@article {70323, title = {Endocytome profiling uncovers cell-surface protein dynamics underlying neuronal connectivity.}, journal = {Neuron}, year = {2026}, month = {2026 Mar 12}, abstract = {

Endocytosis actively remodels the neuronal surface proteome to drive diverse cellular processes, yet its global extent and effects on neural circuit development have defied comprehensive interrogation. Here, we introduce endocytome profiling: a systematic, cell-type-specific approach for mapping cell-surface protein (CSP) dynamics in situ. Quantitative proteomic analysis of developing Drosophila olfactory receptor neuron (ORN) axons generated an endocytic atlas comprising over 1,000 proteins and revealed the extent to which the cell-surface proteome is remodeled to meet developmental demands. Targeted interrogation of a junctional CSP showed that its endosome-to-surface ratio is precisely balanced to enable developmental axon pruning while preserving mature axon integrity. Multi-omic integration uncovered widespread transcellular signaling and identified a growth factor secreted by neighboring neurons to direct ORN axon targeting via endocytic regulation of its receptor. Endocytome profiling provides unprecedented access to cell-surface proteome dynamics and offers a platform to dissect proteome-scale remodeling across diverse cell types and contexts.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2026.01.027}, url = {https://doi.org/10.1016/j.neuron.2026.01.027}, author = {McLaughlin, Colleen N and Ji, Hui and Dong, Katherine X and Xu, Chuanyun and Wong, Kenneth Kin Lam and Li, Zhuoran and Luginbuhl, David J and Xu, Charles and Lyu, Cheng and Qin, Wei and Li, Jiefu and Udeshi, Namrata D and Carr, Steven A and Ting, Alice Y and Luo, Liqun} } @article {70244, title = {Fast dendritic excitations primarily mediate back-propagation in CA1 pyramidal neurons during behavior}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 03}, abstract = {

Dendrites integrate synaptic inputs to trigger action potentials, and dendrites carry back-propagating action potentials (bAPs) to synapses where these signals contribute to plasticity. Despite strong evidence for a rich repertoire of nonlinear dendritic excitations, the in vivo roles of these excitations in dendritic integration and back-propagation remain uncertain. Here, we used high-speed voltage imaging through a chronically implanted microprism to map membrane potential dynamics from basal to apical dendrites of CA1 neurons in mice navigating in a virtual reality environment. Despite complex dendritic branch morphology, the dynamics were largely captured by 2 or 3 electrical compartments: basal, soma, and apical. Fast dendritic spikes almost always started from bAPs, indicating that dendritic spikes are primarily a consequence rather than a cause of somatic spiking. These fast spikes sometimes triggered slower apical dendritic plateau depolarizations, which drove complex spikes at the soma. We found that the biophysics of dendritic excitability determined the distribution of simple and complex spikes across a place field. Our results show how CA1 pyramidal neurons convert synaptic inputs to spiking outputs and suggest a primary role of dendritic nonlinearities in mediating activity-dependent plasticity.

}, doi = {10.64898/2026.01.03.696606}, url = {https://www.biorxiv.org/content/early/2026/01/03/2026.01.03.696606}, author = {Lee, Byung Hun and Park, Pojeong and Wu, Xiang and Wong-Campos, J. David and Xu, Junjie and Xiong, Marley and Qi, Yitong and Huang, Yi-Chieh and Itkis, Daniel G. and Plutkis, Sarah E. and Lavis, Luke D. and Cohen, Adam E.} } @article {70331, title = {NPAS4 refines spatial and temporal firing in CA1 pyramidal neurons}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 22}, abstract = {

NPAS4 is an activity-dependent transcription factor that, in CA1 of the hippocampus, regulates inhibitory synapses made onto the active pyramidal neuron. In principle, NPAS4 thereby allows the past activity of a neuron to influence how it encodes information, although this has not yet been demonstrated. Here, we generated a sparse, CA1-specific knockout (KO) of NPAS4 in the mouse hippocampus and used optogenetic tagging to identify KO neurons in vivo. Recordings from intermingled wild-type (WT) and KO neurons in awake behaving animals revealed that NPAS4 deletion degrades spatial representations and temporal precision of spiking: KO neurons exhibited larger place fields with reduced in-field firing and increased out-of-field firing, less stable place fields, reduced coupling to local field potential theta oscillations, and diminished phase precession. These findings demonstrate that NPAS4 plays a crucial role in refining the spatial and temporal properties of CA1 pyramidal neuron spikes, which themselves are thought to be fundamental building blocks of more complex processes such as learning and memory.

}, doi = {10.64898/2026.03.22.713468}, url = {https://www.biorxiv.org/content/early/2026/03/22/2026.03.22.713468}, author = {Payne, Anja and Heinz, Daniel A. and Santiago, Chiaki and Hagopian, Lara L. and Ganasi, Rolando Sceptre and Quirk, Clare and Hartzell, Andrea L. and Leutgeb, Jill K. and Leutgeb, Stefan and Bloodgood, Brenda L.} } @article {70257, title = {Redefining colocalization analysis with a novel phasor mixing coefficient}, journal = {Journal of Cell Science}, volume = {139}, year = {2026}, month = {2026 Jan 19}, pages = {jcs264388}, abstract = {

The first step to probing any potential interaction between two biomolecules is to determine their spatial association. In other words, if two biomolecules localize similarly within a cell, then it is plausible they could interact. Traditionally, this is quantified through various colocalization metrics. These measures infer this association by estimating the degree to which fluorescent signals from each biomolecule overlap or correlate. However, these metrics are, at best, proxies, and they depend strongly on various experimental choices. Here, we define a new strategy that leverages multispectral imaging and phasor analysis, termed the phasor mixing coefficient (PMC). The PMC measures the precise mixing of fluorescent signals in each pixel. We demonstrate how the PMC captures complex biological subtlety by offering two distinct values, a global measure of overall color mixing and the homogeneity thereof. We additionally show that the PMC exhibits less sensitivity to signal-to-noise ratio, intensity threshold and background signal compared to canonical methods. Moreover, this method provides a means to visualize color mixing at each pixel. We show that the PMC offers users a nuanced and robust metric to quantify biological association.

}, issn = {0021-9533}, doi = {10.1242/jcs.264388}, url = {https://doi.org/10.1242/jcs.264388}, author = {Puls, Owen F. and Aaron, Jesse S. and Quarles, Ellen K. and Khuon, Satya and Eisenman, Leanna R. and Kamaid, Andres and Malacrida, Leonel and Chew, Teng-Leong} } @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 {69719, title = {Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopyAbstract}, journal = {Nature Communications}, volume = {16}, year = {2025}, month = {Jan-12-2025}, abstract = {

Optical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing image acquisition, applying additional dose, or introducing more optics. Our method (i) introduces synthetic aberrations to images acquired on the shallow side of image stacks, making them resemble those acquired deeper into the volume and (ii) trains neural networks to reverse the effect of these aberrations. We use simulations and experiments to show that applying the trained {\textquoteleft}de-aberration{\textquoteright} networks outperforms alternative methods, providing restoration on par with adaptive optics techniques; and subsequently apply the networks to diverse datasets captured with confocal, light-sheet, multi-photon, and super-resolution microscopy. In all cases, the improved quality of the restored data facilitates qualitative image inspection and improves downstream image quantitation, including orientational analysis of blood vessels in mouse tissue and improved membrane and nuclear segmentation in\ C. elegans\ embryos.

}, doi = {10.1038/s41467-024-55267-x}, url = {https://www.nature.com/articles/s41467-024-55267-xhttps://www.nature.com/articles/s41467-024-55267-x.pdfhttps://www.nature.com/articles/s41467-024-55267-x.pdfhttps://www.nature.com/articles/s41467-024-55267-x}, author = {Guo, Min and Wu, Yicong and Hobson, Chad M. and Su, Yijun and Qian, Shuhao and Krueger, Eric and Christensen, Ryan and Kroeschell, Grant and Bui, Johnny and Chaw, Matthew and Zhang, Lixia and Liu, Jiamin and Hou, Xuekai and Han, Xiaofei and Lu, Zhiye and Ma, Xuefei and Zhovmer, Alexander and Combs, Christian and Moyle, Mark and Yemini, Eviatar and Liu, Huafeng and Liu, Zhiyi and Benedetto, Alexandre and La Riviere, Patrick and Col{\'o}n-Ramos, Daniel and Shroff, Hari} } @article {69460, title = {Dendritic excitations govern back-propagation via a spike-rate accelerometer}, journal = {Nature Communications}, volume = {16}, year = {2025}, month = {2025 Feb 04}, abstract = {

Dendrites on neurons support nonlinear electrical excitations, but the computational significance of these events is not well understood. We developed molecular, optical, and analytical tools to map sub-millisecond voltage dynamics throughout the dendritic trees of CA1 pyramidal neurons under diverse optogenetic and synaptic stimulus patterns, in acute brain slices. We observed history-dependent spike back-propagation in distal dendrites, driven by locally generated Na+ spikes (dSpikes). Dendritic depolarization created a transient window for dSpike propagation, opened by A-type KV channel inactivation, and closed by slow NaV inactivation. Collisions of dSpikes with synaptic inputs triggered calcium channel and N-methyl-D-aspartate receptor (NMDAR)-dependent plateau potentials, with accompanying complex spikes at the soma. This hierarchical ion channel network acts as a spike-rate accelerometer, providing an intuitive picture of how dendritic excitations shape associative plasticity rules.

}, doi = {10.1038/s41467-025-55819-9}, url = {https://www.biorxiv.org/content/early/2024/05/18/2023.06.02.543490}, author = {Park, Pojeong and Wong-Campos, David and Itkis, Daniel G. and Lee, Byung Hun and Qi, Yitong and Davis, Hunter and Antin, Benjamin and Pasarkar, Amol and Grimm, Jonathan B. and Plutkis, Sarah E. and Holland, Katie L. and Paninski, Liam and Lavis, Luke D. and Cohen, Adam E.} } @article {69846, title = {Far-red fluorescent genetically encoded calcium ion indicators.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Apr 07}, pages = {3318}, abstract = {

Genetically encoded calcium ion (Ca) indicators (GECIs) are widely-used molecular tools for functional imaging of Ca dynamics and neuronal activities with single-cell resolution. Here we report the design and development of two far-red fluorescent GECIs, FR-GECO1a and FR-GECO1c, based on the monomeric far-red fluorescent proteins mKelly1 and mKelly2. FR-GECOs have excitation and emission maxima at ~596 nm and ~644 nm, respectively, display large responses to Ca in vitro (ΔF/F = 6 for FR-GECO1a, 18 for FR-GECO1c), are bright under both one-photon and two-photon illumination, and have high affinities (apparent K = 29 nM for FR-GECO1a, 83 nM for FR-GECO1c) for Ca. FR-GECOs offer sensitive and fast detection of single action potentials in neurons, and enable in vivo all-optical manipulation and measurement of cellular activities in combination with optogenetic actuators.

Preprint:\ https://doi.org/10.1101/2020.11.12.380089

}, keywords = {Action Potentials, Animals, Calcium, Fluorescent Dyes, HEK293 Cells, Humans, Luminescent Proteins, Mice, Neurons, Optogenetics, Red Fluorescent Protein}, issn = {2041-1723}, doi = {10.1038/s41467-025-58485-z}, url = {https://doi.org/10.1038/s41467-025-58485-z}, author = {Dalangin, Rochelin and Jia, Bill Z and Qi, Yitong and Aggarwal, Abhi and Sakoi, Kenryo and Drobizhev, Mikhail and Molina, Rosana S and Patel, Ronak and Abdelfattah, Ahmed S and Zheng, Jihong and Reep, Daniel and Hasseman, Jeremy P and Zhao, Yufeng and Wu, Jiahui and Podgorski, Kaspar and Tebo, Alison G and Schreiter, Eric R and Hughes, Thomas E and Terai, Takuya and Paquet, Marie-Eve and Megason, Sean G and Cohen, Adam E and Shen, Yi and Campbell, Robert E} } @article {69842, title = {Hedonic eating is controlled by dopamine neurons that oppose GLP-1R satiety.}, journal = {Science}, volume = {387}, year = {2025}, month = {2025 Mar 28}, pages = {eadt0773}, abstract = {

Hedonic eating is defined as food consumption driven by palatability without physiological need. However, neural control of palatable food intake is poorly understood. We discovered that hedonic eating is controlled by a neural pathway from the peri-locus ceruleus to the ventral tegmental area (VTA). Using photometry-calibrated optogenetics, we found that VTA dopamine (VTA) neurons encode palatability to bidirectionally regulate hedonic food consumption. VTA neuron responsiveness was suppressed during food consumption by semaglutide, a glucagon-like peptide receptor 1 (GLP-1R) agonist used as an antiobesity drug. Mice recovered palatable food appetite and VTA neuron activity during repeated semaglutide treatment, which was reversed by consumption-triggered VTA neuron inhibition. Thus, hedonic food intake activates VTA neurons, which sustain further consumption, a mechanism that opposes appetite reduction by semaglutide.

}, keywords = {Animals, Anti-Obesity Agents, Appetite, Dopaminergic Neurons, Eating, Glucagon-Like Peptide 1, Glucagon-Like Peptide-1 Receptor, Glucagon-Like Peptides, Male, Mice, Mice, Inbred C57BL, Neural Pathways, Optogenetics, Satiation, Satiety Response, Ventral Tegmental Area}, issn = {1095-9203}, doi = {10.1126/science.adt0773}, url = {https://doi.org/10.1126/science.adt0773}, author = {Zhu, Zhenggang and Gong, Rong and Rodriguez, Vicente and Quach, Kathleen T and Chen, Xinyu and Sternson, Scott M} } @article {70139, title = {In-situ glial cell-surface proteomics identifies pro-longevity factors in Drosophila}, journal = {eLife}, year = {2025}, month = {2025 Dec 12}, abstract = {

Much focus has shifted towards understanding how glial dysfunction contributes to age-related neurodegeneration due to the critical roles glial cells play in maintaining healthy brain function. Cell-cell interactions, which are largely mediated by cell-surface proteins, control many critical aspects of development and physiology; as such, dysregulation of glial cell-surface proteins in particular is hypothesized to play an important role in age-related neurodegeneration. However, it remains technically difficult to profile glial cell-surface proteins in intact brains. Here, we applied a cell-surface proteomic profiling method to glial cells from intact brains in\ Drosophila,\ which enabled us to fully profile cell-surface proteomes\ in-situ, preserving native cell-cell interactions that would otherwise be omitted using traditional proteomics methods. Applying this platform to young and old flies, we investigated how glial cell-surface proteomes change during aging. We identified candidate genes predicted to be involved in brain aging, including several associated with neural development and synapse wiring molecules not previously thought to be particularly active in glia. Through a functional genetic screen, we identified one surface protein, DIP-β, which is down-regulated in old flies and can increase fly lifespan when overexpressed in adult glial cells. We further performed whole-head single-nucleus RNA-seq, and revealed that DIP-β overexpression mainly impacts glial and fat cells. We also found that glial DIP-β overexpression was associated with improved cell-cell communication, which may contribute to the observed lifespan extension. Our study is the first to apply\ in-situ\ cell-surface proteomics to glial cells in\ Drosophila, and to identify DIP-β as a potential glial regulator of brain aging.

}, doi = {10.7554/eLife.109422.1}, url = {https://doi.org/10.7554/eLife.109422.1}, author = {Marques, Madeline P. and Sun, Bo and Park, Ye-Jin and Jackson, Tyler and Lu, Tzu-Chiao and Qi, Yanyan and Harrison, Erin and Wang, Miranda C. and Venkatachalam, Kartik and Pasha, Omar Moussa and Varanasi, Amogh and Carey, Dominique Kiki and Mani, D.R. and Zirin, Jonathan and Qadiri, Mujeeb and Hu, Yanhui and Perrimon, Norbert and Carr, Steven A. and Udeshi, Namrata D. and Luo, Liqun and Li, Jiefu and Li, Hongjie} } @article {70202, title = {Memory traces bias new learning for hippocampal generalization}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 25}, abstract = {

The ability to use generalized prior experience to guide behavior in novel situations is a fundamental cognitive function. While recent evidence suggests that the hippocampus supports generalization how this is accomplished is poorly understood. Here we combined longitudinal optical imaging in head-fixed mice with computational modeling to examine generalization in hippocampal area CA1. We found that prior training accelerated behavioral adaptation to a novel environment and that this was accompanied by highly stable hippocampal representations. We identified putative memory traces from prior experience that enabled this generalization at multiple levels. At the population level, novel-context network dynamics rapidly aligned with low-dimensional neural subspaces established during prior experience. At the cellular level, spatially-informative weak "residual" activity reflecting generalizable information about the task structure appeared to bias which neurons form place fields (PFs) and where via behavioral timescale synaptic plasticity (BTSP). Finally, this was an active process as many PFs changed their reference frame in the novel environment to reflect the consistent task structure. In sum, the influence of memory traces on new PF formation may allow past experience to guide new learning such that representations are based on generalizable features, thus enabling rapid adaptive behavior in new contexts.

}, doi = {10.1101/2025.11.24.690297}, url = {https://www.biorxiv.org/content/early/2025/11/25/2025.11.24.690297}, author = {Qian, Fish Kunxun and Li, Guanchun and Lipshutz, David and Romani, Sandro and Magee, Jeffrey Charles} } @article {70198, title = {Redefining colocalization analysis with a novel Phasor Mixing Coefficient.}, journal = {J Cell Sci}, year = {2025}, month = {2025 Nov 24}, abstract = {

The first step to probing any potential interaction between two biomolecules is to determine their spatial association. In other words, if two biomolecules localize similarly within a cell, then it is plausible they could interact. Traditionally, this is quantified through various colocalization metrics. These measures infer this association by estimating the degree to which fluorescent signals from each biomolecule overlap or correlate. However, these metrics are, at best, proxies, and they depend strongly on various experimental choices. Alternatively, here we define a new strategy which leverages multispectral imaging and phasor analysis, termed the Phasor Mixing Coefficient (PMC). PMC measures the precise mixing of fluorescent signals in each pixel. We demonstrate how PMC captures complex biological subtlety by offering two distinct values, a global measure of overall color mixing and the homogeneity thereof. We additionally show that PMC exhibits less sensitivity to signal-to-noise ratio, intensity threshold, and background signal compared to canonical methods. Moreover, this method provides a means to visualize color mixing at each pixel. We show that PMC offers users a nuanced and robust metric to quantify biological association.

}, issn = {1477-9137}, doi = {10.1242/jcs.264388}, author = {Puls, Owen F and Aaron, Jesse S and Quarles, Ellen K and Khuon, Satya and Eisenman, Leanna R and Kamaid, Andres and Malacrida, Leonel and Chew, Teng-Leong} } @article {70203, title = {Redefining colocalization analysis with a novel Phasor Mixing Coefficient.}, journal = {J Cell Sci}, year = {2025}, month = {2025 Nov 24}, abstract = {

The first step to probing any potential interaction between two biomolecules is to determine their spatial association. In other words, if two biomolecules localize similarly within a cell, then it is plausible they could interact. Traditionally, this is quantified through various colocalization metrics. These measures infer this association by estimating the degree to which fluorescent signals from each biomolecule overlap or correlate. However, these metrics are, at best, proxies, and they depend strongly on various experimental choices. Alternatively, here we define a new strategy which leverages multispectral imaging and phasor analysis, termed the Phasor Mixing Coefficient (PMC). PMC measures the precise mixing of fluorescent signals in each pixel. We demonstrate how PMC captures complex biological subtlety by offering two distinct values, a global measure of overall color mixing and the homogeneity thereof. We additionally show that PMC exhibits less sensitivity to signal-to-noise ratio, intensity threshold, and background signal compared to canonical methods. Moreover, this method provides a means to visualize color mixing at each pixel. We show that PMC offers users a nuanced and robust metric to quantify biological association.

}, issn = {1477-9137}, doi = {10.1242/jcs.264388}, url = {https://doi.org/10.1242/jcs.264388}, author = {Puls, Owen F and Aaron, Jesse S and Quarles, Ellen K and Khuon, Satya and Eisenman, Leanna R and Kamaid, Andres and Malacrida, Leonel and Chew, Teng-Leong} } @article {70155, title = {Sexual dimorphism in the complete connectome of the Drosophila male central nervous system}, journal = {bioRxiv}, year = {2025}, month = {2025 Oct 09}, abstract = {

Sex differences in behaviour exist across the animal kingdom, typically under strong genetic regulation. In Drosophila, previous work has shown that fruitless and doublesex transcription factors identify neurons driving sexually dimorphic behaviour. However, the organisation of dimorphic neurons into functional circuits remains unclear.We now present the connectome of the entire Drosophila male central nervous system. This contains 166,691 neurons spanning the brain and ventral nerve cord, fully proofread and comprehensively annotated including fruitless and doublesex expression and 11,691 cell types. By comparison with a previous female brain connectome, we provide the first comprehensive description of the differences between male and female brains to synaptic resolution. Of 7,319 cross-matched cell types in the central brain, 114 are dimorphic with an additional 262 male- and 69 female-specific (totalling 4.8\% of neurons in males and 2.4\% in females).This resource enables analysis of full sensory-to-motor circuits underlying complex behaviours as well as the impact of dimorphic elements. Sex-specific and dimorphic neurons are concentrated in higher brain centres while the sensory and motor periphery are largely isomorphic. Within higher centres, male-specific connections are organised into hotspots defined by male-specific neurons or the presence of male-specific arbours on neurons that are otherwise similar between sexes. Numerous circuit switches reroute sensory information to form conserved, antagonistic circuits controlling opposing behaviours.

}, doi = {10.1101/2025.10.09.680999}, url = {https://www.biorxiv.org/content/early/2025/10/09/2025.10.09.680999}, author = {Berg, Stuart and Beckett, Isabella R and Costa, Marta and Schlegel, Philipp and Januszewski, Micha{\l} and Marin, Elizabeth C and Nern, Aljoscha and Preibisch, Stephan and Qiu, Wei and Takemura, Shin-ya and Fragniere, Alexandra MC and Champion, Andrew S and Adjavon, Diane-Yayra and Cook, Michael and Gkantia, Marina and Hayworth, Kenneth J and Huang, Gary B and Katz, William T and K{\"a}mpf, Florian and Lu, Zhiyuan and Ordish, Christopher and Paterson, Tyler and St{\"u}rner, Tomke and Trautman, Eric T and Whittle, Catherine R and Burnett, Laura E and Hoeller, Judith and Li, Feng and Loesche, Frank and Morris, Billy J and Pietzsch, Tobias and Pleijzier, Markus W and Silva, Valeria and Yin, Yijie and Ali, Iris and Badalamente, Griffin and Bates, Alexander Shakeel and Bogovic, John and Brooks, Paul and Cachero, Sebastian and Canino, Brandon S and Chaisrisawatsuk, Bhumpanya and Clements, Jody and Crowe, Arthur and de Haan Vicente, In{\^e}s and Dempsey, Georgia and Don{\`a}, Erika and dos Santos, M{\'a}rcia and Dreher, Marisa and Dunne, Christopher R and Eichler, Katharina and Finley-May, Samantha and Flynn, Miriam A and Hameed, Imran and Hopkins, Gary Patrick and Hubbard, Philip M and Kiassat, Ladann and Kovalyak, Julie and Lauchie, Shirley A and Leonard, Meghan and Lohff, Alanna and Longden, Kit D and Maldonado, Charli A and Mitletton, Myrto and Moitra, Ilina and Moon, Sung Soo and Mooney, Caroline and Munnelly, Eva J and Okeoma, Nneoma and Olbris, Donald J and Pai, Anika and Patel, Birava and Phillips, Emily M and Plaza, Stephen M and Richards, Alana and Rivas Salinas, Jennifer and Roberts, Ruair{\'\i} Jv and Rogers, Edward M and Scott, Ashley L and Scuderi, Louis A and Seenivasan, Pavithraa and Serratosa Capdevila, Laia and Smith, Claire and Svirskas, Rob and Takemura, Satoko and Tastekin, Ibrahim and Thomson, Alexander and Umayam, Lowell and Walsh, John J and Whittome, Holly and Xu, C Shan and Yakal, Emily A and Yang, Tansy and Zhao, Arthur and George, Reed and Jain, Viren and Jayaraman, Vivek and Korff, Wyatt and Meissner, Geoffrey W and Romani, Sandro and Funke, Jan and Knecht, Christopher and Saalfeld, Stephan and Scheffer, Louis K and Waddell, Scott and Card, Gwyneth M and Ribeiro, Carlos and Reiser, Michael B and Hess, Harald F and Rubin, Gerald M and Jefferis, Gregory Sxe} } @article {69490, title = {Spatial transcriptomics reveals human cortical layer and area specification}, journal = {Nature}, year = {2025}, month = {2025 May 14}, abstract = {

The human cerebral cortex, pivotal for advanced cognitive functions, is composed of six distinct layers and dozens of functionally specialized areas. The layers and areas are distinguished both molecularly, by diverse neuronal and glial cell subtypes, and structurally, through intricate spatial organization3,4. While single-cell transcriptomics studies have advanced molecular characterization of human cortical development, a critical gap exists due to the loss of spatial context during cell dissociation. Here, we utilized multiplexed error-robust fluorescence in situ hybridization (MERFISH)9, augmented with deep-learning-based cell segmentation, to examine the molecular, cellular, and cytoarchitectural development of human fetal cortex with spatially resolved single-cell resolution. Our extensive spatial atlas, encompassing 16 million single cells, spans eight cortical areas across four time points in the second and third trimesters. We uncovered an early establishment of the six-layer structure, identifiable in the laminar distribution of excitatory neuronal subtypes by mid-gestation, long before the emergence of cytoarchitectural layers. Notably, while anterior-posterior gradients of neuronal subtypes were generally observed in most cortical areas, a striking exception was the sharp molecular border between primary (V1) and secondary visual cortices (V2) at gestational week 20. Here we discovered an abrupt binary shift in neuronal subtype specification at the earliest stages, challenging the notion that continuous morphogen gradients dictate mid-gestation cortical arealization. Moreover, integrating single-nuclei RNA-sequencing and in situ whole transcriptomics revealed an early upregulation of synaptogenesis in V1-specific Layer 4 neurons, suggesting a role of synaptogenesis in this discrete border formation. Collectively, our findings underscore the crucial role of spatial relationships in determining the molecular specification of cortical layers and areas. This work not only provides a valuable resource for the field, but also establishes a spatially resolved single-cell analysis paradigm that paves the way for a comprehensive developmental atlas of the human brain.

Preprint:\ https://www.biorxiv.org/content/early/2024/06/10/2024.06.05.597673

}, doi = {10.1038/s41586-025-09010-1}, url = {https://doi.org/10.1038/s41586-025-09010-1}, author = {Qian, Xuyu and Coleman, Kyle and Jiang, Shunzhou and Kriz, Andrea J. and Marciano, Jack H. and Luo, Chunyu and Cai, Chunhui and Manam, Monica Devi and Caglayan, Emre and Otani, Aoi and Ghosh, Urmi and Shao, Diane D. and Andersen, Rebecca E. and Neil, Jennifer E. and Johnson, Robert and LeFevre, Alexandra and Hecht, Jonathan L. and Miller, Michael B. and Sun, Liang and Stringer, Carsen and Li, Mingyao and Walsh, Christopher A.} } @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 {69373, title = {Connectome-driven neural inventory of a complete visual system}, journal = {Nature}, year = {2024}, month = {2025 Mar 26}, abstract = {

Vision provides animals with detailed information about their surroundings, conveying diverse features such as color, form, and movement across the visual scene. Computing these parallel spatial features requires a large and diverse network of neurons, such that in animals as distant as flies and humans, visual regions comprise half the brain{\textquoteright}s volume. These visual brain regions often reveal remarkable structure-function relationships, with neurons organized along spatial maps with shapes that directly relate to their roles in visual processing. To unravel the stunning diversity of a complex visual system, a careful mapping of the neural architecture matched to tools for targeted exploration of that circuitry is essential. Here, we report a new connectome of the right optic lobe from a male Drosophila central nervous system FIB-SEM volume and a comprehensive inventory of the fly{\textquoteright}s visual neurons. We developed a computational framework to quantify the anatomy of visual neurons, establishing a basis for interpreting how their shapes relate to spatial vision. By integrating this analysis with connectivity information, neurotransmitter identity, and expert curation, we classified the 53,000 neurons into 727 types, about half of which are systematically described and named for the first time. Finally, we share an extensive collection of split-GAL4 lines matched to our neuron type catalog. Together, this comprehensive set of tools and data unlock new possibilities for systematic investigations of vision in Drosophila, a foundation for a deeper understanding of sensory processing.

}, doi = {10.1038/s41586-025-08746-0}, url = {https://doi.org/10.1038/s41586-025-08746-0}, author = {Aljoscha Nern and Frank Loesche and Shin-ya Takemura and Laura E Burnett and Marisa Dreher and Eyal Gruntman and Judith Hoeller and Gary B Huang and Michal Januszewski and Nathan C Klapoetke and Sanna Koskela and Kit D Longden and Zhiyuan Lu and Stephan Preibisch and Wei Qiu and Edward M Rogers and Pavithraa Seenivasan and Arthur Zhao and John Bogovic and Brandon S Canino and Jody Clements and Michael Cook and Samantha Finley-May and Miriam A Flynn and Imran Hameed and Kenneth J Hayworth and Gary Patrick Hopkins and Philip M Hubbard and William T Katz and Julie Kovalyak and Shirley A Lauchie and Meghan Leonard and Alanna Lohff and Charli A Maldonado and Caroline Mooney and Nneoma Okeoma and Donald J Olbris and Christopher Ordish and Tyler Paterson and Emily M Phillips and Tobias Pietzsch and Jennifer Rivas Salinas and Patricia K Rivlin and Ashley L Scott and Louis A Scuderi and Satoko Takemura and Iris Talebi and Alexander Thomson and Eric T Trautman and Lowell Umayam and Claire Walsh and John J Walsh and C Shan Xu and Emily A Yakal and Tansy Yang and Ting Zhao and Jan Funke and Reed George and Harald F Hess and Gregory S X E Jefferis and Christopher Knecht and Wyatt Korff and Stephen M Plaza and Sandro Romani and Stephan Saalfeld and Louis K Scheffer and Stuart Berg and Gerald M Rubin and Michael B Reiser} } @article {69328, title = {Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses}, journal = {eLife}, year = {2024}, month = {2024 Nov 11}, abstract = {

Chemical synapses are the major sites of communication between neurons in the nervous system and mediate either excitatory or inhibitory signaling. At excitatory synapses, glutamate is the primary neurotransmitter and upon release from presynaptic vesicles, is detected by postsynaptic glutamate receptors, which include ionotropic AMPA and NMDA receptors. Here, we have developed methods to identify glutamatergic synapses in brain tissue slices, label AMPA receptors with small gold nanoparticles (AuNPs), and prepare lamella for cryo-electron tomography studies. The targeted imaging of glutamatergic synapses in the lamella is facilitated by fluorescent pre- and postsynaptic signatures, and the subsequent tomograms allow for the identification of key features of chemical synapses, including synaptic vesicles, the synaptic cleft, and AuNP-labeled AMPA receptors. These methods pave the way for imaging brain regions at high resolution, using unstained, unfixed samples preserved under near-native conditions.

}, doi = {10.7554/eLife.98458}, url = {https://doi.org/10.7554/eLife.98458}, author = {Aya Matsui and Catherine Spangler and Johannes Elferich and Momoko Shiozaki and Nikki Jean and Xiaowei Zhao and Maozhen Qin and Haining Zhong and Zhiheng Yu and Eric Gouaux} } @article {69602, title = {Data Release: High-Resolution Imaging and Segmentation of P7 Mouse Tissue Microarchitecture Using FIB-SEM and Machine Learning}, journal = {bioRxiv}, year = {2024}, month = {2024 Sep 07}, abstract = {

This report presents a comprehensive data release exploring the tissue microarchitecture of P7 aged mice using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) combined with machine learning-based segmentations of nuclei. The study includes high-resolution 3D volumes and nucleus segmentations for seven vital tissues{\textemdash}pancreas, liver, kidney, heart, thymus, hippocampus, and skin{\textemdash}from a single mouse. The detailed datasets are openly accessible on OpenOrganelle.org, providing a valuable resource for the scientific community to support further research and collaboration.

}, doi = {10.1101/2024.09.05.611438}, url = {https://www.doi.org/10.1101/2024.09.05.611438}, author = {Ackerman, David and Avetissian, Emma and Bleck, Christopher K. E. and Bogovic, John A. and Innerberger, Michael and Korff, Wyatt and Li, Wei-Ping and Lu, Zhiyuan and Petruncio, Alyson and Preibisch, Stephan and Qiu, Wei and Jeff L Rhoades and Saalfeld, Stephan and Silva, Malan and Trautman, Eric T. and Vorimo, Rebecca and Weigel, Aubrey and Yu, Zhiheng and Zubov, Yurii and ,} } @article {69256, title = {Dendritic voltage imaging maps the biophysical basis of plateau potentials in the hippocampus}, journal = {bioRxiv}, year = {2024}, month = {2024 Mar 7}, abstract = {

Dendrites on neurons integrate synaptic inputs to determine spike timing. Dendrites also convey back-propagating action potentials (bAPs) which interact with synaptic inputs to produce plateau potentials and to mediate synaptic plasticity. The biophysical rules which govern the timing, spatial structures, and ionic character of dendritic excitations are not well understood. We developed molecular, optical, and computational tools to map sub-millisecond voltage dynamics throughout the dendritic trees of CA1 pyramidal neurons under diverse optogenetic and synaptic stimulus patterns, in acute brain slices. We observed history-dependent bAP propagation in distal dendrites, driven by locally generated Na+ spikes (dSpikes). Dendritic depolarization creates a transient window for dSpike propagation, opened by A-type KV channel inactivation, and closed by slow NaV inactivation. Collisions of dSpikes with synaptic inputs triggered calcium channel and N-methyl-D-aspartate receptor (NMDAR)-dependent plateau potentials, with accompanying complex spikes at the soma. This hierarchical ion channel network acts as a spike-rate accelerometer, providing an intuitive picture of how dendritic excitations shape associative plasticity rules.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2023.06.02.543490}, url = {https://www.biorxiv.org/content/early/2024/03/07/2023.06.02.543490}, author = {Pojeong Park and J. David Wong-Campos and Daniel Itkis and Byung Hun Lee and Yitong Qi and Hunter C. Davis and Jonathan B. Grimm and Sarah E. Plutkis and Luke Lavis and Adam Ezra Cohen} } @article {69327, title = {Development of a First-in-Class RIPK1 Degrader to Enhance Antitumor Immunity}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Dec 16}, pages = {10683}, abstract = {

The scaffolding function of receptor interacting protein kinase 1 (RIPK1) confers intrinsic and extrinsic resistance to immune checkpoint blockades (ICBs) and emerges as a promising target for improving cancer immunotherapies. To address the challenge posed by a poorly defined binding pocket within the intermediate domain of RIPK1, here we harness proteolysis targeting chimera (PROTAC) technology to develop a RIPK1 degrader, LD4172. LD4172 exhibits potent and selective RIPK1 degradation both in vitro and in vivo. Degradation of RIPK1 by LD4172 triggers immunogenic cell death, enhances tumor-infiltrating lymphocyte responses, and sensitizes tumors to anti-PD1 therapy in female C57BL/6J mice. This work reports a RIPK1 degrader that serves as a chemical probe for investigating the scaffolding functions of RIPK1 and as a potential therapeutic agent to enhance tumor responses to ICBs therapy.

}, doi = {10.1038/s41467-024-55006-2}, url = {https://doi.org/10.1038/s41467-024-55006-2}, author = {Xin Yu and Dong Lu and Xiaoli Qi and Hanfeng Lin and Bryan L. Holloman and Feng Jin and Longyong Xu and Lang Ding and Weiyi Peng and Meng C. Wang and Xi Chen and Jin Wang} } @article {69692, title = {Elevated IL-22 as a result of stress-induced gut leakage suppresses septal neuron activation to ameliorate anxiety-like behavior.}, journal = {Immunity}, year = {2024}, month = {2024 Dec 04}, pages = {S1074-7613(24)00523-5}, abstract = {

Psychological stress and its sequelae pose a major challenge to public health. Immune activation is conventionally thought to aggravate stress-related mental diseases such as anxiety disorders and depression. Here, we sought to identify potentially beneficial consequences of immune activation in response to stress. We showed that stress led to increased interleukin (IL)-22 production in the intestine as a result of stress-induced gut leakage. IL-22 was both necessary and sufficient to attenuate stress-induced anxiety behaviors in mice. More specifically, IL-22 gained access to the septal area of the brain and directly suppressed neuron activation. Furthermore, human patients with clinical depression displayed reduced IL-22 levels, and exogenous IL-22 treatment ameliorated depressive-like behavior elicited by chronic stress in mice. Our study thus identifies a gut-brain axis in response to stress, whereby IL-22 reduces neuronal activation and concomitant anxiety behavior, suggesting that early immune activation can provide protection against psychological stress.

}, issn = {1097-4180}, doi = {10.1016/j.immuni.2024.11.008}, author = {Xia, Mengyu and Lu, Junmei and Lan, Jiabin and Teng, Teng and Shiao, Rani and Sun, Hongbin and Jin, Zheyu and Liu, Xueer and Wang, Jie and Wu, Hongyan and Wang, Changchun and Yi, Han and Qi, Qingqing and Li, Jixi and Schneeberger, Marc and Shen, Wei and Lu, Boxun and Chen, Lei and Ilanges, Anoj and Zhou, Xinyu and Yu, Xiaofei} } @article {69649, title = {FITM2 deficiency results in ER lipid accumulation, ER stress, and reduced apolipoprotein B lipidation and VLDL triglyceride secretion in vitro and in mouse liver.}, journal = {Mol Metab}, year = {2024}, month = {2024 Oct 18}, pages = {102048}, abstract = {

OBJECTIVES: Triglycerides (TGs) associate with apolipoprotein B100 (apoB100) to form very low density lipoproteins (VLDLs) in the liver. The repertoire of factors that facilitate this association is incompletely understood. FITM2, an integral endoplasmic reticulum (ER) protein, was originally discovered as a factor participating in cytosolic lipid droplet (LD) biogenesis in tissues that do not form VLDL. We hypothesized that in the liver, in addition to promoting cytosolic LD formation, FITM2 would also transfer TG from its site of synthesis in the ER membrane to nascent VLDL particles within the ER lumen.

METHODS: Experiments were conducted using a rat hepatic cell line (McArdle-RH7777, or McA cells), an established model of mammalian lipoprotein metabolism, and mice. FITM2 expression was reduced using siRNA in cells and by liver specific cre-recombinase mediated deletion of the Fitm2 gene in mice. Effects of FITM2 deficiency on VLDL assembly and secretion in\ vitro and in\ vivo were measured by multiple methods, including density gradient ultracentrifugation, chromatography, mass spectrometry, stimulated Raman scattering (SRS) microscopy, sub-cellular fractionation, immunoprecipitation, immunofluorescence, and electron microscopy.

MAIN FINDINGS: 1) FITM2-deficient hepatic cells in\ vitro and in\ vivo secrete TG-depleted VLDL particles, but the number of particles is unchanged compared to controls; 2) FITM2 deficiency in mice on a high fat diet (HFD) results in decreased plasma TG levels. The number of apoB100-containing lipoproteins remains similar, but shift from VLDL to low density lipoprotein (LDL) density; 3) Both in\ vitro and in\ vivo, when TG synthesis is stimulated and FITM2 is deficient, TG accumulates in the ER, and despite its availability this pool is unable to fully lipidate apoB100 particles; 4) FITM2 deficiency disrupts ER morphology and results in ER stress.

PRINCIPAL CONCLUSIONS: The results suggest that FITM2 contributes to VLDL lipidation, especially when newly synthesized hepatic TG is in abundance. In addition to its fundamental importance in VLDL assembly, the results also suggest that under dysmetabolic conditions, FITM2 may be an important factor in the partitioning of TG between cytosolic LDs and VLDL particles.

}, issn = {2212-8778}, doi = {10.1016/j.molmet.2024.102048}, url = {https://doi.org/10.1016/j.molmet.2024.102048}, author = {Wang, Haizhen and Nikain, Cyrus and Fortounas, Konstantinos I and Amengual, Jaime and Tufanli, Ozlem and La Forest, Maxwell and Yu, Yong and Wang, Meng C and Watts, Russell and Lehner, Richard and Qiu, Yunping and Cai, Min and Kurland, Irwin J and Goldberg, Ira J and Rajan, Sujith and Hussain, M Mahmood and Brodsky, Jeffrey L and Fisher, Edward A} } @article {69622, title = {A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging.}, journal = {Nat Methods}, year = {2024}, month = {2024 Sep 20}, abstract = {

Genetically encoded fluorescent calcium indicators allow cellular-resolution recording of physiology. However, bright, genetically targetable indicators that can be multiplexed with existing tools in vivo are needed for simultaneous imaging of multiple signals. Here we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan. WHaloCaMP is compatible with rhodamine dye-ligands that fluoresce from green to near-infrared, including several that efficiently label the brain in animals. When bound to a near-infrared dye-ligand, WHaloCaMP shows a 7{\texttimes} increase in fluorescence intensity and a 2.1-ns increase in fluorescence lifetime upon calcium binding. We use WHaloCaMP1a to image Ca responses in vivo in flies and mice, to perform three-color multiplexed functional imaging of hundreds of neurons and astrocytes in zebrafish larvae and to quantify Ca concentration using fluorescence lifetime imaging microscopy (FLIM).

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02411-6}, url = {https://doi.org/10.1038/s41592-024-02411-6}, author = {Farrants, Helen and Shuai, Yichun and Lemon, William C and Monroy Hernandez, Christian and Zhang, Deng and Yang, Shang and Patel, Ronak and Qiao, Guanda and Frei, Michelle S and Plutkis, Sarah E and Grimm, Jonathan B and Hanson, Timothy L and Tomaska, Filip and Turner, Glenn C and Stringer, Carsen and Keller, Philipp J and Beyene, Abraham G and Chen, Yao and Liang, Yajie and Lavis, Luke D and Schreiter, Eric R} } @article {69655, title = {Rapid Whole-Organ Characterization via Quantitative Light-Sheet Microscopy}, journal = {Laser \& Photonics Reviews}, year = {2024}, month = {2024 Oct 22}, pages = {2401177}, abstract = {

Whole-organ imaging and characterization at a submicron level provide abundant information on development and diseases while remaining a big challenge, especially in the context of time load. Herein, a quantitative light-sheet microscopy platform that enabled highly time-efficient assessments of fibrous structures within the intact cleared tissue is developed. Dual-view inverted selective plane illumination microscopy (diSPIM), followed by improved registration and deconvolution, led to submicron isotropic imaging of mouse upper genital tract with one hundred-fold speed-ups than previous efforts. Further, optical metrics quantifying 3D local density and structural complexity of targets based on parallel and vectorized convolution in both spatial and frequency domains are developed. Collectively, ≈400{\textendash}2000 fold increases in time efficiency counting for imaging, postprocessing, and quantitative characterization compared to the traditional method is gained. Using this platform, automatic identification of medulla and cortex within the mouse ovary at over 90\% overlap with manual selection by anatomy experts is achieved. Additionally, heterogeneous distributions of immune cells in the mouse ovary and fallopian tube, offering a unique perspective for understanding the immune microenvironment are discovered. This work paves the way for future whole-organ study, and exhibits potential with promise for offering mechanistic insights into physiological and pathological alterations of biological tissues.

}, keywords = {immune microenvironment, light-sheet microscopy, quantitative characterization, whole-organ imaging}, doi = {10.1002/lpor.202401177}, url = {https://doi.org/10.1002/lpor.202401177}, author = {Chen, Lingmei and Su, Yijun and Qian, Shuhao and Zhou, Lingxi and Han, Tao and Wang, Chuncheng and Jiang, Rushan and Ding, Zhihua and Guo, Min and Liu, Zhiyi} } @article {68709, title = {BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Jun 01}, abstract = {

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

}, issn = {1548-7105}, doi = {10.1038/s41592-023-01848-5}, author = {Manubens-Gil, Linus and Zhou, Zhi and Chen, Hanbo and Ramanathan, Arvind and Liu, Xiaoxiao and Liu, Yufeng and Bria, Alessandro and Gillette, Todd and Ruan, Zongcai and Yang, Jian and Radojevi{\'c}, Miroslav and Zhao, Ting and Cheng, Li and Qu, Lei and Liu, Siqi and Bouchard, Kristofer E and Gu, Lin and Cai, Weidong and Ji, Shuiwang and Roysam, Badrinath and Wang, Ching-Wei and Yu, Hongchuan and Sironi, Amos and Iascone, Daniel Maxim and Zhou, Jie and Bas, Erhan and Conde-Sousa, Eduardo and Aguiar, Paulo and Li, Xiang and Li, Yujie and Nanda, Sumit and Wang, Yuan and Muresan, Leila and Fua, Pascal and Ye, Bing and He, Hai-Yan and Staiger, Jochen F and Peter, Manuel and Cox, Daniel N and Simonneau, Michel and Oberlaender, Marcel and Jefferis, Gregory and Ito, Kei and Gonzalez-Bellido, Paloma and Kim, Jinhyun and Rubel, Edwin and Cline, Hollis T and Zeng, Hongkui and Nern, Aljoscha and Chiang, Ann-Shyn and Yao, Jianhua and Roskams, Jane and Livesey, Rick and Stevens, Janine and Liu, Tianming and Dang, Chinh and Guo, Yike and Zhong, Ning and Tourassi, Georgia and Hill, Sean and Hawrylycz, Michael and Koch, Christof and Meijering, Erik and Ascoli, Giorgio A and Peng, Hanchuan} } @article {68933, title = {Biomechanical origins of proprioceptor feature selectivity and topographic maps in the Drosophila leg.}, journal = {Neuron}, year = {2023}, month = {2023 Aug 04}, abstract = {

Our ability to sense and move our bodies relies on proprioceptors, sensory neurons that detect mechanical forces within the body. Different subtypes of proprioceptors detect different kinematic features, such as joint position, movement, and vibration, but the mechanisms that underlie proprioceptor feature selectivity remain poorly understood. Using single-nucleus RNA sequencing (RNA-seq), we found that proprioceptor subtypes in the Drosophila leg lack differential expression of mechanosensitive ion channels. However, anatomical reconstruction of the proprioceptors and connected tendons revealed major biomechanical differences between subtypes. We built a model of the proprioceptors and tendons that identified a biomechanical mechanism for joint angle selectivity and predicted the existence of a topographic map of joint angle, which we confirmed using calcium imaging. Our findings suggest that biomechanical specialization is a key determinant of proprioceptor feature selectivity in Drosophila. More broadly, the discovery of proprioceptive maps reveals common organizational principles between proprioception and other topographically organized sensory systems.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2023.07.009}, author = {Mamiya, Akira and Sustar, Anne and Siwanowicz, Igor and Qi, Yanyan and Lu, Tzu-Chiao and Gurung, Pralaksha and Chen, Chenghao and Phelps, Jasper S and Kuan, Aaron T and Pacureanu, Alexandra and Lee, Wei-Chung Allen and Li, Hongjie and Mhatre, Natasha and Tuthill, John C} } @article {68385, title = {Rationalized deep learning super-resolution microscopy for sustained live imaging of rapid subcellular processes.}, journal = {Nature Biotechnology}, volume = {41}, year = {2023}, month = {2023 Mar 01}, pages = {367-77}, abstract = {

The goal when imaging bioprocesses with optical microscopy is to acquire the most spatiotemporal information with the least invasiveness. Deep neural networks have substantially improved optical microscopy, including image super-resolution and restoration, but still have substantial potential for artifacts. In this study, we developed rationalized deep learning (rDL) for structured illumination microscopy and lattice light sheet microscopy (LLSM) by incorporating prior knowledge of illumination patterns and, thereby, rationally guiding the network to denoise raw images. Here we demonstrate that rDL structured illumination microscopy eliminates spectral bias-induced resolution degradation and reduces model uncertainty by five-fold, improving the super-resolution information by more than ten-fold over other computational approaches. Moreover, rDL applied to LLSM enables self-supervised training by using the spatial or temporal continuity of noisy data itself, yielding results similar to those of supervised methods. We demonstrate the utility of rDL by imaging the rapid kinetics of motile cilia, nucleolar protein condensation during light-sensitive mitosis and long-term interactions between membranous and membrane-less organelles.

}, issn = {1546-1696}, doi = {10.1038/s41587-022-01471-3}, author = {Qiao, Chang and Li, Di and Liu, Yong and Zhang, Siwei and Liu, Kan and Liu, Chong and Guo, Yuting and Jiang, Tao and Fang, Chuyu and Li, Nan and Zeng, Yunmin and He, Kangmin and Zhu, Xueliang and Lippincott-Schwartz, Jennifer and Dai, Qionghai and Li, Dong} } @article {69074, title = {Vagal sensory neurons mediate the Bezold-Jarisch reflex and induce syncope.}, journal = {Nature}, volume = {623}, year = {2023}, month = {2023 Nov 01}, pages = {387-396}, abstract = {

Visceral sensory pathways mediate homeostatic reflexes, the dysfunction of which leads to many neurological disorders. The Bezold-Jarisch reflex (BJR), first described in 1867, is a cardioinhibitory reflex that is speculated to be mediated by vagal sensory neurons (VSNs) that also triggers syncope. However, the molecular identity, anatomical organization, physiological characteristics and behavioural influence of cardiac VSNs remain mostly unknown. Here we leveraged single-cell RNA-sequencing data and HYBRiD tissue clearing to show that VSNs that express neuropeptide Y receptor Y2 (NPY2R) predominately connect the heart ventricular wall to the area postrema. Optogenetic activation of NPY2R VSNs elicits the classic triad of BJR responses-hypotension, bradycardia and suppressed respiration-and causes an animal to faint. Photostimulation during high-resolution echocardiography and laser Doppler flowmetry with behavioural observation revealed a range of phenotypes reflected in clinical syncope, including reduced cardiac output, cerebral hypoperfusion, pupil dilation and eye-roll. Large-scale Neuropixels brain recordings and machine-learning-based modelling showed that this manipulation causes the suppression of activity across a large distributed neuronal population that is not explained by changes in spontaneous behavioural movements. Additionally, bidirectional manipulation of the periventricular zone had a push-pull effect, with inhibition leading to longer syncope periods and activation inducing arousal. Finally, ablating NPY2R VSNs specifically abolished the BJR. Combined, these results demonstrate a genetically defined cardiac reflex that recapitulates characteristics of human syncope at physiological, behavioural and neural network levels.

}, keywords = {Area Postrema, Bradycardia, Cardiac Output, Low, Echocardiography, Heart, Heart Rate, Humans, Hypotension, Laser-Doppler Flowmetry, Nerve Net, Reflex, Sensory Receptor Cells, Single-Cell Gene Expression Analysis, Syncope, vagus nerve}, issn = {1476-4687}, doi = {10.1038/s41586-023-06680-7}, author = {Lovelace, Jonathan W and Ma, Jingrui and Yadav, Saurabh and Chhabria, Karishma and Shen, Hanbing and Pang, Zhengyuan and Qi, Tianbo and Sehgal, Ruchi and Zhang, Yunxiao and Bali, Tushar and Vaissiere, Thomas and Tan, Shawn and Liu, Yuejia and Rumbaugh, Gavin and Ye, Li and Kleinfeld, David and Stringer, Carsen and Augustine, Vineet} } @article {68792, title = {Voltage dynamics of dendritic integration and back-propagation in vivo}, journal = {bioRxiv}, year = {2023}, month = {2023 May 26}, abstract = {

Neurons integrate synaptic inputs within their dendrites and produce spiking outputs, which then propagate down the axon and back into the dendrites where they contribute to plasticity. Mapping the voltage dynamics in dendritic arbors of live animals is crucial for understanding neuronal computation and plasticity rules. Here we combine patterned channelrhodopsin activation with dual-plane structured illumination voltage imaging, for simultaneous perturbation and monitoring of dendritic and somatic voltage in Layer 2/3 pyramidal neurons in anesthetized and awake mice. We examined the integration of synaptic inputs and compared the dynamics of optogenetically evoked, spontaneous, and sensory-evoked back-propagating action potentials (bAPs). Our measurements revealed a broadly shared membrane voltage throughout the dendritic arbor, and few signatures of electrical compartmentalization among synaptic inputs. However, we observed spike rate acceleration-dependent propagation of bAPs into distal dendrites. We propose that this dendritic filtering of bAPs may play a critical role in activity-dependent plasticity.

}, doi = {10.1101/2023.05.25.542363}, url = {https://doi.org/10.1101/2023.05.25.542363}, author = {J. David Wong-Campos and Pojeong Park and Hunter Davis and Yitong Qi and He Tian and Daniel G. Itkis and Doyeon Kim and Sarah E. Plutkis and Luke Lavis and Adam E. Cohen} } @article {68011, title = {BRD2 compartmentalizes the accessible genome.}, journal = {Nature Genetics}, volume = {54}, year = {2022}, month = {2022 Apr 11}, pages = {481-491}, abstract = {

Mammalian chromosomes are organized into megabase-sized compartments that are further subdivided into topologically associating domains (TADs). While the formation of TADs is dependent on cohesin, the mechanism behind compartmentalization remains enigmatic. Here, we show that the bromodomain and extraterminal (BET) family scaffold protein BRD2 promotes spatial mixing and compartmentalization of active chromatin after cohesin loss. This activity is independent of transcription but requires BRD2 to recognize acetylated targets through its double bromodomain and interact with binding partners with its low-complexity domain. Notably, genome compartmentalization mediated by BRD2 is antagonized on the one hand by cohesin and on the other hand by the BET homolog protein BRD4, both of which inhibit BRD2 binding to chromatin. Polymer simulation of our data supports a BRD2-cohesin interplay model of nuclear topology, in which genome compartmentalization results from a competition between loop extrusion and chromatin-state-specific affinity interactions.

}, keywords = {Animals, Cell Cycle Proteins, Chromatin, Chromosomes, Mammals, Nuclear Proteins, Protein Binding, Protein Domains, Transcription Factors}, issn = {1546-1718}, doi = {10.1038/s41588-022-01044-9}, author = {Xie, Liangqi and Dong, Peng and Qi, Yifeng and Hsieh, Tsung-Han S and English, Brian P and Jung, Seolkyoung and Chen, Xingqi and De Marzio, Margherita and Casellas, Rafael and Chang, Howard Y and Zhang, Bin and Tjian, Robert and Liu, Zhe} } @article {68984, title = {Embryo~model completes gastrulation to neurulation and organogenesis.}, journal = {Nature}, volume = {610}, year = {2022}, month = {10/2022}, pages = {143-153}, abstract = {

Embryonic stem (ES) cells can undergo many aspects of mammalian embryogenesis in vitro, but their developmental potential is substantially extended by interactions with extraembryonic stem cells, including trophoblast stem (TS) cells, extraembryonic endoderm stem (XEN) cells and inducible XEN (iXEN) cells. Here we assembled stem cell-derived embryos in vitro from mouse ES cells, TS cells and iXEN cells and showed that they recapitulate the development of whole natural mouse embryo in utero up to day 8.5 post-fertilization. Our embryo model displays headfolds with defined forebrain and midbrain regions and develops a beating heart-like structure, a trunk comprising a neural tube and somites, a tail bud containing neuromesodermal progenitors, a gut tube, and primordial germ cells. This complete embryo model develops within an extraembryonic yolk sac that initiates blood island development. Notably, we demonstrate that the neurulating embryo model assembled from Pax6-knockout ES cells aggregated with wild-type TS cells and iXEN cells recapitulates the ventral domain expansion of the neural tube that occurs in natural, ubiquitous Pax6-knockout embryos. Thus, these complete embryoids are a powerful in vitro model for dissecting the roles of diverse cell lineages and genes in development. Our results demonstrate the self-organization ability of ES cells and two types of extraembryonic stem cells to reconstitute mammalian development through and beyond gastrulation to neurulation and early organogenesis.

}, keywords = {Animals, Cell Lineage, Embryo, Mammalian, Embryonic Stem Cells, Endoderm, Gastrulation, Heart, Mesencephalon, Mice, Models, Biological, Neural Tube, Neurulation, Organogenesis, PAX6 Transcription Factor, Prosencephalon, Somites}, issn = {1476-4687}, doi = {10.1038/s41586-022-05246-3}, author = {Amadei, Gianluca and Handford, Charlotte E and Qiu, Chengxiang and De Jonghe, Joachim and Greenfeld, Hannah and Tran, Martin and Martin, Beth K and Chen, Dong-Yuan and Aguilera-Castrejon, Alejandro and Hanna, Jacob H and Elowitz, Michael B and Hollfelder, Florian and Shendure, Jay and Glover, David M and Zernicka-Goetz, Magdalena} } @article {68422, title = {Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.}, journal = {Science}, volume = {375}, year = {2022}, month = {03/2022}, pages = {eabk2432}, abstract = {

For more than 100 years, the fruit fly has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula , that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to \>250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

}, keywords = {Animals, Cell Nucleus, Databases, Genetic, Drosophila melanogaster, Drosophila Proteins, Female, Gene Expression Regulation, Gene Regulatory Networks, Genes, Insect, Male, RNA-Seq, Sex Characteristics, Single-Cell Analysis, Transcription Factors, Transcriptome}, issn = {1095-9203}, doi = {10.1126/science.abk2432}, author = {Li, Hongjie and Janssens, Jasper and De Waegeneer, Maxime and Kolluru, Sai Saroja and Davie, Kristofer and Gardeux, Vincent and Saelens, Wouter and David, Fabrice P A and Brbi{\'c}, Maria and Spanier, Katina and Leskovec, Jure and McLaughlin, Colleen N and Xie, Qijing and Jones, Robert C and Brueckner, Katja and Shim, Jiwon and Tattikota, Sudhir Gopal and Schnorrer, Frank and Rust, Katja and Nystul, Todd G and Carvalho-Santos, Zita and Ribeiro, Carlos and Pal, Soumitra and Mahadevaraju, Sharvani and Przytycka, Teresa M and Allen, Aaron M and Goodwin, Stephen F and Berry, Cameron W and Fuller, Margaret T and White-Cooper, Helen and Matunis, Erika L and DiNardo, Stephen and Galenza, Anthony and O{\textquoteright}Brien, Lucy Erin and Dow, Julian A T and Jasper, Heinrich and Oliver, Brian and Perrimon, Norbert and Deplancke, Bart and Quake, Stephen R and Luo, Liqun and Aerts, Stein and Agarwal, Devika and Ahmed-Braimah, Yasir and Arbeitman, Michelle and Ariss, Majd M and Augsburger, Jordan and Ayush, Kumar and Baker, Catherine C and Banisch, Torsten and Birker, Katja and Bodmer, Rolf and Bolival, Benjamin and Brantley, Susanna E and Brill, Julie A and Brown, Nora C and Buehner, Norene A and Cai, Xiaoyu Tracy and Cardoso-Figueiredo, Rita and Casares, Fernando and Chang, Amy and Clandinin, Thomas R and Crasta, Sheela and Desplan, Claude and Detweiler, Angela M and Dhakan, Darshan B and Don{\`a}, Erika and Engert, Stefanie and Floc{\textquoteright}hlay, Swann and George, Nancy and Gonz{\'a}lez-Segarra, Amanda J and Groves, Andrew K and Gumbin, Samantha and Guo, Yanmeng and Harris, Devon E and Heifetz, Yael and Holtz, Stephen L and Horns, Felix and Hudry, Bruno and Hung, Ruei-Jiun and Jan, Yuh Nung and Jaszczak, Jacob S and Jefferis, Gregory S X E and Karkanias, Jim and Karr, Timothy L and Katheder, Nadja Sandra and Kezos, James and Kim, Anna A and Kim, Seung K and Kockel, Lutz and Konstantinides, Nikolaos and Kornberg, Thomas B and Krause, Henry M and Labott, Andrew Thomas and Laturney, Meghan and Lehmann, Ruth and Leinwand, Sarah and Li, Jiefu and Li, Joshua Shing Shun and Li, Kai and Li, Ke and Li, Liying and Li, Tun and Litovchenko, Maria and Liu, Han-Hsuan and Liu, Yifang and Lu, Tzu-Chiao and Manning, Jonathan and Mase, Anjeli and Matera-Vatnick, Mikaela and Matias, Neuza Reis and McDonough-Goldstein, Caitlin E and McGeever, Aaron and McLachlan, Alex D and Moreno-Roman, Paola and Neff, Norma and Neville, Megan and Ngo, Sang and Nielsen, Tanja and O{\textquoteright}Brien, Caitlin E and Osumi-Sutherland, David and Ozel, Mehmet Neset and Papatheodorou, Irene and Petkovic, Maja and Pilgrim, Clare and Pisco, Angela Oliveira and Reisenman, Carolina and Sanders, Erin Nicole and Dos Santos, Gilberto and Scott, Kristin and Sherlekar, Aparna and Shiu, Philip and Sims, David and Sit, Rene V and Slaidina, Maija and Smith, Harold E and Sterne, Gabriella and Su, Yu-Han and Sutton, Daniel and Tamayo, Marco and Tan, Michelle and Tastekin, Ibrahim and Treiber, Christoph and Vacek, David and Vogler, Georg and Waddell, Scott and Wang, Wanpeng and Wilson, Rachel I and Wolfner, Mariana F and Wong, Yiu-Cheung E and Xie, Anthony and Xu, Jun and Yamamoto, Shinya and Yan, Jia and Yao, Zepeng and Yoda, Kazuki and Zhu, Ruijun and Zinzen, Robert P} } @article {68419, title = {Transcription factor Acj6 controls dendrite targeting via a combinatorial cell-surface code.}, journal = {Neuron}, volume = {110}, year = {2022}, month = {07/2022}, pages = {2299-2314.e8}, abstract = {

Transcription factors specify the fate and connectivity of developing neurons. We investigate how a lineage-specific transcription factor, Acj6, controls the precise dendrite targeting of Drosophila olfactory projection neurons (PNs) by regulating the expression of cell-surface proteins. Quantitative cell-surface proteomic profiling of wild-type and acj6 mutant PNs in intact developing brains, and a proteome-informed genetic screen identified PN surface proteins that execute Acj6-regulated wiring decisions. These include canonical cell adhesion molecules and proteins previously not associated with wiring, such as Piezo, whose mechanosensitive ion channel activity is dispensable for its function in PN dendrite targeting. Comprehensive genetic analyses revealed that Acj6 employs unique sets of cell-surface proteins in different PN types for dendrite targeting. Combined expression of Acj6 wiring executors rescued acj6 mutant phenotypes with higher efficacy and breadth than expression of individual executors. Thus, Acj6 controls wiring specificity of different neuron types by specifying distinct combinatorial expression of cell-surface executors.

}, keywords = {Animals, Dendrites, Drosophila, Drosophila Proteins, Ion Channels, Membrane Proteins, Nerve Tissue Proteins, Olfactory Pathways, Olfactory Receptor Neurons, POU Domain Factors, Proteomics, Transcription Factors}, issn = {1097-4199}, doi = {10.1016/j.neuron.2022.04.026}, author = {Xie, Qijing and Li, Jiefu and Li, Hongjie and Udeshi, Namrata D and Svinkina, Tanya and Orlin, Daniel and Kohani, Sayeh and Guajardo, Ricardo and Mani, D R and Xu, Chuanyun and Li, Tongchao and Han, Shuo and Wei, Wei and Shuster, S Andrew and Luginbuhl, David J and Quake, Stephen R and Murthy, Swetha E and Ting, Alice Y and Carr, Steven A and Luo, Liqun} } @article {67179, title = {Cryo-EM structures of excitatory amino acid transporter 3 visualize coupled substrate, sodium, and proton binding and transport.}, journal = {Sciences Advances}, volume = {7}, year = {2021}, month = {2021 Mar 03}, abstract = {

Human excitatory amino acid transporter 3 (hEAAT3) mediates glutamate uptake in neurons, intestine, and kidney. Here, we report cryo-EM structures of hEAAT3 in several functional states where the transporter is empty, bound to coupled sodium ions only, or fully loaded with three sodium ions, a proton, and the substrate aspartate. The structures suggest that hEAAT3 operates by an elevator mechanism involving three functionally independent subunits. When the substrate-binding site is near the cytoplasm, it has a remarkably low affinity for the substrate, perhaps facilitating its release and allowing the rapid transport turnover. The mechanism of the coupled uptake of the sodium ions and the substrate is conserved across evolutionarily distant families and is augmented by coupling to protons in EAATs. The structures further suggest a mechanism by which a conserved glutamate residue mediates proton symport.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abf5814}, author = {Qiu, Biao and Matthies, Doreen and Fortea, Eva and Yu, Zhiheng and Boudker, Olga} } @article {67827, title = {Enhanced Photoinduced Electron Transfer Through a Tyrosine Relay in a De Novo Designed Protein Scaffold Bearing a Photoredox Unit and a Fe II S 4 Site}, journal = {ChemPhotoChem}, volume = {5}, year = {2021}, month = {03/2021}, pages = {665 - 668}, abstract = {

Electron transfer (ET) processes in biology over long distances often proceed via a series of hops, which reduces the distance dependence of the rate of ET. The protein matrix itself can be involved in mediating ET directly through the participation of redox-active amino acids. We have designed an electron transfer chain incorporated into a de novo protein scaffold, which is capable of photoinduced intramolecular electron transfer between a photoredox unit and a FeIIS4\ site through a tyrosine amino acid relay. The kinetics were characterized by nanosecond laser pulse photolysis and revealed that electron transfer from [RuIIIbpymal]3+\ proceeds most efficiently via a tyrosine located \~{}16 {\r A} from Rubpymal (bpymal=1-((1-([2,2'-bipyridin]-4-yl)-1H-1,2,3-triazol-4-yl)methyl)-1H-pyrrole-2,5-dione). Removal of the tyrosine as the electron relay station results in a 20-fold decrease in the apparent rate constant for the electron transfer.

}, issn = {2367-0932}, doi = {10.1002/cptc.v5.710.1002/cptc.202100014}, url = {https://onlinelibrary.wiley.com/toc/23670932/5/7}, author = {Tebo, Alison and Quaranta, Annamaria and Pecoraro, Vincent L. and Aukauloo, Ally} } @article {67233, title = {ER-to-Golgi protein delivery through an interwoven, tubular network extending from ER.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Apr 29}, pages = {2412}, abstract = {

Cellular versatility depends on accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by approximately 30\% of all proteins), the physical nature of the vessel conducting the first portage (endoplasmic reticulum [ER] to Golgi apparatus) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to the ER by a thin neck. COPII localizes to this neck region and dynamically regulates cargo entry from the ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.03.035}, author = {Weigel, Aubrey V and Chang, Chi-Lun and Shtengel, Gleb and Xu, C Shan and Hoffman, David P and Freeman, Melanie and Iyer, Nirmala and Aaron, Jesse and Khuon, Satya and Bogovic, John and Qiu, Wei and Hess, Harald F and Lippincott-Schwartz, Jennifer} } @article {67670, title = {Imaging Africa: a strategic approach to optical microscopy training in Africa.}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {2021 Aug 20}, pages = {847-855}, issn = {1548-7105}, doi = {10.1038/s41592-021-01227-y}, author = {Reiche, Michael A and Warner, Digby F and Aaron, Jesse and Khuon, Satya and Fletcher, Daniel A and Hahn, Klaus and Rogers, Kelly L and Mhlanga, Musa and Koch, Anastasia and Quaye, Wendye and Chew, Teng-Leong} } @article {66025, title = {Internal state configures olfactory behavior and early sensory processing in larvae.}, journal = {Science Advances}, volume = {7}, year = {2021}, month = {2021 Jan 01}, abstract = {

Animals exhibit different behavioral responses to the same sensory cue depending on their internal state at a given moment. How and where in the brain are sensory inputs combined with state information to select an appropriate behavior? Here, we investigate how food deprivation affects olfactory behavior in larvae. We find that certain odors repel well-fed animals but attract food-deprived animals and that feeding state flexibly alters neural processing in the first olfactory center, the antennal lobe. Hunger differentially modulates two output pathways required for opposing behavioral responses. Upon food deprivation, attraction-mediating uniglomerular projection neurons show elevated odor-evoked activity, whereas an aversion-mediating multiglomerular projection neuron receives odor-evoked inhibition. The switch between these two pathways is regulated by the lone serotonergic neuron in the antennal lobe, CSD. Our findings demonstrate how flexible behaviors can arise from state-dependent circuit dynamics in an early sensory processing center.

}, issn = {2375-2548}, doi = {10.1126/sciadv.abd6900}, author = {Vogt, Katrin and Zimmerman, David M and Schlichting, Matthias and Hernandez-Nunez, Luis and Qin, Shanshan and Malacon, Karen and Rosbash, Michael and Pehlevan, Cengiz and Cardona, Albert and Samuel, Aravinthan D T} } @article {67794, title = {The organization and development of cortical interneuron presynaptic circuits are area specific.}, journal = {Cell Reports}, volume = {37}, year = {2021}, month = {2021 Nov 09}, pages = {109993}, abstract = {

Parvalbumin and somatostatin inhibitory interneurons gate information flow in discrete cortical areas that compute sensory and cognitive functions. Despite the considerable differences between areas, individual interneuron subtypes are genetically invariant and are thought to form canonical circuits regardless of which area they are embedded in. Here, we investigate whether this is achieved through selective and systematic variations in their afferent connectivity during development. To this end, we examined the development of their inputs within distinct cortical areas. We find that interneuron afferents show little evidence of being globally stereotyped. Rather, each subtype displays characteristic regional connectivity and distinct developmental dynamics by which this connectivity is achieved. Moreover, afferents dynamically regulated during development are disrupted by early sensory deprivation and in a model of fragile X syndrome. These data provide a comprehensive map of interneuron afferents across cortical areas and reveal the logic by which these circuits are established during development.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.109993}, author = {Pouchelon, Gabrielle and Dwivedi, Deepanjali and Bollmann, Yannick and Agba, Chimuanya K and Xu, Qing and Mirow, Andrea M C and Kim, Sehyun and Qiu, Yanjie and Sevier, Elaine and Ritola, Kimberly D and Cossart, Rosa and Fishell, Gord} } @article {67766, title = {A pair of dopamine neurons mediate chronic stress signals to induce learning deficit in Drosophila melanogaster.}, journal = {Proceedings of the National Academy of Sciences of the U. S. A.}, volume = {118}, year = {2021}, month = {2021 Oct 19}, abstract = {

Chronic stress could induce severe cognitive impairments. Despite extensive investigations in mammalian models, the underlying mechanisms remain obscure. Here, we show that chronic stress could induce dramatic learning and memory deficits in The chronic stress-induced learning deficit (CSLD) is long lasting and associated with other depression-like behaviors. We demonstrated that excessive dopaminergic activity provokes susceptibility to CSLD. Remarkably, a pair of PPL1-γ1pedc dopaminergic neurons that project to the mushroom body (MB) γ1pedc compartment play a key role in regulating susceptibility to CSLD so that stress-induced PPL1-γ1pedc hyperactivity facilitates the development of CSLD. Consistently, the mushroom body output neurons (MBON) of the γ1pedc compartment, MBON-γ1pedc\>α/β neurons, are important for modulating susceptibility to CSLD. Imaging studies showed that dopaminergic activity is necessary to provoke the development of chronic stress-induced maladaptations in the MB network. Together, our data support that PPL1-γ1pedc mediates chronic stress signals to drive allostatic maladaptations in the MB network that lead to CSLD.

}, issn = {1091-6490}, doi = {10.1073/pnas.2023674118}, author = {Jia, Jia and He, Lei and Yang, Junfei and Shuai, Yichun and Yang, Jingjing and Wu, Yalan and Liu, Xin and Chen, Tianli and Wang, Guaxiu and Wang, Xingyu and Song, Xiaoxu and Ding, Zhaowen and Zhu, Yan and Ling-Qi Zhang and Chen, Peng and Qin, Hongtao} } @article {68425, title = {Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila}, journal = {Elife}, volume = {10}, year = {2021}, month = {02/2021}, abstract = {

Recognition of environmental cues is essential for the survival of all organisms. Transcriptional changes occur to enable the generation and function of the neural circuits underlying sensory perception. To gain insight into these changes, we generated single-cell transcriptomes of olfactory- (ORNs), thermo-, and hygro-sensory neurons at an early developmental and adult stage using single-cell and single-nucleus RNA sequencing. We discovered that ORNs maintain expression of the same olfactory receptors across development. Using receptor expression and computational approaches, we matched transcriptomic clusters corresponding to anatomically and physiologically defined neuron types across multiple developmental stages. We found that cell-type-specific transcriptomes partly reflected axon trajectory choices in development and sensory modality in adults. We uncovered stage-specific genes that could regulate the wiring and sensory responses of distinct ORN types. Collectively, our data reveal transcriptomic features of sensory neuron biology and provide a resource for future studies of their development and physiology.

}, keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, Female, Male, Olfactory Receptor Neurons, Sequence Analysis, RNA, Single-Cell Analysis, Smell, Transcriptome}, issn = {2050-084X}, doi = {10.7554/eLife.63856}, author = {McLaughlin, Colleen N and Brbi{\'c}, Maria and Xie, Qijing and Li, Tongchao and Horns, Felix and Kolluru, Sai Saroja and Kebschull, Justus M and Vacek, David and Xie, Anthony and Li, Jiefu and Jones, Robert C and Leskovec, Jure and Quake, Stephen R and Luo, Liqun and Li, Hongjie} } @article {68426, title = {Temporal evolution of single-cell transcriptomes of olfactory projection neurons.}, journal = {Elife}, volume = {10}, year = {2021}, month = {01/2021}, abstract = {

Neurons undergo substantial morphological and functional changes during development to form precise synaptic connections and acquire specific physiological properties. What are the underlying transcriptomic bases? Here, we obtained the single-cell transcriptomes of olfactory projection neurons (PNs) at four developmental stages. We decoded the identity of 21 transcriptomic clusters corresponding to 20 PN types and developed methods to match transcriptomic clusters representing the same PN type across development. We discovered that PN transcriptomes reflect unique biological processes unfolding at each stage-neurite growth and pruning during metamorphosis at an early pupal stage; peaked transcriptomic diversity during olfactory circuit assembly at mid-pupal stages; and neuronal signaling in adults. At early developmental stages, PN types with adjacent birth order share similar transcriptomes. Together, our work reveals principles of cellular diversity during brain development and provides a resource for future studies of neural development in PNs and other neuronal types.

}, keywords = {Animals, Drosophila melanogaster, Neurites, Olfactory Nerve, Single-Cell Analysis, Time Factors, Transcriptome}, issn = {2050-084X}, doi = {10.7554/eLife.63450}, author = {Xie, Qijing and Brbi{\'c}, Maria and Horns, Felix and Kolluru, Sai Saroja and Jones, Robert C and Li, Jiefu and Reddy, Anay R and Xie, Anthony and Kohani, Sayeh and Li, Zhuoran and McLaughlin, Colleen N and Li, Tongchao and Xu, Chuanyun and Vacek, David and Luginbuhl, David J and Leskovec, Jure and Quake, Stephen R and Luo, Liqun and Li, Hongjie} } @article {65368, title = {3D ATAC-PALM: super-resolution imaging of the accessible genome.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Apr 01}, pages = {430-6}, abstract = {

To image the accessible genome at nanometer scale in situ, we developed three-dimensional assay for transposase-accessible chromatin-photoactivated localization microscopy (3D ATAC-PALM) that integrates an assay for transposase-accessible chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with oligopaint DNA{\textendash}fluorescence in situ hybridization (FISH), RNA{\textendash}FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, revealing spatially segregated accessible chromatin domains (ACDs) that enclose active chromatin and transcribed genes. Using these methods to analyze genetically perturbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.

}, issn = {1548-7091}, doi = {10.1038/s41592-020-0775-2}, url = {http://www.nature.com/articles/s41592-020-0775-2}, author = {Xie, Liangqi and Dong, Peng and Chen, Xingqi and Hsieh, Tsung-Han S. and Banala, Sambashiva and De Marzio, Margherita and English, Brian P. and Qi, Yifeng and Jung, Seol Kyoung and Kieffer-Kwon, Kyong-Rim and Legant, Wesley R. and Hansen, Anders S. and Schulmann, Anton and Casellas, Rafael and Zhang, Bin and Betzig, Eric and Lavis, Luke D. and Chang, Howard Y. and Tjian, Robert and Liu, Zhe} } @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 {68429, title = {Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators.}, journal = {Cell}, volume = {180}, year = {2020}, month = {01/2020}, pages = {373-386.e15}, abstract = {

Molecular interactions at the cellular interface mediate organized assembly of single cells into tissues and, thus, govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally resolved approach to profile cell-surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed global downregulation of wiring molecules and upregulation of synaptic molecules in the transition from developing to mature PNs. A proteome-instructed in\ vivo screen identified 20 cell-surface molecules regulating neural circuit assembly, many of which belong to evolutionarily conserved protein families not previously linked to neural development. Genetic analysis further revealed that the lipoprotein receptor LRP1 cell-autonomously controls PN dendrite targeting, contributing to the formation of a precise olfactory map. These findings highlight the power of temporally resolved in situ cell-surface proteomic profiling in discovering regulators of brain wiring.

}, keywords = {Animals, Axons, Brain, Dendrites, Drosophila melanogaster, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Developmental, Membrane Proteins, Neurogenesis, Olfactory Nerve, Olfactory Pathways, Olfactory Receptor Neurons, Proteomics, Receptors, Lipoprotein, Smell}, issn = {1097-4172}, doi = {10.1016/j.cell.2019.12.029}, author = {Li, Jiefu and Han, Shuo and Li, Hongjie and Udeshi, Namrata D and Svinkina, Tanya and Mani, D R and Xu, Chuanyun and Guajardo, Ricardo and Xie, Qijing and Li, Tongchao and Luginbuhl, David J and Wu, Bing and McLaughlin, Colleen N and Xie, Anthony and Kaewsapsak, Pornchai and Quake, Stephen R and Carr, Steven A and Ting, Alice Y and Luo, Liqun} } @article {65626, title = {Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na+ channels in nanodisc}, journal = {Proceedings of the National Academy of Sciences of the U.S.A.}, volume = {117}, year = {2020}, month = {2020 Jun 23}, pages = {14187-93}, abstract = {

NaChBac, the first bacterial voltage-gated Na+\ (Nav) channel to be characterized, has been the prokaryotic prototype for studying the structure{\textendash}function relationship of Nav\ channels. Discovered nearly two decades ago, the structure of NaChBac has not been determined. Here we present the single particle electron cryomicroscopy (cryo-EM) analysis of NaChBac in both detergent micelles and nanodiscs. Under both conditions, the conformation of NaChBac is nearly identical to that of the potentially inactivated NavAb. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Nav\ channels in lipid bilayers. To study GMTs in mammalian Nav\ channels, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Nav1.7 replaced the corresponding sequence in NaChBac. Cryo-EM structures of the nanodisc-embedded chimera alone and in complex with HuwenToxin IV (HWTX-IV) were determined to 3.5 and 3.2 {\r A} resolutions, respectively. Compared to the structure of HWTX-IV{\textendash}bound human Nav1.7, which was obtained at an overall resolution of 3.2 {\r A}, the local resolution of the toxin has been improved from \~{}6 to \~{}4 {\r A}. This resolution enabled visualization of toxin docking. NaChBac can thus serve as a convenient surrogate for structural studies of the interactions between GMTs and Nav\ channels in a membrane environment.

}, issn = {0027-8424}, doi = {10.1073/pnas.1922903117}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1922903117https://syndication.highwire.org/content/doi/10.1073/pnas.1922903117}, author = {Gao, Shuai and Valinsky, William C. and On, Nguyen Cam and Houlihan, Patrick R. and Qu, Qian and Liu, Lei and Pan, Xiaojing and Clapham, David E. and Yan, Nieng} } @article {65854, title = {Improved genetically encoded near-infrared fluorescent calcium ion indicators for in vivo imaging.}, journal = {PLoS Biology}, volume = {18}, year = {2020}, month = {2020 Nov 24}, pages = {e3000965}, abstract = {

Near-infrared (NIR) genetically encoded calcium ion (Ca2+) indicators (GECIs) can provide advantages over visible wavelength fluorescent GECIs in terms of reduced phototoxicity, minimal spectral cross talk with visible light excitable optogenetic tools and fluorescent probes, and decreased scattering and absorption in mammalian tissues. Our previously reported NIR GECI, NIR-GECO1, has these advantages but also has several disadvantages including lower brightness and limited fluorescence response compared to state-of-the-art visible wavelength GECIs, when used for imaging of neuronal activity. Here, we report 2 improved NIR GECI variants, designated NIR-GECO2 and NIR-GECO2G, derived from NIR-GECO1. We characterized the performance of the new NIR GECIs in cultured cells, acute mouse brain slices, and Caenorhabditis elegans and Xenopus laevis in vivo. Our results demonstrate that NIR-GECO2 and NIR-GECO2G provide substantial improvements over NIR-GECO1 for imaging of neuronal Ca2+ dynamics.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3000965}, author = {Qian, Yong and Cosio, Danielle M Orozco and Piatkevich, Kiryl D and Aufmkolk, Sarah and Su, Wan-Chi and Celiker, Orhan T and Schohl, Anne and Murdock, Mitchell H and Abhi Aggarwal and Chang, Yu-Fen and Wiseman, Paul W and Ruthazer, Edward S and Boyden, Edward S and Campbell, Robert E} } @article {68428, title = {Single-Cell Transcriptomes Reveal Diverse Regulatory Strategies for Olfactory Receptor Expression and Axon Targeting.}, journal = {Curr Biol}, volume = {30}, year = {2020}, month = {04/2020}, pages = {1189-1198.e5}, abstract = {

The regulatory mechanisms by which neurons coordinate their physiology and connectivity are not well understood. The Drosophila olfactory receptor neurons (ORNs) provide an excellent system to investigate this question. Each ORN type expresses a unique olfactory receptor, or a combination thereof, and sends their axons to a stereotyped glomerulus. Using single-cell RNA sequencing, we identified 33 transcriptomic clusters for ORNs and mapped 20 to their glomerular types, demonstrating that transcriptomic clusters correspond well with anatomically and physiologically defined ORN types. Each ORN type expresses hundreds of transcription factors. Transcriptome-instructed genetic analyses revealed that (1) one broadly expressed transcription factor (Acj6) only regulates olfactory receptor expression in one ORN type and only wiring specificity in another type, (2) one type-restricted transcription factor (Forkhead) only regulates receptor expression, and (3) another type-restricted transcription factor (Unplugged) regulates both events. Thus, ORNs utilize diverse strategies and complex regulatory networks to coordinate their physiology and connectivity.

}, keywords = {Animals, Axons, Drosophila melanogaster, Drosophila Proteins, Forkhead Transcription Factors, Homeodomain Proteins, Nerve Tissue Proteins, Olfactory Receptor Neurons, POU Domain Factors, Receptors, Odorant, Single-Cell Analysis, Smell, Transcriptome}, issn = {1879-0445}, doi = {10.1016/j.cub.2020.01.049}, author = {Li, Hongjie and Li, Tongchao and Horns, Felix and Li, Jiefu and Xie, Qijing and Xu, Chuanyun and Wu, Bing and Kebschull, Justus M and McLaughlin, Colleen N and Kolluru, Sai Saroja and Jones, Robert C and Vacek, David and Xie, Anthony and Luginbuhl, David J and Quake, Stephen R and Luo, Liqun} } @article {65635, title = {Structure of human GABA receptor in an inactive state.}, journal = {Nature}, volume = {584}, year = {2020}, month = {2020 Aug 01}, pages = {304-9}, abstract = {

The human GABA receptor-a member of the class C family of G-protein-coupled receptors (GPCRs)-mediates inhibitory neurotransmission and has been implicated in epilepsy, pain and addiction. A unique GPCR that is known to require heterodimerization for function, the GABA receptor has two subunits, GABA and GABA, that are structurally homologous but perform distinct and complementary functions. GABA recognizes orthosteric ligands, while GABA couples with G proteins. Each subunit is characterized by an extracellular Venus flytrap (VFT) module, a descending peptide linker, a seven-helix transmembrane domain and a cytoplasmic tail. Although the VFT heterodimer structure has been resolved, the structure of the full-length receptor and its transmembrane signalling mechanism remain unknown. Here we present a near full-length structure of the GABA receptor at atomic resolution, captured in an inactive state by cryo-electron microscopy. Our structure reveals several ligands that preassociate with the receptor, including two large endogenous phospholipids that are embedded within the transmembrane domains to maintain receptor integrity and modulate receptor function. We also identify a previously unknown heterodimer interface between transmembrane helices 3 and 5 of both subunits, which serves as a signature of the inactive conformation. A unique {\textquoteright}intersubunit latch{\textquoteright} within this transmembrane interface maintains the inactive state, and its disruption leads to constitutive receptor activity.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2452-0}, author = {Park, Jinseo and Fu, Ziao and Frangaj, Aurel and Liu, Jonathan and Mosyak, Lidia and Shen, Tong and Slavkovich, Vesna N and Ray, Kimberly M and Taura, Jaume and Cao, Baohua and Geng, Yong and Zuo, Hao and Kou, Yongjun and Grassucci, Robert and Chen, Shaoxia and Liu, Zheng and Lin, Xin and Williams, Justin P and Rice, William J and Eng, Edward T and Huang, Rick K and Soni, Rajesh K and Kloss, Brian and Yu, Zhiheng and Javitch, Jonathan A and Hendrickson, Wayne A and Slesinger, Paul A and Quick, Matthias and Graziano, Joseph and Yu, Hongtao and Fiehn, Oliver and Clarke, Oliver B and Frank, Joachim and Fan, Qing R} } @article {65390, title = {Temperature-dependent sex determination is mediated by pSTAT3 repression of Kdm6b..}, journal = {Science}, volume = {368}, year = {2020}, month = {2020 Apr 17}, pages = {303-306}, abstract = {

In many reptiles, including the red-eared slider turtle (), sex is determined by ambient temperature during embryogenesis. We previously showed that the epigenetic regulator is elevated at the male-producing temperature and essential to activate the male pathway. In this work, we established a causal link between temperature and transcriptional regulation of We show that signal transducer and activator of transcription 3 (STAT3) is phosphorylated at the warmer, female-producing temperature, binds the locus, and represses transcription, blocking the male pathway. Influx of Ca, a mediator of STAT3 phosphorylation, is elevated at the female temperature and acts as a temperature-sensitive regulator of STAT3 activation.

}, issn = {1095-9203}, doi = {10.1126/science.aaz4165}, author = {Weber, Ceri and Zhou, Yingjie and Lee, Jong Gwan and Looger, Loren L and Qian, Guoying and Ge, Chutian and Capel, Blanche} } @article {64918, title = {De novo design of tunable, pH-driven conformational changes.}, journal = {Science}, volume = {364}, year = {2019}, month = {2019 May 17}, pages = {658-64}, abstract = {

The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.

}, doi = {10.1126/science.aav7897}, author = {Boyken, Scott E and Benhaim, Mark A and Busch, Florian and Jia, Mengxuan and Back, Matthew J and Choi, Heejun and Klima, Jason C and Chen, Zibo and Walkey, Carl and Mileant, Alexander and Sahasrabuddhe, Aniruddha and Wei, Kathy Y and Hodge, Edgar A and Byron, Sarah and Quijano-Rubio, Alfredo and Sankaran, Banumathi and King, Neil P and Lippincott-Schwartz, Jennifer and Wysocki, Vicki H and et al} } @article {65203, title = {Drosulfakinin signaling in fruitless circuitry antagonizes P1 neurons to regulate sexual arousal in Drosophila.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Oct 18}, pages = {4770}, abstract = {

Animals perform or terminate particular behaviors by integrating external cues and internal states through neural circuits. Identifying neural substrates and their molecular modulators promoting or inhibiting animal behaviors are key steps to understand how neural circuits control behaviors. Here, we identify the Cholecystokinin-like peptide Drosulfakinin (DSK) that functions at single-neuron resolution to suppress male sexual behavior in Drosophila. We found that Dsk neurons physiologically interact with male-specific P1 neurons, part of a command center for male sexual behaviors, and function oppositely to regulate multiple arousal-related behaviors including sex, sleep and spontaneous walking. We further found that the DSK-2 peptide functions through its receptor CCKLR-17D3 to suppress sexual behaviors in flies. Such a neuropeptide circuit largely overlaps with the fruitless-expressing neural circuit that governs most aspects of male sexual behaviors. Thus DSK/CCKLR signaling in the sex circuitry functions antagonistically with P1 neurons to balance arousal levels and modulate sexual behaviors.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-12758-6}, author = {Wu, Shunfan and Guo, Chao and Zhao, Huan and Sun, Mengshi and Chen, Jie and Han, Caihong and Peng, Qionglin and Qiao, Huanhuan and Peng, Ping and Liu, Yan and Luo, Shengzhan D and Pan, Yufeng} } @article {56204, title = {A genetically encoded near-infrared fluorescent calcium ion indicator.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jan 21}, pages = {171-4}, abstract = {

We report an intensiometric, near-infrared fluorescent, genetically encoded calcium ion (Ca) indicator (GECI) with excitation and emission maxima at 678 and 704 nm, respectively. This GECI, designated NIR-GECO1, enables imaging of Ca transients in cultured mammalian cells and brain tissue with sensitivity comparable to that of currently available visible-wavelength GECIs. We demonstrate that NIR-GECO1 opens up new vistas for multicolor Ca imaging in combination with other optogenetic indicators and actuators.

}, issn = {1548-7105}, doi = {10.1038/s41592-018-0294-6}, author = {Qian, Yong and Piatkevich, Kiryl D and Mc Larney, Benedict and Abdelfattah, Ahmed S and Mehta, Sohum and Murdock, Mitchell H and Gottschalk, Sven and Molina, Rosana S and Zhang, Wei and Chen, Yingche and Wu, Jiahui and Drobizhev, Mikhail and Hughes, Thomas E and Zhang, Jin and Schreiter, Eric R and Shoham, Shy and Razansky, Daniel and Boyden, Edward S and Campbell, Robert E} } @article {64904, title = {The glutamine transporter Slc38a1 regulates GABAergic neurotransmission and synaptic plasticity.}, journal = {Cerebal Cortex}, year = {2019}, month = {2019 May 03}, abstract = {

GABA signaling sustains fundamental brain functions, from nervous system development to the synchronization of population activity and synaptic plasticity. Despite these pivotal features, molecular determinants underscoring the rapid and cell-autonomous replenishment of the vesicular neurotransmitter GABA and its impact on synaptic plasticity remain elusive. Here, we show that genetic disruption of the glutamine transporter Slc38a1 in mice hampers GABA synthesis, modifies synaptic vesicle morphology in GABAergic presynapses and impairs critical period plasticity. We demonstrate that Slc38a1-mediated glutamine transport regulates vesicular GABA content, induces high-frequency membrane oscillations and shapes cortical processing and plasticity. Taken together, this work shows that Slc38a1 is not merely a transporter accumulating glutamine for metabolic purposes, but a key component regulating several neuronal functions.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhz055}, author = {Qureshi, Tayyaba and S{\o}rensen, Christina and Berghuis, Paul and Jensen, Vidar and Dobszay, Marton B and Farkas, Tam{\'a}s and Dalen, Knut Tomas and Guo, Caiying and Hassel, Bj{\o}rnar and Utheim, Tor Paaske and Hvalby, {\O}ivind and Hafting, Torkel and Harkany, Tibor and Fyhn, Marianne and Chaudhry, Farrukh Abbas} } @article {64987, title = {NDP52 tunes cortical actin interaction with astral microtubules for accurate spindle orientation.}, journal = {Cell Research}, volume = {29}, year = {2019}, month = {2019 Jun 14}, pages = {666-79}, abstract = {

Oriented cell divisions are controlled by a conserved molecular cascade involving Gαi, LGN, and NuMA. Here, we show that NDP52 regulates spindle orientation via remodeling the polar cortical actin cytoskeleton. siRNA-mediated NDP52 suppression surprisingly revealed a ring-like compact subcortical F-actin architecture surrounding the spindle in prophase/prometaphase cells, which resulted in severe defects of astral microtubule growth and an aberrant spindle orientation. Remarkably, NDP52 recruited the actin assembly factor N-WASP and regulated the dynamics of the subcortical F-actin ring in mitotic cells. Mechanistically, NDP52 was found to bind to phosphatidic acid-containing vesicles, which absorbed cytoplasmic N-WASP to regulate local filamentous actin growth at the polar cortex. Our TIRFM analyses revealed that NDP52-containing vesicles anchored N-WASP and shortened the length of actin filaments in vitro. Based on these results we propose that NDP52-containing vesicles regulate cortical actin dynamics through N-WASP to accomplish a spatiotemporal regulation between astral microtubules and the actin network for proper spindle orientation and precise chromosome segregation. In this way, intracellular vesicles cooperate with microtubules and actin filaments to regulate proper mitotic progression. Since NDP52 is absent from yeast, we reason that metazoans have evolved an elaborate spindle positioning machinery to ensure accurate chromosome segregation in mitosis.

}, issn = {1748-7838}, doi = {10.1038/s41422-019-0189-9}, author = {Yu, Huijuan and Yang, Fengrui and Dong, Peng and Liao, Shanhui and Liu, Wei R and Zhao, Gangyin and Qin, Bo and Dou, Zhen and Liu, Zhe and Liu, Wei and Zang, Jianye and Lippincott-Schwartz, Jennifer and Liu, Xing and Yao, Xuebiao} } @article {65156, title = {RNA granules hitchhike on lysosomes for long-distance transport, Using annexin A11 as a molecular tether.}, journal = {Cell}, volume = {179}, year = {2019}, month = {2019 Sep 19}, pages = {147-164.e20}, abstract = {

Long-distance RNA transport enables local protein synthesis at metabolically-active sites distant from the nucleus. This process ensures an appropriate spatial organization of proteins, vital to polarized cells such as neurons. Here, we present a mechanism for RNA transport in which RNA granules "hitchhike" on moving lysosomes. In\ vitro biophysical modeling, live-cell microscopy, and unbiased proximity labeling proteomics reveal that annexin A11 (ANXA11), an RNA granule-associated phosphoinositide-binding protein, acts as a molecular tether between RNA granules and lysosomes. ANXA11 possesses an N-terminal low complexity domain, facilitating its phase separation into membraneless RNA granules, and a C-terminal membrane binding domain, enabling interactions with lysosomes. RNA granule transport requires ANXA11, and amyotrophic lateral sclerosis (ALS)-associated mutations in ANXA11 impair RNA granule transport by disrupting their interactions with lysosomes. Thus, ANXA11 mediates neuronal RNA transport by tethering RNA granules to actively-transported lysosomes, performing a critical cellular function that is disrupted in ALS.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2019.08.050}, author = {Liao, Ya-Cheng and Fernandopulle, Michael S and Wang, Guozhen and Choi, Heejun and Hao, Ling and Drerup, Catherine M and Patel, Rajan and Qamar, Seema and Nixon-Abell, Jonathon and Shen, Yi and Meadows, William and Vendruscolo, Michele and Knowles, Tuomas P J and Nelson, Matthew and Czekalska, Magdalena A and Musteikyte, Greta and Gachechiladze, Mariam A and Stephens, Christina A and Pasolli, H Amalia and Forrest, Lucy R and St George-Hyslop, Peter and Lippincott-Schwartz, Jennifer and Ward, Michael E} } @article {49010, title = {A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578.}, journal = {BMC Biology}, volume = {16}, year = {2018}, month = {2018 Jan 16}, pages = {9}, abstract = {

BACKGROUND: Genetically encoded calcium ion (Ca2+) indicators (GECIs) are indispensable tools for measuring Ca2+ dynamics and neuronal activities in vitro and in vivo. Red fluorescent protein (RFP)-based GECIs have inherent advantages relative to green fluorescent protein-based GECIs due to the longer wavelength light used for excitation. Longer wavelength light is associated with decreased phototoxicity and deeper penetration through tissue. Red GECI can also enable multicolor visualization with blue- or cyan-excitable fluorophores.

RESULTS: Here we report the development, structure, and validation of a new RFP-based GECI, K-GECO1, based on a circularly permutated RFP derived from the sea anemone Entacmaea quadricolor. We have characterized the performance of K-GECO1 in cultured HeLa cells, dissociated neurons, stem-cell-derived cardiomyocytes, organotypic brain slices, zebrafish spinal cord in vivo, and mouse brain in vivo.

CONCLUSION: K-GECO1 is the archetype of a new lineage of GECIs based on the RFP eqFP578 scaffold. It offers high sensitivity and fast kinetics, similar or better than those of current state-of-the-art indicators, with diminished lysosomal accumulation and minimal blue-light photoactivation. Further refinements of the K-GECO1 lineage could lead to further improved variants with overall performance that exceeds that of the most highly optimized red GECIs.

}, issn = {1741-7007}, doi = {10.1186/s12915-018-0480-0}, author = {Shen, Yi and Dana, Hod and Abdelfattah, Ahmed S and Patel, Ronak and Shea, Jamien and Molina, Rosana S and Rawal, Bijal and Rancic, Vladimir and Chang, Yu-Fen and Wu, Lanshi and Chen, Yingche and Qian, Yong and Wiens, Matthew D and Hambleton, Nathan and Ballanyi, Klaus and Hughes, Thomas E and Drobizhev, Mikhail and Kim, Douglas S and Koyama, Minoru and Schreiter, Eric R and Campbell, Robert E} } @article {49086, title = {Nociceptive interneurons control modular motor pathways to promote escape behavior in Drosophila.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Mar 12}, abstract = {

Rapid and efficient escape behaviors in response to noxious sensory stimuli are essential for protection and survival. Yet, how noxious stimuli are transformed to coordinated escape behaviors remains poorly understood. Inlarvae, noxious stimuli trigger sequential body bending and corkscrew-like rolling behavior. We identified a population of interneurons in the nerve cord of, termed Down-and-Back (DnB) neurons, that are activated by noxious heat, promote nociceptive behavior, and are required for robust escape responses to noxious stimuli. Electron microscopic circuit reconstruction shows that DnBs are targets of nociceptive and mechanosensory neurons, are directly presynaptic to pre-motor circuits, and link indirectly to Goro rolling command-like neurons. DnB activation promotes activity in Goro neurons, and coincident inactivation of Goro neurons prevents the rolling sequence but leaves intact body bending motor responses. Thus, activity from nociceptors to DnB interneurons coordinates modular elements of nociceptive escape behavior.

}, issn = {2050-084X}, doi = {10.7554/eLife.26016}, author = {Burgos, Anita and Honjo, Ken and Ohyama, Tomoko and Qian, Cheng Sam and Shin, Grace Ji-Eun and Gohl, Daryl M and Silies, Marion and Tracey, W Daniel and Zlatic, Marta and Cardona, Albert and Grueber, Wesley B} } @article {48976, title = {Optogenetic dissection of descending behavioral control in Drosophila.}, journal = {eLife}, year = {2018}, month = {2018}, pages = {e34275}, abstract = {

In most animals, the brain makes behavioral decisions that are transmitted by descending neurons to the nerve cord circuitry that produces behaviors. In insects, only a few descending neurons have been associated with specific behaviors. To explore how descending neurons control an insect{\textquoteright}s movements, we developed a novel method to systematically assay the behavioral effects of activating individual neurons on freely behaving terrestrial\ D. melanogaster. We calculated a two-dimensional representation of the entire behavior space explored by these flies and we associated descending neurons with specific behaviors by identifying regions of this space that were visited with increased frequency during optogenetic activation. Applying this approach across a large collection of descending neurons, we found that (1) activation of most of the descending neurons drove stereotyped behaviors, (2) in many cases multiple descending neurons activated similar behaviors, and (3) optogenetically-activated behaviors were often dependent on the behavioral state prior to activation.

}, doi = {10.7554/eLife.34275}, author = {Cande, Jessica and Namiki, Shigehiro and Qiu, Jirui and Korff, Wyatt and Card, Gwyneth M and Shaevitz, Joshua W and Stern, David L and Berman, Gordon J} } @article {48984, title = {Stability, affinity and chromatic variants of the glutamate sensor iGluSnFR.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Nov}, pages = {9386-9}, abstract = {

Single-wavelength fluorescent reporters allow visualization of specific neurotransmitters with high spatial and temporal resolution. We report variants of intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) that are functionally brighter; detect submicromolar to millimolar amounts of glutamate; and have blue, cyan, green, or yellow emission profiles. These variants could be imaged in vivo in cases where original iGluSnFR was too dim, resolved glutamate transients in dendritic spines and axonal boutons, and allowed imaging at kilohertz rates.

}, doi = {10.1038/s41592-018-0171-3}, author = {Marvin, Jonathan S and Scholl, Benjamin and Wilson, Daniel E and Podgorski, Kaspar and Kazemipour, Abbas and Mueller, Johannes Alexander and Schoch-McGovern, Susanne and Wang, Samuel S-H and Quiroz, Francisco Jose Urra and Rebola, Nelson and Bao, Huan and Little, Justin P and Tkachuk, Ariana N and Hantman, Adam W and Chapman, Edwin R and Dietrich, Dirk and DiGregorio, David A and Fitzpatrick, David and Looger, Loren L} } @article {68437, title = {Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-Cell RNA Sequencing.}, journal = {Cell}, volume = {171}, year = {2017}, month = {11/2017}, pages = {1206-1220.e22}, abstract = {

The definition of neuronal type and how it relates to the transcriptome are open questions. Drosophila olfactory projection neurons (PNs) are among the best-characterized neuronal types: different PN classes target dendrites to distinct olfactory glomeruli, while PNs of the same class exhibit indistinguishable anatomical and physiological properties. Using single-cell RNA sequencing, we comprehensively characterized the transcriptomes of most PN classes and unequivocally mapped transcriptomes to specific olfactory function for six classes. Transcriptomes of\ closely related PN classes exhibit the largest differences during circuit assembly but become indistinguishable in adults, suggesting that neuronal subtype diversity peaks during development. Transcription factors and cell-surface molecules are the most differentially expressed genes between classes and are highly informative in encoding cell identity, enabling us to identify a new lineage-specific transcription factor that instructs PN dendrite targeting. These findings establish that neuronal transcriptomic identity corresponds with anatomical and physiological identity defined by connectivity and function.

}, keywords = {Animals, Brain, Cluster Analysis, Dendrites, Drosophila melanogaster, Gene Expression Profiling, Neurons, Olfactory Bulb, Organ Specificity, Pupa, Sequence Analysis, RNA, Single-Cell Analysis, Transcription Factors}, issn = {1097-4172}, doi = {10.1016/j.cell.2017.10.019}, author = {Li, Hongjie and Horns, Felix and Wu, Bing and Xie, Qijing and Li, Jiefu and Li, Tongchao and Luginbuhl, David J and Quake, Stephen R and Luo, Liqun} } @article {65773, title = {Intramolecular Photogeneration of a Tyrosine Radical in a Designed Protein}, journal = {ChemPhotoChem}, volume = {1}, year = {2017}, month = {02/2017}, pages = {89 {\textendash} 92}, abstract = {

Long-distance biological electron transfer occurs through a hopping mechanism and often involves tyrosine as a high potential intermediate, for example in the early charge separation steps during photosynthesis. Protein design allows for the development of minimal systems to study the underlying principles of complex systems. Herein, we report the development of the first ruthenium-linked designed protein for the photogeneration of a tyrosine radical by intramolecular electron transfer.

}, doi = {10.1002/cptc.201600044}, url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cptc.201600044}, author = {Tebo, Alison G and Quaranta, Annamaria and Herrero, Christian and Pecoraro, Vincent L and Aukauloo, Ally} } @article {48495, title = {Semiparametric spectral modeling of the Drosophila connectome.}, journal = {arXiv}, year = {2017}, month = {2017 May 9}, pages = {1705.03297}, abstract = {

We present semiparametric spectral modeling of the complete larval Drosophila mushroom body connectome. Motivated by a thorough exploratory data analysis of the network via Gaussian mixture modeling (GMM) in the adjacency spectral embedding (ASE) representation space, we introduce the latent structure model (LSM) for network modeling and inference. LSM is a generalization of the stochastic block model (SBM) and a special case of the random dot product graph (RDPG) latent position model, and is amenable to semiparametric GMM in the ASE representation space. The resulting connectome code derived via semiparametric GMM composed with ASE captures latent connectome structure and elucidates biologically relevant neuronal properties.

}, url = {https://arxiv.org/abs/1705.03297}, author = {Priebe, Carey E. and Park, Youngser and Tang, Minh and Athreya, Avanti and Lyzinski, Vince and Vogelstein, Joshua T and Qin, Yichen and Cocanougher, Benjamin and Eichler, Katharina and Zlatic, Marta and Cardona, Albert} } @article {48699, title = {Structure and topology around the cleavage site regulate post-translational cleavage of the HIV-1 gp160 signal peptide.}, journal = {eLife}, volume = {6}, year = {2017}, month = {2017 Jul 28}, abstract = {

Like all other secretory proteins, the HIV-1 envelope glycoprotein gp160, is targeted to the endoplasmic reticulum (ER) by its signal peptide during synthesis. Proper gp160 folding in the ER requires core glycosylation, disulfide-bond formation and proline isomerization. Signal-peptide cleavage occurs only late after gp160 chain termination and is dependent on folding of the soluble subunit gp120 to a near-native conformation. We here detail the mechanism by which co-translational signal-peptide cleavage is prevented. Conserved residues from the signal peptide and residues downstream of the canonical cleavage site form an extended alpha-helix in the ER membrane that covers the cleavage site, thus preventing cleavage. A point mutation in the signal peptide breaks the alpha helix allowing co-translational cleavage. We demonstrate that postponed cleavage of gp160 enhances functional folding of the molecule. The change to early cleavage results in decreased viral fitness compared to wild-type HIV.

}, issn = {2050-084X}, doi = {10.7554/eLife.26067}, author = {Snapp, Erik Lee and McCaul, Nicholas and Quandte, Matthias and Cabartova, Zuzana and Bontjer, Ilja and K{\"a}llgren, Carolina and Nilsson, IngMarie and Land, Aafke and von Heijne, Gunnar and Sanders, Rogier W and Braakman, Ineke} } @article {48497, title = {Whole-brain serial-section electron microscopy in larval zebrafish.}, journal = {Nature}, volume = {545}, year = {2017}, month = {2017 May 18}, pages = {345-349}, abstract = {

High-resolution serial-section electron microscopy (ssEM) makes it possible to investigate the dense meshwork of axons, dendrites, and synapses that form neuronal circuits. However, the imaging scale required to comprehensively reconstruct these structures is more than ten orders of magnitude smaller than the spatial extents occupied by networks of interconnected neurons, some of which span nearly the entire brain. Difficulties in generating and handling data for large volumes at nanoscale resolution have thus restricted vertebrate studies to fragments of circuits. These efforts were recently transformed by advances in computing, sample handling, and imaging techniques, but high-resolution examination of entire brains remains a challenge. Here, we present ssEM data for the complete brain of a larval zebrafish (Danio rerio) at 5.5 days post-fertilization. Our approach utilizes multiple rounds of targeted imaging at different scales to reduce acquisition time and data management requirements. The resulting dataset can be analysed to reconstruct neuronal processes, permitting us to survey all myelinated axons (the projectome). These reconstructions enable precise investigations of neuronal morphology, which reveal remarkable bilateral symmetry in myelinated reticulospinal and lateral line afferent axons. We further set the stage for whole-brain structure-function comparisons by co-registering functional reference atlases and in vivo two-photon fluorescence microscopy data from the same specimen. All obtained images and reconstructions are provided as an open-access resource.

}, issn = {1476-4687}, doi = {10.1038/nature22356}, author = {Hildebrand, David Grant Colburn and Cicconet, Marcelo and Torres, Russel Miguel and Choi, Woohyuk and Quan, Tran Minh and Moon, Jungmin and Wetzel, Arthur Willis and Scott Champion, Andrew and Graham, Brett Jesse and Randlett, Owen and Plummer, George Scott and Portugues, Ruben and Bianco, Isaac Henry and Saalfeld, Stephan and Baden, Alexander David and Lillaney, Kunal and Burns, Randal and Vogelstein, Joshua Tzvi and Schier, Alexander Franz and Lee, Wei-Chung Allen and Jeong, Won-Ki and Lichtman, Jeff William and Engert, Florian} } @article {47299, title = {Calcium imaging of neural circuits with extended depth-of-field light-sheet microscopy.}, journal = {Optics Letters}, volume = {41}, year = {2016}, month = {2016 Feb 17}, pages = {855-8}, abstract = {

Increasing the volumetric imaging speed of light-sheet microscopy will improve its ability to detect fast changes in neural activity. Here, a system is introduced for brain-wide imaging of neural activity in the larval zebrafish by coupling structured illumination with cubic phase extended depth-of-field (EDoF) pupil encoding. This microscope enables faster light-sheet imaging and facilitates arbitrary plane scanning{\textemdash}removing constraints on acquisition speed, alignment tolerances, and physical motion near the sample. The usefulness of this method is demonstrated by performing multi-plane calcium imaging in the fish brain with a\ 416{\texttimes}832{\texttimes}160 μm\ field of view at 33\ Hz. The optomotor response behavior of the zebrafish is monitored at high speeds, and time-locked correlations of neuronal activity are resolved across its brain.

}, doi = {10.1364/OL.41.000855}, author = {Quirin, Sean and Vladimirov, Nikita and Yang, Chao-Tsung and Peterka, Darcy S and Yuste, Rafael and Ahrens, Misha B} } @article {47348, title = {High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry.}, journal = {Nature Genetics}, volume = {48}, year = {2016}, month = {2016 Mar}, pages = {323-30}, abstract = {

Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 {\texttimes} 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24\%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.

}, issn = {1546-1718}, doi = {10.1038/ng.3496}, author = {Sun, Celi and Molineros, Julio E and Looger, Loren L and Zhou, Xu-Jie and Kim, Kwangwoo and Okada, Yukinori and Ma, Jianyang and Qi, Yuan-Yuan and Kim-Howard, Xana and Motghare, Prasenjeet and Bhattarai, Krishna and Adler, Adam 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 Kochi, Yuta and Suzuki, Akari and Kubo, Michiaki and Sumida, Takayuki and Yamamoto, Kazuhiko and Lee, Shin-Seok and Kim, Young Jin and Han, Bok-Ghee and Dozmorov, Mikhail and Kaufman, Kenneth M and Wren, Jonathan D and Harley, John B and Shen, Nan and Chua, Kek Heng and Zhang, Hong and Bae, Sang-Cheol and Nath, Swapan K} } @article {47812, title = {Improving data quality in neuronal population recordings.}, journal = {Nature Neuroscience}, volume = {19}, year = {2016}, month = {2016 Aug 26}, pages = {1165-74}, abstract = {

Understanding how the brain operates requires understanding how large sets of neurons function together. Modern recording technology makes it possible to simultaneously record the activity of hundreds of neurons, and technological developments will soon allow recording of thousands or tens of thousands. As with all experimental techniques, these methods are subject to confounds that complicate the interpretation of such recordings, and could lead to erroneous scientific conclusions. Here we discuss methods for assessing and improving the quality of data from these techniques and outline likely future directions in this field.

}, issn = {1546-1726}, doi = {10.1038/nn.4365}, author = {Harris, Kenneth D and Quiroga, Rodrigo Quian and Freeman, Jeremy and Smith, Spencer L} } @article {68765, title = {Non-centrosomal epidermal microtubules act in parallel to LET-502/ROCK to promote C. elegans elongation}, journal = {Development}, volume = {143}, year = {2016}, month = {01/2016}, pages = {160-173}, abstract = {

C. elegans embryonic elongation is a morphogenetic event driven by actomyosin contractility and muscle-induced tension transmitted through hemidesmosomes. A role for the microtubule cytoskeleton has also been proposed, but its contribution remains poorly characterized. Here, we investigate the organization of the non-centrosomal microtubule arrays present in the epidermis and assess their function in elongation. We show that the microtubule regulators γ-tubulin and NOCA-1 are recruited to hemidesmosomes and adherens junctions early in elongation. Several parallel approaches suggest that microtubule nucleation occurs from these sites. Disrupting the epidermal microtubule array by overexpressing the microtubule-severing protein Spastin or by inhibiting the C. elegans ninein homolog NOCA-1 in the epidermis mildly affected elongation. However, microtubules were essential for elongation when hemidesmosomes or the activity of the Rho kinase LET-502/ROCK were partially compromised. Imaging of junctional components and genetic analyses suggest that epidermal microtubules function together with Rho kinase to promote the transport of E-cadherin to adherens junctions and myotactin to hemidesmosomes. Our results indicate that the role of LET-502 in junctional remodeling is likely to be independent of its established function as a myosin II activator, but requires a microtubule-dependent pathway involving the syntaxin SYX-5. Hence, we propose that non-centrosomal microtubules organized by epidermal junctions contribute to elongation by transporting junction remodeling factors, rather than having a mechanical role.

}, issn = {0950-1991}, doi = {10.1242/dev.126615}, url = {https://doi.org/10.1242/dev.126615}, author = {Quintin, Sophie and Wang, Shahoe and Pontabry, Julien and Bender, Ambre and Robin, Fran{\c c}ois and Hyenne, Vincent and Landmann, Fr{\'e}d{\'e}ric and Gally, Christelle and Oegema, Karen and Labouesse, Michel} } @article {48105, title = {Sensitive enhancement of vessel wall imaging with an endoesophageal Wireless Amplified NMR Detector (WAND).}, journal = {Magnetic Resonance in Medicine}, volume = {78}, year = {2016}, month = {2016 Dec 04}, pages = {2048-54}, abstract = {

PURPOSE: To improve the imaging quality of vessel walls with an endoesophageal Wireless Amplified NMR Detector (WAND).

METHODS: A cylindrically shaped double-frequency resonator has been constructed with a single metal wire that is self-connected by a pair of nonlinear capacitors. The double-frequency resonator can convert wirelessly provided pumping power into amplified MR signals. This compact design makes the detector easily insertable into a rodent esophagus.

RESULTS: The detector has good longitudinal and axial symmetry. Compared to an external surface coil, the WAND can enhance detection sensitivity by at least 5 times, even when the distance separation between the region of interest and the detector{\textquoteright}s cylindrical surface is twice the detector{\textquoteright}s own radius. Such detection capability enables us to observe vessel walls near the aortic arch and carotid bifurcation with elevated sensitivity.

CONCLUSION: A cylindrical MRI detector integrated with a wireless-powered amplifier has been developed as an endoesophageal detector to enhance detection sensitivity of vessel walls. This detector can greatly improve the imaging quality for vessel regions that are susceptible to atherosclerotic lesions. Magn Reson Med, 2016. {\textcopyright} 2016 International Society for Magnetic Resonance in Medicine.

}, issn = {1522-2594}, doi = {10.1002/mrm.26562}, author = {Zeng, Xianchun and Barbic, Mladen and Chen, Liangliang and Qian, Chunqi} } @article {46813, title = {BlastNeuron for automated comparison, retrieval and clustering of 3D neuron morphologies.}, journal = {Neuroinformatics}, volume = {13}, year = {2015}, month = {2015 Jun 3}, pages = {487-99}, abstract = {

Characterizing the identity and types of neurons in the brain, as well as their associated function, requires a means of quantifying and comparing 3D neuron morphology. Presently, neuron comparison methods are based on statistics from neuronal morphology such as size and number of branches, which are not fully suitable for detecting local similarities and differences in the detailed structure. We developed BlastNeuron to compare neurons in terms of their global appearance, detailed arborization patterns, and topological similarity. BlastNeuron first compares and clusters 3D neuron reconstructions based on global morphology features and moment invariants, independent of their orientations, sizes, level of reconstruction and other variations. Subsequently, BlastNeuron performs local alignment between any pair of retrieved neurons via a tree-topology driven dynamic programming method. A 3D correspondence map can thus be generated at the resolution of single reconstruction nodes. We applied BlastNeuron to three datasets: (1) 10,000+ neuron reconstructions from a public morphology database, (2) 681 newly and manually reconstructed neurons, and (3) neurons reconstructions produced using several independent reconstruction methods. Our approach was able to accurately and efficiently retrieve morphologically and functionally similar neuron structures from large morphology database, identify the local common structures, and find clusters of neurons that share similarities in both morphology and molecular profiles.

}, issn = {1559-0089}, doi = {10.1007/s12021-015-9272-7}, author = {Wan, Yinan and Long, Fuhui and Qu, Lei and Xiao, Hang and Hawrylycz, Michael and Myers, Eugene W and Peng, Hanchuan} } @article {47620, title = {Deacetylation of nuclear LC3 drives autophagy initiation under starvation.}, journal = {Molecular cell}, volume = {57}, year = {2015}, month = {2015 Feb 5}, pages = {456-66}, abstract = {

Shuttling of macromolecules between different cellular compartments helps regulate the timing and extent of different cellular activities. Here, we report that LC3, a key initiator of autophagy that cycles between the nucleus and cytoplasm, becomes selectively activated in the nucleus during starvation through deacetylation by the nuclear deacetylase Sirt1. Deacetylation of LC3 at K49 and K51 by Sirt1 allows LC3 to interact with the nuclear protein DOR and return to the cytoplasm with DOR, where it is able to bind Atg7 and other autophagy factors and undergo phosphatidylethanolamine conjugation to preautophagic membranes. The association of deacetylated LC3 with autophagic factors shifts LC3{\textquoteright}s distribution from the nucleus toward the cytoplasm. Thus, an acetylation-deacetylation cycle ensures that LC3 effectively redistributes in an activated form from nucleus to cytoplasm, where it plays a central role in autophagy to enable the cell to cope with the lack of external nutrients.

}, keywords = {Acetylation, Autophagy, Cell Nucleus, Cytoplasm, HEK293 Cells, Hela Cells, Humans, Lysine, Microscopy, Confocal, Microtubule-Associated Proteins, Sirtuin 1, Ubiquitin-Activating Enzymes}, issn = {1097-4164}, doi = {10.1016/j.molcel.2014.12.013}, author = {Huang, Rui and Xu, Yinfeng and Wan, Wei and Shou, Xin and Qian, Jiali and You, Zhiyuan and Liu, Bo and Chang, Chunmei and Zhou, Tianhua and Lippincott-Schwartz, Jennifer and Liu, Wei} } @article {68448, title = {NAD$^{+}$/NADH metabolism and NAD$^{+}$-dependent enzymes in cell death and ischemic brain injury: current advances and therapeutic implications.}, journal = {Curr Med Chem}, volume = {22}, year = {2015}, month = {2015}, pages = {1239-47}, abstract = {

NAD(+) and NADH play crucial roles in a variety of biological processes including energy metabolism, mitochondrial functions, and gene expression. Multiple studies have indicated that NAD(+) administration can profoundly decrease oxidative cell death as well as ischemic and traumatic brain injury, suggesting NAD(+) metabolism as a promising therapeutic target for cerebral ischemia and head injury. Cumulating evidence has suggested that NAD(+) can produce its protective effects by multiple mechanisms, including preventing mitochondrial alterations, enhancing energy metabolism, preventing virtually all forms of cell death including apoptosis, necrosis and autophagy, inhibiting inflammation, directly increasing antioxidation capacity of cells and tissues, and activating SIRT1. Increasing evidence has also suggested that NADH metabolism is a potential therapeutic target for treating several neurological disorders. A number of studies have further indicated that multiple NAD(+)-dependent enzymes such as sirtuins, polymerase(ADP-ribose) polymerases (PARPs) and CD38 mediate cell death and multiple biological processes. In this article, an overview of the recent findings regarding the roles of NAD(+)/NADH and NAD(+)-dependent enzymes in cell death and ischemic brain injury is provided. These findings have collectively indicated that NAD(+)/NADH and NAD(+)-dependent enzymes play fundamental roles in oxidative stress-induced cell death and ischemic brain injury, which may become promising therapeutic targets for brain ischemia and multiple other neurological disorders.

}, keywords = {ADP-ribosyl Cyclase 1, Animals, Brain Injuries, Brain Ischemia, Cell Death, Humans, NAD, Poly(ADP-ribose) Polymerases, Sirtuins}, issn = {1875-533X}, doi = {10.2174/0929867322666150209154420}, author = {Ma, Yingxin and Nie, Hui and Chen, Heyu and Li, Jiefu and Hong, Yunyi and Wang, Ban and Wang, Caixia and Zhang, Jie and Cao, Wei and Zhang, Mingchao and Xu, Yongning and Ding, Xianting and Yin, Shan Kai and Qu, Xinkai and Ying, Weihai} } @article {68766, title = {NOCA-1 functions with γ-tubulin and in parallel to Patronin to assemble non-centrosomal microtubule arrays in \textitC. elegans}, journal = {eLife}, volume = {4}, year = {2015}, month = {09/2015}, pages = {e08649}, abstract = {

Non-centrosomal microtubule arrays assemble in differentiated tissues to perform mechanical and transport-based functions. In this study, we identify \textitCaenorhabditis elegans NOCA-1 as a protein with homology to vertebrate ninein. NOCA-1 contributes to the assembly of non-centrosomal microtubule arrays in multiple tissues. In the larval epidermis, NOCA-1 functions redundantly with the minus end protection factor Patronin/PTRN-1 to assemble a circumferential microtubule array essential for worm growth and morphogenesis. Controlled degradation of a γ-tubulin complex subunit in this tissue revealed that γ-tubulin acts with NOCA-1 in parallel to Patronin/PTRN-1. In the germline, NOCA-1 and γ-tubulin co-localize at the cell surface, and inhibiting either leads to a microtubule assembly defect. γ-tubulin targets independently of NOCA-1, but NOCA-1 targeting requires γ-tubulin when a non-essential putatively palmitoylated cysteine is mutated. These results show that NOCA-1 acts with γ-tubulin to assemble non-centrosomal arrays in multiple tissues and highlight functional overlap between the ninein and Patronin protein families.

}, keywords = {ninein, NOCA-1, non-centrosomal microtubule array, Patronin, PTRN-1}, issn = {2050-084X}, doi = {10.7554/eLife.08649}, url = {https://doi.org/10.7554/eLife.08649}, author = {Wang, Shaohe and Wu, Di and Quintin, Sophie and Green, Rebecca A and Cheerambathur, Dhanya K and Ochoa, Stacy D and Desai, Arshad and Oegema, Karen}, editor = {Akhmanova, Anna} } @article {68450, title = {Cytoplasmic tyrosine phosphatase Shp2 coordinates hepatic regulation of bile acid and FGF15/19 signaling to repress bile acid synthesis.}, journal = {Cell Metab}, volume = {20}, year = {2014}, month = {08/2014}, pages = {320-32}, abstract = {

Bile acid (BA) biosynthesis is tightly controlled by intrahepatic negative feedback signaling elicited by BA binding to farnesoid X receptor (FXR) and also by enterohepatic communication involving ileal BA reabsorption and FGF15/19 secretion. However, how these pathways are coordinated is poorly understood. We show here that nonreceptor tyrosine phosphatase Shp2 is a critical player that couples and regulates the intrahepatic and enterohepatic signals for repression of BA synthesis. Ablating Shp2 in hepatocytes suppressed signal relay from FGFR4, receptor for FGF15/19, and attenuated BA activation of FXR signaling, resulting in elevation of systemic BA levels and chronic hepatobiliary disorders in mice. Acting immediately downstream of FGFR4, Shp2 associates with FRS2α and promotes the receptor activation and signal relay to several pathways. These results elucidate a molecular mechanism for the control of BA homeostasis by Shp2 through the orchestration of multiple signals in hepatocytes.

}, keywords = {Animals, Bile Acids and Salts, Bile Ducts, Cell Line, Cholesterol 7-alpha-Hydroxylase, Fibroblast Growth Factors, Liver, Membrane Proteins, Mice, Mice, Knockout, Protein Tyrosine Phosphatase, Non-Receptor Type 11, Receptor, Fibroblast Growth Factor, Type 4, Signal Transduction, Up-Regulation}, issn = {1932-7420}, doi = {10.1016/j.cmet.2014.05.020}, author = {Li, Shuangwei and Hsu, Diane D F and Li, Bing and Luo, Xiaolin and Alderson, Nazilla and Qiao, Liping and Ma, Lina and Zhu, Helen H and He, Zhao and Suino-Powell, Kelly and Ji, Kaihong and Li, Jiefu and Shao, Jianhua and Xu, H Eric and Li, Tiangang and Feng, Gen-Sheng} } @article {45371, title = {Integrated action of pheromone signals in promoting courtship behavior in male mice.}, journal = {eLife}, volume = {3}, year = {2014}, month = {2014 Jul 29}, pages = {e03025}, abstract = {

The mammalian vomeronasal organ encodes pheromone information about gender, reproductive status, genetic background and individual differences. It remains unknown how pheromone information interacts to trigger innate behaviors. In this study, we identify vomeronasal receptors responsible for detecting female pheromones. A sub-group of V1re clade members recognizes gender-identifying cues in female urine. Multiple members of the V1rj clade are cognate receptors for urinary estrus signals, as well as for sulfated estrogen (SE) compounds. In both cases, the same cue activates multiple homologous receptors, suggesting redundancy in encoding female pheromone cues. Neither gender-specific cues nor SEs alone are sufficient to promote courtship behavior in male mice, whereas robust courtship behavior can be induced when the two cues are applied together. Thus, integrated action of different female cues is required in pheromone-triggered mating behavior. These results suggest a gating mechanism in the vomeronasal circuit in promoting specific innate behavior.DOI: http://dx.doi.org/10.7554/eLife.03025.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.03025}, author = {Haga-Yamanaka, Sachiko and Ma, Limei and He, Jie and Qiu, Qiang and Lavis, Luke D and Looger, Loren L and Yu, C Ron} } @article {45852, title = {Live imaging of endogenous PSD-95 using ENABLED: a conditional strategy to fluorescently label endogenous proteins.}, journal = {Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Dec 10}, pages = {16698-712}, abstract = {

Stoichiometric labeling of endogenous synaptic proteins for high-contrast live-cell imaging in brain tissue remains challenging. Here, we describe a conditional mouse genetic strategy termed endogenous labeling via exon duplication (ENABLED), which can be used to fluorescently label endogenous proteins with near ideal properties in all neurons, a sparse subset of neurons, or specific neuronal subtypes. We used this method to label the postsynaptic density protein PSD-95 with mVenus without overexpression side effects. We demonstrated that mVenus-tagged PSD-95 is functionally equivalent to wild-type PSD-95 and that PSD-95 is present in nearly all dendritic spines in CA1 neurons. Within spines, while PSD-95 exhibited low mobility under basal conditions, its levels could be regulated by chronic changes in neuronal activity. Notably, labeled PSD-95 also allowed us to visualize and unambiguously examine otherwise-unidentifiable excitatory shaft synapses in aspiny neurons, such as parvalbumin-positive interneurons and dopaminergic neurons. Our results demonstrate that the ENABLED strategy provides a valuable new approach to study the dynamics of endogenous synaptic proteins in vivo.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3888-14.2014}, author = {Fortin, Dale A and Tillo, Shane E and Yang, Guang and Rah, Jong-Cheol and Melander, Joshua B and Bai, Suxia and Soler-Cede{\~n}o, Omar and Qin, Maozhen and Zemelman, Boris V and Guo, Caiying and Mao, Tianyi and Zhong, Haining} } @article {65783, title = {Protein design: toward functional metalloenzymes.}, journal = {Chemical reviews}, volume = {114}, year = {2014}, month = {03/2014}, pages = {3495 {\textendash} 3578}, doi = {10.1021/cr400458x}, author = {Yu, Fangting and Cangelosi, Virginia M and Zastrow, Melissa L and Tegoni, Matteo and Plegaria, Jefferson S and Tebo, Alison G and Mocny, Catherine S and Ruckthong, Leela and Qayyum, Hira and Pecoraro, Vincent L} } @article {47220, title = {Imaging a population code for odor identity in the Drosophila mushroom body.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {33}, year = {2013}, month = {2013 Jun 19}, pages = {10568-81}, abstract = {

The brain represents sensory information in the coordinated activity of neuronal ensembles. Although the microcircuits underlying olfactory processing are well characterized in Drosophila, no studies to date have examined the encoding of odor identity by populations of neurons and related it to the odor specificity of olfactory behavior. Here we used two-photon Ca(2+) imaging to record odor-evoked responses from \>100 neurons simultaneously in the Drosophila mushroom body (MB). For the first time, we demonstrate quantitatively that MB population responses contain substantial information on odor identity. Using a series of increasingly similar odor blends, we identified conditions in which odor discrimination is difficult behaviorally. We found that MB ensemble responses accounted well for olfactory acuity in this task. Kenyon cell ensembles with as few as 25 cells were sufficient to match behavioral discrimination accuracy. Using a generalization task, we demonstrated that the MB population code could predict the flies{\textquoteright} responses to novel odors. The degree to which flies generalized a learned aversive association to unfamiliar test odors depended upon the relative similarity between the odors{\textquoteright} evoked MB activity patterns. Discrimination and generalization place different demands on the animal, yet the flies{\textquoteright} choices in these tasks were reliably predicted based on the amount of overlap between MB activity patterns. Therefore, these different behaviors can be understood in the context of a single physiological framework.

}, keywords = {Animals, Calcium, Discrimination (Psychology), Drosophila, Generalization (Psychology), Image Processing, Computer-Assisted, Learning, Linear Models, Mushroom Bodies, Neuroimaging, Odors, Olfactory Pathways, Olfactory Perception, Psychomotor Performance, Synaptic Transmission}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0682-12.2013}, author = {Campbell, Robert A A and Honegger, Kyle S and Qin, Hongtao and Li, Wanhe and Demir, Ebru and Turner, Glenn C} } @article {5423, title = {A GAL4-driver line resource for Drosophila neurobiology.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {991-1001}, abstract = {

We established a collection of 7,000 transgenic lines of Drosophila melanogaster. Expression of GAL4 in each line is controlled by a different, defined fragment of genomic DNA that serves as a transcriptional enhancer. We used confocal microscopy of dissected nervous systems to determine the expression patterns driven by each fragment in the adult brain and ventral nerve cord. We present image data on 6,650 lines. Using both manual and machine-assisted annotation, we describe the expression patterns in the most useful lines. We illustrate the utility of these data for identifying novel neuronal cell types, revealing brain asymmetry, and describing the nature and extent of neuronal shape stereotypy. The GAL4 lines allow expression of exogenous genes in distinct, small subsets of the adult nervous system. The set of DNA fragments, each driving a documented expression pattern, will facilitate the generation of additional constructs for manipulating neuronal function. synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For the overall strategy and methods used to produce the GAL4 lines:
Pfeiffer, B.D., Jenett, A., Hammonds, A.S., Ngo, T.T., Misra, S., Murphy, C., Scully, A., Carlson, J.W., Wan, K.H., Laverty, T.R., Mungall, C., Svirskas, R., Kadonaga, J.T., Doe, C.Q., Eisen, M.B., Celniker, S.E., Rubin, G.M. (2008). Tools for neuroanatomy and neurogenetics in Drosophila. Proc. Natl. Acad. Sci. USA 105, 9715-9720. http://www.pnas.org/content/105/28/9715.full.pdf+html synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in the embryo:
Manning, L., Purice, M.D., Roberts, J., Pollard, J.L., Bennett, A.L., Kroll, J.R., Dyukareva, A.V., Doan, P.N., Lupton, J.R., Strader, M.E., Tanner, S., Bauer, D., Wilbur, A., Tran, K.D., Laverty, T.R., Pearson, J.C., Crews, S.T., Rubin, G.M., and Doe, C.Q. (2012) Annotated embryonic CNS expression patterns of 5000 GMR GAL4 lines: a resource for manipulating gene expression and analyzing cis-regulatory motifs. Cell Reports (2012) Doi: 10.1016/j.celrep.2012.09.009 http://www.cell.com/cell-reports/fulltext/S2211-1247(12)00290-2 synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in imaginal discs:
Jory, A., Estella, C., Giorgianni, M.W., Slattery, M., Laverty, T.R., Rubin, G.M., and Mann, R.S. (2012) A survey of 6300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Reports (2012) Doi: 10.1016/j.celrep.2012.09.010 http://www.cell.com/cell-reports/fulltext/S2211-1247(12)00291-4 synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in the larval nervous system:
Li, H.-H., Kroll, J.R., Lennox, S., Ogundeyi, O., Jeter, J., Depasquale, G., and Truman, J.W. (2013) A GAL4 driver resource for developmental and behavioral studies on the larval CNS of Drosophila. Cell Reports (submitted).

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.011}, author = {Jenett, Arnim and Rubin, Gerald M and Ngo, Teri-T B and Shepherd, David and Murphy, Christine and Dionne, Heather and Pfeiffer, Barret D and Cavallaro, Amanda and Hall, Donald and Jeter, Jennifer and Iyer, Nirmala and Fetter, Dona and Hausenfluck, Joanna H and Peng, Hanchuan and Trautman, Eric T and Svirskas, Robert R and Myers, Eugene W and Iwinski, Zbigniew R and Aso, Yoshinori and Depasquale, Gina M and Enos, Adrianne and Hulamm, Phuson and Lam, Shing Chun Benny and Li, Hsing-Hsi and Laverty, Todd R and Long, Fuhui and Qu, Lei and Murphy, Sean D and Rokicki, Konrad and Safford, Todd and Shaw, Kshiti and Simpson, Julie H and Sowell, Allison and Tae, Susana and Yu, Yang and Zugates, Christopher T} } @article {5163, title = {Imaging neural activity using Thy1-GCaMP transgenic mice.}, journal = {Neuron}, volume = {76}, year = {2012}, month = {2012 Oct 18}, pages = {297-308}, abstract = {

The ability to chronically monitor neuronal activity in the living brain is essential for understanding the organization and function of the nervous system. The genetically encoded green fluorescent protein based calcium sensor GCaMP provides a powerful tool for detecting calcium transients in neuronal somata, processes, and synapses that are triggered by neuronal activities. Here we report the generation and characterization of transgenic mice that express improved GCaMPs in various neuronal subpopulations under the control of the Thy1 promoter. In vitro and in vivo studies show that calcium transients induced by spontaneous and stimulus-evoked neuronal activities can be readily detected at the level of individual cells and synapses in acute brain slices, as well as in awake behaving animals. These GCaMP transgenic mice allow investigation of activity patterns in defined neuronal populations in the living brain, and will greatly facilitate dissecting complex structural and functional relationships of neural networks.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.07.011}, author = {Chen, Qian and Cichon, Joseph and Wang, Wenting and Qiu, LI and Lee, Seok-Jin R. and Campbell, Nolan R. and DeStefino, Nicholas and Fu, Zhanyan and Yasuda, Ryohei and Looger, Loren L and Arenkiel, Benjamin R. and Gan, Wenbiao and Feng, Guoping} } @article {6326, title = {Maturation in action: CryoEM study of a viral capsid caught during expansion.}, journal = {Structure}, volume = {20}, year = {2012}, month = {2012 Aug 8}, pages = {1384-90}, abstract = {

Bacteriophage HK97 maturation involves discrete intermediate particle forms, comparable to transitional states in protein folding, before reaching its mature form. The process starts by formation of a metastable prohead, poised for exothermic expansion triggered by DNA packaging. During maturation, the capsid subunit transitions from a strained to a canonical tertiary conformation and this has been postulated to be the driving mechanism for initiating expansion via switching hexameric capsomer architecture from skewed to 6-fold symmetric. We report the subnanometer electron-cryomicroscopy reconstruction of the HK97 first expansion intermediate before any crosslink formation. This form displays 6-fold symmetric hexamers, but capsid subunit tertiary structures exhibit distortions comparable to the prohead forms. We propose that coat subunit strain release acts in synergy with the first crosslinks to drive forward maturation. Finally, we speculate that the energetic features of this transition may result from increased stability of intermediates during maturation via enhanced inter-subunit interactions.

}, keywords = {Amino Acid Substitution, Bacteriophages, Capsid, Capsid Proteins, Cryoelectron Microscopy, Protein Structure, Protein Subunits, Quaternary, Secondary, Tertiary, Virus Assembly}, issn = {1878-4186}, doi = {10.1016/j.str.2012.05.011}, author = {Veesler, David and Quispe, Joel and Grigorieff, Nikolaus and Potter, Clinton S and Carragher, Bridget and Johnson, John E} } @article {5339, title = {Transcriptional control of cell fate specification: lessons from the fly retina.}, journal = {Current Topics in Developmental Biology}, volume = {98}, year = {2012}, month = {2012}, pages = {259-76}, abstract = {

It is now widely recognized that as cells of developing tissues transition through successive states of decreasing pluripotency into a state of terminal differentiation, they undergo significant changes in their gene expression profiles. Interestingly, these successive states of increasing differentiation are marked by the spatially and temporally restricted expression of sets of transcription factors. Each wave of transcription factors not only signals the arrival of a given stage in cellular differentiation, but it is also necessary for the activation of the next set of transcription factors, creating the appearance of a smooth, directed, and deterministic genetic program of cellular differentiation. Until recently, however, it was largely unknown which genes, besides each other, these transcription factors were activating. Thus, the molecular definition of any given step of differentiation, and how it gave rise to the following step remained unclear. Recent advances in transcriptomics, bioinformatics, and molecular genetics resulted in the identification of numerous transcription factor target genes (TGs). These advances have opened the door to using similar approaches in developmental biology to understand what the transcriptional cascades of cellular differentiation might be. Using the development of the Drosophila eye as a model system, we discuss the role of transcription factors and their TGs in cell fate specification and terminal differentiation.

}, keywords = {Animals, Cell Lineage, Developmental, Drosophila melanogaster, Gene Expression Regulation, Genetic, Humans, Retina, Signal Transduction, Transcription}, issn = {1557-8933}, doi = {10.1016/B978-0-12-386499-4.00010-0}, author = {Quan, Xiao-jiang and Ramaekers, Ariane and Hassan, Bassem A} } @article {4157, title = {BrainAligner: 3D registration atlases of Drosophila brains.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 Jun}, pages = {493-500}, abstract = {

Analyzing Drosophila melanogaster neural expression patterns in thousands of three-dimensional image stacks of individual brains requires registering them into a canonical framework based on a fiducial reference of neuropil morphology. Given a target brain labeled with predefined landmarks, the BrainAligner program automatically finds the corresponding landmarks in a subject brain and maps it to the coordinate system of the target brain via a deformable warp. Using a neuropil marker (the antibody nc82) as a reference of the brain morphology and a target brain that is itself a statistical average of data for 295 brains, we achieved a registration accuracy of 2 μm on average, permitting assessment of stereotypy, potential connectivity and functional mapping of the adult fruit fly brain. We used BrainAligner to generate an image pattern atlas of 2954 registered brains containing 470 different expression patterns that cover all the major compartments of the fly brain.

}, keywords = {Algorithms, Animals, Brain, Computer-Assisted, Drosophila melanogaster, Drosophila Proteins, Gene Expression, Genetically Modified, Green Fluorescent Proteins, Image Processing, Neuropil, Recombinant Proteins, Software, Transcription Factors}, issn = {1548-7105}, doi = {10.1038/nmeth.1602}, author = {Peng, Hanchuan and Chung, Phuong and Long, Fuhui and Qu, Lei and Jenett, Arnim and Seeds, Andrew M and Myers, Eugene W and Simpson, Julie H} } @article {6524, title = {A critical role of mitochondrial phosphatase Ptpmt1 in embryogenesis reveals a mitochondrial metabolic stress-induced differentiation checkpoint in embryonic stem cells.}, journal = {Molecular and Cellular Biology}, volume = {31}, year = {2011}, month = {2011 Dec}, pages = {4902-16}, abstract = {

Mitochondria are highly dynamic organelles that play multiple roles in cells. How mitochondria cooperatively modulate embryonic stem (ES) cell function during development is not fully understood. Global disruption of Ptpmt1, a mitochondrial Pten-like phosphatidylinositol phosphate (PIP) phosphatase, resulted in developmental arrest and postimplantation lethality. Ptpmt1(-/-) blastocysts failed to outgrow, and inner-cell-mass cells failed to thrive. Depletion of Ptpmt1 in conditional knockout ES cells decreased proliferation without affecting energy homeostasis or cell survival. Differentiation of Ptpmt1-depleted ES cells was essentially blocked. This was accompanied by upregulation of cyclin-dependent kinase inhibitors and a significant cell cycle delay. Reintroduction of wild-type but not of catalytically deficient Ptpmt1 C132S or truncated Ptpmt1 lacking the mitochondrial localization signal restored the differentiation capabilities of Ptpmt1 knockout ES cells. Intriguingly, Ptpmt1 is specifically important for stem cells, as ablation of Ptpmt1 in differentiated embryonic fibroblasts did not disturb cellular function. Further analyses demonstrated that oxygen consumption of Ptpmt1-depleted cells was decreased, while glycolysis was concomitantly enhanced. In addition, mitochondrial fusion/dynamics were compromised in Ptpmt1 knockout cells due to accumulation of PIPs. These studies, while establishing a crucial role for Ptpmt1 phosphatase in embryogenesis, reveal a mitochondrial metabolic stress-activated checkpoint in the control of ES cell differentiation.

}, keywords = {Alleles, Animals, Apoptosis, Cell Cycle Checkpoints, Cell Differentiation, Cell Proliferation, Cloning, Confocal, Embryonic Development, Embryonic Stem Cells, Fibroblasts, Glycolysis, Immunohistochemistry, In Situ Nick-End Labeling, Knockout, Mice, Microscopy, Mitochondria, Molecular, Phosphatidylinositol Phosphates, Physiological, PTEN Phosphohydrolase, Reactive Oxygen Species, Stress}, issn = {1098-5549}, doi = {10.1128/MCB.05629-11}, author = {Shen, Jinhua and Liu, Xia and Yu, Wen-Mei and Liu, Jie and Nibbelink, Milou Groot and Guo, Caiying and Finkel, Toren and Qu, Cheng-Kui} } @article {2908, title = {N-WASp is required for Schwann cell cytoskeletal dynamics, normal myelin gene expression and peripheral nerve myelination.}, journal = {Development}, volume = {138}, year = {2011}, month = {2011 Apr}, pages = {1329-37}, abstract = {

Schwann cells elaborate myelin sheaths around axons by spirally wrapping and compacting their plasma membranes. Although actin remodeling plays a crucial role in this process, the effectors that modulate the Schwann cell cytoskeleton are poorly defined. Here, we show that the actin cytoskeletal regulator, neural Wiskott-Aldrich syndrome protein (N-WASp), is upregulated in myelinating Schwann cells coincident with myelin elaboration. When N-WASp is conditionally deleted in Schwann cells at the onset of myelination, the cells continue to ensheath axons but fail to extend processes circumferentially to elaborate myelin. Myelin-related gene expression is also severely reduced in the N-WASp-deficient cells and in vitro process and lamellipodia formation are disrupted. Although affected mice demonstrate obvious motor deficits these do not appear to progress, the mutant animals achieving normal body weights and living to advanced age. Our observations demonstrate that N-WASp plays an essential role in Schwann cell maturation and myelin formation.

}, keywords = {Animals, Axons, Blotting, Cells, Cultured, Cytoskeleton, Fluorescent Antibody Technique, Gait, Gene Expression, Knockout, Mice, Myelin Sheath, Neuronal, Peripheral Nerves, Reverse Transcriptase Polymerase Chain Reaction, Schwann Cells, Western, Wiskott-Aldrich Syndrome Protein}, issn = {1477-9129}, doi = {10.1242/dev.058677}, author = {Jin, Fuzi and Dong, Baoxia and Georgiou, John and Jiang, Qiuhong and Zhang, Jinyi and Bharioke, Arjun and Qiu, Frank and Lommel, Silvia and Feltri, M Laura and Wrabetz, Lawrence and Roder, John C and Eyer, Joel and Chen, Xiequn and Peterson, Alan C and Siminovitch, Katherine A} } @article {3839, title = {Simultaneous recognition and segmentation of cells: application in C. elegans.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 Aug 17}, pages = {2895-902}, abstract = {

MOTIVATION: Automatic recognition of cell identities is critical for quantitative measurement, targeting, and manipulation of cells of model animals at single-cell resolution. It has been shown to be a powerful tool for studying gene expression and regulation, cell lineages, and cell fates. Existing methods first segment cells, before applying a recognition algorithm in the second step. As a result, the segmentation errors in the first step directly affect and complicate the subsequent cell recognition step. Moreover, in new experimental settings, some of the image features that have been previously relied upon to recognize cells may not be easy to reproduce, due to limitations on the number of color channels available for fluorescent imaging or to the cost of building transgenic animals. An approach that is more accurate and relies on only a single signal channel is clearly desirable. RESULTS: We have developed a new method, called SRS (for Simultaneous Recognition and Segmentation of cells), and applied it to 3D image stacks of the model organism C. elegans. Given a 3D image stack of the animal and a 3D atlas of target cells, SRS is effectively an atlas-guided voxel classification process: cell recognition is realized by smoothly deforming the atlas to best fit the image, where the segmentation is obtained naturally via classification of all image voxels. The method achieved a 97.7\% overall recognition accuracy in recognizing a key class of marker cells, the body wall muscle (BWM) cells, on a data set of 175 C. elegans image stacks containing 14,118 manually curated BWM cells providing the "ground-truth" for accuracy. This result was achieved without any additional fiducial image features. SRS also automatically identified 14 of the image stacks as involving {\textpm}90-degree rotations. With these stacks excluded from the data set, the recognition accuracy rose to 99.1\%. We also show SRS is generally applicable to other cell-types, e.g. intestinal cells. AVAILABILITY: The supplementary movies can be downloaded from our website http://penglab.janelia.org/proj/celegans_seganno. The method has been implemented as a plug-in program within the V3D system (http://penglab.janelia.org/proj/v3d) and will be released in the V3D plugin source code repository.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btr480}, author = {Qu, Lei and Long, Fuhui and Liu, Xiao and Kim, Stuart and Myers, Eugene and Peng, Hanchuan} } @article {46734, title = {Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast.}, journal = {Cell}, volume = {147}, year = {2011}, month = {2011 Dec 23}, pages = {1484-97}, abstract = {

Messenger RNA decay measurements are typically performed on a population of cells. However, this approach cannot reveal sufficient complexity to provide information on mechanisms that may regulate mRNA degradation, possibly on short timescales. To address this deficiency, we measured cell cycle-regulated decay in single yeast cells using single-molecule FISH. We found that two genes responsible for mitotic progression, SWI5 and CLB2, exhibit a mitosis-dependent mRNA stability switch. Their transcripts are stable until mitosis, when a precipitous decay eliminates the mRNA complement, preventing carryover into the next cycle. Remarkably, the specificity and timing of decay is entirely regulated by their promoter, independent of specific cis mRNA sequences. The mitotic exit network protein Dbf2p binds to SWI5 and CLB2 mRNAs cotranscriptionally and regulates their decay. This work reveals the promoter-dependent control of mRNA stability, a regulatory mechanism that could be employed by a variety of mRNAs and organisms.

}, keywords = {Cell Cycle, Cell Cycle Proteins, Cyclin B, Gene Expression Regulation, Fungal, In Situ Hybridization, Fluorescence, Kinetics, Promoter Regions, Genetic, Protein-Serine-Threonine Kinases, RNA Stability, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors, Transcription, Genetic}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.11.051}, author = {Trcek, Tatjana and Larson, Daniel R and Mold{\'o}n, Alberto and Query, Charles C and Singer, Robert H} } @article {2146, title = {A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems.}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010 Apr 15}, pages = {1091-7}, abstract = {

The fruit fly (Drosophila melanogaster) is a commonly used model organism in biology. We are currently building a 3D digital atlas of the fruit fly larval nervous system (LNS) based on a large collection of fly larva GAL4 lines, each of which targets a subset of neurons. To achieve such a goal, we need to automatically align a number of high-resolution confocal image stacks of these GAL4 lines. One commonly employed strategy in image pattern registration is to first globally align images using an affine transform, followed by local non-linear warping. Unfortunately, the spatially articulated and often twisted LNS makes it difficult to globally align the images directly using the affine method. In a parallel project to build a 3D digital map of the adult fly ventral nerve cord (VNC), we are confronted with a similar problem.

}, keywords = {Algorithms, Animals, Cell Line, Computer-Assisted, Confocal, Drosophila melanogaster, Image Processing, Imaging, Microscopy, Nervous System, Three-Dimensional}, issn = {1367-4811}, doi = {10.1007/s12021-010-9090-x}, author = {Qu, Lei and Peng, Hanchuan} } @article {1556, title = {Engineering human IgG1 affinity to human neonatal Fc receptor: impact of affinity improvement on pharmacokinetics in primates.}, journal = {Journal of Immunology}, volume = {182}, year = {2009}, month = {2009 Jun 15}, pages = {7663-71}, abstract = {

The pH-dependent binding of Igs to the neonatal FcR (FcRn) plays a critical role in the in vivo homeostasis of IgGs. Modulating the interaction between Fc and FcRn through protein engineering is one method for improving the pharmacokinetics of therapeutic Abs. Recent studies disputed the direct relationship between increasing FcRn affinity and improved pharmacokinetic properties. In this work, we studied the pharmacokinetics of two human IgG1 Fc variants in cynomolgus monkey to further clarify the affinity-pharmacokinetic relationship. First, we report a number of novel Fc point mutations and combination variants, including some with primate-specific FcRn-binding improvements. By studying these variants along with some previously described variants across a wide range of affinities, we discovered a direct correlation of pH 6 affinity improvements with neutral pH improvements, suggesting that all of the tested variants exhibit similar pH dependency in FcRn binding. We then evaluated the pharmacokinetics of variants N434A and N434W, which, respectively, gave approximately 4- and 80-fold improvements in pH 6-binding affinity to both human and nonhuman primate FcRn. Surprisingly, clearance of N434W was similar to that of wild type. N434W is the first variant studied in primates that exhibits significant binding to FcRn at pH 7.4, and its clearance substantiates the principle that too much affinity improvement, i.e., beyond that of N434W, does not yield improved pharmacokinetics. In contrast, N434A exhibited a approximately 2-fold decrease in clearance in cynomolgus monkey, supporting the notion that modest increases in pH 6 FcRn affinity can result in improved pharmacokinetics in primates.

}, keywords = {Amino Acid Sequence, Animals, Antibody Affinity, Fc, Histocompatibility Antigens Class I, Humans, Hydrogen-Ion Concentration, Immunoglobulin G, Macaca fascicularis, Mice, Models, Molecular, Mutation, Protein Structure, Quaternary, Receptors, Recombinant Proteins}, issn = {1550-6606}, doi = {10.4049/jimmunol.0804182}, author = {Yeung, Yik Andy and Leabman, Maya K and Marvin, Jonathan S and Qiu, Julia and Adams, Camellia W and Lien, Samantha and Starovasnik, Melissa A and Lowman, Henry B} } @article {2780, title = {Reactive astrocytes in glial scar attract olfactory ensheathing cells migration by secreted TNF-alpha in spinal cord lesion of rat.}, journal = {PLoS One}, volume = {4}, year = {2009}, month = {2009 Dec 3}, pages = {e8141}, abstract = {

After spinal cord injury (SCI), the formation of glial scar contributes to the failure of injured adult axons to regenerate past the lesion. Increasing evidence indicates that olfactory ensheathing cells (OECs) implanted into spinal cord are found to migrate into the lesion site and induce axons regeneration beyond glial scar and resumption of functions. However, little is known about the mechanisms of OECs migrating from injection site to glial scar/lesion site.

}, keywords = {Animals, Astrocytes, Cell Movement, Cicatrix, Conditioned, Culture Media, Enzyme Activation, Mitogen-Activated Protein Kinases, Olfactory Pathways, Rats, Receptors, Spinal Cord, Sprague-Dawley, Tumor Necrosis Factor, Tumor Necrosis Factor-alpha, Type I}, issn = {1932-6203}, doi = {10.1364/AO.50.001792}, author = {Su, Zhida and Yuan, Yimin and Chen, Jingjing and Cao, Li and Zhu, Yanling and Gao, Liang and Qiu, Yang and He, Cheng} } @article {2201, title = {Single-molecule DNA sequencing of a viral genome.}, journal = {Science}, volume = {320}, year = {2008}, month = {2008 Apr 4}, pages = {106-9}, abstract = {

The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of \>25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of \>150x and with 100\% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.

}, keywords = {Algorithms, Bacteriophage M13, Computational Biology, DNA, DNA Primers, Genetic, Genome, Mutation, Sequence Alignment, Sequence Analysis, Software, Templates, Viral}, issn = {1095-9203}, doi = {10.1038/nbt0510-426}, author = {Harris, Timothy D and Buzby, Phillip R and Babcock, Hazen and Beer, Eric and Bowers, Jayson and Braslavsky, Ido and Causey, Marie and Colonell, Jennifer and Dimeo, James and Efcavitch, J William and Giladi, Eldar and Gill, Jaime and Healy, John and Jarosz, Mirna and Lapen, Dan and Moulton, Keith and Quake, Stephen R and Steinmann, Kathleen and Thayer, Edward and Tyurina, Anastasia and Ward, Rebecca and Weiss, Howard and Xie, Zheng} } @article {6494, title = {Evolution of genes and genomes on the Drosophila phylogeny.}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007 Nov 8}, pages = {203-18}, abstract = {

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

}, keywords = {Animals, Codon, DNA, DNA Transposable Elements, Drosophila, Drosophila Proteins, Evolution, Gene Order, Genes, Genome, Genomics, Immunity, Insect, Mitochondrial, Molecular, Multigene Family, Phylogeny, Reproduction, RNA, Sequence Alignment, Sequence Analysis, Synteny, Untranslated}, issn = {1476-4687}, doi = {10.1038/nature06341}, author = {Clark, Andrew G and Eisen, Michael B and Smith, Douglas R and Bergman, Casey M and Oliver, Brian and Markow, Therese A and Kaufman, Thomas C and Kellis, Manolis and Gelbart, William and Iyer, Venky N and Pollard, Daniel A and Sackton, Timothy B and Larracuente, Amanda M and Singh, Nadia D and Abad, Jose P and Abt, Dawn N and Adryan, Boris and Aguade, Montserrat and Akashi, Hiroshi and Anderson, Wyatt W and Aquadro, Charles F and Ardell, David H and Arguello, Roman and Artieri, Carlo G and Barbash, Daniel A and Barker, Daniel and Barsanti, Paolo and Batterham, Phil and Batzoglou, Serafim and Begun, Dave and Bhutkar, Arjun and Blanco, Enrico and Bosak, Stephanie A and Bradley, Robert K and Brand, Adrianne D and Brent, Michael R and Brooks, Angela N and Brown, Randall H and Butlin, Roger K and Caggese, Corrado and Calvi, Brian R and Bernardo de Carvalho, A and Caspi, Anat and Castrezana, Sergio and Celniker, Susan E and Chang, Jean L and Chapple, Charles and Chatterji, Sourav and Chinwalla, Asif and Civetta, Alberto and Clifton, Sandra W and Comeron, Josep M and Costello, James C and Coyne, Jerry A and Daub, Jennifer and David, Robert G and Delcher, Arthur L and Delehaunty, Kim and Do, Chuong B and Ebling, Heather and Edwards, Kevin and Eickbush, Thomas and Evans, Jay D and Filipski, Alan and Findeiss, Sven and Freyhult, Eva and Fulton, Lucinda and Fulton, Robert and Garcia, Ana C L and Gardiner, Anastasia and Garfield, David A and Garvin, Barry E and Gibson, Greg and Gilbert, Don and Gnerre, Sante and Godfrey, Jennifer and Good, Robert and Gotea, Valer and Gravely, Brenton and Greenberg, Anthony J and Griffiths-Jones, Sam and Gross, Samuel and Guigo, Roderic and Gustafson, Erik A and Haerty, Wilfried and Hahn, Matthew W and Halligan, Daniel L and Halpern, Aaron L and Halter, Gillian M and Han, Mira V and Heger, Andreas and Hillier, LaDeana and Hinrichs, Angie S and Holmes, Ian and Hoskins, Roger A and Hubisz, Melissa J and Hultmark, Dan and Huntley, Melanie A and Jaffe, David B and Jagadeeshan, Santosh and Jeck, William R and Johnson, Justin and Jones, Corbin D and Jordan, William C and Karpen, Gary H and Kataoka, Eiko and Keightley, Peter D and Kheradpour, Pouya and Kirkness, Ewen F and Koerich, Leonardo B and Kristiansen, Karsten and Kudrna, Dave and Kulathinal, Rob J and Kumar, Sudhir and Kwok, Roberta and Lander, Eric and Langley, Charles H and Lapoint, Richard and Lazzaro, Brian P and Lee, So-Jeong and Levesque, Lisa and Li, Ruiqiang and Lin, Chiao-Feng and Lin, Michael F and Lindblad-Toh, Kerstin and Llopart, Ana and Long, Manyuan and Low, Lloyd and Lozovsky, Elena and Lu, Jian and Luo, Meizhong and Machado, Carlos A and Makalowski, Wojciech and Marzo, Mar and Matsuda, Muneo and Matzkin, Luciano and McAllister, Bryant and McBride, Carolyn S and McKernan, Brendan and McKernan, Kevin and Mendez-Lago, Maria and Minx, Patrick and Mollenhauer, Michael U and Montooth, Kristi and Mount, Stephen M and Mu, Xu and Myers, Eugene and Negre, Barbara and Newfeld, Stuart and Nielsen, Rasmus and Noor, Mohamed A F and O{\textquoteright}Grady, Patrick and Pachter, Lior and Papaceit, Montserrat and Parisi, Matthew J and Parisi, Michael and Parts, Leopold and Pedersen, Jakob S and Pesole, Graziano and Phillippy, Adam M and Ponting, Chris P and Pop, Mihai and Porcelli, Damiano and Powell, Jeffrey R and Prohaska, Sonja and Pruitt, Kim and Puig, Marta and Quesneville, Hadi and Ram, Kristipati Ravi and Rand, David and Rasmussen, Matthew D and Reed, Laura K and Reenan, Robert and Reily, Amy and Remington, Karin A and Rieger, Tania T and Ritchie, Michael G and Robin, Charles and Rogers, Yu-Hui and Rohde, Claudia and Rozas, Julio and Rubenfield, Marc J and Ruiz, Alfredo and Russo, Susan and Salzberg, Steven L and Sanchez-Gracia, Alejandro and Saranga, David J and Sato, Hajime and Schaeffer, Stephen W and Schatz, Michael C and Schlenke, Todd and Schwartz, Russell and Segarra, Carmen and Singh, Rama S and Sirot, Laura and Sirota, Marina and Sisneros, Nicholas B and Smith, Chris D and Smith, Temple F and Spieth, John and Stage, Deborah E and Stark, Alexander and Stephan, Wolfgang and Strausberg, Robert L and Strempel, Sebastian and Sturgill, David and Sutton, Granger and Sutton, Granger G and Tao, Wei and Teichmann, Sarah and Tobari, Yoshiko N and Tomimura, Yoshihiko and Tsolas, Jason M and Valente, Vera L S and Venter, Eli and Venter, J Craig and Vicario, Saverio and Vieira, Filipe G and Vilella, Albert J and Villasante, Alfredo and Walenz, Brian and Wang, Jun and Wasserman, Marvin and Watts, Thomas and Wilson, Derek and Wilson, Richard K and Wing, Rod A and Wolfner, Mariana F and Wong, Alex and Wong, Gane Ka-Shu and Wu, Chung-I and Wu, Gabriel and Yamamoto, Daisuke and Yang, Hsiao-Pei and Yang, Shiaw-Pyng and Yorke, James A and Yoshida, Kiyohito and Zdobnov, Evgeny and Zhang, Peili and Zhang, Yu and Zimin, Aleksey V and Baldwin, Jennifer and Abdouelleil, Amr and Abdulkadir, Jamal and Abebe, Adal and Abera, Brikti and Abreu, Justin and Acer, St Christophe and Aftuck, Lynne and Alexander, Allen and An, Peter and Anderson, Erica and Anderson, Scott and Arachi, Harindra and Azer, Marc and Bachantsang, Pasang and Barry, Andrew and Bayul, Tashi and Berlin, Aaron and Bessette, Daniel and Bloom, Toby and Blye, Jason and Boguslavskiy, Leonid and Bonnet, Claude and Boukhgalter, Boris and Bourzgui, Imane and Brown, Adam and Cahill, Patrick and Channer, Sheridon and Cheshatsang, Yama and Chuda, Lisa and Citroen, Mieke and Collymore, Alville and Cooke, Patrick and Costello, Maura and D{\textquoteright}Aco, Katie and Daza, Riza and De Haan, Georgius and DeGray, Stuart and DeMaso, Christina and Dhargay, Norbu and Dooley, Kimberly and Dooley, Erin and Doricent, Missole and Dorje, Passang and Dorjee, Kunsang and Dupes, Alan and Elong, Richard and Falk, Jill and Farina, Abderrahim and Faro, Susan and Ferguson, Diallo and Fisher, Sheila and Foley, Chelsea D and Franke, Alicia and Friedrich, Dennis and Gadbois, Loryn and Gearin, Gary and Gearin, Christina R and Giannoukos, Georgia and Goode, Tina and Graham, Joseph and Grandbois, Edward and Grewal, Sharleen and Gyaltsen, Kunsang and Hafez, Nabil and Hagos, Birhane and Hall, Jennifer and Henson, Charlotte and Hollinger, Andrew and Honan, Tracey and Huard, Monika D and Hughes, Leanne and Hurhula, Brian and Husby, M Erii and Kamat, Asha and Kanga, Ben and Kashin, Seva and Khazanovich, Dmitry and Kisner, Peter and Lance, Krista and Lara, Marcia and Lee, William and Lennon, Niall and Letendre, Frances and LeVine, Rosie and Lipovsky, Alex and Liu, Xiaohong and Liu, Jinlei and Liu, Shangtao and Lokyitsang, Tashi and Lokyitsang, Yeshi and Lubonja, Rakela and Lui, Annie and MacDonald, Pen and Magnisalis, Vasilia and Maru, Kebede and Matthews, Charles and McCusker, William and McDonough, Susan and Mehta, Teena and Meldrim, James and Meneus, Louis and Mihai, Oana and Mihalev, Atanas and Mihova, Tanya and Mittelman, Rachel and Mlenga, Valentine and Montmayeur, Anna and Mulrain, Leonidas and Navidi, Adam and Naylor, Jerome and Negash, Tamrat and Nguyen, Thu and Nguyen, Nga and Nicol, Robert and Norbu, Choe and Norbu, Nyima and Novod, Nathaniel and O{\textquoteright}Neill, Barry and Osman, Sahal and Markiewicz, Eva and Oyono, Otero L and Patti, Christopher and Phunkhang, Pema and Pierre, Fritz and Priest, Margaret and Raghuraman, Sujaa and Rege, Filip and Reyes, Rebecca and Rise, Cecil and Rogov, Peter and Ross, Keenan and Ryan, Elizabeth and Settipalli, Sampath and Shea, Terry and Sherpa, Ngawang and Shi, Lu and Shih, Diana and Sparrow, Todd and Spaulding, Jessica and Stalker, John and Stange-Thomann, Nicole and Stavropoulos, Sharon and Stone, Catherine and Strader, Christopher and Tesfaye, Senait and Thomson, Talene and Thoulutsang, Yama and Thoulutsang, Dawa and Topham, Kerri and Topping, Ira and Tsamla, Tsamla and Vassiliev, Helen and Vo, Andy and Wangchuk, Tsering and Wangdi, Tsering and Weiand, Michael and Wilkinson, Jane and Wilson, Adam and Yadav, Shailendra and Young, Geneva and Yu, Qing and Zembek, Lisa and Zhong, Danni and Zimmer, Andrew and Zwirko, Zac and Jaffe, David B and Alvarez, Pablo and Brockman, Will and Butler, Jonathan and Chin, CheeWhye and Gnerre, Sante and Grabherr, Manfred and Kleber, Michael and Mauceli, Evan and MacCallum, Iain} } @article {6249, title = {Global analyses of mRNA translational control during early Drosophila embryogenesis.}, journal = {Genome Biology}, volume = {8}, year = {2007}, month = {2007}, pages = {R63}, abstract = {

BACKGROUND: In many animals, the first few hours of life proceed with little or no transcription, and developmental regulation at these early stages is dependent on maternal cytoplasm rather than the zygotic nucleus. Translational control is critical for early Drosophila embryogenesis and is exerted mainly at the gene level. To understand post-transcriptional regulation during Drosophila early embryonic development, we used sucrose polysomal gradient analyses and GeneChip analysis to illustrate the translation profile of individual mRNAs. RESULTS: We determined ribosomal density and ribosomal occupancy of over 10,000 transcripts during the first ten hours after egg laying. CONCLUSION: We report the extent and general nature of gene regulation at the translational level during early Drosophila embryogenesis on a genome-wide basis. The diversity of the translation profiles indicates multiple mechanisms modulating transcript-specific translation. Cluster analyses suggest that the genes involved in some biological processes are co-regulated at the translational level at certain developmental stages.

}, keywords = {Animals, Cluster Analysis, Developmental, Drosophila, Embryo, Embryonic Development, Gene Expression Regulation, Messenger, Nonmammalian, Polyribosomes, Protein Biosynthesis, Ribosomes, RNA, RNA 5{\textquoteright} Terminal Oligopyrimidine Sequence}, issn = {1465-6914}, doi = {10.1186/gb-2007-8-4-r63}, author = {Qin, Xiaoli and Ahn, Soyeon and Speed, Terence P and Rubin, Gerald M} } @article {46630, title = {Guidelines on nicotine dose selection for in vivo research.}, journal = {Psychopharmacology (Berl)}, volume = {190}, year = {2007}, month = {2007 Feb}, pages = {269-319}, abstract = {

RATIONALE: This review provides insight for the judicious selection of nicotine dose ranges and routes of administration for in vivo studies. The literature is replete with reports in which a dosaging regimen chosen for a specific nicotine-mediated response was suboptimal for the species used. In many cases, such discrepancies could be attributed to the complex variables comprising species-specific in vivo responses to acute or chronic nicotine exposure.

OBJECTIVES: This review capitalizes on the authors{\textquoteright} collective decades of in vivo nicotine experimentation to clarify the issues and to identify the variables to be considered in choosing a dosaging regimen. Nicotine dose ranges tolerated by humans and their animal models provide guidelines for experiments intended to extrapolate to human tobacco exposure through cigarette smoking or nicotine replacement therapies. Just as important are the nicotine dosaging regimens used to provide a mechanistic framework for acquisition of drug-taking behavior, dependence, tolerance, or withdrawal in animal models.

RESULTS: Seven species are addressed: humans, nonhuman primates, rats, mice, Drosophila, Caenorhabditis elegans, and zebrafish. After an overview on nicotine metabolism, each section focuses on an individual species, addressing issues related to genetic background, age, acute vs chronic exposure, route of administration, and behavioral responses.

CONCLUSIONS: The selected examples of successful dosaging ranges are provided, while emphasizing the necessity of empirically determined dose-response relationships based on the precise parameters and conditions inherent to a specific hypothesis. This review provides a new, experimentally based compilation of species-specific dose selection for studies on the in vivo effects of nicotine.

}, keywords = {Animals, Behavioral Research, Dose-Response Relationship, Drug, Ganglionic Stimulants, Guidelines as Topic, Humans, Models, Biological, Nicotine, Species Specificity}, issn = {0033-3158}, doi = {10.1007/s00213-006-0441-0}, author = {Matta, Shannon G and Balfour, David J and Benowitz, Neal L and Boyd, R Thomas and Buccafusco, Jerry J and Caggiula, Anthony R and Craig, Caroline R and Collins, Allan C and Damaj, M Imad and Donny, Eric C and Gardiner, Phillip S and Grady, Sharon R and Heberlein, Ulrike and Leonard, Sherry S and Levin, Edward D and Lukas, Ronald J and Markou, Athina and Marks, Michael J and McCallum, Sarah E and Parameswaran, Neeraja and Perkins, Kenneth A and Picciotto, Marina R and Quik, Maryka and Rose, Jed E and Rothenfluh, Adrian and Schafer, William R and Stolerman, Ian P and Tyndale, Rachel F and Wehner, Jeanne M and Zirger, Jeffrey M} } @article {6250, title = {Lola regulates Drosophila olfactory projection neuron identity and targeting specificity.}, journal = {Neural Development}, volume = {2}, year = {2007}, month = {2007 Jul 16}, pages = {14}, abstract = {

BACKGROUND: Precise connections of neural circuits can be specified by genetic programming. In the Drosophila olfactory system, projection neurons (PNs) send dendrites to single glomeruli in the antenna lobe (AL) based upon lineage and birth order and send axons with stereotyped terminations to higher olfactory centers. These decisions are likely specified by a PN-intrinsic transcriptional code that regulates the expression of cell-surface molecules to instruct wiring specificity. RESULTS: We find that the loss of longitudinals lacking (lola), which encodes a BTB-Zn-finger transcription factor with 20 predicted splice isoforms, results in wiring defects in both axons and dendrites of all lineages of PNs. RNA in situ hybridization and quantitative RT-PCR suggest that most if not all lola isoforms are expressed in all PNs, but different isoforms are expressed at widely varying levels. Overexpression of individual lola isoforms fails to rescue the lola null phenotypes and causes additional phenotypes. Loss of lola also results in ectopic expression of Gal4 drivers in multiple cell types and in the loss of transcription factor gene lim1 expression in ventral PNs. CONCLUSION: Our results indicate that lola is required for wiring of axons and dendrites of most PN classes, and suggest a need for its molecular diversity. Expression pattern changes of Gal4 drivers in lola-/- clones imply that lola normally represses the expression of these regulatory elements in a subset of the cells surrounding the AL. We propose that Lola functions as a general transcription factor that regulates the expression of multiple genes ultimately controlling PN identity and wiring specificity.

}, keywords = {Animals, Body Patterning, Brain, Cell Differentiation, Dendrites, Developmental, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Growth Cones, Larva, Olfactory Pathways, Olfactory Receptor Neurons, Regulatory Elements, Transcription Factors, Transcriptional, Transcriptional Activation}, issn = {1749-8104}, doi = {10.1186/1749-8104-2-14}, author = {Spletter, Maria Lynn and Liu, Jian and Liu, Justin and Su, Helen and Giniger, Edward and Komiyama, Takaki and Quake, Stephen and Luo, Liqun} } @article {2707, title = {The sequence of the human genome.}, journal = {Science}, volume = {291}, year = {2001}, month = {2001 Feb 16}, pages = {1304-51}, abstract = {

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90\% of the genome is in scaffold assemblies of 100,000 bp or more, and 25\% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1\% of the genome is spanned by exons, whereas 24\% is in introns, with 75\% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1\% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

}, keywords = {Algorithms, Animals, Artificial, Bacterial, Chromosome Banding, Chromosome Mapping, Chromosomes, Computational Biology, Consensus Sequence, CpG Islands, Databases, DNA, Evolution, Exons, Factual, Female, Gene Duplication, Genes, Genetic Variation, Genome, Human, Human Genome Project, Humans, Intergenic, Introns, Male, Molecular, Nucleic Acid, Phenotype, Physical Chromosome Mapping, Polymorphism, Proteins, Pseudogenes, Repetitive Sequences, Retroelements, Sequence Analysis, Single Nucleotide, Species Specificity}, issn = {0036-8075}, doi = {10.1126/science.1058040}, author = {Venter, J C and Adams, M D and Myers, E W and Li, P W and Mural, R J and Sutton, G G and Smith, H O and Yandell, M and Evans, C A and Holt, R A and Gocayne, J D and Amanatides, P and Ballew, R M and Huson, D H and Wortman, J R and Zhang, Q and Kodira, C D and Zheng, X H and Chen, L and Skupski, M and Subramanian, G and Thomas, P D and Zhang, J and Gabor Miklos, G L and Nelson, C and Broder, S and Clark, A G and Nadeau, J and McKusick, V A and Zinder, N and Levine, A J and Roberts, R J and Simon, M and Slayman, C and Hunkapiller, M and Bolanos, R and Delcher, A and Dew, I and Fasulo, D and Flanigan, M and Florea, L and Halpern, A and Hannenhalli, S and Kravitz, S and Levy, S and Mobarry, C and Reinert, K and Remington, K and Abu-Threideh, J and Beasley, E and Biddick, K and Bonazzi, V and Brandon, R and Cargill, M and Chandramouliswaran, I and Charlab, R and Chaturvedi, K and Deng, Z and Di Francesco, V and Dunn, P and Eilbeck, K and Evangelista, C and Gabrielian, A E and Gan, W and Ge, W and Gong, F and Gu, Z and Guan, P and Heiman, T J and Higgins, M E and Ji, R R and Ke, Z and Ketchum, K A and Lai, Z and Lei, Y and Li, Z and Li, J and Liang, Y and Lin, X and Lu, F and Merkulov, G V and Milshina, N and Moore, H M and Naik, A K and Narayan, V A and Neelam, B and Nusskern, D and Rusch, D B and Salzberg, S and Shao, W and Shue, B and Sun, J and Wang, Z and Wang, A and Wang, X and Wang, J and Wei, M and Wides, R and Xiao, C and Yan, C and Yao, A and Ye, J and Zhan, M and Zhang, W and Zhang, H and Zhao, Q and Zheng, L and Zhong, F and Zhong, W and Zhu, S and Zhao, S and Gilbert, D and Baumhueter, S and Spier, G and Carter, C and Cravchik, A and Woodage, T and Ali, F and An, H and Awe, A and Baldwin, D and Baden, H and Barnstead, M and Barrow, I and Beeson, K and Busam, D and Carver, A and Center, A and Cheng, M L and Curry, L and Danaher, S and Davenport, L and Desilets, R and Dietz, S and Dodson, K and Doup, L and Ferriera, S and Garg, N and Gluecksmann, A and Hart, B and Haynes, J and Haynes, C and Heiner, C and Hladun, S and Hostin, D and Houck, J and Howland, T and Ibegwam, C and Johnson, J and Kalush, F and Kline, L and Koduru, S and Love, A and Mann, F and May, D and McCawley, S and McIntosh, T and McMullen, I and Moy, M and Moy, L and Murphy, B and Nelson, K and Pfannkoch, C and Pratts, E and Puri, V and Qureshi, H and Reardon, M and Rodriguez, R and Rogers, Y H and Romblad, D and Ruhfel, B and Scott, R and Sitter, C and Smallwood, M and Stewart, E and Strong, R and Suh, E and Thomas, R and Tint, N N and Tse, S and Vech, C and Wang, G and Wetter, J and Williams, S and Williams, M and Windsor, S and Winn-Deen, E and Wolfe, K and Zaveri, J and Zaveri, K and Abril, J F and Guig{\'o}, R and Campbell, M J and Sjolander, K V and Karlak, B and Kejariwal, A and Mi, H and Lazareva, B and Hatton, T and Narechania, A and Diemer, K and Muruganujan, A and Guo, N and Sato, S and Bafna, V and Istrail, S and Lippert, R and Schwartz, R and Walenz, B and Yooseph, S and Allen, D and Basu, A and Baxendale, J and Blick, L and Caminha, M and Carnes-Stine, J and Caulk, P and Chiang, Y H and Coyne, M and Dahlke, C and Mays, A and Dombroski, M and Donnelly, M and Ely, D and Esparham, S and Fosler, C and Gire, H and Glanowski, S and Glasser, K and Glodek, A and Gorokhov, M and Graham, K and Gropman, B and Harris, M and Heil, J and Henderson, S and Hoover, J and Jennings, D and Jordan, C and Jordan, J and Kasha, J and Kagan, L and Kraft, C and Levitsky, A and Lewis, M and Liu, X and Lopez, J and Ma, D and Majoros, W and McDaniel, J and Murphy, S and Newman, M and Nguyen, T and Nguyen, N and Nodell, M and Pan, S and Peck, J and Peterson, M and Rowe, W and Sanders, R and Scott, J and Simpson, M and Smith, T and Sprague, A and Stockwell, T and Turner, R and Venter, E and Wang, M and Wen, M and Wu, D and Wu, M and Xia, A and Zandieh, A and Zhu, X} }