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1661 Janelia Publications

Showing 41-50 of 1661 results
08/27/19 | Constraining computational models using electron microscopy wiring diagrams.
Litwin-Kumar A, Turaga SC
Current Opinion in Neurobiology. 2019 Aug 27;58:94-100. doi: 10.1016/j.conb.2019.07.007

Numerous efforts to generate "connectomes," or synaptic wiring diagrams, of large neural circuits or entire nervous systems are currently underway. These efforts promise an abundance of data to guide theoretical models of neural computation and test their predictions. However, there is not yet a standard set of tools for incorporating the connectivity constraints that these datasets provide into the models typically studied in theoretical neuroscience. This article surveys recent approaches to building models with constrained wiring diagrams and the insights they have provided. It also describes challenges and the need for new techniques to scale these approaches to ever more complex datasets.

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08/27/19 | Idiosyncratic neural coding and neuromodulation of olfactory individuality in .
Honegger KS, Smith MA, Churgin MA, Turner GC, de Bivort BL
Proceedings of the National Academy of Sciences of the United States of America. 2019 Aug 27:. doi: 10.1073/pnas.1901623116

Innate behavioral biases and preferences can vary significantly among individuals of the same genotype. Though individuality is a fundamental property of behavior, it is not currently understood how individual differences in brain structure and physiology produce idiosyncratic behaviors. Here we present evidence for idiosyncrasy in olfactory behavior and neural responses in We show that individual female from a highly inbred laboratory strain exhibit idiosyncratic odor preferences that persist for days. We used in vivo calcium imaging of neural responses to compare projection neuron (second-order neurons that convey odor information from the sensory periphery to the central brain) responses to the same odors across animals. We found that, while odor responses appear grossly stereotyped, upon closer inspection, many individual differences are apparent across antennal lobe (AL) glomeruli (compact microcircuits corresponding to different odor channels). Moreover, we show that neuromodulation, environmental stress in the form of altered nutrition, and activity of certain AL local interneurons affect the magnitude of interfly behavioral variability. Taken together, this work demonstrates that individual exhibit idiosyncratic olfactory preferences and idiosyncratic neural responses to odors, and that behavioral idiosyncrasies are subject to neuromodulation and regulation by neurons in the AL.

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Pavlopoulos Lab
08/22/19 | Regionalized tissue fluidization by an actomyosin cable is required for epithelial gap closure during insect gastrulation.
Jain A, Ulman V, Mukherjee A, Prakash M, Pimpale L, Munster S, Panfilio KA, Jug F, Grill SW, Tomancak P, Pavlopoulos A
bioRxiv. 2019 Aug 22:. doi: https://doi.org/10.1101/744193

Many animal embryos face early on in development the problem of having to pull and close an epithelial sheet around the spherical yolk-sac. During this gastrulation process, known as epiboly, the spherical geometry of the egg dictates that the epithelial sheet first expands and subsequently compacts to close around the sphere. While it is well recognized that contractile actomyosin cables can drive epiboly movements, it is unclear how pulling on the leading edge can lead to simultaneous tissue expansion and compaction. Moreover, the epithelial sheet spreading over the sphere is mechanically stressed and this stress needs to be dissipated for seamless closure. While oriented cell division is known to dissipate tissue stresses during epiboly, it is unclear how this can be achieved without cell division. Here we show that during extraembryonic tissue (serosa) epiboly in the red flour beetle Tribolium castaneum, the non-proliferative serosa becomes regionalized into two distinct territories: a dorsal region under higher tension away from the leading edge with larger, isodiametric and non-rearranging cells, and a more fluid ventral region under lower tension surrounding the leading edge with smaller, anisotropic cells undergoing cell intercalation. Our results suggest that fluidization of the leading edge is effected by a heterogeneous actomyosin cable that drives sequential eviction and intercalation of individual cells away from the serosa margin. Since this developmental solution utilized during epiboly resembles the mechanism of wound healing in other systems, we propose actomyosin cable-driven local tissue fluidization as a conserved morphogenetic module for closure of epithelial gaps.

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08/13/19 | Bright and photostable chemigenetic indicators for extended in vivo voltage imaging.
Abdelfattah AS, Kawashima T, Singh A, Novak O, Liu H, Shuai Y, Huang Y, Campagnola L, Seeman SC, Yu J, Zheng J, Grimm JB, Patel R, Friedrich J, Mensh BD, Paninski L, Macklin JJ, Murphy GJ, Podgorski K, Lin B, Chen T, Turner GC, Liu Z, Koyama M, Svoboda K, Ahrens MB, Lavis LD, Schreiter ER
Science. 2019 Aug 13;365(6454):699-704. doi: 10.1126/science.aav6416

Imaging changes in membrane potential using genetically encoded fluorescent voltage indicators (GEVIs) has great potential for monitoring neuronal activity with high spatial and temporal resolution. Brightness and photostability of fluorescent proteins and rhodopsins have limited the utility of existing GEVIs. We engineered a novel GEVI, "Voltron", that utilizes bright and photostable synthetic dyes instead of protein-based fluorophores, extending the combined duration of imaging and number of neurons imaged simultaneously by more than tenfold relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously, over 15 min of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.

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08/15/19 | Time-variant SRC kinase activation determines endothelial permeability response.
Klomp JE, Shaaya M, Matsche J, Rebiai R, Aaron JS, Collins KB, Huyot V, Gonzalez AM, Muller WA, Chew T, Malik AB, Karginov AV
Cell Chemical Biology. 2019 Aug 15;26(8):1081-94. doi: 10.1016/j.chembiol.2019.04.007

In the current model of endothelial barrier regulation, the tyrosine kinase SRC is purported to induce disassembly of endothelial adherens junctions (AJs) via phosphorylation of VE cadherin, and thereby increase junctional permeability. Here, using a chemical biology approach to temporally control SRC activation, we show that SRC exerts distinct time-variant effects on the endothelial barrier. We discovered that the immediate effect of SRC activation was to transiently enhance endothelial barrier function as the result of accumulation of VE cadherin at AJs and formation of morphologically distinct reticular AJs. Endothelial barrier enhancement via SRC required phosphorylation of VE cadherin at Y731. In contrast, prolonged SRC activation induced VE cadherin phosphorylation at Y685, resulting in increased endothelial permeability. Thus, time-variant SRC activation differentially phosphorylates VE cadherin and shapes AJs to fine-tune endothelial barrier function. Our work demonstrates important advantages of synthetic biology tools in dissecting complex signaling systems.

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08/12/19 | An automatic behavior recognition system classifies animal behaviors using movements and their temporal context.
Ravbar P, Branson K, Simpson JH
Journal of Neuroscience Methods. 2019 Aug 12;326:108352. doi: 10.1016/j.jneumeth.2019.108352

Animals can perform complex and purposeful behaviors by executing simpler movements in flexible sequences. It is particularly challenging to analyze behavior sequences when they are highly variable, as is the case in language production, certain types of birdsong and, as in our experiments, flies grooming. High sequence variability necessitates rigorous quantification of large amounts of data to identify organizational principles and temporal structure of such behavior. To cope with large amounts of data, and minimize human effort and subjective bias, researchers often use automatic behavior recognition software. Our standard grooming assay involves coating flies in dust and videotaping them as they groom to remove it. The flies move freely and so perform the same movements in various orientations. As the dust is removed, their appearance changes. These conditions make it difficult to rely on precise body alignment and anatomical landmarks such as eyes or legs and thus present challenges to existing behavior classification software. Human observers use speed, location, and shape of the movements as the diagnostic features of particular grooming actions. We applied this intuition to design a new automatic behavior recognition system (ABRS) based on spatiotemporal features in the video data, heavily weighted for temporal dynamics and invariant to the animal’s position and orientation in the scene. We use these spatiotemporal features in two steps of supervised classification that reflect two time-scales at which the behavior is structured. As a proof of principle, we show results from quantification and analysis of a large data set of stimulus-induced fly grooming behaviors that would have been difficult to assess in a smaller dataset of human-annotated ethograms. While we developed and validated this approach to analyze fly grooming behavior, we propose that the strategy of combining alignment-invariant features and multi-timescale analysis may be generally useful for movement-based classification of behavior from video data.

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08/09/19 | A Neural Circuit Arbitrates between Persistence and Withdrawal in Hungry Drosophila.
Sayin S, De Backer J, Siju KP, Wosniack ME, Lewis LP, Frisch L, Gansen B, Schlegel P, Edmondson-Stait A, Sharifi N, Fisher CB, Calle-Schuler SA, Lauritzen JS, Bock DD, Costa M, Jefferis GS, Gjorgjieva J, Grunwald Kadow IC
Neuron. 2019 Aug 09:. doi: 10.1016/j.neuron.2019.07.028

In pursuit of food, hungry animals mobilize significant energy resources and overcome exhaustion and fear. How need and motivation control the decision to continue or change behavior is not understood. Using a single fly treadmill, we show that hungry flies persistently track a food odor and increase their effort over repeated trials in the absence of reward suggesting that need dominates negative experience. We further show that odor tracking is regulated by two mushroom body output neurons (MBONs) connecting the MB to the lateral horn. These MBONs, together with dopaminergic neurons and Dop1R2 signaling, control behavioral persistence. Conversely, an octopaminergic neuron, VPM4, which directly innervates one of the MBONs, acts as a brake on odor tracking by connecting feeding and olfaction. Together, our data suggest a function for the MB in internal state-dependent expression of behavior that can be suppressed by external inputs conveying a competing behavioral drive.

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08/07/19 | A small number of cholinergic neurons mediate hyperaggression in female Drosophila.
Palavicino-Maggio CB, Chan Y, McKellar C, Kravitz EA
Proceedings of the National Academy of Sciences of the United States of America. 2019 Aug 07;116(34):17029-38. doi: 10.1073/pnas.1907042116

In the Drosophila model of aggression, males and females fight in same-sex pairings, but a wide disparity exists in the levels of aggression displayed by the 2 sexes. A screen of Drosophila Flylight Gal4 lines by driving expression of the gene coding for the temperature sensitive dTRPA1 channel, yielded a single line (GMR26E01-Gal4) displaying greatly enhanced aggression when thermoactivated. Targeted neurons were widely distributed throughout male and female nervous systems, but the enhanced aggression was seen only in females. No effects were seen on female mating behavior, general arousal, or male aggression. We quantified the enhancement by measuring fight patterns characteristic of female and male aggression and confirmed that the effect was female-specific. To reduce the numbers of neurons involved, we used an intersectional approach with our library of enhancer trap flp-recombinase lines. Several crosses reduced the populations of labeled neurons, but only 1 cross yielded a large reduction while maintaining the phenotype. Of particular interest was a small group (2 to 4 pairs) of neurons in the approximate position of the pC1 cluster important in governing male and female social behavior. Female brains have approximately 20 doublesex (dsx)-expressing neurons within pC1 clusters. Using dsxFLP instead of 357FLP for the intersectional studies, we found that the same 2 to 4 pairs of neurons likely were identified with both. These neurons were cholinergic and showed no immunostaining for other transmitter compounds. Blocking the activation of these neurons blocked the enhancement of aggression.

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08/03/19 | Response to "Fallacies of mice experiments".
Gao Z, Thomas AM, Economo MN, Abrego AM, Svoboda K, De Zeeuw CI, Li N
Neuroinformatics. 2019 Aug 03:. doi: 10.1007/s12021-019-09433-y

In a recent Editorial, De Schutter commented on our recent study on the roles of a cortico-cerebellar loop in motor planning in mice (De Schutter 2019, Neuroinformatics, 17, 181-183, Gao et al. 2018, Nature, 563, 113-116). Two issues were raised. First, De Schutter questions the involvement of the fastigial nucleus in motor planning, rather than the dentate nucleus, given previous anatomical studies in non-human primates. Second, De Schutter suggests that our study design did not delineate different components of the behavior and the fastigial nucleus might play roles in sensory discrimination rather than motor planning. These comments are based on anatomical studies in other species and homology-based arguments and ignore key anatomical data and neurophysiological experiments from our study. Here we outline our interpretation of existing data and point out gaps in knowledge where future studies are needed.

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

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