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2041 Janelia Publications

Showing 51-60 of 2041 results
10/15/21 | Organizing memories for generalization in complementary learning systems.
Weinan Sun , Madhu Advani , Nelson Spruston , Andrew Saxe , James E. Fitzgerald
bioRxiv. 2021 Oct 15:. doi:

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.

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10/14/21 | Rapid synaptic plasticity contributes to a learned conjunctive code of position and choice-related information in the hippocampus
Xinyu Zhao , Ching-Lung Hsu , Nelson Spruston
Neuron. 2021 Oct 14:. doi:

To successfully perform goal-directed navigation, animals must know where they are and what they are doing—e.g., looking for water, bringing food back to the nest, or escaping from a predator. Hippocampal neurons code for these critical variables conjunctively, but little is known about how this where/what code is formed or flexibly routed to other brain regions. To address these questions, we performed intracellular whole-cell recordings in mouse CA1 during a cued, two-choice virtual navigation task. We demonstrate that plateau potentials in CA1 pyramidal neurons rapidly strengthen synaptic inputs carrying conjunctive information about position and choice. Plasticity-induced response fields were modulated by cues only in animals previously trained to collect rewards based on these cues. Thus, we reveal that gradual learning is required for the formation of a conjunctive population code, upstream of CA1, while plateau-potential-induced synaptic plasticity in CA1 enables flexible routing of the code to downstream brain regions.

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10/06/21 | Cre-Dependent Anterograde Transsynaptic Labeling and Functional Imaging in Zebrafish Using VSV With Reduced Cytotoxicity.
Kler S, Ma M, Narayan S, Ahrens MB, Pan YA
Frontiers in Neuroanatomy. 2021 Oct 06;15:758350. doi: 10.3389/fnana.2021.758350

The small size and translucency of larval zebrafish () have made it a unique experimental system to investigate whole-brain neural circuit structure and function. Still, the connectivity patterns between most neuronal types remain mostly unknown. This gap in knowledge underscores the critical need for effective neural circuit mapping tools, especially ones that can integrate structural and functional analyses. To address this, we previously developed a vesicular stomatitis virus (VSV) based approach called Tracer with Restricted Anterograde Spread (TRAS). TRAS utilizes lentivirus to complement replication-incompetent VSV (VSVΔG) to allow restricted (monosynaptic) anterograde labeling from projection neurons to their target cells in the brain. Here, we report the second generation of TRAS (TRAS-M51R), which utilizes a mutant variant of VSVΔG [VSV(M51R)ΔG] with reduced cytotoxicity. Within the primary visual pathway, we found that TRAS-M51R significantly improved long-term viability of transsynaptic labeling (compared to TRAS) while maintaining anterograde spread activity. By using Cre-expressing VSV(M51R)ΔG, TRAS-M51R could selectively label excitatory ( positive) and inhibitory ( positive) retinorecipient neurons. We further show that these labeled excitatory and inhibitory retinorecipient neurons retained neuronal excitability upon visual stimulation at 5-8 days post fertilization (2-5 days post-infection). Together, these findings show that TRAS-M51R is suitable for neural circuit studies that integrate structural connectivity, cell-type identity, and neurophysiology.

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10/04/21 | An adaptive optics module for deep tissue multiphoton imaging in vivo
Cristina Rodríguez , Anderson Chen , José A. Rivera , Manuel A. Mohr , Yajie liang , Wenzhi Sun , Daniel E. Milkie , Thomas G. Bifano , Xiaoke Chen , Na Ji
Nature Methods. 2021 Oct 04:1259-64. doi: 10.1038/s41592-021-01279-0

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

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10/01/21 | A high-throughput predictive method for sequence-similar fold switchers.
Kim AK, Looger LL, Porter LL
Biopolymers. 2021 Oct 01;112(10):e23416. doi: 10.1002/bip.23416

Although most experimentally characterized proteins with similar sequences assume the same folds and perform similar functions, an increasing number of exceptions is emerging. One class of exceptions comprises sequence-similar fold switchers, whose secondary structures shift from α-helix <-> β-sheet through a small number of mutations, a sequence insertion, or a deletion. Predictive methods for identifying sequence-similar fold switchers are desirable because some are associated with disease and/or can perform different functions in cells. Here, we use homology-based secondary structure predictions to identify sequence-similar fold switchers from their amino acid sequences alone. To do this, we predicted the secondary structures of sequence-similar fold switchers using three different homology-based secondary structure predictors: PSIPRED, JPred4, and SPIDER3. We found that α-helix <-> β-strand prediction discrepancies from JPred4 discriminated between the different conformations of sequence-similar fold switchers with high statistical significance (P < 1.8*10 ). Thus, we used these discrepancies as a classifier and found that they can often robustly discriminate between sequence-similar fold switchers and sequence-similar proteins that maintain the same folds (Matthews Correlation Coefficient of 0.82). We found that JPred4 is a more robust predictor of sequence-similar fold switchers because of (a) the curated sequence database it uses to produce multiple sequence alignments and (b) its use of sequence profiles based on Hidden Markov Models. Our results indicate that inconsistencies between JPred4 secondary structure predictions can be used to identify some sequence-similar fold switchers from their sequences alone. Thus, the negative information from inconsistent secondary structure predictions can potentially be leveraged to identify sequence-similar fold switchers from the broad base of genomic sequences.

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10/01/21 | A sequence-based method for predicting extant fold switchers that undergo α-helix <-> β-strand transitions
Soumya Mishra , Loren L. Looger , Lauren L. Porter
Biopolymers. 2021 Oct 01;112(10):. doi: 10.1101/2021.01.14.426714

Extant fold-switching proteins remodel their secondary structures and change their functions in response to cellular stimuli, regulating biological processes and affecting human health. In spite of their biological importance, these proteins remain understudied. Few representative examples of fold switchers are available in the Protein Data Bank, and they are difficult to predict. In fact, all 96 experimentally validated examples of extant fold switchers were stumbled upon by chance. Thus, predictive methods are needed to expedite the process of discovering and characterizing more of these shapeshifting proteins. Previous approaches require a solved structure or all-atom simulations, greatly constraining their use. Here, we propose a high-throughput sequence-based method for predicting extant fold switchers that transition from α-helix in one conformation to β-strand in the other. This method leverages two previous observations: (1) α-helix <-> β-strand prediction discrepancies from JPred4 are a robust predictor of fold switching, and (2) the fold-switching regions (FSRs) of some extant fold switchers have different secondary structure propensities when expressed in isolation (isolated FSRs) than when expressed within the context of their parent protein (contextualized FSRs). Combining these two observations, we ran JPred4 on the sequences of isolated and contextualized FSRs from 14 known extant fold switchers and found α-helix <->β-strand prediction discrepancies in every case. To test the overall robustness of this finding, we randomly selected regions of proteins not expected to switch folds (single-fold proteins) and found significantly fewer α-helix <-> β-strand prediction discrepancies (p < 4.2*10−20, Kolmogorov-Smirnov test). Combining these discrepancies with the overall percentage of predicted secondary structure, we developed a classifier that often robustly identifies extant fold switchers (Matthews Correlation Coefficient of 0.70). Although this classifier had a high false negative rate (6/14), its false positive rate was very low (1/211), suggesting that it can be used to predict a subset of extant fold switchers from billions of available genomic sequences.

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10/01/21 | An adaptive optics module for deep tissue multiphoton imaging in vivo.
Rodriguez C, Chen A, Rivera JA, Mohr MA, Liang Y, Natan RG, Sun W, Milkie DE, Bifano TG, Chen X, Ji N
Nature Methods. 2021 Oct 01;18(10):1259-1264. doi: 10.1038/s41592-021-01279-0

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

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10/01/21 | QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
Glyn Nelson , Ulrike Boehm , Steve Bagley , Peter Bajcsy , Johanna Bischof , Claire M Brown , Aurelien Dauphin , Ian M Dobbie , John E Eriksson , Orestis Faklaris , Julia Fernandez-Rodriguez , Alexia Ferrand , Ali Gheisari , Hella Hartmann , Christian Kukat , Alex Laude , Miso Mitkovski , Sebastian Munck , Alison J North , Tobias M Rasse , Ute Resch-Genger , Lucas C Schuetz , Arne Seitz , Caterina Strambio-De-Castillia , Jason R Swedlow , Ioannis Alexopoulos , Karin Aumayr , Sergiy Avilov , Gert-Jan Bakker , Rodrigo R Bammann , Andrea Bassi , Hannes Beckert , Sebastian Beer , Yury Belyaev , Jakob Bierwagen , Konstantin A Birngruber , Manel Bosch , Juergen Breitlow , Lisa A Cameron , Joe Chalfoun , James J Chambers , Chieh-Li Chen , Eduardo Conde-Sousa , Alexander D Corbett , Fabrice P Cordelieres , Elaine Del Nery , Ralf Dietzel , Frank Eismann , Elnaz Fazeli , Andreas Felscher , Hans Fried , Nathalie Gaudreault , Wah Ing Goh , Thomas Guilbert , Roland Hadleigh , Peter Hemmerich , Gerhard A Holst , Michelle S Itano , Claudia B Jaffe , Helena K Jambor , Stuart C Jarvis , Antje Keppler , David Kirchenbuechler , Marcel Kirchner , Norio Kobayashi , Gabriel Krens , Susanne Kunis , Judith Lacoste , Marco Marcell , Gabriel G Martins , Daniel J Metcalf , Claire A Mitchell , Joshua Moore , Tobias Mueller , Michael S Nelson , Stephen Ogg , Shuichi Onami , Alexandra L Palmer , Perrine Paul-Gilloteaux , Jaime A Pimentel , Laure Plantard , Santosh Podder , Elton Rexhepaj , Arnaud Royon , Markku A Saari , Damien Schapman , Vincent Schoonderwoert , Britta Schroth-Diez , Stanley Schwartz , Michael Shaw , Martin Spitaler , Martin T Stoeckl , Damir Sudar , Jeremie Teillon , Stefan Terjung , Roland Thuenauer , Christian D Wilms , Graham D Wright , Roland Nitschke , Laurent Gelman
Journal of Microscopy. 2021 Oct 01;284(1):56-73

In April 2020, the QUality Assessment and REProducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models, and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper 1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; 2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers, and observers of such; 3) outlines the current actions of the QUAREP-LiMi initiative, and 4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.

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09/30/21 | Cellular bases of olfactory circuit assembly revealed by systematic time-lapse imaging.
Li T, Fu T, Wong KK, Li H, Xie Q, Luginbuhl DJ, Wagner MJ, Betzig E, Luo L
Cell. 2021 Sep 30;184(20):5107. doi: 10.1016/j.cell.2021.08.030

Neural circuit assembly features simultaneous targeting of numerous neuronal processes from constituent neuron types, yet the dynamics is poorly understood. Here, we use the Drosophila olfactory circuit to investigate dynamic cellular processes by which olfactory receptor neurons (ORNs) target axons precisely to specific glomeruli in the ipsi- and contralateral antennal lobes. Time-lapse imaging of individual axons from 30 ORN types revealed a rich diversity in extension speed, innervation timing, and ipsilateral branch locations and identified that ipsilateral targeting occurs via stabilization of transient interstitial branches. Fast imaging using adaptive optics-corrected lattice light-sheet microscopy showed that upon approaching target, many ORN types exhibiting "exploring branches" consisted of parallel microtubule-based terminal branches emanating from an F-actin-rich hub. Antennal nerve ablations uncovered essential roles for bilateral axons in contralateral target selection and for ORN axons to facilitate dendritic refinement of postsynaptic partner neurons. Altogether, these observations provide cellular bases for wiring specificity establishment.

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09/30/21 | The LRRK2 G2019S mutation alters astrocyte-to-neuron communication via extracellular vesicles and induces neuron atrophy in a human iPSC-derived model of Parkinson’s disease
Aurelie de Rus Jacquet , Jenna L. Tancredi , Andrew L. Lemire , Michael C. DeSantis , Wei-Ping Li , Erin K. O’Shea
eLife. 2021 Sep 30:. doi:

Astrocytes are essential cells of the central nervous system, characterized by dynamic relationships with neurons that range from functional metabolic interactions and regulation of neuronal firing activities, to the release of neurotrophic and neuroprotective factors. In Parkinson’s disease (PD), dopaminergic neurons are progressively lost during the course of the disease, but the effects of PD on astrocytes and astrocyte-to-neuron communication remains largely unknown. This study focuses on the effects of the PD-related mutation LRRK2 G2019S in astrocytes generated from patient-derived induced pluripotent stem cells. We report the alteration of extracellular vesicle (EV) biogenesis in astrocytes, and we identify the abnormal accumulation of key PD-related proteins within multi vesicular bodies (MVBs). We found that dopaminergic neurons internalize astrocyte-secreted EVs and that LRRK2 G2019S EVs are abnormally enriched in neurites and fail to provide full neurotrophic support to dopaminergic neurons. Thus, dysfunctional astrocyte-to-neuron communication via altered EV biological properties may participate in the progression of PD.

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