesis of neurodegenerative diseases. However, little is known about the cellular and molecular mechanisms of axon pruning. We use the stereotyped pruning of gamma neurons of the Drosophila mushroom bodies (MB) during metamorphosis to investigate these mechanisms. Detailed time course analyses indicate that MB axon pruning is mediated by local degeneration rather than retraction and that the disruption of the microtubule cytoskeleton precedes axon pruning. In addition, multiple lines of genetic evidence demonstrate an intrinsic role of the ubiquitin-proteasome system in axon pruning; for example, loss-of-function mutations of the ubiquitin activating enzyme (E1) or proteasome subunits in MB neurons block axon pruning. Our findings suggest that some forms of axon pruning during development may share similarities with degeneration of axons in response to injury.

}, keywords = {Animals, Axons, Biological, Cell Adhesion Molecules, Cysteine Endopeptidases, Cytoskeletal Proteins, Cytoskeleton, Cytosol, Drosophila, Endocytosis, Endopeptidases, Gene Expression, Ligases, Metamorphosis, Microtubules, Multienzyme Complexes, Mutation, Nerve Degeneration, Neurons, Proteasome Endopeptidase Complex, Saccharomyces cerevisiae, Synapses, Transfection, Ubiquitin, Ubiquitin-Activating Enzymes, Ubiquitin-Protein Ligases}, issn = {0896-6273}, author = {Watts, Ryan J and Hoopfer, Eric D and Luo, Liqun} } @article {1778, title = {An amino-acid taste receptor.}, journal = {Nature}, volume = {416}, year = {2002}, month = {2002 Mar 14}, pages = {199-202}, abstract = {

The sense of taste provides animals with valuable information about the nature and quality of food. Mammals can recognize and respond to a diverse repertoire of chemical entities, including sugars, salts, acids and a wide range of toxic substances. Several amino acids taste sweet or delicious (umami) to humans, and are attractive to rodents and other animals. This is noteworthy because L-amino acids function as the building blocks of proteins, as biosynthetic precursors of many biologically relevant small molecules, and as metabolic fuel. Thus, having a taste pathway dedicated to their detection probably had significant evolutionary implications. Here we identify and characterize a mammalian amino-acid taste receptor. This receptor, T1R1+3, is a heteromer of the taste-specific T1R1 and T1R3 G-protein-coupled receptors. We demonstrate that T1R1 and T1R3 combine to function as a broadly tuned L-amino-acid sensor responding to most of the 20 standard amino acids, but not to their D-enantiomers or other compounds. We also show that sequence differences in T1R receptors within and between species (human and mouse) can significantly influence the selectivity and specificity of taste responses.

}, keywords = {Alleles, Amino Acids, Animals, Calcium Signaling, Cell Line, Cell Surface, Chorda Tympani Nerve, Dose-Response Relationship, Drug, G-Protein-Coupled, Genetic, Heterotrimeric GTP-Binding Proteins, Humans, Inosine Monophosphate, Mice, Mutation, Polymorphism, Protein Subunits, Receptors, Stereoisomerism, Structure-Activity Relationship, Substrate Specificity, Taste, Taste Buds, Transfection}, issn = {0028-0836}, doi = {10.1038/nature726}, author = {Nelson, Greg and Chandrashekar, Jayaram and Hoon, Mark A and Feng, Luxin and Zhao, Grace and Ryba, Nicholas J P and Zuker, Charles S} } @article {45927, title = {Action potential bursting in subicular pyramidal neurons is driven by a calcium tail current.}, journal = {J Neurosci}, volume = {21}, year = {2001}, month = {2001 May 15}, pages = {3312-21}, abstract = {

Subiculum is the primary output area of the hippocampus and serves as a key relay center in the process of memory formation and retrieval. A majority of subicular pyramidal neurons communicate via bursts of action potentials, a mode of signaling that may enhance the fidelity of information transfer and synaptic plasticity or contribute to epilepsy when unchecked. In the present study, we show that a Ca(2+) tail current drives bursting in subicular pyramidal neurons. An action potential activates voltage-activated Ca(2+) channels, which deactivate slowly enough during action potential repolarization to produce an afterdepolarization that triggers subsequent action potentials in the burst. The Ca(2+) channels underlying bursting are located primarily near the soma, and the amplitude of Ca(2+) tail currents correlates with the strength of bursting across cells. Multiple channel subtypes contribute to Ca(2+) tail current, but the need for an action potential to produce the slow depolarization suggests a central role for high-voltage-activated Ca(2+) channels in subicular neuron bursting.

}, keywords = {Action Potentials, Animals, Calcium, Calcium Channel Blockers, Calcium Channels, T-Type, Dendrites, Dose-Response Relationship, Drug, Electric Stimulation, Fluorescent Dyes, Fura-2, Hippocampus, In Vitro Techniques, Microelectrodes, Microinjections, Nickel, Patch-Clamp Techniques, Perfusion, Potassium Channels, Pyramidal Cells, Rats, Sodium Channels, Tetrodotoxin}, issn = {1529-2401}, author = {Jung, H Y and Staff, N P and Spruston, N} } @article {1142, title = {Are complex behaviors specified by dedicated regularoty genes? Reasoning from Drosophila.}, journal = {Cell}, volume = {105}, year = {2001}, month = {2001 Apr 6}, pages = {13-24}, issn = {0092-8674}, author = {Baker, B.S. and Taylor, B.T. and Hall, Jeffrey C} } @article {2190, title = {An acid- and base-stable o-nitrobenzyl photolabile linker for solid phase organic synthesis.}, journal = {Tetrahedron Letters}, volume = {39}, year = {1998}, month = {1998 Oct 8}, pages = {7451-54}, abstract = {

The synthesis of an o-nitrobenzyl photolabile linker (1) from o-nitrobenzaldehyde is described, and the efficiency of its light-mediated (365 nm) cleavage is found to be comparable to related, previously developed systems. In contrast, 1 is shown to be stable to acid, base, and Lewis acid/amine combinations while the previously developed linker 2 is shown to degrade under the latter two conditions.

}, issn = {0040-4039}, author = {Sternson, Scott M and Schreiber, Stuart L} } @article {45923, title = {Action potential initiation and backpropagation in neurons of the mammalian CNS.}, journal = {Trends Neurosci}, volume = {20}, year = {1997}, month = {1997 Mar}, pages = {125-31}, abstract = {

Most neurons in the mammalian CNS encode and transmit information via action potentials. Knowledge of where these electrical events are initiated and how they propagate within neurons is therefore fundamental to an understanding of neuronal function. While work from the 1950s suggested that action potentials are initiated in the axon, many subsequent investigations have suggested that action potentials can also be initiated in the dendrites. Recently, experiments using simultaneous patch-pipette recordings from different locations on the same neuron have been used to address this issue directly. These studies show that the site of action potential initiation is in the axon, even when synaptic activation is powerful enough to elicit dendritic electrogenesis. Furthermore, these and other studies also show that following initiation, action potentials actively backpropagate into the dendrites of many neuronal types, providing a retrograde signal of neuronal output to the dendritic tree.

}, keywords = {Action Potentials, Animals, Central Nervous System, Neurons}, issn = {0166-2236}, author = {Stuart, G and Spruston, N and Sakmann, B and H{\"a}usser, M} } @article {45913, title = {Activity-dependent action potential invasion and calcium influx into hippocampal CA1 dendrites.}, journal = {Science}, volume = {268}, year = {1995}, month = {1995 Apr 14}, pages = {297-300}, abstract = {

The temporal and spatial profile of activity-evoked changes in membrane potential and intracellular calcium concentration in the dendrites of hippocampal CA1 pyramidal neurons was examined with simultaneous somatic and dendritic patch-pipette recording and calcium imaging experiments. Action potentials are initiated close to the soma of these neurons and backpropagate into the dendrites in an activity-dependent manner; those occurring early in a train propagate actively, whereas those occurring later fail to actively invade the distal dendrites. Consistent with this finding, dendritic calcium transients evoked by single action potentials do not significantly attenuate with distance from the soma, whereas those evoked by trains attenuate substantially. Failure of action potential propagation into the distal dendrites often occurs at branch points. Consequently, neighboring regions of the dendritic tree can experience different voltage and calcium signals during repetitive action potential firing. The influence of backpropagating action potentials on synaptic integration and plasticity will therefore depend on both the extent of dendritic branching and the pattern of neuronal activity.

}, keywords = {Action Potentials, Animals, Calcium, Calcium Channels, Dendrites, Ion Channel Gating, Neuronal Plasticity, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Sodium Channels, Synapses, Tetrodotoxin}, issn = {0036-8075}, author = {Spruston, N and Schiller, Y and Stuart, G and Sakmann, B} } @article {1169, title = {Addition of a 29 residue carboxyl-terminal tail converts a simple HMG box-containing protein into a transcriptional activator.}, journal = {Journal of Molecular Biology}, volume = {249}, year = {1995}, month = {1995 May 26}, pages = {11-28}, abstract = {

Human mitochondrial transcription factor A (h-mtTFA) is essential for initiation of transcription from the two promoters located in the displacement-loop region of human mitochondrial DNA. This 25 kDa protein contains two tandem, HMG box DNA-binding domains separated by a 27 amino acid residue linker region and followed by a 25 residue carboxyl-terminal tail; both the linker and tail are rich in basic amino acid residues. Mutational analysis of h-mtTFA revealed that the tail region is important for specific DNA recognition and essential for transcriptional activation. The critical role of the human tail in transcription was confirmed by constructing chimeric proteins that exchanged similar regions between h-mtTFA and its Saccharomyces cerevisiae homolog, sc-mtTFA. Wild-type sc-mtTFA is unable to activate transcription from the human mitochondrial light-strand promoter (LSP). Addition of the human tail region to sc-mtTFA conferred LSP-specific promoter activation. In all of the different h-mtTFA mutations tested, transcriptional activation was correlated with specific DNA-binding activity, suggesting that these two functions may be inseparable, a situation entirely consistent with previous mutational analyses of human mitochondrial promoters.

}, keywords = {Base Sequence, DNA, DNA-Binding Proteins, Genetic, High Mobility Group Proteins, Humans, Mitochondrial, Mitochondrial Proteins, Molecular Sequence Data, Mutagenesis, Nuclear Proteins, Promoter Regions, Saccharomyces cerevisiae, Site-Directed, Trans-Activators, Transcription Factors}, issn = {0022-2836}, doi = {10.1101/gad.1352105}, author = {Dairaghi, D J and Shadel, G S and Clayton, D A} } @article {963, title = {The activities of two Ets-related transcription factors required for Drosophila eye development are modulated by the Ras/MAPK pathway.}, journal = {Cell}, volume = {78}, year = {1994}, month = {1994 Jul 15}, pages = {137-47}, abstract = {

We show that the activities of two Ets-related transcription factors required for normal eye development in Drosophila, pointed and yan, are regulated by the Ras1/MAPK pathway. The pointed gene codes for two related proteins, and we show that one form is a constitutive activator of transcription, while the activity of the other form is stimulated by the Ras1/MAPK pathway. Mutation of the single consensus MAPK phosphorylation site in the second form abrogates this responsiveness. yan is a negative regulator of photoreceptor determination, and genetic data suggest that it acts as an antagonist of Ras1. We demonstrate that yan can repress transcription and that this repression activity is negatively regulated by the Ras1/MAPK signal, most likely through direct phosphorylation of yan by MAPK.

}, keywords = {Animals, Biological, Calcium-Calmodulin-Dependent Protein Kinases, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Extracellular Signal-Regulated MAP Kinases, Eye, Eye Proteins, Gene Expression Regulation, Genes, Genetic, Insect, Invertebrate, Models, Morphogenesis, Nerve Tissue Proteins, Phenotype, Photoreceptor Cells, Proto-Oncogene Proteins, Proto-Oncogene Proteins p21(ras), ras, Repressor Proteins, Signal Transduction, Transcription, Transcription Factors}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {O{\textquoteright}Neill, E M and Rebay, I and Tjian, R and Rubin, G M} } @article {965, title = {Analysis of genetic mosaics in developing and adult Drosophila tissues.}, journal = {Development}, volume = {117}, year = {1993}, month = {1993 Apr}, pages = {1223-37}, abstract = {

We have constructed a series of strains to facilitate the generation and analysis of clones of genetically distinct cells in developing and adult tissues of Drosophila. Each of these strains carries an FRT element, the target for the yeast FLP recombinase, near the base of a major chromosome arm, as well as a gratuitous cell-autonomous marker. Novel markers that carry epitope tags and that are localized to either the cell nucleus or cell membrane have been generated. As a demonstration of how these strains can be used to study a particular gene, we have analyzed the developmental role of the Drosophila EGF receptor homolog. Moreover, we have shown that these strains can be utilized to identify new mutations in mosaic animals in an efficient and unbiased way, thereby providing an unprecedented opportunity to perform systematic genetic screens for mutations affecting many biological processes.

}, keywords = {Animals, Drosophila, Embryo, Epidermal Growth Factor, Female, Genetic Markers, Genetic Testing, Immunohistochemistry, Male, Mosaicism, Mutation, Nonmammalian, Phenotype, Receptor}, issn = {0950-1991}, doi = {10.1186/gb-2007-8-7-r145}, author = {Xu, T and Rubin, G M} } @article {966, title = {The argos gene encodes a diffusible factor that regulates cell fate decisions in the Drosophila eye.}, journal = {Cell}, volume = {69}, year = {1992}, month = {1992 Jun 12}, pages = {963-75}, abstract = {

The argos gene encodes a protein that is required for viability and that regulates the determination of cells in the Drosophila eye. A developmental analysis of argos mutant eyes indicates that the mystery cells, which are usually nonneuronal, are transformed into extra photoreceptors, and that supernumerary cone cells and pigment cells are also recruited. Clonal analysis indicates that argos acts nonautonomously and can diffuse over the range of several cell diameters. Conceptual translation of the argos gene suggests that it encodes a secreted protein.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Cell Communication, Clone Cells, Cloning, DNA, Drosophila melanogaster, Embryonic Induction, Eye, Gene Expression, Genes, Messenger, Molecular, Molecular Sequence Data, Phenotype, Restriction Mapping, RNA, Signal Transduction}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Freeman, M and Kl{\"a}mbt, C and Goodman, C S and Rubin, G M} } @article {45819, title = {Aphid soldiers discriminate between soldiers and non-soldiers, rather than between kin and non-kin, in Ceratoglyphina bambusae}, journal = {Animal behaviour}, volume = {42}, year = {1991}, pages = {865-866}, abstract = {

Examined kin discrimination and colony defense in soldier-producing aphids from the surface of 3 galls. Soldiers always attacked conspecific nonsoldiers, regardless of origin, and never attacked conspecific soldiers. Soldier attacks of nonsoldiers may exclude unrelated nonsoldier aphids from the gall where they would propagate and compete with resident aphids. (PsycINFO Database Record (c) 2012 APA, all rights reserved)

}, doi = {10.1016/S0003-3472(05)80135-6}, url = {http://psycnet.apa.org/psycinfo/1992-15421-001}, author = {Shigeyuki Aoki and Utako Kurosu and David L Stern} } @article {45823, title = {Agonistic interactions between ants and gall-living soldier aphids}, journal = {Journal of Ethology}, volume = {8}, year = {1990}, pages = {139-141}, issn = {0289-0771}, doi = {10.1007/BF02350284}, author = {Utako Kurosu and David L Stern and Shigeyuki Aoki} } @article {970, title = {Analysis of cis-acting requirements of the Rh3 and Rh4 genes reveals a bipartite organization to rhodopsin promoters in Drosophila melanogaster.}, journal = {Genes \& Development}, volume = {4}, year = {1990}, month = {1990 Mar}, pages = {444-63}, abstract = {

The rhodopsin genes of Drosophila melanogaster are expressed in nonoverlapping subsets of photoreceptor cells within the insect visual system. Two of these genes, Rh3 and Rh4, are known to display complementary expression patterns in the UV-sensitive R7 photoreceptor cell population of the compound eye. In addition, we find that Rh3 is expressed in a small group of paired R7 and R8 photoreceptor cells at the dorsal eye margin that are apparently specialized for the detection of polarized light. In this paper we present a detailed characterization of the cis-acting requirements of both Rh3 and Rh4. Promoter deletion series demonstrate that small regulatory regions (less than 300 bp) of both R7 opsin genes contain DNA sequences sufficient to generate their respective expression patterns. Individual cis-acting elements were further identified by oligonucleotide-directed mutagenesis guided by interspecific sequence comparisons. Our results suggest that the Drosophila rhodopsin genes share a simple bipartite promoter structure, whereby the proximal region constitutes a functionally equivalent promoter "core" and the distal region determines cell-type specificity. The expression patterns of several hybrid rhodopsin promoters, in which all or part of the putative core regions have been replaced with the analogous regions of different rhodopsin promoters, provide additional evidence in support of this model.

}, keywords = {Animals, Base Sequence, DNA Mutational Analysis, Drosophila melanogaster, Eye Proteins, Gene Expression, Genes, Genetic, Histocytochemistry, Molecular Sequence Data, Mutation, Nucleic Acid, Promoter Regions, Retinal Pigments, Rhodopsin, Rod Opsins, Sequence Homology}, issn = {0890-9369}, doi = {10.1186/gb-2007-8-7-r145}, author = {Fortini, M E and Rubin, G M} } @article {978, title = {Analysis of P transposable element functions in Drosophila.}, journal = {Cell}, volume = {38}, year = {1984}, month = {1984 Aug}, pages = {135-46}, abstract = {

We have made a P-element derivative called Pc[ry], which carries the selectable marker gene rosy, but which acts like a nondefective, intact P element. It transposes autonomously into the germline chromosomes of an M-strain Drosophila embryo and it mobilizes in trans the defective P elements of the singed-weak allele. Frameshift mutations introduced into any of the four major open reading frames of the P sequence were each sufficient to eliminate the transposase activity, but none affected signals required in cis for transposition of the element. Complementation tests between pairs of mutant elements suggest that a single polypeptide comprises the transposase. We have examined transcripts of P elements both from natural P strains and from lines containing only nondefective Pc[ry] elements, and have identified two RNA species that appear to be specific for autonomous elements.

}, keywords = {Alleles, Animals, Base Sequence, Crosses, DNA Restriction Enzymes, DNA Transposable Elements, Drosophila, Female, Genes, Genetic, Genetic Complementation Test, Male, Mutation, Nucleic Acid Hybridization}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Karess, R E and Rubin, G M} } @article {1144, title = {On the action of major loci affecting sex determination in Drosophila melanogaster.}, journal = {Genetics}, volume = {94}, year = {1980}, month = {1980 Feb}, pages = {383-423}, abstract = {

Sex determination in Drosophila melanogaster is under the control of the X chromosome:autosome ratio and at least four major regulatory genes: transformer (tra), transformer-2 (tra-2), doublesex (dsx) and intersex (ix). Attention is focused here on the roles of these four loci in sex determination. By examining the sexual phenotype of clones of homozygous mutant cells produced by mitotic recombination in flies heterozygous for a given recessive sex-determination mutant, we have shown that the tra, tra-2 and dsx loci determine sex in a cell-autonomous manner. The effect of removing the wild-type allele of each locus (by mitotic recombination) at a number of times during development has been used to determine when the wild-type alleles of the tra, tra-2 and dsx loci have been transcribed sufficiently to support normal sexual development. The wild-type alleles of all three loci are needed into the early pupal period for normal sex determination in the cells that produce the sexually dimorphic (in pigmentation) cuticle of the fifth and sixth dorsal abdominal segments. tra(+) and tra-2(+) cease being needed shortly before the termination of cell division in the abdomen, whereas dsx(+) is required at least until the end of division. By contrast, in the foreleg, the wild-type alleles of tra(+) and tra-2(+) have functioned sufficiently for normal sexual differentiation to occur by about 24 to 48 hours before pupariation, but dsx(+) is required in the foreleg at least until pupariation.--A comparison of the phenotypes produced in mutant/deficiency and homozygous mutant-bearing flies shows that dsx, tra-2 and tra mutants result in a loss of wild-type function and probably represent null alleles at these genes.-All possible homozygous doublemutant combinations of ix, tra-2 and dsx have been constructed and reveal a clear pattern of epistasis: dsx \> tra, tra-2 \> ix. We conclude that these genes function in a single pathway that determines sex. The data suggest that these mutants are major regulatory loci that control the batteries of genes necessary for the development of many, and perhaps all, secondary sexual characteristics.-The striking similarities between the properties of these loci and those of the homeotic loci that determine segmental and subsegmental specialization during development suggest that the basic mechanisms of regulation are the same in the two situations. The phenotypes and interactions of these sex-determination mutants provide the basis for the model of how the wild-type alleles of these loci act together to effect normal sex determination. Implications of these observations for the function of other homeotic loci are discussed.

}, issn = {0016-6731}, author = {Baker, B.S. and Ridge, K.} }