(Bobby) Kasthuri Neuroscientist, Argonne National Laboratory, and Assistant Professor of Neurobiology, University of Chicago
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Conservation and Divergence of Related Neuronal Lineages in The
RESEARCH ARTICLE Conservation and divergence of related neuronal lineages in the Drosophila central brain Ying-Jou Lee, Ching-Po Yang, Rosa L Miyares, Yu-Fen Huang, Yisheng He, Qingzhong Ren, Hui-Min Chen, Takashi Kawase, Masayoshi Ito, Hideo Otsuna, Ken Sugino, Yoshi Aso, Kei Ito, Tzumin Lee* Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States Abstract Wiring a complex brain requires many neurons with intricate cell specificity, generated by a limited number of neural stem cells. Drosophila central brain lineages are a predetermined series of neurons, born in a specific order. To understand how lineage identity translates to neuron morphology, we mapped 18 Drosophila central brain lineages. While we found large aggregate differences between lineages, we also discovered shared patterns of morphological diversification. Lineage identity plus Notch-mediated sister fate govern primary neuron trajectories, whereas temporal fate diversifies terminal elaborations. Further, morphological neuron types may arise repeatedly, interspersed with other types. Despite the complexity, related lineages produce similar neuron types in comparable temporal patterns. Different stem cells even yield two identical series of dopaminergic neuron types, but with unrelated sister neurons. Together, these phenomena suggest that straightforward rules drive incredible neuronal complexity, and that large changes in morphology can result from relatively simple fating mechanisms. *For correspondence: Introduction [email protected] In order to understand how the genome encodes behavior, we need to study the developmental mechanisms that build and wire complex centers in the brain. The fruit fly is an ideal model system Competing interests: The to research these mechanisms. The Drosophila field has extensive genetic tools. -
The Creation of Neuroscience
The Creation of Neuroscience The Society for Neuroscience and the Quest for Disciplinary Unity 1969-1995 Introduction rom the molecular biology of a single neuron to the breathtakingly complex circuitry of the entire human nervous system, our understanding of the brain and how it works has undergone radical F changes over the past century. These advances have brought us tantalizingly closer to genu- inely mechanistic and scientifically rigorous explanations of how the brain’s roughly 100 billion neurons, interacting through trillions of synaptic connections, function both as single units and as larger ensem- bles. The professional field of neuroscience, in keeping pace with these important scientific develop- ments, has dramatically reshaped the organization of biological sciences across the globe over the last 50 years. Much like physics during its dominant era in the 1950s and 1960s, neuroscience has become the leading scientific discipline with regard to funding, numbers of scientists, and numbers of trainees. Furthermore, neuroscience as fact, explanation, and myth has just as dramatically redrawn our cultural landscape and redefined how Western popular culture understands who we are as individuals. In the 1950s, especially in the United States, Freud and his successors stood at the center of all cultural expla- nations for psychological suffering. In the new millennium, we perceive such suffering as erupting no longer from a repressed unconscious but, instead, from a pathophysiology rooted in and caused by brain abnormalities and dysfunctions. Indeed, the normal as well as the pathological have become thoroughly neurobiological in the last several decades. In the process, entirely new vistas have opened up in fields ranging from neuroeconomics and neurophilosophy to consumer products, as exemplified by an entire line of soft drinks advertised as offering “neuro” benefits. -
BRAIN Neuroethics Working Group Meeting
Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Neuroethics Working Group (NEWG) Meeting January 26th, 2021 On January 26th, 2021, the National Institutes of Health (NIH) Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative Neuroethics Working Group (NEWG) met virtually to discuss emerging ethics themes in the BRAIN portfolio and potential future workshop topics, and revisited neuroethics themes in the BRAIN 2.0 reports. In opening remarks, John Ngai, PhD, Director of the NIH BRAIN Initiative, emphasized the importance of continuing to work towards equity, in general and in the neuroethics space. He also reminded participants of the joint session with the Multi-Council Working Group (MCWG) and NEWG, which took place the following day. Next, Saskia Hendriks, MD, PhD, Faculty in the NIH Bioethics Department and National Institute of Neurological Disorders and Stroke (NINDS) Neuroethics Consultant, presented key findings from an analysis on emerging neuroethical considerations in BRAIN grants awarded during fiscal year 2020. Dr. Hendriks summarized 12 themes identified by the analysis, which fell into two broad groups of potential ethical challenges: conducting research ethically; and the implications of research, tools, and technologies on individuals, groups, and society. The NEWG valued these findings, recognizing that the themes were consistent with concurrent discussions of neuroethics priorities for BRAIN. Participants also considered increasing funding opportunity outreach efforts to neuroscientists interested in partnering with neuroethicists. Further, the group acknowledged the need to raise awareness about the value of integrating neuroethics into neuroscience research, potentially by hosting a workshop on identifying ways to facilitate this integration. Henry (Hank) T. Greely, JD, Director of Law and Biosciences at Stanford University and co-chair of the NEWG, led a discussion on potential future NEWG workshop topics for the next phase of the NIH BRAIN Initiative. -
Obama Administration Proposes Over $434 Million in Funding for the BRAIN Initiative
Obama Administration Proposes Over $434 Million in Funding for the BRAIN Initiative “Last year, I launched the BRAIN Initiative to help unlock the mysteries of the brain, to improve our treatment of conditions like Alzheimer’s and autism and to deepen our understanding of how we think, learn and remember. I’m pleased to announce new steps that my Administration is taking to support this critical research, and I’m heartened to see so many private, philanthropic, and academic institutions joining this effort.” - President Barack Obama September 2014 Since its launch in April 2013, the President’s BRAIN Initiative® - Brain Research through Advancing Innovative Neurotechnologies – has grown to include investments from five Federal agencies: the Defense Advanced Research Projects Agency (DARPA), the National Institutes of Health (NIH), the National Science Foundation (NSF), Intelligence Advanced Research Projects Activity (IARPA), and the Food and Drug Administration (FDA). Federal agencies are supporting the initiative by investing in promising research projects aimed at revolutionizing our understanding of the human brain, developing novel technologies, and supporting further research and development in neurotechnology. The President’s 2017 Budget also proposes funding for the Department of Energy (DOE) to join DARPA, NIH, NSF, IARPA, and FDA in advancing the goals of the BRAIN Initiative. Major foundations, private research institutions, and companies including the Howard Hughes Medical Institute, Allen Institute for Brain Science, the Kavli Foundation, the Simons Foundation, GE, GlaxoSmithKline, as well as patient advocacy organizations and universities, have committed over $500 million to the BRAIN Initiative. There are many opportunities for others across sectors to play a role in this historic initiative through new and expanded commitments to advance the BRAIN Initiative. -
Spiking Allows Neurons to Estimate Their Causal Effect
bioRxiv preprint doi: https://doi.org/10.1101/253351; this version posted January 25, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Spiking allows neurons to estimate their causal effect Benjamin James Lansdell1,+ and Konrad Paul Kording1 1Department of Bioengineering, University of Pennsylvania, PA, USA [email protected] Learning aims at causing better performance and the typical gradient descent learning is an approximate causal estimator. However real neurons spike, making their gradients undefined. Interestingly, a popular technique in economics, regression discontinuity design, estimates causal effects using such discontinuities. Here we show how the spiking threshold can reveal the influence of a neuron's activity on the performance, indicating a deep link between simple learning rules and economics-style causal inference. Learning is typically conceptualized as changing a neuron's properties to cause better performance or improve the reward R. This is a problem of causality: to learn, a neuron needs to estimate its causal influence on reward, βi. The typical solution linearizes the problem and leads to popular gradient descent- based (GD) approaches of the form βGD = @R . However gradient descent is just one possible approximation i @hi to the estimation of causal influences. Focusing on the underlying causality problem promises new ways of understanding learning. Gradient descent is problematic as a model for biological learning for two reasons. First, real neurons spike, as opposed to units in artificial neural networks (ANNs), and their rates are usually quite slow so that the discreteness of their output matters (e.g. -
One Page BRAIN Initiative Overview 2018
® The BRAIN Initiative Over the past 25 years, the burden of At a glance... neurological disorders has increased sub- stantially. This increase, combined with the Launched in 2013, the NIH BRAIN Initia- growing burden of mental and substance tive is revealing how the brain works, by use disorders, reinforces the need for new developing and applying tools to precise- ways to intervene and deepen our ly map and observe brain circuits. st knowledge of the brain. The 21 Century Cures Act provides NIH Not enough is known about the billions of BRAIN Initiative funding through 2026. brain cells—that communicate via trillions NIH has invested over $950 million in the of synapses to make up the circuitry—that BRAIN Initiative, supporting over 550 enable us to perceive, think, feel, and act. new awards. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN)® Ten NIH Institutes and Centers partici- Initiativewww.braininitiative.org ( ) sup- pate in the NIH BRAIN Initiative. ports research to develop and use extra- The BRAIN Initiative Alliance communi- ordinary new technologies that will revolu- cates BRAIN Initiative activities of Federal tionize our understanding of the brain. agencies and private organizations. 12-Year Scientific Vision • Seven priority areas outline the Initiative: • The BRAIN Multi-Council Working Group (MCWG) helps NIH to track the Initiative and assists with Discovering diversity: Identify different brain informing Advisory Councils of the Institutes and cell types and determine their roles in health Centers that contribute to the NIH BRAIN Initiative. and disease. • The BRAIN Neuroethics Working Group (NEWG) Maps at multiple scales: Generate circuit considers ethical implications arising from the diagrams that vary in resolution from synapses development and use of BRAIN neurotechnologies to the whole brain. -
UNDERSTANDING the BRAIN (Utb) $143,930,000 +$37,490,000 / 35.2%
UNDERSTANDING THE BRAIN (UtB) $143,930,000 +$37,490,000 / 35.2% Overview Understanding the Brain (UtB) is a multi-year effort that continues the previously titled “Cognitive Science and Neuroscience” activity and that includes NSF’s participation in the Administration’s Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. For over three decades, NSF has supported fundamental brain research from molecules to cognition and behavior, and enabled technology development, through many disciplinary programs spread across the Foundation. In 2012, Congress encouraged NSF to create a cross-foundation activity in Cognitive Science and Neuroscience, and also encouraged the White House to form an Interagency Working Group on Neuroscience (IWGN) under the National Science and Technology Council, which is co-chaired by NSF. In FY 2013, the President announced the multi-agency BRAIN Initiative, with NSF as one of the lead participating agencies. The Understanding the Brain activity draws together and consolidates NSF’s ongoing activities in Cognitive Science and Neuroscience and the BRAIN Initiative. With UtB, NSF aims to leverage its existing investments and foster greater collaboration among these research and technology disciplines to accelerate fundamental discoveries in neuroscience, cognitive science, and neuroengineering. Understanding the brain is one of the grand scientific challenges at the intersection of the physical, life, behavioral, and engineering sciences. The National Research Council report, “Research at the Intersection of the Physical and Life Sciences” (2010), identified “Understanding the Brain” as one of the top five grand challenges for research that will significantly benefit society. The National Academy of Engineering has also recognized “Reverse-Engineering the Brain” as a Grand Challenge for Engineering (2008). -
Data Mining in Genomics, Metagenomics and Connectomics
Csaba Kerepesi DATA MINING IN GENOMICS, METAGENOMICS AND CONNECTOMICS PhD Thesis Supervisor: Dr. Vince Grolmusz Department of Computer Science E¨otv¨osLor´andUniversity, Hungary PhD School of Computer Science E¨otv¨osLor´andUniversity, Hungary Dr. Erzs´ebet Csuhaj-Varj´u PhD Program of Information Systems Dr. Andr´as Bencz´ur Budapest, 2017 Acknowledgements I would like to thank my supervisor Dr. Vince Grolmusz for his tireless support with which he started my scientific career. I am very grateful to the PhD School of Computer Science and the Faculty of Informatics, ELTE for their inexhaustible support. I would like to thank my co-authors for their precious work and I also would like to thank all my colleagues, who helped me anything in my re- searches. Finally, I would like to thank my family for their everlasting support. 2 Contents 1 Introduction 6 2 Data Mining in Genomics and Metagenomics 14 2.1 AmphoraNet: The Webserver Implementation of the AM- PHORA2 Metagenomic Workflow Suite . 14 2.1.1 Introduction . 14 2.1.2 Results and Discussion . 15 2.2 Visual Analysis of the Quantitative Composition of Metage- nomic Communities: the AmphoraVizu Webserver . 17 2.2.1 Introduction . 17 2.2.2 Results and Discussion . 19 2.3 Evaluating the Quantitative Capabilities of Metagenomic Analysis Software . 21 2.3.1 Introduction . 21 2.3.2 Results and discussion . 22 2.3.3 Methods . 25 2.3.4 Availability . 29 2.4 The \Giant Virus Finder" Discovers an Abundance of Giant Viruses in the Antarctic Dry Valleys . 30 2.4.1 Introduction . 30 3 2.4.2 Results and discussion . -
Polygenic Evidence and Overlapped Brain Functional Connectivities For
Sun et al. Translational Psychiatry (2020) 10:252 https://doi.org/10.1038/s41398-020-00941-z Translational Psychiatry ARTICLE Open Access Polygenic evidence and overlapped brain functional connectivities for the association between chronic pain and sleep disturbance Jie Sun 1,2,3,WeiYan2,Xing-NanZhang2, Xiao Lin2,HuiLi2,Yi-MiaoGong2,Xi-MeiZhu2, Yong-Bo Zheng2, Xiang-Yang Guo3,Yun-DongMa2,Zeng-YiLiu2,LinLiu2,Jia-HongGao4, Michael V. Vitiello 5, Su-Hua Chang 2,6, Xiao-Guang Liu 1,7 and Lin Lu2,6 Abstract Chronic pain and sleep disturbance are highly comorbid disorders, which leads to barriers to treatment and significant healthcare costs. Understanding the underlying genetic and neural mechanisms of the interplay between sleep disturbance and chronic pain is likely to lead to better treatment. In this study, we combined 1206 participants with phenotype data, resting-state functional magnetic resonance imaging (rfMRI) data and genotype data from the Human Connectome Project and two large sample size genome-wide association studies (GWASs) summary data from published studies to identify the genetic and neural bases for the association between pain and sleep disturbance. Pittsburgh sleep quality index (PSQI) score was used for sleep disturbance, pain intensity was measured by Pain Intensity Survey. The result showed chronic pain was significantly correlated with sleep disturbance (r = 0.171, p-value < 0.001). Their genetic correlation was rg = 0.598 using linkage disequilibrium (LD) score regression analysis. Polygenic score (PGS) association analysis showed PGS of chronic pain was significantly associated with sleep and vice versa. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Nine shared functional connectivity (FCs) were identified involving prefrontal cortex, temporal cortex, precentral/ postcentral cortex, anterior cingulate cortex, fusiform gyrus and hippocampus. -
Certificate for Approving the Dissertation
MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Kevin J. Rutherford Candidate for the Degree: Doctor of Philosophy Director (Jason Palmeri) Reader (Michele Simmons) Reader (Heidi McKee) Reader (Kate Ronald) Graduate School Representative (Bo Brinkman) ABSTRACT PACK YOUR THINGS AND GO: BRINGING OBJECTS TO THE FORE IN RHETORIC AND COMPOSITION by Kevin J. Rutherford This dissertation project focuses on object-oriented rhetoric (OOR), a perspective that questions the traditional notions of rhetorical action as solely a human province. The project makes three major, interrelated claims: that OOR provides a unique and productive methodology to examine the inclusion of the non-human in rhetorical study; that to some extent, rhetoric has always been interested in the way nonhuman objects interact with humans; and that these claims have profound implications for our activities as teachers and scholars. Chapter one situates OOR within current scholarship in composition and rhetoric, arguing that it can serve as a useful methodology for the field despite rhetoric’s traditional focus on epistemology and human symbolic action. Chapter two examines rhetorical history to demonstrate that a view of rhetoric that includes nonhuman actors is not new, but has often been marginalized. Chapter three examines two videogames as sites of theory and practice for object-oriented rhetoric, specifically focusing on a sense of metaphor to understand the experience of nonhuman rhetors. Chapter four interrogates the network surrounding a review aggregation website to argue that, while some nonhumans may be unhelpful rhetorical collaborators, OOR can assist us in improving relationships with them. -
Glia and Neurons Glia and Neurons Objective: Role of Glia in Nervous System Agenda: 1
Applied Neuroscience Columbia Science Honors Program Spring 2017 Glia and Neurons Glia and Neurons Objective: Role of Glia in Nervous System Agenda: 1. Glia • Guest Lecture by Dr. Jennifer Ziegenfuss 2. Machine Learning • Applications in Neuroscience Connectomics A connectome is a comprehensive map of neural connections in the brain (wiring diagram). • Fails to illustrate how neurons behave in real-time (neural dynamics) • Fails to show how a behavior is generated • Fails to account for glia A Tiny Piece of the Connectome Serial EM Reconstruction of Axonal Inputs (various colors) onto a section of apical dendrite (grey) of a pyramidal neuron in mouse cerebral cortex. Arrows mark functional synapses. Lichtman Lab (Harvard) Scaling up efforts to map neural connections is unlikely to deliver the promised benefits such as understanding: • how the brain produces memories • Perception • Consciousness • Treatments for epilepsy, depression, and schizophrenia While glia have been neglected in the quest to understand neuronal signaling, they can sense neuronal activity and control it. Are Glia the Genius Cells? Structure-Function Divide in Brain The function of a neural network is critically dependent upon its interconnections. Only C. elegans has a complete connectome. In neuroscience: • many common diseases and disorders have no known histological trace • debates how many cell types there are • questionable plan to image whole volumes by EM • complexity of structure How is the brain’s function related to its complex structure? Worm Connectome Dots are individual neurons and lines represent axons. C. elegans Caenorhabditis elegans (C. elegans) is a transparent nematode commonly used in neuroscience research. They have a simple nervous system: 302 neurons and 7000 synapses. -
A Critical Look at Connectomics
EDITORIAL A critical look at connectomics There is a public perception that connectomics will translate directly into insights for disease. It is essential that scientists and funding institutions avoid misrepresentation and accurately communicate the scope of their work. onnectomes are generating interest and excitement, both among nervous system, dubbed the classic connectome because it is currently neuroscientists and the public. This September, the first grants the only wiring diagram for an animal’s entire nervous system at the level Cunder the Human Connectome Project, totaling $40 million of the synapse. Although major neurobiological insights have been made over 5 years, were awarded by the US National Institutes of Health using C. elegans and its known connectivity and genome, there are still (NIH). In the public arena, striking, colorful pictures of human brains many questions remaining that can only be answered by hypothesis-driven have accompanied claims that imply that understanding the complete experiments. For example, we still don’t completely understand the process connectivity of the human brain’s billions of neurons by a trillion synapses of axon regeneration, relevant to spinal cord injury in humans, in this is not only possible, but that this will also directly translate into insights comparatively simple system. Thus, a connectome, at any resolution, is for neurological and psychiatric disorders. Even a press release from only one of several complementary tools necessary to understand nervous the NIH touted that the Human Connectome Project would map the system disease and injury. wiring diagram of the entire living human brain and would link these There are substantial efforts aimed at generating connectomes for circuits to the full spectrum of brain function in health and disease.