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1999 Janelia Publications

Showing 61-70 of 1999 results
06/11/21 | Pervasive fold switching in a ubiquitous protein superfamily.
Lauren L. Porter , Allen K. Kim , Loren L. Looger , Anaya Majumdar , Mary Starich
bioRxiv. 2021 Jun 11:. doi: 10.1101/2021.06.10.447921

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

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06/11/21 | The functional organization of excitatory synaptic input to place cells.
Adoff MD, Climer JR, Davoudi H, Marvin JS, Looger LL, Dombeck DA
Nature Communications. 2021 Jun 11;12(1):3558. doi: 10.1038/s41467-021-23829-y

Hippocampal place cells contribute to mammalian spatial navigation and memory formation. Numerous models have been proposed to explain the location-specific firing of this cognitive representation, but the pattern of excitatory synaptic input leading to place firing is unknown, leaving no synaptic-scale explanation of place coding. Here we used resonant scanning two-photon microscopy to establish the pattern of synaptic glutamate input received by CA1 place cells in behaving mice. During traversals of the somatic place field, we found increased excitatory dendritic input, mainly arising from inputs with spatial tuning overlapping the somatic field, and functional clustering of this input along the dendrites over ~10 µm. These results implicate increases in total excitatory input and co-activation of anatomically clustered synaptic input in place firing. Since they largely inherit their fields from upstream synaptic partners with similar fields, many CA1 place cells appear to be part of multi-brain-region cell assemblies forming representations of specific locations.

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06/07/21 | Live and Let Dye.
Lavis LD
Biochemistry. 2021 Jun 07:. doi: 10.1021/acs.biochem.1c00299

The measurement of ion concentrations and fluxes inside living cells is key to understanding cellular physiology. Fluorescent indicators that can infiltrate and provide intel on the cellular environment are critical tools for biological research. Developing these molecular informants began with the seminal work of Racker and colleagues ( (1979) 18, 2210), who demonstrated the passive loading of fluorescein in living cells to measure changes in intracellular pH. This work continues, employing a mix of old and new tradecraft to create innovative agents for monitoring ions inside living systems.

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Truman LabCardona Lab
06/04/21 | Unveiling the sensory and interneuronal pathways of the neuroendocrine connectome in Drosophila.
Hückesfeld S, Schlegel P, Miroschnikow A, Schoofs A, Zinke I, Haubrich AN, Schneider-Mizell CM, Truman JW, Fetter RD, Cardona A, Pankratz MJ
eLife. 2021 Jun 04;10:. doi: 10.7554/eLife.65745

Neuroendocrine systems in animals maintain organismal homeostasis and regulate stress response. Although a great deal of work has been done on the neuropeptides and hormones that are released and act on target organs in the periphery, the synaptic inputs onto these neuroendocrine outputs in the brain are less well understood. Here, we use the transmission electron microscopy reconstruction of a whole central nervous system in the larva to elucidate the sensory pathways and the interneurons that provide synaptic input to the neurosecretory cells projecting to the endocrine organs. Predicted by network modeling, we also identify a new carbon dioxide-responsive network that acts on a specific set of neurosecretory cells and that includes those expressing corazonin (Crz) and diuretic hormone 44 (Dh44) neuropeptides. Our analysis reveals a neuronal network architecture for combinatorial action based on sensory and interneuronal pathways that converge onto distinct combinations of neuroendocrine outputs.

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06/02/21 | Learning to represent continuous variables in heterogeneous neural networks
Ran Darshan , Alexander Rivkind
bioRxiv. 2021 Jun 02:. doi: 10.1101/2021.06.01.446635

Manifold attractors are a key framework for understanding how continuous variables, such as position or head direction, are encoded in the brain. In this framework, the variable is represented along a continuum of persistent neuronal states which forms a manifold attactor. Neural networks with symmetric synaptic connectivity that can implement manifold attractors have become the dominant model in this framework. In addition to a symmetric connectome, these networks imply homogeneity of individual-neuron tuning curves and symmetry of the representational space; these features are largely inconsistent with neurobiological data. Here, we developed a theory for computations based on manifold attractors in trained neural networks and show how these manifolds can cope with diverse neuronal responses, imperfections in the geometry of the manifold and a high level of synaptic heterogeneity. In such heterogeneous trained networks, a continuous representational space emerges from a small set of stimuli used for training. Furthermore, we find that the network response to external inputs depends on the geometry of the representation and on the level of synaptic heterogeneity in an analytically tractable and interpretable way. Finally, we show that a too complex geometry of the neuronal representation impairs the attractiveness of the manifold and may lead to its destabilization. Our framework reveals that continuous features can be represented in the recurrent dynamics of heterogeneous networks without assuming unrealistic symmetry. It suggests that the representational space of putative manifold attractors in the brain dictates the dynamics in their vicinity.

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06/02/21 | The anterior cingulate cortex directs exploration of alternative strategies.
Tervo DG, Kuleshova E, Manakov M, Proskurin M, Karlsson M, Lustig A, Behnam R, Karpova AY
Neuron. 2021 Jun 2;109(11):1876-87. doi: 10.1016/j.neuron.2021.03.028

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

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06/01/21 | Attractor dynamics gate cortical information flow during decision-making.
Finkelstein A, Fontolan L, Economo MN, Li N, Romani S, Svoboda K
Nature Neuroscience. 2021 Jun 1;24(6):843-50. doi: 10.1038/s41593-021-00840-6

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

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05/31/21 | Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications
Alex Rigano , Shannon Ehmsen , Serkan Utku Ozturk , Joel Ryan , Alexander Balashov , Mathias Hammer , Koray Kirli , Karl Bellve , Ulrike Boehm , Claire M. Brown , James J. Chambers , Robert A. Coleman , Andrea Cosolo , Orestis Faklaris , Kevin Fogarty , Thomas Guilbert , Anna B. Hamacher , Michelle S. Itano , Daniel P. Keeley , Susanne Kunis , Judith Lacoste , Alex Laude , Willa Ma , Marco Marcello , Paula Montero-Llopis , Glyn Nelson , Roland Nitschke , Jaime A. Pimentel , Stefanie Weidtkamp-Peters , Peter J. Park , Burak Alver , David Grunwald , Caterina Strambio-De-Castillia
bioRxiv. 2021 May 31:

For the information content of microscopy images to be appropriately interpreted, reproduced, and meet FAIR (Findable Accessible Interoperable and Reusable) principles, they should be accompanied by detailed descriptions of microscope hardware, image acquisition settings, image pixel and dimensional structure, and instrument performance. Nonetheless, the thorough documentation of imaging experiments is significantly impaired by the lack of community-sanctioned easy-to-use software tools to facilitate the extraction and collection of relevant microscopy metadata. Here we present Micro-Meta App, an intuitive open-source software designed to tackle these issues that was developed in the context of nascent global bioimaging community organizations, including BioImaging North America (BINA) and QUAlity Assessment and REProducibility in Light Microscopy (QUAREP-LiMi), whose goal is to improve reproducibility, data quality and sharing value for imaging experiments. The App provides a user-friendly interface for building comprehensive descriptions of the conditions utilized to produce individual microscopy datasets as specified by the recently proposed 4DN-BINA-OME tiered-system of Microscopy Metadata model. To achieve this goal the App provides a visual guide for a microscope-user to: 1) interactively build diagrammatic representations of hardware configurations of given microscopes that can be easily reused and shared with colleagues needing to document similar instruments. 2) Automatically extracts relevant metadata from image files and facilitates the collection of missing image acquisition settings and calibration metrics associated with a given experiment. 3) Output all collected Microscopy Metadata to interoperable files that can be used for documenting imaging experiments and shared with the community. In addition to significantly lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training users that have limited knowledge of the intricacies of light microscopy experiments. To ensure wide-adoption by microscope-users with different needs Micro-Meta App closely interoperates with MethodsJ2 and OMERO.mde, two complementary tools described in parallel manuscripts.

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05/28/21 | Advances in Confocal Microscopy and Selected Applications.
Reilly WM, Obara CJ
Methods in Molecular Biology. 2021 May 28;2304:1-35. doi: 10.1007/978-1-0716-1402-0_1

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

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05/28/21 | FLIM Imaging for Metabolic Studies in Live Cells.
Choi H
Methods in Molecular Biology. 2021 May 28;2304:339-346. doi: 10.1007/978-1-0716-1402-0_18

Fluorescent biochemical sensors allow probing metabolic states in a living cell with high spatiotemporal dynamics. This chapter describes a method for the in situ detection of changes in NAD level in living cells using fluorescence lifetime imaging (FLIM).

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