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9 results on '"Stephen M. Plaza"'

1. Information flow, cell types and stereotypy in a full olfactory connectome

Author

Sridhar R. Jagannathan, Asa Barth-Maron, Marta Costa, Gerald M. Rubin, Feng Li, Alexandre Javier, Philipp Schlegel, Stephen M. Plaza, Nikolas Drummond, Tomke Stürner, Joseph Hsu, Laia Serratosa Capdevila, Imaan F.M. Tamimi, Elizabeth C. Marin, Gregory S.X.E. Jefferis, Alexander Shakeel Bates, Schlegel, Philipp [0000-0002-5633-1314], Bates, Alexander Shakeel [0000-0002-1195-0445], Stürner, Tomke [0000-0003-4054-0784], Jagannathan, Sridhar R [0000-0002-2078-1145], Marin, Elizabeth C [0000-0001-6333-0072], Li, Feng [0000-0002-6658-9175], Rubin, Gerald M [0000-0001-8762-8703], Plaza, Stephen M [0000-0001-7425-8555], Costa, Marta [0000-0001-5948-3092], Jefferis, Gregory SXE [0000-0002-0587-9355], Apollo - University of Cambridge Repository, and Jefferis, Gregory S X E [0000-0002-0587-9355]

Subjects
0301 basic medicine, Olfactory system, Property (programming), Datasets as Topic, neuroscience, 0302 clinical medicine, Biology (General), 0303 health sciences, D. melanogaster, General Neuroscience, General Medicine, Olfactory Pathways, 3. Good health, medicine.anatomical_structure, Drosophila melanogaster, Mushroom bodies, Connectome, Medicine, Drosophila, Female, Research Article, olfaction, Cell type, Connectomics, QH301-705.5, neuroanatomy, Science, Olfaction, Biology, stereotypy, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Interneurons, medicine, Animals, connectomics, 030304 developmental biology, General Immunology and Microbiology, biology.organism_classification, Stereotypy (non-human), 030104 developmental biology, nervous system, Antennal lobe, synapses, Neuroscience, 030217 neurology & neurosurgery, Neuroanatomy
Abstract

The hemibrain connectome (Scheffer et al., 2020) provides large scale connectivity and morphology information for the majority of the central brain of Drosophila melanogaster. Using this data set, we provide a complete description of the most complex olfactory system studied at synaptic resolution to date, covering all first, second and third-order neurons of the olfactory system associated with the antennal lobe and lateral horn (mushroom body neurons are described in a parallel paper, Li et al., 2020). We develop a generally applicable strategy to extract information flow and layered organisation from synaptic resolution connectome graphs, mapping olfactory input to descending interneurons. This identifies a range of motifs including highly lateralised circuits in the antennal lobe and patterns of convergence downstream of the mushroom body and lateral horn. We also leverage a second data set (FAFB, Zheng et al., 2018) to provide a first quantitative assessment of inter- versus intra-individual stereotypy. Complete reconstruction of select developmental lineages in two brains (three brain hemispheres) reveals striking similarity in neuronal morphology across brains for >170 cell types. Within and across brains, connectivity correlates with morphology. Notably, neurons of the same morphological type show similar connection variability within one brain as across brains; this property should enable a rigorous quantitative approach to cell typing.

Published
2021

2. Author response: Information flow, cell types and stereotypy in a full olfactory connectome

Author

Imaan F.M. Tamimi, Marta Costa, Asa Barth-Maron, Philipp Schlegel, Gregory S.X.E. Jefferis, Alexander Shakeel Bates, Laia Serratosa Capdevila, Elizabeth C. Marin, Joseph Hsu, Feng Li, Stephen M. Plaza, Sridhar R. Jagannathan, Alexandre Javier, Gerald M. Rubin, Nikolas Drummond, and Tomke Stürner

Subjects
Cell type, Stereotypy (non-human), Connectome, Information flow, Biology, Neuroscience
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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5. Comparisons between the ON- and OFF-edge motion pathways in the Drosophila brain

Author

Natasha Cheatham, Iris Talebi, Aya Shinomiya, C. Shan Xu, Claire Smith, Omotara Ogundeyi, David Peel, Kazunori Shinomiya, Shirley Lauchie, Erika Neace, Namra Ansari, Louis K. Scheffer, Roxanne Aniceto, Patricia K. Rivlin, Toufiq Parag, Zhiyuan Lu, Ian A. Meinertzhagen, Gary B. Huang, Aljoscha Nern, Christopher Ordish, Satoko Takemura, and Stephen M. Plaza

Subjects
Computer science, QH301-705.5, neuroanatomy, Science, Models, Neurological, Motion Perception, General Biochemistry, Genetics and Molecular Biology, Motion (physics), Synapse, medicine, motion detection, Image Processing, Computer-Assisted, Animals, Biology (General), Crosses, Genetic, Neurons, optic lobe, General Immunology and Microbiology, biology, electron microscopy, D. melanogaster, General Neuroscience, connectome, Homozygote, Optic Lobe, Nonmammalian, Brain, Motion detection, General Medicine, Dendrites, biology.organism_classification, Lobe, medicine.anatomical_structure, Drosophila melanogaster, Receptive field, Synapses, Connectome, Medicine, visual system, Female, Photoreceptor Cells, Invertebrate, Neuroscience, Neuroanatomy, Research Article
Abstract

Understanding the circuit mechanisms behind motion detection is a long-standing question in visual neuroscience. In Drosophila melanogaster, recently discovered synapse-level connectomes in the optic lobe, particularly in ON-pathway (T4) receptive-field circuits, in concert with physiological studies, suggest a motion model that is increasingly intricate when compared with the ubiquitous Hassenstein-Reichardt model. By contrast, our knowledge of OFF-pathway (T5) has been incomplete. Here, we present a conclusive and comprehensive connectome that, for the first time, integrates detailed connectivity information for inputs to both the T4 and T5 pathways in a single EM dataset covering the entire optic lobe. With novel reconstruction methods using automated synapse prediction suited to such a large connectome, we successfully corroborate previous findings in the T4 pathway and comprehensively identify inputs and receptive fields for T5. Although the two pathways are probably evolutionarily linked and exhibit many similarities, we uncover interesting differences and interactions that may underlie their distinct functional properties.

Published
2019

6. Author response: Comparisons between the ON- and OFF-edge motion pathways in the Drosophila brain

Author

Toufiq Parag, Claire Smith, C. Shan Xu, Roxanne Aniceto, David Peel, Shirley Lauchie, Aljoscha Nern, Zhiyuan Lu, Iris Talebi, Aya Shinomiya, Erika Neace, Namra Ansari, Louis K. Scheffer, Gary B. Huang, Natasha Cheatham, Ian A. Meinertzhagen, Christopher Ordish, Kazunori Shinomiya, Omotara Ogundeyi, Patricia K. Rivlin, Stephen M. Plaza, and Satoko Takemura

Subjects
Physics, biology, Motion (geometry), Drosophila (subgenus), Edge (geometry), biology.organism_classification, Neuroscience
Published
2018
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8. A connectome of a learning and memory center in the adult Drosophila brain

Author

Christopher Ordish, Toufiq Parag, Shin-ya Takemura, William T. Katz, Roxanne Aniceto, Shirley Lauchie, Stephen M. Plaza, Christopher Sigmund, C. Shan Xu, Satoko Takemura, Stuart Berg, Allan M. Wong, Aya Shinomiya, Donald J. Olbris, Louis K. Scheffer, Lei-Ann Chang, Lowell Umayam, Glenn C. Turner, Omotara Ogundeyi, Harald F. Hess, Ting Zhao, Toshihide Hige, Patricia K. Rivlin, Julie Tran, Zhiyuan Lu, Yoshinori Aso, Gary B. Huang, and Gerald M. Rubin

Subjects
0301 basic medicine, QH301-705.5, Science, En passant, Sensory system, Biology, General Biochemistry, Genetics and Molecular Biology, Synapse, EM reconstruction, 03 medical and health sciences, Memory, dopaminergic neuron, Connectome, Animals, Learning, Biology (General), Mushroom Bodies, D. melanogaster, General Immunology and Microbiology, General Neuroscience, Compartment (ship), Depolarization, General Medicine, memory recall, mushroom body, Associative learning, 030104 developmental biology, Mushroom bodies, Medicine, Drosophila, Neuroscience, Research Article
Abstract

Understanding memory formation, storage and retrieval requires knowledge of the underlying neuronal circuits. In Drosophila, the mushroom body (MB) is the major site of associative learning. We reconstructed the morphologies and synaptic connections of all 983 neurons within the three functional units, or compartments, that compose the adult MB’s α lobe, using a dataset of isotropic 8 nm voxels collected by focused ion-beam milling scanning electron microscopy. We found that Kenyon cells (KCs), whose sparse activity encodes sensory information, each make multiple en passant synapses to MB output neurons (MBONs) in each compartment. Some MBONs have inputs from all KCs, while others differentially sample sensory modalities. Only 6% of KC>MBON synapses receive a direct synapse from a dopaminergic neuron (DAN). We identified two unanticipated classes of synapses, KC>DAN and DAN>MBON. DAN activation produces a slow depolarization of the MBON in these DAN>MBON synapses and can weaken memory recall. DOI: http://dx.doi.org/10.7554/eLife.26975.001

Published
2017
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9. Author response: A connectome of a learning and memory center in the adult Drosophila brain

Author

Toshihide Hige, Christopher Sigmund, Toufiq Parag, Stephen M. Plaza, Aya Shinomiya, C. Shan Xu, Patricia K. Rivlin, Julie Tran, Roxanne Aniceto, Omotara Ogundeyi, Christopher Ordish, Lei-Ann Chang, Harald F. Hess, Louis K. Scheffer, Glenn C. Turner, Lowell Umayam, Gary B. Huang, Gerald M. Rubin, Satoko Takemura, Stuart Berg, Shirley Lauchie, Donald J. Olbris, Zhiyuan Lu, Yoshinori Aso, Shin-ya Takemura, William T. Katz, Allan M. Wong, and Ting Zhao

Subjects
biology, Connectome, Center (algebra and category theory), Drosophila (subgenus), biology.organism_classification, Neuroscience
Published
2017
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