@article {70287, title = {Orofacial behaviors, not eye movements, govern neural activity in mouse visual cortex}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 05}, abstract = {

Neural activity in mouse primary visual cortex (V1) correlates strongly with orofacial movements. Such strong modulation has not been found in the primate visual cortex during eye fixation [1], which led to the suggestion that the modulation may primarily depend on eye movements in both species [2]. Here we examined the influence of eye movements on neural activity in mouse visual cortex both in complete darkness and in the presence of different types of visual input. In all cases, we found that eye movements explain a smaller fraction of neural activity variance compared to orofacial behaviors. Additionally, we found that eye movements were correlated to orofacial movements, such as whisking and sniffing, and thus may be indirectly correlated to neural activity. These results further emphasize the impact of movement signals on mouse visual cortex during free viewing behavior.

}, doi = {10.64898/2026.02.04.703800}, url = {https://www.biorxiv.org/content/early/2026/02/05/2026.02.04.703800}, author = {Syeda, Atika and N{\'u}{\~n}ez-Ochoa, Miguel Angel and Zhong, Lin and Pachitariu, Marius and Stringer, Carsen} } @article {70250, title = {Oxytocin modulation of spinal circuits drives therapeutic benefits of massage}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 12}, abstract = {

Across social species, social touch enhances well-being and reduces pain {\textemdash} two seemingly distinct benefits that enhance survival. Yet where and how the nervous system integrates these functions, and whether a single mechanism could serve both, remains unknown. Here we show that massage triggers oxytocin release, which shapes both pain and touch reward at the earliest stage of central processing {\textemdash} the spinal cord {\textemdash} through a single, state-dependent circuit mechanism. We report that in humans, massage enhances well-being, effects that correlate with endogenous oxytocin release. In mice, gentle touch activates hypothalamic oxytocin neurons that project directly to the spinal dorsal horn. Genetic manipulation of spinal oxytocin circuits alters behavioral responses to both gentle touch and noxious stimuli. Spinal calcium imaging and slice electrophysiology reveal that oxytocin acts on both excitatory and inhibitory spinal neurons to sculpt the relative activity of spinal ascending systems that convey both social touch and pain to the brain. Extending these findings to humans, we show that oxytocin receptors are also expressed on spinal excitatory and inhibitory neurons, and that endogenous oxytocin during massage correlates with altered spinal touch processing. Thus, spinal oxytocin signaling provides an evolutionarily conserved mechanism for the therapeutic benefits of massage.

}, doi = {10.64898/2026.01.11.698886}, url = {https://www.biorxiv.org/content/early/2026/01/12/2026.01.11.698886}, author = {Bohic, Manon and Salamone, Paula Celeste and Zuo, Wanhong and Negm, Ahmed and Fulton, Sasha Leilani and Du, Shibin and Jayakumar, Swathi and Keating, Jessica and Soubeyre, Vanessa and Gradwell, Mark Andrew and Upadhyay, Aman and Shorter, Lucero and Kim, Joel and Inoue, Yukiko Ueno and Inoue, Takayoshi and Mensch, Brett and Ye, Jiang-Hong and Peirs, Cedric and Poulen, Gaetan and Lonjon, Nicolas and Vachiery-Lahaye, Florence and Bauchet, Luc and Bourinet, Emmanuel and Olausson, Hakan and Abdus-Saboor, Ishmail and Tao, Yuan-Xiang and Boehme, Rebecca and Abraira, Victoria E.} } @article {70226, title = {Octopamine instructs head direction plasticity}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 15}, abstract = {

Many plasticity rules rely on adjusting the strength of synapses between pairs of cells based on their coincident activity. We uncovered a new mechanism for coincidence detection in the Drosophila head direction network. To maintain an accurate sense of direction, head direction neurons that signal orientation during navigation must learn to anchor to relevant external sensory cues in novel environments. Yet the synaptic mechanism for this form of unsupervised learning is unknown in any organism. In Drosophila, GABAergic visual inputs converge onto head direction neurons, and these inhibitory synapses change strength with experience to learn the relationship between visual landmarks and head direction. However, how coincident pre- and postsynaptic activity is detected across this inhibitory synapse is not understood. We discovered that neurons which release the monoamine octopamine close a feedback loop that conveys postsynaptic head direction activity onto presynaptic terminals of visual inputs. This octopamine pathway is required for anchoring the head direction network to visual cues. Furthermore, pairing structured activation of octopamine neurons with a visual cue is sufficient to drive rapid plasticity, even without postsynaptic head direction cell activity. Previous work has extensively characterized coincidence detection mechanisms at excitatory synapses; our work defines a novel mechanism for coincidence detection at an inhibitory synapse, in which postsynaptic activity is relayed via a neuromodulatory neuron onto presynaptic terminals

}, doi = {10.64898/2025.12.11.693783}, url = {https://www.biorxiv.org/content/early/2025/12/15/2025.12.11.693783}, author = {Plitt, Mark H. and Turner-Evans, Daniel B. and Co, Jessica C. and Layden, Aryanna and Eddison, Mark and Ray, Robert P. and Jayaraman, Vivek and Fisher, Yvette E.} } @article {70169, title = {Optimizing multifunctional fluorescent ligands for intracellular labeling.}, journal = {Proc Natl Acad Sci USA}, volume = {122}, year = {2025}, month = {2025 Nov 04}, pages = {e2510046122}, abstract = {

Enzyme-based self-labeling tags enable the covalent attachment of synthetic molecules to proteins inside living cells. A frontier of this field is designing cell-permeable multifunctional ligands that contain fluorophores in combination with affinity tags or pharmacological agents. This is challenging since attachment of additional chemical moieties onto fluorescent ligands can adversely affect membrane permeability. To address this problem, we examined the chemical properties of rhodamine-based self-labeling tag ligands through the lens of medicinal chemistry. We found that the lactone-zwitterion equilibrium constant () of rhodamines inversely correlates with their distribution coefficients (log), suggesting that ligands based on dyes exhibiting low and high log values, such as Si-rhodamines, would efficiently enter cells. We designed cell-permeable multifunctional HaloTag ligands with a biotin moiety to purify mitochondria or a JQ1 appendage to translocate BRD4 within the nucleus. We found that translocation of BRD4 to constitutive heterochromatin in cells leads to apparent increases in transcriptional activity. These fluorescent reagents enable affinity capture and translocation of intracellular proteins in living cells, and our general design concepts will facilitate the design of multifunctional chemical tools for biology.

Preprint:\ https://doi.org/10.1101/2022.07.02.498544
Preprint:\ https://doi.org/10.32388/0xcyuc

}, keywords = {Bromodomain Containing Proteins, Cell Cycle Proteins, Fluorescent Dyes, Humans, Ligands, Mitochondria, Nuclear Proteins, Rhodamines, Staining and Labeling, Transcription Factors}, issn = {1091-6490}, doi = {10.1073/pnas.2510046122}, url = {https://doi.org/10.1073/pnas.2510046122}, author = {Kumar, Pratik and Vevea, Jason D and Tkachuk, Ariana N and Campbell, Kirby R and Watson, Emma T and Ayala, Anthony X and Grimm, Jonathan B and Chapman, Edwin R and Solecki, David J and Lavis, Luke D} } @article {70243, title = {The organization of visual pathways in the Drosophila brain}, journal = {bioRxiv}, year = {2025}, month = {2025 Dec 26}, abstract = {

Visual systems across species transform photoreceptor inputs into diverse perceptual representations through hierarchical networks that extract features via parallel pathways. In Drosophila, the optic lobes are layered, retinotopic visual processing centers that contain two-thirds of the brain{\textquoteright}s neurons and support diverse visually guided behaviors. Although this architecture has long suggested hierarchical and parallel organization, a system-wide account of how behaviorally relevant visual features are routed and integrated across a complete visual system{\textemdash}in any animal{\textemdash}has remained elusive. The new male fly connectome now provides the synapse-level wiring needed to trace visual information from photoreceptors through the optic lobes and across the central brain. Applying a network-based analysis of information flow, we reveal a multi-layered architecture organized into distinct, functionally interpretable pathways. Using this framework to propagate signals through these pathways predicts receptive-field structure and feature selectivity consistent with physiological data, enabling large-scale functional annotation of thousands of neuron types. We find that distinct visual input channels are broadly distributed throughout the brain, yet converge in focal regions of feature specificity and acute spatial vision. Together, these analyses provide a neuron-level, connectome-based view of how a brain organizes and transforms visual input.

}, doi = {10.64898/2025.12.22.696097}, url = {https://www.biorxiv.org/content/early/2025/12/26/2025.12.22.696097}, author = {Hoeller, Judith and Zhao, Arthur and Nern, Aljoscha and Rogers, Edward M and Romani, Sandro and Reiser, Michael B} } @article {69010, title = {Olfactory sensory neuron population expansions influence projection neuron adaptation and enhance odour tracking}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Aug 15}, pages = {7041}, abstract = {

The evolutionary expansion of sensory neuron populations detecting important environmental cues is widespread, but functionally enigmatic. We investigated this phenomenon through comparison of homologous olfactory pathways of Drosophila melanogaster and its close relative Drosophila sechellia, an extreme specialist for Morinda citrifolia noni fruit. D. sechellia has evolved species-specific expansions in select, noni-detecting olfactory sensory neuron (OSN) populations, through multigenic changes. Activation and inhibition of defined proportions of neurons demonstrate that OSN number increases contribute to stronger, more persistent, noni-odour tracking behaviour. These expansions result in increased synaptic connections of sensory neurons with their projection neuron (PN) partners, which are conserved in number between species. Surprisingly, having more OSNs does not lead to greater odour-evoked PN sensitivity or reliability. Rather, pathways with increased sensory pooling exhibit reduced PN adaptation, likely through weakened lateral inhibition. Our work reveals an unexpected functional impact of sensory neuron population expansions to explain ecologically-relevant, species-specific behaviour.

}, doi = {10.1038/s41467-024-50808-w}, url = {https://doi.org/10.1038/s41467-024-50808-w}, author = {Suguru Takagi and Liliane Abuin and S. David Stupski and J. Roman Arguello and Lucia Prieto-Godino and David L. Stern and Steeve Cruchet and Raquel {\'A}lvarez-Oca{\~n}a and Carl F. R. Wienecke and Floris van Breugel and Thomas O. Auer and Richard Benton} } @article {69669, title = {ONIX: a unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior.}, journal = {Nat Methods}, year = {2024}, month = {2024 Nov 11}, abstract = {

Behavioral neuroscience faces two conflicting demands: long-duration recordings from large neural populations and unimpeded animal behavior. To meet this challenge we developed ONIX, an open-source data acquisition system with high data throughput (2 GB s) and low closed-loop latencies (\<1 ms) that uses a 0.3-mm thin tether to minimize behavioral impact. Head position and rotation are tracked in three dimensions and used to drive active commutation without torque measurements. ONIX can acquire data from combinations of passive electrodes, Neuropixels probes, head-mounted microscopes, cameras, three-dimensional trackers and other data sources. We performed uninterrupted, long (~7 h) neural recordings in mice as they traversed complex three-dimensional terrain, and multiday sleep-tracking recordings (~55 h). ONIX enabled exploration with similar mobility as nonimplanted animals, in contrast to conventional tethered systems, which have restricted movement. By combining long recordings with full mobility, our technology will enable progress on questions that require high-quality neural recordings during ethologically grounded behaviors.

}, issn = {1548-7105}, doi = {10.1038/s41592-024-02521-1}, url = {https://doi.org/10.1038/s41592-024-02521-1}, author = {Newman, Jonathan P and Zhang, Jie and Cuevas-L{\'o}pez, Aar{\'o}n and Miller, Nicholas J and Honda, Takato and van der Goes, Marie-Sophie H and Leighton, Alexandra H and Carvalho, Filipe and Lopes, Gon{\c c}alo and Lakunina, Anna and Siegle, Joshua H and Harnett, Mark T and Wilson, Matthew A and Voigts, Jakob} } @article {69399, title = {Optimization in Visual Motion Estimation.}, journal = {Annu Rev Vis Sci}, year = {2024}, month = {2024 Apr 25}, abstract = {

Sighted animals use visual signals to discern directional motion in their environment. Motion is not directly detected by visual neurons, and it must instead be computed from light signals that vary over space and time. This makes visual motion estimation a near universal neural computation, and decades of research have revealed much about the algorithms and mechanisms that generate directional signals. The idea that sensory systems are optimized for performance in natural environments has deeply impacted this research. In this article, we review the many ways that optimization has been used to quantitatively model visual motion estimation and reveal its underlying principles. We emphasize that no single optimization theory has dominated the literature. Instead, researchers have adeptly incorporated different computational demands and biological constraints that are pertinent to the specific brain system and animal model under study. The successes and failures of the resulting optimization models have thereby provided insights into how computational demands and biological constraints together shape neural computation.

}, issn = {2374-4650}, doi = {10.1146/annurev-vision-101623-025432}, author = {Clark, Damon A and Fitzgerald, James E} } @article {68531, title = {Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity}, journal = {eLife}, year = {2024}, month = {2024 Jan 19}, abstract = {

Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins enriched at lysosomes mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked with longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using large-scale proteomic profiling, we systemically profiled lysosome- enriched proteomes in association with different longevity mechanisms. We further discovered the lysosomal recruitment of AMPK and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we discovered lysosomal heterogeneity across tissues as well as the specific enrichment of the Ragulator complex on Cystinosin positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity at different levels and provides resources for understanding the contribution of lysosomal proteome dynamics in modulating signal transduction, organelle crosstalk and organism longevity.

}, doi = {10.7554/eLife.85214}, url = {https://doi.org/10.7554/eLife.85214}, author = {Yong Yu and Shihong M. Gao and Youchen Guan and Pei-Wen Hu and Qinghao Zhang and Jiaming Liu and Bentian Jing and Qian Zhao and David M Sabatini and Monther Abu-Remaileh and Sung Yun Jung and Meng C. Wang} } @article {69229, title = {Organization of an ascending circuit that conveys flight motor state in Drosophila.}, journal = {Current Biology}, year = {2024}, month = {2024 Feb 13}, abstract = {

Natural behaviors are a coordinated symphony of motor acts that drive reafferent (self-induced) sensory activation. Individual sensors cannot disambiguate exafferent (externally induced) from reafferent sources. Nevertheless, animals readily differentiate between these sources of sensory signals to carry out adaptive behaviors through corollary discharge circuits (CDCs), which provide predictive motor signals from motor pathways to sensory processing and other motor pathways. Yet, how CDCs comprehensively integrate into the nervous system remains unexplored. Here, we use connectomics, neuroanatomical, physiological, and behavioral approaches to resolve the network architecture of two pairs of ascending histaminergic neurons (AHNs) in Drosophila, which function as a predictive CDC in other insects. Both AHN pairs receive input primarily from a partially overlapping population of descending neurons, especially from DNg02, which controls wing motor output. Using Ca imaging and behavioral recordings, we show that AHN activation is correlated to flight behavior and precedes wing motion. Optogenetic activation of DNg02 is sufficient to activate AHNs, indicating that AHNs are activated by descending commands in advance of behavior and not as a consequence of sensory input. Downstream, each AHN pair targets predominantly non-overlapping networks, including those that process visual, auditory, and mechanosensory information, as well as networks controlling wing, haltere, and leg sensorimotor control. These results support the conclusion that the AHNs provide a predictive motor signal about wing motor state to mostly non-overlapping sensory and motor networks. Future work will determine how AHN signaling is driven by other descending neurons and interpreted by AHN downstream targets to maintain adaptive sensorimotor performance.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.01.071}, author = {Cheong, Han S J and Boone, Kaitlyn N and Bennett, Marryn M and Salman, Farzaan and Ralston, Jacob D and Hatch, Kaleb and Allen, Raven F and Phelps, Alec M and Cook, Andrew P and Phelps, Jasper S and Erginkaya, Mert and Lee, Wei-Chung A and Card, Gwyneth M and Daly, Kevin C and Dacks, Andrew M} } @article {68635, title = {OME-Zarr: a cloud-optimized bioimaging file format with international community support.}, journal = {Histochemistry and Cell Biology}, volume = {160}, year = {2023}, month = {2023 Feb 25}, pages = {223-251}, abstract = {

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the format itself {\textendash} OME-Zarr {\textendash} along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain {\textemdash} the file format that underlies so many personal, institutional, and global data management and analysis tasks.

}, doi = {10.1007/s00418-023-02209-1}, url = {https://doi.org/10.1007/s00418-023-02209-1}, author = {Josh Moore and Daniela Basurto-Lozada and S{\'e}bastien Besson and John Bogovic and Eva M. Brown and Jean-Marie Burel and Gustavo de Medeiros and Erin E. Diel and David Gault and Satrajit S. Ghosh and Ilan Gold and Yaroslav O. Halchenko and Matthew Hartley and Dave Horsfall and Mark S. Keller and Mark Kittisopikul and Gabor Kovacs and Ayb{\"u}ke K{\"u}pc{\"u} Yolda{\c s} and Albane le Tournoulx de la Villegeorges and Tong Li and Prisca Liberali and Melissa Linkert and Dominik Lindner and Joel L{\"u}thi and Jeremy Maitin-Shepard and Trevor Manz and Matthew McCormick and Khaled Mohamed and William Moore and Bugra {\"O}zdemir and Constantin Pape and Lucas Pelkmans and Martin Prete and Tobias Pietzsch and Stephan Preibisch and Norman Rzepka and David R. Stirling and Jonathan Striebel and Christian Tischer and Daniel Toloudis and Petr Walczysko and Alan M. Watson and Frances Wong and Kevin A. Yamauchi and Omer Bayraktar and Muzlifah Haniffa and Stephan Saalfeld and Jason R. Swedlow} } @article {69042, title = {Optimized Red-Absorbing Dyes for Imaging and Sensing}, journal = {Journal of the American Chemical Society}, year = {2023}, month = {2023 Oct 16}, abstract = {

Rhodamine dyes are excellent scaffolds for developing a broad range of fluorescent probes. A key property of rhodamines is their equilibrium between a colorless lactone and fluorescent zwitterion. Tuning the lactone{\textendash}zwitterion equilibrium constant (KL{\textendash}Z) can optimize dye properties for specific biological applications. Here, we use known and novel organic chemistry to prepare a comprehensive collection of rhodamine dyes to elucidate the structure{\textendash}activity relationships that govern\ KL{\textendash}Z. We discovered that the auxochrome substituent strongly affects the lactone{\textendash}zwitterion equilibrium, providing a roadmap for the rational design of improved rhodamine dyes. Electron-donating auxochromes, such as julolidine, work in tandem with fluorinated pendant phenyl rings to yield bright, red-shifted fluorophores for live-cell single-particle tracking (SPT) and multicolor imaging. The\ N-aryl auxochrome combined with fluorination yields red-shifted F{\"o}rster resonance energy transfer (FRET) quencher dyes useful for creating a new semisynthetic indicator to sense cAMP using fluorescence lifetime imaging microscopy (FLIM). Together, this work expands the synthetic methods available for rhodamine synthesis, generates new reagents for advanced fluorescence imaging experiments, and describes structure{\textendash}activity relationships that will guide the design of future probes.

}, issn = {0002-7863}, doi = {10.1021/jacs.3c0527310.1021/jacs.3c05273}, url = {https://pubs.acs.org/doi/10.1021/jacs.3c05273}, author = {Grimm, Jonathan B. and Tkachuk, Ariana N. and Patel, Ronak and Hennigan, S. Thomas and Gutu, Alina and Dong, Peng and Gandin, Valentina and Osowski, Anastasia M. and Holland, Katie L. and Liu, Zhe J. and Brown, Timothy A. and Lavis, Luke D.} } @article {68828, title = {Organization of an Ascending Circuit that Conveys Flight Motor State}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 09}, abstract = {

Natural behaviors are a coordinated symphony of motor acts which drive self-induced or reafferent sensory activation. Single sensors only signal presence and magnitude of a sensory cue; they cannot disambiguate exafferent (externally-induced) from reafferent sources. Nevertheless, animals readily differentiate between these sources of sensory signals to make appropriate decisions and initiate adaptive behavioral outcomes. This is mediated by predictive motor signaling mechanisms, which emanate from motor control pathways to sensory processing pathways, but how predictive motor signaling circuits function at the cellular and synaptic level is poorly understood. We use a variety of techniques, including connectomics from both male and female electron microscopy volumes, transcriptomics, neuroanatomical, physiological and behavioral approaches to resolve the network architecture of two pairs of ascending histaminergic neurons (AHNs), which putatively provide predictive motor signals to several sensory and motor neuropil. Both AHN pairs receive input primarily from an overlapping population of descending neurons, many of which drive wing motor output. The two AHN pairs target almost exclusively non-overlapping downstream neural networks including those that process visual, auditory and mechanosensory information as well as networks coordinating wing, haltere, and leg motor output. These results support the conclusion that the AHN pairs multi-task, integrating a large amount of common input, then tile their output in the brain, providing predictive motor signals to non-overlapping sensory networks affecting motor control both directly and indirectly.

}, doi = {10.1101/2023.06.07.544074}, url = {https://doi.org/10.1101/2023.06.07.544074}, author = {Han S. J. Cheong and Kaitlyn N. Boone and Marryn M. Bennett and Farzaan Salman and Jacob D. Ralston and Kaleb Hatch and Raven F. Allen and Alec M. Phelps and Andrew P. Cook and Jasper S. Phelps and Mert Erginkaya and Wei-Chung A. Lee and Gwyneth M. Card and Kevin C. Daly and Andrew M. Dacks} } @article {67789, title = {Organizing memories for generalization in complementary learning systems.}, journal = {Nature Neuroscience}, volume = {26}, year = {2023}, month = {2023 Aug 01}, pages = {1438-1448}, abstract = {

Our ability to remember the past is essential for guiding our future behavior. Psychological and neurobiological features of declarative memories are known to transform over time in a process known as systems consolidation. While many theories have sought to explain the time-varying role of hippocampal and neocortical brain areas, the computational principles that govern these transformations remain unclear. Here we propose a theory of systems consolidation in which hippocampal-cortical interactions serve to optimize generalizations that guide future adaptive behavior. We use mathematical analysis of neural network models to characterize fundamental performance tradeoffs in systems consolidation, revealing that memory components should be organized according to their predictability. The theory shows that multiple interacting memory systems can outperform just one, normatively unifying diverse experimental observations and making novel experimental predictions. Our results suggest that the psychological taxonomy and neurobiological organization of declarative memories reflect a system optimized for behaving well in an uncertain future.

}, doi = {10.1038/s41593-023-01382-9}, url = {https://doi.org/10.1038/s41593-023-01382-9}, author = {Weinan Sun and Madhu Advani and Nelson Spruston and Andrew Saxe and James E. Fitzgerald} } @article {68675, title = {Origin of wiring specificity in an olfactory map revealed by neuron type-specific, time-lapse imaging of dendrite targeting.}, journal = {eLife}, volume = {12}, year = {2023}, month = {2023 Mar 28}, abstract = {

How does wiring specificity of neural maps emerge during development? Formation of the adult olfactory glomerular map begins with patterning of projection neuron (PN) dendrites at the early pupal stage. To better understand the origin of wiring specificity of this map, we created genetic tools to systematically characterize dendrite patterning across development at PN type-specific resolution. We find that PNs use lineage and birth order combinatorially to build the initial dendritic map. Specifically, birth order directs dendrite targeting in rotating and binary manners for PNs of the anterodorsal and lateral lineages, respectively. Two-photon- and adaptive optical lattice light-sheet microscope-based time-lapse imaging reveals that PN dendrites initiate active targeting with direction-dependent branch stabilization on the timescale of seconds. Moreover, PNs that are used in both the larval and adult olfactory circuits prune their larval-specific dendrites and re-extend new dendrites simultaneously to facilitate timely olfactory map organization. Our work highlights the power and necessity of type-specific neuronal access and time-lapse imaging in identifying wiring mechanisms that underlie complex patterns of functional neural maps.

}, issn = {2050-084X}, doi = {10.7554/eLife.85521}, author = {Wong, Kenneth Kin Lam and Li, Tongchao and Fu, Tian-Ming and Liu, Gaoxiang and Lyu, Cheng and Kohani, Sayeh and Xie, Qijing and Luginbuhl, David J and Upadhyayula, Srigokul and Betzig, Eric and Luo, Liqun} } @article {68512, title = {Oligodendrocyte precursor cells ingest axons in the mouse neocortex.}, journal = {Proceedings of the National Academies of Science of the U.S.A.}, volume = {119}, year = {2022}, month = {2022 Nov 29}, pages = {e2202580119}, abstract = {

Neurons in the developing brain undergo extensive structural refinement as nascent circuits adopt their mature form. This physical transformation of neurons is facilitated by the engulfment and degradation of axonal branches and synapses by surrounding glial cells, including microglia and astrocytes. However, the small size of phagocytic organelles and the complex, highly ramified morphology of glia have made it difficult to define the contribution of these and other glial cell types to this crucial process. Here, we used large-scale, serial section transmission\ electron microscopy (TEM) with computational volume segmentation to reconstruct the complete 3D morphologies of distinct glial types in the mouse visual cortex, providing unprecedented resolution of their morphology and composition. Unexpectedly, we discovered that the fine processes of oligodendrocyte precursor cells (OPCs), a population of abundant, highly dynamic glial progenitors, frequently surrounded small branches of axons. Numerous phagosomes and phagolysosomes (PLs) containing fragments of axons and vesicular structures were present inside their processes, suggesting that OPCs engage in axon pruning. Single-nucleus RNA sequencing from the developing mouse cortex revealed that OPCs express key phagocytic genes at this stage, as well as neuronal transcripts, consistent with active axon engulfment. Although microglia are thought to be responsible for the majority of synaptic pruning and structural refinement, PLs were ten times more abundant in OPCs than in microglia at this stage, and these structures were markedly less abundant in newly generated oligodendrocytes, suggesting that OPCs contribute substantially to the refinement of neuronal circuits during cortical development.

}, keywords = {Animals, Axons, Mice, Neocortex, Neurons, Oligodendrocyte Precursor Cells, Oligodendroglia}, issn = {1091-6490}, doi = {10.1073/pnas.2202580119}, author = {Buchanan, JoAnn and Elabbady, Leila and Collman, Forrest and Jorstad, Nikolas L and Bakken, Trygve E and Ott, Carolyn and Glatzer, Jenna and Bleckert, Adam A and Bodor, Agnes L and Brittain, Derrick and Bumbarger, Daniel J and Mahalingam, Gayathri and Seshamani, Sharmishtaa and Schneider-Mizell, Casey and Takeno, Marc M and Torres, Russel and Yin, Wenjing and Hodge, Rebecca D and Castro, Manuel and Dorkenwald, Sven and Ih, Dodam and Jordan, Chris S and Kemnitz, Nico and Lee, Kisuk and Lu, Ran and Macrina, Thomas and Mu, Shang and Popovych, Sergiy and Silversmith, William M and Tartavull, Ignacio and Turner, Nicholas L and Wilson, Alyssa M and Wong, William and Wu, Jingpeng and Zlateski, Aleksandar and Zung, Jonathan and Lippincott-Schwartz, Jennifer and Lein, Ed S and Seung, H Sebastian and Bergles, Dwight E and Reid, R Clay and da Costa, Nuno Ma{\c c}arico} } @article {68254, title = {Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation}, journal = {bioRxiv}, year = {2022}, month = {2022 Jul 27}, abstract = {

Advances in microscopy hold great promise for allowing quantitative and precise readouts of morphological and molecular phenomena at the single cell level in bacteria. However, the potential of this approach is ultimately limited by the availability of methods to perform unbiased cell segmentation, defined as the ability to faithfully identify cells independent of their morphology or optical characteristics. In this study, we present a new algorithm, Omnipose, which accurately segments samples that present significant challenges to current algorithms, including mixed bacterial cultures, antibiotic-treated cells, and cells of extended or branched morphology. We show that Omnipose achieves generality and performance beyond leading algorithms and its predecessor, Cellpose, by virtue of unique neural network outputs such as the gradient of the distance field. Finally, we demonstrate the utility of Omnipose in the characterization of extreme morphological phenotypes that arise during interbacterial antagonism and on the segmentation of non-bacterial objects. Our results distinguish Omnipose as a uniquely powerful tool for answering diverse questions in bacterial cell biology.

}, doi = {10.1101/2021.11.03.467199}, url = {https://doi.org/10.1101/2021.11.03.467199}, author = {Kevin J. Cutler and Carsen Stringer and Paul A. Wiggins and Joseph D. Mougous} } @article {68410, title = {Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation.}, journal = {Nature Methods}, year = {2022}, month = {2022 Oct 17}, abstract = {

Advances in microscopy hold great promise for allowing quantitative and precise measurement of morphological and molecular phenomena at the single-cell level in bacteria; however, the potential of this approach is ultimately limited by the availability of methods to faithfully segment cells independent of their morphological or optical characteristics. Here, we present Omnipose, a deep neural network image-segmentation algorithm. Unique network outputs such as the gradient of the distance field allow Omnipose to accurately segment cells on which current algorithms, including its predecessor, Cellpose, produce errors. We show that Omnipose achieves unprecedented segmentation performance on mixed bacterial cultures, antibiotic-treated cells and cells of elongated or branched morphology. Furthermore, the benefits of Omnipose extend to non-bacterial subjects, varied imaging modalities and three-dimensional objects. Finally, we demonstrate the utility of Omnipose in the characterization of extreme morphological phenotypes that arise during interbacterial antagonism. Our results distinguish Omnipose as a powerful tool for characterizing diverse and arbitrarily shaped cell types from imaging data.

}, issn = {1548-7105}, doi = {10.1038/s41592-022-01639-4}, author = {Cutler, Kevin J and Stringer, Carsen and Lo, Teresa W and Rappez, Luca and Stroustrup, Nicholas and Brook Peterson, S and Wiggins, Paul A and Mougous, Joseph D} } @article {68113, title = {One engram two readouts: stimulus dynamics switch a learned behavior in Drosophila}, journal = {bioRxiv}, year = {2022}, month = {2022 May 26}, abstract = {

Memory guides the choices an animal makes across widely varying conditions in dynamic environments. Consequently, the most adaptive choice depends on the options available. How can a single memory support optimal behavior across different sets of choice options? We address this using olfactory learning in Drosophila. Even when we restrict an odor-punishment association to a single set of synapses using optogenetics, we find that flies still show choice behavior that depends on the options it encounters. Here we show that how the odor choices are presented to the animal influences memory recall itself. Presenting two similar odors in sequence enabled flies to not only discriminate them behaviorally but also at the level of neural activity. However, when the same odors were encountered as solitary stimuli, no such differences were detectable. These results show that memory recall is not simply a comparison to a static learned template, but can be adaptively modulated by stimulus dynamics.

}, doi = {10.1101/2022.05.24.492551}, url = {https://doi.org/10.1101/2022.05.24.492551}, author = {Mehrab N Modi and Adithya Rajagopalan and Herv{\'e} Rouault and Yoshinori Aso and Glenn C Turner} } @article {67930, title = {Online learning for orientation estimation during translation in an insect ring attractor network.}, journal = {Scientific Reports}, volume = {12}, year = {2022}, month = {2022 Feb 25}, pages = {3210}, abstract = {

Insect neural systems are a promising source of inspiration for new navigation algorithms, especially on low size, weight, and power platforms. There have been unprecedented recent neuroscience breakthroughs with Drosophila in behavioral and neural imaging experiments as well as the mapping of detailed connectivity of neural structures. General mechanisms for learning orientation in the central complex (CX) of Drosophila have been investigated previously; however, it is unclear how these underlying mechanisms extend to cases where there is translation through an environment (beyond only rotation), which is critical for navigation in robotic systems. Here, we develop a CX neural connectivity-constrained model that performs sensor fusion, as well as unsupervised learning of visual features for path integration; we demonstrate the viability of this circuit for use in robotic systems in simulated and physical environments. Furthermore, we propose a theoretical understanding of how distributed online unsupervised network weight modification can be leveraged for learning in a trajectory through an environment by minimizing orientation estimation error. Overall, our results may enable a new class of CX-derived low power robotic navigation algorithms and lead to testable predictions to inform future neuroscience experiments.

}, issn = {2045-2322}, doi = {10.1038/s41598-022-05798-4}, author = {Robinson, Brian S and Norman-Tenazas, Raphael and Cervantes, Martha and Symonette, Danilo and Johnson, Erik C and Joyce, Justin and Rivlin, Patricia K and Hwang, Grace and Zhang, Kechen and Gray-Roncal, William} } @article {67873, title = {Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Jan 19}, 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. Here, we outline the system{\textquoteright}s design and rationale, present validation experiments characterising system performance, and demonstrate example applications in freely moving and head-fixed mouse behaviour.

}, issn = {2050-084X}, doi = {10.7554/eLife.67846}, author = {Akam, Thomas and Lustig, Andy and Rowland, James M and Kapanaiah, Sampath Kt and Esteve-Agraz, Joan and Panniello, Mariangela and M{\'a}rquez, Cristina and Kohl, Michael M and K{\"a}tzel, Dennis and Costa, Rui M and Walton, Mark E} } @article {68300, title = {Organization of translating secretome mRNAS on endoplasmic reticulum}, journal = {Biophysical Journal}, volume = {121}, year = {2022}, month = {2022 Feb 01}, pages = {33a}, abstract = {

The endoplasmic reticulum (ER) has a complex morphology comprised of stacked sheets, tubules, and three-way junctions, which together function as a platform for protein synthesis of membrane and secretory proteins. Specific ER subdomains are thought to be spatially organized to enable protein synthesis activity, but precisely where these domains are localized is unclear, especially relative to the plethora of organelle interactions taking place on the ER. Here, we use single-molecule tracking of ribosomes and mRNA in combination with simultaneous imaging of ER to assess the sites of membrane protein synthesis on the ER. We found that ribosomes were widely distributed throughout different ER morphologies, but the synthesis of membrane proteins (including Type I, II, and multi-spanning) and an ER luminal protein (Calreticulin) occurred primarily at three-way junctions. Lunapark played a key role in stabilizing transmembrane protein mRNA at three-way junctions. We additionally found that translating mRNAs coding for transmembrane proteins are in the vicinity of lysosomes and translate through a cap-independent but eIF2-dependent mechanism. These results support the idea that discrete ER subdomains co-exist with lysosomes to support specific types of protein synthesis activities, with ER-lysosome interactions playing an important role in the translation of secretome mRNAs.

}, issn = {00063495}, doi = {10.1016/j.bpj.2021.11.2550}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0006349521035256}, author = {Choi, Heejun and Liao, Ya-Cheng and Yoon, Young J. and Grimm, Jonathan and Lavis, Luke D. and Singer, Robert H. and Lippincott-Schwartz, Jennifer} } @article {67788, title = {Open Chemistry: What if we just give everything away?}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Nov 05}, abstract = {

A group leader decided that his lab would share the fluorescent dyes they create, for free and without authorship requirements. Nearly 12,000 aliquots later, he reveals what has happened since.

}, issn = {2050-084X}, doi = {10.7554/eLife.74981}, author = {Lavis, Luke D} } @article {67753, title = {An open-access volume electron microscopy atlas of whole cells and tissues.}, journal = {Nature}, volume = {599}, year = {2021}, month = {2021 Nov 1}, pages = {147-51}, abstract = {

Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structures with nanometre resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations in that they visualize only a single slice or a relatively small volume of the cell, respectively. Focused ion beam-scanning electron microscopy (FIB-SEM) has demonstrated the ability to image small volumes of cellular samples with 4-nm isotropic voxels. Owing to advances in the\ precision and stability of FIB milling, together with enhanced signal detection and faster SEM scanning, we have increased the volume that can be imaged with 4-nm\ voxels by two orders of magnitude. Here we present a volume EM atlas at such resolution comprising ten three-dimensional datasets for whole cells and tissues, including cancer cells, immune cells, mouse pancreatic islets and Drosophila neural tissues. These open access data (via OpenOrganelle) represent the foundation of a field of high-resolution whole-cell volume EM and subsequent analyses, and we invite researchers to explore this atlas and\ pose questions.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-03992-4}, author = {Xu, C Shan and Pang, Song and Shtengel, Gleb and M{\"u}ller, Andreas and Ritter, Alex T and Hoffman, Huxley K and Takemura, Shin-ya and Lu, Zhiyuan and Pasolli, H Amalia and Iyer, Nirmala and Chung, Jeeyun and Bennett, Davis and Weigel, Aubrey V and Freeman, Melanie and Van Engelenburg, Schuyler B and Walther, Tobias C and Farese, Robert V and Lippincott-Schwartz, Jennifer and Mellman, Ira and Solimena, Michele and Hess, Harald F} } @article {67274, title = {An open-source semi-automated robotics pipeline for embryo immunohistochemistry.}, journal = {Scientific Reports}, volume = {11}, year = {2021}, month = {2021 May 13}, pages = {10314}, abstract = {

A significant challenge for developmental systems biology is balancing throughput with controlled conditions that minimize experimental artifacts. Large-scale developmental screens such as unbiased mutagenesis surveys have been limited in their applicability to embryonic systems, as the technologies for quantifying precise expression patterns in whole animals has not kept pace with other sequencing-based technologies. Here, we outline an open-source semi-automated pipeline to chemically fixate, stain, and 3D-image Drosophila embryos. Central to this pipeline is a liquid handling robot, Flyspresso, which automates the steps of classical embryo fixation and staining. We provide the schematics and an overview of the technology for an engineer or someone equivalently trained to reproduce and further improve upon Flyspresso, and highlight the Drosophila embryo fixation and colorimetric or antibody staining protocols. Additionally, we provide a detailed overview and stepwise protocol for our adaptive-feedback pipeline for automated embryo imaging on confocal microscopes. We demonstrate the efficiency of this pipeline compared to classical techniques, and how it can be repurposed or scaled to other protocols and biological systems. We hope our pipeline will serve as a platform for future research, allowing a broader community of users to build, execute, and share similar experiments.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-89676-5}, author = {Fuqua, Timothy and Jordan, Jeff and Halavatyi, Aliaksandr and Tischer, Christian and Richter, Kerstin and Crocker, Justin} } @article {67178, title = {Optogenetic Tools for Manipulating Protein Subcellular Localization and Intracellular Signaling at Organelle Contact Sites}, journal = {Current Protocols}, volume = {1}, year = {2021}, month = {2021 Mar 03}, abstract = {

Intracellular signaling processes are frequently based on direct interactions between proteins and organelles. A fundamental strategy to elucidate the physiological significance of such interactions is to utilize optical dimerization tools. These tools are based on the use of small proteins or domains that interact with each other upon light illumination. Optical dimerizers are particularly suitable for reproducing and interrogating a given protein-protein interaction and for investigating a protein{\textquoteright}s intracellular role in a spatially and temporally precise manner. Described in this article are genetic engineering strategies for the generation of modular light-activatable protein dimerization units and instructions for the preparation of optogenetic applications in mammalian cells. Detailed protocols are provided for the use of light-tunable switches to regulate protein recruitment to intracellular compartments, induce intracellular organellar membrane tethering, and reconstitute protein function using enhanced Magnets (eMags), a recently engineered optical dimerization system. {\textcopyright} 2021 Wiley Periodicals LLC.

}, issn = {2691-1299}, doi = {https://doi.org/10.1002/cpz1.71}, url = {https://doi.org/10.1002/cpz1.71}, author = {Benedetti, Lorena} } @inbook {67667, title = {Optogenetics}, booktitle = {Molecular Imaging: Principles and Practice, 2nd Edition}, year = {2021}, publisher = {Academic Press}, organization = {Academic Press}, edition = {2}, chapter = {16}, abstract = {

To truly understand biological systems, one must possess the ability to selectively manipulate their parts and observe the outcome. (For purposes of this review, we refer mostly to targets of neuroscience; however, the principles covered here largely extend to myriad samples from microbes to plants to the intestine, etc.).

Drugs are the most commonly employed way of introducing such perturbations, but they act on endogenous proteins that frequently exist in multiple cell types, complicating the interpretation of experiments. Whatever the applied stimulus, it is best to introduce optimized exogenous reagents into the systems under studydenabling manipulations to be targeted to speci!c cells and pathways. (It is also possible to target manipulations through other means, such as drugs that acquire cell-type speci!city through targeting via antibodies and/or cell surface receptor ligands, but as far as we are aware, existing reagents fall short in terms of necessary speci!city.) Many types of perturbations are useful in living systems and can be divided into rough categories such as the following: depolarize or hyperpolarize cells, induce or repress the activity of a speci!c pathway, induce or inhibit expression of a particular gene, activate or repress a speci!c protein, degrade a speci!c protein, etc. User-supplied triggers for such manipulations to occur include the following: addition of a small molecule ({\textquotedblleft}chemogenetics{\textquotedblright}dideally inert on endogenous proteins) [1], sound waves ({\textquotedblleft}sonogenetics{\textquotedblright}) [2], alteration of temperature ({\textquotedblleft}thermogenetics{\textquotedblright}d almost exclusively used for small invertebrates) [3], and light ({\textquotedblleft}optogenetics{\textquotedblright}). There are reports of using magnetic !elds ({\textquotedblleft}magnetogenetics{\textquotedblright}) [4], but there is no evidence that such effects are reproducible or even physically possible [5,6]. Of these, the most commonly used, for multiple reasons, is light.

Many factors make light an ideal user-controlled stimulus for the manipulation of samples. Light is quickly delivered, and most light-sensitive proteins and other molecules respond quickly to light stimuli, making many optogenetic systems relatively rapid in comparison to, for instance, drug-modulated systems. Light is also quite easy to deliver in localized patterns, allowing for targeted stimulation. Multiple wavelengths can be delivered separately to distinct (or overlapping) regions, potentially allowing combinatorial control of diverse components. Finally, light can be delivered to shallow brain regions (and peripheral sites) relatively noninvasively, and to deeper brain regions with some effort.

However, there are also a number of shortcomings of using light for control. Robust and uniform penetration of light into the sample is the most signi!cant concern. For systems requiring modulation of many cells, particularly at depth, the use of systems controlled by small molecule drugs would generally be recommended instead of optogenetic approaches. When light is delivered through the use of !bers, lenses, or other optical devices, such interventions can produce signi!- cant cellular death, scar formation, and biofouling. The foreign-body response of tissue to objects triggers substantial molecular alterations, the implications of which are incompletely de!ned, but can involve reactive astrogliosis, oxidative stress, and perturbed vascularization. Head-mounted lightdelivery devices can be heavy and/or restrictive, and thus perturb behavior, particularly for small animals (e.g., mouse behavior is much more disrupted than rat behavior). More generally, all light causes tissue heating, which can have dramatic effects on cell health, physiology, and animal behavior. This is most concerning for tiny animals such as "ies. Light itself also damages tissue, most obviously through photochemistry (e.g., oxidation and radicalization) and photobleaching of critical endogenousmolecules. Furthermore, of course, light is ubiquitous, meaning that the sample is never completely unstimulated, despite precautions. Light passes through the eyes into the brain with surprising ease, and even through the skull with modest ef!cacy [7]dwhich can disrupt animal behavior (as can the converse: stimulating light in the brain perceived as a visual stimulus through the back of the eyes.) Light-responsive proteins exist in all samples, particularly in the eyes but to some extent in all tissuesdnotably, deep-brain photoreceptors [8].

The use of optogenetic tools has accelerated research on many fronts in disparate !elds. Additional, perhaps most, limitations on the utility of optogenetics must, however, be placed squarely on the shortcomings of the current suite of tools (and potential inherent limits in their performance.) The vast majority of optogenetic effectors are gated by blue light, which has signi!cant penetration issues and can be phototoxic under high intensity; redder wavelengths would in general be preferred. Furthermore, multiplexing requires tools making use of other parts of the visible spectrum (and redder wavelengths). A related issue is that most chromophores for optogenetic reagents have very broad action spectra (w250 nm bandwidth for retinal; w200 nm bandwidth for "avin), complicating both multiplexing and their use alongside many optical imaging reagentsdnarrower action spectra would be preferred for effectors in most situations. More generally, the current classes of optogenetic effectors are\ few, mostly limited to (1) channels and pumps (most with poor ion selectivity), (2) dimerizers, and (3) a handful of enzymes. The number of optogenetic tools that perform a very speci!c function in cells is small. Although progress has undeniably been made, much additional research and engineering will be required to dramatically expand the optogenetic toolkit.

Rather than providing a survey of research !ndings, this review covers general considerations of optogenetics experiments, and then focuses largely on molecular tools: the existing suite, their features and limitations, and goals for the creation and validation of additional reagents.

}, author = {Looger, Loren L and Maria G. Paez Segala} } @article {67794, title = {The organization and development of cortical interneuron presynaptic circuits are area specific.}, journal = {Cell Reports}, volume = {37}, year = {2021}, month = {2021 Nov 09}, pages = {109993}, abstract = {

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

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.109993}, author = {Pouchelon, Gabrielle and Dwivedi, Deepanjali and Bollmann, Yannick and Agba, Chimuanya K and Xu, Qing and Mirow, Andrea M C and Kim, Sehyun and Qiu, Yanjie and Sevier, Elaine and Ritola, Kimberly D and Cossart, Rosa and Fishell, Gord} } @article {67668, title = {Optimization of Fluorescent Proteins and Techniques for In-resin Correlative Light and Electron Microscopy}, journal = {Microscopy and Microanalysis}, volume = {26}, year = {2020}, month = {07/2020}, pages = {1036{\textendash}1039}, abstract = {

Correlative light and electron microscopy (CLEM) combines the power of electron microscopy, with its excellent resolution and contrast, with that of fluorescence imaging, which allows the staining of specific molecules, organelles, and cell populations. Fluorescence imaging is also readily compatible with live cells and behaving animals, facilitating real-time visualization of cellular processes, potentially followed by electron microscopic reconstruction. Super-resolution single-molecule localization microscopy is a relatively new modality that harnesses the ability of some fluorophores to photoconvert, through which localization precision better than Abbe{\textquoteright}s diffraction limit is achieved through iterative high-resolution localization of single-molecule emitters. Here we describe our lab{\textquoteright}s recent progress in the development of reagents and techniques for super-resolution single-molecule localization CLEM and their applications to biological problems.

}, doi = {10.1017/S143192762001675X}, author = {Paez-Segala, Maria and Wang, Yalin and Iyer, Nirmala and Li, Wei-Ping and Rivlin, Patricia and Looger, Loren} } @article {65827, title = {Optimized Vivid-derived Magnets photodimerizers for subcellular optogenetics in mammalian cells.}, journal = {Elife}, volume = {9}, year = {2020}, month = {2020 Nov 11}, abstract = {

Light-inducible dimerization protein modules enable precise temporal and spatial control of biological processes in non-invasive fashion. Among them, Magnets are small modules engineered from the photoreceptor Vivid by orthogonalizing the homodimerization interface into complementary heterodimers. Both Magnets components, which are well-tolerated as protein fusion partners, are photoreceptors requiring simultaneous photoactivation to interact, enabling high spatiotemporal confinement of dimerization with a single-excitation wavelength. However, Magnets require concatemerization for efficient responses and cell preincubation at 28C to be functional. Here we overcome these limitations by engineering an optimized Magnets pair requiring neither concatemerization nor low temperature preincubation. We validated these {\textquoteright}enhanced{\textquoteright} Magnets (eMags) by using them to rapidly and reversibly recruit proteins to subcellular organelles, to induce organelle contacts, and to reconstitute OSBP-VAP ER-Golgi tethering implicated in phosphatidylinositol-4-phosphate transport and metabolism. eMags represent a very effective tool to optogenetically manipulate physiological processes over whole cells or in small subcellular volumes.

}, issn = {2050-084X}, doi = {10.7554/eLife.63230}, author = {Benedetti, Lorena and Marvin, Jonathan S and Falahati, Hanieh and Guill{\'e}n-Samander, Andres and Looger, Loren L and De Camilli, Pietro} } @article {65761, title = {Orthogonal fluorescent chemogenetic reporters for multicolor imaging}, journal = {Nature Chemical Biology}, year = {2020}, month = {04/2020}, pages = {1{\textendash}9}, abstract = {

Spectrally separated fluorophores allow the observation of multiple targets simultaneously inside living cells, leading to a deeper understanding of the molecular interplay that regulates cell function and fate. Chemogenetic systems combining a tag and a synthetic fluorophore provide certain advantages over fluorescent proteins since there is no requirement for chromophore maturation. Here, we present the engineering of a set of spectrally orthogonal fluorogen-activating tags based on the fluorescence-activating and absorption shifting tag (FAST) that are compatible with two-color, live-cell imaging. The resulting tags, greenFAST and redFAST, demonstrate orthogonality not only in their fluorogen recognition capabilities, but also in their one- and two-photon absorption profiles. This pair of orthogonal tags allowed the creation of a two-color cell cycle sensor capable of detecting very short, early cell cycles in zebrafish development and the development of split complementation systems capable of detecting multiple protein{\textendash}protein interactions by live-cell fluorescence microscopy. The fluorescent chemogenetic reporters greenFAST and redFAST were engineered by protein engineering. They display orthogonal fluorogen recognition and spectral properties allowing efficient multicolor imaging of proteins in live cells and organisms.

}, issn = {1552-4450}, doi = {10.1038/s41589-020-0611-0}, author = {Tebo, Alison G. and Moeyaert, Benjamien and Thauvin, Marion and Carlon-Andres, Irene and B{\"o}ken, Dorothea and Volovitch, Michel and Padilla-Parra, Sergi and Dedecker, Peter and Vriz, Sophie and Gautier, Arnaud} } @article {51792, title = {An orderly single-trial organization of population dynamics in premotor cortex predicts behavioral variability.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Jan 15}, pages = {216}, abstract = {

Animals are not simple input-output machines. Their responses to even very similar stimuli are variable. A key, long-standing question in neuroscience is to understand the neural correlates of such behavioral variability. To reveal these correlates, behavior and neural population activity must be related to one another on single trials. Such analysis is challenging due to the dynamical nature of brain function (e.g., in decision making), heterogeneity across neurons and limited sampling of the relevant neural population. By analyzing population recordings from mouse frontal cortex in perceptual decision-making tasks, we show that an analysis approach tailored to the coarse grain features of the dynamics is able to reveal previously unrecognized structure in the organization of population activity. This structure is similar on error and correct trials, suggesting dynamics that may be constrained by the underlying circuitry, is able to predict multiple aspects of behavioral variability and reveals long time-scale modulation of population activity.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-08141-6}, author = {Wei, Ziqiang and Inagaki, Hidehiko and Li, Nuo and Svoboda, Karel and Druckmann, Shaul} } @article {65206, title = {The organization of the second optic chiasm of the optic lobe.}, journal = {Frontiers in Neural Circuits}, volume = {13}, year = {2019}, month = {2019 Oct 11}, pages = {65}, abstract = {

Visual pathways from the compound eye of an insect relay to four neuropils, successively the lamina, medulla, lobula, and lobula plate in the underlying optic lobe. Among these neuropils, the medulla, lobula, and lobula plate are interconnected by the complex second optic chiasm, through which the anteroposterior axis undergoes an inversion between the medulla and lobula. Given their complex structure, the projection patterns through the second optic chiasm have so far lacked critical analysis. By densely reconstructing axon trajectories using a volumetric scanning electron microscopy (SEM) technique, we reveal the three-dimensional structure of the second optic chiasm of , which comprises interleaving bundles and sheets of axons insulated from each other by glial sheaths. These axon bundles invert their horizontal sequence in passing between the medulla and lobula. Axons connecting the medulla and lobula plate are also bundled together with them but do not decussate the sequence of their horizontal positions. They interleave with sheets of projection neuron axons between the lobula and lobula plate, which also lack decussations. We estimate that approximately 19,500 cells per hemisphere, about two thirds of the optic lobe neurons, contribute to the second chiasm, most being Tm cells, with an estimated additional 2,780 T4 and T5 cells each. The chiasm mostly comprises axons and cell body fibers, but also a few synaptic elements. Based on our anatomical findings, we propose that a chiasmal structure between the neuropils is potentially advantageous for processing complex visual information in parallel. The EM reconstruction shows not only the structure of the chiasm in the adult brain, the previously unreported main topic of our study, but also suggest that the projection patterns of the neurons comprising the chiasm may be determined by the proliferation centers from which the neurons develop. Such a complex wiring pattern could, we suggest, only have arisen in several evolutionary steps.

}, issn = {1662-5110}, doi = {10.3389/fncir.2019.00065}, author = {Shinomiya, Kazunori and Horne, Jane Anne and McLin, Sari and Wiederman, Meagan and Nern, Aljoscha and Plaza, Stephen M and Meinertzhagen, Ian A} } @article {49173, title = {Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms.}, journal = {Science (New York, N.Y.)}, volume = {360}, year = {2018}, month = {2018 Apr 20}, abstract = {

True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes that we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution, without inducing undue stress on either. We combined lattice light-sheet microscopy with adaptive optics to achieve, across large multicellular volumes, noninvasive aberration-free imaging of subcellular processes, including endocytosis, organelle remodeling during mitosis, and the migration of axons, immune cells, and metastatic cancer cells in vivo. The technology reveals the phenotypic diversity within cells across different organisms and developmental stages and may offer insights into how cells harness their intrinsic variability to adapt to different physiological environments.

}, issn = {1095-9203}, doi = {10.1126/science.aaq1392}, author = {Liu, Tsung-Li and Upadhyayula, Srigokul and Milkie, Daniel E and Singh, Ved and Wang, Kai and Swinburne, Ian A and Mosaliganti, Kishore R and Collins, Zach M and Hiscock, Tom W and Shea, Jamien and Kohrman, Abraham Q and Medwig, Taylor N and Dambournet, Daphne and Forster, Ryan and Cunniff, Brian and Ruan, Yuan and Yashiro, Hanako and Scholpp, Steffen and Meyerowitz, Elliot M and Hockemeyer, Dirk and Drubin, David G and Martin, Benjamin L and Matus, David Q and Koyama, Minoru and Megason, Sean G and Kirchhausen, Tom and Betzig, Eric} } @article {49141, title = {Odorant binding protein 69a connects social interaction to modulation of social responsiveness in Drosophila.}, journal = {PLoS Genetics}, volume = {14}, year = {2018}, month = {2018 Apr 09}, pages = {e1007328}, abstract = {

Living in a social environment requires the ability to respond to specific social stimuli and to incorporate information obtained from prior interactions into future ones. One of the mechanisms that facilitates social interaction is pheromone-based communication. In Drosophila melanogaster, the male-specific pheromone cis-vaccenyl acetate (cVA) elicits different responses in male and female flies, and functions to modulate behavior in a context and experience-dependent manner. Although it is the most studied pheromone in flies, the mechanisms that determine the complexity of the response, its intensity and final output with respect to social context, sex and prior interaction, are still not well understood. Here we explored the functional link between social interaction and pheromone-based communication and discovered an odorant binding protein that links social interaction to sex specific changes in cVA related responses. Odorant binding protein 69a (Obp69a) is expressed in auxiliary cells and secreted into the olfactory sensilla. Its expression is inversely regulated in male and female flies by social interactions: cVA exposure reduces its levels in male flies and increases its levels in female flies. Increasing or decreasing Obp69a levels by genetic means establishes a functional link between Obp69a levels and the extent of male aggression and female receptivity. We show that activation of cVA-sensing neurons is sufficeint to regulate Obp69a levels in the absence of cVA, and requires active neurotransmission between the sensory neuron to the second order olfactory neuron. The cross-talk between sensory neurons and non-neuronal auxiliary cells at the olfactory sensilla, represents an additional component in the machinery that promotes behavioral plasticity to the same sensory stimuli in male and female flies.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1007328}, author = {Bentzur, Assa and Shmueli, Anat and Omesi, Liora and Ryvkin, Julia and Knapp, Jon-Michael and Parnas, Moshe and Davis, Fred P and Shohat-Ophir, Galit} } @article {49235, title = {Of what use is connectomics? A personal perspective on the connectome.}, journal = {The Journal of Experimental Biology}, volume = {221}, year = {2018}, month = {2018 May 20}, abstract = {

The brain is a network of neurons and its biological output is behaviour. This is an exciting age, with a growing acknowledgement that the comprehensive compilation of synaptic circuits densely reconstructed in the brains of model species is now both technologically feasible and a scientifically enabling possibility in neurobiology, much as 30 years ago genomics was in molecular biology and genetics. Implemented by huge advances in electron microscope technology, especially focused ion beam-scanning electron microscope (FIB-SEM) milling (see Glossary), image capture and alignment, and computer-aided reconstruction of neuron morphologies, enormous progress has been made in the last decade in the detailed knowledge of the actual synaptic circuits formed by real neurons, in various brain regions of the fly It is useful to distinguish synaptic pathways that are major, with 100 or more presynaptic contacts, from those that are minor, with fewer than about 10; most neurites are both presynaptic and postsynaptic, and all synaptic sites have multiple postsynaptic dendrites. Work on has spearheaded these advances because cell numbers are manageable, and neuron classes are morphologically discrete and genetically identifiable, many confirmed by reporters. Recent advances are destined within the next few years to reveal the complete connectome in an adult fly, paralleling advances in the larval brain that offer the same prospect possibly within an even shorter time frame. The final amendment and validation of segmented bodies by human proof-readers remains the most time-consuming step, however. The value of a complete connectome in is that, by targeting to specific neurons transgenes that either silence or activate morphologically identified circuits, and then identifying the resulting behavioural outcome, we can determine the causal mechanism for behaviour from its loss or gain. More importantly, the connectome reveals hitherto unsuspected pathways, leading us to seek novel behaviours for these. Circuit information will eventually be required to understand how differences between brains underlie differences in behaviour, and especially to herald yet more advanced connectomic strategies for the vertebrate brain, with an eventual prospect of understanding cognitive disorders having a connectomic basis. Connectomes also help us to identify common synaptic circuits in different species and thus to reveal an evolutionary progression in candidate pathways.

}, issn = {1477-9145}, doi = {10.1242/jeb.164954}, author = {Meinertzhagen, Ian A} } @article {49115, title = {Opportunities and obstacles for deep learning in biology and medicine.}, journal = {Journal of The Royal Society Interface}, year = {2018}, month = {2018 Apr 4}, abstract = {

Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems{\textemdash}patient classification, fundamental biological processes and treatment of patients{\textemdash}and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network{\textquoteright}s prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.

}, doi = {10.1098/rsif.2017.0387}, author = {Ching, Travers and Himmelstein, Daniel S and Beaulieu-Jones, Brett K and Kalinin, Alexandr A and Do, Brian T and Way, Gregory P and Ferrero, Enrico and Agapow, Paul-Michael and Zietz, Michael and Hoffman, Michael M and Xie, Wei and Rosen, Gail L and Lengerich, Benjamin J and Israeli, Johnny and Lanchantin, Jack and Woloszynek, Stephen and Carpenter, Anne E and Shrikumar, Avanti and Xu, Jinbo and Cofer, Evan M} } @article {49381, title = {Optical alignment device for two-photon microscopy.}, journal = {Biomedical Optics Express}, volume = {9}, year = {2018}, month = {2018 Aug 1}, pages = {3624-9}, abstract = {

Two-photon excitation fluorescence microscopy has revolutionized our understanding of brain structure and function through the high resolution and large penetration depth it offers. Investigating neural structures\ in vivo\ requires gaining optical access to the brain, which is typically achieved by replacing a part of the skull with one or several layers of cover glass windows. To compensate for the spherical aberrations caused by the presence of these layers of glass, collar-correction objectives are typically used. However, the efficiency of this correction has been shown to depend significantly on the tilt angle between the glass window surface and the optical axis of the imaging system. Here, we first expand these observations and characterize the effect of the tilt angle on the collected fluorescence signal with thicker windows (double cover slide) and compare these results with an objective devoid of collar-correction. Second, we present a simple optical alignment device designed to rapidly minimize the tilt angle\ in vivo\ and align the optical axis of the microscope perpendicularly to the glass window to an angle below 0.25{\textdegree}, thereby significantly improving the imaging quality. Finally, we describe a tilt-correction procedure for users in an\ in vivo\ setting, enabling the accurate alignment with a resolution of \<0.2{\textdegree} in only few iterations.

}, doi = {10.1364/BOE.9.003624}, author = {Gali{\~n}anes, Gregorio L and Marchand, Paul J and Turcotte, Raphael and Pellat, Sebastien and Ji, Na and Huber, Daniel} } @article {49366, title = {Optimization of fluorophores for chemical tagging and immunohistochemistry of Drosophila neurons.}, journal = {PLoS One}, volume = {13}, year = {2018}, month = {2018 Aug 15}, pages = {e0200759}, abstract = {

The use of genetically encoded {\textquoteright}self-labeling tags{\textquoteright} with chemical fluorophore ligands enables rapid labeling of specific cells in neural tissue. To improve the chemical tagging of neurons, we synthesized and evaluated new fluorophore ligands based on Cy, Janelia Fluor, Alexa Fluor, and ATTO dyes and tested these with recently improved Drosophila melanogaster transgenes. We found that tissue clearing and mounting in DPX substantially improves signal quality when combined with specific non-cyanine fluorophores. We compared and combined this labeling technique with standard immunohistochemistry in the Drosophila brain.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0200759}, author = {Meissner, Geoffrey W and Grimm, Jonathan B and Johnston, Rebecca M and Sutcliffe, Ben and Ng, Julian and Jefferis, Gregory S X E and Cachero, Sebastian and Lavis, Luke D and Malkesman, Oz} } @article {48976, title = {Optogenetic dissection of descending behavioral control in Drosophila.}, journal = {eLife}, year = {2018}, month = {2018}, pages = {e34275}, abstract = {

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

}, doi = {10.7554/eLife.34275}, author = {Cande, Jessica and Namiki, Shigehiro and Qiu, Jirui and Korff, Wyatt and Card, Gwyneth M and Shaevitz, Joshua W and Stern, David L and Berman, Gordon J} } @article {48642, title = {The Ol1mpiad: concordance of behavioural faculties of stage 1 and stage 3 Drosophila larvae.}, journal = {The Journal of Experimental Biology}, volume = {220}, year = {2017}, month = {2017 Jul 01}, pages = {2452-2475}, abstract = {

Mapping brain function to brain structure is a fundamental task for neuroscience. For such an endeavour, the Drosophila larva is simple enough to be tractable, yet complex enough to be interesting. It features about 10,000 neurons and is capable of various taxes, kineses and Pavlovian conditioning. All its neurons are currently being mapped into a light-microscopical atlas, and Gal4 strains are being generated to experimentally access neurons one at a time. In addition, an electron microscopic reconstruction of its nervous system seems within reach. Notably, this electron microscope-based connectome is being drafted for a stage 1 larva - because stage 1 larvae are much smaller than stage 3 larvae. However, most behaviour analyses have been performed for stage 3 larvae because their larger size makes them easier to handle and observe. It is therefore warranted to either redo the electron microscopic reconstruction for a stage 3 larva or to survey the behavioural faculties of stage 1 larvae. We provide the latter. In a community-based approach we called the Ol1mpiad, we probed stage 1 Drosophila larvae for free locomotion, feeding, responsiveness to substrate vibration, gentle and nociceptive touch, burrowing, olfactory preference and thermotaxis, light avoidance, gustatory choice of various tastants plus odour-taste associative learning, as well as light/dark-electric shock associative learning. Quantitatively, stage 1 larvae show lower scores in most tasks, arguably because of their smaller size and lower speed. Qualitatively, however, stage 1 larvae perform strikingly similar to stage 3 larvae in almost all cases. These results bolster confidence in mapping brain structure and behaviour across developmental stages.

}, issn = {1477-9145}, doi = {10.1242/jeb.156646}, author = {Almeida-Carvalho, Maria J and Berh, Dimitri and Braun, Andreas and Chen, Yi-chun and Eichler, Katharina and Eschbach, Claire and Fritsch, Pauline M J and Gerber, Bertram and Hoyer, Nina and Jiang, Xiaoyi and Kleber, J{\"o}rg and Kl{\"a}mbt, Christian and K{\"o}nig, Christian and Louis, Matthieu and Michels, Birgit and Miroschnikow, Anton and Mirth, Christen and Miura, Daisuke and Niewalda, Thomas and Otto, Nils and Paisios, Emmanouil and Pankratz, Michael J and Petersen, Meike and Ramsperger, Noel and Randel, Nadine and Risse, Benjamin and Saumweber, Timo and Schlegel, Philipp and Schleyer, Michael and Soba, Peter and Sprecher, Simon G and Tanimura, Teiichi and Thum, Andreas S and Toshima, Naoko and Truman, Jim W and Yarali, Ayse and Zlatic, Marta} } @article {48649, title = {Opening a path to commercialization.}, journal = {Optics and Photonics News}, volume = {28}, year = {2017}, month = {2017 Jul 01}, pages = {42-9}, abstract = {

To smooth the academic-to-industry transition, one institution is experimenting with offering biomedical researchers pre-commercial open access to new optical imaging systems still under development. The approach, the authors of this case study suggest, can be a win on both sides.

}, doi = {10.1364/OPN.28.7.000042} } @article {48371, title = {Optical measurement of receptor tyrosine kinase oligomerization on live cells.}, journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes}, volume = {1859}, year = {2017}, month = {2017 Apr 04}, pages = {1436-44}, abstract = {

Receptor tyrosine kinases (RTK) are important cell surface receptors that transduce extracellular signals across the plasma membrane. The traditional view of how these receptors function is that ligand binding to the extracellular domains acts as a master-switch that enables receptor monomers to dimerize and subsequently trans-phosphorylate each other on their intracellular domains. However, a growing body of evidence suggests that receptor oligomerization is not merely a consequence of ligand binding, but is instead part of a complex process responsible for regulation of receptor activation. Importantly, the oligomerization dynamics and subsequent activation of these receptors are affected by other cellular components, such as cytoskeletal machineries and cell membrane lipid characteristics. Thus receptor activation is not an isolated molecular event mediated by the ligand-receptor interaction, but instead involves orchestrated interactions between the receptors and other cellular components. Measuring receptor oligomerization dynamics on live cells can yield important insights into the characteristics of these interactions. Therefore, it is imperative to develop techniques that can probe receptor movements on the plasma membrane with optimal temporal and spatial resolutions. Various microscopic techniques have been used for this purpose. Optical techniques including single molecule tracking (SMT) and fluorescence correlation spectroscopy (FCS) measure receptor diffusion on live cells. Receptor-receptor interactions can also be assessed by detecting F{\"o}rster resonance energy transfer (FRET) between fluorescently-labeled receptors situated in close proximity or by counting the number of receptors within a diffraction limited fluorescence spot (stepwise bleaching). This review will describe recent developments of optical techniques that have been used to study receptor oligomerization on living cells. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova.

}, doi = {10.1016/j.bbamem.2017.03.026}, author = {Chung, Inhee} } @article {48799, title = {Optogenetic control with a photocleavable protein, PhoCl.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Apr}, pages = {391-394}, abstract = {

To expand the range of experiments that are accessible with optogenetics, we developed a photocleavable protein (PhoCl) that spontaneously dissociates into two fragments after violet-light-induced cleavage of a specific bond in the protein backbone. We demonstrated that PhoCl can be used to engineer light-activatable Cre recombinase, Gal4 transcription factor, and a viral protease that in turn was used to activate opening of the large-pore ion channel Pannexin-1.

}, keywords = {Connexins, Directed Molecular Evolution, Green Fluorescent Proteins, HEK293 Cells, HSP90 Heat-Shock Proteins, Humans, Luminescent Proteins, Nerve Tissue Proteins, Nuclear Localization Signals, Optogenetics, Patch-Clamp Techniques, Photochemistry, Protein Engineering, Recombinant Proteins, Viral Nonstructural Proteins}, issn = {1548-7105}, doi = {10.1038/nmeth.4222}, author = {Zhang, Wei and Lohman, Alexander W and Zhuravlova, Yevgeniya and Lu, Xiaocen and Wiens, Matthew D and Hoi, Hiofan and Yaganoglu, Sine and Mohr, Manuel A and Kitova, Elena N and Klassen, John S and Pantazis, Periklis and Thompson, Roger J and Campbell, Robert E} } @article {48847, title = {Organization of the drosophila larval visual circuit.}, journal = {eLife}, year = {2017}, month = {2017 Aug 8}, pages = {e28387}, abstract = {

Visual systems transduce, process and transmit light-dependent environmental cues. Computation of visual features depends on photoreceptor neuron types (PR) present, organization of the eye and wiring of the underlying neural circuit. Here, we describe the circuit architecture of the visual system of\ Drosophila\ larvae by mapping the synaptic wiring diagram and neurotransmitters. By contacting different targets, the two larval PR-subtypes create two converging pathways potentially underlying the computation of ambient light intensity and temporal light changes already within this first visual processing center. Locally processed visual information then signals via dedicated projection interneurons to higher brain areas including the lateral horn and mushroom body. The stratified structure of the larval optic neuropil (LON) suggests common organizational principles with the adult fly and vertebrate visual systems. The complete synaptic wiring diagram of the LON paves the way to understanding how circuits with reduced numerical complexity control wide ranges of behaviors.

}, doi = {10.7554/eLife.28387}, author = {Larderet, Ivan and Fritsch, Pauline M J and Gendre, Nanae and Neagu-Maier, G Larisa and Fetter, Richard D and Schneider-Mizell, Casey M and Truman, James W and Zlatic, Marta and Cardona, Albert and Sprecher, Simon G} } @article {47468, title = {Opponent and bidirectional control of movement velocity in the basal ganglia.}, journal = {Nature}, year = {2016}, month = {2016 May 2}, abstract = {

For goal-directed behaviour it is critical that we can both select the appropriate action and learn to modify the underlying movements (for example, the pitch of a note or velocity of a reach) to improve outcomes. The basal ganglia are a critical nexus where circuits necessary for the production of behaviour, such as the neocortex and thalamus, are integrated with reward signalling to reinforce successful, purposive actions. The dorsal striatum, a major input structure of basal ganglia, is composed of two opponent pathways, direct and indirect, thought to select actions that elicit positive outcomes and suppress actions that do not, respectively. Activity-dependent plasticity modulated by reward is thought to be sufficient for selecting actions in the striatum. Although perturbations of basal ganglia function produce profound changes in movement, it remains unknown whether activity-dependent plasticity is sufficient to produce learned changes in movement kinematics, such as velocity. Here we use cell-type-specific stimulation in mice delivered in closed loop during movement to demonstrate that activity in either the direct or indirect pathway is sufficient to produce specific and sustained increases or decreases in velocity, without affecting action selection or motivation. These behavioural changes were a form of learning that accumulated over trials, persisted after the cessation of stimulation, and were abolished in the presence of dopamine antagonists. Our results reveal that the direct and indirect pathways can each bidirectionally control movement velocity, demonstrating unprecedented specificity and flexibility in the control of volition by the basal ganglia.

}, issn = {1476-4687}, doi = {10.1038/nature17639}, author = {Yttri, Eric A and Dudman, Joshua T} } @article {48096, title = {Opportunities for Technology and Tool Development.}, journal = {Neuron}, volume = {92}, year = {2016}, month = {2016 Nov 2}, pages = {564-566}, abstract = {

Major resources are now available to develop tools and technologies aimed at dissecting the circuitry and computations underlying behavior, unraveling the underpinnings of brain disorders, and understanding the neural substrates of cognition. Scientists from around the world shared their views around new tools and technologies to drive advances in neuroscience.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2016.10.042} } @article {47936, title = {The Oscillating Stimulus Transporter Assay, OSTA: Quantitative functional imaging of transporter protein activity in time and frequency domains.}, journal = {Molecular Cell}, volume = {64}, year = {2016}, month = {2016 Oct 6}, pages = {199-212}, abstract = {

Transmembrane transporter proteins allow the passage of essentially all biologically important molecules across the lipid membranes of cells and organelles and are therefore of central importance to all forms of life. Current methods of transporter measurement, however, are lacking in several dimensions. Herein, a method is presented in which oscillating stimuli are presented to transporter-expressing cells, and activity is measured through imaging the corresponding oscillating responses of intracellular fluorescent sensors. This approach yields continuous temporal readouts of transporter activity and can therefore be used to measure time-dependent responses to drugs and other stimuli. Because of the periodic nature of the response, temporal Fourier transforms can be used to identify and quantify regions of interest in the xy plane and to overcome noise. This technique, called the Oscillating Stimulus Transporter Assay (OSTA), should greatly facilitate both functional characterization of transporters as well as high-throughput screening of drugs for transporters of particular pathophysiological interest.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2016.09.001}, author = {Keller, Jacob P and Looger, Loren L} } @article {46861, title = {Open source tools for large-scale neuroscience.}, journal = {Current Opinion in Neurobiology}, volume = {32}, year = {2015}, month = {2015 Jun}, pages = {156-63}, abstract = {

New technologies for monitoring and manipulating the nervous system promise exciting biology but pose challenges for analysis and computation. Solutions can be found in the form of modern approaches to distributed computing, machine learning, and interactive visualization. But embracing these new technologies will require a cultural shift: away from independent efforts and proprietary methods and toward an open source and collaborative neuroscience.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2015.04.002}, author = {Freeman, Jeremy} } @proceedings {65005, title = {An open-source VAA3D plugin for real-time 3D visualization of terabyte-sized volumetric images.}, year = {2015}, month = {2015 Apr 19}, abstract = {

Modern high-throughput bioimaging techniques pose the unprecedented challenge of exploring and analyzing the produced Terabyte-scale volumetric images directly in their 3D space. Without expensive virtual reality devices and/or parallel computing infrastructures, this becomes even more demanding and calls for new, more scalable tools that help exploring these very large 3D data also on common laptops and graphic hardware. To this end, we developed a plugin for the open-source, cross-platform Vaa3D system to extend its powerful 3D visualization and analysis capabilities to images of potentially unlimited size. When used with large volumetric images up to 2.5 Terabyte in size, Vaa3D-TeraFly exhibited real-time (subsecond) performance that scaled constantly on image size. The tool has been implemented in C++ with Qt and OpenGL and it is freely and publicly available both as open-source and as binary package along with the main Vaa3D distribution.

}, doi = {10.1109/ISBI.2015.7163925}, author = {Alessandro Bria and Giulio Iannello and Hanchuan Peng} } @article {47126, title = {Opposing intrinsic temporal gradients guide neural stem cell production of varied neuronal fates.}, journal = {Science (New York, N.Y.)}, volume = {350}, year = {2015}, month = {2015 Oct 16}, pages = {317-20}, abstract = {

Neural stem cells show age-dependent developmental potentials, as evidenced by their production of distinct neuron types at different developmental times. Drosophila neuroblasts produce long, stereotyped lineages of neurons. We searched for factors that could regulate neural temporal fate by RNA-sequencing lineage-specific neuroblasts at various developmental times. We found that two RNA-binding proteins, IGF-II mRNA-binding protein (Imp) and Syncrip (Syp), display opposing high-to-low and low-to-high temporal gradients with lineage-specific temporal dynamics. Imp and Syp promote early and late fates, respectively, in both a slowly progressing and a rapidly changing lineage. Imp and Syp control neuronal fates in the mushroom body lineages by regulating the temporal transcription factor Chinmo translation. Together, the opposing Imp/Syp gradients encode stem cell age, specifying multiple cell fates within a lineage.

}, issn = {1095-9203}, doi = {10.1126/science.aad1886}, author = {Liu, Zhiyong and Yang, Ching-Po and Sugino, Ken and Fu, Chi-Cheng and Liu, Ling-Yu and Yao, Xiaohao and Lee, Luke P and Lee, Tzumin} } @article {46745, title = {Optimized tools for multicolor stochastic labeling reveal diverse stereotyped cell arrangements in the fly visual system.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015 May 11}, pages = {E2967-76}, abstract = {

We describe the development and application of methods for high-throughput neuroanatomy in Drosophila using light microscopy. These tools enable efficient multicolor stochastic labeling of neurons at both low and high densities. Expression of multiple membrane-targeted and distinct epitope-tagged proteins is controlled both by a transcriptional driver and by stochastic, recombinase-mediated excision of transcription-terminating cassettes. This MultiColor FlpOut (MCFO) approach can be used to reveal cell shapes and relative cell positions and to track the progeny of precursor cells through development. Using two different recombinases, the number of cells labeled and the number of color combinations observed in those cells can be controlled separately. We demonstrate the utility of MCFO in a detailed study of diversity and variability of Distal medulla (Dm) neurons, multicolumnar local interneurons in the adult visual system. Similar to many brain regions, the medulla has a repetitive columnar structure that supports parallel information processing together with orthogonal layers of cell processes that enable communication between columns. We find that, within a medulla layer, processes of the cells of a given Dm neuron type form distinct patterns that reflect both the morphology of individual cells and the relative positions of their arbors. These stereotyped cell arrangements differ between cell types and can even differ for the processes of the same cell type in different medulla layers. This unexpected diversity of coverage patterns provides multiple independent ways of integrating visual information across the retinotopic columns and implies the existence of multiple developmental mechanisms that generate these distinct patterns.

}, issn = {1091-6490}, doi = {10.1073/pnas.1506763112}, author = {Nern, Aljoscha and Pfeiffer, Barret D and Rubin, Gerald M} } @article {47017, title = {Optogenetics: 10 years after ChR2 in neurons-views from the community.}, journal = {Nature Neuroscience}, volume = {18}, year = {2015}, month = {2015 Aug 26}, pages = {1202-12}, issn = {1546-1726}, doi = {10.1038/nn.4106}, author = {Adamantidis, Antoine and Arber, Silvia and Bains, Jaideep S and Bamberg, Ernst and Bonci, Antonello and Buzs{\'a}ki, Gy{\"o}rgy and Cardin, Jessica A and Costa, Rui M and Dan, Yang and Goda, Yukiko and Graybiel, Ann M and H{\"a}usser, Michael and Hegemann, Peter and Huguenard, John R and Insel, Thomas R and Janak, Patricia H and Johnston, Daniel and Josselyn, Sheena A and Koch, Christof and Kreitzer, Anatol C and L{\"u}scher, Christian and Malenka, Robert C and Miesenb{\"o}ck, Gero and Nagel, Georg and Roska, Botond and Schnitzer, Mark J and Shenoy, Krishna V and Soltesz, Ivan and Sternson, Scott M and Tsien, Richard W and Tsien, Roger Y and Turrigiano, Gina G and Tye, Kay M and Wilson, Rachel I} } @article {46924, title = {Oscillatory patterns in hippocampus under light and deep isoflurane anesthesia closely mirror prominent brain states in awake animals.}, journal = {Hippocampus}, volume = {26}, year = {2015}, month = {2015 Jul 18}, pages = {102-9}, abstract = {

The hippocampus exhibits a variety of distinct states of activity under different conditions. For instance the rhythmic patterns of activity orchestrated by the theta oscillation during running and REM sleep are markedly different from the large irregular activity (LIA) observed during awake resting and slow wave sleep. We found that under different levels of isoflurane anesthesia activity in the hippocampus of rats displays two distinct states which have several qualities that mirror the theta and LIA states. These data provide further evidence that the two states are intrinsic modes of the hippocampus; while also characterizing a preparation that could be useful for studying the natural activity states in hippocampus. This article is protected by copyright. All rights reserved.

}, issn = {1098-1063}, doi = {10.1002/hipo.22494}, author = {Lustig, Brian and Wang, Yingxue and Pastalkova, Eva} } @article {47218, title = {OpenStage: a low-cost motorized microscope stage with sub-micron positioning accuracy.}, journal = {PloS One}, volume = {9}, year = {2014}, month = {2014 Feb 26}, pages = {e88977}, abstract = {

Recent progress in intracellular calcium sensors and other fluorophores has promoted the widespread adoption of functional optical imaging in the life sciences. Home-built multiphoton microscopes are easy to build, highly customizable, and cost effective. For many imaging applications a 3-axis motorized stage is critical, but commercially available motorization hardware (motorized translators, controller boxes, etc) are often very expensive. Furthermore, the firmware on commercial motor controllers cannot easily be altered and is not usually designed with a microscope stage in mind. Here we describe an open-source motorization solution that is simple to construct, yet far cheaper and more customizable than commercial offerings. The cost of the controller and motorization hardware are under $1000. Hardware costs are kept low by replacing linear actuators with high quality stepper motors. Electronics are assembled from commonly available hobby components, which are easy to work with. Here we describe assembly of the system and quantify the positioning accuracy of all three axes. We obtain positioning repeatability of the order of 1 μm in X/Y and 0.1 μm in Z. A hand-held control-pad allows the user to direct stage motion precisely over a wide range of speeds (10(-1) to 10(2) μm{\textperiodcentered}s(-1)), rapidly store and return to different locations, and execute "jumps" of a fixed size. In addition, the system can be controlled from a PC serial port. Our "OpenStage" controller is sufficiently flexible that it could be used to drive other devices, such as micro-manipulators, with minimal modifications.

}, keywords = {Costs and Cost Analysis, Equipment Design, Microscopy, Reproducibility of Results}, issn = {1932-6203}, doi = {10.1371/journal.pone.0088977}, author = {Campbell, Robert A A and Eifert, Robert W and Turner, Glenn C} } @article {45063, title = {Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Jul 22}, pages = {E2967-76}, abstract = {

The type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has emerged recently as a powerful method to manipulate the genomes of various organisms. Here, we report a toolbox for high-efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids. Systematic evaluation reveals Cas9 lines with ubiquitous or germ-line-restricted patterns of activity. We also demonstrate differential activity of the same gRNA expressed from different U6 snRNA promoters, with the previously untested U6:3 promoter giving the most potent effect. An appropriate combination of Cas9 and gRNA allows targeting of essential and nonessential genes with transmission rates ranging from 25-100\%. We also demonstrate that our optimized CRISPR/Cas tools can be used for offset nicking-based mutagenesis. Furthermore, in combination with oligonucleotide or long double-stranded donor templates, our reagents allow precise genome editing by homology-directed repair with rates that make selection markers unnecessary. Last, we demonstrate a novel application of CRISPR/Cas-mediated technology in revealing loss-of-function phenotypes in somatic cells following efficient biallelic targeting by Cas9 expressed in a ubiquitous or tissue-restricted manner. Our CRISPR/Cas tools will facilitate the rapid evaluation of mutant phenotypes of specific genes and the precise modification of the genome with single-nucleotide precision. Our results also pave the way for high-throughput genetic screening with CRISPR/Cas.

}, issn = {1091-6490}, doi = {10.1073/pnas.1405500111}, author = {Port, Fillip and Chen, Hui-Min and Lee, Tzumin and Bullock, Simon L} } @article {6892, title = {Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Feb}, pages = {175-82}, abstract = {

The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sensor. These {\textquoteright}Twitch{\textquoteright} sensors are based on the C-terminal domain of Opsanus troponin C. Their FRET responses were optimized by a large-scale functional screen in bacterial colonies, refined by a secondary screen in rat hippocampal neuron cultures. We tested the in vivo performance of the most sensitive variants in the brain and lymph nodes of mice. The sensitivity of the Twitch sensors matched that of synthetic calcium dyes and allowed visualization of tonic action potential firing in neurons and high resolution functional tracking of T lymphocytes. Given their ratiometric readout, their brightness, large dynamic range and linear response properties, Twitch sensors represent versatile tools for neuroscience and immunology.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2773}, author = {Thestrup, Thomas and Litzlbauer, Julia and Bartholom{\"a}us, Ingo and Mues, Marsilius and Russo, Luigi and Dana, Hod and Kovalchuk, Yuri and Liang, Yajie and Kalamakis, Georgios and Laukat, Yvonne and Becker, Stefan and Witte, Gregor and Geiger, Anselm and Allen, Taylor and Rome, Lawrence C and Chen, Tsai-Wen and Kim, Douglas S. and Garaschuk, Olga and Griesinger, Christian and Griesbeck, Oliver} } @article {45698, title = {Oscillatory activity in the medial prefrontal cortex and nucleus accumbens correlates with impulsivity and reward outcome.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014 Oct 21}, pages = {e111300}, abstract = {

Actions expressed prematurely without regard for their consequences are considered impulsive. Such behaviour is governed by a network of brain regions including the prefrontal cortex (PFC) and nucleus accumbens (NAcb) and is prevalent in disorders including attention deficit hyperactivity disorder (ADHD) and drug addiction. However, little is known of the relationship between neural activity in these regions and specific forms of impulsive behaviour. In the present study we investigated local field potential (LFP) oscillations in distinct sub-regions of the PFC and NAcb on a 5-choice serial reaction time task (5-CSRTT), which measures sustained, spatially-divided visual attention and action restraint. The main findings show that power in gamma frequency (50-60 Hz) LFP oscillations transiently increases in the PFC and NAcb during both the anticipation of a cue signalling the spatial location of a nose-poke response and again following correct responses. Gamma oscillations were coupled to low-frequency delta oscillations in both regions; this coupling strengthened specifically when an error response was made. Theta (7-9 Hz) LFP power in the PFC and NAcb increased during the waiting period and was also related to response outcome. Additionally, both gamma and theta power were significantly affected by upcoming premature responses as rats waited for the visual cue to respond. In a subgroup of rats showing persistently high levels of impulsivity we found that impulsivity was associated with increased error signals following a nose-poke response, as well as reduced signals of previous trial outcome during the waiting period. Collectively, these in-vivo neurophysiological findings further implicate the PFC and NAcb in anticipatory impulsive responses and provide evidence that abnormalities in the encoding of rewarding outcomes may underlie trait-like impulsive behaviour.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0111300}, author = {Donnelly, Nicholas A and Holtzman, Tahl and Rich, P Dylan and Nevado-Holgado, Alejo J and Fernando, Anushka B P and Van Dijck, Gert and Holzhammer, Tobias and Paul, Oliver and Ruther, Patrick and Paulsen, Ole and Robbins, Trevor W and Dalley, Jeffrey W} } @article {48165, title = {Omnidirectional displacements for deformable surfaces.}, journal = {Medical image analysis}, volume = {17}, year = {2013}, month = {2013 May}, pages = {429-41}, abstract = {

Deformable surface models are often represented as triangular meshes in image segmentation applications. For a fast and easily regularized deformation onto the target object boundary, the vertices of the mesh are commonly moved along line segments (typically surface normals). However, in case of high mesh curvature, these lines may not intersect with the target boundary at all. Consequently, certain deformations cannot be achieved. We propose omnidirectional displacements for deformable surfaces (ODDS) to overcome this limitation. ODDS allow each vertex to move not only along a line segment but within the volumetric inside of a surrounding sphere, and achieve globally optimal deformations subject to local regularization constraints. However, allowing a ball-shaped instead of a linear range of motion per vertex significantly increases runtime and memory. To alleviate this drawback, we propose a hybrid approach, fastODDS, with improved runtime and reduced memory requirements. Furthermore, fastODDS can also cope with simultaneous segmentation of multiple objects. We show the theoretical benefits of ODDS with experiments on synthetic data, and evaluate ODDS and fastODDS quantitatively on clinical image data of the mandible and the hip bones. There, we assess both the global segmentation accuracy as well as local accuracy in high curvature regions, such as the tip-shaped mandibular coronoid processes and the ridge-shaped acetabular rims of the hip bones.

}, keywords = {Algorithms, Computer Simulation, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Models, Biological, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity}, issn = {1361-8423}, doi = {10.1016/j.media.2012.11.006}, author = {Kainmueller, Dagmar and Lamecker, Hans and Heller, Markus O and Weber, Britta and Hege, Hans-Christian and Zachow, Stefan} } @article {6904, title = {The Open Connectome Project Data Cluster: Scalable analysis and vision for high-throughput neuroscience.}, journal = {Scientific and Statistical Database Management: International Conference, SSDBM ... : Proceedings. International Conference on Scientific and Statistical Database Management}, year = {2013}, month = {2013 Jun 18}, abstract = {

We describe a scalable database cluster for the spatial analysis and annotation of high-throughput brain imaging data, initially for 3-d electron microscopy image stacks, but for time-series and multi-channel data as well. The system was designed primarily for workloads that build connectomes- neural connectivity maps of the brain-using the parallel execution of computer vision algorithms on high-performance compute clusters. These services and open-science data sets are publicly available at openconnecto.me. The system design inherits much from NoSQL scale-out and data-intensive computing architectures. We distribute data to cluster nodes by partitioning a spatial index. We direct I/O to different systems-reads to parallel disk arrays and writes to solid-state storage-to avoid I/O interference and maximize throughput. All programming interfaces are RESTful Web services, which are simple and stateless, improving scalability and usability. We include a performance evaluation of the production system, highlighting the effec-tiveness of spatial data organization.

}, doi = {10.1145/2484838.2484870}, author = {Burns, Randal and Roncal, William Gray and Kleissas, Dean and Lillaney, Kunal and Manavalan, Priya and Perlman, Eric and Berger, Daniel R. and Bock, Davi D and Chung, Kwanghun and Grosenick, Logan and Kasthuri, Narayanan and Weiler, Nicholas C and Deisseroth, Karl and Kazhdan, Michael and Lichtman, Jeff and Reid, R Clay and Smith, Stephen J and Szalay, Alexander S and Vogelstein, Joshua T and Vogelstein, R Jacob} } @article {6128, title = {An optimized fluorescent probe for visualizing glutamate neurotransmission.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2013 Feb}, pages = {162-70}, abstract = {

We describe an intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) with signal-to-noise ratio and kinetics appropriate for in vivo imaging. We engineered iGluSnFR in vitro to maximize its fluorescence change, and we validated its utility for visualizing glutamate release by neurons and astrocytes in increasingly intact neurological systems. In hippocampal culture, iGluSnFR detected single field stimulus-evoked glutamate release events. In pyramidal neurons in acute brain slices, glutamate uncaging at single spines showed that iGluSnFR responds robustly and specifically to glutamate in situ, and responses correlate with voltage changes. In mouse retina, iGluSnFR-expressing neurons showed intact light-evoked excitatory currents, and the sensor revealed tonic glutamate signaling in response to light stimuli. In worms, glutamate signals preceded and predicted postsynaptic calcium transients. In zebrafish, iGluSnFR revealed spatial organization of direction-selective synaptic activity in the optic tectum. Finally, in mouse forelimb motor cortex, iGluSnFR expression in layer V pyramidal neurons revealed task-dependent single-spine activity during running.

}, keywords = {Animals, Astrocytes, Biosensing Techniques, Caenorhabditis elegans, Calcium Signaling, Escherichia coli Proteins, Excitatory Postsynaptic Potentials, Fluorescent Dyes, Glutamic Acid, Green Fluorescent Proteins, Hippocampus, Mice, Motor Cortex, Neurons, Photic Stimulation, Pyramidal Cells, Recombinant Fusion Proteins, Retina, Signal-To-Noise Ratio, Synaptic Transmission, Zebrafish}, issn = {1548-7105}, doi = {10.1038/nmeth.2333}, author = {Marvin, Jonathan S and Borghuis, Bart G and Tian, Lin and Cichon, Joseph and Harnett, Mark T and Akerboom, Jasper and Gordus, Andrew and Renninger, Sabine L. and Chen, Tsai-Wen and Bargmann, Cornelia I and Orger, Michael B. and Schreiter, Eric R and Demb, Jonathan B and Gan, Wen-Biao and Hires, S Andrew and Looger, Loren L} } @article {6581, title = {Optimizing the quantity/quality trade-off in connectome inference.}, journal = {Communications in Statistics-Theory and Methods}, volume = {42}, year = {2013}, month = {2013 Oct}, pages = {3455-62}, chapter = {3455}, abstract = {

We demonstrate a meaningful prospective power analysis for an (admittedly idealized) illustrative connectome inference task. Modeling neurons as vertices and synapses as edges in a simple random graph model, we optimize the trade-off between the number of (putative) edges identified and the accuracy of the edge identification procedure. We conclude that explicit analysis of the quantity/quality trade-off is imperative for optimal neuroscientific experimental design. In particular, identifying edges faster/more cheaply, but with more error, can yield superior inferential performance.

}, issn = {0361-0926}, doi = {10.1080/03610926.2011.630768}, author = {Priebe, C. E. and Vogelstein, J. and Bock, D.} } @article {5677, title = {Optogenetics in a transparent animal: circuit function in the larval zebrafish.}, journal = {Current Opinion in Neurobiology}, volume = {23}, year = {2013}, month = {2013 Feb}, pages = {119-26}, abstract = {

Optogenetic tools can be used to manipulate neuronal activity in a reversible and specific manner. In recent years, such methods have been applied to uncover causal relationships between activity in specified neuronal circuits and behavior in the larval zebrafish. In this small, transparent, genetic model organism, noninvasive manipulation and monitoring of neuronal activity with light is possible throughout the nervous system. Here we review recent work in which these new tools have been applied to zebrafish, and discuss some of the existing challenges of these approaches.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2012.11.001}, author = {Portugues, Ruben and Severi, Kristen E and Wyart, Claire and Ahrens, Misha B} } @article {48275, title = {Optogenetics through windows on the brain in the nonhuman primate.}, journal = {Journal of neurophysiology}, volume = {110}, year = {2013}, month = {2013 Sep}, pages = {1455-67}, abstract = {

Optogenetics combines optics and genetics to control neuronal activity with cell-type specificity and millisecond temporal precision. Its use in model organisms such as rodents, Drosophila, and Caenorhabditis elegans is now well-established. However, application of this technology in nonhuman primates (NHPs) has been slow to develop. One key challenge has been the delivery of viruses and light to the brain through the thick dura mater of NHPs, which can only be penetrated with large-diameter devices that damage the brain. The opacity of the NHP dura prevents visualization of the underlying cortex, limiting the spatial precision of virus injections, electrophysiological recordings, and photostimulation. Here, we describe a new optogenetics approach in which the native dura is replaced with an optically transparent artificial dura. This artificial dura can be penetrated with fine glass micropipettes, enabling precisely targeted injections of virus into brain tissue with minimal damage to cortex. The expression of optogenetic agents can be monitored visually over time. Most critically, this optical window permits targeted, noninvasive photostimulation and concomitant measurements of neuronal activity via intrinsic signal imaging and electrophysiological recordings. We present results from both anesthetized-paralyzed (optical imaging) and awake-behaving NHPs (electrophysiology). The improvements over current methods made possible by the artificial dura should enable the widespread use of optogenetic tools in NHP research, a key step toward the development of therapies for neuropsychiatric and neurological diseases in humans.

}, keywords = {Animals, Brain, Dura Mater, Gene Transfer Techniques, Haplorhini, Neurosurgical Procedures, Optogenetics}, issn = {1522-1598}, doi = {10.1152/jn.00153.2013}, author = {Ruiz, Octavio and Lustig, Brian R and Nassi, Jonathan J and Cetin, Ali and Reynolds, John H and Albright, Thomas D and Callaway, Edward M and Stoner, Gene R and Roe, Anna W} } @article {6295, title = {Organization of cortical and thalamic input to pyramidal neurons in mouse motor cortex.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Jan 9}, pages = {748-60}, abstract = {

Determining how long-range synaptic inputs engage pyramidal neurons in primary motor cortex (M1) is important for understanding circuit mechanisms involved in regulating movement. We used channelrhodopsin-2-assisted circuit mapping to characterize the long-range excitatory synaptic connections made by multiple cortical and thalamic areas onto pyramidal neurons in mouse vibrissal motor cortex (vM1). Each projection innervated vM1 pyramidal neurons with a unique laminar profile. Collectively, the profiles for different sources of input partially overlapped and spanned all cortical layers. Specifically, orbital cortex (OC) inputs primarily targeted neurons in L6. Secondary motor cortex (M2) inputs excited neurons mainly in L5B, including pyramidal tract neurons. In contrast, thalamocortical inputs from anterior motor-related thalamic regions, including VA/VL (ventral anterior thalamic nucleus/ventrolateral thalamic nucleus), targeted neurons in L2/3 through L5B, but avoided L6. Inputs from posterior sensory-related thalamic areas, including POm (posterior thalamic nuclear group), targeted neurons only in the upper layers (L2/3 and L5A), similar to inputs from somatosensory (barrel) cortex. Our results show that long-range excitatory inputs target vM1 pyramidal neurons in a layer-specific manner. Inputs from sensory-related cortical and thalamic areas preferentially target the upper-layer pyramidal neurons in vM1. In contrast, inputs from OC and M2, areas associated with volitional and cognitive aspects of movements, bypass local circuitry and have direct monosynaptic access to neurons projecting to brainstem and thalamus.

}, keywords = {Animals, Cerebral Cortex, Data Interpretation, Efferent Pathways, Electric Stimulation, Electrophysiological Phenomena, Female, Inbred C57BL, Male, Mice, Motor Cortex, Neurons, Patch-Clamp Techniques, Pons, Pyramidal Tracts, Statistical, Thalamus}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4338-12.2013}, author = {Hooks, Bryan M and Mao, Tianyi and Gutnisky, Diego A and Yamawaki, Naoki and Svoboda, Karel and Shepherd, Gordon M G} } @article {5959, title = {Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.}, journal = {Current Protocols in Protein Science }, volume = {Chapter 17}, year = {2013}, month = {2013 Apr 2}, pages = {Unit 17.15}, abstract = {

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

}, issn = {1934-3663}, doi = {10.1002/0471140864.ps1715s72}, author = {Nannenga, Brent L and Iadanza, Matthew G and Vollmar, Breanna S and Gonen, Tamir} } @article {6526, title = {The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.}, journal = {PLoS Biology}, volume = {11}, year = {2013}, month = {2013 Jan}, pages = {e1001473}, abstract = {

The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (\~{}5\%) of its precursor "silent" germline micronuclear genome by a process of "unscrambling" and fragmentation. The tiny macronuclear "nanochromosomes" typically encode single, protein-coding genes (a small portion, 10\%, encode 2-8 genes), have minimal noncoding regions, and are differentially amplified to an average of \~{}2,000 copies. We report the high-quality genome assembly of \~{}16,000 complete nanochromosomes (\~{}50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean \~{}3.2 kb) and encode \~{}18,500 genes. Alternative DNA fragmentation processes \~{}10\% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is \~{}4.0\%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease.

}, keywords = {Base Sequence, DNA, DNA Copy Number Variations, DNA Fragmentation, Gene Amplification, Gene Rearrangement, Genes, Genetic Variation, Genome, Macronucleus, Messenger, Molecular Sequence Data, Oxytricha, Protein Binding, Protozoan, RNA, Sequence Analysis, Telomere}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1001473}, author = {Swart, Estienne C and Bracht, John R and Magrini, Vincent and Minx, Patrick and Chen, Xiao and Zhou, Yi and Khurana, Jaspreet S and Goldman, Aaron D and Nowacki, Mariusz and Schotanus, Klaas and Jung, Seolkyoung and Fulton, Robert S and Ly, Amy and McGrath, Sean and Haub, Kevin and Wiggins, Jessica L and Storton, Donna and Matese, John C and Parsons, Lance and Chang, Wei-Jen and Bowen, Michael S and Stover, Nicholas A and Jones, Thomas A and Eddy, Sean R. and Herrick, Glenn A and Doak, Thomas G and Wilson, Richard K and Mardis, Elaine R and Landweber, Laura F} } @article {65017, title = {An olfactory subsystem that mediates high-sensitivity detection of volatile amines.}, journal = {Cell Rep}, volume = {2}, year = {2012}, month = {2012 Jul 26}, pages = {76-88}, abstract = {

Olfactory stimuli are detected by over 1,000 odorant receptors in mice, with each receptor being mapped to specific glomeruli in the olfactory bulb. The trace amine-associated receptors (TAARs) are a small family of evolutionarily conserved olfactory receptors whose contribution to olfaction remains enigmatic. Here, we show that a majority of the TAARs are mapped to a discrete subset of glomeruli in the dorsal olfactory bulb of the mouse. This TAAR projection is distinct from the previously described class I and class II domains, and is formed by a sensory neuron population that is restricted to express TAAR genes prior to choice. We also show that the dorsal TAAR glomeruli are selectively activated by amines at low concentrations. Our data uncover a hard-wired, parallel input stream in the main olfactory pathway that is specialized for the detection of volatile amines.

}, keywords = {Amines, Animals, Female, Gene Targeting, Mice, Mice, Inbred C57BL, Mice, Transgenic, Models, Biological, Multigene Family, Olfactory Pathways, Olfactory Perception, Olfactory Receptor Neurons, Receptors, Cell Surface, Receptors, G-Protein-Coupled, Substrate Specificity, Volatile Organic Compounds, Volatilization}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.06.006}, author = {Pacifico, Rodrigo and Dewan, Adam and Cawley, Dillon and Guo, Caiying and Bozza, Thomas} } @article {6328, title = {Optimal noise reduction in 3D reconstructions of single particles using a volume-normalized filter.}, journal = {Journal of Structural Biology}, volume = {180}, year = {2012}, month = {2012 Oct}, pages = {26-38}, abstract = {

The high noise level found in single-particle electron cryo-microscopy (cryo-EM) image data presents a special challenge for three-dimensional (3D) reconstruction of the imaged molecules. The spectral signal-to-noise ratio (SSNR) and related Fourier shell correlation (FSC) functions are commonly used to assess and mitigate the noise-generated error in the reconstruction. Calculation of the SSNR and FSC usually includes the noise in the solvent region surrounding the particle and therefore does not accurately reflect the signal in the particle density itself. Here we show that the SSNR in a reconstructed 3D particle map is linearly proportional to the fractional volume occupied by the particle. Using this relationship, we devise a novel filter (the "single-particle Wiener filter") to minimize the error in a reconstructed particle map, if the particle volume is known. Moreover, we show how to approximate this filter even when the volume of the particle is not known, by optimizing the signal within a representative interior region of the particle. We show that the new filter improves on previously proposed error-reduction schemes, including the conventional Wiener filter as well as figure-of-merit weighting, and quantify the relationship between all of these methods by theoretical analysis as well as numeric evaluation of both simulated and experimentally collected data. The single-particle Wiener filter is applicable across a broad range of existing 3D reconstruction techniques, but is particularly well suited to the Fourier inversion method, leading to an efficient and accurate implementation.

}, keywords = {Algorithms, Capsid, Cryoelectron Microscopy, Data Interpretation, Fourier Analysis, Imaging, Kinesin, Models, Molecular, Papillomaviridae, Protein Structure, Quaternary, Signal-To-Noise Ratio, Software, Statistical, Tertiary, Three-Dimensional}, issn = {1095-8657}, doi = {10.1016/j.jsb.2012.05.005}, author = {Sindelar, Charles V and Grigorieff, Nikolaus} } @article {5164, title = {Optimization of a GCaMP calcium indicator for neural activity imaging.}, journal = {The Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Oct 3}, pages = {13819-40}, chapter = {13819}, abstract = {

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo . Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by severalfold, creating a family of {\textquotedblleft}GCaMP5{\textquotedblright} sensors. We tested GCaMP5s in several systems: cultured neurons and astrocytes, mouse retina, and in vivo in Caenorhabditis chemosensory neurons, Drosophila larval neuromuscular junction and adult antennal lobe, zebrafish retina and tectum, and mouse visual cortex. Signal-to-noise ratio was improved by at least 2- to 3-fold. In the visual cortex, two GCaMP5 variants detected twice as many visual stimulus-responsive cells as GCaMP3. By combining in vivo imaging with electrophysiology we show that GCaMP5 fluorescence provides a more reliable measure of neuronal activity than its predecessor GCaMP3.GCaMP5allows more sensitive detection of neural activity in vivo andmayfind widespread applications for cellular imaging in general.

}, doi = {10.1523/​JNEUROSCI.2601-12.2012}, author = {Akerboom, Jasper and Chen, Tsai-Wen and Wardill, Trevor J. and Marvin, Jonathan S and Mutlu, Sevinc and Carreras Caldero, Nicole and Esposti, Federico and Borghuis, Bart G and Sun, Xiaonan Richard and Gordus, Andrew and Orger, Michael B. and Portugues, Ruben and Engert, Florian and Macklin, John J and Filosa, Alessandro and Aggarwal, Aman and Kerr, Rex and Takagi, Ryousuke and Kracun, Sebastian and Shigetomi, Eiji and Khakh, Baljit S. and Baier, Herwig and Lagnado, Leon and Wang, Samuel S-H and Bargmann, Cornelia and Kimmel, Bruce and Jayaraman, Vivek and Svoboda, Karel and Kim, Douglas S. and Schreiter, Eric R and Looger, Loren L} } @article {5329, title = {Optogenetic analysis of a nociceptor neuron and network reveals ion channels acting downstream of primary sensors.}, journal = {Current Biology}, volume = {22}, year = {2012}, month = {2012 May 8}, pages = {743-52}, abstract = {

Nociception generally evokes rapid withdrawal behavior in order to protect the tissue from harmful insults. Most nociceptive neurons responding to mechanical insults display highly branched dendrites, an anatomy shared by Caenorhabditis elegans FLP and PVD neurons, which mediate harsh touch responses. Although several primary molecular nociceptive sensors have been characterized, less is known about modulation and amplification of noxious signals within nociceptor neurons. First, we analyzed the FLP/PVD network by optogenetics and studied integration of signals from these cells in downstream interneurons. Second, we investigated which genes modulate PVD function, based on prior single-neuron mRNA profiling of PVD.

}, keywords = {Ion Channels, Neurons}, issn = {1879-0445}, doi = {10.1016/j.cub.2012.02.066}, author = {Husson, Steven J and Costa, Wagner Steuer and Wabnig, Sebastian and Stirman, Jeffrey N and Watson, Joseph D and Spencer, W Clay and Akerboom, Jasper and Looger, Loren L and Treinin, Millet and Miller, David M and Lu, Hang and Gottschalk, Alexander} } @article {6501, title = {Organization and metamorphosis of glia in the Drosophila visual system.}, journal = {The Journal of Comparative Neurology}, volume = {520}, year = {2012}, month = {2012 Jul 1}, pages = {2067-85}, abstract = {

The visual system of Drosophila is an excellent model for determining the interactions that direct the differentiation of the nervous system{\textquoteright}s many unique cell types. Glia are essential not only in the development of the nervous system, but also in the function of those neurons with which they become associated in the adult. Given their role in visual system development and adult function we need to both accurately and reliably identify the different subtypes of glia, and to relate the glial subtypes in the larval brain to those previously described for the adult. We viewed driver expression in subsets of larval eye disc glia through the earliest stages of pupal development to reveal the counterparts of these cells in the adult. Two populations of glia exist in the lamina, the first neuropil of the adult optic lobe: those that arise from precursors in the eye-disc/optic stalk and those that arise from precursors in the brain. In both cases, a single larval source gives rise to at least three different types of adult glia. Furthermore, analysis of glial cell types in the second neuropil, the medulla, has identified at least four types of astrocyte-like (reticular) glia. Our clarification of the lamina{\textquoteright}s adult glia and identification of their larval origins, particularly the respective eye disc and larval brain contributions, begin to define developmental interactions which establish the different subtypes of glia.

}, keywords = {Animals, Biological, Drosophila, Drosophila Proteins, Electron, Eye, Genetically Modified, Green Fluorescent Proteins, Horseradish Peroxidase, Metamorphosis, Microscopy, Neuroglia, Neuropil, Nonmammalian, Optic Chiasm, Optic Lobe, Transmission, Visual Pathways}, issn = {1096-9861}, doi = {10.1002/cne.23071}, author = {Edwards, Tara N and Nuschke, Andrea C and Nern, Aljoscha and Meinertzhagen, Ian A.} } @article {6330, title = {Outcome of the first electron microscopy validation task force meeting.}, journal = {Structure}, volume = {20}, year = {2012}, month = {2012 Feb 8}, pages = {205-14}, abstract = {

This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the Unified Data Resource for 3DEM (http://www.emdatabank.org) and held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. At the workshop, a group of scientists involved in collecting electron microscopy data, using the data to determine three-dimensional electron microscopy (3DEM) density maps, and building molecular models into the maps explored how to assess maps, models, and other data that are deposited into the Electron Microscopy Data Bank and Protein Data Bank public data archives. The specific recommendations resulting from the workshop aim to increase the impact of 3DEM in biology and medicine.

}, keywords = {Animals, Databases, Electron, Factual, Guidelines as Topic, Humans, Information Storage and Retrieval, Macromolecular Substances, Microscopy, Models, Molecular, Molecular Conformation, Molecular Sequence Annotation}, issn = {1878-4186}, doi = {10.1016/j.str.2011.12.014}, author = {Henderson, Richard and Sali, Andrej and Baker, Matthew L and Carragher, Bridget and Devkota, Batsal and Downing, Kenneth H and Egelman, Edward H and Feng, Zukang and Frank, Joachim and Grigorieff, Nikolaus and Jiang, Wen and Ludtke, Steven J and Medalia, Ohad and Penczek, Pawel A and Rosenthal, Peter B and Rossmann, Michael G and Schmid, Michael F and Schr{\"o}der, Gunnar F and Steven, Alasdair C and Stokes, David L and Westbrook, John D and Wriggers, Willy and Yang, Huanwang and Young, Jasmine and Berman, Helen M and Chiu, Wah and Kleywegt, Gerard J and Lawson, Catherine L} } @article {5295, title = {Observations on clustered synaptic plasticity and highly structured input patterns.}, journal = {Neuron}, volume = {72}, year = {2011}, month = {2011 Dec 22}, pages = {887-8}, abstract = {

In this issue of Neuron, Makino and Malinow and Kleindienst et\ al. present evidence of a behaviorally induced form of synaptic plasticity that would encourage the development of fine-scale structured input patterns and\ the binding of features within single neurons.

}, keywords = {Action Potentials, Animals, Cell Compartmentation, Dendrites, Female, Hippocampus, Neuronal Plasticity, Pregnancy, Sensory Deprivation, Synapses, Synaptic Transmission}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.12.009}, author = {Magee, Jeffrey C} } @article {5672, title = {Observers exploit stochastic models of sensory change to help judge the passage of time.}, journal = {Current Biology}, volume = {21}, year = {2011}, month = {2011 Feb 8}, pages = {200-6}, abstract = {

Sensory stimulation can systematically bias the perceived passage of time, but why and how this happens is mysterious. In this report, we provide evidence that such biases may ultimately derive from an innate and adaptive use of stochastically evolving dynamic stimuli to help refine estimates derived from internal timekeeping mechanisms. A simplified statistical model based on probabilistic expectations of stimulus change derived from the second-order temporal statistics of the natural environment makes three predictions. First, random noise-like stimuli whose statistics violate natural expectations should induce timing bias. Second, a previously unexplored obverse of this effect is that similar noise stimuli with natural statistics should reduce the variability of timing estimates. Finally, this reduction in variability should scale with the interval being timed, so as to preserve the overall Weber law of interval timing. All three predictions are borne out experimentally. Thus, in the context of our novel theoretical framework, these results suggest that observers routinely rely on sensory input to augment their sense of the passage of time, through a process of Bayesian inference based on expectations of change in the natural environment.

}, keywords = {Biological, Humans, Models, Photic Stimulation, Stochastic Processes, Time Perception}, issn = {1879-0445}, doi = {10.1016/j.cub.2010.12.043}, author = {Ahrens, Misha B and Sahani, Maneesh} } @article {6488, title = {Optogenetics: potentials for addiction research.}, journal = {Addiction Biology}, volume = {16}, year = {2011}, month = {2011 Oct}, pages = {519-31}, abstract = {

Research on the biology of addiction has advanced significantly over the last 50 years expanding our understanding of the brain mechanisms underlying reward, reinforcement and craving. Novel experimental approaches and techniques have provided an ever increasing armory of tools to dissect behavioral processes, neural networks and molecular mechanisms. The ultimate goal is to reintegrate this knowledge into a coherent, mechanistic framework of addiction to help identify new treatment. This can be greatly facilitated by using tools that allow, with great spatial and temporal specificity, to link molecular changes with altered activation of neural circuits and behavior. Such specificity can now be achieved by using optogenetic tools. Our review describes the general principles of optogenetics and its use to understand the links between neural activity and behavior. We also provide an overview of recent studies using optogenetic tools in addiction and consider some outstanding questions of addiction research that are particularly amenable for optogenetic approaches.

}, keywords = {Animals, Brain, Dopamine, Gene Expression, Genetic Techniques, Humans, Light, Nerve Net, Nerve Tissue Proteins, Neurons, Neurosciences, Optical Tweezers, Rhodopsin, Substance-Related Disorders, Translational Medical Research, Voltage-Sensitive Dye Imaging}, issn = {1369-1600}, doi = {10.1111/j.1369-1600.2011.00386.x}, author = {Cao, Zhen Fang Huang and Burdakov, Denis and Sarnyai, Zolt{\'a}n} } @article {65019, title = {Orphan nuclear receptors control neuronal remodeling during fly metamorphosis.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2010 Dec 27}, pages = {6-7}, abstract = {

News \& Views\ |\ Published:\ 27 December 2010

Orphan nuclear receptors control neuronal remodeling during fly metamorphosis

Nature Neuroscience\ volume\ 14,\ pages\ 6{\textendash}7\ (2011)\ |\ Download Citation

Pruning of excess branches is essential for the maturation of developing neuronal circuits. Cross-talk between TGF-β signaling and two antagonistic orphan nuclear receptors governs the pruning of larval γ neurons in the\ Drosophila\ pupa.

Neural circuits are remodeled as the brain matures or acquires new functions. Such developmental remodeling involves complex cellular changes that are tightly regulated in space and time. During metamorphosis of holometabolous insect brains, most larval functional neurons are rewired into the adult circuitry, and study of these processes has been particularly fruitful for the elucidation of the mechanisms that underlie neuron remodeling1. In metamorphosing\ Drosophila, nuclear signaling of the steroid hormone receptor ecdysone receptor B1 isoform (EcR-B1) cell-autonomously orchestrates neuron remodeling. Only neurons destined to remodel upregulate EcR-B1 expression before a crucial pre-pupal ecdysone pulse2. It is therefore necessary to determine the mechanisms that pattern EcR-B1 expression to understand how developmental neuronal remodeling is programmed in\ Drosophila.

}, doi = {10.1038/nn0111-6}, author = {Tzumin Lee and Takeshi Awasaki} } @article {47686, title = {The open reading frame 3a protein of severe acute respiratory syndrome-associated coronavirus promotes membrane rearrangement and cell death.}, journal = {Journal of virology}, volume = {84}, year = {2010}, month = {2010 Jan}, pages = {1097-109}, abstract = {

The genome of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) contains eight open reading frames (ORFs) that encode novel proteins. These accessory proteins are dispensable for in vitro and in vivo replication and thus may be important for other aspects of virus-host interactions. We investigated the functions of the largest of the accessory proteins, the ORF 3a protein, using a 3a-deficient strain of SARS-CoV. Cell death of Vero cells after infection with SARS-CoV was reduced upon deletion of ORF 3a. Electron microscopy of infected cells revealed a role for ORF 3a in SARS-CoV induced vesicle formation, a prominent feature of cells from SARS patients. In addition, we report that ORF 3a is both necessary and sufficient for SARS-CoV-induced Golgi fragmentation and that the 3a protein accumulates and localizes to vesicles containing markers for late endosomes. Finally, overexpression of ADP-ribosylation factor 1 (Arf1), a small GTPase essential for the maintenance of the Golgi apparatus, restored Golgi morphology during infection. These results establish an important role for ORF 3a in SARS-CoV-induced cell death, Golgi fragmentation, and the accumulation of intracellular vesicles.

}, keywords = {ADP-Ribosylation Factor 1, Animals, Cell Death, Cell Membrane, Cercopithecus aethiops, Cytoplasmic Vesicles, Gene Deletion, Golgi Apparatus, Host-Pathogen Interactions, Humans, SARS Virus, Transfection, Vero Cells, Viral Structural Proteins}, issn = {1098-5514}, doi = {10.1128/JVI.01662-09}, author = {Freundt, Eric C and Yu, Li and Goldsmith, Cynthia S and Welsh, Sarah and Cheng, Aaron and Yount, Boyd and Liu, Wei and Frieman, Matthew B and Buchholz, Ursula J and Screaton, Gavin R and Lippincott-Schwartz, Jennifer and Zaki, Sherif R and Xu, Xiao-Ning and Baric, Ralph S and Subbarao, Kanta and Lenardo, Michael J} } @proceedings {5829, title = {Over-complete representations on recurrent neural networks can support persistent percepts.}, volume = {23}, year = {2010}, month = {2010}, pages = {541-9}, publisher = {MIT Press}, abstract = {

A striking aspect of cortical neural networks is the divergence of a relatively small number of input channels from the peripheral sensory apparatus into a large number of cortical neurons, an over-complete representation strategy. Cortical neurons are then connected by a sparse network of lateral synapses. Here we propose that such architecture may increase the persistence of the representation of an incoming stimulus, or a percept. We demonstrate that for a family of networks in which the receptive field of each neuron is re-expressed by its outgoing connections, a represented percept can remain constant despite changing activity. We term this choice of connectivity REceptive FIeld REcombination (REFIRE) networks. The sparse REFIRE network may serve as a high-dimensional integrator and a biologically plausible model of the local cortical circuit.

}, author = {Druckmann, S and Chklovskii, D} } @article {6496, title = {The overlap of small molecule and protein binding sites within families of protein structures.}, journal = {PLoS Computational Biology}, volume = {6}, year = {2010}, month = {2010 Feb}, pages = {e1000668}, abstract = {

Protein-protein interactions are challenging targets for modulation by small molecules. Here, we propose an approach that harnesses the increasing structural coverage of protein complexes to identify small molecules that may target protein interactions. Specifically, we identify ligand and protein binding sites that overlap upon alignment of homologous proteins. Of the 2,619 protein structure families observed to bind proteins, 1,028 also bind small molecules (250-1000 Da), and 197 exhibit a statistically significant (p\<0.01) overlap between ligand and protein binding positions. These "bi-functional positions", which bind both ligands and proteins, are particularly enriched in tyrosine and tryptophan residues, similar to "energetic hotspots" described previously, and are significantly less conserved than mono-functional and solvent exposed positions. Homology transfer identifies ligands whose binding sites overlap at least 20\% of the protein interface for 35\% of domain-domain and 45\% of domain-peptide mediated interactions. The analysis recovered known small-molecule modulators of protein interactions as well as predicted new interaction targets based on the sequence similarity of ligand binding sites. We illustrate the predictive utility of the method by suggesting structural mechanisms for the effects of sanglifehrin A on HIV virion production, bepridil on the cellular entry of anthrax edema factor, and fusicoccin on vertebrate developmental pathways. The results, available at http://pibase.janelia.org, represent a comprehensive collection of structurally characterized modulators of protein interactions, and suggest that homologous structures are a useful resource for the rational design of interaction modulators.

}, keywords = {Binding Sites, Computational Biology, Ligands, Models, Molecular, Nonparametric, Protein Binding, Protein Interaction Domains and Motifs, Proteins, Statistics}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000668}, author = {Davis, Fred P and Sali, Andrej} } @article {3925, title = {Odor coding by modules of coherent mitral/tufted cells in the vertebrate olfactory bulb.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Feb 17}, pages = {2401-6}, abstract = {

Odor representation in the olfactory bulb (OB) undergoes a transformation from a combinatorial glomerular map to a distributed mitral/tufted (M/T) cell code. To understand this transformation, we analyzed the odor representation in large populations of individual M/T cells in the Xenopus OB. The spontaneous [Ca(2+)] activities of M/T cells appeared to be irregular, but there were groups of spatially distributed neurons showing synchronized [Ca(2+)] activities. These neurons were always connected to the same glomerulus. Odorants elicited complex spatiotemporal response patterns in M/T cells where nearby neurons generally showed little correlation. But the responses of neurons connected to the same glomerulus were virtually identical, irrespective of whether the responses were excitatory or inhibitory, and independent of the distance between them. Synchronous neurons received correlated EPSCs and were coupled by electrical conductances that could account for the correlated responses. Thus, at the output stage of the OB, odors are represented by modules of distributed and synchronous M/T cells associated with the same glomeruli. This allows for parallel input to higher brain centers.

}, keywords = {Animals, Biological, Brain, Calcium, Electrophysiology, Fluorescent Dyes, Models, Neurons, Odors, Olfactory Bulb, Olfactory Pathways, Patch-Clamp Techniques, Smell, Time Factors, Vertebrates, Xenopus laevis}, issn = {1091-6490}, doi = {10.1073/pnas.0810151106}, author = {Chen, Tsai-Wen and Lin, Bei-Jung and Schild, Detlev} } @article {47226, title = {Olfactory information processing in Drosophila.}, journal = {Current Biology : CB}, volume = {19}, year = {2009}, month = {2009 Aug 25}, pages = {R700-13}, abstract = {

In both insect and vertebrate olfactory systems only two synapses separate the sensory periphery from brain areas required for memory formation and the organisation of behaviour. In the\ Drosophila\ olfactory system, which is anatomically very similar to its vertebrate counterpart, there has been substantial recent progress in understanding the flow of information from experiments using\ molecular genetic, electrophysiological and optical imaging techniques. In this review, we shall focus on how olfactory information is processed and transformed in order to extract behaviourally relevant information. We follow the progress from olfactory receptor neurons, through the first processing area, the antennal lobe, to higher olfactory centres. We address both the underlying anatomy and mechanisms that govern the transformation of neural activity. We emphasise our emerging understanding of how different elementary computations, including signal averaging, gain control, decorrelation and integration, may be mapped onto different circuit elements.

}, doi = {10.1016/j.cub.2009.06.026}, author = {Masse, Nicolas Y and Turner, Glenn C and Jeffers, Gregory SXE} } @article {1097, title = {Onconase cytotoxicity relies on the distribution of its positive charge.}, journal = {The FEBS Journal}, volume = {276}, year = {2009}, month = {2009 Jul}, pages = {3846-57}, abstract = {

Onconase (ONC) is a member of the ribonuclease A superfamily that is toxic to cancer cells in vitro and in vivo. ONC is now in Phase IIIb clinical trials for the treatment of malignant mesothelioma. Internalization of ONC to the cytosol of cancer cells is essential for its cytotoxic activity, despite the apparent absence of a cell-surface receptor protein. Endocytosis and cytotoxicity do, however, appear to correlate with the net positive charge of ribonucleases. To dissect the contribution made by the endogenous arginine and lysine residues of ONC to its cytotoxicity, 22 variants were created in which cationic residues were replaced with alanine. Variants with the same net charge (+2 to +5) as well as equivalent catalytic activity and conformational stability were found to exhibit large (\> 10-fold) differences in toxicity for the cells of a human leukemia line. In addition, a more cationic ONC variant could be either much more or much less cytotoxic than a less cationic variant, again depending on the distribution of its cationic residues. The endocytosis of variants with widely divergent cytotoxic activity was quantified by flow cytometry using a small-molecule fluorogenic label, and was found to vary by twofold or less. This small difference in endocytosis did not account for the large difference in cytotoxicity, implicating the distribution of cationic residues as being critical for lipid-bilayer translocation subsequent to endocytosis. This finding has fundamental implications for understanding the interaction of ribonucleases and other proteins with mammalian cells.

}, keywords = {Amino Acid Sequence, Animals, Antineoplastic Agents, Cations, Cell Line, Cell Proliferation, Endocytosis, Genetic Variation, Humans, Models, Molecular, Molecular Sequence Data, Protein Structure, Rana pipiens, Ribonucleases, Sequence Alignment, Tertiary, Tumor}, issn = {1742-4658}, doi = {10.1111/j.1742-4658.2009.07098.x}, author = {Turcotte, Rebecca F and Lavis, Luke D and Raines, Ronald T} } @article {5486, title = {Oviposition preference for and positional avoidance of acetic acid provide a model for competing behavioral drives in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Jul 7}, pages = {11352-7}, abstract = {

Selection of appropriate oviposition sites is essential for progeny survival and fitness in generalist insect species, such as Drosophila melanogaster, yet little is known about the mechanisms regulating how environmental conditions and innate adult preferences are evaluated and balanced to yield the final substrate choice for egg-deposition. Female D. melanogaster are attracted to food containing acetic acid (AA) as an oviposition substrate. However, our observations reveal that this egg-laying preference is a complex process, as it directly opposes an otherwise strong, default behavior of positional avoidance for the same food. We show that 2 distinct sensory modalities detect AA. Attraction to AA-containing food for the purpose of egg-laying relies on the gustatory system, while positional repulsion depends primarily on the olfactory system. Similarly, distinct central brain regions are involved in AA attraction and repulsion. Given this unique situation, in which a single environmental stimulus yields 2 opposing behavioral outputs, we propose that the interaction of egg-laying attraction and positional aversion for AA provides a powerful model for studying how organisms balance competing behavioral drives and integrate signals involved in choice-like processes.

}, keywords = {Acetic Acid, Animal, Animal Feed, Animals, Avoidance Learning, Biological, Brain, Drosophila melanogaster, Female, Hydrogen-Ion Concentration, Models, Neurons, Olfactory Pathways, Oviposition, Sexual Behavior, Taste}, issn = {1091-6490}, doi = {10.1073/pnas.0901419106}, author = {Joseph, Ryan M and Devineni, Anita V and King, Ian F G and Heberlein, Ulrike} } @article {47223, title = {Olfactory representations by Drosophila mushroom body neurons.}, journal = {Journal of Neurophysiology}, volume = {99}, year = {2008}, month = {2008 Feb}, pages = {734-46}, abstract = {

Learning and memory has been studied extensively in Drosophila using behavioral, molecular, and genetic approaches. These studies have identified the mushroom body as essential for the formation and retrieval of olfactory memories. We investigated odor responses of the principal neurons of the mushroom body, the Kenyon cells (KCs), in Drosophila using whole cell recordings in vivo. KC responses to odors were highly selective and, thus sparse, compared with those of their direct inputs, the antennal lobe projection neurons (PNs). We examined the mechanisms that might underlie this transformation and identified at least three contributing factors: excitatory synaptic potentials (from PNs) decay rapidly, curtailing temporal integration, PN convergence onto individual KCs is low ( approximately 10 PNs per KC on average), and KC firing thresholds are high. Sparse activity is thought to be useful in structures involved in memory in part because sparseness tends to reduce representation overlaps. By comparing activity patterns evoked by the same odors across olfactory receptor neurons and across KCs, we show that representations of different odors do indeed become less correlated as they progress through the olfactory system.

}, keywords = {Anesthetics, Local, Animals, Brain Mapping, Drosophila, Electric Stimulation, Excitatory Postsynaptic Potentials, Membrane Potentials, Mushroom Bodies, Nerve Net, Neurons, Afferent, Odors, Olfactory Pathways, Patch-Clamp Techniques, Spectrum Analysis, Tetrodotoxin}, issn = {0022-3077}, doi = {10.1152/jn.01283.2007}, author = {Turner, Glenn C and Bazhenov, Maxim and Laurent, Gilles} } @article {46302, title = {Optimizing one-shot learning with binary synapses.}, journal = {Neural Computation}, volume = {20}, year = {2008}, month = {2008 Aug}, pages = {1928-50}, abstract = {

A network of excitatory synapses trained with a conservative version of Hebbian learning is used as a model for recognizing the familiarity of thousands of once-seen stimuli from those never seen before. Such networks were initially proposed for modeling memory retrieval (selective delay activity). We show that the same framework allows the incorporation of both familiarity recognition and memory retrieval, and estimate the network{\textquoteright}s capacity. In the case of binary neurons, we extend the analysis of Amit and Fusi (1994) to obtain capacity limits based on computations of signal-to-noise ratio of the field difference between selective and non-selective neurons of learned signals. We show that with fast learning (potentiation probability approximately 1), the most recently learned patterns can be retrieved in working memory (selective delay activity). A much higher number of once-seen learned patterns elicit a realistic familiarity signal in the presence of an external field. With potentiation probability much less than 1 (slow learning), memory retrieval disappears, whereas familiarity recognition capacity is maintained at a similarly high level. This analysis is corroborated in simulations. For analog neurons, where such analysis is more difficult, we simplify the capacity analysis by studying the excess number of potentiated synapses above the steady-state distribution. In this framework, we derive the optimal constraint between potentiation and depression probabilities that maximizes the capacity.

}, keywords = {Algorithms, Brain, Computer Simulation, Learning, Models, Statistical, Neural Networks (Computer), Neurons, Pattern Recognition, Automated, Synapses, Synaptic Transmission}, issn = {0899-7667}, doi = {10.1162/neco.2008.10-07-618}, author = {Romani, Sandro and Amit, Daniel J and Amit, Yali} } @article {795, title = {Organization and postembryonic development of glial cells in the adult central brain of Drosophila.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Dec 17}, pages = {13742-53}, abstract = {

Glial cells exist throughout the nervous system, and play essential roles in various aspects of neural development and function. Distinct types of glia may govern diverse glial functions. To determine the roles of glia requires systematic characterization of glia diversity and development. In the adult Drosophila central brain, we identify five different types of glia based on its location, morphology, marker expression, and development. Perineurial and subperineurial glia reside in two separate single-cell layers on the brain surface, cortex glia form a glial mesh in the brain cortex where neuronal cell bodies reside, while ensheathing and astrocyte-like glia enwrap and infiltrate into neuropils, respectively. Clonal analysis reveals that distinct glial types derive from different precursors, and that most adult perineurial, ensheathing, and astrocyte-like glia are produced after embryogenesis. Notably, perineurial glial cells are made locally on the brain surface without the involvement of gcm (glial cell missing). In contrast, the widespread ensheathing and astrocyte-like glia derive from specific brain regions in a gcm-dependent manner. This study documents glia diversity in the adult fly brain and demonstrates involvement of different developmental programs in the derivation of distinct types of glia. It lays an essential foundation for studying glia development and function in the Drosophila brain.

}, keywords = {Animals, Antigens, Brain, Cell Count, Cell Differentiation, Cell Lineage, Clone Cells, Differentiation, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Embryo, Genetically Modified, Homeodomain Proteins, Larva, Neuroglia, Neurons, Neuropil, Nonmammalian, Transcription Factors}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4844-08.2008}, author = {Awasaki, Takeshi and Lai, Sen-Lin and Ito, Kei and Lee, Tzumin} } @article {1414, title = {Organization of the songbird basal ganglia, including area X.}, journal = {The Journal of Comparative Neurology}, volume = {508}, year = {2008}, month = {2008 Jun 10}, pages = {840-66}, abstract = {

Area X is a songbird basal ganglia nucleus that is required for vocal learning. Both Area X and its immediate surround, the medial striatum (MSt), contain cells displaying either striatal or pallidal characteristics. We used pathway-tracing techniques to compare directly the targets of Area X and MSt with those of the lateral striatum (LSt) and globus pallidus (GP). We found that the zebra finch LSt projects to the GP, substantia nigra pars reticulata (SNr) and pars compacta (SNc), but not the thalamus. The GP is reciprocally connected with the subthalamic nucleus (STN) and projects to the SNr and motor thalamus analog, the ventral intermediate area (VIA). In contrast to the LSt, Area X and surrounding MSt project to the ventral pallidum (VP) and dorsal thalamus via pallidal-like neurons. A dorsal strip of the MSt contains spiny neurons that project to the VP. The MSt, but not Area X, projects to the ventral tegmental area (VTA) and SNc, but neither MSt nor Area X projects to the SNr. Largely distinct populations of SNc and VTA dopaminergic neurons innervate Area X and surrounding the MSt. Finally, we provide evidence consistent with an indirect pathway from the cerebellum to the basal ganglia, including Area X. Area X projections thus differ from those of the GP and LSt, but are similar to those of the MSt. These data clarify the relationships among different portions of the oscine basal ganglia as well as among the basal ganglia of birds and mammals.

}, keywords = {Animals, Basal Ganglia, Finches, Male, Neural Pathways, Songbirds}, issn = {1096-9861}, doi = {10.1002/cne.21699}, author = {Person, Abigail L and Gale, Samuel D and Farries, Michael A and Perkel, David J} } @article {67285, title = {Observability of Higgs produced with top quarks and decaying to bottom quarks}, journal = {Journal of Physics G: Nuclear and Particle Physics}, volume = {34}, year = {2007}, month = {04/20027}, pages = {N221 - N250}, abstract = {

The decay,\ , is dominant for a Standard Model Higgs boson in the mass range just above the exclusion limit of 114.4 GeV/c2\ reported by the LEP experiments. Unfortunately, an overwhelming abundance of\ \ events arising from more mundane sources, together with the lack of precision inherent in the reconstruction of the Higgs mass, renders this decay mode\ a priori\ undetectable in the case of direct Higgs production at the LHC. It is therefore of no small interest to investigate whether\ \ can be observed in those cases where the Higgs is produced in association with other massive particles. In this note, the results of a study of Higgs bosons produced in association with top quarks and decaying via\ \ are presented. The study was performed as realistically as possible by employing a full and detailed Monte Carlo simulation of the CMS detector followed by the application of trigger and reconstruction algorithms that were developed for use with real data. Important systematic effects resulting from such sources as the uncertainties in the jet energy scale and the estimated rates for correctly tagging b jets or mistagging non-b jets have been taken into account. The impact of large theoretical uncertainties in the cross sections for\ \ plus\ N\ jets processes due to an absence of next-to-leading order calculations is also considered.

}, issn = {0954-3899}, doi = {10.1088/0954-3899/34/5/N03}, url = {https://iopscience.iop.org/article/10.1088/0954-3899/34/5/N03}, author = {Benedetti, D and Cucciarelli, S and Hill, C and Incandela, J and Koay, S A and Riccardi, C and Santocchia, A and Schmidt, A and Torre, P and Weiser, C} } @article {2364, title = {Olfactory coding with all-or-nothing glomeruli.}, journal = {Journal of Neurophysiology}, volume = {98}, year = {2007}, month = {2007 Dec}, pages = {3134-42}, abstract = {

We present a model for olfactory coding based on spatial representation of glomerular responses. In this model distinct odorants activate specific subsets of glomeruli, dependent on the odorant{\textquoteright}s chemical identity and concentration. The glomerular response specificities are understood statistically, based on experimentally measured distributions of activation thresholds. A simple version of the model, in which glomerular responses are binary (the all-or-nothing model), allows us to account quantitatively for the following results of human/rodent olfactory psychophysics: 1) just noticeable differences in the perceived concentration of a single odor (Weber ratios) are as low as dC/C approximately 0.04; 2) the number of simultaneously perceived odors can be as high as 12; and 3) extensive lesions of the olfactory bulb do not lead to significant changes in detection or discrimination thresholds. We conclude that a combinatorial code based on a binary glomerular response is sufficient to account for several important features of the discrimination capacity of the mammalian olfactory system.

}, keywords = {Algorithms, Animals, Discrimination (Psychology), Mice, Models, Neurological, Odors, Olfactory Bulb, Olfactory Pathways, Olfactory Receptor Neurons, Psychomotor Performance, Psychophysics, Rats, Smell}, issn = {0022-3077}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Koulakov, Alexei and Gelperin, Alan and Rinberg, Dmitry} } @article {2368, title = {Olfactory neuronal dynamics in behaving animals.}, journal = {Seminars in Cell \& Developmental Biology}, volume = {17}, year = {2006}, month = {2006 Aug}, pages = {454-61}, abstract = {

More than 50 years have passed since the first recording of neuronal responses to an odor stimulus from the primary olfactory brain area, the main olfactory bulb. During this time very little progress has been achieved in understanding neuronal dynamics in the olfactory bulb in awake behaving animals, which is very different from that in anesthetized preparations. In this paper we formulate a new framework containing the main reasons for studying olfactory neuronal dynamics in awake animals and review advances in the field within this new framework.

}, keywords = {Anesthesia, Animal, Animals, Behavior, Brain, Conditioning (Psychology), Neuronal Plasticity, Olfactory Bulb, Olfactory Receptor Neurons, Rabbits, Rats, Synaptic Transmission}, issn = {1084-9521}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Rinberg, Dmitry and Gelperin, Alan} } @article {1238, title = {Optimal information storage in noisy synapses under resource constraints.}, journal = {Neuron}, volume = {52}, year = {2006}, month = {2006 Nov 9}, pages = {409-23}, abstract = {

Experimental investigations have revealed that synapses possess interesting and, in some cases, unexpected properties. We propose a theoretical framework that accounts for three of these properties: typical central synapses are noisy, the distribution of synaptic weights among central synapses is wide, and synaptic connectivity between neurons is sparse. We also comment on the possibility that synaptic weights may vary in discrete steps. Our approach is based on maximizing information storage capacity of neural tissue under resource constraints. Based on previous experimental and theoretical work, we use volume as a limited resource and utilize the empirical relationship between volume and synaptic weight. Solutions of our constrained optimization problems are not only consistent with existing experimental measurements but also make nontrivial predictions.

}, keywords = {Animals, Excitatory Postsynaptic Potentials, Information Storage and Retrieval, Memory, Models, Neurological, Synapses, Synaptic Transmission}, issn = {0896-6273}, doi = {10.1371/journal.pcbi.1001066}, author = {Varshney, Lav R and Sj{\"o}str{\"o}m, Per Jesper and Chklovskii, Dmitri B} } @article {45755, title = {The origin of a mutualism: a morphological trait promoting the evolution of ant-aphid mutualisms.}, journal = {Evolution}, volume = {59}, year = {2005}, month = {2005 Apr}, pages = {921-6}, abstract = {

Mutualisms are mutually beneficial interactions between species and are fundamentally important at all levels of biological organization. It is not clear, however, why one species participates in a particular mutualism whereas another does not. Here we show that pre-existing traits can dispose particular species to evolve a mutualistic interaction. Combining morphological, ecological, and behavioral data in a comparative analysis, we show that resource use in Chaitophorus aphids (Hemiptera: Aphididae) modulates the origin of their mutualism with ants. We demonstrate that aphid species that feed on deeper phloem elements have longer mouthparts, that this inhibits their ability to withdraw their mouthparts and escape predators and that, consequently, this increases their need for protection by mutualist ants.

}, keywords = {Animals, Ants, Aphids, Biological Evolution, Body Weights and Measures, Feeding Behavior, Great Britain, Mouth, Symbiosis}, issn = {0014-3820}, author = {Shingleton, Alexander W and Stern, David L and Foster, William A} } @article {45901, title = {Output-mode transitions are controlled by prolonged inactivation of sodium channels in pyramidal neurons of subiculum.}, journal = {PLoS Biol}, volume = {3}, year = {2005}, month = {2005 Jun}, pages = {e175}, abstract = {

Transitions between different behavioral states, such as sleep or wakefulness, quiescence or attentiveness, occur in part through transitions from action potential bursting to single spiking. Cortical activity, for example, is determined in large part by the spike output mode from the thalamus, which is controlled by the gating of low-voltage-activated calcium channels. In the subiculum--the major output of the hippocampus--transitions occur from bursting in the delta-frequency band to single spiking in the theta-frequency band. We show here that these transitions are influenced strongly by the inactivation kinetics of voltage-gated sodium channels. Prolonged inactivation of sodium channels is responsible for an activity-dependent switch from bursting to single spiking, constituting a novel mechanism through which network dynamics are controlled by ion channel gating.

}, keywords = {Adenosine Diphosphate, Animals, Cognition, Evoked Potentials, Hippocampus, In Vitro Techniques, Membrane Potentials, Pyramidal Cells, Rats, Sodium Channels}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0030175}, author = {Cooper, Donald C and Chung, Sungkwon and Spruston, Nelson} } @article {2349, title = {Object-location memory impairment in patients with thermal lesions to the right or left hippocampus.}, journal = {Neuropsychologia}, volume = {42}, year = {2004}, month = {2004 Feb 25}, pages = {1017-28}, abstract = {

Memory for object-location was investigated by testing subjects with small unilateral thermolesions to the medial temporal lobe using small-scale 2D (Abstract) or large-scale 3D (Real) recall conditions. Four patients with lesions of the left hippocampus (LH), 10 patients with damage to the right hippocampus (RH) and 9 matched normal controls (NC) were tested. Six task levels were presented in a pseudorandom order. During each level, subjects viewed one to six different objects on the floor of a circular curtained arena 2.90 m in diameter for 10 s. Recall was tested by marking the locations of objects on a map of the arena (Abstract recall) and then by replacing the objects in the arena (Real recall). Two component errors were studied by calculating the Location Error (LE), independent of the object identity and the configuration error by finding the best match to the presented configuration. The RH group was impaired relative to the NC for nearly all combinations of recall and error types. An impairment was observed in this group even for one object and it deepened sharply with an increasing object number. Damage to the right perirhinal or parahippocampal cortices did not add to the impairment. Deficits in the LH group were also observed, but less consistently. The data indicate that spatial memory is strongly but not exclusively lateralised to the right medial temporal lobe.

}, keywords = {Adult, Anterior Temporal Lobectomy, Brain Damage, Brain Mapping, Cerebral, Chronic, Dominance, Electrocoagulation, Epilepsy, Female, Hippocampus, Humans, Male, Memory, Mental Recall, Middle Aged, Orientation, Pattern Recognition, Postoperative Complications, Reference Values, Short-Term, Temporal Lobe, Visual}, issn = {0028-3932}, doi = {10.1016/j.neuropsychologia.2004.01.002}, author = {Stepankova, Katerina and Fenton, Andr{\'e} A and Pastalkova, Eva and Kalina, Miroslav and Bohbot, V{\'e}ronique D} } @article {1738, title = {Optically active sum frequency generation from molecules with a chiral center: amino acids as model systems.}, journal = {Journal of the American Chemical Society}, volume = {126}, year = {2004}, month = {2004 Nov 24}, pages = {15008-9}, abstract = {

With amino acids as model systems, optically active sum frequency generation (OA-SFG) was used to probe the chirality of molecules with a chiral center and an intrinsically achiral chromophore in isotropic solution for the first time. Like that of circular dichroism (CD), the OA-SFG{\textquoteright}s near electronic resonance originates from the extrachromophoric chiral perturbation on the carboxyl chromophore. The difference in the relative strengths of OA-SFG and CD among different amino acids can be explained by the difference in the details of perturbations.

}, keywords = {Amino Acids, Chemical, Circular Dichroism, Models, Optics and Photonics, Stereoisomerism}, issn = {0002-7863}, doi = {10.1021/ja045708i}, author = {Ji, Na and Shen, Yuen-Ron} } @article {2513, title = {Overexpression of broad: a new insight into its role in the Drosophila prothoracic gland cells.}, journal = {The Journal of Experimental Biology}, volume = {207}, year = {2004}, month = {2004 Mar}, pages = {1151-61}, abstract = {

Insect molting is triggered by ecdysteroids, which are produced in the prothoracic glands (PG). The broad (br) gene is one of the {\textquoteright}early genes{\textquoteright} directly regulated by ecdysteroids. Ectopic expression of the BR-Z3 isoform in early second instar Drosophila larvae (L2) before the rise of the ecdysteroid titer prevented molting to the third instar, but the larvae subsequently formed L2 prepupae after prolonged feeding. When these larvae were fed on diet containing 20-hydroxyecdysone (20E), they formed pharate third instar larvae. The critical weight for normal L3 pupariation of w(1118) larvae was found to be 0.8 mg and that for L2 pupariation was 0.45 mg. We also defined a threshold weight for metamorphosis of 0.3 mg, above which L2 larvae will metamorphose when provided with 20E. BR-Z3 apparently works through the PG cells of the ring gland but not the putative neurosecretory cells that drive ecdysone secretion, because ectopic expression of BR-Z3 specifically in the ring gland caused 53\% of the larvae to become permanent first instar larvae. Driving other BR isoforms in the ring gland prevented larval molting or pupariation to varying degrees. These molting defects were rescued by feeding 20E. Overexpression of each of the BR isoforms caused degeneration of the PG cells but on different time courses, indicating that BR is a signal for the degeneration of the PG cells that normally occurs during the pupal-adult transition.

}, keywords = {Animals, Body Weights and Measures, Drosophila, Drosophila Proteins, Ecdysterone, Exocrine Glands, Gene Expression Regulation, Genetically Modified, Immunohistochemistry, Larva, Molting, Protein Isoforms, Transcription Factors}, issn = {0022-0949}, author = {Zhou, Xiaofeng and Zhou, Baohua and Truman, James W and Riddiford, Lynn M} } @article {3087, title = {Operant behavior can be triggered by the position of the rat relative to objects rotating on an inaccessible platform.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, year = {2003}, month = {2003 Feb 18}, pages = {2094-9}, abstract = {

The present study describes a task testing the ability of rats to trigger operant behavior by their relative spatial position to inaccessible rotating objects. Rats were placed in a Skinner box with a transparent front wall through which they could observe one or two adjacent objects fixed on a slowly rotating arena (d = 1 m) surrounded by an immobile black cylinder. The direction of arena rotation was alternated at a sequence of different time intervals. Rats were reinforced for the first bar-press that was emitted when a radius separating the two adjacent objects or dividing a single object into two halves (pointing radius) entered a 60 degrees sector of its circular trajectory defined with respect to the stationary Skinner box (reward sector). Well trained rats emitted 62.1 +/- 3.6\% of responses in a 60 degrees sector preceding the reward sector and in the first 30 degrees of the reward sector. Response rate increased only when the pointing radius was approaching the reward sector, regardless of the time elapsed from the last reward. In the extinction session, when no reward was delivered, rats responded during the whole passage of the pointing radius through the former reward sector and spontaneously decreased responding after the pointing radius left this area. This finding suggests that rats perceived the reward sector as a continuous single region. The same results were obtained when the Skinner box with the rat was orbiting around the immobile scene. It is concluded that rats can recognize and anticipate their position relative to movable objects.

}, keywords = {Animal, Animals, Behavior, Conditioning, Long-Evans, Male, Operant, Rats, Reward}, issn = {0027-8424}, doi = {10.1073/pnas.0438002100}, author = {Pastalkova, E and Kelemen, E and Bures, J} } @article {47225, title = {Oscillations and sparsening of odor representations in the mushroom body.}, journal = {Science (New York, N.Y.)}, volume = {297}, year = {2002}, month = {2002 Jul 19}, pages = {359-65}, abstract = {

In the insect olfactory system, oscillatory synchronization is functionally relevant and reflects the coherent activation of dynamic neural assemblies. We examined the role of such oscillatory synchronization in information transfer between networks in this system. The antennal lobe is the obligatory relay for olfactory afferent signals and generates oscillatory output. The mushroom body is responsible for formation and retrieval of olfactory and other memories. The format of odor representations differs significantly across these structures. Whereas representations are dense, dynamic, and seemingly redundant in the antennal lobe, they are sparse and carried by more selective neurons in the mushroom body. This transformation relies on a combination of oscillatory dynamics and intrinsic and circuit properties that act together to selectively filter and synthesize the output from the antennal lobe. These results provide direct support for the functional relevance of correlation codes and shed some light on the role of oscillatory synchronization in sensory networks.

}, keywords = {Action Potentials, Animals, Electric Stimulation, Electrodes, Evoked Potentials, Excitatory Postsynaptic Potentials, Female, gamma-Aminobutyric Acid, Grasshoppers, Interneurons, Male, Mushroom Bodies, Nerve Net, Neural Inhibition, Neurons, Odors, Patch-Clamp Techniques, Picrotoxin, Smell, Synaptic Transmission, Time Factors}, issn = {1095-9203}, doi = {10.1126/science.1070502}, author = {Perez-Orive, Javier and Mazor, Ofer and Turner, Glenn C and Cassenaer, Stijn and Wilson, Rachel I and Laurent, Gilles} } @article {1267, title = {Orientation preference maps in mammalian visual cortex: A wire length minimization approach.}, journal = {Neuron}, volume = {29}, year = {2001}, month = {2001 Feb}, pages = {519-27}, abstract = {

In the visual cortex of many mammals, orientation preference changes smoothly along the cortical surface, with the exception of singularities such as pinwheels and fractures. The reason for the existence of these singularities has remained elusive, suggesting that they are developmental artifacts. We show that singularities reduce the length of intracortical neuronal connections for some connection rules. Therefore, pinwheels and fractures could be evolutionary adaptations keeping cortical volume to a minimum. Wire length minimization approach suggests that interspecies differences in orientation preference maps reflect differences in intracortical neuronal circuits, thus leading to experimentally testable predictions. We discuss application of our model to direction preference maps.

}, issn = {0896-6273}, author = {Koulakov, Alexei A and Chklovskii, Dmitri B} } @article {2016, title = {Optical imaging of calcium transients in neurons and pharyngeal muscle of C. elegans.}, journal = {Neuron}, volume = {26}, year = {2000}, month = {2000 Jun}, pages = {583-94}, abstract = {

Electrophysiology and optical indicators have been used in vertebrate systems to investigate excitable cell firing and calcium transients, but both techniques have been difficult to apply in organisms with powerful reverse genetics. To overcome this limitation, we expressed cameleon proteins, genetically encoded calcium indicators, in the pharyngeal muscle of the nematode worm Caenorhabditis elegans. In intact transgenic animals expressing cameleons, fluorescence ratio changes accompanied muscular contraction, verifying detection of calcium transients. By comparing the magnitude and duration of calcium influx in wild-type and mutant animals, we were able to determine the effects of calcium channel proteins on pharyngeal calcium transients. We also successfully used cameleons to detect electrically evoked calcium transients in individual C. elegans neurons. This technique therefore should have broad applications in analyzing the regulation of excitable cell activity in genetically tractable organisms.

}, keywords = {Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Calcium, Calcium Channels, Down-Regulation, Electrophysiology, Helminth Proteins, Muscle Proteins, Mutation, Neurons, Optics and Photonics, Pharyngeal Muscles, Protein Isoforms}, issn = {0896-6273}, author = {Kerr, R and Lev-Ram, V and Baird, G and Vincent, P and Tsien, R Y and Schafer, W R} } @article {1268, title = {Optimal sizes of dendritic and axonal arbors in a topographic projection.}, journal = {Journal of Neurophysiology}, volume = {83}, year = {2000}, month = {2000}, pages = {2113-19}, chapter = {2113}, abstract = {

I consider a topographic projection between two neuronal layers with different densities of neurons. Given the number of output neurons connected to each input neuron (divergence) and the number of input neurons synapsing on each output neuron (convergence), I determine the widths of axonal and dendritic arbors which minimize the total volume of axons and dendrites. Analytical results for one-dimensional and two-dimensional projections can be summarized qualitatively in the following rule: neurons of the sparser layer should have arbors wider than those of the denser layer. This agrees with the anatomic data for retinal, cerebellar, olfactory bulb, and neocortical neurons the morphology and connectivity of which are known. The rule may be used to infer connectivity of neurons from their morphology.

}, issn = {0022-3077}, author = {Chklovskii, Dmitri B} } @article {2455, title = {The origins of insect metamorphosis.}, journal = {Nature}, volume = {401}, year = {1999}, month = {1999 Sep 30}, pages = {447-52}, abstract = {

Insect metamorphosis is a fascinating and highly successful biological adaptation, but there is much uncertainty as to how it evolved. Ancestral insect species did not undergo metamorphosis and there are still some existing species that lack metamorphosis or undergo only partial metamorphosis. Based on endocrine studies and morphological comparisons of the development of insect species with and without metamorphosis, a novel hypothesis for the evolution of metamorphosis is proposed. Changes in the endocrinology of development are central to this hypothesis. The three stages of the ancestral insect species-pronymph, nymph and adult-are proposed to be equivalent to the larva, pupa and adult stages of insects with complete metamorphosis. This proposal has general implications for insect developmental biology.

}, keywords = {Animals, Biological, Biological Evolution, Insect Hormones, Insects, Juvenile Hormones, Metamorphosis, Nymph, Wing}, issn = {0028-0836}, doi = {10.1038/46737}, author = {Truman, J W and Riddiford, L M} } @article {968, title = {The optic lobe projection pattern of polarization-sensitive photoreceptor cells in Drosophila melanogaster.}, journal = {Cell and Tissue Research}, volume = {265}, year = {1991}, month = {1991 Jul}, pages = {185-91}, abstract = {

Histological staining of wild-type and sevenless transgenic Drosophila melanogaster bearing Rh3-lacZ fusion genes permits the selective visualization of polarization-sensitive R7 and R8 photoreceptor cells located along the dorsal anterior eye margin. Diffusion of beta-galactosidase throughout these cells reveals that they project long axons to the two most peripheral synaptic target rows of the dorsal posterior medulla, defining a specialized marginal zone of this optic lobe. Comparison of the staining patterns of marginal and nonmarginal Rh3-lacZ-expressing photoreceptor cells in the same histological preparations suggest that the marginal cells possess morphologically specialized axons and synaptic terminals. These findings are discussed with reference to the neuroanatomy of the corresponding dorsal marginal eye and optic lobe regions of the larger dipterans Musca and Calliphora, and in relation to the ability of Drosophila to orient to polarized light.

}, keywords = {Animals, beta-Galactosidase, Cloning, Drosophila melanogaster, Eye, Gene Expression, Histocytochemistry, Light, Molecular, Nonmammalian, Ocular, Ocular Physiological Phenomena, Optic Lobe, Photoreceptor Cells, Vision}, issn = {0302-766X}, doi = {10.1186/gb-2007-8-7-r145}, author = {Fortini, M E and Rubin, G M} } @article {2723, title = {An O(ND) difference algorithm and its variations.}, journal = {Algorithmica}, volume = {1}, year = {1986}, month = {1986 Nov}, pages = {251-66}, abstract = {

The problems of finding a longest common subsequence of two sequences A and B and a shortest edit script for transforming A into B have long been known to be dual problems. In this paper, they are shown to be equivalent to finding a shortest/longest path in an edit graph. Using this perspective, a simple O(ND) time and space algorithm is developed where N is the sum of the lengths of A and B and D is the size of the minimum edit script for A and B. The algorithm performs well when differences are small (sequences are similar) and is consequently fast in typical applications. The algorithm is shown to have O(N +D expected-time performance under a basic stochastic model. A refinement of the algorithm requires only O(N) space, and the use of suffix trees leads to an O(NlgN +D ) time variation.

}, author = {Myers, Eugene} }