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Bioenergetics Unbelievable
HISTORICAL PERSPECTIVES Bioenergetics Unbelievable ... ... but true! MARS - The easiest Data Analysis for Microplate Readers. Key features that the MARS software can do: Standard curve calculation wizard Linear, 4-parameter, cubic-spline, segmental curve fits Enzyme kinetics - Michaelis-Menten, Lineweaver-Burk, Scatchard Automatic DNA / RNA concentration determination 3D well scanning for cell-based assays Delta F% calculation for HTRF® Z’ calculation User-defined formula generator FDA 21 CFR Part 11 compliant Overlay plot of esterase catalysed pNPA Multi-user software license included reactions at different concentrations. Find our microplate readers on www.bmglabtech.com FLUOstar PHERAstar FS NOVOstar NEPHELOstar Stacker HTRF is a registered trademark of Cisbio International. The Journal of Biological Chemistry TABLE OF CONTENTS 2010 HISTORICAL PERSPECTIVES ON BIOENERGETICS PROLOGUE REFLECTIONS H1 JBC Historical Perspectives: Bioenergetics. Nicole Kresge, Robert H13 A Research Journey with ATP Synthase. Paul D. Boyer D. Simoni, and Robert L. Hill H30 Happily at Work. Henry Lardy CLASSICS H41 Keilin, Cytochrome, and the Respiratory Chain. E. C. Slater H2 Polyribonucleotide Synthesis and Bacterial Amino Acid Uptake: the Work of Leon A. Heppel H48 Reminiscences of Leon A. Heppel. Leon A. Heppel H5 Unraveling the Enzymology of Oxidative Phosphorylation: the Work of Efraim Racker H8 Ion Transport in the Sarcoplasmic Reticulum: the Work of David H. MacLennan H10 ATP Synthesis and the Binding Change Mechanism: the Work of Paul D. Boyer JOURNAL OF BIOLOGICAL CHEMISTRY i PROLOGUE This paper is available online at www.jbc.org © 2010 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in the U.S.A. JBC Historical Perspectives: Bioenergetics* Nicole Kresge, Robert D. -
An Error Detection and Correction Framework for Connectomics
An Error Detection and Correction Framework for Connectomics Jonathan Zung Ignacio Tartavull∗ Kisuk Leey Princeton University Princeton University MIT [email protected] [email protected] [email protected] H. Sebastian Seung Princeton University [email protected] Abstract We define and study error detection and correction tasks that are useful for 3D reconstruction of neurons from electron microscopic imagery, and for image seg- mentation more generally. Both tasks take as input the raw image and a binary mask representing a candidate object. For the error detection task, the desired output is a map of split and merge errors in the object. For the error correction task, the desired output is the true object. We call this object mask pruning, because the candidate object mask is assumed to be a superset of the true object. We train multiscale 3D convolutional networks to perform both tasks. We find that the error-detecting net can achieve high accuracy. The accuracy of the error-correcting net is enhanced if its input object mask is “advice” (union of erroneous objects) from the error-detecting net. 1 Introduction While neuronal circuits can be reconstructed from volumetric electron microscopic imagery, the process has historically [39] and even recently [37] been highly laborious. One of the most time- consuming reconstruction tasks is the tracing of the brain’s “wires,” or neuronal branches. This task is an example of instance segmentation, and can be automated through computer detection of the boundaries between neurons. Convolutional networks were first applied to neuronal boundary detection a decade ago [14, 38]. Since then convolutional nets have become the standard approach, arXiv:1708.02599v2 [cs.CV] 3 Dec 2017 and the accuracy of boundary detection has become impressively high [40, 3, 21, 9]. -
The Neural Circuit for Touch Sensitivity in Caenorhabditis Elegans'
0270.6474/85/0504-0956$02.0’3/0 The Journal of Neuroscience Copyright 0 Society for Neuroscience Vol. 5. No. 4, pp. 9X-964 Printed in U.S.A. April 1985 The Neural Circuit for Touch Sensitivity in Caenorhabditis elegans’ MARTIN CHALFIE,*$*, JOHN E. SULSTON,* JOHN G. WHITE,* EILEEN SOUTHGATE,* J. NICHOL THOMSON,+ AND SYDNEY BRENNERS * Deoartment of Biolooical Sciences, Columbia University, New York, New York 10027 and $ Medical Research Council Laboratory of Molecular Biology, Hiis Road, Cambridge CB2 2QH, En&and Abstract In this paper, we use an alternative approach to analyze the function of specific cells and synapses in that part of the C. elegans The neural pathways for touch-induced movement in Cae- nervous system that mediates touch-induced movement. The recon- norhabditis ekgans contain six touch receptors, five pairs of structions are used to identify cells that are likely to be involved in interneurons, and 69 motor neurons. The synaptic relation- the touch reflex. The role of these cells is then tested by killing them ships among these cells have been deduced from recon- with a laser microbeam (Sulston and White, 1980) and observing structions from serial section electron micrographs, and the the effects of cell loss on the touch response. This method has roles of the cells were assessed by examining the behavior enabled us to confirm the functional importance of certain synapses of animals after selective killing of precursors of the cells by seen in the electron microscope and to generate a plausible model laser microsurgery. This analysis revealed that there are two of the touch reflex circuit. -
General Developments 1944-1986
Chapter 3 General Developments 1944-1986 3.1 Introduction 3.2 Administrative Developments 3.3 Legal Status of the Society 3.4 General Post-War Planning 3.5 Biological Council 3.6 Anniversary Meetings 3.7 General Pattern of Ordinary Meetings 3.8 Proceedings, Agenda Papers, Bulletin 3.9 Travel Funds 3.10 Medals and Named Lectures 3.1 1 Fellowships and Scholarships 3.12 Awards Committees 3.13 The Harden Conferences 3.14 Honorary Membership 3.15 The Society’s Nobel Laureates 3.16 A Royal Charter - To Be or Not To Be? 3.17 The Chemical Society Library 3.18 Archives and the Science Museum 3.19 The Society’s Logo 3.1 Introduction As with many aspects of our national life, the years 1944- 1985 can be considered a watershed in the development of the Biochemical Society. The end of the Second World War left the Country exhausted but a spirit of optimism was in the air. Thanks to the efforts of the Honorary Officers, the Society successfully survived the War and the mood of optimism within the Society was fully justified and has lasted well after the hopes of a brave new world have long faded in other areas of human activity. Biochemistry rapidly developed into a thriving discipline and this has been maintained throughout the post-War period, although in recent years the pace has slackened somewhat mainly owing to the parsimony of recent Government policy on support of Science. This blossoming of Biochemistry in the post-War years has been one of the great scientific successes of all time and in the DEVELOPMENT 1944- 1986 37 U.K.the simultaneous expansion of the Biochemical Society has been equally impressive. -
Applications of the Free-Living Nematode, Caenorhabditis Elegans: a Review
Journal of Zoological Research Volume 3, Issue 4, 2019, PP 19-30 ISSN 2637-5575 Applications of the Free-Living Nematode, Caenorhabditis Elegans: A Review Marwa I. Saad El-Din* Assistant Professor, Zoology Department, Faculty of Science, Suez Canal University, Egypt *Corresponding Author: Marwa I. Saad El-Din, Assistant Professor, Zoology Department, Faculty of Science, Suez Canal University, Egypt. Email: [email protected]. ABSTRACT The free-living nematode, Caenorhabditis elegans, has been suggested as an excellent model organism in ecotoxicological studies. It is a saprophytic nematode species that inhabits soil and leaf-litter environments in many parts of the world. It has emerged to be an important experimental model in a broad range of areas including neuroscience, developmental biology, molecular biology, genetics, and biomedical science. Characteristics of this animal model that have contributed to its success include its genetic manipulability, invariant and fully described developmental program, well-characterized genome, ease of culture and maintenance, short and prolific life cycle, and small and transparent body. These features have led to an increasing use of C. elegans for environmental toxicology and ecotoxicology studies since the late 1990s. Although generally considered a soil organism, it lives in the interstitial water between soil particles and can be easily cultured in aquatic medium within the laboratory. It has been successfully used to study toxicity of a broad range of environmental toxicants using both lethal and sub lethal endpoints including behavior, growth and reproduction and feeding. In this work we review the choice, use and applications of this worm as an experimental organism for biological and biomedical researches that began in the 1960s. -
SYDNEY BRENNER Salk Institute, 100010 N
NATURE’S GIFT TO SCIENCE Nobel Lecture, December 8, 2002 by SYDNEY BRENNER Salk Institute, 100010 N. Torrey Pines Road, La Jolla, California, USA, and King’s College, Cambridge, England. The title of my lecture is “Nature’s gift to Science.” It is not a lecture about one scientific journal paying respects to another, but about how the great di- versity of the living world can both inspire and serve innovation in biological research. Current ideas of the uses of Model Organisms spring from the ex- emplars of the past and choosing the right organism for one’s research is as important as finding the right problems to work on. In all of my research these two decisions have been closely intertwined. Without doubt the fourth winner of the Nobel prize this year is Caenohabditis elegans; it deserves all of the honour but, of course, it will not be able to share the monetary award. I intend to tell you a little about the early work on the nematode to put it into an intellectual perspective. It bridges, both in time and concept, the biol- ogy we practice today and the biology that was initiated some fifty years ago with the revolutionary discovery of the double-helical structure of DNA by Watson and Crick. My colleagues who follow will tell you more about the worm and also recount their incisive research on the cell lineage and on the genetic control of all death. To begin with, I can do no better than to quote from the paper I published in 1974 (1). -
Research Organizations and Major Discoveries in Twentieth-Century Science: a Case Study of Excellence in Biomedical Research Hollingsworth, J
www.ssoar.info Research organizations and major discoveries in twentieth-century science: a case study of excellence in biomedical research Hollingsworth, J. Rogers Veröffentlichungsversion / Published Version Arbeitspapier / working paper Zur Verfügung gestellt in Kooperation mit / provided in cooperation with: SSG Sozialwissenschaften, USB Köln Empfohlene Zitierung / Suggested Citation: Hollingsworth, J. R. (2002). Research organizations and major discoveries in twentieth-century science: a case study of excellence in biomedical research. (Papers / Wissenschaftszentrum Berlin für Sozialforschung, 02-003). Berlin: Wissenschaftszentrum Berlin für Sozialforschung gGmbH. https://nbn-resolving.org/urn:nbn:de:0168-ssoar-112976 Nutzungsbedingungen: Terms of use: Dieser Text wird unter einer Deposit-Lizenz (Keine This document is made available under Deposit Licence (No Weiterverbreitung - keine Bearbeitung) zur Verfügung gestellt. Redistribution - no modifications). We grant a non-exclusive, non- Gewährt wird ein nicht exklusives, nicht übertragbares, transferable, individual and limited right to using this document. persönliches und beschränktes Recht auf Nutzung dieses This document is solely intended for your personal, non- Dokuments. Dieses Dokument ist ausschließlich für commercial use. All of the copies of this documents must retain den persönlichen, nicht-kommerziellen Gebrauch bestimmt. all copyright information and other information regarding legal Auf sämtlichen Kopien dieses Dokuments müssen alle protection. You are not allowed -
{PDF} Charles Darwin, the Copley Medal, and the Rise of Naturalism
CHARLES DARWIN, THE COPLEY MEDAL, AND THE RISE OF NATURALISM 1862-1864 1ST EDITION PDF, EPUB, EBOOK Marsha Driscoll | 9780205723171 | | | | | Charles Darwin, the Copley Medal, and the Rise of Naturalism 1862-1864 1st edition PDF Book In recognition of his distinguished work in the development of the quantum theory of atomic structure. In recognition of his distinguished studies of tissue transplantation and immunological tolerance. Dunn, Dann Siems, and B. Alessandro Volta. Tomas Lindahl. Thomas Henry Huxley. Andrew Huxley. Adam Sedgwick. Ways and Means, Science and Society Picture Library. John Smeaton. Each year the award alternates between the physical and biological sciences. On account of his curious Experiments and Discoveries concerning the different refrangibility of the Rays of Light, communicated to the Society. David Keilin. For his seminal work on embryonic stem cells in mice, which revolutionised the field of genetics. Derek Barton. This game is set in and involves debates within the Royal Society on whether Darwin should receive the Copley Medal, the equivalent of the Nobel Prize in its day. Frank Fenner. For his Paper communicated this present year, containing his Experiments relating to Fixed Air. Read and download Log in through your school or library. In recognition of his pioneering work on the structure of muscle and on the molecular mechanisms of muscle contraction, providing solutions to one of the great problems in physiology. James Cook. Wilhelm Eduard Weber. For his investigations on the morphology and histology of vertebrate and invertebrate animals, and for his services to biological science in general during many past years. Retrieved John Ellis. -
A Cellular and Regulatory Map of the Cholinergic Nervous System of C
TOOLS AND RESOURCES A cellular and regulatory map of the cholinergic nervous system of C. elegans Laura Pereira1,2,3*, Paschalis Kratsios1,2,3†, Esther Serrano-Saiz1,2,3†, Hila Sheftel4, Avi E Mayo4, David H Hall5, John G White6, Brigitte LeBoeuf7, L Rene Garcia7,8, Uri Alon4, Oliver Hobert1,2,3* 1Department of Biological Sciences, Columbia University, New York, United States; 2Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States; 3Howard Hughes Medical Institute, Columbia University, New York, United States; 4Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; 5Department of Neuroscience, Albert Einstein College of Medicine, New York, United States; 6MRC Laboratory of Molecular Biology, Cambridge, United Kingdom; 7Department of Biology, Texas A&M University, College Station, United States; 8Howard Hughes Medical Institute, Texas A&M University, College Station, United States Abstract Nervous system maps are of critical importance for understanding how nervous systems develop and function. We systematically map here all cholinergic neuron types in the male and hermaphrodite C. elegans nervous system. We find that acetylcholine (ACh) is the most broadly used neurotransmitter and we analyze its usage relative to other neurotransmitters within the context of the entire connectome and within specific network motifs embedded in the connectome. We reveal several dynamic aspects of cholinergic neurotransmitter identity, including *For correspondence: pereira. a sexually dimorphic glutamatergic to cholinergic neurotransmitter switch in a sex-shared [email protected] (LP); or38@ interneuron. An expression pattern analysis of ACh-gated anion channels furthermore suggests that columbia.edu (OH) ACh may also operate very broadly as an inhibitory neurotransmitter. -
C. Elegans Multi-Dendritic Sensory Neurons: Morphology and Function
YMCNE-02539; No of Pages 10 Molecular and Cellular Neuroscience xxx (2010) xxx–xxx Contents lists available at ScienceDirect Molecular and Cellular Neuroscience journal homepage: www.elsevier.com/locate/ymcne C. elegans multi-dendritic sensory neurons: Morphology and function Adi Albeg a, Cody J. Smith b, Marios Chatzigeorgiou c, Dror G. Feitelson d, David H. Hall e, William R. Schafer c, David M. Miller III b, Millet Treinin a,⁎ a Department of Medical Neurobiology, Institute for Medical Research – Israel-Canada, Hebrew University – Hadassah Medical School, Jerusalem 91120, Israel b Department of Cell and Developmental Biology and Program in Neuroscience, Vanderbilt University, Nashville, TN 37232-8240, USA c Cell Biology Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge UK d Department of Computer Science, Hebrew University, Jerusalem 91904, Israel e Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA article info abstract Article history: PVD and FLP sensory neurons envelope the body of the C. elegans adult with a highly branched network of thin Received 3 June 2010 sensory processes. Both PVD and FLP neurons are mechanosensors. PVD is known to mediate the response to Revised 2 October 2010 high threshold mechanical stimuli. Thus PVD and FLP neurons are similar in both morphology and function to Accepted 13 October 2010 mammalian nociceptors. To better understand the function of these neurons we generated strains lacking Available online xxxx them. Behavioral analysis shows that PVD and FLP regulate movement under normal growth conditions, as animals lacking these neurons demonstrate higher dwelling behavior. In addition, PVD—whose thin branches Keywords: — C. -
Getting Into the Mind of a Worm—A Personal View* John G
Getting into the mind of a worm—a personal view* John G. White§ Laboratory of Optical and Computational Instrumentation, University of Wisconsin, Madison WI 53706, USA Table of Contents 1. References ............................................................................................................................ 10 2. Author biography ................................................................................................................... 10 Ever since I can remember, I liked to take things to bits to see how they work. My parents thought that this trait was not to be encouraged when applied to living animals, so diverted my attention to things mechanical and electronic. I was given the use of a shed in the garden. This became my beloved workshop where I made bombs, rockets, and radios. After one of my bombs caused a local scare, my activities were restricted to electronics. On finishing school, I worked in a factory for a time and then progressed onto a couple of other jobs in industrial development labs on the basis of my self-taught skills in electronics. Eventually, I got a job as an electronics technician in the Medical Research Council's labs in Mill Hill (MRC National Institute for Medical Research, Mill Hill, London, UK). It was here that I got my first (ethical) exposure to biology. I developed a voltage clamp apparatus for neurophysiological research, a project that piqued my curiosity about nervous systems. I also developed a computer system for displaying 3D images of molecular structures. The MRC encouraged and supported me to study for a physics degree at Brunel University. However, after I graduated in 1969, there seemed no good career path where I could pursue my developing interest in computers in the lab where I was working, so I sought and obtained a job offer from industry. -
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Nonlinear Dynamics on a Novel Neural Topology a Thesis Submitted in Partial Fulfilment O
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Nonlinear Dynamics on a Novel Neural Topology A thesis submitted in partial fulfilment of the requirements For the degree of Master of Science in Physics By Alan Perstin May 2019 The thesis of Alan Perstin is approved: __________________________________ ___________ Dr. Eric Collins Date __________________________________ ___________ Dr. Tyler Luchko Date __________________________________ ___________ Dr. Yohannes Shiferaw, Chair Date California State University, Northridge ii Table of Contents Signature Page ii List of Figures v Abstract vii Chapter 1: Introduction 1 Chapter 2: Preliminary Biomedical Physics 5 2.1: Preliminaries Concerning Neurophysiology 5 2.2: Preliminaries Concerning Neural Diagnostics 11 2.3: Motivating the Island Network 15 Chapter 3: An Introduction to Graph Theory 20 3.1: Preliminaries Concerning Graphs 20 3.2: Graph Topology 21 3.2.1: The Adjacency Matrix 21 3.2.2: Degree Distribution and Edge Density 23 3.2.3: Average Shortest Path Length 25 3.2.4: Clustering Coefficient 27 3.2.5: Small-Worldness 29 3.2.6: Measures of Centrality 30 3.2.7: Hubs 34 3.2.8: Communities 37 3.2.9: Modularity 39 3.3: Topologies of Common Graphs 43 3.3.1: Random Networks 44 3.3.2: Small-World Networks 46 3.3.3: Scale-Free Networks 49 3.3.4: Closing Remarks 50 Chapter 4: Topology of the Island Network 52 4.1: Generating the Island Network 52 4.1.1: Properties of the Island Network 53 4.2: General Metrics 60 4.2.1 Degree Distribution and Edge Density 61 4.2.2 Small-Worldness 61 4.2.3 Hubs 63 4.2.4