Getting Into the Mind of a Worm—A Personal View* John G
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A Damage Sensor Associated with the Cuticle Coordinates Three Core Environmental Stress Responses in Caenorhabditis Elegans
HIGHLIGHTED ARTICLE | INVESTIGATION A Damage Sensor Associated with the Cuticle Coordinates Three Core Environmental Stress Responses in Caenorhabditis elegans William Dodd,*,1 Lanlan Tang,*,1 Jean-Christophe Lone,† Keon Wimberly,* Cheng-Wei Wu,* Claudia Consalvo,* Joni E. Wright,* Nathalie Pujol,†,2 and Keith P. Choe*,2 *Department of Biology, University of Florida, Gainesville, Florida 32611 and †Aix Marseille University, CNRS, INSERM, CIML, Marseille, France ORCID ID: 0000-0001-8889-3197 (N.P.) ABSTRACT Extracellular matrix barriers and inducible cytoprotective genes form successive lines of defense against chemical and microbial environmental stressors. The barrier in nematodes is a collagenous extracellular matrix called the cuticle. In Caenorhabditis elegans, disruption of some cuticle collagen genes activates osmolyte and antimicrobial response genes. Physical damage to the epidermis also activates antimicrobial responses. Here, we assayed the effect of knocking down genes required for cuticle and epidermal integrity on diverse cellular stress responses. We found that disruption of specific bands of collagen, called annular furrows, coactivates detoxification, hyperosmotic, and antimicrobial response genes, but not other stress responses. Disruption of other cuticle structures and epidermal integrity does not have the same effect. Several transcription factors act downstream of furrow loss. SKN-1/ Nrf and ELT-3/GATA are required for detoxification, SKN-1/Nrf is partially required for the osmolyte response, and STA-2/Stat and ELT- 3/GATA for antimicrobial gene expression. Our results are consistent with a cuticle-associated damage sensor that coordinates de- toxification, hyperosmotic, and antimicrobial responses through overlapping, but distinct, downstream signaling. KEYWORDS damage sensor; collagen; detoxification; osmotic stress; antimicrobial response XTRACELLULAR matrices (ECMs) are ubiquitous features Internal and epidermal tissues secrete ECMs as mechanical Eof animal tissues composed of secreted fibrous proteins support. -
A Transparent Window Into Biology: a Primer on Caenorhabditis Elegans* Ann K
A Transparent window into biology: A primer on Caenorhabditis elegans* Ann K. Corsi1§, Bruce Wightman2§, and Martin Chalfie3§ 1Biology Department, The Catholic University of America, Washington, DC 20064 2Biology Department, Muhlenberg College, Allentown, PA 18104 3Department of Biological Sciences, Columbia University, New York, NY 10027 Table of Contents 1. Introduction ............................................................................................................................2 2. C. elegans basics .....................................................................................................................4 2.1. Growth and maintenance ................................................................................................ 4 2.2. Sexual forms and their importance .................................................................................... 5 2.3. Life cycle ....................................................................................................................7 3. C. elegans genetics ...................................................................................................................8 4. Why choose C. elegans? ......................................................................................................... 10 5. C. elegans tissues ................................................................................................................... 11 5.1. Epidermis: a model for extracellular matrix production, wound healing, and cell fusion ............ 12 5.2. Muscles—controlling -
Web Resources for C. Elegans Studies* §
Web resources for C. elegans studies* § Raymond Lee , Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Table of Contents 1. Introduction ............................................................................................................................1 2. Portal and knowledge environment .............................................................................................. 2 2.1. WormBase ...................................................................................................................2 2.2. Caenorhabditis elegans WWW Server ..............................................................................3 3. Literature search ...................................................................................................................... 4 3.1. Textpresso ................................................................................................................... 4 3.2. NCBI PubMed ..............................................................................................................5 3.3. Caenorhabditis elegans WWW Server Worm Literature Index ............................................... 5 4. Gene function .........................................................................................................................6 4.1. WormBase Gene Summary ............................................................................................. 6 4.2. NCBI AceView ........................................................................................................... -
TGF-Β Signaling in C. Elegans * Tina L
TGF-β signaling in C. elegans * Tina L. Gumienny1 and Cathy Savage-Dunn2§ 1Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College Station, TX 77843 USA 2Department of Biology, Queens College, and the Graduate School and University Center, City University of New York, Flushing, NY 11367 USA Table of Contents 1. Overview ...............................................................................................................................2 2. DBL-1 pathway .......................................................................................................................4 2.1. Body size regulation ...................................................................................................... 5 2.2. Male tail development .................................................................................................... 6 2.3. Innate immunity ............................................................................................................ 6 2.4. Aging and longevity ...................................................................................................... 7 2.5. Mesodermal patterning ................................................................................................... 8 2.6. Chemosensation and neuronal function .............................................................................. 8 2.7. Ligand, receptors, and their modulators ............................................................................. 8 2.8. Intracellular -
Molecular Evolution Inferences from the C. Elegans Genome* Asher D
Molecular evolution inferences from the C. elegans genome* Asher D. Cutter§, Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada Table of Contents 1. Introduction ............................................................................................................................1 2. Mutation ................................................................................................................................2 3. Recombination ........................................................................................................................ 3 4. Natural Selection ..................................................................................................................... 4 5. Genetic Drift ...........................................................................................................................6 6. Population dynamics ................................................................................................................ 7 7. Summary ...............................................................................................................................7 8. Acknowledgements .................................................................................................................. 8 9. References ..............................................................................................................................8 Abstract An understanding of evolution at the molecular level requires the simultaneous -
The Biology of Strongyloides Spp.* Mark E
The biology of Strongyloides spp.* Mark E. Viney1§ and James B. Lok2 1School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK 2Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-6008, USA Table of Contents 1. Strongyloides is a genus of parasitic nematodes ............................................................................. 1 2. Strongyloides infection of humans ............................................................................................... 2 3. Strongyloides in the wild ...........................................................................................................2 4. Phylogeny, morphology and taxonomy ........................................................................................ 4 5. The life-cycle ..........................................................................................................................6 6. Sex determination and genetics of the life-cycle ............................................................................. 8 7. Controlling the life-cycle ........................................................................................................... 9 8. Maintaining the life-cycle ........................................................................................................ 10 9. The parasitic phase of the life-cycle ........................................................................................... 10 10. Life-cycle plasticity ............................................................................................................. -
Natural Variation and Population Genetics of Caenorhabditis Elegans* §
Natural variation and population genetics of Caenorhabditis elegans* § Antoine Barrière and Marie-Anne Félix , Institut Jacques Monod, CNRS - Universities of Paris, 75251 Paris cedex 05, France Table of Contents 1. Molecular polymorphisms and population genetics ......................................................................... 2 1.1. Low molecular diversity of C. elegans ...............................................................................2 1.2. Population structure and geographic differentiation .............................................................. 7 1.3. Comparison with C. briggsae and C. remanei .....................................................................8 1.4. Outcrossing versus selfing in C. elegans ............................................................................9 2. Phenotypic diversity ............................................................................................................... 11 2.1. Phenotypic change upon mutation accumulation ................................................................ 11 2.2. Polymorphic phenotypes ............................................................................................... 11 2.3. Genetic analysis of a natural phenotypic variation .............................................................. 14 3. References ............................................................................................................................ 16 Abstract C. elegans presents a low level of molecular diversity, which may be explained -
The C. Elegans Eggshell* Kathryn K
The C. elegans eggshell* Kathryn K. Stein1,2 and Andy Golden1,§ 1Laboratory of Biochemistry and Genetics, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA 2Translational Genomics Research Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA Table of Contents 1. Overview of the structure of the C. elegans eggshell ....................................................................... 2 2. Timeline for eggshell formation .................................................................................................. 3 3. Layer one: the vitelline layer ...................................................................................................... 4 4. Layer two: the chitin layer ......................................................................................................... 4 4.1. CHS-1 .........................................................................................................................5 4.2. GNA-2 ........................................................................................................................6 4.3. EGG-1, EGG-2 ............................................................................................................. 6 4.4. EGG-3, EGG-4, EGG-5 .................................................................................................. 6 4.5. SPE-11 ........................................................................................................................7 -
Wormbase: a Comprehensive Resource for Nematode Research Todd W
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2010 Wormbase: A comprehensive resource for nematode research Todd W. Harris Ontario Institute for Cancer Research Igor Antoshechkin California Institute of Technology Tamberlyn Bieri Washington University School of Medicine in St. Louis Darin Blasiar Washington University School of Medicine in St. Louis Juancarlos Chan California Institute of Technology See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Part of the Medicine and Health Sciences Commons Recommended Citation Harris, Todd W.; Antoshechkin, Igor; Bieri, Tamberlyn; Blasiar, Darin; Chan, Juancarlos; Chen, Wen J.; De La Cruz, Norie; Davis, Paul; Duesbury, Margaret; Fang, Ruihua; Fernandes, Jolene; Han, Michael; Kishore, Ranjana; Lee, Raymond; Muller, Hans-Michael; Nakamura, Cecilia; Ozersky, Philip; Petcherski, Andrei; Rangarajan, Arun; Rogers, Anthony; Schindelman, Gary; Schwarz, Erich M.; Tuli, Mary Ann; Van Auken, Kimberly; Wang, Daniel; Wang, Xiaodong; Williams, Gary; Yook, Karen; Durbin, Richard; Stein, Lincoln D.; Spieth, John; and Sternberg, Paul W., ,"Wormbase: A comprehensive resource for nematode research." Nucleic Acids Research.,. D463-D467. (2010). https://digitalcommons.wustl.edu/open_access_pubs/110 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Todd W. Harris, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Juancarlos Chan, Wen J. Chen, Norie De La Cruz, Paul Davis, Margaret Duesbury, Ruihua Fang, Jolene Fernandes, Michael Han, Ranjana Kishore, Raymond Lee, Hans-Michael Muller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. -
Genetic Suppression* §
Genetic suppression* § Jonathan Hodgkin , Genetics Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK Table of Contents 1. Introduction ............................................................................................................................2 2. Intragenic suppression by same site replacement ............................................................................ 2 3. Intragenic suppression by compensatory second site mutation .......................................................... 2 4. Intragenic suppression by altered splicing ..................................................................................... 2 5. Intragenic suppression of dominant mutations by loss-of-function in cis. ............................................2 6. Extragenic suppression — overview ............................................................................................ 3 7. Informational suppression — overview ........................................................................................ 4 8. Nonsense suppression ............................................................................................................... 4 9. Extragenic suppression by modified splicing ................................................................................. 5 10. Suppression by loss of NMD (Nonsense Mediated Decay) ............................................................. 6 11. Extragenic suppression by non-specific physiological effects ......................................................... -
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.