@article {70177, title = {A pair of interneurons that assign positive valence to sweet sensation in Drosophila}, journal = {Curr Bill}, year = {2026}, month = {2026 Jan 29}, abstract = {

Assigning valence-appeal or aversion-to gustatory stimuli and relaying it to higher-order brain regions to guide flexible behaviors is crucial to survival. Yet the neural circuits that transform taste into motivationally relevant signals remain poorly defined in any model system. In Drosophila melanogaster, substantial progress has been made in mapping the sensorimotor pathways encoding intrinsic valence for feeding and the architecture of the dopaminergic reinforcement system. However, where and how "effective" (i.e., real-time) valence is first imposed on a taste has long been a mystery. Here, we identified a pair of subesophageal zone interneurons in Drosophila, termed Fox, that impart reinforcing positive valence to sweet taste and convey this signal to the mushroom body, the fly{\textquoteright}s associative learning center. We show that Fox neuron activity is necessary and sufficient to drive appetitive behaviors and can override a tastant{\textquoteright}s intrinsic neutral or aversive valence without impairing taste quality discrimination. Furthermore, Fox neurons relay the positive valence to specific dopaminergic neurons that mediate appetitive memory formation. Our findings reveal a circuit mechanism through which effective valence is bestowed upon sweet sensation and transformed into a reinforcing signal that supports learned sugar responses. The Fox neurons form a convergent-divergent "hourglass" circuit motif, acting as a bottleneck for valence assignment and distributing motivational signals to higher-order centers. This architecture confers both robustness and flexibility in reward processing-an organizational principle that may generalize across species.

}, doi = {10.1016/j.cub.2025.12.058}, url = {https://doi.org/10.1016/j.cub.2025.12.058}, author = {Christie, Kevin William and Dadyala, Tarandeep Singh and Sinakevitch, Irina Troufakina and Chung, Phuong and Ito, Masayoshi and Shao, Lisha} } @article {70294, title = {Phasor analysis of RGB camera data enables fluorescence microscopy unmixing and brightfield segmentation in a commercial microscope}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 16}, abstract = {

Spectral information plays a crucial role in biological imaging, yet conventional epifluorescence and histological techniques often rely on RGB image acquisition, limiting the resolution of spectrally overlapping components. Here, we present a phasor-based spectral analysis framework adapted for RGB images, enabling unsupervised segmentation and unmixing without the need for hyperspectral systems or sequential acquisition. By applying a discrete Fourier transform to the red, green, and blue intensities at each pixel, we generate a two-dimensional phasor plot where spectral relationships are encoded in modulation and phase. We demonstrate the utility of this approach across three distinct applications: segmentation of lung histology images stained with hematoxylin and eosin to quantify alveolar collapse, analysis of autofluorescence in skin lesions (nevi and melanoma) to highlight pathological spectral signatures, and spectral unmixing in multicolor-labeled U2OS cells to resolve overlapping fluorophores. Our method improves signal separation, reduces noise, and enhances biological interpretability using standard RGB acquisition. These findings establish RGB phasor analysis as a practical and powerful tool for spectral decomposition and segmentation in microscopy, bridging the gap between conventional imaging and advanced spectral analysis.

}, doi = {10.64898/2026.02.13.705652}, url = {https://www.biorxiv.org/content/early/2026/02/16/2026.02.13.705652}, author = {Schuty, Bruno and Garcia, Maria Jose and Khuon, Satya and Malacrida, Leonel S} } @article {70302, title = {Phenotypic CRISPR screens identify NLRX1 as an essential activator of the human mitochondrial permeability transition}, journal = {Proceedings of the National Academy of Sciences}, volume = {123}, year = {2026}, month = {2026 Feb 25}, pages = {e2535298123}, abstract = {

Mitochondria utilize calcium to increase ATP synthesis. However, excessive matrix calcium activates the mitochondrial permeability transition (mPT), a process that permeabilizes the mitochondrial inner membrane and leads to cell death. While initially characterized 50 y ago, the proteins underlying the process are unclear, although integral membrane proteins were expected to be the porous entities during calcium overload. Here, we designed two assays to study the mPT using high-throughput methodologies. By surveying 19,113 proteins in human cells, we identified four proteins that sensitize the human mPT, but only one that was essential for mPT activation, mitochondrial-localized NRLX1. Surprisingly, NLRX1 is not an integral membrane protein, and our work did not identify any essential integral membrane proteins for the human mPT. The mitochondrial permeability transition (mPT) is an evolutionarily conserved destructive process that permeabilizes the inner mitochondrial membrane in response to calcium overload. The molecular mechanism underlying the mPT is not established. To unambiguously identify essential proteins, we designed two phenotypic assays for mitochondrial calcium overload and applied them to FACS-based CRISPR screening in human cells, ultimately evaluating 19,113 genes. The first screen studied mitochondrial membrane potential (MMP) collapse in response to calcium overload. Top-ranked genes were the essential proteins of the mitochondrial calcium uniporter complex, MCU and EMRE, reflecting that the calcium-induced MMP collapse results from mitochondrial calcium entry and not the mPT. The second screen measured the permeability of the inner mitochondrial membrane. Here, the fluorescent interaction of a membrane impermeant 600 Da dye and a mitochondrial-targeted HaloTag protein was studied under mPT activating conditions; calcium overload and the thiol-reactive molecule phenylarsine oxide. With secondary validation, we identified four protein-encoding genes that delayed or prevented the mPT under knockout: NF2, REST, BPTF, and NRLX1. Knockout of the nonmitochondrial proteins BPTF, NF2, or REST increased mitochondrial calcium retention capacity (CRC). However, calcium release or sensitivity to cyclosporin A (CsA) persisted, indicative of mPT sensitizers. Only knockout of the mitochondrial matrix protein, NLRX1, increased CRC, abolished calcium release, and was CsA-insensitive. This top-ranked hit of the mitochondrial permeability screen meets the definition of an essential mPT activator. Integral membrane proteins, including all previously proposed mPT candidates, were not essential activators.

}, doi = {10.1073/pnas.2535298123}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.2535298123}, author = {William C. Valinsky and Robert P. Ray and Kathy S. Schaefer and Jonathan B. Grimm and Carla Nicolini and Luke D. Lavis and David E. Clapham} } @article {69949, title = {Proprioceptive limit detectors mediate sensorimotor control of the Drosophila leg}, journal = {Nat Commun}, year = {2026}, month = {2026 Feb 12}, abstract = {

Many animals possess mechanosensory neurons that fire when a limb nears the limit of its physical range, but the function of these proprioceptive limit detectors remains poorly understood. Here, we investigate a class of proprioceptors on the Drosophila leg called hair plates. Using calcium imaging in behaving flies, we find that a hair plate on the fly coxa (CxHP8) detects the limits of anterior leg movement. By reconstructing CxHP8 axons in an electron microscopy dataset, we found that they are wired to excite posterior leg movement and inhibit anterior leg movement. Consistent with this connectivity, optogenetic activation of CxHP8 neurons elicited posterior postural reflexes, while silencing altered the swing-to-stance transition during walking. Finally, we use comprehensive reconstruction of peripheral morphology and downstream connectivity to predict the function of other hair plates distributed across the fly leg. Our results suggest that each hair plate is specialized to control specific sensorimotor reflexes that are matched to the joint limit it detects. They also illustrate the feasibility of predicting sensorimotor reflexes from a connectome with identified proprioceptive inputs and motor outputs.

}, doi = {10.1038/s41467-026-69333-z}, url = {https://doi.org/10.1038/s41467-026-69333-z}, author = {Pratt, Brandon G. and Dallmann, Chris J. and Chou, Grant M. and Siwanowicz, Igor and Walling-Bell, Sarah and Cook, Andrew and Sustar, Anne and Azevedo, Anthony and Tuthill, John C.} } @article {70225, title = {Parallel neuronal ensembles control behavior across sensorimotor levels in Drosophila}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 16}, abstract = {

Nervous systems can process information in serial or in parallel, trading off efficiency for flexibility and speed. How these network architectures are implemented across sensorimotor pathways to control behavior is unclear. We investigate this tradeoff directly in Drosophila by comparing neuronal circuits underlying landing and takeoff, behaviors transforming similar visual cues to whole-body motor output. Using a whole-CNS connectome, electrophysiology, and behavioral analysis, we reconstruct the complete feedforward pathway for landing, including visual feature detectors, a dedicated ensemble of descending neurons (DNs), and a core premotor circuit in the nerve cord. Comparison to the takeoff pathway reveals that, despite encoding the same sensory feature and engaging similar muscle groups, neuronal circuits controlling the two behaviors are separated at every sensorimotor level. Extending this analysis to the complete DN population reveals a blueprint for descending motor control: DNs across the behavioral space utilized by the fly are organized as a set of parallel, loosely-overlapping ensembles that form a continuum from command-like control, with individual DNs determining behavioral output, to population coding, with multiple DNs controlling behavior synergistically. Distinct combinations of sensory feature detectors differentially recruit DN ensembles to enable flexible, context-dependent behavioral control.

}, doi = {10.64898/2025.12.13.693955}, url = {https://www.biorxiv.org/content/early/2025/12/16/2025.12.13.693955}, author = {Liessem, Sander and Asinof, Samuel K. and Nern, Aljoscha and Sumathipala, Marissa and Rogers, Edward and Erginkaya, Mert and Dallmann, Chris J. and Card, Gwyneth M and Ache, Jan M.} } @article {68716, title = {PEELing: an integrated and user-centric platform for cell-surface proteomics analysis}, journal = {Bioinformatics}, year = {2025}, month = {2025 Aug 06}, abstract = {

Summary:\ Molecular compartmentalization is vital for cellular physiology. Spatially-resolved proteomics allows biologists to survey protein composition and dynamics with subcellular resolution. Here we present PEELing, an integrated package and user-friendly web service for analyzing spatially-resolved proteomics data. PEELing assesses data quality using curated or user-defined references, performs cutoff analysis to remove contaminants, connects to databases for functional annotation, and generates data visualizations-providing a streamlined and reproducible workflow to explore spatially-resolved proteomics data.

Availability and implementation:\ PEELing and its tutorial are publicly available at https://peeling.janelia.org/ (Zenodo DOI: 10.5281/zenodo.15692517). A Python package of PEELing is available at https://github.com/JaneliaSciComp/peeling/ (Zenodo DOI: 10.5281/zenodo.15692434).

Contact:Technical support for PEELing: peeling@janelia.hhmi.org.

bioRxiv Preprint:\ https://doi.org/10.1101/2023.04.21.537871

}, doi = {10.1093/bioinformatics/btaf439}, url = {https://doi.org/10.1093/bioinformatics/btaf439}, author = {Xi Peng and Jody Clements and Zuzhi Jiang and Stephan Preibisch and Jiefu Li} } @article {70194, title = {Pericyte and Endothelial Primary Cilia and Centrioles have Disparate Organization Across the Brain Microvasculature}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 19}, abstract = {

The brain microvascular functions are strongly influenced by the local microenvironment and cellular organization. Intracellular organelles, including primary cilia and centrioles, play critical roles in sensing and transmitting environmental cues and maintaining vascular integrity. However, their distribution across the brain vasculature remains poorly understood. In this study, we utilized publicly available large-volume electron microscopy datasets encompassing the cerebral vasculature from pial arterioles through parenchymal capillaries to pial venules. We systematically analyzed the cellular organization and characterized the distribution of primary cilia and centrioles in the mouse and human brain microvasculature. We found primary cilia exclusively on human cortical endothelial cells (ECs), indicating inter-species differences between mouse and human. Primary cilia were frequently present on mural cells (MCs, smooth muscle cells or pericytes) surrounding venules and capillaries but rarely observed on arterioles in both mouse and human brains. These MC primary cilia exhibited heterogeneity in ciliogenesis, including cells with ciliary pockets, surface cilia, and a hybrid configuration we refer as a partial pocket. In the mouse brain, many MC primary cilia were closely ensheathed by astrocytic endfeet and occasionally extended between them to establish proximity to synapses, whereas all primary cilia in the human brain were confined within the basal lamina. Our analysis of cellular density revealed similar EC densities between arterioles and venules in mice, but not in human. EC centrioles were consistently positioned against the direction of blood flow relative to the nuclei, suggesting that they may serve as a structural marker for flow direction. Collectively, these findings provide a comprehensive characterization of primary cilia and centrioles, highlighting distinct interspecies differences between mouse and human brain microvasculature. The proximity to neural cells and gradient distribution of these subcellular structures suggest that they may act as antennae for sensing mechanical and chemical signals within the brain microvascular environment.

}, doi = {10.1101/2025.11.19.689283}, url = {https://www.biorxiv.org/content/early/2025/11/19/2025.11.19.689283}, author = {Grubb, Soren and Chanddha, Vanshika and Lippincott-Schwartz, Jennifer and Ott, Carolyn and Mughal, Amreen} } @article {69756, title = {Periodic ER-plasma membrane junctions support long-range Ca signal integration in dendrites.}, journal = {Cell}, volume = {188}, year = {2025}, month = {01/2025}, pages = {484-500.e22}, abstract = {

Neuronal dendrites must relay synaptic inputs over long distances, but the mechanisms by which activity-evoked intracellular signals propagate over macroscopic distances remain unclear. Here, we discovered a system of periodically arranged endoplasmic reticulum-plasma membrane (ER-PM) junctions tiling the plasma membrane of dendrites at \~{}1\ μm intervals, interlinked by a meshwork of ER tubules patterned in a ladder-like array. Populated with Junctophilin-linked plasma membrane voltage-gated Ca channels and ER Ca-release channels (ryanodine receptors), ER-PM junctions are hubs for ER-PM crosstalk, fine-tuning of Ca homeostasis, and local activation of the Ca/calmodulin-dependent protein kinase II. Local spine stimulation activates the Ca modulatory machinery, facilitating signal transmission and ryanodine-receptor-dependent Ca release at ER-PM junctions over 20\ μm away. Thus, interconnected ER-PM junctions support signal propagation and Ca release from the spine-adjacent ER. The capacity of this subcellular architecture to modify both local and distant membrane-proximal biochemistry potentially contributes to dendritic computations.

}, keywords = {Animals, Calcium, Calcium Signaling, Calcium-Calmodulin-Dependent Protein Kinase Type 2, Cell Membrane, Dendrites, Endoplasmic Reticulum, Hippocampus, Humans, Male, Mice, Rats, Ryanodine Receptor Calcium Release Channel}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.11.029}, author = {Benedetti, Lorena and Fan, Ruolin and Weigel, Aubrey V and Moore, Andrew S and Houlihan, Patrick R and Kittisopikul, Mark and Park, Grace and Petruncio, Alyson and Hubbard, Philip M and Pang, Song and Xu, C Shan and Hess, Harald F and Saalfeld, Stephan and Rangaraju, Vidhya and Clapham, David E and De Camilli, Pietro and Ryan, Timothy A and Lippincott-Schwartz, Jennifer} } @article {70164, title = {Place-cell heterogeneity underlies power-laws in hippocampal activity}, journal = {arXiv}, year = {2025}, month = {2025 Jul 30}, abstract = {

Power-law scaling in coarse-grained data suggests critical dynamics, but the true source of this scaling often remains unclear. Here, we analyze neural activity recorded during spatial navigation, reproducing power-law scaling under a phenomenological renormalization group (PRG) procedure that clusters units by activity similarity. Such scaling was previously linked to criticality. Here, we show that the iterative nature of the procedure itself leads to the emergence of power laws when applied to heterogeneous, non-interacting units obeying spatially structured activity without requiring critical interactions. Furthermore, the scaling exponents produced by heteregeneous non-interacting units match the observed exponents in recorded neural data. A simplified version of the PRG further reveals how heterogeneity smooths transitions across scales, mimicking critical behavior. The resulting exponents depend systematically on system and population size, predictions confirmed by subsampling the data.

}, doi = {10.48550/arXiv.2507.23030}, url = {https://arxiv.org/abs/2507.23030}, author = {John J. Briguglio and Jaesung Lee and Albert K. Lee and Vincent Hakim and Sandro Romani} } @article {70193, title = {Population morphology implies a common developmental blueprint for Drosophila motion detectors}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 15}, abstract = {

Quantitative analysis of neuron morphology is essential in order to develop our understanding of circuit organisation and development. The recent acquisition of whole-brain electron microscopy-based (EM) reconstructions of the Drosophila melanogaster nervous system now provide the resolution needed to examine morphology at scale. Utilising these data, together with new computational tools, we extract and analyse the dendrites of all T4 and T5 neurons within one hemisphere (n \~ 6000).T4 and T5 neurons are the first uniquely direction-selective neurons in the visual pathway, and are classified into four subtypes (a,b,c, and d). Each subtype encodes one of four cardinal motion directions (up, down, forwards, backwards). The dendrites of these neurons form in two distinct neuropils, the Medulla (T4) and the Lobula (T5), and are asymmetrically oriented in a direction inverse to the direction of motion which they encode. However, their densely overlapping and compact arbours has made rigorous morphological quantification challenging. The presence of differences beyond their characteristic orientation, both between T4 and T5, as well as within subtypes, has remained poorly understood.Our analysis reveals a high degree of structural similarity across both types and subtypes. Particularly, measures of geometry and graph topology show only minor variation, with no consistent separation between T4 and T5, or their subtypes.These results indicate that, despite forming in different neuropils, and serving distinct motion directions, T4 and T5 dendrites follow closely aligned morphological patterns. This suggests that their arborization may be governed by shared developmental constraints and mechanisms.

}, doi = {10.1101/2025.11.15.688637}, url = {https://www.biorxiv.org/content/early/2025/11/16/2025.11.15.688637}, author = {Drummond, Nikolas and Zhao, Arthur and Borst, Alexander} } @article {70119, title = {A priming circuit controls the olfactory response and memory in Drosophila}, journal = {eLife}, year = {2025}, month = {2025 Sep 23}, abstract = {

Priming is a process by which exposure to a stimulus affects the response to a subsequent stimulus in humans. In this study we found that in\ Drosophila, a prior encounter with an aversive stimulus results in enhanced preference for a following novel odor, while an appetitive stimulus leads to reduced preference for a new odor. This priming behavior of flies relies on the well-studied olfactory memory circuits including Kenyon cells (KC), dopaminergic neurons (DANs), and mushroom body output neurons (MBONs). Aversive stimulus results in increased odor responses in reward DANs that innervate the γ4 lobe of the mushroom body (MB) and decreased odor responses in a γ4γ5-innvervating repulsive MBON. We concluded that these neurons are required for the priming effects in flies. These results characterized the newly found priming behavior in flies and demonstrated the sheer influence of unconditioned stimulus on odor perception during associative learning.

}, doi = {10.7554/elife.107736.1}, url = {http://dx.doi.org/10.7554/eLife.107736.1}, author = {Yang, He and Jiang, Yang and Kunes, Samuel} } @article {70011, title = {Programmable Liposome Organization via DNA Origami Templates.}, journal = {J Am Chem Soc}, year = {2025}, month = {2025 Jul 02}, abstract = {

Liposomes are essential vehicles for membrane protein reconstitution and drug delivery, making them vital tools in both in vivo and in vitro studies. However, the lack of robust techniques for the precise arrangement of these synthetic vesicles limits their potential applications. Here, we present a modular polymerization platform based on square DNA origami to template the formation and organization of liposomes. By programming the sequence, number, position, chirality, and flexibility of sticky ends on each square, we assemble uniformly sized liposomes into diverse two-dimensional (2D) arrays, as well as finite lattices and rings. Additionally, we demonstrate stepwise assembly and targeted disassembly, enabling dynamic structural control. These complex liposome architectures represent a significant advancement in the fields of biotechnology, nanotechnology, and bottom-up biology.

}, issn = {1520-5126}, doi = {10.1021/jacs.5c05196}, url = {https://doi.org/10.1021/jacs.5c05196}, author = {Zhang, Zhao and Feng, Zhaomeng and Zhao, Xiaowei and Yu, Zhiheng and Chapman, Edwin R} } @article {70022, title = {Programmable Liposome Organization via DNA Origami Templates.}, journal = {J Am Chem Soc}, volume = {147}, year = {2025}, month = {2025 Jul 16}, pages = {24548-24554}, abstract = {

Liposomes are essential vehicles for membrane protein reconstitution and drug delivery, making them vital tools in both in vivo and in vitro studies. However, the lack of robust techniques for the precise arrangement of these synthetic vesicles limits their potential applications. Here, we present a modular polymerization platform based on square DNA origami to template the formation and organization of liposomes. By programming the sequence, number, position, chirality, and flexibility of sticky ends on each square, we assemble uniformly sized liposomes into diverse two-dimensional (2D) arrays, as well as finite lattices and rings. Additionally, we demonstrate stepwise assembly and targeted disassembly, enabling dynamic structural control. These complex liposome architectures represent a significant advancement in the fields of biotechnology, nanotechnology, and bottom-up biology.

}, keywords = {DNA, Liposomes, Nucleic Acid Conformation}, issn = {1520-5126}, doi = {10.1021/jacs.5c05196}, url = {https://doi.org/10.1021/jacs.5c05196}, author = {Zhang, Zhao and Feng, Zhaomeng and Zhao, Xiaowei and Yu, Zhiheng and Chapman, Edwin R} } @article {70082, title = {A protein tunnel helps stressed lysosomes swell.}, journal = {Science}, volume = {389}, year = {2025}, month = {2025 Aug 21}, pages = {782-783}, abstract = {

The endoplasmic reticulum donates lipids through a tunnel-like protein to help lysosomes expand.

}, keywords = {Adaptor Proteins, Signal Transducing, Animals, Endoplasmic Reticulum, Humans, Lipid Metabolism, Lysosomes}, issn = {1095-9203}, doi = {10.1126/science.aea5377}, url = {https://doi.org/10.1126/science.aea5377}, author = {Lippincott-Schwartz, Jennifer} } @article {69325, title = {Patch-walking: Coordinated multi-pipette patch clamp for efficiently finding synaptic connections}, journal = {eLife}, volume = {13}, year = {2024}, month = {2024 Nov 18}, pages = {RP97399}, abstract = {

Significant technical challenges exist when measuring synaptic connections between neurons in living brain tissue. The patch clamping technique, when used to probe for synaptic connections, is manually laborious and time-consuming. To improve its efficiency, we pursued another approach: instead of retracting all patch clamping electrodes after each recording attempt, we cleaned just one of them and reused it to obtain another recording while maintaining the others. With one new patch clamp recording attempt, many new connections can be probed. By placing one pipette in front of the others in this way, one can {\textquoteright}walk{\textquoteright} across the mouse brain slice, termed {\textquoteright}patch-walking.{\textquoteright} We performed 136 patch clamp attempts for two pipettes, achieving 71 successful whole cell recordings (52.2\%). Of these, we probed 29 pairs (i.e. 58 bidirectional probed connections) averaging 91 μm intersomatic distance, finding three connections. Patch-walking yields 80-92\% more probed connections, for experiments with 10-100 cells than the traditional synaptic connection searching method.

}, doi = {10.7554/elife.97399}, url = {https://doi.org/10.7554/elife.97399}, author = {Mighten C. Yip and Mercedes M. Gonzalez and Colby F. Lewallen and Corey R. Landry and Ilya Kolb and Bo Yang and William M. Stoy and Ming-fai Fong and Matthew JM Rowan and Edward S. Boyden and Craig R. Forest} } @article {69707, title = {Pearling Drives Mitochondrial DNA Nucleoid Distribution}, journal = {bioRxiv}, year = {2024}, month = {12/2024}, abstract = {

The regular distribution of mitochondrial DNA-containing nucleoids is essential for mitochondrial function and genome inheritance; however, the underlying mechanisms remain unknown. Our data reveal that mitochondria frequently undergo spontaneous and reversible pearling - a biophysical instability in which tubules undulate into regularly spaced beads. We discovered that pearling imposes a characteristic length scale, simultaneously mediating nucleoid disaggregation and establishing inter-nucleoid distancing with near-maximally achievable precision. Cristae invaginations play a dual role: lamellar cristae density determines pearling frequency and duration, and preserves the resulting nucleoid spacing after recovery. The distribution of mitochondrial genomes is thus fundamentally governed by the interplay between spontaneous pearling and cristae ultrastructure.

}, doi = {10.1101/2024.12.21.629917}, url = {https://www.biorxiv.org/content/early/2024/12/22/2024.12.21.629917}, author = {Landoni, Juan C. and Lycas, Matthew D. and Macuada, Josefa and Jaccard, Romeo and Obara, Christopher J. and Moore, Andrew S. and Ben Nejma, Sheda and Hoffman, David and Lippincott-Schwartz, Jennifer and Marshall, Wallace and Sturm, Gabriel and Manley, Suliana} } @article {69704, title = {Periodic ER-plasma membrane junctions support long-range Ca signal integration in dendrites.}, journal = {Cell}, year = {2024}, month = {2024 Dec 18}, abstract = {

Neuronal dendrites must relay synaptic inputs over long distances, but the mechanisms by which activity-evoked intracellular signals propagate over macroscopic distances remain unclear. Here, we discovered a system of periodically arranged endoplasmic reticulum-plasma membrane (ER-PM) junctions tiling the plasma membrane of dendrites at \~{}1\ μm intervals, interlinked by a meshwork of ER tubules patterned in a ladder-like array. Populated with Junctophilin-linked plasma membrane voltage-gated Ca channels and ER Ca-release channels (ryanodine receptors), ER-PM junctions are hubs for ER-PM crosstalk, fine-tuning of Ca homeostasis, and local activation of the Ca/calmodulin-dependent protein kinase II. Local spine stimulation activates the Ca modulatory machinery, facilitating signal transmission and ryanodine-receptor-dependent Ca release at ER-PM junctions over 20\ μm away. Thus, interconnected ER-PM junctions support signal propagation and Ca release from the spine-adjacent ER. The capacity of this subcellular architecture to modify both local and distant membrane-proximal biochemistry potentially contributes to dendritic computations.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.11.029}, author = {Benedetti, Lorena and Fan, Ruolin and Weigel, Aubrey V and Moore, Andrew S and Houlihan, Patrick R and Kittisopikul, Mark and Park, Grace and Petruncio, Alyson and Hubbard, Philip M and Pang, Song and Xu, C Shan and Hess, Harald F and Saalfeld, Stephan and Rangaraju, Vidhya and Clapham, David E and De Camilli, Pietro and Ryan, Timothy A and Lippincott-Schwartz, Jennifer} } @article {69705, title = {Permanent cilia loss during cerebellar granule cell neurogenesis involves withdrawal of cilia maintenance and centriole capping.}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Dec 24}, pages = {e2408083121}, abstract = {

Brain neurons utilize the primary cilium as a privileged compartment to detect and respond to extracellular ligands such as Sonic hedgehog (SHH). However, cilia in cerebellar granule cell (GC) neurons disassemble during differentiation through ultrastructurally unique intermediates, a process we refer to as cilia deconstruction. In addition, mature neurons do not reciliate despite having docked centrioles. Here, we identify molecular changes that accompany cilia deconstruction and centriole docking in GC neurons. We used single cell transcriptomic and immunocytological analyses to compare the transcript levels and subcellular localization of proteins between progenitor, differentiating, and mature GCs. Differentiating GCs lacked transcripts for key activators of premitotic cilia resorption, indicating that cilia disassembly in differentiating cells is distinct from premitotic cilia resorption. Instead, during differentiation, transcripts of many genes required for cilia maintenance-specifically those encoding components of intraflagellar transport, pericentrosomal material, and centriolar satellites-decreased. The abundance of several corresponding proteins in and around cilia and centrosomes also decreased. These changes coincided with downregulation of SHH signaling prior to differentiation, even in a mutant with excessive SHH activation. Finally, mother centrioles in maturing granule neurons recruited the cap complex protein, CEP97. These data suggest that a global, developmentally programmed decrease in cilium maintenance in differentiating GCs mediates cilia deconstruction, while capping of docked mother centrioles prevents cilia regrowth and dysregulated SHH signaling. Our study provides mechanistic insights expanding our understanding of permanent cilia loss in multiple tissue-specific contexts.

}, keywords = {Animals, Cell Differentiation, Centrioles, Cerebellum, Cilia, Hedgehog Proteins, Mice, Neurogenesis, Neurons, Signal Transduction}, issn = {1091-6490}, doi = {10.1073/pnas.2408083121}, author = {Constable, Sandii and Ott, Carolyn M and Lemire, Andrew L and White, Kevin and Xun, Yu and Lim, Amin and Lippincott-Schwartz, Jennifer and Mukhopadhyay, Saikat} } @article {69136, title = {Permanent deconstruction of intracellular primary cilia in differentiating granule cell neurons.}, journal = {J Cell Biol.}, volume = {223}, year = {2024}, month = {2024 Aug 13}, pages = {e202404038}, abstract = {

Primary cilia on granule cell neuron progenitors in the developing cerebellum detect sonic hedgehog to facilitate proliferation. Following differentiation, cerebellar granule cells become the most abundant neuronal cell type in the brain. While granule cell cilia are essential during early developmental stages, they become infrequent upon maturation. Here, we provide nanoscopic resolution of cilia in situ using large-scale electron microscopy volumes and immunostaining of mouse cerebella. In many granule cells, we found intracellular cilia, concealed from the external environment. Cilia were disassembled in differentiating granule cell neurons-in a process we call cilia deconstruction-distinct from premitotic cilia resorption in proliferating progenitors. In differentiating granule cells, cilia deconstruction involved unique disassembly intermediates, and, as maturation progressed, mother centriolar docking at the plasma membrane. Unlike ciliated neurons in other brain regions, our results show the deconstruction of concealed cilia in differentiating granule cells, which might prevent mitogenic hedgehog responsiveness. Ciliary deconstruction could be paradigmatic of cilia removal during differentiation in other tissues.

}, doi = {10.1016/j.cub.2024.07.036}, url = {https://doi.org/10.1016/j.cub.2024.07.036 }, author = {Ott, Carolyn M and Constable, Sandii and Nguyen, Tri M and White, Kevin and Lee, Wei-Chung Allen and Lippincott-Schwartz, Jennifer and Mukhopadhyay, Saikat} } @article {69139, title = {Petascale pipeline for precise alignment of images from serial section electron microscopy.}, journal = {Nature Communications}, volume = {15}, year = {2024}, month = {2024 Jan 04}, pages = {289}, abstract = {

The reconstruction of neural circuits from serial section electron microscopy (ssEM) images is being accelerated by automatic image segmentation methods. Segmentation accuracy is often limited by the preceding step of aligning 2D section images to create a 3D image stack. Precise and robust alignment in the presence of image artifacts is challenging, especially as datasets are attaining the petascale. We present a computational pipeline for aligning ssEM images with several key elements. Self-supervised convolutional nets are trained via metric learning to encode and align image pairs, and they are used to initialize iterative fine-tuning of alignment. A procedure called vector voting increases robustness to image artifacts or missing image data. For speedup the series is divided into blocks that are distributed to computational workers for alignment. The blocks are aligned to each other by composing transformations with decay, which achieves a global alignment without resorting to a time-consuming global optimization. We apply our pipeline to a whole fly brain dataset, and show improved accuracy relative to prior state of the art. We also demonstrate that our pipeline scales to a cubic millimeter of mouse visual cortex. Our pipeline is publicly available through two open source Python packages.

}, keywords = {Animals, Brain, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Mice, Microscopy, Electron}, issn = {2041-1723}, doi = {10.1038/s41467-023-44354-0}, author = {Popovych, Sergiy and Macrina, Thomas and Kemnitz, Nico and Castro, Manuel and Nehoran, Barak and Jia, Zhen and Bae, J Alexander and Mitchell, Eric and Mu, Shang and Trautman, Eric T and Saalfeld, Stephan and Li, Kai and Seung, H Sebastian} } @article {69128, title = {Phase diversity-based wavefront sensing for fluorescence microscopy.}, journal = {Optica}, volume = {11}, year = {2024}, month = {2024 Jun 10}, pages = {806-820}, abstract = {

Fluorescence microscopy is an invaluable tool in biology, yet its performance is compromised when the wavefront of light is distorted due to optical imperfections or the refractile nature of the sample. Such optical aberrations can dramatically lower the information content of images by degrading image contrast, resolution, and signal. Adaptive optics (AO) methods can sense and subsequently cancel the aberrated wavefront, but are too complex, inefficient, slow, or expensive for routine adoption by most labs. Here we introduce a rapid, sensitive, and robust wavefront sensing scheme based on phase diversity, a method successfully deployed in astronomy but underused in microscopy. Our method enables accurate wavefront sensing to less than λ/35 root mean square (RMS) error with few measurements, and AO with no additional hardware besides a corrective element. After validating the method with simulations, we demonstrate calibration of a deformable mirror \> 100-fold faster than comparable methods (corresponding to wavefront sensing on the ~100 ms scale), and sensing and subsequent correction of severe aberrations (RMS wavefront distortion exceeding λ/2), restoring diffraction-limited imaging on extended biological samples.

}, doi = {10.1364/OPTICA.518559}, url = {https://doi.org/10.1364/OPTICA.518559}, author = {Johnson, Courtney and Guo, Min and Schneider, Magdalena C and Su, Yijun and Khuon, Satya and Reiser, Nikolaj and Wu, Yicong and Riviere, Patrick La and Shroff, Hari} } @article {69472, title = {The physical and cellular mechanism of structural color change in zebrafish.}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Jun 04}, pages = {e2308531121}, abstract = {

Many animals exhibit remarkable colors that are produced by the constructive interference of light reflected from arrays of intracellular guanine crystals. These animals can fine-tune their crystal-based structural colors to communicate with each other, regulate body temperature, and create camouflage. While it is known that these changes in color are caused by changes in the angle of the crystal arrays relative to incident light, the cellular machinery that drives color change is not understood. Here, using a combination of 3D focused ion beam scanning electron microscopy (FIB-SEM), micro-focused X-ray diffraction, superresolution fluorescence light microscopy, and pharmacological perturbations, we characterized the dynamics and 3D cellular reorganization of crystal arrays within zebrafish iridophores during norepinephrine (NE)-induced color change. We found that color change results from a coordinated 20{\textdegree} tilting of the intracellular crystals, which alters both crystal packing and the angle at which impinging light hits the crystals. Importantly, addition of the dynein inhibitor dynapyrazole-a completely blocked this NE-induced red shift by hindering crystal dynamics upon NE addition. FIB-SEM and microtubule organizing center (MTOC) mapping showed that microtubules arise from two MTOCs located near the poles of the iridophore and run parallel to, and in between, individual crystals. This suggests that dynein drives crystal angle change in response to NE by binding to the limiting membrane surrounding individual crystals and walking toward microtubule minus ends. Finally, we found that intracellular cAMP regulates the color change process. Together, our results provide mechanistic insight into the cellular machinery that drives structural color change.

}, keywords = {Animals, Color, Microscopy, Electron, Scanning, Norepinephrine, Pigmentation, Zebrafish, Zebrafish Proteins}, issn = {1091-6490}, doi = {10.1073/pnas.2308531121}, author = {Gur, Dvir and Moore, Andrew S and Deis, Rachael and Song, Pang and Wu, Xufeng and Pinkas, Iddo and Deo, Claire and Iyer, Nirmala and Hess, Harald F and Hammer, John A and Lippincott-Schwartz, Jennifer} } @article {69579, title = {Plasticity-induced actin polymerization in the dendritic shaft regulates intracellular AMPA receptor trafficking.}, journal = {Elife}, volume = {13}, year = {2024}, month = {2024 Aug 15}, abstract = {

AMPA-type receptors (AMPARs) are rapidly inserted into synapses undergoing plasticity to increase synaptic transmission, but it is not fully understood if and how AMPAR-containing vesicles are selectively trafficked to these synapses. Here, we developed a strategy to label AMPAR GluA1 subunits expressed from their endogenous loci in cultured rat hippocampal neurons and characterized the motion of GluA1-containing vesicles using single-particle tracking and mathematical modeling. We find that GluA1-containing vesicles are confined and concentrated near sites of stimulation-induced structural plasticity. We show that confinement is mediated by actin polymerization, which hinders the active transport of GluA1-containing vesicles along the length of the dendritic shaft by modulating the rheological properties of the cytoplasm. Actin polymerization also facilitates myosin-mediated transport of GluA1-containing vesicles to exocytic sites. We conclude that neurons utilize F-actin to increase vesicular GluA1 reservoirs and promote exocytosis proximal to the sites of synaptic activity.

}, keywords = {Actins, Animals, Cells, Cultured, Dendrites, Exocytosis, Hippocampus, Neuronal Plasticity, Neurons, Polymerization, Protein Transport, Rats, Receptors, AMPA}, issn = {2050-084X}, doi = {10.7554/eLife.80622}, url = {https://doi.org/10.7554/eLife.80622}, author = {Wong, Victor C and Houlihan, Patrick R and Liu, Hui and Walpita, Deepika and DeSantis, Michael C and Liu, Zhe and O{\textquoteright}Shea, Erin K} } @article {69149, title = {Prediction of Cellular Identities from Trajectory and Cell Fate Information}, journal = {arXiv}, year = {2024}, month = {2024 Jan 11}, abstract = {

Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative approach to cell identification during early C. elegans embryogenesis using machine learning. We employed random forest, MLP, and LSTM models, and tested cell classification accuracy on 3D time-lapse confocal datasets spanning the first 4 hours of embryogenesis. By leveraging a small number of spatial-temporal features of individual cells, including cell trajectory and cell fate information, our models achieve an accuracy of over 90\%, even with limited data. We also determine the most important feature contributions and can interpret these features in the context of biological knowledge. Our research demonstrates the success of predicting cell identities in 4D imaging sequences directly from simple spatio-temporal features.

}, doi = {10.48550/arXiv.2401.06182}, url = {https://doi.org/10.48550/arXiv.2401.06182}, author = {Baiyang Dai and Jiamin Yang and Hari Shroff and Patrick La Riviere} } @article {68631, title = {Phase separation of Hippo signalling complexes.}, journal = {EMBO Journal}, volume = {42}, year = {2023}, month = {2023 Feb 20}, pages = {e112863}, abstract = {

The Hippo pathway was originally discovered to control tissue growth in Drosophila and includes the Hippo kinase (Hpo; MST1/2 in mammals), scaffold protein Salvador (Sav; SAV1 in mammals) and the Warts kinase (Wts; LATS1/2 in mammals). The Hpo kinase is activated by binding to Crumbs-Expanded (Crb-Ex) and/or Merlin-Kibra (Mer-Kib) proteins at the apical domain of epithelial cells. Here we show that activation of Hpo also involves the formation of supramolecular complexes with properties of a biomolecular condensate, including concentration dependence and\ sensitivity to starvation, macromolecular crowding, or 1,6-hexanediol treatment. Overexpressing Ex or Kib induces formation of micron-scale Hpo condensates in the cytoplasm, rather than at the apical membrane. Several Hippo pathway components contain unstructured low-complexity domains and purified Hpo-Sav complexes undergo phase separation in\ vitro. Formation of Hpo condensates is conserved in human cells. We propose that apical Hpo kinase activation occurs in phase separated "signalosomes" induced by clustering of upstream pathway components.

}, issn = {1460-2075}, doi = {10.15252/embj.2022112863}, author = {Bonello, Teresa T and Cai, Danfeng and Fletcher, Georgina C and Wiengartner, Kyler and Pengilly, Victoria and Lange, Kimberly S and Liu, Zhe and Lippincott-Schwartz, Jennifer and Kavran, Jennifer M and Thompson, Barry J} } @article {68917, title = {Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment}, journal = {bioRxiv}, year = {2023}, month = {2023 Jul 15}, abstract = {

Targeting deep brain structures during electrophysiology and injections requires intensive training and expertise. Even with experience, researchers often can{\textquoteright}t be certain that a probe is placed precisely in a target location and this complexity scales with the number of simultaneous probes used in an experiment. Here, we present Pinpoint, open-source software that allows for interactive exploration of stereotaxic insertion plans. Once an insertion plan is created, Pinpoint allows users to save these online and share them with collaborators. 3D modeling tools allow users to explore their insertions alongside rig and implant hardware and ensure plans are physically possible. Probes in Pinpoint can be linked to electronic micro-manipulators allowing real-time visualization of current brain region targets alongside neural data. In addition, Pinpoint can control manipulators to automate and parallelize the insertion process. Compared to previously available software, Pinpoint{\textquoteright}s easy access through web browsers, extensive features, and real-time experiment integration enable more efficient and reproducible recordings.

}, doi = {10.1101/2023.07.14.548952}, url = {https://doi.org/10.1101/2023.07.14.548952}, author = {Daniel Birman and Kenneth J. Yang and Steven J. West and Bill Karsh and Yoni Browning and the International Brain Laboratory and Joshua H. Siegle and Nicholas A. Steinmetz} } @article {68770, title = {The power of peer networking for improving STEM faculty job applications: a successful pilot programme.}, journal = {Proceedings. Biological Sciences}, volume = {290}, year = {2023}, month = {2023 Apr 26}, pages = {20230124}, abstract = {

To attain a faculty position, postdoctoral fellows submit job applications that require considerable time and effort to produce. Although mentors and colleagues review these applications, postdocs rarely receive iterative feedback from reviewers with the breadth of expertise typically found on an academic search committee. To address this gap, we describe an international peer-reviewing programme for postdocs across disciplines to receive reciprocal, iterative feedback on faculty applications. A participant survey revealed that nearly all participants would recommend the programme to others. Furthermore, our programme was more likely to attract postdocs who struggled to find mentoring, possibly because of their identity as a woman or member of an underrepresented population in STEM or because they changed fields. Between 2018 and 2021, our programme provided nearly 150 early career academics with a diverse and supportive community of peer mentors during the difficult search for a faculty position and continues to do so today. As the transition from postdoc to faculty represents the largest {\textquoteright}leak{\textquoteright} in the academic pipeline, implementation of similar programmes by universities or professional societies would provide psycho-social support necessary to prevent attrition of individuals from underrepresented populations as well as increase the chances of success for early career academics in their search for independence.

}, keywords = {Faculty, Female, Humans, Mentoring, Mentors, Peer Group, Pilot Projects}, issn = {1471-2954}, doi = {10.1098/rspb.2023.0124}, author = {Guardia, Carlos M and Kane, Erin and Tebo, Alison G and Sanders, Anna A W M and Kaya, Devrim and Grogan, Kathleen E} } @article {68708, title = {Predictive and robust gene selection for spatial transcriptomics.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Apr 12}, pages = {2091}, abstract = {

A prominent trend in single-cell transcriptomics is providing spatial context alongside a characterization of each cell{\textquoteright}s molecular state. This typically requires targeting an a priori selection of genes, often covering less than 1\% of the genome, and a key question is how to optimally determine the small gene panel. We address this challenge by introducing a flexible deep learning framework, PERSIST, to identify informative gene targets for spatial transcriptomics studies by leveraging reference scRNA-seq data. Using datasets spanning different brain regions, species, and scRNA-seq technologies, we show that PERSIST reliably identifies panels that provide more accurate prediction of the genome-wide expression profile, thereby capturing more information with fewer genes. PERSIST can be adapted to specific biological goals, and we demonstrate that PERSIST{\textquoteright}s binarization of gene expression levels enables models trained on scRNA-seq data to generalize with to spatial transcriptomics data, despite the complex shift between these technologies.

}, keywords = {Gene Expression Profiling, Sequence Analysis, RNA, Single-Cell Analysis, Transcriptome}, issn = {2041-1723}, doi = {10.1038/s41467-023-37392-1}, author = {Covert, Ian and Gala, Rohan and Wang, Tim and Svoboda, Karel and S{\"u}mb{\"u}l, Uygar and Lee, Su-In} } @article {69075, title = {Preserved neural dynamics across animals performing similar behaviour.}, journal = {Nature}, year = {2023}, month = {2023 Nov 08}, abstract = {

Animals of the same species exhibit similar behaviours that are advantageously adapted to their body and environment. These behaviours are shaped at the species level by selection pressures over evolutionary timescales. Yet, it remains unclear how these common behavioural adaptations emerge from the idiosyncratic neural circuitry of each individual. The overall organization of neural circuits is preserved across individuals because of their common evolutionarily specified developmental programme. Such organization at the circuit level may constrain neural activity, leading to low-dimensional latent dynamics across the neural population. Accordingly, here we suggested that the shared circuit-level constraints within a species would lead to suitably preserved latent dynamics across individuals. We analysed recordings of neural populations from monkey and mouse motor cortex to demonstrate that neural dynamics in individuals from the same species are surprisingly preserved when they perform similar behaviour. Neural population dynamics were also preserved when animals consciously planned future movements without overt behaviour and enabled the decoding of planned and ongoing movement across different individuals. Furthermore, we found that preserved neural dynamics extend beyond cortical regions to the dorsal striatum, an evolutionarily older structure. Finally, we used neural network models to demonstrate that behavioural similarity is necessary but not sufficient for this preservation. We posit that these emergent dynamics result from evolutionary constraints on brain development and thus reflect fundamental properties of the neural basis of behaviour.

}, issn = {1476-4687}, doi = {10.1038/s41586-023-06714-0}, author = {Safaie, Mostafa and Chang, Joanna C and Park, Junchol and Miller, Lee E and Dudman, Joshua T and Perich, Matthew G and Gallego, Juan A} } @article {68042, title = {Partial resistance to citalopram in a Wistar-Kyoto rat model of depression: An evaluation using resting-state functional MRI and graph analysis.}, journal = {Journal of Psychiatric Research}, volume = {151}, year = {2022}, month = {2022 Jul 01}, pages = {242-251}, abstract = {

Wistar-Kyoto (WKY) rats as an endogenous depression model partially lack a response to classic selective serotonin reuptake inhibitors (SSRIs). Thus, this strain has the potential to be established as a model of treatment-resistant depression (TRD). However, the SSRI resistance in WKY rats is still not fully understood. In this study, WKY and control rats were subjected to a series of tests, namely, a forced swim test (FST), a sucrose preference test (SPT), and an open field test (OFT), and were scanned in a 7.0-T MRI scanner before and after three-week citalopram or saline administration. Behavioral results demonstrated that WKY rats had increased immobility in the FST and decreased sucrose preference in the SPT and central time spent in the OFT. However, citalopram did not improve immobility in the FST. The amplitude of low-frequency fluctuation (ALFF) analysis showed regional changes in the striatum and hippocampus of WKY rats. However, citalopram partially reversed the ALFF value in the dorsal part of the two regions. Functional connectivity (FC) analysis showed that FC strengths were decreased in WKY rats compared with controls. Nevertheless, citalopram partially increased FC strengths in WKY rats. Based on FC, global graph analysis demonstrated decreased network efficiency in WKY\ +\ saline group compared with control\ +\ saline group, but citalopram showed weak network efficiency improvement. In conclusion, resting-state fMRI results implied widely affected brain function at both regional and global levels in WKY rats. Citalopram had only partial effects on these functional changes, indicating a potential treatment resistance mechanism.

}, issn = {1879-1379}, doi = {10.1016/j.jpsychires.2022.04.010}, author = {Li, Qi and Zhao, Wentao and Liu, Sha and Zhao, Yu and Pan, Weixing and Wang, Xiao and Liu, Zhifen and Xu, Yong} } @article {68102, title = {Perceptual decisions exhibit hallmarks of dynamic Bayesian inference}, journal = {bioRxiv}, year = {2022}, month = {2022 May 24}, abstract = {

To interpret the sensory environment, the brain combines ambiguous sensory measurements with context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages the statistical structure of the task to maximize decision accuracy and show that its decisions are biased by task context. The magnitude of this decision bias is not a fixed property of the sensory measurement but depends on the observer{\textquoteright}s belief about the current context. The model therefore predicts that decision bias will grow with the reliability of the context cue, the stability of the environment, and with the number of trials since the last context switch. Analysis of human choice data validates all three predictions, providing evidence that the brain continuously updates probabilistic representations of the environment to best interpret an uncertain, ever-changing world.

}, doi = {10.1101/2022.05.23.493109}, url = {https://doi.org/10.1101/2022.05.23.493109}, author = {Julie A. Charlton and Wiktor F. M{\l}ynarski and Yoon H. Bai and Ann M. Hermundstad and Robbe L. T. Goris} } @article {67994, title = {Petascale pipeline for precise alignment of images from serial section electron microscopy.}, journal = {bioRxiv}, year = {2022}, month = {2022 Mar 27}, abstract = {

The reconstruction of neural circuits from serial section electron microscopy (ssEM) images is being accelerated by automatic image segmentation methods. Segmentation accuracy is often limited by the preceding step of aligning 2D section images to create a 3D image stack. Precise and robust alignment in the presence of image artifacts is challenging, especially as datasets are attaining the petascale. We present a computational pipeline for aligning ssEM images with several key elements. Self-supervised convolutional nets are trained via metric learning to encode and align image pairs, and they are used to initialize iterative fine-tuning of alignment. A procedure called vector voting increases robustness to image artifacts or missing image data. For speedup the series is divided into blocks that are distributed to computational workers for alignment. The blocks are aligned to each other by composing transformations with decay, which achieves a global alignment without resorting to a time-consuming global optimization. We apply our pipeline to a whole fly brain dataset, and show improved accuracy relative to prior state of the art. We also demonstrate that our pipeline scales to a cubic millimeter of mouse visual cortex. Our pipeline is publicly available through two open source Python packages.

}, doi = {10.1101/2022.03.25.485816}, url = {https://doi.org/10.1101/2022.03.25.485816}, author = {Sergiy Popovych and Thomas Macrina and Nico Kemnitz and Manuel Castro and Barak Nehoran and Zhen Jia and J. Alexander Bae and Eric Mitchell and Shang Mu and Eric T. Trautman and Stephan Saalfeld and Kai Li and Sebastian Seung} } @article {68116, title = {Plasticity-induced actin polymerization in the dendritic shaft regulates intracellular AMPA receptor trafficking.}, journal = {bioRxiv}, year = {2022}, month = {2022 May 29}, abstract = {

AMPA-type receptors (AMPARs) are rapidly inserted into synapses undergoing long-term potentiation (LTP) to increase synaptic transmission, but how AMPAR-containing vesicles are selectively trafficked to these synapses during LTP is not known. Here we developed a strategy to label AMPAR GluA1 subunits expressed from the endogenous loci of rat hippocampal neurons such that the motion of GluA1-containing vesicles in time-lapse sequences can be characterized using single-particle tracking and mathematical modeling. We find that GluA1-containing vesicles are confined and concentrated near sites of stimulation-induced plasticity. We show that confinement is mediated by actin polymerization, which hinders the active transport of GluA1-containing vesicles along the length of the dendritic shaft by modulating the rheological properties of the cytoplasm. Actin polymerization also facilitates myosin-mediated transport of GluA1-containing vesicles to exocytic sites. We conclude that neurons utilize F-actin to increase vesicular GluA1 reservoirs and promote exocytosis proximal to the sites of neuronal activity.

}, doi = {10.1101/2022.05.29.493906}, url = {https://doi.org/10.1101/2022.05.29.493906}, author = {V. C. Wong and P.R. Houlihan and H. Liu and D. Walpita and M.C. DeSantis and Z. Liu and E. K. O{\textquoteright}Shea} } @article {67892, title = {A population of descending neurons that regulates the flight motor of Drosophila.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 Mar 14}, pages = {1189-1196}, abstract = {

Similar to many insect species, Drosophila melanogaster is capable of maintaining a stable flight trajectory for periods lasting up to several hours. Because aerodynamic torque is roughly proportional to the fifth power of wing length, even small asymmetries in wing size require the maintenance of subtle bilateral differences in flapping motion to maintain a stable path. Flies can even fly straight after losing half of a wing, a feat they accomplish via very large, sustained kinematic changes to both the damaged and intact wings. Thus, the neural network responsible for stable flight must be capable of sustaining fine-scaled control over wing motion across a large dynamic range. In this study, we describe an unusual type of descending neuron (DNg02) that projects directly from visual output regions of the brain to the dorsal flight neuropil of the ventral nerve cord. Unlike many descending neurons, which exist as single bilateral pairs with unique morphology, there is a population of at least 15 DNg02 cell pairs with nearly identical shape. By optogenetically activating different numbers of DNg02 cells, we demonstrate that these neurons regulate wingbeat amplitude over a wide dynamic range via a population code. Using two-photon functional imaging, we show that DNg02 cells are responsive to visual motion during flight in a manner that would make them well suited to continuously regulate bilateral changes in wing kinematics. Collectively, we have identified a critical set of descending neurons that provides the sensitivity and dynamic range required for flight control.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.01.008}, author = {Namiki, Shigehiro and Ros, Ivo G and Morrow, Carmen and Rowell, William J and Card, Gwyneth M and Korff, Wyatt and Dickinson, Michael H} } @article {68983, title = {Post-gastrulation synthetic embryos generated ex utero from mouse naive ESCs}, journal = {Cell}, volume = {185}, year = {2022}, month = {09/2022}, pages = {3290-3306.e25}, abstract = {

Summary In\ vitro cultured stem cells with distinct developmental capacities can contribute to embryonic or extraembryonic tissues after microinjection into pre-implantation mammalian embryos. However, whether cultured stem cells can independently give rise to entire gastrulating embryo-like structures with embryonic and extraembryonic compartments remains unknown. Here, we adapt a recently established platform for prolonged ex utero growth of natural embryos to generate mouse post-gastrulation synthetic whole embryo models (sEmbryos), with both embryonic and extraembryonic compartments, starting solely from naive ESCs. This was achieved by co-aggregating non-transduced ESCs, with naive ESCs transiently expressing Cdx2 or Gata4 to promote their priming toward trophectoderm and primitive endoderm lineages, respectively. sEmbryos adequately accomplish gastrulation, advance through key developmental milestones, and develop organ progenitors within complex extraembryonic compartments similar to E8.5 stage mouse embryos. Our findings highlight the plastic potential of naive pluripotent cells to self-organize and functionally reconstitute and model the entire mammalian embryo beyond gastrulation.

}, keywords = {embryogenesis, embryoids, ESCs, ex utero, extra-embryonic Tissues, iPSCs, naive pluripotency, PGCs, synthetic embryos}, issn = {0092-8674}, doi = {https://doi.org/10.1016/j.cell.2022.07.028}, url = {https://www.sciencedirect.com/science/article/pii/S0092867422009813}, author = {Shadi Tarazi and Alejandro Aguilera-Castrejon and Carine Joubran and Nadir Ghanem and Shahd Ashouokhi and Francesco Roncato and Emilie Wildschutz and Montaser Haddad and Bernardo Oldak and Elidet Gomez-Cesar and Nir Livnat and Sergey Viukov and Dmitry Lokshtanov and Segev Naveh-Tassa and Max Rose and Suhair Hanna and Calanit Raanan and Ori Brenner and Merav Kedmi and Hadas Keren-Shaul and Tsvee Lapidot and Itay Maza and Noa Novershtern and Jacob H. Hanna} } @article {68409, title = {Practical considerations for quantitative light sheet fluorescence microscopy.}, journal = {Nature Methods}, volume = {19}, year = {2022}, month = {2022 Dec 01}, pages = {1538-49}, abstract = {

Fluorescence microscopy has evolved from a purely observational tool to a platform for quantitative, hypothesis-driven research. As such, the demand for faster and less phototoxic imaging modalities has spurred a rapid growth in light sheet fluorescence microscopy (LSFM). By restricting the excitation to a thin plane, LSFM reduces the overall light dose to a specimen while simultaneously improving image contrast. However, the defining characteristics of light sheet microscopes subsequently warrant unique considerations in their use for quantitative experiments. In this Perspective, we outline many of the pitfalls in LSFM that can compromise analysis and confound interpretation. Moreover, we offer guidance in addressing these caveats when possible. In doing so, we hope to provide a useful resource for life scientists seeking to adopt LSFM to quantitatively address complex biological hypotheses.

}, issn = {1548-7105}, doi = {10.1038/s41592-022-01632-x}, author = {Hobson, Chad M and Guo, Min and Vishwasrao, Harshad D and Wu, Yicong and Shroff, Hari and Chew, Teng-Leong} } @article {68370, title = {A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGF-β2 signaling.}, journal = {Cell Reports}, volume = {40}, year = {2022}, month = {2022 Sep 20}, pages = {111358}, abstract = {

Many breast cancer (BC) patients suffer from complications of metastatic disease. To form metastases, cancer cells must become migratory and coordinate both invasive and proliferative programs at distant organs. Here, we identify srGAP1 as a regulator of a proliferative-to-invasive switch in BC cells. High-resolution light-sheet microscopy demonstrates that BC cells can form actin-rich protrusions during extravasation. srGAP1 cells display a motile and invasive phenotype that facilitates their extravasation from blood vessels, as shown in zebrafish and mouse models, while attenuating tumor growth. Interestingly, a population of srGAP1 cells remain as solitary disseminated tumor cells in the lungs of mice bearing BC tumors. Overall, srGAP1 cells have increased Smad2 activation and TGF-β2 secretion, resulting in increased invasion and p27 levels to sustain quiescence. These findings identify srGAP1 as a mediator of a proliferative to invasive phenotypic switch in BC cells in\ vivo through a TGF-β2-mediated signaling axis.

}, keywords = {Actins, Animals, Cell Line, Tumor, Down-Regulation, Mice, Transforming Growth Factor beta2, Zebrafish}, issn = {2211-1247}, doi = {10.1016/j.celrep.2022.111358}, author = {Mondal, Chandrani and Gacha-Garay, Majo J and Larkin, Kathryn A and Adikes, Rebecca C and Di Martino, Julie S and Chien, Chen-Chi and Fraser, Madison and Eni-Aganga, Ireti and Agullo-Pascual, Esperanza and Cialowicz, Katarzyna and Ozbek, Umut and Naba, Alexandra and Gaitas, Angelo and Fu, Tian-Ming and Upadhyayula, Srigokul and Betzig, Eric and Matus, David Q and Martin, Benjamin L and Bravo-Cordero, Jose Javier} } @article {68043, title = {The PV2 cluster of parvalbumin neurons in the murine periaqueductal gray: connections and gene expression.}, journal = {Brain Structure and Function}, volume = {227}, year = {2022}, month = {2022 Jul 01}, pages = {2049-72}, abstract = {

The PV2 (Celio 1990), a cluster of parvalbumin-positive neurons located in the ventromedial region of the distal periaqueductal gray (PAG) has not been previously described as its own entity, leading us to study its extent, connections, and gene expression. It is an oval, bilateral, elongated cluster composed of approximately 475 parvalbumin-expressing neurons in a single mouse hemisphere. In its anterior portion it impinges upon the paratrochlear nucleus (Par4) and in its distal portion it is harbored in the posterodorsal raphe nucleus (PDR). It is known to receive inputs from the orbitofrontal cortex and from the parvafox nucleus in the ventrolateral hypothalamus. Using anterograde tracing methods in parvalbumin-Cre mice, the main projections of the PV2 cluster innervate the supraoculomotor periaqueductal gray (Su3) of the PAG, the parvafox nucleus of the lateral hypothalamus, the gemini nuclei of the posterior hypothalamus, the septal regions, and the diagonal band in the forebrain, as well as various nuclei within the reticular formation in the midbrain and brainstem. Within the brainstem, projections were discrete, but involved areas implicated in autonomic control. The PV2 cluster expressed various peptides and receptors, including the receptor for Adcyap1, a peptide secreted by one of its main afferences, namely, the parvafox nucleus. The expression of GAD1 and GAD2 in the region of the PV2, the presence of Vgat-1 in a subpopulation of PV2-neurons as well as the coexistence of GAD67 immunoreactivity with parvalbumin in terminal endings indicates the inhibitory nature of a subpopulation of PV2-neurons. The PV2 cluster may be part of a feedback controlling the activity of the hypothalamic parvafox and the Su3 nuclei in the periaqueductal gray.

}, issn = {1863-2661}, doi = {10.1007/s00429-022-02491-0}, author = {Leemann, Siri and Babalian, Alexandre and Girard, Franck and Davis, Fred and Celio, Marco R} } @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 {67241, title = {A perspective on Microscopy Metadata: data provenance and quality control}, journal = {arXiv}, year = {2021}, month = {2021 Apr 26}, abstract = {

The application of microscopy in biomedical research has come a long way since Antonie van Leeuwenhoek discovered unicellular organisms. Countless innovations have positioned light microscopy as a cornerstone of modern biology and a method of choice for connecting omics datasets to their biological and clinical correlates. Still, regardless of how convincing published imaging data looks, it does not always convey meaningful information about the conditions in which it was acquired, processed, and analyzed. Adequate record-keeping, reporting, and quality control are therefore essential to ensure experimental rigor and data fidelity, allow experiments to be reproducibly repeated, and promote the proper evaluation, interpretation, comparison, and re-use. To this end, microscopy images should be accompanied by complete descriptions detailing experimental procedures, biological samples, microscope hardware specifications, image acquisition parameters, and image analysis procedures, as well as metrics accounting for instrument performance and calibration. However, universal, community-accepted Microscopy Metadata standards and reporting specifications that would result in Findable Accessible Interoperable and Reproducible (FAIR) microscopy data have not yet been established. To understand this shortcoming and to propose a way forward, here we provide an overview of the nature of microscopy metadata and its importance for fostering data quality, reproducibility, scientific rigor, and sharing value in light microscopy. The proposal for tiered Microscopy Metadata Specifications that extend the OME Data Model put forth by the 4D Nucleome Initiative and by Bioimaging North America [1-3] as well as a suite of three complementary and interoperable tools are being developed to facilitate the process of image data documentation and are presented in related manuscripts [4-6].

}, url = {https://arxiv.org/abs/1910.11370}, author = {Maximiliaan Huisman and Mathias Hammer and Alex Rigano and Ulrike Boehm and James J. Chambers and Nathalie Gaudreault and Alison J. North and Jaime A. Pimentel and Damir Sudar and Peter Bajcsy and Claire M. Brown and Alexander D. Corbett and Orestis Faklaris and Judith Lacoste and Alex Laude and Glyn Nelson and Roland Nitschke and David Grunwald and Caterina Strambio-De-Castillia} } @article {67702, title = {Pervasive fold switching in a ubiquitous protein superfamily.}, journal = {bioRxiv}, year = {2021}, month = {2021 Jun 11}, abstract = {

Fold-switching proteins challenge the one-sequence-one-structure paradigm by adopting multiple stable folds. Nevertheless, it is uncertain whether fold switchers are naturally pervasive or rare exceptions to the well-established rule. To address this question, we developed a predictive method and applied it to the NusG superfamily of \>15,000 transcription factors. We predicted that a substantial population (25\%) of the proteins in this family switch folds. Circular dichroism and nuclear magnetic resonance spectroscopies of 10 sequence-diverse variants confirmed our predictions. Thus, we leveraged family-wide predictions to determine both conserved contacts and taxonomic distributions of fold-switching proteins. Our results indicate that fold switching is pervasive in the NusG superfamily and that the single-fold paradigm significantly biases structure-prediction strategies.

}, doi = {10.1101/2021.06.10.447921}, author = {Lauren L. Porter and Allen K. Kim and Loren L. Looger and Anaya Majumdar and Mary Starich} } @article {68751, title = {Polo-like kinase 1 independently controls microtubule-nucleating capacity and size of the centrosome}, journal = {Journal of Cell Biology}, volume = {220}, year = {2021}, month = {01/2021}, abstract = {

Centrosomes are composed of a centriolar core surrounded by a pericentriolar material (PCM) matrix that docks microtubule-nucleating γ-tubulin complexes. During mitotic entry, the PCM matrix increases in size and nucleating capacity in a process called centrosome maturation. Polo-like kinase 1 (PLK1) is recruited to centrosomes and phosphorylates PCM matrix proteins to drive their self-assembly, which leads to PCM expansion. Here, we show that in addition to controlling PCM expansion, PLK1 independently controls the generation of binding sites for γ-tubulin complexes on the PCM matrix. Selectively preventing the generation of PLK1-dependent γ-tubulin docking sites led to spindle defects and impaired chromosome segregation without affecting PCM expansion, highlighting the importance of phospho-regulated centrosomal γ-tubulin docking sites in spindle assembly. Inhibiting both γ-tubulin docking and PCM expansion by mutating substrate target sites recapitulated the effects of loss of centrosomal PLK1 on the ability of centrosomes to catalyze spindle assembly.

}, issn = {0021-9525}, doi = {10.1083/jcb.202009083}, url = {https://doi.org/10.1083/jcb.202009083}, author = {Ohta, Midori and Zhao, Zhiling and Wu, Di and Wang, Shaohe and Harrison, Jennifer L. and G{\'o}mez-Cavazos, J. Sebasti{\'a}n and Desai, Arshad and Oegema, Karen F.} } @article {67825, title = {The power of peer networking for improving STEM faculty job applications: a successful pilot program}, journal = {bioRxiv}, year = {2021}, month = {10/2021}, abstract = {

In order to successfully obtain a faculty position, postdoctoral fellows or {\textquoteleft}postdocs{\textquoteright}, must submit an application which requires considerable time and effort to produce. These job applications are often reviewed by mentors and colleagues, but rarely are postdocs offered the opportunity to solicit feedback multiple times from reviewers with the same breadth of expertise often found on an academic search committee. To address this gap, this manuscript describes an international peer reviewing program for small groups of postdocs with a broad range of expertise to reciprocally and iteratively provide feedback to each other on their application materials. Over 145 postdocs have participated, often multiple times, over three years. A survey of participants in this program revealed that nearly all participants would recommend participation in such a program to other faculty applicants. Furthermore, this program was more likely to attract participants who struggled to find mentoring and support elsewhere, either because they changed fields or because of their identity as a woman or member of an underrepresented population in STEM. Participation in programs like this one could provide early career academics like postdocs with a diverse and supportive community of peer mentors during the difficult search for a faculty position. Such psychosocial support and encouragement has been shown to prevent attrition of individuals from these populations and programs like this one target the largest {\textquoteleft}leak{\textquoteright} in the pipeline, that of postdoc to faculty. Implementation of similar peer reviewing programs by universities or professional scientific societies could provide a valuable mechanism of support and increased chances of success for early-career academics in their search for independence.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.10.16.464662}, url = {https://www.biorxiv.org/content/early/2021/10/18/2021.10.16.464662}, author = {Guardia, Carlos M. and Kane, Erin and Tebo, Alison G. and Sanders, Anna A.W.M. and Kaya, Devrim and Grogan, Kathleen E.} } @article {66000, title = {Precision Mapping of COVID-19 Vulnerable Locales by Epidemiological and Socioeconomic Risk Factors, Developed Using South Korean Data.}, journal = {International Journal of Environmental Research and Public Health}, volume = {18}, year = {2021}, month = {2021 Jan 12}, abstract = {

COVID-19 has severely impacted socioeconomically disadvantaged populations. To support pandemic control strategies, geographically weighted negative binomial regression (GWNBR) mapped COVID-19 risk related to epidemiological and socioeconomic risk factors using South Korean incidence data (January 20, 2020 to July 1, 2020). We constructed COVID-19-specific socioeconomic and epidemiological themes using established social theoretical frameworks and created composite indexes through principal component analysis. The risk of COVID-19 increased with higher area morbidity, risky health behaviours, crowding, and population mobility, and with lower social distancing, healthcare access, and education. Falling COVID-19 risks and spatial shifts over three consecutive time periods reflected effective public health interventions. This study provides a globally replicable methodological framework and precision mapping for COVID-19 and future pandemics.

}, issn = {1660-4601}, doi = {10.3390/ijerph18020604}, author = {Weinstein, Bayarmagnai and da Silva, Alan R and Kouzoukas, Dimitrios E and Bose, Tanima and Kim, Gwang-Jin and Correa, Paola A and Pondugula, Santhi and Lee, YoonJung and Kim, Jihoo and Carpenter, David O} } @article {68990, title = {Principles of signaling pathway modulation for enhancing human naive pluripotency induction.}, journal = {Cell Stem Cell}, volume = {28}, year = {2021}, month = {09/2021}, pages = {1549-1565.e12}, abstract = {

Isolating human MEK/ERK signaling-independent pluripotent stem cells (PSCs) with naive pluripotency characteristics while maintaining differentiation competence and (epi)genetic integrity remains challenging. Here, we engineer reporter systems that allow the screening for defined conditions that induce molecular and functional features of human naive pluripotency. Synergistic inhibition of WNT/β-CATENIN, protein kinase C (PKC), and SRC signaling consolidates the induction of teratoma-competent naive human PSCs, with the capacity to differentiate into trophoblast stem cells (TSCs) and extraembryonic naive endodermal (nEND) cells in\ vitro. Divergent signaling and transcriptional requirements for boosting naive pluripotency were found between mouse and human. P53 depletion in naive hPSCs increased their contribution to mouse-human cross-species chimeric embryos upon priming and differentiation. Finally, MEK/ERK inhibition can be substituted with the inhibition of NOTCH/RBPj, which induces alternative naive-like hPSCs with a diminished risk for deleterious global DNA hypomethylation. Our findings set a framework for defining the signaling foundations of human naive pluripotency.

}, keywords = {Animals, Cell Differentiation, Embryo, Mammalian, Humans, Mice, Pluripotent Stem Cells, Signal Transduction, Trophoblasts}, issn = {1875-9777}, doi = {10.1016/j.stem.2021.04.001}, author = {Bayerl, Jonathan and Ayyash, Muneef and Shani, Tom and Manor, Yair Shlomo and Gafni, Ohad and Massarwa, Rada and Kalma, Yael and Aguilera-Castrejon, Alejandro and Zerbib, Mirie and Amir, Hadar and Sheban, Daoud and Geula, Shay and Mor, Nofar and Weinberger, Leehee and Naveh Tassa, Segev and Krupalnik, Vladislav and Oldak, Bernardo and Livnat, Nir and Tarazi, Shadi and Tawil, Shadi and Wildschutz, Emilie and Ashouokhi, Shahd and Lasman, Lior and Rotter, Varda and Hanna, Suhair and Ben-Yosef, Dalit and Novershtern, Noa and Viukov, Sergey and Hanna, Jacob H} } @booklet {67972, title = {Programmable 3D snapshot microscopy with Fourier convolutional networks}, year = {2021}, abstract = {

3D snapshot microscopy enables fast volumetric imaging by capturing a 3D volume in a single 2D camera image and performing computational reconstruction. Fast volumetric imaging has a variety of biological applications such as whole brain imaging of rapid neural activity in larval zebrafish. The optimal microscope design for this optical 3D-to-2D encoding is both sample- and task-dependent, with no general solution known. Deep learning based decoders can be combined with a differentiable simulation of an optical encoder for end-to-end optimization of both the deep learning decoder and optical encoder. This technique has been used to engineer local optical encoders for other problems such as depth estimation, 3D particle localization, and lensless photography. However, 3D snapshot microscopy is known to require a highly non-local optical encoder which existing UNet-based decoders are not able to engineer. We show that a neural network architecture based on global kernel Fourier convolutional neural networks can efficiently decode information from multiple depths in a volume, globally encoded across a 3D snapshot image. We show in simulation that our proposed networks succeed in engineering and reconstructing optical encoders for 3D snapshot microscopy where the existing state-of-the-art UNet architecture fails. We also show that our networks outperform the state-of-the-art learned reconstruction algorithms for a computational photography dataset collected on a prototype lensless camera which also uses a highly non-local optical encoding.

}, keywords = {Computer Vision and Pattern Recognition (cs.CV), electronic engineering, FOS: Computer and information sciences, FOS: Electrical engineering, Image and Video Processing (eess.IV), information engineering, Machine Learning (cs.LG)}, doi = {10.48550/ARXIV.2104.10611}, url = {https://arxiv.org/abs/2104.10611}, author = {Deb, Diptodip and Jiao, Zhenfei and Chen, Alex B. and Broxton, Michael and Ahrens, Misha B. and Podgorski, Kaspar and Turaga, Srinivas C.} } @article {67300, title = {Protein-Retention Expansion Microscopy (ExM): Scalable and Convenient Super-Resolution Microscopy.}, journal = {Methods in Molecular Biology}, volume = {2304}, year = {2021}, month = {2021 May 28}, pages = {147-156}, abstract = {

Expansion microscopy (ExM) is a method to expand biological specimens ~fourfold in each dimension by embedding in a hyper-swellable gel material. The expansion is uniform across observable length scales, enabling imaging of structures previously too small to resolve. ExM is compatible with any microscope and does not require expensive materials or specialized software, offering effectively sub-diffraction-limited imaging capabilities to labs that are not equipped to use traditional super-resolution imaging methods. Expanded specimens are ~99\% water, resulting in strongly reduced optical scattering and enabling imaging of sub-diffraction-limited structures throughout specimens up to several hundred microns in (pre-expansion) thickness.

}, issn = {1940-6029}, doi = {10.1007/978-1-0716-1402-0_7}, author = {Tillberg, Paul} } @article {66901, title = {Protocol for preparation of heterogeneous biological samples for 3D electron microscopy: a case study for insects.}, journal = {Scientific Reports}, volume = {11}, year = {2021}, month = {2021 Feb 25}, pages = {4717}, abstract = {

Modern morphological and structural studies are coming to a new level by incorporating the latest methods of three-dimensional electron microscopy (3D-EM). One of the key problems for the wide usage of these methods is posed by difficulties with sample preparation, since the methods work poorly with heterogeneous (consisting of tissues different in structure and in chemical composition) samples and require expensive equipment and usually much time. We have developed a simple protocol allows preparing heterogeneous biological samples suitable for 3D-EM in a laboratory that has a standard supply of equipment and reagents for electron microscopy. This protocol, combined with focused ion-beam scanning electron microscopy, makes it possible to study 3D ultrastructure of complex biological samples, e.g., whole insect heads, over their entire volume at the cellular and subcellular levels. The protocol provides new opportunities for many areas of study, including connectomics.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-83936-0}, author = {Polilov, Alexey A and Makarova, Anastasia A and Pang, Song and Shan Xu, C and Hess, Harald} } @article {66900, title = {pyControl: Open source, Python based, hardware and software for controlling behavioural neuroscience experiments}, journal = {bioRxiv}, year = {2021}, month = {2021 Feb 23}, abstract = {

Laboratory behavioural tasks are an essential research tool. As questions asked of behaviour and brain activity become more sophisticated, the ability to specify and run richly structured tasks becomes more important. An increasing focus on reproducibility also necessitates accurate communication of task logic to other researchers. To these ends we developed pyControl, a system of open source hardware and software for controlling behavioural experiments comprising; a simple yet flexible Python-based syntax for specifying tasks as extended state machines, hardware modules for building behavioural setups, and a graphical user interface designed for efficiently running high throughput experiments on many setups in parallel, all with extensive online documentation. These tools make it quicker, easier and cheaper to implement rich behavioural tasks at scale. As important, pyControl facilitates communication and reproducibility of behavioural experiments through a highly readable task definition syntax and self-documenting features.

}, doi = {https://doi.org/10.1101/2021.02.22.432227}, author = {Thomas Akam and Andy Lustig and James Rowland and Sampath K.T. Kapanaiah and Joan Esteve-Agraz and Mariangela Panniello and Cristina Marquez and Michael Kohl and Dennis K{\"a}tzel and Rui M. Costa and Mark Walton} } @article {67905, title = {PyNeval: A Python Toolbox for Evaluating Neuron Reconstruction Performance.}, journal = {Frontiers in Neuroinformatics}, volume = {15}, year = {2021}, month = {2022 Jan 28}, pages = {767936}, abstract = {

Quality assessment of tree-like structures obtained from a neuron reconstruction algorithm is necessary for evaluating the performance of the algorithm. The lack of user-friendly software for calculating common metrics motivated us to develop a Python toolbox called PyNeval, which is the first open-source toolbox designed to evaluate reconstruction results conveniently as far as we know. The toolbox supports popular metrics in two major categories, geometrical metrics and topological metrics, with an easy way to configure custom parameters for each metric. We tested the toolbox on both synthetic data and real data to show its reliability and robustness. As a demonstration of the toolbox in real applications, we used the toolbox to improve the performance of a tracing algorithm successfully by integrating it into an optimization procedure.

}, issn = {1662-5196}, doi = {10.3389/fninf.2021.767936}, author = {Zhang, Han and Liu, Chao and Yu, Yifei and Dai, Jianhua and Zhao, Ting and Zheng, Nenggan} } @article {65312, title = {Parvalbumin+ and Npas1+ Pallidal neurons have distinct circuit topology and function.}, journal = {Journal of Neuroscience}, year = {2020}, month = {2020 Aug 30}, author = {Pamukcu, Arin and Cui, Qiaoling and Xenias, Harry S. and Berceau, Brianna L. and Augustine, Elizabeth C. and Fan, Isabel and Hantman, Adam W and Lerner, Talia N. and Boca, Simina M. and Chan, C. Savio} } @article {65694, title = {A post-invasion role for type III effector TarP in modulating the dynamics and organization of host cell focal adhesions.}, journal = {Journal of Biological Chemistry}, volume = {295}, year = {2020}, month = {2020 Oct 23}, pages = {14763-14779}, abstract = {

The human pathogen targets epithelial cells lining the genital mucosa. We observed that infection of various cell types, including fibroblasts and epithelial cells resulted in the formation of unusually stable and mature focal adhesions that resisted disassembly induced by the myosin II inhibitor, blebbistatin. Super-resolution microscopy revealed in infected cells the vertical displacement of paxillin and FAK from the signaling layer of focal adhesions; while vinculin remained in its normal position within the force transduction layer. The candidate type III effector TarP which localized to focal adhesions during infection and when expressed ectopically, was sufficient to mimic both the reorganization and blebbistatin-resistant phenotypes. These effects of TarP, including its localization to focal adhesions, required a post-invasion interaction with the host protein vinculin through a specific domain at the C-terminus of TarP. This interaction is repurposed from an actin-recruiting and -remodeling complex to one that mediates nano-architectural and dynamic changes of focal adhesions. The consequence of -stabilized focal adhesions was restricted cell motility and enhanced attachment to the extracellular matrix. Thus, via a novel mechanism, inserts TarP within focal adhesions to alter their organization and stability.

}, issn = {1083-351X}, doi = {10.1074/jbc.RA120.015219}, author = {Pedrosa, Antonio T and Murphy, Korinn N and Nogueira, Ana T and Brinkworth, Amanda J and Thwaites, Tristan R and Aaron, Jesse and Chew, Teng-Leong and Carabeo, Rey A} } @article {65634, title = {Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator.}, journal = {Neuron}, volume = {107}, year = {2020}, month = {2020 Aug 01}, pages = {470}, abstract = {

Methods for one-photon fluorescent imaging of calcium dynamics can capture the activity of hundreds of neurons across large fields of view at a low equipment complexity and cost. In contrast to two-photon methods, however, one-photon methods suffer from higher levels of crosstalk from neuropil, resulting in a decreased signal-to-noise ratio and artifactual correlations of neural activity. We address this problem by engineering cell-body-targeted variants of the fluorescent calcium indicators GCaMP6f and GCaMP7f. We screened fusions of GCaMP to natural, as well as artificial, peptides and identified fusions that localized GCaMP to within 50\ μm of the cell body of neurons in mice and larval zebrafish. One-photon imaging of soma-targeted GCaMP in dense neural circuits reported fewer artifactual spikes from neuropil, an increased signal-to-noise ratio, and decreased artifactual correlation across neurons. Thus, soma-targeting of fluorescent calcium indicators facilitates usage of simple, powerful, one-photon methods for imaging neural calcium dynamics.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2020.05.029}, author = {Shemesh, Or A and Linghu, Changyang and Piatkevich, Kiryl D and Goodwin, Daniel and Celiker, Orhan Tunc and Gritton, Howard J and Romano, Michael F and Gao, Ruixuan and Yu, Chih-Chieh Jay and Tseng, Hua-An and Bensussen, Seth and Narayan, Sujatha and Yang, Chao-Tsung and Freifeld, Limor and Siciliano, Cody A and Gupta, Ishan and Wang, Joyce and Pak, Nikita and Yoon, Young-Gyu and Ullmann, Jeremy F P and Guner-Ataman, Burcu and Noamany, Habiba and Sheinkopf, Zoe R and Park, Won Min and Asano, Shoh and Keating, Amy E and Trimmer, James S and Reimer, Jacob and Tolias, Andreas S and Bear, Mark F and Tye, Kay M and Han, Xue and Ahrens, Misha B and Boyden, Edward S} } @article {65721, title = {Preventing cytokine storm syndrome in COVID-19 using α-1 adrenergic receptor antagonists.}, journal = {The Journal of Clinical Investigatio}, volume = {130}, year = {2020}, month = {2020 Jul 01}, pages = {3345-47}, keywords = {Adrenergic alpha-1 Receptor Antagonists, Clinical Trials as Topic, Coronavirus Infections, Cytokine Release Syndrome, Humans, Pandemics, Pneumonia, Viral}, issn = {1558-8238}, doi = {10.1172/JCI139642}, author = {Konig, Maximilian F and Powell, Mike and Staedtke, Verena and Bai, Ren-Yuan and Thomas, David L and Fischer, Nicole and Huq, Sakibul and Khalafallah, Adham M and Koenecke, Allison and Xiong, Ruoxuan and Mensh, Brett and Papadopoulos, Nickolas and Kinzler, Kenneth W and Vogelstein, Bert and Vogelstein, Joshua T and Athey, Susan and Zhou, Shibin and Bettegowda, Chetan} } @article {65884, title = {Probabilistic Models of Larval Zebrafish Behavior Reveal Structure on Many Scales}, journal = {Current Biology}, volume = {30}, year = {2020}, month = {01/2020}, pages = {70 - 82.e4}, abstract = {

Nervous systems have evolved to combine environmental information with internal state to select and generate adaptive behavioral sequences. To better understand these computations and their implementation in neural circuits, natural behavior must be carefully measured and quantified. Here, we collect high spatial resolution video of single zebrafish larvae swimming in a naturalistic environment and develop models of their action selection across exploration and hunting. Zebrafish larvae swim in punctuated bouts separated by longer periods of rest called interbout intervals. We take advantage of this structure by categorizing bouts into discrete types and representing their behavior as labeled sequences of bout types emitted over time. We then construct probabilistic models{\textemdash}specifically, marked renewal processes{\textemdash}to evaluate how bout types and interbout intervals are selected by the fish as a function of its internal hunger state, behavioral\ history, and the locations and properties of nearby prey. Finally, we evaluate the models by their predictive likelihood and their ability to generate realistic trajectories of virtual fish swimming through simulated environments. Our simulations capture multiple timescales of structure in larval zebrafish behavior and expose many ways in which hunger state influences their action selection to promote food seeking during hunger and safety during satiety.

}, keywords = {behavioral models, behavioral simulations, exploration, hunger, hunting, natural behavior, Zebrafish}, issn = {0960-9822}, doi = {https://doi.org/10.1016/j.cub.2019.11.026}, url = {http://www.sciencedirect.com/science/article/pii/S0960982219314654}, author = {Robert Evan Johnson and Scott Linderman and Thomas Panier and Caroline Lei Wee and Erin Song and Kristian Joseph Herrera and Andrew Miller and Florian Engert} } @article {65669, title = {A programmable sequence of reporters for lineage analysis.}, journal = {Nature Neuroscience}, volume = {23}, year = {2020}, month = {2020 Dec 01}, pages = {1618-28}, abstract = {

We present CLADES (cell lineage access driven by an edition sequence), a technology for cell lineage studies based on CRISPR-Cas9 techniques. CLADES relies on a system of genetic switches to activate and inactivate reporter genes in a predetermined order. Targeting CLADES to progenitor cells allows the progeny to inherit a sequential cascade of reporters, thereby coupling birth order to reporter expression. This system, which can also be temporally induced by heat shock, enables the temporal resolution of lineage development and can therefore be used to deconstruct an extended cell lineage by tracking the reporters expressed in the progeny. When targeted to the germ line, the same cascade progresses across animal generations, predominantly marking each generation with the corresponding combination of reporters. CLADES therefore offers an innovative strategy for making programmable cascades of genes that can be used for genetic manipulation or to record serial biological events.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-0676-9}, author = {Garcia-Marques, Jorge and Isabel Espinosa Medina and Ku, Kai-Yuan and Yang, Ching-Po and Koyama, Minoru and Yu, Hung-Hsiang and Lee, Tzumin} } @article {64902, title = {Parametric amplification of reversible transverse susceptibility in single domain magnetic nanoparticles.}, journal = {AIP Advances}, volume = {9}, year = {2019}, month = {2019 Apr 25}, pages = {045031}, abstract = {
We propose, model, and experimentally demonstrate the enhancement of reversible transverse susceptibility in single domain magnetic nanoparticles through the principle of parametric amplification. It has previously been demonstrated that properly oriented anisotropic single domain magnetic nanoparticles have an appreciable peak in transverse susceptibility at the particle anisotropy field. Here we show theoretically and experimentally that an additional parametric AC magnetic field applied at a proper phase and at twice the frequency (2f) of the transverse field further enhances transverse susceptibility peaks through the process of parametric amplification. We model this effect numerically and describe it through the energy formalism of the single magnetic domain Stoner-Wohlfarth model. The proper phase relationships of the transverse and parametric fields to obtain either parametric amplification or attenuation of the transverse susceptibility signals are also described. We experimentally demonstrate such parametric tuning of transverse susceptibility in single domain magnetic nanoparticles of a commercial audio tape in a prototypical inductive transverse susceptibility set-up.
}, doi = {10.1063/1.5079980}, author = {El Bidweihy, Hatem and Smith, Richard D and Barbic, Mladen} } @article {51254, title = {The Pearson{\textquoteright}s correlation coefficient is not a universally superior colocalization metric. Response to {\textquoteright}Quantifying colocalization: the MOC is a hybrid coefficient - an uninformative mix of co-occurrence and correlation{\textquoteright}.}, journal = {Journal of Cell Science}, volume = {132}, year = {2019}, month = {2019 Jan 09}, issn = {1477-9137}, doi = {10.1242/jcs.227074}, author = {Aaron, Jesse S and Taylor, Aaron B and Chew, Teng-Leong} } @article {65245, title = {Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression.}, journal = {Nature Cell Biology}, volume = {21}, year = {2019}, month = {2019 Dec}, pages = {1578-1589}, abstract = {

Yes-associated protein (YAP) is a transcriptional co-activator that regulates cell proliferation and survival by binding to a select set of enhancers for target gene activation. How YAP coordinates these transcriptional responses is unknown. Here, we demonstrate that YAP forms liquid-like condensates in the nucleus. Formed within seconds of hyperosmotic stress, YAP condensates compartmentalized the YAP transcription factor TEAD1 and other YAP-related co-activators, including TAZ, and subsequently induced the transcription of YAP-specific proliferation genes. Super-resolution imaging using assay for transposase-accessible chromatin with photoactivated localization microscopy revealed that the YAP nuclear condensates were areas enriched in accessible chromatin domains organized as super-enhancers. Initially devoid of RNA polymerase II, the accessible chromatin domains later acquired RNA polymerase II, transcribing RNA. The removal of the intrinsically-disordered YAP transcription activation domain prevented the formation of YAP condensates and diminished downstream YAP signalling. Thus, dynamic changes in genome organization and gene activation during YAP reprogramming is mediated by liquid-liquid phase separation.

}, issn = {1476-4679}, doi = {10.1038/s41556-019-0433-z}, author = {Cai, Danfeng and Feliciano, Daniel and Dong, Peng and Flores, Eduardo and Gruebele, Martin and Porat-Shliom, Natalie and Sukenik, Shahar and Liu, Zhe and Lippincott-Schwartz, Jennifer} } @article {66014, title = {Physical Principles of Membrane Shape Regulation by the Glycocalyx}, journal = {Cell}, volume = {177}, year = {2019}, month = {Jan-06-2019}, pages = {1757 - 1770.e21}, abstract = {

Cells bend their plasma membranes into highly curved forms to interact with the local environment, but how shape generation is regulated is not fully resolved. Here, we report a synergy between shape-generating processes in the cell interior and the external organization and composition of the cell-surface\ glycocalyx.\ Mucinbiopolymers\ and long-chain\ polysaccharides\ within the glycocalyx can generate entropic forces that favor or disfavor the projection of spherical and finger-like extensions from the cell surface. A polymer brush model of the glycocalyx successfully predicts the effects of polymer size and cell-surface density on membrane morphologies. Specific glycocalyx compositions can also induce plasma membrane instabilities to generate more exotic undulating and pearled\ membrane structures\ and drive secretion of extracellular vesicles. Together, our results suggest a fundamental role for the glycocalyx in regulating curved membrane features that serve in communication between cells and with the\ extracellular matrix.

}, issn = {00928674}, doi = {10.1016/j.cell.2019.04.017}, url = {https://www.sciencedirect.com/science/article/pii/S0092867419304039?via\%3Dihub}, author = {Shurer, Carolyn R. and Kuo, Joe Chin-Hun and Roberts, LaDeidra Mon{\'e}t and Gandhi, Jay G. and Colville, Marshall J. and Enoki, Thais A. and Pan, Hao and Su, Jin and Noble, Jade M. and Hollander, Michael J. and O{\textquoteright}Donnell, John P. and Yin, Rose and Pedram, Kayvon and M{\"o}ckl, Leonhard and Kourkoutis, Lena F. and Moerner, W.E. and Bertozzi, Carolyn R. and Feigenson, Gerald W. and Reesink, Heidi L. and Paszek, Matthew J.} } @article {64944, title = {Pleiotropic effects of ebony and tan on pigmentation and cuticular hydrocarbon composition in Drosophila melanogaster.}, journal = {Frontiers in Physiology}, volume = {10}, year = {2019}, month = {05/2019}, pages = {518}, abstract = {

Pleiotropic genes are genes that affect more than one trait. For example, many genes required for pigmentation in the fruit fly also affect traits such as circadian rhythms, vision, and mating behavior. Here, we present evidence that two pigmentation genes, and , which encode enzymes catalyzing reciprocal reactions in the melanin biosynthesis pathway, also affect cuticular hydrocarbon (CHC) composition in females. More specifically, we report that loss-of-function mutants have a CHC profile that is biased toward long (\>25C) chain CHCs, whereas loss-of-function mutants have a CHC profile that is biased toward short (\<25C) chain CHCs. Moreover, pharmacological inhibition of dopamine synthesis, a key step in the melanin synthesis pathway, reversed the changes in CHC composition seen in mutants, making the CHC profiles similar to those seen in mutants. These observations suggest that genetic variation affecting and/or activity might cause correlated changes in pigmentation and CHC composition in natural populations. We tested this possibility using the Genetic Reference Panel (DGRP) and found that CHC composition covaried with pigmentation as well as levels of and expression in newly eclosed adults in a manner consistent with the and mutant phenotypes. These data suggest that the pleiotropic effects of and might contribute to covariation of pigmentation and CHC profiles in .

}, issn = {1664-042X}, doi = {10.3389/fphys.2019.00518}, author = {Massey, Jonathan H and Akiyama, Noriyoshi and Bien, Tanja and Dreisewerd, Klaus and Wittkopp, Patricia J and Yew, Joanne Y and Takahashi, Aya} } @article {64786, title = {Possible magneto-mechanical and magneto-thermal mechanisms of ion channel activation by iron-loaded ferritin in magnetogenetics.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Aug 02}, abstract = {

The palette of tools for stimulation and regulation of neural activity is continually expanding. One of the new methods being introduced is magnetogenetics, where mechano-sensitive and thermo-sensitive ion channels are genetically engineered to be closely coupled to the iron-storage protein ferritin. Such genetic constructs could provide a powerful new way of non-invasively activating ion channels in-vivo using external magnetic fields that easily penetrate biological tissue. Initial reports that introduced this new technology have sparked a vigorous debate on the plausibility of physical mechanisms of ion channel activation by means of external magnetic fields. I argue that the initial criticisms leveled against magnetogenetics as being physically implausible were possibly based on the overly simplistic and unnecessarily pessimistic assumptions about the magnetic spin configurations of iron in ferritin protein. Additionally, all the possible magnetic-field-based mechanisms of ion channel activation in magnetogenetics might not have been fully considered. I present and propose several new magneto-mechanical and magneto-thermal mechanisms of ion channel activation by iron-loaded ferritin protein that may elucidate and clarify some of the mysteries that presently challenge our understanding of the reported biological experiments. Finally, I present some additional puzzles that will require further theoretical and experimental investigation.

}, doi = {10.7554/eLife.45807}, author = {Barbic, Mladen} } @article {64903, title = {Practical considerations in particle and object tracking and analysis.}, journal = {Current Protocols in Cell Biology}, volume = {83}, year = {2019}, month = {2019 Jun 01}, pages = {e88}, abstract = {

The rapid advancement of live-cell imaging technologies has enabled biologists to generate high-dimensional data to follow biological movement at the microscopic level. Yet, the "perceived" ease of use of modern microscopes has led to challenges whereby sub-optimal data are commonly generated that cannot support quantitative tracking and analysis as a result of various ill-advised decisions made during image acquisition. Even optimally acquired images often require further optimization through digital processing before they can be analyzed. In writing this article, we presume our target audience to be biologists with a foundational understanding of digital image acquisition and processing, who are seeking to understand the essential steps for particle/object tracking experiments. It is with this targeted readership in mind that we review the basic principles of image-processing techniques as well as analysis strategies commonly used for tracking experiments. We conclude this technical survey with a discussion of how movement behavior can be mathematically modeled and described. {\textcopyright} 2019 by John Wiley \& Sons, Inc.

}, issn = {1934-2616}, doi = {10.1002/cpcb.88}, author = {Aaron, Jesse and Wait, Eric and DeSantis, Michael and Chew, Teng-Leong} } @article {64832, title = {Prediction of choice from competing mechanosensory and choice-memory cues during active tactile decision making.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {39}, year = {2019}, month = {2019 May 15}, pages = {3921-33}, abstract = {

Perceptual decision making is an active process where animals move their sense organs to extract task-relevant information. To investigate how the brain translates sensory input into decisions during active sensation, we developed a mouse active touch task where the mechanosensory input can be precisely measured and that challenges animals to use multiple mechanosensory cues. Male mice were trained to localise a pole using a single whisker and to report their decision by selecting one of three choices. Using high-speed imaging and machine vision we estimated whisker-object mechanical forces at millisecond resolution. Mice solved the task by a sensory-motor strategy where both the strength and direction of whisker bending were informative cues to pole location. We found competing influences of immediate sensory input and choice memory on mouse choice. On correct trials, choice could be predicted from the direction and strength of whisker bending, but not from previous choice. In contrast, on error trials, choice could be predicted from previous choice but not from whisker bending. This study shows that animal choices during active tactile decision making can be predicted from mechanosenory and choice-memory signals; and provides a new task, well-suited for future study of the neural basis of active perceptual decisions.Due to the difficulty of measuring the sensory input to moving sense organs, active perceptual decision making remains poorly understood. The whisker system provides a way forward since it is now possible to measure the mechanical forces due to whisker-object contact during behaviour. Here we train mice in a novel behavioural task that challenges them to use rich mechanosensory cues, but can be performed using one whisker and enables task-relevant mechanical forces to be precisely estimated. This approach enables rigorous study of how sensory cues translate into action during active, perceptual decision making. Our findings provide new insight into active touch and how sensory/internal signals interact to determine behavioural choices.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2217-18.2019}, author = {Campagner, Dario and Evans, Mathew H and Chlebikova, Katarina and Colins-Rodriguez, Andrea and Loft, Michaela S E and Fox, Sarah and Pettifer, David and Humphries, Mark D and Svoboda, Karel and Petersen, Rasmus S} } @article {65236, title = {Preparation and co-culture of iPSC-derived dopaminergic neurons and astrocytes.}, journal = {Current Protocols in Cell Biology}, volume = {85}, year = {2019}, month = {2019 Dec 04}, pages = {e98}, abstract = {

Induced pluripotent stem cell (iPSC)-based models are powerful tools to study neurodegenerative diseases such as Parkinson{\textquoteright}s disease. The differentiation of patient-derived neurons and astrocytes allows investigation of the molecular mechanisms responsible for disease onset and development. In particular, these two cell types can be mono- or co-cultured to study the influence of cell-autonomous and non-cell-autonomous contributors to neurodegenerative diseases. We developed a streamlined procedure to produce high-quality/high-purity cultures of dopaminergic neurons and astrocytes that originate from the same population of midbrain floor-plate progenitors. This unit describes differentiation, quality control, culture parameters, and troubleshooting tips to ensure the highest quality and reproducibility of research results. {\textcopyright} 2019 The Authors. Basic Protocol 1: Differentiation of iPSCs into midbrain-patterned neural progenitor cells Support Protocol: Quality control of neural progenitor cells Basic Protocol 2: Differentiation of neural progenitor cells into astrocytes Basic Protocol 3: Differentiation of neural progenitor cells into dopaminergic neurons Basic Protocol 4: Co-culture of iPSC-derived neurons and astrocytes.

}, issn = {1934-2616}, doi = {10.1002/cpcb.98}, author = {de Rus Jacquet, Aurelie} } @article {64813, title = {Principles governing the dynamics of GABAergic interneurons in the barrel cortex.}, journal = {bioRxiv}, year = {2019}, month = {2019 Feb 21}, abstract = {

Information processing in the neocortex is performed by GABAergic interneurons that are integrated with excitatory neurons into precisely structured circuits. To reveal how each neuron type shapes sensory representations, we measured spikes and membrane potential of specific types of neurons in the barrel cortex while mice performed an active, whisker-dependent object localization task. Whiskers were tracked with millisecond precision. Fast-spiking (FS) neurons were activated by touch with short latency and by whisking. FS neurons track thalamic input and provide feedforward inhibition. Somatostatin (SOM)-expressing neurons were also excited by touch, but with a delay (5 ms) compared to excitatory (E) and FS neurons. SOM neurons monitor local excitation and provide feedback inhibition. Vasoactive intestinal polypeptide (VIP)-expressing neurons were not driven by touch but elevated their spike rate during whisking, disinhibiting E and FS neurons. Our data reveal rules of recruitment for specific interneuron types, providing foundations for understanding cortical computations.

}, doi = {10.1101/554949}, author = {Yu, Jianing and Hu, Hang and Agmon, Ariel and Svoboda, Karel} } @article {64780, title = {Probing nicotinic acetylcholine receptor function in mouse brain slices via laser flash photolysis of photoactivatable nicotine.}, journal = {Journal of Visualized Experiments : JoVE}, year = {2019}, month = {2019 Jan 25}, abstract = {

Acetylcholine (ACh) acts through receptors to modulate a variety of neuronal processes, but it has been challenging to link ACh receptor function with subcellular location within cells where this function is carried out. To study the subcellular location of nicotinic ACh receptors (nAChRs) in native brain tissue, an optical method was developed for precise release of nicotine at discrete locations near neuronal membranes during electrophysiological recordings. Patch-clamped neurons in brain slices are filled with dye to visualize their morphology during 2-photon laser scanning microscopy, and nicotine uncaging is executed with a light flash by focusing a 405 nm laser beam near one or more cellular membranes. Cellular current deflections are measured, and a high-resolution three-dimensional (3D) image of the recorded neuron is made to allow reconciliation of nAChR responses with cellular morphology. This method allows for detailed analysis of nAChR functional distribution in complex tissue preparations, promising to enhance the understanding of cholinergic neurotransmission.

}, issn = {1940-087X}, doi = {10.3791/58873}, author = {Arvin, Matthew C and Wokosin, David L and Banala, Sambashiva and Lavis, Luke D and Drenan, Ryan M} } @article {49522, title = {Paring down to the essentials.}, journal = {Science (New York, N.Y.)}, volume = {362}, year = {2018}, month = {2018 Nov 23}, pages = {904}, issn = {1095-9203}, doi = {10.1126/science.aav6872}, author = {Wang, Tim} } @article {49002, title = {Persistent activity in a recurrent circuit underlies courtship memory in Drosophila.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Jan 11}, abstract = {

Recurrent connections are thought to be a common feature of the neural circuits that encode memories, but how memories are laid down in such circuits is not fully understood. Here we present evidence that courtship memory in Drosophila relies on the recurrent circuit between mushroom body gamma (MBg), M6 output, and aSP13 dopaminergic neurons. We demonstrate persistent neuronal activity of aSP13 neurons and show that it transiently potentiates synaptic transmission from MBγ\>M6 neurons. M6 neurons in turn provide input to aSP13 neurons, prolonging potentiation of MBγ\>M6 synapses over time periods that match short-term memory. These data support a model in which persistent aSP13 activity within a recurrent circuit lays the foundation for a short-term memory.

}, issn = {2050-084X}, doi = {10.7554/eLife.31425}, author = {Zhao, Xiaoliang and Lenek, Daniela and Dag, Ugur and Dickson, Barry and Keleman, Krystyna} } @article {49274, title = {Persistent sodium current mediates the steep voltage dependence of spatial coding in hippocampal pyramidal neurons.}, journal = {Neuron}, year = {2018}, month = {2018 Jun 05}, abstract = {

The mammalian hippocampus forms a cognitive map using neurons that fire according to an animal{\textquoteright}s position ("place cells") and many other behavioral and cognitive variables. The responses of these neurons are shaped by their presynaptic inputs and the nature of their postsynaptic integration. In CA1 pyramidal neurons, spatial responses in\ vivo exhibit a strikingly supralinear dependence on baseline membrane potential. The biophysical mechanisms underlying this nonlinear cellular computation are unknown. Here, through a combination of in\ vitro, in\ vivo, and in silico approaches, we show that persistent sodium current mediates the strong membrane potential dependence of place cell activity. This current operates at membrane potentials below the action potential threshold and over seconds-long timescales, mediating a powerful and rapidly reversible amplification of synaptic responses, which drives place cell firing. Thus, we identify a biophysical mechanism that shapes the coding properties of neurons composing the hippocampal cognitive map.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2018.05.025}, author = {Hsu, Ching-Lung and Zhao, Xinyu and Milstein, Aaron D and Spruston, Nelson} } @article {49121, title = {Photoactivatable drugs for nicotinic optopharmacology.}, journal = {Nature Methods}, volume = {15}, year = {2018}, month = {2018 Mar 26}, pages = {347-50}, abstract = {

Photoactivatable pharmacological agents have revolutionized neuroscience, but the palette of available compounds is limited. We describe a general method for caging tertiary amines by using a stable quaternary ammonium linkage that elicits a red shift in the activation wavelength. We prepared a photoactivatable nicotine (PA-Nic), uncageable via one- or two-photon excitation, that is useful to study nicotinic acetylcholine receptors (nAChRs) in different experimental preparations and spatiotemporal scales.

}, issn = {1548-7105}, doi = {10.1038/nmeth.4637}, author = {Banala, Sambashiva and Arvin, Matthew C and Bannon, Nicholas M and Jin, Xiao-Tao and Macklin, John J and Wang, Yong and Peng, Can and Zhao, Guiqing and Marshall, John J and Gee, Kyle R and Wokosin, David L and Kim, Veronica J and McIntosh, J Michael and Contractor, Anis and Lester, Henry A and Kozorovitskiy, Yevgenia and Drenan, Ryan M and Lavis, Luke D} } @article {49049, title = {Physical basis of amyloid fibril polymorphism.}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {2018 Feb 16}, pages = {699}, abstract = {

Polymorphism is a key feature of amyloid fibril structures but it remains challenging to explain these variations for a particular sample. Here, we report electron cryomicroscopy-based reconstructions from different fibril morphologies formed by a peptide fragment from an amyloidogenic immunoglobulin light chain. The observed fibril morphologies vary in the number and cross-sectional arrangement of a structurally conserved building block. A comparison with the theoretically possible constellations reveals the experimentally observed spectrum of fibril morphologies to be governed by opposing sets of forces that primarily arise from the β-sheet twist, as well as peptide-peptide interactions within the fibril cross-section. Our results provide a framework for rationalizing and predicting the structure and polymorphism of cross-β fibrils, and suggest that a small number of physical parameters control the observed fibril architectures.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-03164-5}, author = {Close, William and Neumann, Matthias and Schmidt, Andreas and Hora, Manuel and Annamalai, Karthikeyan and Schmidt, Matthias and Reif, Bernd and Schmidt, Volker and Grigorieff, Nikolaus and F{\"a}ndrich, Marcus} } @conference {65885, title = {Point process latent variable models of larval zebrafish behavior}, booktitle = {NeurIPS}, year = {2018}, month = {12/2018}, abstract = {

A fundamental goal of systems neuroscience is to understand how neural activity gives rise to natural behavior. In order to achieve this goal, we must first build comprehensive models that offer quantitative descriptions of behavior. We develop a new class of probabilistic models to tackle this challenge in the study of larval zebrafish, an important model organism for neuroscience. Larval zebrafish locomote via sequences of punctate swim bouts--brief flicks of the tail--which are naturally modeled as a marked point process. However, these sequences of swim bouts belie a set of discrete and continuous internal states, latent variables that are not captured by standard point process models. We incorporate these variables as latent marks of a point process and explore various models for their dynamics. To infer the latent variables and fit the parameters of this model, we develop an amortized variational inference algorithm that targets the collapsed posterior distribution, analytically marginalizing out the discrete latent variables. With a dataset of over 120,000 swim bouts, we show that our models reveal interpretable discrete classes of swim bouts and continuous internal states like hunger that modulate their dynamics. These models are a major step toward understanding the natural behavioral program of the larval zebrafish and, ultimately, its neural underpinnings.

}, url = {http://papers.nips.cc/paper/8289-point-process-latent-variable-models-of-larval-zebrafish-behavior}, author = {Anuj Sharma and Robert Johnson and Florian Engert and Scott W. Linderman} } @article {49487, title = {A practical guide to adaptive light-sheet microscopy.}, journal = {Nature Protocols}, volume = {13}, year = {2018}, month = {2018 Oct 26}, pages = {2462{\textendash}2500}, abstract = {

We describe the implementation and use of an adaptive imaging framework for optimizing spatial resolution and signal strength in a light-sheet microscope. The framework, termed AutoPilot, comprises hardware and software modules for automatically measuring and compensating for mismatches between light-sheet and detection focal planes in living specimens. Our protocol enables researchers to introduce adaptive imaging capabilities in an existing light-sheet microscope or use our SiMView microscope blueprint to set up a new adaptive multiview light-sheet microscope. The protocol describes (i) the mechano-optical implementation of the adaptive imaging hardware, including technical drawings for all custom microscope components; (ii) the algorithms and software library for automated adaptive imaging, including the pseudocode and annotated source code for all software modules; and (iii) the execution of adaptive imaging experiments, as well as the configuration and practical use of the AutoPilot framework. Setup of the adaptive imaging hardware and software takes 1-2 weeks each. Previous experience with light-sheet microscopy and some familiarity with software engineering and building of optical instruments are recommended. Successful implementation of the protocol recovers near diffraction-limited performance in many parts of typical multicellular organisms studied with light-sheet microscopy, such as fruit fly and zebrafish embryos, for which resolution and signal strength are improved two- to fivefold.

}, issn = {1750-2799}, doi = {10.1038/s41596-018-0043-4}, author = {Royer, Lo{\"\i}c A and Lemon, William C and Chhetri, Raghav K and Keller, Philipp J} } @article {49012, title = {A preferred curvature-based continuum mechanics framework for modeling embryogenesis.}, journal = {Biophysical Journal}, volume = {114}, year = {2018}, month = {2018 Jan 23}, pages = {267-77}, abstract = {

Mechanics plays a key role in the development of higher organisms. However, understanding this relationship is complicated by the difficulty of modeling the link between local forces generated at the subcellular level and deformations observed at the tissue and whole-embryo levels. Here we propose an approach first developed for lipid bilayers and cell membranes, in which force-generation by cytoskeletal elements enters a continuum mechanics formulation for the full system in the form of local changes in preferred curvature. This allows us to express and solve the system using only tissue strains. Locations of preferred curvature are simply related to products of gene expression. A solution, in that context, means relaxing the system{\textquoteright}s mechanical energy to yield global morphogenetic predictions that accommodate a tendency toward the local preferred curvature, without a need to explicitly model force-generation mechanisms at the molecular level. Our computational framework, which we call SPHARM-MECH, extends a 3D spherical harmonics parameterization known as SPHARM to combine this level of abstraction with a sparse shape representation. The integration of these two principles allows computer simulations to be performed in three dimensions on highly complex shapes, gene expression patterns, and mechanical constraints. We demonstrate our approach by modeling mesoderm invagination in the fruit-fly embryo, where local forces generated by the acto-myosin meshwork in the region of the future mesoderm lead to formation of a ventral tissue fold. The process is accompanied by substantial changes in cell shape and long-range cell movements. Applying SPHARM-MECH to whole-embryo live imaging data acquired with light-sheet microscopy reveals significant correlation between calculated and observed tissue movements. Our analysis predicts the observed cell shape anisotropy on the ventral side of the embryo and suggests an active mechanical role of mesoderm invagination in supporting the onset of germ-band extension.

}, doi = {10.1016/j.bpj.2017.11.015}, author = {Khairy, Khaled and Lemon, William C and Amat, Fernando and Keller, Philipp J} } @article {65027, title = {Primed Conversion: The New Kid on the Block for Photoconversion.}, journal = {Chemistry}, volume = {24}, year = {2018}, month = {2018 Jun 12}, pages = {8268-8274}, abstract = {

In 2015, a novel way to convert photoconvertible fluorescent proteins was reported that uses the intercept of blue and far-red light instead of traditional violet or near-UV light illumination. This Minireview describes and contrasts this distinct two-step mechanism termed primed conversion with traditional photoconversion. We provide a comprehensive overview of what is known to date about primed conversion and focus on the molecular requirements for it to take place. We provide examples of its application to axially confined photoconversion in complex tissues as well as super-resolution microscopy. Further, we describe why and when it is useful, including its advantages and disadvantages, and give an insight into potential future development in the field.

}, issn = {1521-3765}, doi = {10.1002/chem.201705651}, author = {Mohr, Manuel Alexander and Pantazis, Periklis} } @article {49414, title = {Probing synaptic transmission and behavior in Drosophila with optogenetics: a laboratory exercise}, journal = {Journal of Undergraduate Neuroscience Education}, volume = {16}, year = {2018}, month = {2018 Summer}, pages = {A289-95}, abstract = {

Optogenetics is possibly the most revolutionary advance in neuroscience research techniques within the last decade. Here, we describe lab modules, presented at a workshop for undergraduate neuroscience educators, using optogenetic control of neurons in the fruit fly Drosophila melanogaster. Drosophila is a genetically accessible model system that combines behavioral and neurophysiological complexity, ease of use, and high research relevance. One lab module utilized two transgenic Drosophila strains, each activating specific circuits underlying startle behavior and backwards locomotion, respectively. The red-shifted channelrhodopsin, CsChrimson, was expressed in neurons sharing a common transcriptional profile, with the expression pattern further refined by the use of a Split GAL4 intersectional activation system. Another set of strains was used to investigate\ synaptic transmission at the larval neuromuscular junction. These expressed Channelrhodopsin 2 (ChR2) in glutamatergic neurons, including the motor neurons. The first strain expressed ChR2 in a wild type background, while the second contained the SNAP-25ts mutant allele, which confers heightened evoked potential amplitude and greatly increased spontaneous vesicle release frequency at the larval neuromuscular junction. These modules introduced educators and students to the use of optogenetic stimulation to control behavior and evoked release at a model synapse, and establish a basis for students to explore neurophysiology using this technique, through recapitulating classic experiments and conducting independent research.\ 

}, url = {http://www.funjournal.org/wp-content/uploads/2018/09/june-16-289.pdf?x91298}, author = {Vilinksy, Ilya and Hibbard, Karen L and Johnson Bruce R and Deitcher, David L} } @article {49122, title = {A proposed circuit computation in basal ganglia: History-dependent gain.}, journal = {Movement Disorders : official journal of the Movement Disorder Society}, year = {2018}, month = {2018 Mar 24}, abstract = {

In this Scientific Perspectives we first review the recent advances in our understanding of the functional architecture of basal ganglia circuits. Then we argue that these data can best be explained by a model in which basal ganglia act to control the gain of movement kinematics to shape performance based on prior experience, which we refer to as a history-dependent gain computation. Finally, we discuss how insights from the history-dependent gain model might translate from the bench to the bedside, primarily the implications for the design of adaptive deep brain stimulation. Thus, we explicate the key empirical and conceptual support for a normative, computational model with substantial explanatory power for the broad role of basal ganglia circuits in health and disease. {\textcopyright} 2018 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.

}, issn = {1531-8257}, doi = {10.1002/mds.27321}, author = {Yttri, Eric Allen and Dudman, Joshua Tate} } @article {68434, title = {Proximity labeling: spatially resolved proteomic mapping for neurobiology.}, journal = {Curr Opin Neurobiol}, volume = {50}, year = {2018}, month = {06/2018}, pages = {17-23}, abstract = {

Understanding signaling pathways in neuroscience requires high-resolution maps of the underlying protein networks. Proximity-dependent biotinylation with engineered enzymes, in combination with mass spectrometry-based quantitative proteomics, has emerged as a powerful method to dissect molecular interactions and the localizations of endogenous proteins. Recent applications to neuroscience have provided insights into the composition of sub-synaptic structures, including the synaptic cleft and inhibitory post-synaptic density. Here we compare the different enzymes and small-molecule probes for proximity labeling in the context of cultured neurons and tissue, review existing studies, and provide technical suggestions for the in vivo application of proximity labeling.

}, keywords = {Animals, Biotinylation, Humans, Neurobiology, Neuroimaging, Proteome, Proteomics}, issn = {1873-6882}, doi = {10.1016/j.conb.2017.10.015}, author = {Han, Shuo and Li, Jiefu and Ting, Alice Y} } @article {68763, title = {Patterned cell and matrix dynamics in branching morphogenesis}, journal = {Journal of Cell Biology}, volume = {216}, year = {2017}, month = {02/2017}, pages = {559-570}, abstract = {

Many embryonic organs undergo branching morphogenesis to maximize their functional epithelial surface area. Branching morphogenesis requires the coordinated interplay of multiple types of cells with the extracellular matrix (ECM). During branching morphogenesis, new branches form by {\textquotedblleft}budding{\textquotedblright} or {\textquotedblleft}clefting.{\textquotedblright} Cell migration, proliferation, rearrangement, deformation, and ECM dynamics have varied roles in driving budding versus clefting in different organs. Elongation of the newly formed branch and final maturation of the tip involve cellular mechanisms that include cell elongation, intercalation, convergent extension, proliferation, and differentiation. New methodologies such as high-resolution live imaging, tension sensors, and force-mapping techniques are providing exciting new opportunities for future research into branching morphogenesis.

}, issn = {0021-9525}, doi = {10.1083/jcb.201610048}, url = {https://doi.org/10.1083/jcb.201610048}, author = {Wang, Shaohe and Sekiguchi, Rei and Daley, William P. and Yamada, Kenneth M.} } @article {48433, title = {Pavlovian conditioning of larval Drosophila: an illustrated, multilingual, hands-on manual for odor-taste associative learning in maggots.}, journal = {Frontiers in Behavioral Neuroscience}, volume = {11}, year = {2017}, month = {2017 Apr 19}, pages = {45}, abstract = {

Larval Drosophila offer a study case for behavioral neurogenetics that is simple enough to be experimentally tractable, yet complex enough to be worth the effort. We provide a detailed, hands-on manual for Pavlovian odor-reward learning in these animals. Given the versatility of Drosophila for genetic analyses, combined with the evolutionarily shared genetic heritage with humans, the paradigm has utility not only in behavioral neurogenetics and experimental psychology, but for translational biomedicine as well. Together with the upcoming total synaptic connectome of the Drosophila nervous system and the possibilities of single-cell-specific transgene expression, it offers enticing opportunities for research. Indeed, the paradigm has already been adopted by a number of labs and is robust enough to be used for teaching in classroom settings. This has given rise to a demand for a detailed, hands-on manual directed at newcomers and/or at laboratory novices, and this is what we here provide. The paradigm and the present manual have a unique set of features: {\textbullet} The paradigm is cheap, easy, and robust; {\textbullet} The manual is detailed enough for newcomers or laboratory novices; {\textbullet} It briefly covers the essential scientific context; {\textbullet} It includes sheets for scoring, data analysis, and display; {\textbullet} It is multilingual: in addition to an English version we provide German, French, Japanese, Spanish and Italian language versions as well. The present manual can thus foster science education at an earlier age and enable research by a broader community than has been the case to date.

}, doi = {10.3389/fnbeh.2017.00045}, author = {Michels, Birgit and Saumweber, Timo and Biernacki, Roland and Thur, Jeanette and Glasgow, Rupert DV and Schleyer, Michael and Chen, Yi-chun and Eschbach, Claire and Stocker, Reinhard F and Toshima, Naoko and Tanimura, Teiichi and Louis, Matthieu and Arias-Gil, Gonzalo and Marescotti, Manuela and Benfenati, Fabio and Gerber, Bertram} } @article {48535, title = {Perceptually accurate display of two greyscale images as a single colour image.}, journal = {Journal of Microscopy}, year = {2017}, month = {2017 May 30}, abstract = {

Life scientists often desire to display the signal from two different molecular probes as a single colour image, so as to convey information about the probes{\textquoteright} relative concentrations as well as their spatial corelationship. Traditionally, such colour images are created through a merge display, where each greyscale signal is assigned to different channels of an RGB colour image. However, human perception of colour and greyscale intensity is not equivalent. Thus, a merged image display conveys to the typical viewer only a subset of the absolute and relative intensity information present in and between two greyscale images. The Commission Internationale de l{\textquoteright}Eclairage L*a*b* colour space (CIELAB) has been designed to specify colours according to the perceptually defined quantities of hue (perceived colour) and luminosity (perceived brightness). Here, we use the CIELAB colour space to encode two dimensions of information about two greyscale images within these two perceptual dimensions of a single colour image. We term our method a Perceptually Uniform Projection display and show using biological image examples how these displays convey more information about two greyscale signals than comparable RGB colour space-based techniques.

}, issn = {1365-2818}, doi = {10.1111/jmi.12588}, author = {Taylor, A B and Ioannou, M S and Watanabe, T and Hahn, K and Chew, T-L} } @article {49452, title = {Pleiotropy in enhancer function is encoded through diverse genetic architectures.}, journal = {bioRxiv}, year = {2017}, month = {2017 Sep 14}, abstract = {

Developmental genes can have complex cis-regulatory regions, with multiple enhancers scattered across stretches of DNA spanning tens or hundreds of kilobases. Early work revealed remarkable modularity of enhancers, where distinct regions of DNA, bound by combinations of transcription factors, drive gene expression in defined spatio-temporal domains. Nevertheless, a few reports have shown that enhancer function may be required in multiple developmental stages, implying that regulatory elements can be pleiotropic. In these cases, it is not clear whether the pleiotropic enhancers employ the same transcription factor binding sites to drive expression at multiple developmental stages or whether enhancers function as chromatin scaffolds, where independent sets of transcription factor binding sites act at different stages. In this work we have studied the activity of the enhancers of the shavenbaby gene throughout D. melanogaster development. We found that all seven shavenbaby enhancers drive gene expression in multiple tissues and developmental stages at varying levels of redundancy. We have explored how this pleiotropy is encoded in two of these enhancers. In one enhancer, the same transcription factor binding sites contribute to embryonic and pupal expression, whereas for a second enhancer, these roles are largely encoded by distinct transcription factor binding sites. Our data suggest that enhancer pleiotropy might be a common feature of cis-regulatory regions of developmental genes and that this pleiotropy can be encoded through multiple genetic architectures.

}, doi = {10.1101/188532}, author = {Preger-Ben Noon, Ella and Sabar{\'\i}s, Gonzalo and Ortiz, Daniela M and Sager, Jonathan and Liebowitz, Anna and Stern, David L and Frankel, Nicol{\'a}s} } @article {67286, title = {Predictive Coding of Novel versus Familiar Stimuli in the Primary Visual Cortex}, journal = {bioRxiv}, year = {2017}, month = {10/2017}, abstract = {

To explore theories of predictive coding, we presented mice with repeated sequences of images with novel images sparsely substituted. Under these conditions, mice could be rapidly trained to lick in response to a novel image, demonstrating a high level of performance on the first day of testing. Using 2-photon calcium imaging to record from layer 2/3 neurons in the primary visual cortex, we found that novel images evoked excess activity in the majority of neurons. When a new stimulus sequence was repeatedly presented, a majority of neurons had similarly elevated activity for the first few presentations, which then decayed to almost zero activity. The decay time of these transient responses was not fixed, but instead scaled with the length of the stimulus sequence. However, at the same time, we also found a small fraction of the neurons within the population (\~2\%) that continued to respond strongly and periodically to the repeated stimulus. Decoding analysis demonstrated that both the transient and sustained responses encoded information about stimulus identity. We conclude that the layer 2/3 population uses a two-channel predictive code: a dense transient code for novel stimuli and a sparse sustained code for familiar stimuli. These results extend and unify existing theories about the nature of predictive neural codes.

}, doi = {10.1101/197608}, url = {https://www.biorxiv.org/content/early/2017/10/03/197608}, author = {Homann, Jan and Koay, Sue Ann and Glidden, Alistair M. and Tank, David W. and Berry, Michael J.} } @article {48418, title = {PreMosa: Extracting 2D surfaces from 3D microscopy mosaics.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, year = {2017}, month = {2017 Apr 05}, pages = {2563-9}, abstract = {

Motivation: A significant focus of biological research is to understand the development, organization and function of tissues. A particularly productive area of study is on single layer epithelial tissues in which the adherence junctions of cells form a 2D manifold that is fluorescently labeled. Given the size of the tissue, a microscope must collect a mosaic of overlapping 3D stacks encompassing the stained surface. Downstream interpretation is greatly simplified by preprocessing such a dataset as follows: (a) extracting and mapping the stained manifold in each stack into a single 2D projection plane, (b) correcting uneven illumination artifacts, (c) stitching the mosaic planes into a single, large 2D image, and (d) adjusting the contrast.

Results: We have developed PreMosa, an efficient, fully automatic pipeline to perform the four preprocessing tasks above resulting in a single 2D image of the stained manifold across which contrast is optimized and illumination is even. Notable features are as follows. First, the 2D projection step employs a specially developed algorithm that actually finds the manifold in the stack based on maximizing contrast, intensity and smoothness. Second, the projection step comes first, implying all subsequent tasks are more rapidly solved in 2D. And last, the mosaic melding employs an algorithm that globally adjusts contrasts amongst the 2D tiles so as to produce a seamless, high-contrast image. We conclude with an evaluation using ground-truth datasets and present results on datasets from Drosophila melanogaster wings and Schmidtae mediterranea ciliary components.

Availability: PreMosa is available under https://cblasse.github.io/premosa.

Contact: blasse@mpi-cbg.de, myers@mpi-cbg.de.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btx195}, author = {Blasse, Corinna and Saalfeld, Stephan and Etournay, Rapha{\"e}l and Sagner, Andreas and Eaton, Suzanne and Myers, Eugene W} } @article {48992, title = {Protein-templated gold nanoparticle synthesis: protein organization, controlled gold sequestration, and unexpected reaction products.}, journal = {Dalton Transactions (Cambridge, England : 2003)}, volume = {46}, year = {2017}, month = {2017 Dec 21}, pages = {16465-16473}, abstract = {

Emerging applications that exploit the properties of nanoparticles for biotechnology require that the nanoparticles be biocompatible or support biological recognition. These types of particles can be produced through syntheses that involve biologically relevant molecules (proteins or natural extracts, for example). Many of the protocols that rely on these molecules are performed without a clear understanding of the mechanism by which the materials are produced. We have investigated a previously described reaction in which gold nanoparticles are produced from the reaction of chloroauric acid and proteins in solution. We find that modifications to the starting conditions can alter the product from the expected solution-suspended colloids to a product where colloids are formed within a solid, fibrous protein structure. We have interrogated this synthesis, exploiting the change in products to better understand this reaction. We have evaluated the kinetics and products for 7 different proteins over a range of concentrations and temperatures. The key factor that controls the synthetic outcome (colloid or fiber) is the concentration of the protein relative to the gold concentration. We find that the observed fibrous structures are more likely to form at low protein concentrations and when hydrophilic proteins are used. An analysis of the reaction kinetics shows that AuNP formation occurs faster at lower protein (fiber-forming) concentrations than at higher protein (colloid-forming) concentrations. These results contradict traditional expectations for reaction kinetics and protein-fiber formation and are instructive of the manner in which proteins template gold nanoparticle production.

}, issn = {1477-9234}, doi = {10.1039/c7dt03275g}, author = {Hart, Cassidy and Abuladel, Nouf and Bee, Madeleine and Kreider, Megan C and CVitan, Alexander C and Esson, Moira M and Farag, Andrew and Ibeh, Trisha and Kalivas, Eleni N and Larco, Daniel-Mario and Walker Long, Andrew and Lymperopoulos, Loukas and Mendel, Zachary and Miles, Nancy and Zareba, Carly M and Schwabacher, James C and Slucher, Helen and Vinals, Javier and Heddleston, John M and Li, Wenyue and Fox, Douglas M and Hartings, Matthew R} } @article {48542, title = {A protocol demonstrating 60 different Drosophila behaviors in one assay.}, journal = {Journal of Undergraduate Neuroscience Education (JUNE)}, volume = {15}, year = {2017}, month = {2017 Spring}, pages = {A110-6}, abstract = {

The fruit fly Drosophila melanogaster performs many behaviors, from simple motor actions to complex social interactions, that are of interest to neurobiologists studying how the brain controls behavior. Here, an undergraduate laboratory exercise uses cutting-edge methods to activate sets of neurons thermogenetically, triggering 60 different behaviors. Students learn how to recognize this large repertoire of behaviors from 16 fly strains that are publicly available, and from a large set of training videos provided here. A full protocol, timeline and handouts are included. Instructors need not have any experience working with flies. Student feedback is reported; in our experience, students are fascinated and highly engaged by watching animals perform such a broad array of behaviors. This exercise teaches fly husbandry and crossing, careful scientific observation, and principles of behavioral screening.

}, url = {http://www.funjournal.org/wp-content/uploads/2017/01/june-15-110.pdf}, author = {McKellar, Claire E and Wyttenbach, Robert A} } @article {48118, title = {A plasma membrane template for macropinocytic cups.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Dec 13}, abstract = {

Macropinocytosis is a fundamental mechanism that allows cells to take up extracellular liquid into large vesicles. It critically depends on the formation of a ring of protrusive actin beneath the plasma membrane, which develops into the macropinocytic cup. We show that macropinocytic cups in Dictyostelium are organised around coincident intense patches of PIP3, active Ras and active Rac. These signalling patches are invariably associated with a ring of active SCAR/WAVE at their periphery, as are all examined structures based on PIP3 patches, including phagocytic cups and basal waves. Patch formation does not depend on the enclosing F-actin ring, and patches become enlarged when the RasGAP NF1 is mutated, showing that Ras plays an instructive role. New macropinocytic cups predominantly form by splitting from existing ones. We propose that cup-shaped plasma membrane structures form from self-organizing patches of active Ras/PIP3, which recruit a ring of actin nucleators to their periphery.

}, issn = {2050-084X}, doi = {10.7554/eLife.20085}, author = {Veltman, Douwe M and Williams, Thomas D and Bloomfield, Gareth and Chen, Bi-Chang and Betzig, Eric and Insall, Robert H and Kay, Robert R} } @article {47274, title = {A platform for brain-wide imaging and reconstruction of individual neurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Jan 20}, abstract = {

The structure of axonal arbors controls how signals from individual neurons are routed within the mammalian brain. However, the arbors of very few long-range projection neurons have been reconstructed in their entirety, as axons with diameters as small as 100 nm arborize in target regions dispersed over many millimeters of tissue. We introduce a platform for high-resolution, three-dimensional fluorescence imaging of complete tissue volumes that enables the visualization and reconstruction of long-range axonal arbors. This platform relies on a high-speed two-photon microscope integrated with a tissue vibratome and a suite of computational tools for large-scale image data. We demonstrate the power of this approach by reconstructing the axonal arbors of multiple neurons in the motor cortex across a single mouse brain.

}, issn = {2050-084X}, doi = {10.7554/eLife.10566}, author = {Economo, Michael N and Clack, Nathan G and Lavis, Luke D and Gerfen, Charles R and Svoboda, Karel and Myers, Eugene W and Chandrashekar, Jayaram} } @article {47305, title = {Postembryonic lineages of the Drosophila ventral nervous system: Neuroglian expression reveals the adult hemilineage associated fiber tracts in the adult thoracic neuromeres.}, journal = {The Journal of Comparative Neurology}, volume = {524}, year = {2016}, month = {2016 Feb 15}, pages = {2677-95}, abstract = {

During larval life most of the thoracic neuroblasts (NBs) in Drosophila undergo a second phase of neurogenesis to generate adult-specific neurons that remain in an immature, developmentally stalled state until pupation. Using a combination of MARCM and immunostaining with a neurotactin antibody Truman et al. (2004) identified 24 adult specific NB lineages within each thoracic hemineuromere of the larval ventral nervous system (VNS) but because the neurotactin labeling of lineage tracts disappearing early in metamorphosis they were unable extend the identification of the these lineages into the adult. Here we show that immunostaining with an antibody against the cell adhesion molecule Neuroglian reveals the same larval secondary lineage projections through metamorphosis and by identifying each neuroglian positive tract at selected stages we have traced the larval hemilineage tracts for all three thoracic neuromeres through metamorphosis into the adult. To validate tract identifications we used the genetic toolkit developed by Harris et al. (2015) to preserve hemilineage specific GAL4 expression patterns from larval into the adult stage. The immortalized expression proved a powerful confirmation of the analysis of the neuroglian scaffold. This work has enabled us to directly link the secondary, larval NB lineages to their adult counterparts. The data provide an anatomical framework that 1) makes it possible to assign most neurons to their parent lineage and 2) allows more precise definitions of the neuronal organization of the adult VNS based in developmental units/rules. This article is protected by copyright. All rights reserved.

}, issn = {1096-9861}, doi = {10.1002/cne.23988}, author = {Shepherd, David and Harris, Robin and Williams, Darren and Truman, James W} } @article {47731, title = {A practical guide to light sheet microscopy.}, journal = {Methods in Molecular Biology (Clifton, N.J.)}, volume = {1451}, year = {2016}, month = {2016}, pages = {321-31}, abstract = {

Light sheet fluorescence microscopy is an efficient method for imaging large volumes of biological tissue, including brains of larval zebrafish, at high spatial and fairly high temporal resolution with minimal phototoxicity.Here, we provide a practical guide for those who intend to build a light sheet microscope for fluorescence imaging in live larval zebrafish brains or other tissues.

}, issn = {1940-6029}, doi = {10.1007/978-1-4939-3771-4_22}, author = {Bennett, Davis V and Ahrens, Misha B} } @article {47382, title = {Practice makes perfect in memory recall.}, journal = {Learning \& Memory (Cold Spring Harbor, N.Y.)}, volume = {23}, year = {2016}, month = {2016 Apr}, pages = {169-73}, abstract = {

A large variability in performance is observed when participants recall briefly presented lists of words. The sources of such variability are not known. Our analysis of a large data set of free recall revealed a small fraction of participants that reached an extremely high performance, including many trials with the recall of complete lists. Moreover, some of them developed a number of consistent input-position-dependent recall strategies, in particular recalling words consecutively ("chaining") or in groups of consecutively presented words ("chunking"). The time course of acquisition and particular choice of positional grouping were variable among participants. Our results show that acquiring positional strategies plays a crucial role in improvement of recall performance.

}, issn = {1549-5485}, doi = {10.1101/lm.041178.115}, author = {Romani, Sandro and Katkov, Mikhail and Tsodyks, Misha} } @article {47410, title = {A primer on the Bayesian approach to high-density single-molecule trajectories analysis.}, journal = {Biophysical Journal}, volume = {110}, year = {2016}, month = {2016 Mar 29}, pages = {1209-15}, abstract = {

Tracking single molecules in living cells provides invaluable information on their environment and on the interactions that underlie their motion. New experimental techniques now permit the recording of large amounts of individual trajectories, enabling the implementation of advanced statistical tools for data analysis. In this primer, we present a Bayesian approach toward treating these data, and we discuss how it can be fruitfully employed to infer physical and biochemical parameters from single-molecule trajectories.

}, issn = {1542-0086}, doi = {10.1016/j.bpj.2016.01.018}, author = {El Beheiry, Mohamed and T{\"u}rkcan, Silvan and Richly, Maximilian U and Triller, Antoine and Alexandrou, Antigone and Dahan, Maxime and Masson, Jean-Baptiste} } @article {47602, title = {Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies.}, journal = {Nature Biotechnology}, volume = {34}, year = {2016}, month = {2016 Jul 4}, pages = {987-92}, abstract = {

Expansion microscopy (ExM) enables imaging of preserved specimens with nanoscale precision on diffraction-limited instead of specialized super-resolution microscopes. ExM works by physically separating fluorescent probes after anchoring them to a swellable gel. The first ExM method did not result in the retention of native proteins in the gel and relied on custom-made reagents that are not widely available. Here we describe protein retention ExM (proExM), a variant of ExM in which proteins are anchored to the swellable gel, allowing the use of conventional fluorescently labeled antibodies and streptavidin, and fluorescent proteins. We validated and demonstrated the utility of proExM for multicolor super-resolution (\~{}70 nm) imaging of cells and mammalian tissues on conventional microscopes.

}, issn = {1546-1696}, doi = {10.1038/nbt.3625}, author = {Tillberg, Paul and Chen, Fei and Piatkevich, Kiryl D and Zhao, Yongxin and Yu, Chih-Chieh Jay and English, Brian P and Gao, Linyi and Martorell, Anthony and Suk, Ho-Jun and Yoshida, Fumiaki and DeGennaro, Ellen M and Roossien, Douglas H and Gong, Guanyu and Seneviratne, Uthpala and Tannenbaum, Steven R and Desimone, Robert and Cai, Dawen and Boyden, Edward S} } @article {47419, title = {PSF engineering in multifocus microscopy for increased depth volumetric imaging.}, journal = {Biomedical Optics Express}, volume = {7}, year = {2016}, month = {2016 Feb 16}, pages = {726-31}, abstract = {

Imaging and localizing single molecules with high accuracy in a 3D volume is a challenging task. Here we combine multifocal microscopy, a recently developed volumetric imaging technique, with point spread function engineering to achieve an increased depth for single molecule imaging. Applications in 3D single molecule localization-based super-resolution imaging is shown over an axial depth of 4 {\textmu}m as well as for the tracking of diffusing beads in a fluid environment over 8 {\textmu}m.

}, doi = {10.1364/BOE.7.000726}, author = {Hajj, Bassam and El Beheiry, Mohamed and Dahan, Maxime} } @article {47304, title = {P1 interneurons promote a persistent internal state that enhances inter-male aggression in Drosophila.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Dec 29}, abstract = {

How brains are hardwired to produce aggressive behavior, and how aggression circuits are related to those that mediate courtship, is not well understood. A large-scale screen for aggression-promoting neurons in Drosophila identified several independent hits that enhanced both inter-male aggression and courtship. Genetic intersections revealed that 8-10 P1 interneurons, previously thought to exclusively control male courtship, were sufficient to promote fighting. Optogenetic experiments indicated that P1 activation could promote aggression at a threshold below that required for wing extension. P1 activation in the absence of wing extension triggered persistent aggression via an internal state that could endure for minutes. High-frequency P1 activation promoted wing extension and suppressed aggression during photostimulation, whereas aggression resumed and wing extension was inhibited following photostimulation offset. Thus, P1 neuron activation promotes a latent, internal state that facilitates aggression and courtship, and controls the overt expression of these social behaviors in a threshold-dependent, inverse manner.

}, issn = {2050-084X}, doi = {10.7554/eLife.11346}, author = {Hoopfer, Eric D and Jung, Yonil and Inagaki, Hidehiko K and Rubin, Gerald M and Anderson, David J} } @article {48313, title = {Peptide dimer structure in an Aβ(1-42) fibril visualized with cryo-EM.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Sep 22}, pages = {11858-63}, abstract = {

Alzheimer{\textquoteright}s disease (AD) is a fatal neurodegenerative disorder in humans and the main cause of dementia in aging societies. The disease is characterized by the aberrant formation of β-amyloid (Aβ) peptide oligomers and fibrils. These structures may damage the brain and give rise to cerebral amyloid angiopathy, neuronal dysfunction, and cellular toxicity. Although the connection between AD and Aβ fibrillation is extensively documented, much is still unknown about the formation of these Aβ aggregates and their structures at the molecular level. Here, we combined electron cryomicroscopy, 3D reconstruction, and integrative structural modeling methods to determine the molecular architecture of a fibril formed by Aβ(1-42), a particularly pathogenic variant of Aβ peptide. Our model reveals that the individual layers of the Aβ fibril are formed by peptide dimers with face-to-face packing. The two peptides forming the dimer possess identical tilde-shaped conformations and interact with each other by packing of their hydrophobic C-terminal β-strands. The peptide C termini are located close to the main fibril axis, where they produce a hydrophobic core and are surrounded by the structurally more flexible and charged segments of the peptide N termini. The observed molecular architecture is compatible with the general chemical properties of Aβ peptide and provides a structural basis for various biological observations that illuminate the molecular underpinnings of AD. Moreover, the structure provides direct evidence for a steric zipper within a fibril formed by full-length Aβ peptide.

}, keywords = {Amino Acid Sequence, Amyloid, Amyloid beta-Peptides, Cryoelectron Microscopy, Epitope Mapping, Image Processing, Computer-Assisted, Immunoglobulin Fab Fragments, Models, Molecular, Molecular Sequence Data, Peptide Fragments, Peptides, Protein Multimerization, Protein Structure, Secondary}, issn = {1091-6490}, doi = {10.1073/pnas.1503455112}, author = {Schmidt, Matthias and Rohou, Alexis and Lasker, Keren and Yadav, Jay K and Schiene-Fischer, Cordelia and F{\"a}ndrich, Marcus and Grigorieff, Nikolaus} } @article {47409, title = {Plasticity-driven individualization of olfactory coding in mushroom body output neurons.}, journal = {Nature}, volume = {526}, year = {2015}, month = {2015 Oct 8}, pages = {258-62}, abstract = {

Although all sensory circuits ascend to higher brain areas where stimuli are represented in sparse, stimulus-specific activity patterns, relatively little is known about sensory coding on the descending side of neural circuits, as a network converges. In insects, mushroom bodies have been an important model system for studying sparse coding in the olfactory system, where this format is important for accurate memory formation. In Drosophila, it has recently been shown that the 2,000 Kenyon cells of the mushroom body converge onto a population of only 34 mushroom body output neurons (MBONs), which fall into 21 anatomically distinct cell types. Here we provide the first, to our knowledge, comprehensive view of olfactory representations at the fourth layer of the circuit, where we find a clear transition in the principles of sensory coding. We show that MBON tuning curves are highly correlated with one another. This is in sharp contrast to the process of progressive decorrelation of tuning in the earlier layers of the circuit. Instead, at the population level, odour representations are reformatted so that positive and negative correlations arise between representations of different odours. At the single-cell level, we show that uniquely identifiable MBONs display profoundly different tuning across different animals, but that tuning of the same neuron across the two hemispheres of an individual fly was nearly identical. Thus, individualized coordination of tuning arises at this level of the olfactory circuit. Furthermore, we find that this individualization is an active process that requires a learning-related gene, rutabaga. Ultimately, neural circuits have to flexibly map highly stimulus-specific information in sparse layers onto a limited number of different motor outputs. The reformatting of sensory representations we observe here may mark the beginning of this sensory-motor transition in the olfactory system.

}, keywords = {Adenylyl Cyclases, Animals, Drosophila melanogaster, Drosophila Proteins, Female, Learning, Male, Mushroom Bodies, Mutation, Neuronal Plasticity, Neurons, Olfactory Pathways, Olfactory Perception, Psychomotor Performance}, issn = {1476-4687}, doi = {10.1038/nature15396}, author = {Hige, Toshihide and Aso, Yoshinori and Rubin, Gerald M and Turner, Glenn C} } @inbook {46570, title = {Population genomic and phylogenomic insights into the evolution of physiology and behaviour in social insects}, booktitle = {Advances in Insect Physiology}, number = {48}, year = {2015}, pages = {293{\textendash}324}, abstract = {

Genomics revolutionized the field of social insect research by providing powerful tools to understand the relationship between genes, physiology and behaviour of social insects. Notably, analysis of gene expression and methylation patterns in the different castes of insect colonies highlighted many genes that likely underlie caste-specific physiological and behavioural phenotypes. However, earlier studies of social insect genomes lacked an {\textquoteleft}evolutionary{\textquoteright} context.\ Out of the millions of DNA bases found in the genome of a social insect, which pieces were most important to fitness over the timescale of social evolution?\ Here, we review a burgeoning body of literature that utilizes between-species or within-species genomic comparisons to highlight the evolutionary forces that have shaped social insect genomes. These pioneering phylogenetic and population genomic studies provide a critically needed evolutionary context to social insect genomes and underscore the importance of adaptive changes in physiology and behaviour in social evolution.

}, doi = {10.1016/bs.aiip.2015.01.002}, author = {Kent, Clement F and Zayed, Amro} } @article {46788, title = {Post-acquisition image based compensation for thickness variation in microscopy section series.}, journal = {IEEE International Symposium on Biomedical Imaging}, year = {2015}, month = {2014 Nov 25}, pages = {507-11}, abstract = {

Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as that of Drosophila melanogaster. The process of removing ultrathin layers from a solid block containing the specimen, however, is a fragile procedure and has limited precision with respect to section thickness. We have developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series. First experiments show promising results on both serial section Transmission Electron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) series. We made our solution available as Open Source plugins for the TrakEM2 software and the ImageJ distribution Fiji.

}, url = {http://arxiv.org/abs/1411.6970}, author = {Hanslovsky, Philpp and Bogovic, John A and Saalfeld, Stephan} } @conference {47129, title = {Post-acquisition image based compensation for thickness variation in microscopy section series.}, booktitle = {IEEE 12th International Symposium on Biomedical Imaging (ISBI)}, year = {2015}, month = {2015 Jul 01}, abstract = {

Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as that of Drosophila melanogaster. The process of removing ultrathin layers from a solid block containing the specimen, however, is a fragile procedure and has limited precision with respect to section thickness. We have developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series. First experiments show promising results on both serial section Transmission Electron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) series. We made our solution available as Open Source plugins for the TrakEM2 software and the ImageJ distribution Fiji.

}, doi = {10.1109/ISBI.2015.7163922}, author = {Hanslovsky, Philipp and Bogovic, John and Saalfeld, Stephan} } @article {46571, title = {A primer to single-particle cryo-electron microscopy}, journal = {Cell }, volume = {161}, year = {2015}, month = {2015 Apr 23}, pages = {438-49}, chapter = {438-49}, abstract = {

Cryo-electron microscopy (cryo-EM) of single-particle specimens is used to determine the structure of proteins and macromolecular complexes without the need for crystals. Recent advances in detector technology and software algorithms now allow images of unprecedented quality to be recorded and structures to be determined at near-atomic resolution. However, compared with X-ray crystallography, cryo-EM is a young technique with distinct challenges. This primer explains the different steps and considerations involved in structure determination by single-particle cryo-EM to provide an overview for scientists wishing to understand more about this technique and the interpretation of data obtained with it, as well as a starting guide for new practitioners.

}, doi = {10.1016/j.cell.2015.03.050}, author = {Cheng, Yifan and Grigorieff, Nikolaus and Penczek, Pawel A and Walz, Thomas} } @article {46883, title = {Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015 Jul 7}, pages = {7357}, abstract = {

Many cellular functions rely on DNA-binding proteins finding and associating to specific sites in the genome. Yet the mechanisms underlying the target search remain poorly understood, especially in the case of the highly organized mammalian cell nucleus. Using as a model Tet repressors (TetRs) searching for a multi-array locus, we quantitatively analyse the search process in human cells with single-molecule tracking and single-cell protein-DNA association measurements. We find that TetRs explore the nucleus and reach their target by 3D diffusion interspersed with transient interactions with non-cognate sites, consistent with the facilitated diffusion model. Remarkably, nonspecific binding times are broadly distributed, underlining a lack of clear delimitation between specific and nonspecific interactions. However, the search kinetics is not determined by diffusive transport but by the low association rate to nonspecific sites. Altogether, our results provide a comprehensive view of the recruitment dynamics of proteins at specific loci in mammalian cells.

}, issn = {2041-1723}, doi = {10.1038/ncomms8357}, author = {Normanno, Davide and Boudarene, Lydia and Dugast-Darzacq, Claire and Chen, Jiji and Richter, Christian and Proux, Florence and B{\'e}nichou, Olivier and Voituriez, Rapha{\"e}l and Darzacq, Xavier and Dahan, Maxime} } @article {47616, title = {Profile of Eric Betzig, Stefan Hell, and W. E. Moerner, 2014 Nobel Laureates in Chemistry.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 Mar 3}, pages = {2630-2}, issn = {1091-6490}, doi = {10.1073/pnas.1500784112}, author = {Lippincott-Schwartz, Jennifer} } @article {46658, title = {Projection-specific characteristics of retinal input to the brain.}, journal = {The Journal of Neuroscience}, volume = {35}, year = {2015}, month = {2015 Apr 22}, pages = {6575-83}, abstract = {

The brain receives information about the direction of object motion from several types of retinal ganglion cells (RGCs). On-Off direction-selective (DS) RGCs respond preferentially to stimuli moving quickly in one of four directions and provide a significant (but difficult to quantify) fraction of RGC input to the SC. On DS RGCs, in comparison, respond preferentially to stimuli moving slowly in one of three directions and are thought to only target retinorecipient nuclei comprising the accessory optic system, e.g., the medial terminal nucleus (MTN). To determine the fraction of SC-projecting RGCs that exhibit direction selectivity, and the specificity with which On-Off and On DS RGCs target retinorecipient areas, we performed optical and electrophysiological recordings from RGCs retrogradely labeled from the mouse SC and MTN. We found, surprisingly, that both On-Off and On DS RGCs innervate the SC; collectively they constitute nearly 40\% of SC-projecting RGCs. In comparison, only On DS RGCs project to the MTN. Subsequent experiments revealed that individual On DS RGCs innervate either the SC or MTN and exhibit robust projection-specific differences in somatodendritic morphology, cellular excitability, and light-evoked activity; several projection-specific differences in the output of On DS RGCs correspond closely to differences in excitatory synaptic input the cells receive. Our results reveal a robust projection of On DS RGCs to the SC, projection-specific differences in the response properties of On DS RGCs, and biophysical and synaptic mechanisms that underlie these functional differences.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4298-14.2015}, author = {Gauvain, Gregory and Murphy, Gabe J} } @article {47202, title = {Propagation of homeostatic sleep signals by segregated synaptic microcircuits of the Drosophila mushroom body.}, journal = {Current Biology : CB}, volume = {25}, year = {2015}, month = {2015 Nov 16}, pages = {2915-27}, abstract = {

The Drosophila mushroom body (MB) is a key associative memory center that has also been implicated in the control of sleep. However, the identity of MB neurons underlying homeostatic sleep regulation, as well as the types of sleep signals generated by specific classes of MB neurons, has remained poorly understood. We recently identified two MB output neuron (MBON) classes whose axons convey sleep control signals from the MB to converge in the same downstream target region: a cholinergic sleep-promoting MBON class and a glutamatergic wake-promoting MBON class. Here, we deploy a combination of neurogenetic, behavioral, and physiological approaches to identify and mechanistically dissect sleep-controlling circuits of the MB. Our studies reveal the existence of two segregated excitatory synaptic microcircuits that propagate homeostatic sleep information from different populations of intrinsic MB\ "Kenyon cells" (KCs) to specific sleep-regulating MBONs: sleep-promoting KCs increase sleep by preferentially activating the cholinergic MBONs, while wake-promoting KCs decrease sleep by preferentially activating the glutamatergic MBONs. Importantly, activity of the sleep-promoting MB microcircuit is increased by sleep deprivation and is necessary for homeostatic rebound sleep (i.e., the increased sleep that occurs after, and in compensation for, sleep lost during deprivation). These studies reveal for the first time specific functional connections between subsets of KCs and particular MBONs and establish the identity of synaptic microcircuits underlying transmission of homeostatic sleep signals in the MB.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.09.017}, author = {Sitaraman, Divya and Aso, Yoshinori and Jin, Xin and Chen, Nan and Felix, Mario and Rubin, Gerald M and Nitabach, Michael N} } @article {46497, title = {Proper migration and axon outgrowth of zebrafish cranial motoneuron subpopulations require the cell adhesion molecule MDGA2A.}, journal = {Biology Open}, volume = {4}, year = {2015}, month = {2015}, pages = {146-54}, abstract = {

The formation of functional neuronal circuits relies on accurate migration and proper axonal outgrowth of neuronal precursors. On the route to their targets migrating cells and growing axons depend on both, directional information from neurotropic cues and adhesive interactions mediated via extracellular matrix molecules or neighbouring cells. The inactivation of guidance cues or the interference with cell adhesion can cause severe defects in neuronal migration and axon guidance. In this study we have analyzed the function of the MAM domain containing glycosylphosphatidylinositol anchor 2A (MDGA2A) protein in zebrafish cranial motoneuron development. MDGA2A is prominently expressed in distinct clusters of cranial motoneurons, especially in the ones of the trigeminal and facial nerves. Analyses of MDGA2A knockdown embryos by light sheet and confocal microscopy revealed impaired migration and aberrant axonal outgrowth of these neurons; suggesting that adhesive interactions mediated by MDGA2A are required for the proper arrangement and outgrowth of cranial motoneuron subtypes.

}, issn = {2046-6390}, doi = {10.1242/bio.20148482}, author = {Ingold, Esther and Vom Berg-Maurer, Colette M and Burckhardt, Christoph J and Lehnherr, Andr{\'e} and Rieder, Philip and Keller, Philipp J and Stelzer, Ernst H and Greber, Urs F and Neuhauss, Stephan C F and Gesemann, Matthias} } @article {45719, title = {The PAR complex controls the spatiotemporal dynamics of F-actin and the MTOC in directionally migrating leukocytes.}, journal = {Journal of Cell Science}, volume = {127}, year = {2014}, month = {2014 Oct 15}, pages = {4381-95}, abstract = {

Inflammatory cells acquire a polarized phenotype to migrate towards sites of infection or injury. A conserved polarity complex comprising PAR-3, PAR-6 and atypical protein kinase C (aPKC) relays extracellular polarizing cues to control cytoskeletal and signaling networks affecting morphological and functional polarization. However, there is no evidence that myeloid cells use PAR signaling to migrate vectorially in three-dimensional (3D) environments in vivo. Using genetically encoded bioprobes and high-resolution live imaging, we reveal the existence of F-actin oscillations in the trailing edge and constant repositioning of the microtubule organizing center (MTOC) to direct leukocyte migration in wounded medaka fish larvae (Oryzias latipes). Genetic manipulation in live myeloid cells demonstrates that the catalytic activity of aPKC and the regulated interaction with PAR-3 and PAR-6 are required for consistent F-actin oscillations, MTOC perinuclear mobility, aPKC repositioning and wound-directed migration upstream of Rho kinase (also known as ROCK or ROK) activation. We propose that the PAR complex coordinately controls cytoskeletal changes affecting both the generation of traction force and the directionality of leukocyte migration to sites of injury.

}, issn = {1477-9137}, doi = {10.1242/jcs.146217}, author = {Crespo, Carolina and Vernieri, Claudio and Keller, Philipp J and Garr{\`e}, Massimiliano and Bender, Jeffrey R and Wittbrodt, Joachim and Pardi, Ruggero} } @article {68336, title = {Parasympathetic ganglia derive from Schwann cell precursors}, journal = {Science}, volume = {345}, year = {2014}, month = {06/2014}, pages = {87-90}, abstract = {

The parasympathetic nervous system helps regulate the functions of many tissues and organs, including the salivary glands and the esophagus. To do so, it needs to reach throughout the body, connecting central systems to peripheral ones. Dyachuk et al. and Espinosa-Medina et al. explored how these connections are established in mice (see the Perspective by Kalcheim and Rohrer). Progenitor cells that travel along with the developing nerves can give rise to both myelinforming Schwann cells and to parasympathetic neurons. That means the interacting nerves do not have to find each other. Instead, the beginnings of the connections are laid down as the nervous system develops. Science, this issue p. 82, p. 87; see also p. 32 Parasympathetic neurons are born from Schwann cell precursors located in the nerves that carry preganglionic fibers. [Also see Perspective by Kalcheim and Rohrer] Neural crest cells migrate extensively and give rise to most of the peripheral nervous system, including sympathetic, parasympathetic, enteric, and dorsal root ganglia. We studied how parasympathetic ganglia form close to visceral organs and what their precursors are. We find that many cranial nerve-associated crest cells coexpress the pan-autonomic determinant Paired-like homeodomain 2b (Phox2b) together with markers of Schwann cell precursors. Some give rise to Schwann cells after down-regulation of PHOX2b. Others form parasympathetic ganglia after being guided to the site of ganglion formation by the nerves that carry preganglionic fibers, a parsimonious way of wiring the pathway. Thus, cranial Schwann cell precursors are the source of parasympathetic neurons during normal development.

}, doi = {10.1126/science.1253286}, url = {https://www.science.org/doi/abs/10.1126/science.1253286}, author = {I. Espinosa-Medina and E. Outin and C. A. Picard and Z. Chettouh and S. Dymecki and G. G. Consalez and E. Coppola and J.-F. Brunet} } @article {6886, title = {Pfam: the protein families database.}, journal = {Nucleic acids research}, volume = {42}, year = {2014}, month = {2014 Jan}, pages = {D222-30}, abstract = {Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80\%, despite a 50\% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. Here, we describe the changes to Pfam content. Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures.}, keywords = {Databases, DNA, Internet, Intrinsically Disordered Proteins, Protein, Protein Conformation, Proteins, Proteome, Sequence Alignment, Sequence Analysis}, issn = {1362-4962}, doi = {10.1093/nar/gkt1223}, author = {Finn, Robert D and Bateman, Alex and Clements, Jody and Coggill, Penelope and Eberhardt, Ruth Y and Sean R. Eddy and Heger, Andreas and Hetherington, Kirstie and Holm, Liisa and Mistry, Jaina and Sonnhammer, Erik L L and Tate, John and Punta, Marco} } @article {45053, title = {Phase shifts in binaural stimuli provide directional cues for sound localisation in the field cricket Gryllus bimaculatus.}, journal = {Journal of Experimental Biology}, volume = {217}, year = {2014}, month = {2014 Jul 1}, pages = {2390-8}, abstract = {

The cricket{\textquoteright}s auditory system is a highly directional pressure difference receiver whose function is hypothesised to depend on phase relationships between the sound waves propagating through the auditory trachea that connects the left and right hearing organs. We tested this hypothesis by measuring the effect of experimentally constructed phase shifts in acoustic stimuli on phonotactic behavior of Gryllus bimaculatus, the oscillatory response patterns of the tympanic membrane, and the activity of the auditory afferents. The same artificial calling song was played simultaneously at the left and right sides of the cricket, but one sound pattern was shifted in phase by 90 deg (carrier frequencies between 3.6 and 5.4 kHz). All three levels of auditory processing are sensitive to experimentally induced acoustic phase shifts, and the response characteristics are dependent on the carrier frequency of the sound stimulus. At lower frequencies, crickets steered away from the sound leading in phase, while tympanic membrane vibrations and auditory afferent responses were smaller when the ipsilateral sound was leading. In contrast, opposite responses were observed at higher frequencies in all three levels of auditory processing. Minimal responses occurred near the carrier frequency of the cricket{\textquoteright}s calling song, suggesting a stability at this frequency. Our results indicate that crickets may use directional cues arising from phase shifts in acoustic signals for sound localisation, and that the response properties of pressure difference receivers may be analysed with phase-shifted sound stimuli to further our understanding of how insect auditory systems are adapted for directional processing.

}, issn = {1477-9145}, doi = {10.1242/jeb.101402}, author = {Seagraves, Kelly M and Hedwig, Berthold} } @article {47628, title = {Photocontrollable fluorescent proteins for superresolution imaging.}, journal = {Annual review of biophysics}, volume = {43}, year = {2014}, month = {2014}, pages = {303-29}, abstract = {

Superresolution fluorescence microscopy permits the study of biological processes at scales small enough to visualize fine subcellular structures that are unresolvable by traditional diffraction-limited light microscopy. Many superresolution techniques, including those applicable to live cell imaging, utilize genetically encoded photocontrollable fluorescent proteins. The fluorescence of these proteins can be controlled by light of specific wavelengths. In this review, we discuss the biochemical and photophysical properties of photocontrollable fluorescent proteins that are relevant to their use in superresolution microscopy. We then describe the recently developed photoactivatable, photoswitchable, and reversibly photoswitchable fluorescent proteins, and we detail their particular usefulness in single-molecule localization-based and nonlinear ensemble-based superresolution techniques. Finally, we discuss recent applications of photocontrollable proteins in superresolution imaging, as well as how these applications help to clarify properties of intracellular structures and processes that are relevant to cell and developmental biology, neuroscience, cancer biology and biomedicine.

}, keywords = {Animals, Cells, Luminescent Proteins, Mammals, Microscopy, Fluorescence}, issn = {1936-1238}, doi = {10.1146/annurev-biophys-051013-022836}, author = {Shcherbakova, Daria M and Sengupta, Prabuddha and Lippincott-Schwartz, Jennifer and Verkhusha, Vladislav V} } @article {45699, title = {Photoswitchable red fluorescent protein with a large stokes shift.}, journal = {Chemistry \& Biology}, volume = {21}, year = {2014}, month = {2014 Oct 23}, pages = {1402-14}, abstract = {

A subclass of fluorescent proteins (FPs), large Stokes shift (LSS) FP, are characterized by increased spread between excitation and emission maxima. We report a photoswitchable variant of a red FP with an LSS, PSLSSmKate, which initially exhibits excitation and emission at 445 and 622\ nm, but violet irradiation photoswitches PSLSSmKate into a common red form with excitation and emission at 573 and 621\ nm. We characterize spectral, photophysical, and biochemical properties of PSLSSmKate in\ vitro and in mammalian cells and determine its crystal structure in the LSS form. Mass spectrometry, mutagenesis, and spectroscopy of PSLSSmKate allow us\ to propose molecular mechanisms for the LSS, pH dependence, and light-induced chromophore transformation. We demonstrate the applicability of PSLSSmKate to superresolution photoactivated localization microscopy and protein dynamics in live cells. Given its promising properties, we expect that PSLSSmKate-like phenotype will be further used for photoactivatable imaging and tracking multiple populations of intracellular objects.

}, issn = {1879-1301}, doi = {10.1016/j.chembiol.2014.08.010}, author = {Piatkevich, Kiryl D and English, Brian P and Malashkevich, Vladimir N and Xiao, Hui and Almo, Steven C and Singer, Robert H and Verkhusha, Vladislav V} } @article {6717, title = {Population genomics of the honey bee reveals strong signatures of positive selection on worker traits.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Jan 31}, pages = {2614-19}, abstract = {

Most theories used to explain the evolution of eusociality rest upon two key assumptions: mutations affecting the phenotype of sterile workers evolve by positive selection if the resulting traits benefit fertile kin, and that worker traits provide the primary mechanism allowing social insects to adapt to their environment. Despite the common view that positive selection drives phenotypic evolution of workers, we know very little about the prevalence of positive selection acting on the genomes of eusocial insects. We mapped the footprints of positive selection in Apis mellifera through analysis of 40 individual genomes, allowing us to identify thousands of genes and regulatory sequences with signatures of adaptive evolution over multiple timescales. We found Apoidea- and Apis-specific genes to be enriched for signatures of positive selection, indicating that novel genes play a disproportionately large role in adaptive evolution of eusocial insects. Worker-biased proteins have higher signatures of adaptive evolution relative to queen-biased proteins, supporting the view that worker traits are key to adaptation. We also found genes regulating worker division of labor to be enriched for signs of positive selection. Finally, genes associated with worker behavior based on analysis of brain gene expression were highly enriched for adaptive protein and cis-regulatory evolution. Our study highlights the significant contribution of worker phenotypes to adaptive evolution in social insects, and provides a wealth of knowledge on the loci that influence fitness in honey bees.

}, issn = {1091-6490}, doi = {10.1073/pnas.1315506111}, author = {Harpur, Brock A and Kent, Clement F and Molodtsova, Daria and Lebon, Jonathan M D and Alqarni, Abdulaziz S and Owayss, Ayman A and Zayed, Amro} } @article {45336, title = {Population of sensory neurons essential for asthmatic hyperreactivity of inflamed airways.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Aug 5}, pages = {11515-20}, abstract = {

Asthma is a common debilitating inflammatory lung disease affecting over 200 million people worldwide. Here, we investigated neurogenic components involved in asthmatic-like attacks using the ovalbumin-sensitized murine model of the disease, and identified a specific population of neurons that are required for airway hyperreactivity. We show that ablating or genetically silencing these neurons abolished the hyperreactive broncho-constrictions, even in the presence of a fully developed lung inflammatory immune response. These neurons are found in the vagal ganglia and are characterized by the expression of the transient receptor potential vanilloid 1 (TRPV1) ion channel. However, the TRPV1 channel itself is not required for the asthmatic-like hyperreactive airway response. We also demonstrate that optogenetic stimulation of this population of TRP-expressing cells with channelrhodopsin dramatically exacerbates airway hyperreactivity of inflamed airways. Notably, these cells express the sphingosine-1-phosphate receptor 3 (S1PR3), and stimulation with a S1PR3 agonist efficiently induced broncho-constrictions, even in the absence of ovalbumin sensitization and inflammation. Our results show that the airway hyperreactivity phenotype can be physiologically dissociated from the immune component, and provide a platform for devising therapeutic approaches to asthma that target these pathways separately.

}, issn = {1091-6490}, doi = {10.1073/pnas.1411032111}, author = {Tr{\"a}nkner, Dimitri and Hahne, Nadeau and Sugino, Ken and Hoon, Mark A and Zuker, Charles} } @inbook {65784, title = {Porphyrins and Metalloporphyrins at Components in Artificial Photosynthesis Research}, booktitle = {Handbook of Porphyrin Science}, volume = {34}, year = {2014}, pages = {196 {\textendash} 233}, publisher = {World Scientific Pulishing}, organization = {World Scientific Pulishing}, isbn = {978-981-4425-10-0}, doi = {10.1142/9789814417297_0016}, author = {Tebo, Alison G. and Herrero, C and Aukauloo, A}, editor = {Kadish, Karl M and Smith, Kevin M and undefined, and Guilard, Roger} } @article {45374, title = {The practical and fundamental limits of optical imaging in mammalian brains.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Sep 17}, pages = {1242-1245}, abstract = {

Advances in chemistry and physics have profound effects on neuroimaging. Current and future progress in\ these disciplines will continue to aid in efforts to visualize neural circuitry, particularly in deeper layers of the brain.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.08.009}, author = {Ji, Na} } @article {45067, title = {Precise spatial coding is preserved along the longitudinal hippocampal axis.}, journal = {Hippocampus}, volume = {24}, year = {2014}, month = {2014 Jul 18}, pages = {1-16}, abstract = {

Compared to the dorsal hippocampus, relatively few studies have characterized neuronal responses in the ventral hippocampus. In particular, it is unclear whether and how cells in the ventral region represent space and/or respond to contextual changes. We recorded from dorsal and ventral CA1 neurons in freely moving mice exposed to manipulations of visuospatial and olfactory contexts. We found that ventral cells respond to alterations of the visuospatial environment such as exposure to novel local cues, cue rotations, and contextual expansion in similar ways to dorsal cells, with the exception of cue rotations. Furthermore, we found that ventral cells responded to odors much more strongly than dorsal cells, particularly to odors of high valence. Similar to earlier studies recording from the ventral hippocampus in CA3, we also found increased scaling of place cell field size along the longitudinal hippocampal axis. Although the increase in place field size observed toward the ventral pole has previously been taken to suggest a decrease in spatial information coded by ventral place cells, we hypothesized that a change in spatial scaling could instead signal a shift in representational coding that preserves the resolution of spatial information. To explore this possibility, we examined population activity using principal component analysis (PCA) and neural location reconstruction techniques. Our results suggest that ventral populations encode a distributed representation of space, and that the resolution of spatial information at the population level is comparable to that of dorsal populations of similar size. Finally, through the use of neural network modeling, we suggest that the redundancy in spatial representation along the longitudinal hippocampal axis may allow the hippocampus to overcome the conflict between memory interference and generalization inherent in neural network memory. Our results suggest that ventral population activity is well suited for generalization across locations and contexts. {\textcopyright} 2014 Wiley Periodicals, Inc.

}, issn = {1098-1063}, doi = {10.1002/hipo.22333}, author = {Keinath, Alexander T and Wang, Melissa E and Wann, Ellen G and Yuan, Robin K and Dudman, Joshua T and Muzzio, Isabel A} } @article {47625, title = {Probing the stochastic, motor-driven properties of the cytoplasm using force spectrum microscopy.}, journal = {Cell}, volume = {158}, year = {2014}, month = {2014 Aug 14}, pages = {822-32}, abstract = {

Molecular motors in cells typically produce highly directed motion; however, the aggregate, incoherent effect of all active processes also creates randomly fluctuating forces, which drive diffusive-like, nonthermal motion. Here, we introduce force-spectrum-microscopy (FSM) to directly quantify random forces within the cytoplasm of cells and thereby probe stochastic motor activity. This technique combines measurements of the random motion of probe particles with independent micromechanical measurements of the cytoplasm to quantify the spectrum of force fluctuations. Using FSM, we show that force\ fluctuations substantially enhance intracellular movement of small and large components. The fluctuations are three times larger in malignant cells than in their benign counterparts. We further demonstrate that vimentin acts globally to anchor organelles against randomly fluctuating forces in the cytoplasm, with no effect on their magnitude. Thus, FSM has broad applications for understanding the cytoplasm and its intracellular processes in relation to cell physiology in healthy and diseased states.

}, keywords = {Animals, Biomechanical Phenomena, Cytoplasm, Embryo, Mammalian, Fibroblasts, Mice, Microscopy, Atomic Force, Proteins, Vimentin}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.06.051}, author = {Guo, Ming and Ehrlicher, Allen J and Jensen, Mikkel H and Renz, Malte and Moore, Jeffrey R and Goldman, Robert D and Lippincott-Schwartz, Jennifer and Mackintosh, Frederick C and Weitz, David A} } @article {6897, title = {Procedures for behavioral experiments in head-fixed mice.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e88678}, abstract = {

The mouse is an increasingly prominent model for the analysis of mammalian neuronal circuits. Neural circuits ultimately have to be probed during behaviors that engage the circuits. Linking circuit dynamics to behavior requires precise control of sensory stimuli and measurement of body movements. Head-fixation has been used for behavioral research, particularly in non-human primates, to facilitate precise stimulus control, behavioral monitoring and neural recording. However, choice-based, perceptual decision tasks by head-fixed mice have only recently been introduced. Training mice relies on motivating mice using water restriction. Here we describe procedures for head-fixation, water restriction and behavioral training for head-fixed mice, with a focus on active, whisker-based tactile behaviors. In these experiments mice had restricted access to water (typically 1 ml/day). After ten days of water restriction, body weight stabilized at approximately 80\% of initial weight. At that point mice were trained to discriminate sensory stimuli using operant conditioning. Head-fixed mice reported stimuli by licking in go/no-go tasks and also using a forced choice paradigm using a dual lickport. In some cases mice learned to discriminate sensory stimuli in a few trials within the first behavioral session. Delay epochs lasting a second or more were used to separate sensation (e.g. tactile exploration) and action (i.e. licking). Mice performed a variety of perceptual decision tasks with high performance for hundreds of trials per behavioral session. Up to four months of continuous water restriction showed no adverse health effects. Behavioral performance correlated with the degree of water restriction, supporting the importance of controlling access to water. These behavioral paradigms can be combined with cellular resolution imaging, random access photostimulation, and whole cell recordings.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0088678}, author = {Guo, Zengcai V and Hires, S Andrew and Li, Nuo and O{\textquoteright}Connor, Daniel H and Komiyama, Takaki and Ophir, Eran and Huber, Daniel and Bonardi, Claudia and Morandell, Karin and Gutnisky, Diego and Peron, Simon and Xu, Ning-long and Cox, James and Svoboda, Karel} } @article {46941, title = {Protecting integrated circuits from piracy with test-aware logic locking.}, journal = {ICCAD {\textquoteright}14 Proceedings of the 2014 IEEE/ACM International Conference on Computer-Aided Design}, year = {2014}, month = {2014 Nov 03}, pages = {262-269}, abstract = {The increasing IC manufacturing cost encourages a business model where design houses outsource IC fabrication to remote foundries. Despite cost savings, this model exposes design houses to IC piracy as remote foundries can manufacture in excess to sell on the black market. Recent efforts in digital hardware security aim to thwart piracy by using XOR-based chip locking, cryptography, and active metering. To counter direct attacks and lower the exposure of unlocked circuits to the foundry, we introduce a multiplexor-based locking strategy that preserves test response allowing IC testing by an untrusted party before activation. We demonstrate a simple yet effective attack against a locked circuit that does not preserve test response, and validate the effectiveness of our locking strategy on IWLS 2005 benchmarks.}, doi = {10.1109/ICCAD.2014.7001361}, author = {Plaza, Stephen M and Markov, Igor L} } @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 {6933, title = {Protein structure determination by MicroED.}, journal = {Current Opinion in Structural Biology}, volume = {27C}, year = {2014}, month = {2014 Apr 4}, pages = {24-31}, abstract = {

In this review we discuss the current advances relating to structure determination from protein microcrystals with special emphasis on the newly developed method called MicroED. This method uses a transmission electron cryo-microscope to collect electron diffraction data from extremely small 3-dimensional (3D) crystals. MicroED has been used to solve the 3D structure of the model protein lysozyme to 2.9A resolution. As the method further matures, MicroED promises to offer a unique and widely applicable approach to protein crystallography using nanocrystals.

}, issn = {1879-033X}, doi = {10.1016/j.sbi.2014.03.004}, author = {Nannenga, Brent L and Gonen, Tamir} } @article {6936, title = {Proteome analysis and conditional deletion of the EAAT2 glutamate transporter provide evidence against a role of EAAT2 in pancreatic insulin secretion in mice.}, journal = {The Journal of Biological Chemistry}, volume = {289}, year = {2014}, month = {2014 Jan 17}, pages = {1329-44}, abstract = {

Islet function is incompletely understood in part because key steps in glutamate handling remain undetermined. The glutamate (excitatory amino acid) transporter 2 (EAAT2; Slc1a2) has been hypothesized to (a) provide islet cells with glutamate, (b) protect islet cells against high extracellular glutamate concentrations, (c) mediate glutamate release, or (d) control the pH inside insulin secretory granules. Here we floxed the EAAT2 gene to produce the first conditional EAAT2 knock-out mice. Crossing with Nestin-cyclization recombinase (Cre) eliminated EAAT2 from the brain, resulting in epilepsy and premature death, confirming the importance of EAAT2 for brain function and validating the genetic construction. Crossing with insulin-Cre lines (RIP-Cre and IPF1-Cre) to obtain pancreas-selective deletion did not appear to affect survival, growth, glucose tolerance, or β-cell number. We found (using TaqMan RT-PCR, immunoblotting, immunocytochemistry, and proteome analysis) that the EAAT2 levels were too low to support any of the four hypothesized functions. The proteome analysis detected more than 7,000 islet proteins of which more than 100 were transporters. Although mitochondrial glutamate transporters and transporters for neutral amino acids were present at high levels, all other transporters with known ability to transport glutamate were strikingly absent. Glutamate-metabolizing enzymes were abundant. The level of glutamine synthetase was 2 orders of magnitude higher than that of glutaminase. Taken together this suggests that the uptake of glutamate by islets from the extracellular fluid is insignificant and that glutamate is intracellularly produced. Glutamine synthetase may be more important for islets than assumed previously.

}, keywords = {Animals, Crosses, Excitatory Amino Acid Transporter 2, Gene Deletion, Genetic, Glutamic Acid, Insulin, Insulin-Secreting Cells, Knockout, Mice, Proteome}, issn = {1083-351X}, doi = {10.1074/jbc.M113.529065}, author = {Zhou, Yun and Waanders, Leonie F and Holmseth, Silvia and Guo, Caiying and Berger, Urs V and Li, Yuchuan and Lehre, Anne-Catherine and Lehre, Knut P and Danbolt, Niels C} } @article {45904, title = {Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE.}, journal = {Nature Communication}, volume = {5}, year = {2014}, month = {2014 - Aug}, pages = {4521}, abstract = {

The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins.

}, issn = {2041-1723}, doi = {10.1038/ncomms5521}, author = {Wisedchaisri, Goragot and Park, Min-Sun and Iadanza, Matthew G and Zheng, Hongjin and Gonen, Tamir} } @article {45784, title = {Purification of mitochondria by sucrose step density gradient centrifugation.}, journal = {Cold Spring Harbor Protocols}, volume = {2014}, year = {2014}, month = {2014 Oct}, pages = {pdb.prot080028}, abstract = {

Mitochondrial fractions isolated from tissue culture cells or tissue such as liver after differential centrifugation can be purified further by density gradient centrifugation. Here we describe the use of sucrose for this purpose because it is commonly used and inexpensive and the resulting mitochondria preparations are useful for many purposes.

}, issn = {1559-6095}, doi = {10.1101/pdb.prot080028}, author = {Clayton, David A and Shadel, Gerald S} } @article {6827, title = {Parallel neural pathways mediate CO2 avoidance responses in Drosophila.}, journal = {Science}, volume = {340}, year = {2013}, month = {2013 Jun 14}, pages = {1338-41}, abstract = {

Different stimulus intensities elicit distinct perceptions, implying that input signals are either conveyed through an overlapping but distinct subpopulation of sensory neurons or channeled into divergent brain circuits according to intensity. In Drosophila, carbon dioxide (CO2) is detected by a single type of olfactory sensory neuron, but information is conveyed to higher brain centers through second-order projection neurons (PNs). Two distinct pathways, PN(v)-1 and PN(v)-2, are necessary and sufficient for avoidance responses to low and high CO2 concentrations, respectively. Whereas low concentrations activate PN(v)-1, high concentrations activate both PN(v)s and GABAergic PN(v)-3, which may inhibit PN(v)-1 pathway-mediated avoidance behavior. Channeling a sensory input into distinct neural pathways allows the perception of an odor to be further modulated by both stimulus intensity and context.

}, keywords = {Animals, Carbon Dioxide, Drosophila melanogaster, Escape Reaction, Olfactory Pathways, Olfactory Receptor Neurons}, issn = {1095-9203}, doi = {10.1126/science.1236693}, author = {Lin, Hui-Hao and Chu, Li-An and Fu, Tsai-Feng and Dickson, Barry J and Chiang, Ann-Shyn} } @article {6672, title = {Parallel, redundant circuit organization for homeostatic control of feeding behavior.}, journal = {Cell}, volume = {155}, year = {2013}, month = {2013 Dec 5}, pages = {1337-50}, abstract = {

Neural circuits for essential natural behaviors are shaped by selective pressure to coordinate reliable execution of flexible goal-directed actions. However, the structural and functional organization of survival-oriented circuits is poorly understood due to exceptionally complex neuroanatomy. This is exemplified by AGRP neurons, which are a molecularly defined population that is sufficient to rapidly coordinate voracious food seeking and consumption behaviors. Here, we use cell-type-specific techniques for neural circuit manipulation and projection-specific anatomical analysis to examine the organization of this critical homeostatic circuit that regulates feeding. We show that AGRP neuronal circuits use a segregated, parallel, and redundant output configuration. AGRP neuron axon projections that target different brain regions originate from distinct subpopulations, several of which are sufficient to independently evoke feeding. The concerted anatomical and functional analysis of AGRP neuron projection populations reveals a constellation of core forebrain nodes, which are part of an extended circuit that mediates feeding behavior.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.11.002}, author = {Betley, J Nicholas and Cao, Zhen Fang Huang and Ritola, Kimberly D and Sternson, Scott M} } @article {45715, title = {The pea aphid uses a version of the terminal system during oviparous, but not viviparous, development.}, journal = {Evodevo}, volume = {4}, year = {2013}, month = {2013}, pages = {10}, abstract = {

BACKGROUND: In most species of aphid, female nymphs develop into either sexual or asexual adults depending on the length of the photoperiod to which their mothers were exposed. The progeny of these sexual and asexual females, in turn, develop in dramatically different ways. The fertilized oocytes of sexual females begin embryogenesis after being deposited on leaves (oviparous development) while the oocytes of asexual females complete embryogenesis within the mother (viviparous development). Compared with oviparous development, viviparous development involves a smaller transient oocyte surrounded by fewer somatic epithelial cells and a smaller early embryo that comprises fewer cells. To investigate whether patterning mechanisms differ between the earliest stages of the oviparous and viviparous modes of pea aphid development, we examined the expression of pea aphid orthologs of genes known to specify embryonic termini in other insects.

RESULTS: Here we show that pea aphid oviparous ovaries express torso-like in somatic posterior follicle cells and activate ERK MAP kinase at the posterior of the oocyte. In addition to suggesting that some posterior features of the terminal system are evolutionarily conserved, our detection of activated ERK in the oocyte, rather than in the embryo, suggests that pea aphids may transduce the terminal signal using a mechanism distinct from the one used in Drosophila. In contrast with oviparous development, the pea aphid version of the terminal system does not appear to be used during viviparous development, since we did not detect expression of torso-like in the somatic epithelial cells that surround either the oocyte or the blastoderm embryo and we did not observe restricted activated ERK in the oocyte.

CONCLUSIONS: We suggest that while oviparous oocytes and embryos may specify posterior fate through an aphid terminal system, viviparous oocytes and embryos employ a different mechanism, perhaps one that does not rely on an interaction between the oocyte and surrounding somatic cells. Together, these observations provide a striking example of a difference in the fundamental events of early development that is both environmentally induced and encoded by the same genome.

}, issn = {2041-9139}, doi = {10.1186/2041-9139-4-10}, author = {Bickel, Ryan D and Cleveland, Hillary C and Barkas, Joanna and Jeschke, Caitlin C and Raz, Amelie A and Stern, David L and Davis, Gregory K} } @article {4058, title = {Phasing electron diffraction data by molecular replacement: strategy for structure determination and refinement.}, journal = {Methods in Molecular Biology}, volume = {955}, year = {2013}, month = {2013}, pages = {243-72}, abstract = {

Electron crystallography is arguably the only electron cryomicroscopy (cryo EM) technique able to deliver atomic resolution data (better then 3 {\r A}) for membrane proteins embedded in a membrane. The progress in hardware improvements and sample preparation for diffraction analysis resulted in a number of recent examples where increasingly higher resolutions were achieved. Other chapters in this book detail the improvements in hardware and delve into the intricate art of sample preparation for microscopy and electron diffraction data collection and processing. In this chapter, we describe in detail the protocols for molecular replacement for electron diffraction studies. The use of a search model for phasing electron diffraction data essentially eliminates the need of acquiring image data rendering it immune to aberrations from drift and charging effects that effectively lower the attainable resolution.

}, issn = {1940-6029}, doi = {10.1007/978-1-62703-176-9_14}, author = {Wisedchaisri, G and Gonen, T} } @article {47635, title = {Photohighlighting approaches to access membrane dynamics of the Golgi apparatus.}, journal = {Methods in cell biology}, volume = {118}, year = {2013}, month = {2013}, pages = {217-34}, abstract = {

By providing quantitative, visual data of live cells, fluorescent protein-based microscopy techniques are furnishing novel insights into the complexities of membrane trafficking pathways and organelle dynamics. In this chapter, we describe experimental protocols employing fluorescent protein-based photohighlighting techniques to quantify protein movement into and out of the Golgi apparatus, an organelle that serves as the central sorting and processing station of the secretory pathway. The methods allow kinetic characteristics of Golgi-associated protein trafficking to be deciphered, which can help clarify how the Golgi maintains itself as a steady-state structure despite a continuous flux of secretory cargo passing into and out of this organelle. The guidelines presented in this chapter can also be applied to examine the dynamics of other intracellular organelle systems, elucidating mechanisms for how proteins are maintained in specific organelles and/or circulated to other destinations within the cell.

}, keywords = {Animals, Cercopithecus aethiops, CHO Cells, COS Cells, Cricetinae, Cricetulus, Fluorescence Recovery After Photobleaching, Golgi Apparatus, Green Fluorescent Proteins, Hela Cells, Humans, Membrane Glycoproteins, Protein Transport, Recombinant Fusion Proteins, Secretory Pathway, Viral Envelope Proteins}, issn = {0091-679X}, doi = {10.1016/B978-0-12-417164-0.00013-6}, author = {Sengupta, Prabuddha and Lippincott-Schwartz, Jennifer} } @article {48391, title = {Photon shot noise limits on optical detection of neuronal spikes and estimation of spike timing.}, journal = {Biophysical journal}, volume = {104}, year = {2013}, month = {2013 Jan 08}, pages = {51-62}, abstract = {

Optical approaches for tracking neural dynamics are of widespread interest, but a theoretical framework quantifying the physical limits of these techniques has been lacking. We formulate such a framework by using signal detection and estimation theory to obtain physical bounds on the detection of neural spikes and the estimation of their occurrence times as set by photon counting statistics (shot noise). These bounds are succinctly expressed via a discriminability index that depends on the kinetics of the optical indicator and the relative fluxes of signal and background photons. This approach facilitates quantitative evaluations of different indicators, detector technologies, and data analyses. Our treatment also provides optimal filtering techniques for optical detection of spikes. We compare various types of Ca(2+) indicators and show that background photons are a chief impediment to voltage sensing. Thus, voltage indicators that change color in response to membrane depolarization may offer a key advantage over those that change intensity. We also examine fluorescence resonance energy transfer indicators and identify the regimes in which the widely used ratiometric analysis of signals is substantially suboptimal. Overall, by showing how different optical factors interact to affect signal quality, our treatment offers a valuable guide to experimental design and provides measures of confidence to assess optically extracted traces of neural activity.

}, keywords = {Action Potentials, Animals, Computer Simulation, Fluorescence Resonance Energy Transfer, Neurons, Optical Imaging, Photons, Signal Processing, Computer-Assisted, Time Factors}, issn = {1542-0086}, doi = {10.1016/j.bpj.2012.07.058}, author = {Wilt, Brian A and Fitzgerald, James E and Schnitzer, Mark J} } @article {6267, title = {Potassium channels control the interaction between active dendritic integration compartments in layer 5 cortical pyramidal neurons.}, journal = {Neuron}, volume = {79}, year = {2013}, month = {2013 Aug 7}, pages = {516-29}, abstract = {

Active dendritic synaptic integration enhances the computational power of neurons. Such nonlinear processing generates an object-localization signal in the apical dendritic tuft of layer 5B cortical pyramidal neurons during sensory-motor behavior. Here, we employ electrophysiological and optical approaches in brain slices and behaving animals to investigate how excitatory synaptic input to this distal dendritic compartment influences neuronal output. We find that active dendritic integration throughout the apical dendritic tuft is highly compartmentalized by voltage-gated potassium (KV) channels. A high density of both transient and sustained KV channels was observed in all apical dendritic compartments. These channels potently regulated the interaction between apical dendritic tuft, trunk, and axosomatic integration zones to control neuronal output in\ vitro as well as the engagement of dendritic nonlinear processing in\ vivo during sensory-motor behavior. Thus, KV channels dynamically tune the interaction between active dendritic integration compartments in layer 5B pyramidal neurons to shape behaviorally relevant neuronal computations.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.06.005}, author = {Harnett, Mark T and Xu, Ning-long and Magee, Jeffrey C and Williams, Stephen R} } @proceedings {45794, title = {Potential Patterning Differences Underlying Oviparous and Viviparous Development in the Pea Aphid}, volume = {53}, year = {2013}, month = {01/2013}, pages = {E247-E247}, publisher = {OXFORD UNIV PRESS INC}, abstract = {

The pea aphid, Acyrthosiphon pisum, exhibits several environmentally cued, discrete, alternate phenotypes (polyphenisms) during its life cycle. In the case of the reproductive polyphenism, differences in day length determine whether mothers will produce daughters that reproduce either sexually by laying fertilized eggs (oviparous sexual reproduction), or asexually by allowing oocytes to complete embryogenesis within the mother without fertilization (viviparous parthenogenesis). Oocytes and embryos that are produced asexually develop more rapidly, are yolk-free, and much smaller than oocytes and embryos that are produced sexually. Perhaps most striking, the process of oocyte differentiation is truncated in the case of asexual/viviparous development, potentially precluding interactions between the oocyte and surrounding follicle cells that might take place during sexual/oviparous development. Given the important patterning roles that oocyte-follicle cell interactions play in Drosophila, these overt differences suggest that there may be underlying differences in the molecular mechanisms of pattern formation. We have found differences in the expression of homologs of torso-like and tailless, as well as activated MAP kinase, suggesting that there are important differences in the hemipteran version of the terminal patterning system between viviparous and oviparous development. Establishing such differences in the expression of patterning genes between these developmental modes is a first step toward understanding how a single genome manages to direct patterning events in such different embryological contexts.

}, url = {http://www.sicb.org/meetings/2013/schedule/abstractdetails.php?id=1253}, author = {R Bickel and H Cleveland and J Barkas and N Belletier and DL Stern and GK Davis} } @article {45716, title = {Pupariation site preference within and between Drosophila sibling species.}, journal = {Evolution}, volume = {67}, year = {2013}, month = {2013 Sep}, pages = {2714-27}, abstract = {

Holometabolous insects pass through a sedentary pupal stage and often choose a location for pupation that is different from the site of larval feeding. We have characterized a difference in pupariation site choice within and between sibling species of Drosophila. We found that, in nature, Drosophila sechellia pupariate within their host fruit, Morinda citrifolia, and that they perform this behavior in laboratory assays. In contrast, in the laboratory, geographically diverse strains of Drosophila simulans vary in their pupariation site preference; D. simulans lines from the ancestral range in southeast Africa pupariate on fruit, or a fruit substitute, whereas populations from Europe or the New World select sites off of fruit. We explored the genetic basis for the evolved preference in puariation site preference by performing quantitative trait locus mapping within and between species. We found that the interspecific difference is controlled largely by loci on chromosomes X and II. In contrast, variation between two strains of D. simulans appears to be highly polygenic, with the majority of phenotypic effects due to loci on chromosome III. These data address the genetic basis of how new traits arise as species diverge and populations disperse.

}, keywords = {Africa, Animal Distribution, Animals, Chromosomes, Insect, Drosophila, Europe, Evolution, Molecular, Genetic Speciation, Genetic Variation, Morinda, Phylogeography, Pupa, Quantitative Trait Loci, X Chromosome}, issn = {1558-5646}, doi = {10.1111/evo.12146}, author = {Erezyilmaz, Deniz F and Stern, David L} } @article {5389, title = {Parallel wavefront measurements in ultrasound pulse guided digital phase conjugation.}, journal = {Optics Express}, volume = {20}, year = {2012}, month = {2012 Oct 22}, pages = {24827-34}, abstract = {

Ultrasound pulse guided digital phase conjugation has emerged to realize fluorescence imaging inside random scattering media. Its major limitation is the slow imaging speed, as a new wavefront needs to be measured for each voxel. Therefore 3D or even 2D imaging can be time consuming. For practical applications on biological systems, we need to accelerate the imaging process by orders of magnitude. Here we propose and experimentally demonstrate a parallel wavefront measurement scheme towards such a goal. Multiple focused ultrasound pulses of different carrier frequencies can be simultaneously launched inside a scattering medium. Heterodyne interferometry is used to measure all of the wavefronts originating from every sound focus in parallel. We use these wavefronts in sequence to rapidly excite fluorescence at all the voxels defined by the focused ultrasound pulses. In this report, we employed a commercially available sound transducer to generate two sound foci in parallel, doubled the wavefront measurement speed, and reduced the mechanical scanning steps of the sound transducer to half.

}, issn = {1094-4087}, doi = {http://dx.doi.org/10.1364/OE.20.024827}, author = {Fiolka, Reto and Si, Ke and Cui, Meng} } @article {66011, title = {Pediatric epilepsy surgery: long-term 5-year seizure remission and medication use}, journal = {Neurosurgery}, volume = {71}, year = {2012}, month = {Feb-08-2013}, pages = {985 - 993}, abstract = {

Background:\ It is unclear whether long-term seizure outcomes in children are similar to those in adult epilepsy surgery patients.

Objective:\ To determine 5-year outcomes and antiepilepsy drug (AED) use in pediatric epilepsy surgery patients from a single institution.

Methods:\ The cohort consisted of children younger than 18 years of age whose 5-year outcome data would have been available by 2010. Comparisons were made between patients with and without 5-year data (n = 338), patients with 5-year data for seizure outcome (n = 257), and seizure-free patients on and off AEDs (n = 137).

Results:\ Five-year data were available from 76\% of patients. More seizure-free patients with focal resections for hippocampal sclerosis and tumors lacked 5-year data compared with other cases. Of those with 5-year data, 53\% were continuously seizure free, 18\% had late seizure recurrence, 3\% became seizure free after initial failure, and 25\% were never seizure free. Patients were more likely to be continuously seizure free if their surgery was performed during the period 2001 to 2005 (68\%) compared with surgery performed from 1996 to 2000 (61\%), 1991 to 1995 (36\%), and 1986 to 1990 (46\%). More patients had 1 or fewer seizures per month in the late seizure recurrence (47\%) compared with the not seizure-free group (20\%). Four late deaths occurred in the not seizure-free group compared with 1 in the seizure-free group. Of patients who were continuously seizure free, 55\% were not taking AEDs, and more cortical dysplasia patients (74\%) had stopped taking AEDs compared with hemimegalencephaly patients (18\%).

Conclusion:\ In children, 5-year outcomes improved over 20 years of clinical experience. Our results are similar to those of adult epilepsy surgery patients despite mostly extratemporal and hemispheric operations for diverse developmental etiologies.

}, issn = {0148-396X}, doi = {10.1227/NEU.0b013e31826cdd5a}, url = {https://academic.oup.com/neurosurgery/article/71/5/985/2595469http://academic.oup.com/neurosurgery/article-pdf/71/5/985/32585196/00006123-201211000-00011.pdfhttp://academic.oup.com/neurosurgery/article-pdf/71/5/985/32585196/00006123-201211000-00011.pdf}, author = {Hauptman, Jason S. and Pedram, Kayvon and Sison, Christia Angela and Sankar, Raman and Salamon, Noriko and Vinters, Harry V. and Mathern, Gary W.} } @article {6296, title = {The Pfam protein families database.}, journal = {Nucleic acids research}, volume = {40}, year = {2012}, month = {2012 Jan}, pages = {D290-301}, abstract = {

Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that have occurred since our 2010 NAR paper (release 24.0). Over the last 2 years, we have generated 1840 new families and increased coverage of the UniProt Knowledgebase (UniProtKB) to nearly 80\%. Notably, we have taken the step of opening up the annotation of our families to the Wikipedia community, by linking Pfam families to relevant Wikipedia pages and encouraging the Pfam and Wikipedia communities to improve and expand those pages. We continue to improve the Pfam website and add new visualizations, such as the {\textquoteright}sunburst{\textquoteright} representation of taxonomic distribution of families. In this work we additionally address two topics that will be of particular interest to the Pfam community. First, we explain the definition and use of family-specific, manually curated gathering thresholds. Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam.

}, keywords = {Amino Acid, Databases, Encyclopedias as Topic, Internet, Protein, Protein Structure, Proteins, Sequence Homology, Tertiary}, issn = {1362-4962}, doi = {10.1093/nar/gkr1065}, author = {Punta, Marco and Coggill, Penny C and Eberhardt, Ruth Y and Mistry, Jaina and Tate, John and Boursnell, Chris and Pang, Ningze and Forslund, Kristoffer and Ceric, Goran and Clements, Jody and Heger, Andreas and Holm, Liisa and Sonnhammer, Erik L L and Sean R. Eddy and Bateman, Alex and Finn, Robert D} } @article {47646, title = {Plasticity of the asialoglycoprotein receptor deciphered by ensemble FRET imaging and single-molecule counting PALM imaging.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Oct 30}, pages = {E2989-97}, abstract = {

The stoichiometry and composition of membrane protein receptors are critical to their function. However, the inability to assess receptor subunit stoichiometry in situ has hampered efforts to relate receptor structures to functional states. Here, we address this problem for the asialoglycoprotein receptor using ensemble FRET imaging, analytical modeling, and single-molecule counting with photoactivated localization microscopy (PALM). We show that the two subunits of asialoglycoprotein receptor [rat hepatic lectin 1 (RHL1) and RHL2] can assemble into both homo- and hetero-oligomeric complexes, displaying three forms with distinct ligand specificities that coexist on the plasma membrane: higher-order homo-oligomers of RHL1, higher-order hetero-oligomers of RHL1 and RHL2 with two-to-one stoichiometry, and the homo-dimer RHL2 with little tendency to further homo-oligomerize. Levels of these complexes can be modulated in the plasma membrane by exogenous ligands. Thus, even a simple two-subunit receptor can exhibit remarkable plasticity in structure, and consequently function, underscoring the importance of deciphering oligomerization in single cells at the single-molecule level.

}, keywords = {Asialoglycoprotein Receptor, Fluorescence Resonance Energy Transfer, Ligands, Microscopy, Confocal}, issn = {1091-6490}, doi = {10.1073/pnas.1211753109}, author = {Renz, Malte and Daniels, Brian R and V{\'a}mosi, Gy{\"o}rgy and Arias, Irwin M and Lippincott-Schwartz, Jennifer} } @article {47656, title = {Plasticity of the asialoglycoprotein receptor deciphered by ensemble FRET imaging and single-molecule counting PALM imaging.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Oct 30}, pages = {E2989-97}, abstract = {

The stoichiometry and composition of membrane protein receptors are critical to their function. However, the inability to assess receptor subunit stoichiometry in situ has hampered efforts to relate receptor structures to functional states. Here, we address this problem for the asialoglycoprotein receptor using ensemble FRET imaging, analytical modeling, and single-molecule counting with photoactivated localization microscopy (PALM). We show that the two subunits of asialoglycoprotein receptor [rat hepatic lectin 1 (RHL1) and RHL2] can assemble into both homo- and hetero-oligomeric complexes, displaying three forms with distinct ligand specificities that coexist on the plasma membrane: higher-order homo-oligomers of RHL1, higher-order hetero-oligomers of RHL1 and RHL2 with two-to-one stoichiometry, and the homo-dimer RHL2 with little tendency to further homo-oligomerize. Levels of these complexes can be modulated in the plasma membrane by exogenous ligands. Thus, even a simple two-subunit receptor can exhibit remarkable plasticity in structure, and consequently function, underscoring the importance of deciphering oligomerization in single cells at the single-molecule level.

}, keywords = {Asialoglycoprotein Receptor, Fluorescence Resonance Energy Transfer, Ligands, Microscopy, Confocal}, issn = {1091-6490}, doi = {10.1073/pnas.1211753109}, author = {Renz, Malte and Daniels, Brian R and V{\'a}mosi, Gy{\"o}rgy and Arias, Irwin M and Lippincott-Schwartz, Jennifer} } @article {45730, title = {Preparation and mounting of adult Drosophila structures in Canada balsam.}, journal = {Cold Spring Harb Protoc}, volume = {2012}, year = {2012}, month = {2012 Mar}, pages = {373-5}, abstract = {

The Drosophila cuticle carries a rich array of morphological details. Thus, cuticle examination has had a central role in the history of genetics. To prepare fine "museum-quality," permanent slides, it is best to mount specimens in Canada Balsam. It is difficult to give precise recipes for Canada Balsam, because every user seems to prefer a slightly different viscosity. Dilute solutions spread easily and do not dry too rapidly while mounting specimens. The disadvantage is that there is actually less Balsam in a "drop" of the solution, and when dried, it can contract from the sides of the coverslip, sometimes disturbing the specimen. Unfortunately, there is no substitute for experience when using Canada Balsam. This protocol describes a procedure for mounting adult cuticles in Canada Balsam.

}, keywords = {Animals, Balsams, Drosophila, Microscopy, Preservation, Biological, Specimen Handling}, issn = {1559-6095}, doi = {10.1101/pdb.prot067389}, author = {Stern, David L and Sucena, Elio} } @article {5460, title = {Proprioceptive coupling within motor neurons drives C. elegans forward locomotion.}, journal = {Neuron}, volume = {76}, year = {2012}, month = {2012 Nov 21}, pages = {750-61}, abstract = {

Locomotion requires coordinated motor activity throughout an animal{\textquoteright}s body. In both vertebrates and invertebrates, chains of coupled central pattern generators (CPGs) are commonly evoked to explain local rhythmic behaviors. In C.\ elegans, we report that proprioception within the motor circuit is responsible for propagating and coordinating rhythmic undulatory waves from head to tail during forward movement. Proprioceptive coupling between adjacent body regions transduces rhythmic movement initiated near the head into bending waves driven along the body by a chain of reflexes. Using optogenetics and calcium imaging to manipulate and monitor motor circuit activity of moving C.\ elegans held in microfluidic devices, we found that the B-type cholinergic motor neurons transduce the proprioceptive signal. In C.\ elegans, a sensorimotor feedback loop operating within a specific type of motor neuron both drives and organizes body movement.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.08.039}, author = {Wen, Quan and Po, Michelle D. and Hulme, Elizabeth and Chen, Sway and Liu, Xinyu and Kwok, Sen Wai and Gershow, Marc and Leifer, Andrew M. and Butler, Victoria and Fang-Yen, Christopher and Kawano, Taizo and Schafer, William R and Whitesides, George and Wyart, Matthieu and Chklovskii, Dmitri B and Samuel, Aravinthan D. T.} } @article {4900, title = {Pupil-segmentation-based adaptive optical correction of a high-numerical-aperture gradient refractive index lens for two-photon fluorescence endoscopy.}, journal = {Optics Letters}, volume = {37}, year = {2012}, month = {2012 Jun}, pages = {2001-3}, abstract = {

The intrinsic aberrations of high-NA gradient refractive index (GRIN) lenses limit their image quality as well as field of view. Here we used a pupil-segmentation-based adaptive optical approach to correct the inherent aberrations in a two-photon fluorescence endoscope utilizing a 0.8\ NA GRIN lens. By correcting the field-dependent aberrations, we recovered diffraction-limited performance across a large imaging field. The consequent improvements in imaging signal and resolution allowed us to detect fine structures that were otherwise invisible inside mouse brain slices.

}, doi = {10.1364/OL.37.002001}, url = {http://dx.doi.org/10.1364/OL.37.002001}, author = {Wang, Chan and Ji, Na} } @article {6489, title = {PALM and STORM: unlocking live-cell super-resolution.}, journal = {Biopolymers}, volume = {95}, year = {2011}, month = {2011 May}, pages = {322-31}, abstract = {

Live-cell fluorescence light microscopy has emerged as an important tool in the study of cellular biology. The development of fluorescent markers in parallel with super-resolution imaging systems has pushed light microscopy into the realm of molecular visualization at the nanometer scale. Resolutions previously only attained with electron microscopes are now within the grasp of light microscopes. However, until recently, live-cell imaging approaches have eluded super-resolution microscopy, hampering it from reaching its full potential for revealing the dynamic interactions in biology occurring at the single molecule level. Here we examine recent advances in the super-resolution imaging of living cells by reviewing recent breakthroughs in single molecule localization microscopy methods such as PALM and STORM to achieve this important goal.

}, keywords = {Buffers, Fluorescence, Fluorescent Dyes, Luminescent Proteins, Microscopy, Nanotechnology, Photochemical Processes, Single-Cell Analysis}, issn = {0006-3525}, doi = {10.1002/bip.21586}, author = {Henriques, Ricardo and Griffiths, Caron and Hesper Rego, E and Mhlanga, Musa M} } @article {2475, title = {Parallel wavefront optimization method for focusing light through random scattering media.}, journal = {Optics Letters}, volume = {36}, year = {2011}, month = {2011 Mar 15}, pages = {870-2}, abstract = {

A parallel wavefront optimization method is demonstrated experimentally to focus light through random scattering media. The simultaneous modulation of multiple phase elements, each at a unique frequency, enables a parallel determination of the optimal wavefront. Compared to a pixel-by-pixel measurement, the reported parallel method uses the target signal in a highly efficient way. With 441 phase elements, a high-quality focus was formed through a glass diffuser with a peak-to-background ratio of \~{}270. The accuracy and repeatability of the system were tested through experiments.

}, issn = {1539-4794}, doi = {10.1364/OL.36.000870}, author = {Cui, Meng} } @article {4308, title = {The past, present, and future of single neuron reconstruction.}, journal = {Neuroinformatics}, volume = {9}, year = {2011}, month = {2011 Sep}, pages = {97-8}, issn = {1559-0089}, doi = {10.1007/s12021-011-9097-y}, author = {Svoboda, Karel} } @article {4148, title = {Perception of sniff phase in mouse olfaction.}, journal = {Nature}, volume = {14}, year = {2011}, month = {2011 Oct 12}, pages = {1039-44}, abstract = {

Olfactory systems encode odours by which neurons respond and by when they respond. In mammals, every sniff evokes a precise, odour-specific sequence of activity across olfactory neurons. Likewise, in a variety of neural systems, ranging from sensory periphery to cognitive centres, neuronal activity is timed relative to sampling behaviour and/or internally generated oscillations. As in these neural systems, relative timing of activity may represent information in the olfactory system. However, there is no evidence that mammalian olfactory systems read such cues. To test whether mice perceive the timing of olfactory activation relative to the sniff cycle ({\textquoteright}sniff phase{\textquoteright}), we used optogenetics in gene-targeted mice to generate spatially constant, temporally controllable olfactory input. Here we show that mice can behaviourally report the sniff phase of optogenetically driven activation of olfactory sensory neurons. Furthermore, mice can discriminate between light-evoked inputs that are shifted in the sniff cycle by as little as 10 milliseconds, which is similar to the temporal precision of olfactory bulb odour responses. Electrophysiological recordings in the olfactory bulb of awake mice show that individual cells encode the timing of photoactivation in relation to the sniff in both the timing and the amplitude of their responses. Our work provides evidence that the mammalian olfactory system can read temporal patterns, and suggests that timing of activity relative to sampling behaviour is a potent cue that may enable accurate olfactory percepts to form quickly.

}, issn = {1476-4687}, doi = {10.1038/nature10521}, author = {Smear, Matthew and Shusterman, Roman and O{\textquoteright}Connor, Rodney and Bozza, Thomas and Rinberg, Dmitry} } @article {3602, title = {Phase resolved interferometric spectral modulation (PRISM) for ultrafast pulse measurement and compression.}, journal = {Optics Express}, volume = {19}, year = {2011}, month = {2011 Jul 4}, pages = {12961-8}, abstract = {

We show through experiments and simulations that parallel phase modulation, a technique developed in the field of adaptive optics, can be employed to quickly determine the spectral phase profile of ultrafast laser pulses and to perform phase compensation as well as pulse shaping. Different from many existing ultrafast pulse measurement methods, the technique reported here requires no spectrum measurements of nonlinear signals. Instead, the power of nonlinear signals is used directly to quickly measure the spectral phase, a convenient feature for applications such as two-photon fluorescence microscopy. The method is found to work with both smooth and even completely random distortions. The experimental results are verified with MIIPS measurements.

}, issn = {1094-4087}, doi = {10.1364/OE.19.012961}, author = {Wu, Tsai-Wei and Tang, Jianyong and Hajj, Bassam and Cui, Meng} } @article {6495, title = {Phosphorylation at the interface.}, journal = {Structure }, volume = {19}, year = {2011}, month = {2011 Dec 7}, pages = {1726-7}, abstract = {

Proteomic studies have identified thousands of eukaryotic phosphorylation sites (phosphosites), but few are functionally characterized. Nishi et\ al., in this issue of Structure, characterize phosphosites at protein-protein interfaces and estimate the effect of their phosphorylation on interaction affinity, by combining proteomics data with protein structures.

}, issn = {1878-4186}, doi = {10.1016/j.str.2011.11.006}, author = {Davis, Fred P} } @article {3421, title = {Precise olfactory responses tile the sniff cycle.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Jul 17}, pages = {1039-44}, abstract = {

In terrestrial vertebrates, sniffing controls odorant access to receptors, and therefore sets the timescale of olfactory stimuli. We found that odorants evoked precisely sniff-locked activity in mitral/tufted cells in the olfactory bulb of awake mouse. The trial-to-trial response jitter averaged 12 ms, a precision comparable to other sensory systems. Individual cells expressed odor-specific temporal patterns of activity and, across the population, onset times tiled the duration of the sniff cycle. Responses were more tightly time-locked to the sniff phase than to the time after inhalation onset. The spikes of single neurons carried sufficient information to discriminate odors. In addition, precise locking to sniff phase may facilitate ensemble coding by making synchrony relationships across neurons robust to variation in sniff rate. The temporal specificity of mitral/tufted cell output provides a potentially rich source of information for downstream olfactory areas.

}, issn = {1546-1726}, doi = {10.1038/nn.2877}, author = {Shusterman, Roman and Smear, Matthew C and Koulakov, Alexei A and Rinberg, Dmitry} } @article {45732, title = {Preparation of cuticles from feeding Drosophila larvae.}, journal = {Cold Spring Harb Protoc}, volume = {2011}, year = {2011}, month = {2011 Nov}, pages = {1394-8}, abstract = {

The Drosophila cuticle carries a rich array of morphological details. Thus, cuticle examination has had a central role in the history of genetics. Studies of the Drosophila cuticle have focused mainly on first-instar larvae and adult cuticular morphology. Although the cuticles of second- and third-instar larvae are strikingly different from those of the first instar, these differences have been poorly studied. This protocol describes three methods for preparing cuticles from fed larvae. One commonly used procedure involves manually pricking the larvae. A simpler method for preparing larval cuticles is to burst the larvae once they have been mounted. This method is used for first- and second-instar larvae and does not require pricking; it removes the gut contents by "popping" the rear of the embryo using pressure from the coverslip. If just the right amount of medium is used, the coverslip will be pulled toward the slide, applying pressure on the samples. The larvae usually burst from their posterior ends. Also presented is an alternative procedure designed specifically for the use with third-instar larvae, although the "pricking" method can be used at this stage.

}, keywords = {Animals, Dissection, Drosophila, Entomology, Female, Integumentary System, Larva}, issn = {1559-6095}, doi = {10.1101/pdb.prot066498}, author = {Stern, David L and Sucena, Elio} } @article {45733, title = {Preparation of cuticles from unhatched first-instar Drosophila larvae.}, journal = {Cold Spring Harb Protoc}, volume = {2011}, year = {2011}, month = {2011 Sep}, abstract = {

The finely sculpted cuticle of Drosophila carries a rich array of morphological details. Thus, cuticle examination has had a central role in the history of genetics. Studies of the Drosophila cuticle have focused mainly on first-instar larvae and adult cuticular morphology. This protocol describes the preparation of cuticles from larvae that have not yet hatched from the egg. It is designed for sampling all eggs laid by one or more females. This can be particularly useful, for example, when a mutation produces embryos that are unable to hatch from the egg.

}, keywords = {Animals, Drosophila, Entomology, Female, Integumentary System, Larva}, issn = {1559-6095}, doi = {10.1101/pdb.prot065532}, author = {Stern, David L and Sucena, Elio} } @article {47673, title = {Principles and current strategies for targeting autophagy for cancer treatment.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {17}, year = {2011}, month = {2011 Feb 15}, pages = {654-66}, abstract = {

Autophagy is an evolutionarily conserved, intracellular self-defense mechanism in which organelles and proteins are sequestered into autophagic vesicles that are subsequently degraded through fusion with lysosomes. Cells, thereby, prevent the toxic accumulation of damaged or unnecessary components, but also recycle these components to sustain metabolic homoeostasis. Heightened autophagy is a mechanism of resistance for cancer cells faced with metabolic and therapeutic stress, revealing opportunities for exploitation as a therapeutic target in cancer. We summarize recent developments in the field of autophagy and cancer and build upon the results presented at the Cancer Therapy Evaluation Program (CTEP) Early Drug Development meeting in March 2010. Herein, we describe our current understanding of the core components of the autophagy machinery and the functional relevance of autophagy within the tumor microenvironment, and we outline how this knowledge has informed preclinical investigations combining the autophagy inhibitor hydroxychloroquine (HCQ) with chemotherapy, targeted therapy, and immunotherapy. Finally, we describe ongoing clinical trials involving HCQ as a first generation autophagy inhibitor, as well as strategies for the development of novel, more potent, and specific inhibitors of autophagy.

}, keywords = {Animals, Antineoplastic Agents, Autophagy, Clinical Trials, Phase III as Topic, Combined Modality Therapy, Cytoplasmic Vesicles, Humans, Hydroxychloroquine, Immune Tolerance, Immunotherapy, Inflammation, Metabolic Networks and Pathways, Molecular Targeted Therapy, Neoplasms, Proteasome Endopeptidase Complex, Signal Transduction}, issn = {1078-0432}, doi = {10.1158/1078-0432.CCR-10-2634}, author = {Amaravadi, Ravi K and Lippincott-Schwartz, Jennifer and Yin, Xiao-Ming and Weiss, William A and Takebe, Naoko and Timmer, William and DiPaola, Robert S and Lotze, Michael T and White, Eileen} } @article {47667, title = {Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis.}, journal = {Nature methods}, volume = {8}, year = {2011}, month = {2011 Nov}, pages = {969-75}, abstract = {

Photoactivated localization microscopy (PALM) is a powerful approach for investigating protein organization, yet tools for quantitative, spatial analysis of PALM datasets are largely missing. Combining pair-correlation analysis with PALM (PC-PALM), we provide a method to analyze complex patterns of protein organization across the plasma membrane without determination of absolute protein numbers. The approach uses an algorithm to distinguish a single protein with multiple appearances from clusters of proteins. This enables quantification of different parameters of spatial organization, including the presence of protein clusters, their size, density and abundance in the plasma membrane. Using this method, we demonstrate distinct nanoscale organization of plasma-membrane proteins with different membrane anchoring and lipid partitioning characteristics in COS-7 cells, and show dramatic changes in glycosylphosphatidylinositol (GPI)-anchored protein arrangement under varying perturbations. PC-PALM is thus an effective tool with broad applicability for analysis of protein heterogeneity and function, adaptable to other single-molecule strategies.

}, keywords = {Algorithms, Membrane Proteins}, issn = {1548-7105}, doi = {10.1038/nmeth.1704}, author = {Sengupta, Prabuddha and Jovanovic-Talisman, Tijana and Skoko, Dunja and Renz, Malte and Veatch, Sarah L and Lippincott-Schwartz, Jennifer} } @article {5383, title = {Probing tension and dynamics in actomyosin mediated cell shape change.}, journal = {Molecular Biology of the Cell}, volume = {22}, year = {2011}, month = {2011}, author = {Higgins, C. D. and Tulu, U. S. and Gao, L. and Betzig, E and Kiehart, D. P. and Goldstein, B.} } @article {5297, title = {Proof-editing is the bottleneck of 3D neuron reconstruction: the problem and solutions.}, journal = {Neuroinformatics}, volume = {9}, year = {2011}, month = {2011 Sep}, pages = {103-5}, keywords = {Algorithms, Animals, Computer-Assisted, Data Mining, Humans, Image Cytometry, Image Processing, Imaging, Neuroanatomical Tract-Tracing Techniques, Neurons, Software, Software Design, Three-Dimensional}, issn = {1559-0089}, doi = {10.1007/s12021-010-9090-x}, author = {Peng, Hanchuan and Long, Fuhui and Zhao, Ting and Myers, Eugene} } @article {5299, title = {Proteome-wide prediction of overlapping small molecule and protein binding sites using structure.}, journal = {Molecular BioSystems}, volume = {7}, year = {2011}, month = {2011 Feb}, pages = {545-57}, abstract = {

Small molecules that modulate protein-protein interactions are of great interest for chemical biology and therapeutics. Here I present a structure-based approach to predict {\textquoteright}bi-functional{\textquoteright} sites able to bind both small molecule ligands and proteins, in proteins of unknown structure. First, I develop a homology-based annotation method that transfers binding sites of known three-dimensional structure onto protein sequences, predicting residues in ligand and protein binding sites with estimated true positive rates of 98\% and 88\%, respectively, at 1\% false positive rates. Applying this method to the human proteome predicts 8463 proteins with bi-functional residues and correctly recovers the targets of known interaction modulators. Proteins with significantly (p \< 0.01) more bi-functional residues than expected were found to be enriched in regulatory and depleted in metabolism functions. Finally, I demonstrate the utility of the method by describing examples of predicted overlap and evidence of their biological and therapeutic relevance. The results suggest that combining the structures of known binding sites with established fold detection algorithms can predict regions of protein-protein interfaces that are amenable to small molecule modulation. Open-source software and the results for several complete proteomes are available at http://pibase.janelia.org/homolobind.

}, keywords = {Algorithms, Binding Sites, Humans, Ligands, Protein Binding, Protein Conformation, Proteome}, issn = {1742-2051}, doi = {10.1039/c0mb00200c}, author = {Davis, Fred P} } @article {4392, title = {Pupil-segmentation-based adaptive optical microscopy with full-pupil illumination.}, journal = {Optics Letters}, volume = {36}, year = {2011}, month = {2011 Nov 1}, pages = {4206-8}, abstract = {

Optical aberrations deteriorate the performance of microscopes. Adaptive optics can be used to improve imaging performance via wavefront shaping. Here, we demonstrate a pupil-segmentation based adaptive optical approach with full-pupil illumination. When implemented in a two-photon fluorescence microscope, it recovers diffraction-limited performance and improves imaging signal and resolution.

}, issn = {1539-4794}, doi = {10.1364/OL.36.004206}, author = {Milkie, Daniel E and Betzig, Eric and Ji, Na} } @article {6309, title = {Pupil-segmentation-based adaptive optics for microscopy.}, journal = {Proceedings of SPIE}, volume = {7931}, year = {2011}, month = {2011}, pages = {79310I}, abstract = {

Inhomogeneous optical properties of biological samples make it difficult to obtain diffraction-limited resolution in depth. Correcting the sample-induced optical aberrations needs adaptive optics (AO). However, the direct wavefront-sensing approach commonly used in astronomy is not suitable for most biological samples due to their strong scattering of light. We developed an image-based AO approach that is insensitive to sample scattering. By comparing images of the sample taken with different segments of the pupil illuminated, local tilt in the wavefront is measured from image shift. The aberrated wavefront is then obtained either by measuring the local phase directly using interference or with phase reconstruction algorithms similar to those used in astronomical AO. We implemented this pupil-segmentation-based approach in a two-photon fluorescence microscope and demonstrated that diffraction-limited resolution can be recovered from nonbiological and biological samples.

}, doi = {10.1117/12.876398}, author = {Ji, Na and Milkie, Daniel E and Betzig, Eric} } @article {46618, title = {A pair of dopamine neurons target the D1-like dopamine receptor DopR in the central complex to promote ethanol-stimulated locomotion in Drosophila.}, journal = {PLoS One}, volume = {5}, year = {2010}, month = {2010 Apr 1}, pages = {e9954}, abstract = {

Dopamine is a mediator of the stimulant properties of drugs of abuse, including ethanol, in mammals and in the fruit fly Drosophila. The neural substrates for the stimulant actions of ethanol in flies are not known. We show that a subset of dopamine neurons and their targets, through the action of the D1-like dopamine receptor DopR, promote locomotor activation in response to acute ethanol exposure. A bilateral pair of dopaminergic neurons in the fly brain mediates the enhanced locomotor activity induced by ethanol exposure, and promotes locomotion when directly activated. These neurons project to the central complex ellipsoid body, a structure implicated in regulating motor behaviors. Ellipsoid body neurons are required for ethanol-induced locomotor activity and they express DopR. Elimination of DopR blunts the locomotor activating effects of ethanol, and this behavior can be restored by selective expression of DopR in the ellipsoid body. These data tie the activity of defined dopamine neurons to D1-like DopR-expressing neurons to form a neural circuit that governs acute responding to ethanol.

}, keywords = {Animals, Behavior, Animal, Central Nervous System Depressants, Dopamine, Drosophila, Drosophila Proteins, Ethanol, Locomotion, Motor Activity, Neurons, Receptors, Dopamine}, issn = {1932-6203}, doi = {10.1371/journal.pone.0009954}, author = {Kong, Eric C and Woo, Katherine and Li, Haiyan and Lebestky, Tim and Mayer, Nasima and Sniffen, Melissa R and Heberlein, Ulrike and Bainton, Roland J and Hirsh, Jay and Wolf, Fred W} } @proceedings {45797, title = {A patterning difference underlying viviparous and oviparous development in the pea aphid}, volume = {50}, year = {2010}, month = {01/2010}, pages = {E205-E205}, publisher = {OXFORD UNIV PRESS INC}, abstract = {

The pea aphid, Acyrthosiphon pisum, exhibits several environmentally cued, discrete, alternate phenotypes (polyphenisms) during its life cycle. In the case of the reproductive polyphenism, differences in day length determine whether mothers will produce daughters that reproduce either sexually by laying fertilized eggs (oviparous sexual reproduction), or asexually by allowing oocytes to complete embryogenesis within the mother without fertilization (viviparous parthenogenesis). Oocytes and embryos that are produced asexually and develop within the mother develop more rapidly, are yolk-free, and much smaller than oocytes and embryos that are produced sexually. These overt differences suggest that there may be underlying differences in the molecular mechanisms of pattern formation. Indeed, our preliminary comparative gene expression work suggests that there are important differences in the terminal patterning system, involving the Torso pathway, between viviparous and oviparous development. We have so far examined the expression of homologs of torso-like and capicua, members of the Drosophila Torso pathway. We have detected clear differential expression of torso-like and possible differential expression of capicua. Establishing such differences in the expression of patterning genes between these developmental modes is a first step toward understanding how a single genome manages to direct patterning events in such different embryological contexts.

}, author = {R Bickel and N Belletier and H Cleveland and DL Stern and G Davis} } @article {46041, title = {Persistence of coordinated long-term potentiation and dendritic spine enlargement at mature hippocampal CA1 synapses requires N-cadherin.}, journal = {Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Jul 28}, pages = {9984-9}, abstract = {

Persistent changes in spine shape are coupled to long-lasting synaptic plasticity in hippocampus. The molecules that coordinate such persistent structural and functional plasticity are unknown. Here, we generated mice in which the cell adhesion molecule N-cadherin was conditionally ablated from postnatal, excitatory synapses in hippocampus. We applied to adult mice of either sex a combination of whole-cell recording, two-photon microscopy, and spine morphometric analysis to show that postnatal ablation of N-cadherin has profound effects on the stability of coordinated spine enlargement and long-term potentiation (LTP) at mature CA1 synapses, with no effects on baseline spine density or morphology, baseline properties of synaptic neurotransmission, or long-term depression. Thus, N-cadherin couples persistent spine structural modifications with long-lasting synaptic functional modifications associated selectively with LTP, revealing unexpectedly distinct roles at mature synapses in comparison with earlier, broader functions in synapse and spine development.

}, keywords = {Action Potentials, Animals, Biophysics, CA1 Region, Hippocampal, Cadherins, Dendritic Spines, Electric Stimulation, Excitatory Postsynaptic Potentials, In Vitro Techniques, Long-Term Potentiation, Mice, Mice, Inbred C57BL, Mice, Knockout, Microscopy, Immunoelectron, Patch-Clamp Techniques, Pyramidal Cells, Statistics, Nonparametric, Synapses}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1223-10.2010}, author = {Bozdagi, Ozlem and Wang, Xiao-bin and Nikitczuk, Jessica S and Anderson, Tonya R and Bloss, Erik B and Radice, Glenn L and Zhou, Qiang and Benson, Deanna L and Huntley, George W} } @article {4253, title = {The Pfam protein families database.}, journal = {Nucleic Acids Research}, volume = {38}, year = {2010}, month = {2010 Jan}, pages = {D211-22}, abstract = {

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Archaeal, Computational Biology, Databases, Fungal, Genome, Humans, Information Storage and Retrieval, Internet, Molecular Sequence Data, Nucleic Acid, Protein, Protein Structure, Sequence Alignment, Sequence Homology, Software, Tertiary}, issn = {1362-4962}, doi = {10.1093/nar/gkp985}, author = {Finn, Robert D and Mistry, Jaina and Tate, John and Coggill, Penny and Heger, Andreas and Pollington, Joanne E and Gavin, O Luke and Gunasekaran, Prasad and Ceric, Goran and Forslund, Kristoffer and Holm, Liisa and Sonnhammer, Erik L L and Eddy, Sean R. and Bateman, Alex} } @article {4401, title = {Phenotypic robustness conferred by apparently redundant transcriptional enhancers.}, journal = {Nature}, volume = {466}, year = {2010}, month = {2010 Jul 22}, pages = {490-3}, abstract = {

Genes include cis-regulatory regions that contain transcriptional enhancers. Recent reports have shown that developmental genes often possess multiple discrete enhancer modules that drive transcription in similar spatio-temporal patterns: primary enhancers located near the basal promoter and secondary, or {\textquoteright}shadow{\textquoteright}, enhancers located at more remote positions. It has been proposed that the seemingly redundant activity of primary and secondary enhancers contributes to phenotypic robustness. We tested this hypothesis by generating a deficiency that removes two newly discovered enhancers of shavenbaby (svb, a transcript of the ovo locus), a gene encoding a transcription factor that directs development of Drosophila larval trichomes. At optimal temperatures for embryonic development, this deficiency causes minor defects in trichome patterning. In embryos that develop at both low and high extreme temperatures, however, absence of these secondary enhancers leads to extensive loss of trichomes. These temperature-dependent defects can be rescued by a transgene carrying a secondary enhancer driving transcription of the svb cDNA. Finally, removal of one copy of wingless, a gene required for normal trichome patterning, causes a similar loss of trichomes only in flies lacking the secondary enhancers. These results support the hypothesis that secondary enhancers contribute to phenotypic robustness in the face of environmental and genetic variability.

}, keywords = {Animal Structures, Animals, Developmental, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Enhancer Elements, Gene Expression Regulation, Genetic, Larva, Models, Phenotype, Temperature, Transcription, Transcription Factors, Transgenes}, issn = {1476-4687}, doi = {10.1038/nature09158}, author = {Frankel, Nicol{\'a}s and Davis, Gregory K and Vargas, Diego and Wang, Shu and Payre, Fran{\c c}ois and Stern, David L} } @article {6780, title = {A post-burst after depolarization is mediated by group i metabotropic glutamate receptor-dependent upregulation of Ca(v)2.3 R-type calcium channels in CA1 pyramidal neurons.}, journal = {PLoS Biology}, volume = {8}, year = {2010}, month = {2010}, pages = {e1000534}, abstract = {

Activation of group I metabotropic glutamate receptors (subtypes mGluR1 and mGluR5) regulates neural activity in a variety of ways. In CA1 pyramidal neurons, activation of group I mGluRs eliminates the post-burst afterhyperpolarization (AHP) and produces an afterdepolarization (ADP) in its place. Here we show that upregulation of Ca(v)2.3 R-type calcium channels is responsible for a component of the ADP lasting several hundred milliseconds. This medium-duration ADP is rapidly and reversibly induced by activation of mGluR5 and requires activation of phospholipase C (PLC) and release of calcium from internal stores. Effects of mGluR activation on subthreshold membrane potential changes are negligible but are large following action potential firing. Furthermore, the medium ADP exhibits a biphasic activity dependence consisting of short-term facilitation and longer-term inhibition. These findings suggest that mGluRs may dramatically alter the firing of CA1 pyramidal neurons via a complex, activity-dependent modulation of Ca(v)2.3 R-type channels that are activated during spiking at physiologically relevant rates and patterns.

}, keywords = {Action Potentials, Animals, Calcium Channels, Cation Transport Proteins, Female, Inbred C57BL, Ion Channel Gating, Male, Metabotropic Glutamate, Methoxyhydroxyphenylglycol, Mice, Neurons, Patch-Clamp Techniques, Pyramidal Cells, R-Type, Rats, Receptors, Up-Regulation, Wistar, Xenopus}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000534}, author = {Park, Jin-Yong and Remy, Stefan and Varela, Juan and Cooper, Donald C and Chung, Sungkwon and Kang, Ho-Won and Lee, Jung-Ha and Spruston, Nelson} } @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 {68824, title = {Proneural gene-linked neurogenesis in zebrafish cerebellum}, journal = {Developmental Biology}, volume = {343}, year = {2010}, month = {07/2010}, pages = {1-17}, abstract = {

In mammals, cerebellar neurons are categorized as glutamatergic or GABAergic, and are derived from progenitors that express the proneural genes atoh1 or ptf1a, respectively. In zebrafish, three atoh1 genes, atoh1a, atoh1b, and atoh1c, are expressed in overlapping but distinct expression domains in the upper rhombic lip (URL): ptf1a is expressed exclusively in the ventricular zone (VZ). Using transgenic lines expressing fluorescent proteins under the control of the regulatory elements of atoh1a and ptf1a, we traced the lineages of the cerebellar neurons. The atoh1+ progenitors gave rise not only to granule cells but also to neurons of the anteroventral rhombencephalon. The ptf1a+ progenitors generated Purkinje cells. The olig2+ eurydendroid cells, which are glutamatergic, were derived mostly from ptf1a+ progenitors in the VZ but some originated from the atoh1+ progenitors in the URL. In the adult cerebellum, atoh1a, atoh1b, and atoh1c are expressed in the molecular layer of the valvula cerebelli and of the medial corpus cerebelli, and ptf1a was detected in the VZ. The proneural gene expression patterns coincided with the sites of proliferating neuronal progenitors in the adult cerebellum. Our data indicate that proneural gene-linked neurogenesis is evolutionarily conserved in the cerebellum among vertebrates, and that the continuously generated neurons help remodel neural circuits in the adult zebrafish cerebellum.

}, keywords = {Adult neurogenesis, Cerebellum, GABAergic neuron, Glutamatergic neuron, Hindbrain, Proneural gene, Zebrafish}, issn = {0012-1606}, doi = {https://doi.org/10.1016/j.ydbio.2010.03.024}, url = {https://www.sciencedirect.com/science/article/pii/S0012160610002071}, author = {Shuichi Kani and Young-Ki Bae and Takashi Shimizu and Koji Tanabe and Chie Satou and Michael J. Parsons and Ethan Scott and Shin-ichi Higashijima and Masahiko Hibi} } @article {46617, title = {Protein Phosphatase 2a and glycogen synthase kinase 3 signaling modulate prepulse inhibition of the acoustic startle response by altering cortical M-Type potassium channel activity.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Jun 30}, pages = {8830-40}, abstract = {

There is considerable interest in the regulation of sensorimotor gating, since deficits in this process could play a critical role in the symptoms of schizophrenia and other psychiatric disorders. Sensorimotor gating is often studied in humans and rodents using the prepulse inhibition of the acoustic startle response (PPI) model, in which an acoustic prepulse suppresses behavioral output to a startle-inducing stimulus. However, the molecular and neural mechanisms underlying PPI are poorly understood. Here, we show that a regulatory pathway involving protein phosphatase 2A (PP2A), glycogen synthase kinase 3 beta (GSK3beta), and their downstream target, the M-type potassium channel, regulates PPI. Mice (Mus musculus) carrying a hypomorphic allele of Ppp2r5delta, encoding a regulatory subunit of PP2A, show attenuated PPI. This PPP2R5delta reduction increases the phosphorylation of GSK3beta at serine 9, which inactivates GSK3beta, indicating that PPP2R5delta positively regulates GSK3beta activity in the brain. Consistently, genetic and pharmacological manipulations that reduce GSK3beta function attenuate PPI. The M-type potassium channel subunit, KCNQ2, is a putative GSK3beta substrate. Genetic reduction of Kcnq2 also reduces PPI, as does systemic inhibition of M-channels with linopirdine. Importantly, both the GSK3 inhibitor 3-(2,4-dichlorophenyl)-4-(1-methyl-1H-indol-3-yl)1H-pyrrole-2,5-dione (SB216763) and linopirdine reduce PPI when directly infused into the medial prefrontal cortex (mPFC). Whole-cell electrophysiological recordings of mPFC neurons show that SB216763 and linopirdine have similar effects on firing, and GSK3 inhibition occludes the effects of M-channel inhibition. These data support a previously uncharacterized mechanism by which PP2A/GSK3beta signaling regulates M-type potassium channel activity in the mPFC to modulate sensorimotor gating.

}, keywords = {Amino Acid Sequence, Animals, Auditory Perception, Brain, Glycogen Synthase Kinase 3, Inhibition (Psychology), KCNQ2 Potassium Channel, Mice, Mice, Inbred C57BL, Mice, Transgenic, Models, Neurological, Neurons, Phosphorylation, Potassium Channels, Prefrontal Cortex, Protein Phosphatase 2, Reflex, Startle, Signal Transduction}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1292-10.2010}, author = {Kapfhamer, David and Berger, Karen H and Hopf, F Woodward and Seif, Taban and Kharazia, Viktor and Bonci, Antonello and Heberlein, Ulrike} } @article {3637, title = {The prototypical H+/galactose symporter GalP assembles into functional trimers.}, journal = {Journal of Molecular Biology}, volume = {396}, year = {2010}, month = {2010 Feb 26}, pages = {593-601}, abstract = {

Glucose is a primary source of energy for human cells. Glucose transporters form specialized membrane channels for the transport of sugars into and out of cells. Galactose permease (GalP) is the closest bacterial homolog of human facilitated glucose transporters. Here, we report the functional reconstitution and 2D crystallization of GalP. Single particle electron microscopy analysis of purified GalP shows that the protein assembles as an oligomer with three distinct densities. Reconstitution assays yield 2D GalP crystals that exhibit a hexagonal array having p3 symmetry. The projection structure of GalP at 18 A resolution shows that the protein is trimeric. Each monomer in the trimer forms its own channel, but an additional cavity (10 approximately 15 A in diameter) is apparent at the 3-fold axis of the oligomer. We show that the crystalline GalP is able to selectively bind substrate, suggesting that the trimeric form is biologically active.

}, keywords = {Calcium-Binding Proteins, Computer-Assisted, Crystallization, Electron, Escherichia coli, Escherichia coli Proteins, Galactose, Image Processing, Microscopy, Monosaccharide Transport Proteins, Periplasmic Binding Proteins, Protein Binding, Protein Multimerization, Protein Structure, Quaternary}, issn = {1089-8638}, doi = {10.1016/j.jmb.2009.12.010}, author = {Zheng, Hongjin and Taraska, Justin and Merz, Alexey J and Gonen, Tamir} } @article {3914, title = {Pathway interactions and synaptic plasticity in the dendritic tuft regions of CA1 pyramidal neurons.}, journal = {Neuron}, volume = {62}, year = {2009}, month = {2009 Apr 16}, pages = {102-11}, abstract = {

Input comparison is thought to occur in many neuronal circuits, including the hippocampus, where functionally important interactions between the Schaffer collateral and perforant pathways have been hypothesized. We investigated this idea using multisite, whole-cell recordings and Ca2+ imaging and found that properly timed, repetitive stimulation of both pathways results in the generation of large plateau potentials in distal dendrites of CA1 pyramidal neurons. These dendritic plateau potentials produce widespread Ca2+ influx, large after-depolarizations, burst firing output, and long-term potentiation of perforant path synapses. Plateau duration is directly related to the strength and temporal overlap of pathway activation and involves back-propagating action potentials and both NMDA receptors and voltage-gated Ca2+ channels. Thus, the occurrence of highly correlated SC and PP input to CA1 is signaled by a dramatic change in output mode and an increase in input efficacy, all induced by a large plateau potential in the distal dendrites of CA1 pyramidal neurons.

}, keywords = {Anesthetics, Animals, Biophysics, Calcium, Calcium Channel Blockers, Dendrites, Electric Stimulation, Excitatory Amino Acid Antagonists, Hippocampus, Inhibitory Postsynaptic Potentials, Local, Long-Term Potentiation, Membrane Potentials, Neural Pathways, Neuronal Plasticity, Newborn, Patch-Clamp Techniques, Pyramidal Cells, Rats, Spider Venoms, Sprague-Dawley, Synapses, Tetrodotoxin}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.03.007}, author = {Takahashi, Hiroto and Magee, Jeffrey C} } @article {6341, title = {Pentameric assembly of potassium channel tetramerization domain-containing protein 5.}, journal = {Journal of Molecular Biology}, volume = {387}, year = {2009}, month = {2009 Mar 20}, pages = {175-91}, abstract = {

We report the X-ray crystal structure of human potassium channel tetramerization domain-containing protein 5 (KCTD5), the first member of the family to be so characterized. Four findings were unexpected. First, the structure reveals assemblies of five subunits while tetramers were anticipated; pentameric stoichiometry is observed also in solution by scanning transmission electron microscopy mass analysis and analytical ultracentrifugation. Second, the same BTB (bric-a-brac, tramtrack, broad complex) domain surface mediates the assembly of five KCTD5 and four voltage-gated K(+) (Kv) channel subunits; four amino acid differences appear crucial. Third, KCTD5 complexes have well-defined N- and C-terminal modules separated by a flexible linker that swivels by approximately 30 degrees; the C-module shows a new fold and is required to bind Golgi reassembly stacking protein 55 with approximately 1 microM affinity, as judged by surface plasmon resonance and ultracentrifugation. Fourth, despite the homology reflected in its name, KCTD5 does not impact the operation of Kv4.2, Kv3.4, Kv2.1, or Kv1.2 channels.

}, keywords = {Amino Acid, Amino Acid Sequence, Biopolymers, Crystallography, Humans, Models, Molecular, Molecular Sequence Data, Potassium Channels, Protein Conformation, Sequence Homology, Static Electricity, Surface Plasmon Resonance, X-Ray}, issn = {1089-8638}, doi = {10.1016/j.jmb.2009.01.030}, author = {Dementieva, Irina S and Tereshko, Valentina and McCrossan, Zoe A and Solomaha, Elena and Araki, Daniel and Xu, Chen and Grigorieff, Nikolaus and Goldstein, Steve A N} } @article {4441, title = {The phase diagram and the pathway of phase transitions for traffic flow in a circular one-lane roadway.}, journal = {Physica A: Statistical Mechanics and its Applications}, volume = {388}, year = {2009}, month = {2009 Apr 15}, pages = {1665-72}, abstract = {

This paper demonstrates that patient driving habits lead to homogenous congested flow while impatient driving habits lead to wide-moving jam flow in the high density region based on the numerical simulation of the intelligent driver model proposed by M.Treiber [M. Treiber, A.Hennecke, D. Helbing, Phys. Rev. E 62 (2) (2000), 1805{\textendash}1824]. In a circular one lane traffic system which includes homogeneous drivers, we obtain the stable condition of homogenous flow and the phase diagram of traffic flow based on the linearization analysis. The phase diagram shows three possible pathways of phase transition along with the increase of global density: from the homogenous free flow to the homogenous congested flow directly, from the homogenous free flow to the synchronized flow then to the homogenous congested flow, or from the homogenous free flow to synchronized flow then to the wide-moving jam flow. The paper also analyzes the traffic flow including heterogenous drivers, and the results indicate that homogenous congested flow will lose its stability when the proportion of impatient drivers reaches a critical value and some new kinds of traffic flow emerge: wide-moving jam flow or a mixture of synchronized flow and wide-moving jam flow.

}, author = {Wei, Ziqiang and Hong, Yiguang and Wang, Dahui} } @article {45911, title = {Plasticity of burst firing induced by synergistic activation of metabotropic glutamate and acetylcholine receptors.}, journal = {Neuron}, volume = {61}, year = {2009}, month = {2009 Jan 29}, pages = {287-300}, abstract = {

Subiculum, the primary efferent pathway of hippocampus, participates in memory for spatial tasks, relapse to drug abuse, and temporal lobe seizures. Subicular pyramidal neurons exhibit low-threshold burst firing driven by a spike afterdepolarization. Here we report that burst firing can be regulated by stimulation of afferent projections to subiculum. Unlike synaptic plasticity, burst plasticity did not require synaptic depolarization, activation of AMPA or NMDA receptors, or action potential firing. Rather, enhancement of burst firing required synergistic activation of group I, subtype 1 metabotropic glutamate receptors (mGluRs) and muscarinic acetylcholine receptors (mAChR). When either of these receptors was blocked, a suppression of bursting was revealed, which in turn was blocked by antagonists of group I, subtype 5 mGluRs. These results indicate that the output of subiculum can be strongly and bidirectionally regulated by activation of glutamatergic inputs within the hippocampus and cholinergic afferents from the medial septum.

}, keywords = {Acetylcholine, Action Potentials, Afferent Pathways, Animals, Cholinergic Fibers, Electric Stimulation, Excitatory Amino Acid Antagonists, Glutamic Acid, Hippocampus, Male, Neuronal Plasticity, Pyramidal Cells, Rats, Rats, Wistar, Receptors, Cholinergic, Receptors, Metabotropic Glutamate, Receptors, Muscarinic, Septal Nuclei, Synaptic Transmission, Theta Rhythm}, issn = {1097-4199}, doi = {10.1016/j.neuron.2008.12.013}, author = {Moore, Shannon J and Cooper, Donald C and Spruston, Nelson} } @article {2377, title = {Positional cues in the Drosophila nerve cord: semaphorins pattern the dorso-ventral axis.}, journal = {PLoS Biology}, volume = {7}, year = {2009}, month = {2009 Jun 16}, pages = {e1000135}, abstract = {

During the development of neural circuitry, neurons of different kinds establish specific synaptic connections by selecting appropriate targets from large numbers of alternatives. The range of alternative targets is reduced by well organised patterns of growth, termination, and branching that deliver the terminals of appropriate pre- and postsynaptic partners to restricted volumes of the developing nervous system. We use the axons of embryonic Drosophila sensory neurons as a model system in which to study the way in which growing neurons are guided to terminate in specific volumes of the developing nervous system. The mediolateral positions of sensory arbors are controlled by the response of Robo receptors to a Slit gradient. Here we make a genetic analysis of factors regulating position in the dorso-ventral axis. We find that dorso-ventral layers of neuropile contain different levels and combinations of Semaphorins. We demonstrate the existence of a central to dorsal and central to ventral gradient of Sema 2a, perpendicular to the Slit gradient. We show that a combination of Plexin A (Plex A) and Plexin B (Plex B) receptors specifies the ventral projection of sensory neurons by responding to high concentrations of Semaphorin 1a (Sema 1a) and Semaphorin 2a (Sema 2a). Together our findings support the idea that axons are delivered to particular regions of the neuropile by their responses to systems of positional cues in each dimension.

}, keywords = {Animals, Axons, Cell Surface, Drosophila, Drosophila Proteins, Nerve Net, Nerve Tissue Proteins, Neurogenesis, Neuropil, Receptors, Semaphorins, Sensory Receptor Cells, Synapses}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000135}, author = {Zlatic, Marta and Li, Feng and Strigini, Maura and Grueber, Wesley and Bate, Michael} } @article {4526, title = {Preferential ethanol consumption in Drosophila models features of addiction.}, journal = {Current Biology}, volume = {19}, year = {2009}, month = {2009 Dec 29}, pages = {2126-32}, abstract = {

Alcohol addiction is a common affliction with a strong genetic component [1]. Although mammalian studies have provided significant insight into the molecular mechanisms underlying ethanol consumption [2], other organisms such as Drosophila melanogaster are better suited for unbiased, forward genetic approaches to identify novel genes. Behavioral responses to ethanol, such as hyperactivity, sedation, and tolerance, are conserved between flies and mammals [3, 4], as are the underlying molecular pathways [5-9]. However, few studies have investigated ethanol self-administration in flies [10]. Here we characterize ethanol consumption and preference in Drosophila. Flies prefer to consume ethanol-containing food over regular food, and this preference increases over time. Flies are attracted to the smell of ethanol, which partially mediates ethanol preference, but are averse to its taste. Preference for consuming ethanol is not entirely explained by attraction to either its sensory or caloric properties. We demonstrate that flies can exhibit features of alcohol addiction. First, flies self-administer ethanol to pharmacologically relevant concentrations. Second, flies will overcome an aversive stimulus in order to consume ethanol. Third, flies rapidly return to high levels of ethanol consumption after a period of imposed abstinence. Thus, ethanol preference in Drosophila provides a new model for studying aspects of addiction.

}, keywords = {Alcohol Drinking, Alcoholism, Analysis of Variance, Animal, Animals, Disease Models, Drosophila melanogaster, Drosophila Proteins, Ethanol, Eukaryotic Initiation Factor-5, Food Preferences, Smell, Taste}, issn = {1879-0445}, doi = {10.1016/j.cub.2009.10.070}, author = {Devineni, Anita V and Heberlein, Ulrike} } @article {6359, title = {Probing the evolution of appendage specialization by Hox gene misexpression in an emerging model crustacean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Aug 18}, pages = {13897-902}, abstract = {

Changes in the expression of Hox genes have been widely linked to the evolution of animal body plans, but functional demonstrations of this relationship have been impeded by the lack of suitable model organisms. A classic case study involves the repeated evolution of specialized feeding appendages, called maxillipeds, from anterior thoracic legs, in many crustacean lineages. These leg-to-maxilliped transformations correlate with the loss of Ultrabithorax (Ubx) expression from corresponding segments, which is proposed to be the underlying genetic cause. To functionally test this hypothesis, we establish tools for conditional misexpression and use these to misexpress Ubx in the crustacean Parhyale hawaiensis. Ectopic Ubx leads to homeotic transformations of anterior appendages toward more posterior thoracic fates, including maxilliped-to-leg transformations, confirming the capacity of Ubx to control thoracic (leg) versus gnathal (feeding) segmental identities. We find that maxillipeds not only are specified in the absence of Ubx, but also can develop in the presence of low/transient Ubx expression. Our findings suggest a path for the gradual evolutionary transition from thoracic legs to maxillipeds, in which stepwise changes in Hox gene expression have brought about this striking morphological and functional transformation.

}, keywords = {Animals, Cloning, Crustacea, Down-Regulation, Electron, Extremities, Gene Expression Regulation, Genes, Genetic, Genetically Modified, Heat-Shock Proteins, Homeobox, Homeodomain Proteins, Immunohistochemistry, Microscopy, Models, Molecular, Phenotype, Scanning, Transgenes}, issn = {1091-6490}, doi = {10.1073/pnas.0902804106}, author = {Pavlopoulos, Anastasios and Kontarakis, Zacharias and Liubicich, Danielle M and Serano, Julia M and Akam, Michael and Patel, Nipam H and Averof, Michalis} } @article {6491, title = {A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale.}, journal = {PLoS Computational Biology}, volume = {5}, year = {2009}, month = {2009 Mar}, pages = {e1000334}, abstract = {

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brainwide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brainwide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open-access data repository; compatibility with existing resources; and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.

}, keywords = {Animals, Brain, Databases, Factual, Humans, Macaca, Mice, Models, Nerve Net, Neuroanatomy, Neurological, Research Design}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000334}, author = {Bohland, Jason W and Wu, Caizhi and Barbas, Helen and Bokil, Hemant and Bota, Mihail and Breiter, Hans C and Cline, Hollis T and Doyle, John C and Freed, Peter J and Greenspan, Ralph J and Haber, Suzanne N and Hawrylycz, Michael and Herrera, Daniel G and Hilgetag, Claus C and Huang, Z Josh and Jones, Allan and Jones, Edward G and Karten, Harvey J and Kleinfeld, David and K{\"o}tter, Rolf and Lester, Henry A and Lin, John M and Mensh, Brett D and Mikula, Shawn and Panksepp, Jaak and Price, Joseph L and Safdieh, Joseph and Saper, Clifford B and Schiff, Nicholas D and Schmahmann, Jeremy D and Stillman, Bruce W and Svoboda, Karel and Swanson, Larry W and Toga, Arthur W and Van Essen, David C and Watson, James D and Mitra, Partha P} } @article {5412, title = {Purification, characterization and crystallization of pyrroline-5-carboxylate reductase from the hyperthermophilic archeon Sulfolobus Solfataricus.}, journal = {Protein Expression and Purification}, volume = {64}, year = {2009}, month = {2009 Apr}, pages = {125-30}, abstract = {

The gene SSO0495 (proC), which encodes pyrroline-5-carboxylate reductase (P5CR) from the thermoacidophilic archeon Sulfolobus solfataricus P2 (Ss-P5CR), was cloned and expressed. The purified recombinant enzyme catalyzes the thioproline dehydrogenase with concomitant oxidation of NAD(P)H to NAD(P)+. This archeal enzyme has an optimal alkaline pH in this reversible reaction and is thermostable with a half-life of approximately 30 min at 80 degrees C. At pH 9.0, the reverse activation rate is nearly 3-fold higher than at pH 7.0. The homopolymer was characterized by cross-linking and size exclusion gel filtration chromatography. Ss-P5CR was crystallized by the hanging-drop vapor-diffusion method at 37 degrees C. Diffraction data were obtained to a resolution of 3.5A and were suitable for X-ray structure determination.

}, keywords = {Archaeal Proteins, Chromatography, Crystallization, Crystallography, Gel, Kinetics, NADP, Pyrroline Carboxylate Reductases, Sulfolobus solfataricus, Temperature, Thiazolidines, X-Ray}, issn = {1096-0279}, doi = {10.1016/j.pep.2008.10.018}, author = {Meng, Zhaohui and Liu, Zhe and Lou, Zhiyong and Gong, Xiaocui and Cao, Yi and Bartlam, Mark and Zhang, Keqin and Rao, Zihe} } @article {46420, title = {A parasite cysteine protease is key to host protein degradation and iron acquisition.}, journal = {Journal of Biological Chemistry}, volume = {283}, year = {2008}, month = {2008 Oct 24}, pages = {28934-43}, abstract = {

Cysteine proteases of the Clan CA (papain) family are the predominant protease group in primitive invertebrates. Cysteine protease inhibitors arrest infection by the protozoan parasite, Trypanosoma brucei. RNA interference studies implicated a cathepsin B-like protease, tbcatB, as a key inhibitor target. Utilizing parasites in which one of the two alleles of tbcatb has been deleted, the key role of this protease in degradation of endocytosed host proteins is delineated. TbcatB deficiency results in a decreased growth rate and dysmorphism of the flagellar pocket and the subjacent endocytic compartment. Western blot and microscopic analysis indicate that deficiency in tbcatB results in accumulation of both host and parasite proteins, including the lysosomal marker p67. A critical function for parasitism is the degradation of host transferrin, which is necessary for iron acquisition. Substrate specificity analysis of recombinant tbcatB revealed the optimal peptide cleavage sequences for the enzyme and these were confirmed experimentally using FRET-based substrates. Degradation of transferrin was validated by SDS-PAGE and the specific cleavage sites identified by N-terminal sequencing. Because even a modest deficiency in tbcatB is lethal for the parasite, tbcatB is a logical target for the development of new anti-trypanosomal chemotherapy.

}, keywords = {Animals, Animals, Genetically Modified, Catalytic Domain, Cysteine, Cysteine Endopeptidases, Endocytosis, Fluorescence Resonance Energy Transfer, Iron, Lysosomes, Microscopy, Electron, Transmission, Models, Biological, Protein Structure, Tertiary, RNA Interference, Transferrin, Trypanosoma brucei brucei}, issn = {0021-9258}, doi = {10.1074/jbc.M805824200}, author = {O{\textquoteright}Brien, Theresa C and Mackey, Zachary B and Fetter, Richard D and Choe, Youngchool and O{\textquoteright}Donoghue, Anthony J and Zhou, Min and Craik, Charles S and Caffrey, Conor R and McKerrow, James H} } @article {2170, title = {Performance trade-offs in the flight initiation of Drosophila.}, journal = {The Journal of Experimental Biology}, volume = {211}, year = {2008}, month = {2008 Feb}, pages = {341-53}, abstract = {

The fruit fly Drosophila melanogaster performs at least two distinct types of flight initiation. One kind is a stereotyped escape response to a visual stimulus that is mediated by the hard-wired giant fiber neural pathway, and the other is a more variable ;voluntary{\textquoteright} response that can be performed without giant fiber activation. Because the simpler escape take-offs are apparently successful, it is unclear why the fly has multiple pathways to coordinate flight initiation. In this study we use high-speed videography to observe flight initiation in unrestrained wild-type flies and assess the flight performance of each of the two types of take-off. Three-dimensional kinematic analysis of take-off sequences indicates that wing use during the jumping phase of flight initiation is essential for stabilizing flight. During voluntary take-offs, early wing elevation leads to a slower and more stable take-off. In contrast, during visually elicited escapes, the wings are pulled down close to the body during take-off, resulting in tumbling flights in which the fly translates faster but also rotates rapidly about all three of its body axes. Additionally, we find evidence that the power delivered by the legs is substantially greater during visually elicited escapes than during voluntary take-offs. Thus, we find that the two types of Drosophila flight initiation result in different flight performances once the fly is airborne, and that these performances are distinguished by a trade-off between speed and stability.

}, keywords = {Animal, Animals, Biological, Biomechanics, Drosophila melanogaster, Escape Reaction, Extremities, Female, Flight, Models, Time Factors, Video Recording, Wing}, issn = {0022-0949}, doi = {10.1242/jeb.012682}, author = {Card, Gwyneth and Dickinson, Michael} } @article {45849, title = {The Pfam protein families database.}, journal = {Nucleic Acids Research}, volume = {36}, year = {2008}, month = {2008 Jan}, pages = {D281-8}, abstract = {

Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on sequences from selected metagenomics projects. Pfam is available on the web from the consortium members using a new, consistent and improved website design in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/), as well as from mirror sites in France (http://pfam.jouy.inra.fr/) and South Korea (http://pfam.ccbb.re.kr/).

}, keywords = {Animals, Databases, Protein, Genomics, Internet, Protein Structure, Tertiary, Proteins, Sequence Alignment, Sequence Analysis, Protein, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkm960}, author = {Finn, Robert D and Tate, John and Mistry, Jaina and Coggill, Penny C and Sammut, Stephen John and Hotz, Hans-Rudolf and Ceric, Goran and Forslund, Kristoffer and Eddy, Sean R and Sonnhammer, Erik L L and Bateman, Alex} } @article {1115, title = {Phenylglycine and phenylalanine derivatives as potent and selective HDAC1 inhibitors (SHI-1).}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {18}, year = {2008}, month = {2008 Mar 15}, pages = {1859-63}, abstract = {

An HTS screening campaign identified a series of low molecular weight phenols that showed excellent selectivity (\>100-fold) for HDAC1/HDAC2 over other Class I and Class II HDACs. Evolution and optimization of this HTS hit series provided HDAC1-selective (SHI-1) compounds with excellent anti-proliferative activity and improved physical properties. Dose-dependent efficacy in a mouse HCT116 xenograft model was demonstrated with a phenylglycine SHI-1 analog.

}, keywords = {Acetylation, Amides, Animals, Cell Proliferation, Colonic Neoplasms, Cultured, Dogs, Enzyme Inhibitors, Ether-A-Go-Go Potassium Channels, Glycine, Histone Deacetylase 1, Histone Deacetylase Inhibitors, Humans, Macaca mulatta, Mice, Molecular Structure, Phenylalanine, Structure-Activity Relationship, Tumor Cells, Xenograft Model Antitumor Assays}, issn = {1464-3405}, doi = {10.1016/j.bmcl.2008.02.012}, author = {Wilson, Kevin J and Witter, David J and Grimm, Jonathan B and Siliphaivanh, Phieng and Otte, Karin M and Kral, Astrid M and Fleming, Judith C and Harsch, Andreas and Hamill, Julie E and Cruz, Jonathan C and Chenard, Melissa and Szewczak, Alexander A and Middleton, Richard E and Hughes, Bethany L and Dahlberg, William K and Secrist, J Paul and Miller, Thomas A} } @article {2078, title = {Photoactivated localization microscopy (PALM) of adhesion complexes. (With commentary)}, journal = {Current Protocols in Cell Biology}, volume = {Chapter 4}, year = {2008}, month = {2008 Dec}, pages = {21}, abstract = {

Key to understanding a protein{\textquoteright}s biological function is the accurate determination of its spatial distribution inside a cell. Although fluorescent protein markers allow the targeting of specific proteins with molecular precision, much of this information is lost when the resultant fusion proteins are imaged with conventional, diffraction-limited optics. In response, several imaging modalities that are capable of resolution below the diffraction limit (approximately 200 nm) have emerged. Here, both single- and dual-color superresolution imaging of biological structures using photoactivated localization microscopy (PALM) are described. The examples discussed focus on adhesion complexes: dense, protein-filled assemblies that form at the interface between cells and their substrata. A particular emphasis is placed on the instrumentation and photoactivatable fluorescent protein (PA-FP) tags necessary to achieve PALM images at approximately 20 nm resolution in 5 to 30 min in fixed cells.

Commentary: A paper spearheaded by Hari which gives a thorough description of the methods and hardware needed to successfully practice PALM, including cover slip preparation, cell transfection and fixation, drift correction with fiducials, characterization of on/off contrast ratios for different photoactivted fluorescent proteins, identifying PALM-suitable cells, and mechanical and optical components of a PALM system.

}, keywords = {Animals, Cell Line, Cell-Matrix Junctions, Cells, Fluorescence, Humans, Microscopy, Photobleaching, Transfection}, issn = {1934-2616}, doi = {10.1002/0471143030.cb0421s41}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19085989}, author = {Shroff, Hari and White, Helen and Betzig, Eric} } @article {45962, title = {Polymorphic assemblies and crystalline arrays of lens tetraspanin MP20.}, journal = {Journal of Molecular Biology}, volume = {376}, year = {2008}, month = {2008 Feb 15}, pages = {380-92}, abstract = {

Members of the tetraspanin superfamily function as transmembrane scaffold proteins that mediate the assembly of membrane proteins into specific signaling complexes. Tetraspanins also interact with each other and concentrate membrane proteins into tetraspanin-enriched microdomains (TEMs). Here we report that lens-specific tetraspanin MP20 can form multiple types of higher-order assemblies and we present crystalline arrays of MP20. When isolated in the absence of divalent cations, MP20 is solubilized predominantly in tetrameric form, whereas the presence of divalent cations during solubilization promotes the association of MP20 tetramers into higher-order species. This effect only occurs when divalent cations are present during solubilization but not when divalent cations are added to solubilized tetrameric MP20, suggesting that other factors may also be involved. When purified MP20 tetramers are reconstituted with native lens lipids in the presence of magnesium, MP20 forms two-dimensional (2D) crystals. A projection map at 18 A resolution calculated from negatively stained 2D crystals showed that the building block of the crystal is an octamer consisting of two tetramers related to each other by 2-fold symmetry. In addition to 2D crystals, reconstitution of MP20 with native lipids also produced a variety of large protein-lipid complexes, and we present three-dimensional (3D) reconstructions of the four most abundant of these complexes in negative stain. The various complexes formed by MP20 most likely reflect the many ways in which tetraspanins can interact with each other to allow formation of TEMs.

}, keywords = {Animals, Buffers, Cations, Divalent, Cell Membrane, Chelating Agents, Crystallization, Detergents, Edetic Acid, Egtazic Acid, Eye Proteins, Hydrogen-Ion Concentration, Imaging, Three-Dimensional, Lens, Crystalline, Lipid Metabolism, Magnesium, Membrane Microdomains, Membrane Proteins, Protein Structure, Secondary, Protein Structure, Tertiary, Sheep, Silver Staining, Solubility, Tromethamine}, issn = {1089-8638}, doi = {10.1016/j.jmb.2007.09.001}, author = {Gonen, Tamir and Hite, Richard K and Cheng, Yifan and Petre, Benjamin M and Kistler, Joerg and Walz, Thomas} } @article {1770, title = {Preserving cell shape under environmental stress.}, journal = {Nature}, volume = {452}, year = {2008}, month = {2008 Mar 20}, pages = {361-4}, abstract = {

Maintaining cell shape and tone is crucial for the function and survival of cells and tissues. Mechanotransduction relies on the transformation of minuscule mechanical forces into high-fidelity electrical responses. When mechanoreceptors are stimulated, mechanically sensitive cation channels open and produce an inward transduction current that depolarizes the cell. For this process to operate effectively, the transduction machinery has to retain integrity and remain unfailingly independent of environmental changes. This is particularly challenging for poikilothermic organisms, where changes in temperature in the environment may impact the function of mechanoreceptor neurons. Thus, we wondered how insects whose habitat might quickly vary over several tens of degrees of temperature manage to maintain highly effective mechanical senses. We screened for Drosophila mutants with defective mechanical responses at elevated ambient temperatures, and identified a gene, spam, whose role is to protect the mechanosensory organ from massive cellular deformation caused by heat-induced osmotic imbalance. Here we show that Spam protein forms an extracellular shield that guards mechanosensory neurons from environmental insult. Remarkably, heterologously expressed Spam protein also endowed other cells with superb defence against physically and chemically induced deformation. We studied the mechanical impact of Spam coating and show that spam-coated cells are up to ten times stiffer than uncoated controls. Together, these results help explain how poikilothermic organisms preserve the architecture of critical cells during environmental stress, and illustrate an elegant and simple solution to such challenge.

}, keywords = {Animals, Biological, Cell Line, Cell Shape, Cellular, Chemical, Drosophila melanogaster, Drosophila Proteins, Electrophysiology, Environment, Eye Proteins, Hot Temperature, Humidity, Mechanical, Mechanoreceptors, Mechanotransduction, Models, Osmotic Pressure, Stimulation, Stress}, issn = {1476-4687}, doi = {10.1038/nature06603}, author = {Cook, Boaz and Hardy, Robert W and McConnaughey, William B and Zuker, Charles S} } @article {46419, title = {A presynaptic giant ankyrin stabilizes the NMJ through regulation of presynaptic microtubules and transsynaptic cell adhesion.}, journal = {Neuron}, volume = {58}, year = {2008}, month = {2008 Apr 24}, pages = {195-209}, abstract = {

In a forward genetic screen for mutations that destabilize the neuromuscular junction, we identified a novel long isoform of Drosophila ankyrin2 (ank2-L). We demonstrate that loss of presynaptic Ank2-L not only causes synapse disassembly and retraction but also disrupts neuronal excitability and NMJ morphology. We provide genetic evidence that ank2-L is necessary to generate the membrane constrictions that normally separate individual synaptic boutons and is necessary to achieve the normal spacing of subsynaptic protein domains, including the normal organization of synaptic cell adhesion molecules. Mechanistically, synapse organization is correlated with a lattice-like organization of Ank2-L, visualized using extended high-resolution structured-illumination microscopy. The stabilizing functions of Ank2-L can be mapped to the extended C-terminal domain that we demonstrate can directly bind and organize synaptic microtubules. We propose that a presynaptic Ank2-L lattice links synaptic membrane proteins and spectrin to the underlying microtubule cytoskeleton to organize and stabilize the presynaptic terminal.

}, keywords = {Amino Acid Motifs, Animals, Animals, Genetically Modified, Ankyrins, Cell Adhesion Molecules, Neuronal, Drosophila, Drosophila Proteins, Gene Expression Regulation, Horseradish Peroxidase, Larva, Luminescent Proteins, Microscopy, Electron, Transmission, Microtubules, Mutation, Neuromuscular Junction, Presynaptic Terminals, Synapsins, Synaptic Transmission}, issn = {1097-4199}, doi = {10.1016/j.neuron.2008.02.017}, author = {Pielage, Jan and Cheng, Ling and Fetter, Richard D and Carlton, Pete M and Sedat, John W and Davis, Graeme W} } @article {4252, title = {A probabilistic model of local sequence alignment that simplifies statistical significance estimation.}, journal = {PLoS Computational Biology}, volume = {4}, year = {2008}, month = {2008 May 30}, pages = {e1000069}, abstract = {

Sequence database searches require accurate estimation of the statistical significance of scores. Optimal local sequence alignment scores follow Gumbel distributions, but determining an important parameter of the distribution (lambda) requires time-consuming computational simulation. Moreover, optimal alignment scores are less powerful than probabilistic scores that integrate over alignment uncertainty ("Forward" scores), but the expected distribution of Forward scores remains unknown. Here, I conjecture that both expected score distributions have simple, predictable forms when full probabilistic modeling methods are used. For a probabilistic model of local sequence alignment, optimal alignment bit scores ("Viterbi" scores) are Gumbel-distributed with constant lambda = log 2, and the high scoring tail of Forward scores is exponential with the same constant lambda. Simulation studies support these conjectures over a wide range of profile/sequence comparisons, using 9,318 profile-hidden Markov models from the Pfam database. This enables efficient and accurate determination of expectation values (E-values) for both Viterbi and Forward scores for probabilistic local alignments.

}, keywords = {Algorithms, Base Sequence, Chromosome Mapping, Computer Simulation, Data Interpretation, DNA, Genetic, Models, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, Statistical}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000069}, author = {Sean R. Eddy} } @article {4259, title = {Probabilistic phylogenetic inference with insertions and deletions.}, journal = {PLoS Computational Biology}, volume = {4}, year = {2008}, month = {2008 Sep 19}, pages = {e1000172}, abstract = {

A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth-death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new "concordance test" benchmark on real ribosomal RNA alignments, we show that the extended program dnamlepsilon improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm.

}, keywords = {Algorithms, Computational Biology, Computer Simulation, DNA, Evolution, Genetic, Insertional, Markov Chains, Models, Molecular, Mutagenesis, Phylogeny, Poisson Distribution, Ribosomal, RNA, Sequence Alignment, Sequence Deletion, Software, Statistical}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000172}, author = {Rivas, Elena and Sean R. Eddy} } @article {45920, title = {Pyramidal neurons: dendritic structure and synaptic integration.}, journal = {Nature Reviews Neuroscience}, volume = {9}, year = {2008}, month = {2008 Mar}, pages = {206-21}, abstract = {

Pyramidal neurons are characterized by their distinct apical and basal dendritic trees and the pyramidal shape of their soma. They are found in several regions of the CNS and, although the reasons for their abundance remain unclear, functional studies--especially of CA1 hippocampal and layer V neocortical pyramidal neurons--have offered insights into the functions of their unique cellular architecture. Pyramidal neurons are not all identical, but some shared functional principles can be identified. In particular, the existence of dendritic domains with distinct synaptic inputs, excitability, modulation and plasticity appears to be a common feature that allows synapses throughout the dendritic tree to contribute to action-potential generation. These properties support a variety of coincidence-detection mechanisms, which are likely to be crucial for synaptic integration and plasticity.

}, keywords = {Animals, Dendrites, Hippocampus, Models, Neurological, Neocortex, Pyramidal Cells, Synapses}, issn = {1471-0048}, doi = {10.1038/nrn2286}, author = {Spruston, Nelson} } @article {1733, title = {Phase-sensitive sum-frequency vibrational spectroscopy and its application to studies of interfacial alkyl chains.}, journal = {Journal of the American Chemical Society}, volume = {129}, year = {2007}, month = {2007 Aug 22}, pages = {10056-7}, abstract = {

The first general phase-sensitive sum-frequency vibrational spectroscopy (SFVS) was described, which recovers the phase information lost in conventional SFVS measurements. Using a self-assembled monolayer, we demonstrated that this novel technique measures the absolute orientation of surface molecular moieties and is very powerful in resolving spectral features.

}, issn = {0002-7863}, doi = {10.1021/ja071989t}, author = {Ji, Na and Ostroverkhov, Victor and Chen, Chao-Yuan and Shen, Yuen-Ron} } @article {2155, title = {Phenotype clustering of breast epithelial cells in confocal images based on nuclear protein distribution analysis.}, journal = {BMC Cell Biology}, volume = {8 }, year = {2007}, month = {2007 Jul 10}, pages = {S3}, abstract = {

The distribution of chromatin-associated proteins plays a key role in directing nuclear function. Previously, we developed an image-based method to quantify the nuclear distributions of proteins and showed that these distributions depended on the phenotype of human mammary epithelial cells. Here we describe a method that creates a hierarchical tree of the given cell phenotypes and calculates the statistical significance between them, based on the clustering analysis of nuclear protein distributions.

}, keywords = {Breast, Breast Neoplasms, Cell Line, Cluster Analysis, Computer-Assisted, Confocal, Epithelial Cells, Female, Humans, Image Processing, Imaging, Microscopy, Models, Nuclear Proteins, Phenotype, Statistical, Three-Dimensional}, issn = {1471-2121}, doi = {10.1007/s12021-010-9090-x}, author = {Long, Fuhui and Peng, Hanchuan and Sudar, Damir and Leli{\`e}vre, Sophie A and Knowles, David W} } @article {48397, title = {Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors.}, journal = {Biochemistry}, volume = {46}, year = {2007}, month = {2007 Jan 23}, pages = {669-82}, abstract = {

To identify basic local backbone motions in unfolded chains, simulations are performed for a variety of peptide systems using three popular force fields and for implicit and explicit solvent models. A dominant "crankshaft-like" motion is found that involves only a localized oscillation of the plane of the peptide group. This motion results in a strong anticorrelated motion of the phi angle of the ith residue (phi(i)) and the psi angle of the residue i - 1 (psi(i-1)) on the 0.1 ps time scale. Only a slight correlation is found between the motions of the two backbone dihedral angles of the same residue. Aside from the special cases of glycine and proline, no correlations are found between backbone dihedral angles that are separated by more than one torsion angle. These short time, correlated motions are found both in equilibrium fluctuations and during the transit process between Ramachandran basins, e.g., from the beta to the alpha region. A residue{\textquoteright}s complete transit from one Ramachandran basin to another, however, occurs in a manner independent of its neighbors{\textquoteright} conformational transitions. These properties appear to be intrinsic because they are robust across different force fields, solvent models, nonbonded interaction routines, and most amino acids.

}, keywords = {Alanine, Computer Simulation, Glycine, Models, Molecular, Molecular Conformation, Motion, Peptides, Proline, Protein Folding}, issn = {0006-2960}, doi = {10.1021/bi061575x}, author = {Fitzgerald, James E and Jha, Abhishek K and Sosnick, Tobin R and Freed, Karl F} } @article {45959, title = {Projection map of aquaporin-9 at 7 A resolution.}, journal = {Journal of Molecular Biology}, volume = {367}, year = {2007}, month = {2007 Mar 16}, pages = {80-8}, abstract = {

Aquaporin-9, an aquaglyceroporin present in diverse tissues, is unique among aquaporins because it is not only permeable to water, urea and glycerol, but also allows passage of larger uncharged solutes. Single particle analysis of negatively stained recombinant rat aquaporin-9 revealed a particle size characteristic of the tetrameric organization of all members of the aquaporin family. Reconstitution of aquaporin-9 into two-dimensional crystals enabled us to calculate a projection map at 7 A resolution. The projection structure indicates a tetrameric structure, similar to GlpF, with each square-like monomer forming a pore. A comparison of the pore-lining residues between the crystal structure of GlpF and a homology model of aquaporin-9 locates substitutions in these residues predominantly to the hydrophobic edge of the tripathic pore of GlpF, providing first insights into the structural basis for the broader substrate specificity of aquaporin-9.

}, keywords = {Animals, Aquaporins, Crystallography, Escherichia coli, Escherichia coli Proteins, Gene Expression, Models, Molecular, Protein Conformation, Rats, Recombinant Proteins}, issn = {0022-2836}, doi = {10.1016/j.jmb.2006.12.042}, author = {Viadiu, Hector and Gonen, Tamir and Walz, Thomas} } @article {1584, title = {Purification, crystallization and preliminary crystallographic analysis of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus.}, journal = {Acta Crystallographica. Section F, Structural Biology and Crystallization Communications}, volume = {63}, year = {2007}, month = {2007 Mar 1}, pages = {239-41}, abstract = {

A predicted GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus, termed SsGBP, has been cloned and overexpressed in Escherichia coli. The purified protein was crystallized using the hanging-drop vapour-diffusion technique in the presence of 0.05 M cadmium sulfate and 0.8 M sodium acetate pH 7.5. A single-wavelength anomalous dispersion data set was collected to a maximum resolution of 2.0 A using a single cadmium-incorporated crystal. The crystal form belongs to space group P2(1)2(1)2(1), with approximate unit-cell parameters a = 65.0

}, keywords = {Archaeal Proteins, Crystallization, Crystallography, GTP-Binding Proteins, Hot Temperature, Sulfolobus solfataricus, X-Ray}, issn = {1744-3091}, doi = {10.1107/S1744309107008500}, author = {Wu, Hao and Sun, Lei and Brouns, Stan J J and Fu, Sheng and Akerboom, Jasper and Li, Xuemei and van der Oost, John} } @article {45748, title = {The pea aphid, Acyrthosiphon pisum: an emerging genomic model system for ecological, developmental and evolutionary studies.}, journal = {Bioessays}, volume = {28}, year = {2006}, month = {2006 Jul}, pages = {747-55}, abstract = {

Aphids display an abundance of adaptations that are not easily studied in existing model systems. Here we review the biology of a new genomic model system, the pea aphid, Acyrthosiphon pisum. We then discuss several phenomena that are particularly accessible to study in the pea aphid: the developmental genetic basis of polyphenisms, aphid-bacterial symbioses, the genetics of adaptation and mechanisms of virus transmission. The pea aphid can be maintained in the laboratory and natural populations can be studied in the field. These properties allow controlled experiments to be performed on problems of direct relevance to natural aphid populations. Combined with new genomic approaches, the pea aphid is poised to become an important model system for understanding the molecular and developmental basis of many ecologically and evolutionarily relevant problems.

}, keywords = {Adaptation, Biological, Animals, Aphids, Biological Evolution, Ecology, Female, Genome, Insect, Life Cycle Stages, Male, Models, Genetic, Peas, Plant Viruses, Polymorphism, Genetic, Symbiosis}, issn = {0265-9247}, doi = {10.1002/bies.20436}, author = {Brisson, Jennifer A and Stern, David L} } @article {4007, title = {Perturbation of auditory feedback causes systematic perturbation in vocal structure in adult cotton-top tamarins.}, journal = {The Journal of Experimental Biology}, volume = {209}, year = {2006}, month = {2006 Sep}, pages = {3652-63}, abstract = {

Auditory feedback is critical for the development and maintenance of speech in humans. In contrast, studies of nonhuman primate vocal production generally report that subjects show little reliance on auditory input. We examined the extent to which cotton-top tamarin (Saguinus oedipus) vocal production is sensitive to perturbation of auditory feedback by manipulating the predictability of presentation of a 1 s burst of white noise during the production of the species-specific contact call, the combination long call (CLC). We used three experimental conditions: the Begin condition, in which white noise was presented only during the first half of a recording session, the End condition, in which white noise was presented only in the last half, and the Random condition, in which each call had a 50\% probability of receiving white noise playback throughout the recording session, making the auditory feedback unpredictable. In addition we recorded calls before and after the experimental series (Baseline condition) to determine whether any changes induced by modification of auditory feedback persisted. Results showed that playback of white noise during the production of the CLC produced changes in the temporal structure of the CLC: calls were shorter and had fewer pulses, indicating that modification of auditory feedback can interrupt vocal production. In addition, calls that received modified feedback were louder and had longer inter-pulse intervals than those that did not, consistent with an adaptive response to the masking effect of white noise playback. The magnitude of this compensatory effect and the interruption rate were both sensitive to whether the feedback modification occurred at the beginning or end of the experimental session: early feedback produced less interruption and more compensation. Finally, when auditory feedback modification was unpredictable, adaptive changes were observed in both calls that received modified feedback and those that received normal feedback, suggesting that tamarins can generate an expectation of noise playback and increase vocal amplitude in anticipation of masking.

}, keywords = {Acoustic Stimulation, Adaptation, Animal, Animals, Female, Male, Perceptual Masking, Psychological, Saguinus, Vocalization}, issn = {0022-0949}, doi = {10.1242/jeb.02420}, author = {Egnor, S E Roian and Iguina, Carmen G and Hauser, Marc D} } @article {1407, title = {Physiological properties of zebra finch ventral tegmental area and substantia nigra pars compacta neurons.}, journal = {Journal of Neurophysiology}, volume = {96}, year = {2006}, month = {2006 Nov}, pages = {2295-306}, abstract = {

The neurotransmitter dopamine plays important roles in motor control, learning, and motivation in mammals and probably other animals as well. The strong dopaminergic projection to striatal regions and more moderate dopaminergic projections to other regions of the telencephalon predominantly arise from midbrain dopaminergic neurons in the substantia nigra pars compacta (SNc) and ventral tegmental area (VTA). Homologous dopaminergic cell groups in songbirds project anatomically in a manner that may allow dopamine to influence song learning or song production. The electrophysiological properties of SNc and VTA neurons have not previously been studied in birds. Here we used whole cell recordings in brain slices in combination with tyrosine-hydroxylase immunolabeling as a marker of dopaminergic neurons to determine electrophysiological and pharmacological properties of dopaminergic and nondopaminergic neurons in the zebra finch SNc and VTA. Our results show that zebra finch dopaminergic neurons possess physiological properties very similar to those of mammalian dopaminergic neurons, including broad action potentials, calcium- and apamin-sensitive membrane-potential oscillations underlying pacemaker firing, powerful spike-frequency adaptation, and autoinhibition via D2 dopamine receptors. Moreover, the zebra finch SNc and VTA also contain nondopaminergic neurons with similarities (fast-firing, inhibition by the mu-opioid receptor agonist [d-Ala(2), N-Me-Phe(4), Gly-ol(5)]-enkephalin (DAMGO)) and differences (strong h-current that contributes to spontaneous firing) compared with GABAergic neurons in the mammalian SNc and VTA. Our results provide insight into the intrinsic membrane properties that regulate the activity of dopaminergic neurons in songbirds and add to strong evidence for anatomical, physiological, and functional similarities between the dopaminergic systems of mammals and birds.

}, keywords = {Action Potentials, Ala(2)-MePhe(4)-Gly(5)-, Animals, Cholera Toxin, Dopamine D2, Electrophysiology, Enkephalin, Finches, Lysine, Male, mu, Neurons, Opioid, Patch-Clamp Techniques, Quinpirole, Receptors, Substantia Nigra, Tetrodotoxin, Tyrosine 3-Monooxygenase, Ventral Tegmental Area}, issn = {0022-3077}, doi = {10.1152/jn.01040.2005}, author = {Gale, Samuel D and Perkel, David J} } @article {2446, title = {The pupal specifier broad directs progressive morphogenesis in a direct-developing insect.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {2006 May 2}, pages = {6925-30}, abstract = {

A key regulatory gene in metamorphosing (holometabolous) insect life histories is the transcription factor broad (br), which specifies pupal development. To determine the role of br in a direct-developing (hemimetabolous) insect that lacks a pupal stage, we cloned br from the milkweed bug, Oncopeltus fasciatus (Of{\textquoteright}br). We find that, unlike metamorphosing insects, in which br expression is restricted to the larval-pupal transition, Of{\textquoteright}br mRNA is expressed during embryonic development and is maintained at each nymphal molt but then disappears at the molt to the adult. Induction of a supernumerary nymphal stage with a juvenile hormone (JH) mimic prevented the disappearance of br mRNA. In contrast, induction of a precocious adult molt by application of precocene II to third-stage nymphs caused a loss of br mRNA at the precocious adult molt. Thus, JH is necessary to maintain br expression during the nymphal stages. Injection of Of{\textquoteright}br dsRNA into either early third- or fourth-stage nymphs caused a repetition of stage-specific pigmentation patterns and prevented the normal anisometric growth of the wing pads without affecting isometric growth or molting. Therefore, br is necessary for the mutable (heteromorphic) changes that occur during hemimetabolous development. Our results suggest that metamorphosis in insects arose as expression of br, which conveys competence for change, became restricted to one postembryonic instar. After this shift in br expression, the progressive changes that occur within the nymphal series in basal insects became compressed to the one short period of morphogenesis seen in the larva-to-pupa transition of holometabolous insects.

}, keywords = {Animals, Biological, Drosophila Proteins, Heteroptera, Insect Proteins, Juvenile Hormones, Metamorphosis, Molecular Sequence Data, Morphogenesis, Nymph, Pigmentation, RNA, Transcription Factors, Wing}, issn = {0027-8424}, doi = {10.1073/pnas.0509983103}, author = {Erezyilmaz, Deniz F and Riddiford, Lynn M and Truman, James W} } @article {5414, title = {Purification, characterization, and crystallization of human pyrroline-5-carboxylate reductase.}, journal = {Protein Expression and Purification}, volume = {49}, year = {2006}, month = {2006 Sep}, pages = {83-7}, abstract = {

Pyrroline-5-carboxylate reductase (P5CR) catalyzes the reduction of Delta1-pyrroline-5-carboxylate (P5C) to proline with concomitant oxidation of NAD(P)H to NAD(P)(+). The enzymatic cycle between P5C and proline is very important in many physiological and pathological processes. Human P5CR was over-expressed in Escherichia coli and purified to homogeneity by chromatography. Enzymatic assays of the wild-type protein were carried out using 3,4-dehydro-L-proline as substrate and NAD(+) as cofactor. The homopolymer was characterized by cross-linking and size exclusion gel filtration chromatography. Human P5CR was crystallized by the hanging-drop vapor-diffusion method at 37 degrees C. Diffraction data were obtained to a resolution of 2.8A and were suitable for high resolution X-ray structure determination.

}, keywords = {Crystallization, Crystallography, Gene Expression, Humans, Polymers, Proline, Pyrroline Carboxylate Reductases, Solubility, Water, X-Ray}, issn = {1046-5928}, doi = {10.1016/j.pep.2006.02.019}, author = {Meng, Zhaohui and Lou, Zhiyong and Liu, Zhe and Hui, Dong and Bartlam, Mark and Rao, Zihe} } @article {2132, title = {Plasticity of dendritic function.}, journal = {Current Opinion in Neurobiology}, volume = {15}, year = {2005}, month = {2005 Jun}, pages = {334-42}, abstract = {

The various properties of neuronal dendrites{\textendash}their morphology, active membrane and synaptic properties{\textendash}all play important roles in determining the functional capabilities of central nervous system neurons. Because of their fundamental involvement in both synaptic integration and synaptic plasticity, the active dendritic properties are important for both neuronal information processing and storage. The active properties of dendrites are determined by the densities of voltage-gated ion channels located within the dendrites in addition to the biophysical characteristics of those channels. The real power of this system resides in the level of plasticity that is provided by the many forms of channel modulation known to exist in neurons. Indeed, voltage gated ion channel modulation shapes the active properties of neuronal dendrites to specific conditions, thus tailoring the functional role of the single neuron within its circuit.

}, keywords = {Action Potentials, Brain, Dendrites, Ion Channel Gating, Ion Channels, Neuronal Plasticity}, issn = {0959-4388}, doi = {10.1002/cbic.201000254}, author = {Magee, Jeffrey C and Johnston, Daniel} } @article {45753, title = {Pleiotropic functions of a conserved insect-specific Hox peptide motif.}, journal = {Development}, volume = {132}, year = {2005}, month = {2005 Dec}, pages = {5261-70}, abstract = {

The proteins that regulate developmental processes in animals have generally been well conserved during evolution. A few cases are known where protein activities have functionally evolved. These rare examples raise the issue of how highly conserved regulatory proteins with many roles evolve new functions while maintaining old functions. We have investigated this by analyzing the function of the ;QA{\textquoteright} peptide motif of the Hox protein Ultrabithorax (Ubx), a motif that has been conserved throughout insect evolution since its establishment early in the lineage. We precisely deleted the QA motif at the endogenous locus via allelic replacement in Drosophila melanogaster. Although the QA motif was originally characterized as involved in the repression of limb formation, we have found that it is highly pleiotropic. Curiously, deleting the QA motif had strong effects in some tissues while barely affecting others, suggesting that QA function is preferentially required for a subset of Ubx target genes. QA deletion homozygotes had a normal complement of limbs, but, at reduced doses of Ubx and the abdominal-A (abd-A) Hox gene, ectopic limb primordia and adult abdominal limbs formed when the QA motif was absent. These results show that redundancy and the additive contributions of activity-regulating peptide motifs play important roles in moderating the phenotypic consequences of Hox protein evolution, and that pleiotropic peptide motifs that contribute quantitatively to several functions are subject to intense purifying selection.

}, keywords = {Amino Acid Motifs, Animals, Conserved Sequence, Drosophila melanogaster, Drosophila Proteins, Extremities, Genes, Homeobox, Homeodomain Proteins, Phenotype, Sequence Deletion, Transcription Factors}, issn = {0950-1991}, doi = {10.1242/dev.02146}, author = {Hittinger, Chris Todd and Stern, David L and Carroll, Sean B} } @article {3432, title = {Pneumatic capillary gun for ballistic delivery of microparticles.}, journal = {Applied Physics Letters}, volume = {87}, year = {2005}, month = {2005 Jun 29}, pages = {014103}, abstract = {

A pneumatic gun for ballistic delivery of microparticles to soft targets is proposed and demonstrated. The particles are accelerated by a high-speed flow of helium in a capillary tube. Vacuum suction applied to a concentric larger diameter tube is used to divert substantially all of the flow of helium from the gun nozzle, thereby preventing the gas from hitting and damaging the target. Speed of ejection of micron-sized gold particles from the gun nozzle, and their depth of penetration into agarose gels are reported.

}, author = {Rinberg, Dmitry and Simonnet, C and Groisman, A} } @article {45921, title = {Postsynaptic depolarization requirements for LTP and LTD: a critique of spike timing-dependent plasticity.}, journal = {Nat Neurosci}, volume = {8}, year = {2005}, month = {2005 Jul}, pages = {839-41}, abstract = {

Long-term potentiation and long-term depression require postsynaptic depolarization, which many current models attribute to backpropagating action potentials. New experimental work suggests, however, that other mechanisms can lead to dendritic depolarization, and that backpropagating action potentials may be neither necessary nor sufficient for synaptic plasticity in vivo.

}, keywords = {Action Potentials, Animals, Dendrites, Electrophysiology, Excitatory Postsynaptic Potentials, Humans, Long-Term Potentiation, Long-Term Synaptic Depression, Neuronal Plasticity, Reaction Time, Synapses}, issn = {1097-6256}, author = {Lisman, John and Spruston, Nelson} } @article {1405, title = {Properties of dopamine release and uptake in the songbird basal ganglia.}, journal = {Journal of Neurophysiology}, volume = {93}, year = {2005}, month = {2005 Apr}, pages = {1871-9}, abstract = {

Vocal learning in songbirds requires a basal ganglia circuit termed the anterior forebrain pathway (AFP). The AFP is not required for song production, and its role in song learning is not well understood. Like the mammalian striatum, the striatal component of the AFP, Area X, receives dense dopaminergic innervation from the midbrain. Since dopamine (DA) clearly plays a crucial role in basal ganglia-mediated motor control and learning in mammals, it seems likely that DA signaling contributes importantly to the functions of Area X as well. In this study, we used voltammetric methods to detect subsecond changes in extracellular DA concentration to gain better understanding of the properties and regulation of DA release and uptake in Area X. We electrically stimulated Ca(2+)- and action potential-dependent release of an electroactive substance in Area X brain slices and identified the substance as DA by the voltammetric waveform, electrode selectivity, and neurochemical and pharmacological evidence. As in the mammalian striatum, DA release in Area X is depressed by autoinhibition, and the lifetime of extracellular DA is strongly constrained by monoamine transporters. These results add to the known physiological similarities of the mammalian and songbird striatum and support further use of voltammetry in songbirds to investigate the role of basal ganglia DA in motor learning.

}, keywords = {Animals, Basal Ganglia, Dopamine, Male, Neural Pathways, Presynaptic, Receptors, Songbirds}, issn = {0022-3077}, doi = {10.1152/jn.01053.2004}, author = {Gale, Samuel D and Perkel, David J} } @article {4008, title = {A paradox in the evolution of primate vocal learning.}, journal = {Trends in Neurosciences}, volume = {27}, year = {2004}, month = {2004 Nov}, pages = {649-54}, abstract = {

The importance of auditory feedback in the development of spoken language in humans is striking. Paradoxically, although auditory-feedback-dependent vocal plasticity has been shown in a variety of taxonomic groups, there is little evidence that our nearest relatives{\textendash}non-human primates{\textendash}require auditory feedback for the development of species-typical vocal signals. Because of the apparent lack of developmental plasticity in the vocal production system, neuroscientists have largely ignored the neural mechanisms of non-human primate vocal production and perception. Recently, the absence of evidence for vocal plasticity from developmental studies has been contrasted with evidence for vocal plasticity in adults. We argue that this new evidence makes non-human primate vocal behavior an attractive model system for neurobiological analysis.

}, keywords = {Acoustic Stimulation, Animal, Animals, Biological Evolution, Humans, Learning, Vocalization}, issn = {0166-2236}, doi = {10.1016/j.tins.2004.08.009}, author = {Egnor, S E Roian and Hauser, Marc D} } @article {2416, title = {Polybromo protein BAF180 functions in mammalian cardiac chamber maturation.}, journal = {Genes \& Development}, volume = {18}, year = {2004}, month = {2004 Dec 15}, pages = {3106-16}, abstract = {

BAF and PBAF are two related mammalian chromatin remodeling complexes essential for gene expression and development. PBAF, but not BAF, is able to potentiate transcriptional activation in vitro mediated by nuclear receptors, such as RXRalpha, VDR, and PPARgamma. Here we show that the ablation of PBAF-specific subunit BAF180 in mouse embryos results in severe hypoplastic ventricle development and trophoblast placental defects, similar to those found in mice lacking RXRalpha and PPARgamma. Embryonic aggregation analyses reveal that in contrast to PPARgamma-deficient mice, the heart defects are likely a direct result of BAF180 ablation, rather than an indirect consequence of trophoblast placental defects. We identified potential target genes for BAF180 in heart development, such as S100A13 as well as retinoic acid (RA)-induced targets RARbeta2 and CRABPII. Importantly, BAF180 is recruited to the promoter of these target genes and BAF180 deficiency affects the RA response for CRABPII and RARbeta2. These studies reveal unique functions of PBAF in cardiac chamber maturation.

}, keywords = {Animals, Cell Aggregation, Chromatin Assembly and Disassembly, Congenital, Developmental, DNA Primers, Gene Expression Regulation, Heart Defects, Immunoprecipitation, In Situ Hybridization, In Situ Nick-End Labeling, Knockout, Mice, Nuclear Proteins, Oligonucleotide Array Sequence Analysis, Placenta, Receptors, Retinoic Acid, Reverse Transcriptase Polymerase Chain Reaction, S100 Proteins, Transcription Factors}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {Wang, Zhong and Zhai, Weiguo and Richardson, James A and Olson, Eric N and Meneses, Juanito J and Firpo, Meri T and Kang, Chulho and Skarnes, William C and Tjian, Robert} } @conference {45802, title = {Prospects in aphid genetics}, booktitle = {Aphids in a new millennium. Proceedings of the Sixth International Symposium on Aphids}, year = {2004}, month = {09/2004}, publisher = {Institut National de la Recherche Agronomique}, organization = {Institut National de la Recherche Agronomique}, address = {Rennes, France}, abstract = {

This paper identifies the prospects of using aphid species as ideal genetic model systems for the study of evolutionary developmental biology and genetic control of polyphenisms. The advantages and disadvantages of using aphids as genetic model organisms are discussed.

}, isbn = {2-7380-1113-6}, url = {http://www.cabdirect.org/abstracts/20043046841.html;jsessionid=4C6865DD4D971042FEB329F0DD6166E5}, author = {DL Stern and JC Simon and CA Dedryver and C Rispe and M Hull{\'e}} } @article {1257, title = {Power-law for axon diameters at branch point.}, journal = {BMC Neuroscience}, volume = {4}, year = {2003}, month = {2003 Aug 28}, pages = {18}, abstract = {

Axon calibers vary widely among different animals, neuron classes, and even within the same neuron. What determines the diameter of axon branches?

}, keywords = {Animals, Axons, Biological Evolution, Humans, Models, Neural Conduction, Neurological, Predictive Value of Tests, Reaction Time}, issn = {1471-2202}, doi = {10.1016/j.tins.2005.05.006}, author = {Chklovskii, Dmitri B and Stepanyants, Armen} } @article {1987, title = {Presynaptic cyclic nucleotide-gated ion channels modulate neurotransmission in the mammalian olfactory bulb.}, journal = {Neuron}, volume = {37}, year = {2003}, month = {2003 Feb 20}, pages = {639-47}, abstract = {

Cyclic nucleotide-gated channels (CNGCs) on the dendritic cilia of olfactory receptor neurons (ORNs) are critical for sensory transduction in the olfactory system. Do CNGCs also play a role in the axons and/or nerve terminals of ORNs? We find that the cyclic nucleotides cAMP and cGMP can both facilitate and depress synaptic transmission between olfactory nerve fibers and their targets in olfactory bulb glomeruli. Cyclic nucleotides increase intracellular Ca(2+) in ORN terminals and enhance spontaneous transmitter release; at higher concentrations, cyclic nucleotides depress evoked transmission by altering olfactory nerve excitability. Cyclic nucleotides have no effect on transmission or nerve excitability, however, in mice lacking olfactory CNGCs. Taken together, our results identify a novel role for presynaptic CNGCs in modulating neurotransmission.

}, keywords = {Animals, Calcium, Cyclic, Cyclic GMP, Electric Stimulation, Enzyme Inhibitors, Excitatory Postsynaptic Potentials, Forskolin, GABA Agonists, Inbred C57BL, Ion Channel Gating, Ion Channels, Mice, Nucleotides, Olfactory Bulb, Patch-Clamp Techniques, Presynaptic Terminals, Rats, Sprague-Dawley, Synaptic Transmission}, issn = {0896-6273}, author = {Murphy, Gabe J and Isaacson, Jeffry S} } @article {2141, title = {A prominent role for intrinsic neuronal properties in temporal coding.}, journal = {Trends in Neurosciences}, volume = {26}, year = {2003}, month = {2003 Jan}, pages = {14-6}, abstract = {

A recent report presents evidence that the exact timing of action potential output in rat hippocampal pyramidal neurons is similarly modulated during several diverse forms of behavior. These data suggest that it is, to a large degree, the intrinsic properties of the neurons themselves that produce this temporal coding of information. Thus, this report provides an outstanding example of the importance of single neuronal properties, even during complex behaviors.

}, keywords = {Animals, Automatic Data Processing, Hippocampus, Interneurons, Membrane Potentials, Neurons, Rats, Theta Rhythm, Time Factors}, issn = {0166-2236}, doi = {10.1002/cbic.201000254}, author = {Magee, Jeffrey C} } @article {1591, title = {Purification, crystallization and preliminary crystallographic analysis of phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus.}, journal = {Acta Crystallographica. Section D, Biological Crystallography}, volume = {59}, year = {2003}, month = {2003 Oct 19}, pages = {1822-3}, abstract = {

The glycolytic enzyme phosphoglucose isomerase catalyses the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus, which shows no sequence similarity to any known bacterial or eukaryotic phosphoglucose isomerase, has been cloned and overexpressed in Escherichia coli, purified and subsequently crystallized by the hanging-drop method of vapour diffusion using 1.6 M sodium citrate as the precipitant at pH 6.5. Multiple-wavelength anomalous dispersive X-ray data have been collected to a maximum resolution of 1.92 A on a single selenomethionine-incorporated crystal. This crystal belongs to space group C2, with approximate unit-cell parameters a = 84.7

}, keywords = {Crystallization, Crystallography, Escherichia coli, Glucose-6-Phosphate Isomerase, Protein Conformation, Pyrococcus furiosus, Recombinant Proteins, Selenomethionine, X-Ray}, issn = {0907-4449}, author = {Akerboom, Jasper and Turnbull, Andrew P and Hargreaves, David and Fisher, Martin and de Geus, Daniel and Sedelnikova, Svetlana E and Berrisford, John M and Baker, Patrick J and Verhees, Corn{\'e} H and van der Oost, John and Rice, David W} } @article {2142, title = {Phosphorylation-dependent differences in the activation properties of distal and proximal dendritic Na+ channels in rat CA1 hippocampal neurons.}, journal = {The Journal of Physiology}, volume = {541}, year = {2002}, month = {2002 Jun 15}, pages = {665-72}, abstract = {

{At distal dendritic locations, the threshold for action potential generation is higher and the amplitude of back-propagating spikes is decreased. To study whether these characteristics depend upon Na+ channels, their voltage-dependent properties at proximal and distal dendritic locations were compared in CA1 hippocampal neurons. Distal Na+ channels activated at more hyperpolarized voltages than proximal (half-activation voltages were -20.4 +/- 2.4 mV vs. -12.0 +/- 1.7 mV for distal and proximal patches, respectively

}, keywords = {Algorithms, Animals, Axons, Dendrites, Electrophysiology, Enzyme Inhibitors, Hippocampus, Membrane Potentials, Neurons, Patch-Clamp Techniques, Phosphorylation, Protein Kinase Inhibitors, Rats, Sodium Channels, Sprague-Dawley, Staurosporine}, issn = {0022-3751}, doi = {10.1002/cbic.201000254}, author = {Gasparini, Sonia and Magee, Jeffrey C} } @article {1989, title = {Postnatal development of spike generation in rat medial vestibular nucleus neurons.}, journal = {Journal of Neurophysiology}, volume = {85}, year = {2001}, month = {2001 May}, pages = {1899-906}, abstract = {

Image stability during self motion depends on the combined actions of the vestibuloocular and optokinetic reflexes (VOR and OKR, respectively). Neurons in the medial vestibular nucleus (MVN) participate in the VOR and OKR by firing in response to both head and image motion. Their intrinsic spike-generating properties enable MVN neurons to modulate firing rates linearly over a broad range of input amplitudes and frequencies such as those that occur during natural head and image motion. This study examines the postnatal development of the intrinsic spike-generating properties of rat MVN neurons with respect to maturation of peripheral vestibular and visual function. Spike generation was studied in a brain stem slice preparation by recording firing responses to current injected intracellularly through whole cell patch electrodes. MVN neurons fired spontaneously and modulated their firing rate in response to injected current at all postnatal ages. However, the input-output properties of the spike generator changed dramatically during the first two postnatal weeks. Neurons younger than postnatal day 10 could not fire faster than 80 spikes/s, modulated their firing rates over a limited range of input amplitudes, and tended to exhibit a nonlinear relationship between input current and mean evoked firing rate. In response to sustained depolarization, firing rates declined significantly in young neurons. Response gains tended to be highest in the first few postnatal days but varied widely across neurons and were not correlated with age. By about the beginning of the third postnatal week, MVN neurons could fire faster than 100 spikes/s in response to a broad range of input amplitudes, exhibited predominantly linear current-firing rate relationships, and adapted little in response to sustained depolarization. Concomitant decreases in action potential width and the time course of the afterhyperpolarization suggest that changes in potassium currents contribute to the maturation of the MVN neuronal spike generator. The results demonstrate that developmental changes in intrinsic membrane properties enable MVN neurons to fire linearly in response to a broad range of stimuli in time for the onset of visual function at the beginning of the third postnatal week.

}, keywords = {Action Potentials, Age Factors, Animals, Electric Stimulation, Eye Movements, Head Movements, Ion Transport, Movement, Nerve Tissue Proteins, Nystagmus, Optokinetic, Potassium Channels, Rats, Reflex, Sodium Channels, Vestibular Nuclei, Vestibulo-Ocular, Visual Perception}, issn = {0022-3077}, author = {Murphy, G J and Du Lac, S} } @article {45928, title = {Properties of slow, cumulative sodium channel inactivation in rat hippocampal CA1 pyramidal neurons.}, journal = {Biophys J}, volume = {76}, year = {1999}, month = {1999 Feb}, pages = {846-60}, abstract = {

Sodium channels in the somata and dendrites of hippocampal CA1 pyramidal neurons undergo a form of long-lasting, cumulative inactivation that is involved in regulating back-propagating action potential amplitude and can influence dendritic excitation. Using cell-attached patch-pipette recordings in the somata and apical dendrites of CA1 pyramidal neurons, we determined the properties of slow inactivation on response to trains of brief depolarizations. We find that the amount of slow inactivation gradually increases as a function of distance from the soma. Slow inactivation is also frequency and voltage dependent. Higher frequency depolarizations increase both the amount of slow inactivation and its rate of recovery. Hyperpolarized resting potentials and larger command potentials accelerate recovery from slow inactivation. We compare this form of slow inactivation to that reported in other cell types, using longer depolarizations, and construct a simplified biophysical model to examine the possible gating mechanisms underlying slow inactivation. Our results suggest that sodium channels can enter slow inactivation rapidly from the open state during brief depolarizations or slowly from a fast inactivation state during longer depolarizations. Because of these properties of slow inactivation, sodium channels will modulate neuronal excitability in a way that depends in a complicated manner on the resting potential and previous history of action potential firing.

}, keywords = {Animals, Electrophysiology, Hippocampus, Ion Channel Gating, Patch-Clamp Techniques, Pyramidal Cells, Rats, Rats, Wistar, Sodium Channels}, issn = {0006-3495}, author = {Mickus, T and Jung, H Y and Spruston, N} } @article {45805, title = {Phylogeny of the Tribe Cerataphidini (Homoptera) and the Evolution of the Horned Soldier Aphids}, journal = {Evolution}, volume = {52}, year = {1998}, month = {02/1998}, pages = {155-165}, abstract = {

The horned soldier aphids of the Cerataphidini, unlike most social insects that reside in nests, live on the open surface of plants. The lack of a nest and other obvious ecological correlates makes it unclear why secondary-host soldiers might have evolved. Here I present a molecular phylogenetic analysis of 32 species of the Cerataphidini, including 10 species from the genera Ceratovacuna and Pseudoregma that produce horned soldiers. The phylogeny suggests that horned soldiers evolved once and were lost once or twice. Most horned soldiers are a morphologically specialized caste and two species that have unspecialized soldiers are independently derived from species with specialized castes. The genus Ceratovacuna appears to have undergone a relatively rapid radiation. Mapping secondary-host plants and geographic ranges onto the phylogeny suggests that bamboos were the ancestral secondary-host plants and that the Asian tropics and subtropics were the ancestral geographic regions for the genera Astegopteryx, Ceratoglyphina, Ceratovacuna Chaitoregma, and Pseudoregma and possibly for the entire tribe. There is evidence for vicariant events that separate the tropical and subtropical lineages in all of the major lineages of the tribe and for dispersal of some lineages. Based on these results, I present hypotheses for the causes and consequences of horned-soldier evolution.

}, url = {http://www.jstor.org/stable/2410930}, author = {David L Stern} } @article {1562, title = {Protein engineering and the development of generic biosensors.}, journal = {Trends in Biotechnology}, volume = {16}, year = {1998}, month = {1998 Apr}, pages = {183-9}, abstract = {

Biosensors exploit the remarkable specificity of biomolecular recognition to provide analytical tools that can measure the presence of a single molecular species in a complex mixture. A new strategy is emerging in the development of biosensor technologies: molecular-engineering techniques are being used to adapt the properties of proteins to simple, generic detector instrumentation, rather than adapting instruments to the unique requirements of a natural molecule.

}, keywords = {Binding Sites, Biosensing Techniques, Protein Binding, Protein Engineering, Proteins, Signal Transduction}, issn = {0167-7799}, author = {Hellinga, H W and Marvin, J S} } @article {45916, title = {Prolonged sodium channel inactivation contributes to dendritic action potential attenuation in hippocampal pyramidal neurons.}, journal = {J Neurosci}, volume = {17}, year = {1997}, month = {1997 Sep 1}, pages = {6639-46}, abstract = {

During low-frequency firing, action potentials actively invade the dendrites of CA1 pyramidal neurons. At higher firing rates, however, activity-dependent processes result in the attenuation of back-propagating action potentials, and propagation failures occur at some dendritic branch points. We tested two major hypotheses related to this activity-dependent attenuation of back-propagating action potentials: (1) that it is mediated by a prolonged form of sodium channel inactivation and (2) that it is mediated by a persistent dendritic shunt activated by back-propagating action potentials. We found no evidence for a persistent shunt, but we did find that cumulative, prolonged inactivation of sodium channels develops during repetitive action potential firing. This inactivation is significant after a single action potential and continues to develop during several action potentials thereafter, until a steady-state sodium current is established. Recovery from this form of inactivation is much slower than its induction, but recovery can be accelerated by hyperpolarization. The similarity of these properties to the time and voltage dependence of attenuation and recovery of dendritic action potentials suggests that dendritic sodium channel inactivation contributes to the activity dependence of action potential back-propagation in CA1 neurons. Hence, the biophysical properties of dendritic sodium channels will be important determinants of action potential-mediated effects on synaptic integration and plasticity in hippocampal neurons.

}, keywords = {Action Potentials, Animals, Dendrites, Electrophysiology, Hippocampus, In Vitro Techniques, Neurons, Pyramidal Cells, Rats, Rats, Wistar, Sodium Channels, Tetrodotoxin, Time Factors}, issn = {0270-6474}, author = {Jung, H Y and Mickus, T and Spruston, N} } @article {2374, title = {Parametric generation of second sound by first sound in superfluid helium.}, journal = {Physical Review Letters}, volume = {76}, year = {1996}, month = {1996 Mar 18}, pages = {2105-8}, abstract = {

We report the experimental studies of a parametric excitation of a second sound (SS) by a first sound (FS) in a superfluid helium in a resonance cavity. The results on several topics in this system are presented: (i) The linear properties of the instability, namely, the threshold, its temperature and geometrical dependencies, and the spectra of SS just above the onset were measured. They were found to be in a good quantitative agreement with the theory. (ii) It was shown that the mechanism of SS amplitude saturation is due to the nonlinear attenuation of SS via three wave interactions between the SS waves. Strong low frequency amplitude fluctuations of SS above the threshold were observed. The spectra of these fluctuations had a universal shape with exponentially decaying tails. Furthermore, the spectral width grew continuously with the FS amplitude. The role of three and four wave interactions are discussed with respect to the nonlinear SS behavior. The first evidence of Gaussian statistics of the wave amplitudes for the parametrically generated wave ensemble was obtained. (iii) The experiments on simultaneous pumping of the FS and independent SS waves revealed new effects. Below the instability threshold, the SS phase conjugation as a result of three-wave interactions between the FS and SS waves was observed. Above the threshold two new effects were found: a giant amplification of the SS wave intensity and strong resonance oscillations of the SS wave amplitude as a function of the FS amplitude. Qualitative explanations of these effects are suggested.

}, issn = {1079-7114}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Rinberg, D and Cherepanov, V and Steinberg, V} } @article {45814, title = {A phylogenetic reanalysis of allozyme variation among populations of Galapagos finches}, journal = {Zoological Journal of the Linnean Society}, volume = {118}, year = {1996}, pages = {119-134}, abstract = {

We reanalysed Yang \& Pattern{\textquoteright}s allozyme data, published in Auk in 1981, of Darwin{\textquoteright}s finches with a variety of distance and cladistic methods to estimate the phylogeny of the group. Different methods yielded different results, nevertheless there was widespread agreement among the distance methods on several groupings. First, the two species of Camarhynchus grouped near one another, but not always as a monophyletic group. Second, Cactospiza pallida and Platyspiza crassirostris formed a monophyletic group. Finally, all the methods (including parsimony) supported the monophyly of the ground finches. The three distance methods also found close relationships generally between each of two populations of Geospiza scandens, G. difficilis and G. conirostris. There is evidence for inconstancy of evolutionary rates among species. Results from distance methods allowing for rate variation among lineages suggest three conclusions which differ from Yang and Patton{\textquoteright}s findings. First, the monophyletic ground finches arose from the paraphyletic tree finches. Yang and Patton found that the ground finches and tree finches were sister monophyletic taxa. Second, Geospiza scandens appears to be a recently derived species, and not the most basal ground finch. Third, G. fuliginosa is not a recently derived species of ground finch, but was derived from an older split from the remaining ground finches. Most of these conclusions should be considered tentative both because the parsimony trees disagreed sharply with the distance trees and because no clades were strongly supported by the results of bootstrapping and statistical tests of alternative hypotheses. Absence of strong support for clades was probably due to insufficient data. Future phylogenetic studies, preferably using DNA sequence data from several unlinked loci, should sample several populations of each species, and should attempt to assess the importance of hybridization in species phylogeny.

}, doi = {10.1111/j.1096-3642.1996.tb00222.x}, author = {David L. Stern and Peter R. Grant} } @article {1170, title = {A persistent RNA-DNA hybrid is formed during transcription at a phylogenetically conserved mitochondrial DNA sequence.}, journal = {Molecular and Cellular Biology}, volume = {15}, year = {1995}, month = {1995 Jan}, pages = {580-9}, abstract = {

Critical features of the mitochondrial leading-strand DNA replication origin are conserved from Saccharomyces cerevisiae to humans. These include a promoter and a downstream GC-rich sequence block (CSBII) that encodes rGs within the primer RNA. During in vitro transcription at yeast mitochondrial replication origins, there is stable and persistent RNA-DNA hybrid formation that begins at the 5{\textquoteright} end of the rG region. The short rG-dC sequence is the necessary and sufficient nucleic acid element for establishing stable hybrids, and the presence of rGs within the RNA strand of the RNA-DNA hybrid is required. The efficiency of hybrid formation depends on the length of RNA synthesized 5{\textquoteright} to CSBII and the type of RNA polymerase employed. Once made, the RNA strand of an RNA-DNA hybrid can serve as an effective primer for mitochondrial DNA polymerase. These results reveal a new mechanism for persistent RNA-DNA hybrid formation and suggest a step in priming mitochondrial DNA replication that requires both mitochondrial RNA polymerase and an rG-dC sequence-specific event to form an extensive RNA-DNA hybrid.

}, keywords = {Base Sequence, DNA, DNA Primers, DNA Replication, DNA-Directed DNA Polymerase, DNA-Directed RNA Polymerases, Genetic, Mitochondrial, Molecular Sequence Data, Nucleic Acid, Nucleic Acid Hybridization, Phylogeny, Regulatory Sequences, Ribonuclease H, RNA, Saccharomyces cerevisiae, Transcription}, issn = {0270-7306}, doi = {10.1101/gad.1352105}, author = {Xu, B and Clayton, D A} } @article {45816, title = {Phylogenetic evidence that aphids, rather than plants, determine gall morphology}, journal = {Proceedings of the Royal Society of London. Series B: Biological Sciences}, volume = {260}, year = {1995}, pages = {85-89}, abstract = {

Many diverse taxa have evolved independently the habit of living in plant galls. For all but some viral galls, it is unknown whether plants produce galls as a specialized plant reaction to certain types of herbivory, or whether herbivores direct gall development. Here I present a phylogenetic analysis of gallforming cerataphidine aphids which demonstrates that gall morphology is extremely conservative with respect to aphid phylogeny, but variable with respect to plant taxonomy. In addition, the phylogeny reveals at least three host plant switches where the aphids produce galls most similar to the galls of their closest relatives, rather than galls similar to the galls of aphids already present on the host plant. These results suggest that aphids determine the details of gall morphology essentially extending their phenotype to include plant material. Based on this and other evidence, I suggest that the aphids and other galling insects manipulate latent plant developmental programmes to produce modified atavistic plant morphologies rather than create new forms de novo.

}, doi = {10.1098/rspb.1995.0063}, url = {http://rspb.royalsocietypublishing.org/content/260/1357/85.short}, author = {David L Stern} } @article {45892, title = {Probing dendritic function with patch pipettes.}, journal = {Curr Opin Neurobiol}, volume = {5}, year = {1995}, month = {1995 Jun}, pages = {389-94}, abstract = {

Most neurons in the CNS have complex, branching dendritic trees, which receive the majority of all synaptic input. As it is difficult to make electrical recordings from dendrites because of their small size, most of what is known about their electrical properties has been inferred from recordings made at the soma. By taking advantage of the higher resolution offered by improved optics, it is now possible to make patch-pipette recordings from the dendrites of neurons in brain slices under visual control. This new technique promises to provide valuable new information concerning dendritic function.

}, keywords = {Animals, Dendritic Cells, Electrophysiology, Hippocampus, Patch-Clamp Techniques}, issn = {0959-4388}, author = {Stuart, G and Spruston, N} } @article {2092, title = {Proposed method for molecular optical imaging. (With commentary)}, journal = {Optics Letters}, volume = {20}, year = {1995}, month = {1995 Feb 1}, pages = {237-9}, abstract = {

We can resolve multiple discrete features within a focal region of m spatial dimensions by first isolating each on the basis of n \>/= 1 unique optical characteristics and then measuring their relative spatial coordinates. The minimum acceptable separation between features depends on the point-spread function in the (m + n)d-dimensional space formed by the spatial coordinates and the optical parameters, whereas the absolute spatial resolution is determined by the accuracy to which the coordinates can be measured. Estimates of each suggest that near-field fluorescence excitation microscopy/spectroscopy with molecular sensitivity and spatial resolution is possible.

Commentary: Inspired by my earlier work (see below) in single molecule imaging and the isolation of multiple exciton recombination sites within a single probe volume, here I proposed the principle which would eventually lead to PALM. Indeed, all methods of localization microscopy, including PALM, fPALM, PALMIRA, STORM, dSTORM, PAINT, GSDIM, etc. are specific embodiments of the general principle of single molecule isolation and localization I introduced here.

}, issn = {0146-9592}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19859146}, author = {Betzig, E} } @article {45775, title = {A phylogenetic analysis of soldier evolution in the aphid family Hormaphididae.}, journal = {Proc Biol Sci}, volume = {256}, year = {1994}, month = {1994 May 23}, pages = {203-9}, abstract = {

Aphid soldiers, altruistic larvae that protect the colony from predators, are an example of highly social behaviour in an insect group with a natural history different from the eusocial Hymenoptera and Isoptera. Aphids therefore allow independent tests of theory developed to explain the evolution of eusociality. Although soldiers have been discovered in five tribes from two families, the number and pattern of origins and losses of soldiers is unknown due to a lack of phylogenetic data. Here I present a mtDNA based phylogeny for the Hormaphididae, and test the hypothesis that soldiers in the tribe Cerataphidini produced during two points in the life cycle represent independent origins. The results support this hypothesis. In addition, a minimum of five evolutionary events, either four origins and one loss or five origins, are required to explain the distribution of soldiers in the family. The positions of the origins and losses are well resolved, and this phylogeny provides an historical framework for studies on the causes of soldier aphid evolution.

}, keywords = {Animals, Aphids, Base Sequence, DNA Primers, DNA, Mitochondrial, Electron Transport Complex IV, Genes, Insect, Molecular Sequence Data, Phylogeny, Sequence Homology, Nucleic Acid}, issn = {0962-8452}, doi = {10.1098/rspb.1994.0071}, author = {Stern, D L} } @article {45902, title = {Perforated patch-clamp analysis of the passive membrane properties of three classes of hippocampal neurons.}, journal = {J Neurophysiol}, volume = {67}, year = {1992}, month = {1992 Mar}, pages = {508-29}, abstract = {

1. Perforated patch-clamp recordings were made from the three major classes of hippocampal neurons in conventional in vitro slices prepared from adult guinea pigs. This technique provided experimental estimates of passive membrane properties (input resistance, RN, and membrane time constant, tau m) determined in the absence of the leak conductance associated with microelectrode impalement or the washout of cytoplasmic constituents associated with conventional whole-cell recordings. 2. To facilitate comparison of our data with previous results and to determine the passive membrane properties under conditions as physiological as possible, recordings were made at the resting potential, in physiological saline, and without any added blockers of voltage-dependent conductances. 3. Membrane-potential responses to current steps were analyzed, and four criteria were used to identify voltage responses that were the least affected by activation of voltage-dependent conductances. tau m was estimated from the slowest component (tau 0) of multiexponential fits of responses deemed passive by these criteria. RN was estimated from the slope of the linear region in the hyperpolarizing direction of the voltage-current relation. 4. It was not possible to measure purely passive membrane properties that were completely independent of membrane potential in any of the three classes of hippocampal neurons. Changing the membrane potential by constant current injection resulted in changes in RN and tau 0; subthreshold depolarization produced an increase, and hyperpolarization a decrease, in both RN and tau 0 for all three classes of hippocampal neurons. 5. Each of the three classes of hippocampal neurons also displayed a depolarizing "sag" during larger hyperpolarizing voltage transients. To evaluate the effect of the conductances underlying this sag on passive membrane properties, 2-5 mM Cs+ was added to the physiological saline. Extracellular Cs+ effectively blocked the sag in all three classes of hippocampal neurons, but the effect of Cs+ on RN, tau 0, and the voltage dependence of these parameters was unique for each class of neurons. 6. CA1 pyramidal neurons had an RN of 104 +/- 10 (SE) M omega and tau 0 of 28 +/- 2 ms at a resting potential of -64 +/- 2 mV (n = 12). RN and tau 0 were larger at more depolarized potentials in these neurons, but the addition of Cs+ to the physiological saline reversed this voltage dependence. 7. CA3 pyramidal neurons had an RN of 135 +/- 8 M omega and tau 0 of 66 +/- 4 ms at a resting potential of -64 +/- 1 mV (n = 14).(ABSTRACT TRUNCATED AT 400 WORDS)

}, keywords = {Animals, Cesium, Electrophysiology, Guinea Pigs, Hippocampus, In Vitro Techniques, Membrane Potentials, Membranes, Microelectrodes, Neurons, Pyramidal Tracts}, issn = {0022-3077}, author = {Spruston, N and Johnston, D} } @article {2563, title = {Polarization contrast in near-field scanning optical microscopy.}, journal = {Applied Optics}, volume = {31}, year = {1992}, month = {1992 Aug 1}, pages = {4563-8}, abstract = {

Recent advances in probe design have led to enhanced resolution (currently as significant as \  12 nm) in optical microscopes based on near-field imaging. We demonstrate that the polarization of emitted and detected light in such microscopes can be manipulated sensitively to generate contrast. We show that the contrast on certain patterns is consistent with a simple interpretation of the requisite boundary conditions, whereas in other cases a more complicated interaction between the probe and the sample is involved. Finally application of the technique to near-filed magneto-optic imaging is demonstrated.

}, issn = {0003-6935}, doi = {10.1364/AO.31.004563}, author = {Betzig, E and Trautman, J K and Weiner, J S and Harris, T D and Wolfe, R} } @article {2463, title = {Postmetamorphic cell death in the nervous and muscular systems of Drosophila melanogaster.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {10}, year = {1990}, month = {1990 Feb}, pages = {403-1}, abstract = {

Programmed cell death occurs in the nervous and muscular system of newly emerged adult Drosophila melanogaster. Many of the abdominal muscles that were used for eclosion and wing-spreading behavior degenerate by 12 hr after eclosion. Related neurons in the ventral ganglion also die within the first 24 hr. Ligation experiments showed that the muscle breakdown is triggered by a signal from the anterior region, presumably the head, that occurs about 1 hr before adult emergence. The timing of this signal suggests that eclosion hormone may be involved. Although muscle death is triggered prior to ecdysis, it can be delayed, at least temporarily, by forcing the emerging flies to show a prolonged ecdysis behavior. In contrast to the muscles, the death of the neurons is triggered after emergence. The signal for neuronal degeneration is closely correlated with the initiation of wing inflation behavior. Ligation and digging experiments and behavioral manipulations that either blocked or delayed wing expansion behavior had a parallel effect in suppressing or delaying neuronal death.

}, keywords = {Animal, Animals, Behavior, Biological, Cell Survival, Drosophila melanogaster, Female, Ligation, Male, Metamorphosis, Muscles, Nervous System, Neurons}, issn = {0270-6474}, author = {Kimura, K I and Truman, J W} } @article {2464, title = {Postembryonic neurogenesis in the CNS of the tobacco hornworm, Manduca sexta. I. Neuroblast arrays and the fate of their progeny during metamorphosis.}, journal = {The Journal of Comparative Neurology}, volume = {255}, year = {1987}, month = {1987 Jan 22}, pages = {548-59}, abstract = {

The tobacco hornworm Manduca sexta exhibits dramatic changes in its body morphology and behavior as it is transformed from a larva into an adult during metamorphosis. Accompanying these changes is an extensive reorganization of this moth{\textquoteright}s central nervous system (CNS), which involves both the death and remodeling of subsets of larval neurons. We report here that the segmental ganglia of the larvae also contain a stereotyped array of identifiable neuronal stem cells (neuroblasts) that contribute over 2,000 cells to each thoracic ganglion and about 40-80 cells to each abdominal ganglion. The distribution of these neuroblasts varies in a segment specific manner. Dormant neuroblasts are found adjacent to the neuropil in late embryos and early first instar larvae. After the molt to the second instar, these cells enlarge and begin to divide. Through a series of asymmetrical divisions, each neuroblast generates a discrete nest of 10-90 progeny by the end of larval life. These progeny (the imaginal nest cells) are developmentally arrested at an early stage of differentiation and remain so until metamorphosis. At the onset of metamorphosis, a wave of cell death sweeps through the nests, the extent of the death being much greater within the abdominal nests than in the thoracic nests. The surviving imaginal nest cells then differentiate to become functional neurons that are incorporated into the adult CNS.

}, keywords = {Animals, Biological, Cell Division, Central Nervous System, Larva, Lepidoptera, Metamorphosis, Moths, Neurons}, issn = {0021-9967}, doi = {10.1002/cne.902550407}, author = {Booker, R and Truman, J W} } @article {1177, title = {Promoter selection in human mitochondria involves binding of a transcription factor to orientation-independent upstream regulatory elements.}, journal = {Cell}, volume = {50}, year = {1987}, month = {1987 Jul 17}, pages = {247-58}, abstract = {

Selective transcription of human mitochondrial DNA requires a transcription factor (mtTF) in addition to an essentially nonselective RNA polymerase. Partially purified mtTF is able to sequester promoter-containing DNA in preinitiation complexes in the absence of mitochondrial RNA polymerase, suggesting a DNA-binding mechanism for factor activity. Functional domains, required for positive transcriptional regulation by mtTF, are identified within both major promoters of human mtDNA through transcription of mutant promoter templates in a reconstituted in vitro system. These domains are essentially coextensive with DNA sequences protected from nuclease digestion by mtTF-binding. Comparison of the sequences of the two mtTF-responsive elements reveals significant homology only when one sequence is inverted; the binding sites are in opposite orientations with respect to the predominant direction of transcription. Thus mtTF may function bidirectionally, requiring additional protein-DNA interactions to dictate transcriptional polarity. The mtTF-responsive elements are arrayed as direct repeats, separated by approximately 80 bp within the displacement-loop region of human mitochondrial DNA; this arrangement may reflect duplication of an ancestral bidirectional promoter, giving rise to separate, unidirectional promoters for each strand.

}, keywords = {DNA, DNA-Directed RNA Polymerases, Genes, Genetic, Humans, KB Cells, Mitochondria, Mitochondrial, Promoter Regions, Regulator, Templates, Transcription, Transcription Factors}, issn = {0092-8674}, doi = {10.1101/gad.1352105}, author = {Fisher, R P and Topper, J N and Clayton, D A} } @article {1183, title = {Precise identification of individual promoters for transcription of each strand of human mitochondrial DNA.}, journal = {Cell}, volume = {36}, year = {1984}, month = {1984 Mar}, pages = {635-43}, abstract = {

The major site of in vivo transcriptional initiation for both heavy and light strands of human mitochondrial DNA is the displacement-loop region. Transcripts synthesized in vitro by human mitochondrial RNA polymerase were mapped to the nucleotide level and have identical 5{\textquoteright} end map positions to those reported for in vivo primary transcripts. An ordered series of deletion clones, whose template sequences were truncated at either the 5{\textquoteright} or 3{\textquoteright} end, was used to identify the precise mitochondrial DNA sequence required for initiation of transcription. The data provide a definitive assignment of the promoter for heavy-strand transcription occurring within -16 to +7 of the transcriptional start site 16 nucleotides upstream of the 5{\textquoteright} end of the gene for tRNAPhe and of the promoter for light-strand transcription occurring within -28 to +16 of the transcriptional start site at the 5{\textquoteright} end of "7S RNA." Within each control sequence is a candidate promoter whose consensus sequence is 5{\textquoteright}-CANACC(G)CC(A)AAAGAPyA-3{\textquoteright} and in both cases transcriptional initiation occurs within six to eight nucleotides of the 3{\textquoteright} end of this sequence. The transcriptional start site is an integral part of each promoter and each promoter can function in the absence of the other.

}, keywords = {Chromosome Deletion, Chromosome Mapping, DNA, DNA-Directed RNA Polymerases, Genes, Genetic, Humans, Mitochondrial, Operon, Regulator, RNA, Transcription, Transfer}, issn = {0092-8674}, doi = {10.1101/gad.1352105}, author = {Chang, D D and Clayton, D A} } @article {2518, title = {Pheromone binding and inactivation by moth antennae.}, journal = {Nature}, volume = {293}, year = {1981}, month = {1981 Sep 10-16}, pages = {161-3}, abstract = {

The antennae of male silk moths are extremely sensitive to the female sex pheromone such that a male moth can find a female up to 4.5 km away. This remarkable sensitivity is due to both the morphological and biochemical design of these antennae. Along the branches of the plumose antennae are the sensilla trichodea, each consisting of a hollow cuticular hair containing two unbranched dendrites bathed in a fluid, the receptor lymph ,3. The dendrites and receptor lymph are isolated from the haemolymph by a barrier of epidermal cells which secreted the cuticular hair. Pheromone molecules are thought to diffuse down 100 A-wide pore tubules through the cuticular wall and across the receptor lymph space to receptors located in the dendritic membrane. To prevent the accumulation of residual stimulant and hence sensory adaptation, the pheromone molecules are subsequently inactivated in an apparent two-step process of rapid {\textquoteright}early inactivation{\textquoteright} followed by much slower enzymatic degradation. The biochemistry involved in this sequence of events is largely unknown. We report here the identification of three proteins which interact with the pheromone of the wild silk moth Antheraea polyphemus: a pheromone-binding protein and a pheromone-degrading esterase, both uniquely located in the pheromone-sensitive sensilla; and a second esterase common to all cuticular tissues except the sensilla.

}, keywords = {Animal Structures, Animals, Bombyx, Esterases, Extremities, Female, Insect Proteins, Male, Protein Binding, Sex Attractants, Substrate Specificity, Tissue Extracts}, issn = {0028-0836}, author = {Vogt, R G and Riddiford, L M} }