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Your search keyword '"Vivek Jayaraman"' showing total 9 results
Start Over Author "Vivek Jayaraman" Publisher elife sciences publications, ltd
9 results on '"Vivek Jayaraman"'

1. A connectome of the Drosophila central complex reveals network motifs suitable for flexible navigation and context-dependent action selection

Author

Gerald M. Rubin, Marcella Noorman, Shin-ya Takemura, Brad K. Hulse, Hannah Haberkern, Daniel B. Turner-Evans, Tanya Wolff, Romain Franconville, Chuntao Dan, Vivek Jayaraman, Ruchi Parekh, Marisa Dreher, and Ann M Hermundstad

Subjects
General Immunology and Microbiology, Computer science, General Neuroscience, Behavioral pattern, Sensory system, Context (language use), General Medicine, Network dynamics, Spatial memory, Action selection, General Biochemistry, Genetics and Molecular Biology, Recurrent neural network, Connectome, Neuroscience
Abstract

Flexible behaviors over long timescales are thought to engage recurrent neural networks in deep brain regions, which are experimentally challenging to study. In insects, recurrent circuit dynamics in a brain region called the central complex (CX) enable directed locomotion, sleep, and context- and experience-dependent spatial navigation. We describe the first complete electron microscopy-based connectome of the Drosophila CX, including all its neurons and circuits at synaptic resolution. We identified new CX neuron types, novel sensory and motor pathways, and network motifs that likely enable the CX to extract the fly’s head direction, maintain it with attractor dynamics, and combine it with other sensorimotor information to perform vector-based navigational computations. We also identified numerous pathways that may facilitate the selection of CX-driven behavioral patterns by context and internal state. The CX connectome provides a comprehensive blueprint necessary for a detailed understanding of network dynamics underlying sleep, flexible navigation, and state-dependent action selection.

Published
2021
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3. A connectome and analysis of the adult Drosophila central brain

Author

Temour Tokhi, Tom Dolafi, Nneoma Okeoma, Tanya Wolff, Philip M Hubbard, Kazunori Shinomiya, Madelaine K Robertson, Gerald M. Rubin, Gregory S.X.E. Jefferis, Christopher J Knecht, Laramie Leavitt, Alia Suleiman, Satoko Takemura, Christopher Ordish, Jody Clements, Ian A. Meinertzhagen, Alexander Shakeel Bates, Takashi Kawase, Samantha Finley, Nicholas Padilla, Jackie Swift, C. Shan Xu, Stuart Berg, Tyler Paterson, Ashley L Scott, Erika Neace, Shirley Lauchie, Sean M Ryan, Emily M Joyce, Shin-ya Takemura, Tim Blakely, Michael A Cook, Christopher Patrick, Bryon Eubanks, Audrey Francis, Robert Svirskas, William T. Katz, Eric T. Trautman, Caroline Mooney, Ting Zhao, Nicole A Kirk, Megan Sammons, Brandon S Canino, Reed A. George, Louis K. Scheffer, Jolanta A. Borycz, Jon Thomson Rymer, Natasha Cheatham, Dagmar Kainmueller, Gary B. Huang, Khaled Khairy, Nicole Neubarth, Elliott E Phillips, John A. Bogovic, Neha Rampally, Larry Lindsey, Viren Jain, David G. Ackerman, Jane Anne Horne, Kelli Fairbanks, Lowell Umayam, Jens Goldammer, Emily M Phillips, Donald J. Olbris, Feng Li, Emily A Manley, Philipp Schlegel, Hideo Otsuna, Marta Costa, Stephen M. Plaza, Omotara Ogundeyi, Samantha Ballinger, Charli Maldonado, Kelsey Smith, Gary Patrick Hopkins, Vivek Jayaraman, Emily Tenshaw, Julie Kovalyak, Peter H. Li, Tansy Yang, Masayoshi Ito, Miatta Ndama, Claire Smith, Michał Januszewski, Alanna Lohff, SungJin Kim, Anne K Scott, Kei Ito, Iris Talebi, Jeremy Maitlin-Shepard, Nora Forknall, Marisa Dreher, Harald F. Hess, Sari McLin, Patricia K. Rivlin, Dennis A Bailey, Kenneth J. Hayworth, Octave Duclos, Caitlin Ribeiro, John J. Walsh, Zhiyuan Lu, Dorota Tarnogorska, Ruchi Parekh, Aya Shinomiya, Stephan Saalfeld, Margaret A Sobeski, Natalie L Smith, Chelsea X Alvarado, Scheffer, Louis K [0000-0002-3289-6564], Xu, C Shan [0000-0002-8564-7836], Januszewski, Michal [0000-0002-3480-2744], Lu, Zhiyuan [0000-0002-4128-9774], Takemura, Shin-ya [0000-0003-2400-6426], Huang, Gary B [0000-0002-9606-3510], Shinomiya, Kazunori [0000-0003-0262-6421], Maitlin-Shepard, Jeremy [0000-0001-8453-7961], Hubbard, Philip M [0000-0002-6746-5035], Katz, William T [0000-0002-9417-6212], Ackerman, David [0000-0003-0172-6594], Blakely, Tim [0000-0003-0995-5471], Bogovic, John [0000-0002-4829-9457], Kainmueller, Dagmar [0000-0002-9830-2415], Khairy, Khaled A [0000-0002-9274-5928], Li, Peter H [0000-0001-6193-4454], Trautman, Eric T [0000-0001-8588-0569], Bates, Alexander S [0000-0002-1195-0445], Goldammer, Jens [0000-0002-5623-8339], Wolff, Tanya [0000-0002-8681-1749], Svirskas, Robert [0000-0001-8374-6008], Schlegel, Philipp [0000-0002-5633-1314], Knecht, Christopher J [0000-0002-5663-5967], Alvarado, Chelsea X [0000-0002-5973-7512], Bailey, Dennis A [0000-0002-4675-8373], Borycz, Jolanta A [0000-0002-4402-9230], Canino, Brandon S [0000-0002-8454-865X], Cook, Michael [0000-0002-7892-6845], Dreher, Marisa [0000-0002-0041-9229], Eubanks, Bryon [0000-0002-9288-2009], Fairbanks, Kelli [0000-0002-6601-4830], Finley, Samantha [0000-0002-8086-206X], Forknall, Nora [0000-0003-2139-7599], Francis, Audrey [0000-0003-1974-7174], Joyce, Emily M [0000-0001-5794-6321], Kovalyak, Julie [0000-0001-7864-7734], Lauchie, Shirley A [0000-0001-8223-9522], Lohff, Alanna [0000-0002-1242-1836], McLin, Sari [0000-0002-9120-1136], Patrick, Christopher M [0000-0001-8830-1892], Phillips, Elliott E [0000-0002-4918-2058], Phillips, Emily M [0000-0001-7615-301X], Robertson, Madelaine K [0000-0002-1764-0245], Rymer, Jon Thomson [0000-0002-4271-6774], Ryan, Sean M [0000-0002-8879-6108], Sammons, Megan [0000-0003-4516-5928], Shinomiya, Aya [0000-0002-6358-9567], Smith, Natalie L [0000-0002-8271-9873], Swift, Jackie [0000-0003-1321-8183], Takemura, Satoko [0000-0002-2863-0050], Talebi, Iris [0000-0002-0173-8053], Tarnogorska, Dorota [0000-0002-7063-6165], Walsh, John J [0000-0002-7176-4708], Yang, Tansy [0000-0003-1131-0410], Horne, Jane Anne [0000-0001-9673-2692], Parekh, Ruchi [0000-0002-8060-2807], Jayaraman, Vivek [0000-0003-3680-7378], Costa, Marta [0000-0001-5948-3092], Jefferis, Gregory SXE [0000-0002-0587-9355], Ito, Kei [0000-0002-7274-5533], Saalfeld, Stephan [0000-0002-4106-1761], Rubin, Gerald M [0000-0001-8762-8703], Hess, Harald F [0000-0003-3000-1533], Plaza, Stephen M [0000-0001-7425-8555], Apollo - University of Cambridge Repository, Takemura, Shin-Ya [0000-0003-2400-6426], and Jefferis, Gregory Sxe [0000-0002-0587-9355]

Subjects
Male, Computer science, computational biology, 0302 clinical medicine, Drosophila Proteins, Research article, Biology (General), Neurons, Cognitive science, 0303 health sciences, biology, D. melanogaster, General Neuroscience, connectome, Brain, systems biology, graph properties, General Medicine, Human brain, Drosophila melanogaster, medicine.anatomical_structure, Connectome, Medicine, Drosophila, Female, synapse detecton, Insight, Function and Dysfunction of the Nervous System, cell types, Research Article, Computational and Systems Biology, brain regions, Connectomes, QH301-705.5, Ubiquitin-Protein Ligases, Science, connectome reconstuction methods, Small mammal, Central region, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, medicine, Animals, 030304 developmental biology, General Immunology and Microbiology, biology.organism_classification, synapse detection, Synapses, 030217 neurology & neurosurgery, Neuroscience
Abstract

The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly’s brain., eLife digest Animal brains of all sizes, from the smallest to the largest, work in broadly similar ways. Studying the brain of any one animal in depth can thus reveal the general principles behind the workings of all brains. The fruit fly Drosophila is a popular choice for such research. With about 100,000 neurons – compared to some 86 billion in humans – the fly brain is small enough to study at the level of individual cells. But it nevertheless supports a range of complex behaviors, including navigation, courtship and learning. Thanks to decades of research, scientists now have a good understanding of which parts of the fruit fly brain support particular behaviors. But exactly how they do this is often unclear. This is because previous studies showing the connections between cells only covered small areas of the brain. This is like trying to understand a novel when all you can see is a few isolated paragraphs. To solve this problem, Scheffer, Xu, Januszewski, Lu, Takemura, Hayworth, Huang, Shinomiya et al. prepared the first complete map of the entire central region of the fruit fly brain. The central brain consists of approximately 25,000 neurons and around 20 million connections. To prepare the map – or connectome – the brain was cut into very thin 8nm slices and photographed with an electron microscope. A three-dimensional map of the neurons and connections in the brain was then reconstructed from these images using machine learning algorithms. Finally, Scheffer et al. used the new connectome to obtain further insights into the circuits that support specific fruit fly behaviors. The central brain connectome is freely available online for anyone to access. When used in combination with existing methods, the map will make it easier to understand how the fly brain works, and how and why it can fail to work correctly. Many of these findings will likely apply to larger brains, including our own. In the long run, studying the fly connectome may therefore lead to a better understanding of the human brain and its disorders. Performing a similar analysis on the brain of a small mammal, by scaling up the methods here, will be a likely next step along this path.

Published
2020

4. Author response: A connectome and analysis of the adult Drosophila central brain

Author

Dennis A Bailey, Kenneth J. Hayworth, Aya Shinomiya, Madelaine K Robertson, Tim Blakely, C. Shan Xu, Temour Tokhi, Jon Thomson Rymer, Nicole Neubarth, Zhiyuan Lu, Dorota Tarnogorska, Shirley Lauchie, Sean M Ryan, Nneoma Okeoma, Erika Neace, Khaled Khairy, Emily M Phillips, Margaret A Sobeski, Bryon Eubanks, Christopher Patrick, Marisa Dreher, Natalie L Smith, Philipp Schlegel, John A. Bogovic, David G. Ackerman, Jane Anne Horne, Tom Dolafi, Gary B. Huang, Kelli Fairbanks, Claire Smith, Michał Januszewski, Octave Duclos, Satoko Takemura, Christopher Ordish, Chelsea X Alvarado, Jody Clements, Viren Jain, Samantha Finley, John J. Walsh, Nicole A Kirk, Kelsey Smith, Omotara Ogundeyi, Takashi Kawase, Reed A. George, Tyler Paterson, Laramie Leavitt, Kazunori Shinomiya, SungJin Kim, Christopher J Knecht, Nicholas Padilla, Anne K Scott, Tansy Yang, Ashley L Scott, Hideo Otsuna, Jeremy Maitlin-Shepard, Marta Costa, Nora Forknall, Stuart Berg, Alia Suleiman, Harald F. Hess, Audrey Francis, Donald J. Olbris, Caroline Mooney, Emily M Joyce, Eric T. Trautman, Gerald M. Rubin, Jackie Swift, Philip M Hubbard, Ting Zhao, Brandon S Canino, Gary Patrick Hopkins, Kei Ito, Jolanta A. Borycz, Shin-ya Takemura, Masayoshi Ito, Stephen M. Plaza, Ian A. Meinertzhagen, Louis K. Scheffer, Dagmar Kainmueller, Larry Lindsey, Miatta Ndama, Elliott E Phillips, Lowell Umayam, Jens Goldammer, Vivek Jayaraman, Emily Tenshaw, Gregory S.X.E. Jefferis, Alexander Shakeel Bates, William T. Katz, Sari McLin, Neha Rampally, Emily A Manley, Patricia K. Rivlin, Charli Maldonado, Peter H. Li, Samantha Ballinger, Tanya Wolff, Megan Sammons, Julie Kovalyak, Stephan Saalfeld, Alanna Lohff, Natasha Cheatham, Iris Talebi, Michael A Cook, Robert Svirskas, Feng Li, Caitlin Ribeiro, and Ruchi Parekh

Subjects
biology, Connectome, Drosophila (subgenus), biology.organism_classification, Neuroscience
Published
2020
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7. Author response: Sensitive red protein calcium indicators for imaging neural activity

Author

Douglas S. Kim, Boaz Mohar, Sujatha Narayan, Amy Hu, Hod Dana, Cornelia I. Bargmann, Yi Sun, Deepika Walpita, Misha B. Ahrens, Loren L. Looger, John J. Macklin, Vivek Jayaraman, Andrew Gordus, Karel Svoboda, Jeremy P. Hasseman, Ronak Patel, Graham T Holt, Eric R. Schreiter, and Getahun Tsegaye

Subjects
0301 basic medicine, 03 medical and health sciences, Neural activity, 030104 developmental biology, Biochemistry, Chemistry, Protein calcium
Published
2016
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9. Author response: Dynamical feature extraction at the sensory periphery guides chemotaxis

Author

Vani G. Rajendran, David Jarriault, Marco Musy, Matthieu Louis, Shaul Druckmann, Alex Gomez-Marin, Vivek Jayaraman, Gus K. Lott, Eric T. Trautman, Christopher Werner, Ajinkya Deogade, James Sharpe, Parvez Ahammad, Madhusudhan Venkadesan, Julia Riedl, and Aljoscha Schulze

Subjects
Computer science, Feature extraction, Sensory system, Chemotaxis, Neuroscience
Published
2015
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