REVIEW Endocrine Signaling in Caenorhabditis Elegans Controls
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A Review and Appraisal of the DNA Damage Theory of Ageing
Mutation Research 728 (2011) 12–22 Contents lists available at ScienceDirect Mutation Research/Reviews in Mutation Research jo urnal homepage: www.elsevier.com/locate/reviewsmr Co mmunity address: www.elsevier.com/locate/mutres Review A review and appraisal of the DNA damage theory of ageing a,b a, Alex A. Freitas , Joa˜o Pedro de Magalha˜es * a Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK b School of Computing and Centre for BioMedical Informatics, University of Kent, Canterbury, CT2 7NF, UK A R T I C L E I N F O A B S T R A C T Article history: Given the central role of DNA in life, and how ageing can be seen as the gradual and irreversible Received 10 February 2011 breakdown of living systems, the idea that damage to the DNA is the crucial cause of ageing remains a Received in revised form 2 May 2011 powerful one. DNA damage and mutations of different types clearly accumulate with age in mammalian Accepted 3 May 2011 tissues. Human progeroid syndromes resulting in what appears to be accelerated ageing have been Available online 10 May 2011 linked to defects in DNA repair or processing, suggesting that elevated levels of DNA damage can accelerate physiological decline and the development of age-related diseases not limited to cancer. Keywords: Higher DNA damage may trigger cellular signalling pathways, such as apoptosis, that result in a faster Ageing depletion of stem cells, which in turn contributes to accelerated ageing. -
Network Access to the Genome and Biology of Caenorhabditis Elegans
82–86 Nucleic Acids Research, 2001, Vol. 29, No. 1 © 2001 Oxford University Press WormBase: network access to the genome and biology of Caenorhabditis elegans Lincoln Stein*, Paul Sternberg1, Richard Durbin2, Jean Thierry-Mieg3 and John Spieth4 Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA, 1Howard Hughes Medical Institute and California Institute of Technology, Pasadena, CA, USA, 2The Sanger Centre, Hinxton, UK, 3National Center for Biotechnology Information, Bethesda, MD, USA and 4Genome Sequencing Center, Washington University, St Louis, MO, USA Received September 18, 2000; Accepted October 4, 2000 ABSTRACT and a page that shows the locus in the context of the physical map. WormBase (http://www.wormbase.org) is a web-based WormBase uses HTML linking to represent the relationships resource for the Caenorhabditis elegans genome and between objects. For example, a segment of genomic sequence its biology. It builds upon the existing ACeDB data- object is linked with the several predicted gene objects base of the C.elegans genome by providing data contained within it, and each predicted gene is linked to its curation services, a significantly expanded range of conceptual protein translation. subject areas and a user-friendly front end. The major components of the resource are described below. The C.elegans genome DESCRIPTION WormBase contains the ‘essentially complete’ genome of Caenorhabditis elegans (informally known as ‘the worm’) is a C.elegans, which now stands at 99.3 Mb of finished DNA small, soil-dwelling nematode that is widely used as a model interrupted by approximately 25 small gaps. In addition, the system for studies of metazoan biology (1). -
Lower Organisms As Alternatives for Toxicity Testing in Rodents with a Focus on Ceanorhabditis Elegans and the Zebrafish (Danio Rerio)
Report 340720003/2009 L.T.M. van der Ven Lower organisms as alternatives for toxicity testing in rodents With a focus on Ceanorhabditis elegans and the zebrafish (Danio rerio) RIVM report 340720003/2009 Lower organisms as alternatives for toxicity testing in rodents With a focus on Caenorhabditis elegans and the zebrafish (Danio rerio) L.T.M. van der Ven Contact: L.T.M. van der Ven Laboratory for Health Protection Research [email protected] This investigation has been performed by order and for the account of the Ministry of Health, Welfare and Sport, within the framework of V/340720 Alternatives for animal testing RIVM, P.O. Box 1, 3720 BA Bilthoven, the Netherlands Tel +31 30 274 91 11 www.rivm.nl © RIVM 2009 Parts of this publication may be reproduced, provided acknowledgement is given to the 'National Institute for Public Health and the Environment', along with the title and year of publication. RIVM report 340720003 2 Abstract Lower organisms as alternatives for toxicity testing in rodents With a focus on Caenorhabiditis elegans and the zebrafish (Danio rerio) The nematode C. elegans and the zebrafish embryo are promising alternative test models for assessment of toxic effects in rodents. Tests with these lower organisms may have a good predictive power for effects in humans and are thus complementary to tests with in vitro models (cell cultures). However, all described tests need further validation. This is the outcome of a literature survey, commissioned by the ministry of Health, Welfare and Sport of the Netherlands. The survey is part of the policy to reduce, refine and replace animal testing (3R policy). -
“This Is Getting Really Old . . . ” the Genetics of Aging
“This is getting really old . ” The Genetics of Aging Prof. Mike Kuchka Department of Biological Sciences OBJECTIVES • Explain how mutations in genes can increase lifespan in various organisms (METHUSELAH gene of Drosophila) • Relate chromosome length with aging (TELOMERE SHORTENING) • Understand how alteration of intracelluar signaling pathway impacts aging (INSULIN-LIKE GROWTH FACTOR) • Relate caloric restriction with aging (Role of SIRTUIN proteins) • Describe accelerated aging disorders in humans (WERNER’S SYNDROME, HUTCHINSON-GILFORD PROGERIA) Aging – the decline in survival and fecundity with advancing age, caused by the accumulation of damage to macromolecules, intracellular organelles, cells, tissues, organs. SOME INTRODUCTORY POINTS • Natural selection does not select for genes that cause aging or determine lifespan. Rather, aging occurs as a result of the pleiotropic effects of genes that specify other processes [Christensen et al. (2006)]. • Genes that influence longevity are involved in stress response and nutrient sensing, generally, intracellular signaling pathways. • In the past century, mean life expectancy in Western countries increased from ~50 to 75 – 80. • Twin studies (human) suggest that 25% of variation in lifespan is caused by genetic differences. • Manipulation of >100 genes in experimental animal models increases longevity. • Most of these genes are also present in the human genome. • Gene manipulations that increase longevity also postpone age-related diseases. Nematode Worm (C. elegans) as a Model Experimental Organism For the Study of Aging OLD YOUNG MUTANT 2 weeks old 2 days old 2 weeks old From: Hopkin, K. (2004) Scientific American, 14: 12 – 17. Mouse (Mus musculus) as a Model Experimental Organism For the Study of Aging From: Hampton, K. -
Calorie Restriction and Sirtuins Revisited
Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Calorie restriction and sirtuins revisited Leonard Guarente1 Department of Biology, Glenn Laboratory for the Science of Aging, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Calorie or dietary restriction (CR) has attracted attention Toward the resolution of discordances because it is the oldest and most robust way to extend rodent life span. The idea that the nutrient sensors, termed Sirtuins and aging sirtuins, might mediate effects of CR was proposed 13 years Perhaps the greatest challenge to the idea that sirtuins ago and has been challenged in the intervening years. This mediate effects of CR was a study describing the failure to review addresses these challenges and draws from a great observe extension of life span in worms or flies transgenic body of new data in the sirtuin field that shows a systematic for the corresponding SIR2 orthologs after controlling for redirection of mammalian physiology in response to diet by genetic background (Burnett et al. 2011). These findings sirtuins. The prospects for drugs that can deliver at least contradicted other, earlier studies that showed extension a subset of the benefits of CR seems very real. of life span in transgenic worms (Tissenbaum and Guarente 2001; Viswanathan et al. 2005; Berdichevsky et al. 2006) A review published previously in Genes & Development and flies (Rogina and Helfand 2004; Wood et al. 2004; (Guarente 2000) stated the hypothesis that calorie re- Bauer et al. 2009). In fact, a subset of these earlier studies striction (CR) slowed aging and the accompanying de- did control for genetic background (e.g., Bauer et al. -
“This Is Getting Really Old . . . ” the Genetics of Aging
“This is getting really old . ” The Genetics of Aging Prof. Mike Kuchka Department of Biological Sciences OBJECTIVES • Explain how mutations in genes can increase lifespan in various organisms (METHUSELAH gene of Drosophila) • Relate chromosome length with aging (TELOMERE SHORTENING) • Understand how alteration of intracellular signaling pathway impacts aging (INSULIN-LIKE GROWTH FACTOR) • Relate caloric restriction with aging (Role of SIRTUIN proteins) • Describe accelerated aging disorders in humans (WERNER’S SYNDROME, HUTCHINSON-GILFORD PROGERIA) Aging – the decline in survival and fecundity with advancing age, caused by the accumulation of damage to macromolecules, intracellular organelles, cells, tissues, organs. SOME INTRODUCTORY POINTS • Natural selection does not select for genes that cause aging or determine lifespan. Rather, aging occurs as a result of the pleiotropic effects of genes that specify other processes [Christensen et al. (2006)]. • Genes that influence longevity are involved in stress response and nutrient sensing, generally, intracellular signaling pathways. • In the past century, mean life expectancy in Western countries increased from ~50 to 75 – 80. • Twin studies (human) suggest that 25% of variation in lifespan is caused by genetic differences. • Manipulation of >100 genes in experimental animal models increases longevity. • Most of these genes are also present in the human genome. • Gene manipulations that increase longevity also postpone age-related diseases. Nematode Worm (C. elegans) as a Model Experimental Organism For the Study of Aging OLD YOUNG MUTANT 2 weeks old 2 days old 2 weeks old From: Hopkin, K. (2004) Scientific American, 14: 12 – 17. Mouse (Mus musculus) as a Model Experimental Organism For the Study of Aging From: Hampton, K. -
Study Questions 2 (Through Arthropod 1)
Study Questions 2 (through Arthropod 1) 1. Name the three embryonic germ layers found in all triploblastic animals. 2. What is a coelom? Which Phyla that we have discussed thus far have a true coelom? 3. Define cephalization. What is the name of the most primitive Phylum we have discussed that displays cephalization? 4. How is the digestive system of a Turbellarian similar to the digestive system of a Hydrozoan? Describe one way that they are different. 5. What is the function of flame cells? 6. How is the nervous system of a flatworm (Phylum Platyhelminthes) different from that of a Cnidarian? 7. Which two classes of flatworms are entirely parasitic? Describe some adaptations for parasitism that are found in these classes. 8. What are some of the major differences between Nemertine worms (Phylum Nemertea) and flatworms (Phylum Platyhelminthes)? In what major way are these two phyla similar? 9. What is a pseudocoelom? What are some of the functions of the pseudocoelom in Phylum Nematoda? 10. Nematodes have move in a characteristic whip like fashion. What aspect of their anatomy is responsible for this type of movement? 11. Describe the general structure of the Nematode nervous system. How is it different from the nervous system of Platyhelminthes? 12. What is unique about Nematode muscle cells? 13. What is unique about the way Nematode sperm move? 14. Many Nematodes are parasitic. Describe some adaptations that Nematodes have for parasitism. 15. What characteristics of the Nematode Caenorhabditis elegans make such an important model organism for the study of developmental genetics? 16. List two functions of the Rotifer corona. -
Genome and Transcriptome of the Regeneration- Competent Flatworm, Macrostomum Lignano
Genome and transcriptome of the regeneration- competent flatworm, Macrostomum lignano Kaja Wasika,1, James Gurtowskia,1, Xin Zhoua,b, Olivia Mendivil Ramosa, M. Joaquina Delása,c, Giorgia Battistonia,c, Osama El Demerdasha, Ilaria Falciatoria,c, Dita B. Vizosod, Andrew D. Smithe, Peter Ladurnerf, Lukas Schärerd, W. Richard McCombiea, Gregory J. Hannona,c,2, and Michael Schatza,2 aWatson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; bMolecular and Cellular Biology Graduate Program, Stony Brook University, NY 11794; cCancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; dDepartment of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland; eDepartment of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089; and fDepartment of Evolutionary Biology, Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria Contributed by Gregory J. Hannon, August 23, 2015 (sent for review June 25, 2015; reviewed by Ian Korf and Robert E. Steele) The free-living flatworm, Macrostomum lignano has an impressive of all cells (15), and have a very high proliferation rate (16, 17). Of regenerative capacity. Following injury, it can regenerate almost M. lignano neoblasts, 89% enter S-phase every 24 h (18). This high an entirely new organism because of the presence of an abundant mitotic activity results in a continuous stream of progenitors, somatic stem cell population, the neoblasts. This set of unique replacing tissues that are likely devoid of long-lasting, differentiated properties makes many flatworms attractive organisms for study- cell types (18). This makes M. -
Longevity, Genes, and Aging: a View Provided by a Genetic Model System1
Experimental Gerontology, Vol. 34, No. 1, pp. 1–6, 1999 Copyright © 1999 Elsevier Science Inc. Printed in the USA. All rights reserved 0531-5565/99 $–see front matter PII S0531-5565(98)00053-9 LONGEVITY, GENES, AND AGING: A VIEW PROVIDED BY A GENETIC MODEL SYSTEM1 1 S. MICHAL JAZWINSKI Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, Box P7-2, 1901 Perdido Street, New Orleans, Louisiana 70112 Abstract—The genetic analysis of aging in the yeast Saccharomyces cerevisiae has revealed the importance of metabolic capacity, resistance to stress, integrity of gene regulation, and genetic stability for longevity. A balance between these life maintenance processes is sustained by the RAS2 gene, which channels cellular resources among them. This gene cooperates with mitochondria and PHB1 in metabolic adjustments important for longevity. It also modulates stress responses. Transcriptional silencing of heterochromatic regions of the genome is lost during aging, suggesting that gene dysregulation accompanies the aging process. There is evidence that this age change plays a causal role. Aging possesses features of a nonlinear process, and it is likely that application of nonlinear system methodology to aging will be productive. © 1999 Elsevier Science Inc. All rights reserved. Key words: metabolism, stress responses, gene dysregulation, nonlinear system INTRODUCTION IF WE WERE to design an organism, we would endow it with sufficient lifetime metabolic capacity, stress resistance, integrity of gene regulation, and genetic stability. Given a limit to the resources available, we would need to strike a balance between these processes and reproduc- tion. Genetic analysis of the aging process has confirmed the soundness of these engineering principles (Jazwinski, 1996). -
Biology of the Caenorhabditis Elegans Germline Stem Cell System
| WORMBOOK CELL FATE, SIGNALING, AND DEVELOPMENT Biology of the Caenorhabditis elegans Germline Stem Cell System E. Jane Albert Hubbard*,1 and Tim Schedl†,1 *Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, † New York 10016 and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110 ORCID IDs: 0000-0001-5893-7232 (E.J.A.H.); 0000-0003-2148-2996 (T.S.) ABSTRACT Stem cell systems regulate tissue development and maintenance. The germline stem cell system is essential for animal reproduction, controlling both the timing and number of progeny through its influence on gamete production. In this review, we first draw general comparisons to stem cell systems in other organisms, and then present our current understanding of the germline stem cell system in Caenorhabditis elegans. In contrast to stereotypic somatic development and cell number stasis of adult somatic cells in C. elegans, the germline stem cell system has a variable division pattern, and the system differs between larval development, early adult peak reproduction and age-related decline. We discuss the cell and developmental biology of the stem cell system and the Notch regulated genetic network that controls the key decision between the stem cell fate and meiotic development, as it occurs under optimal laboratory conditions in adult and larval stages. We then discuss alterations of the stem cell system in response to environ- mental perturbations and aging. A recurring distinction is between processes that control stem cell fate and those that control cell cycle regulation. C. elegans is a powerful model for understanding germline stem cells and stem cell biology. -
A Model for Evolutionary Ecology of Disease: the Case for Caenorhabditis Nematodes and Their Natural Parasites
Journal of Nematology 49(4):357–372. 2017. Ó The Society of Nematologists 2017. A Model for Evolutionary Ecology of Disease: The Case for Caenorhabditis Nematodes and Their Natural Parasites AMANDA K. GIBSON AND LEVI T. M ORRAN Abstract: Many of the outstanding questions in disease ecology and evolution call for combining observation of natural host– parasite populations with experimental dissection of interactions in the field and the laboratory. The ‘‘rewilding’’ of model systems holds great promise for this endeavor. Here, we highlight the potential for development of the nematode Caenorhabditis elegans and its close relatives as a model for the study of disease ecology and evolution. This powerful laboratory model was disassociated from its natural habitat in the 1960s. Today, studies are uncovering that lost natural history, with several natural parasites described since 2008. Studies of these natural Caenorhabditis–parasite interactions can reap the benefits of the vast array of experimental and genetic tools developed for this laboratory model. In this review, we introduce the natural parasites of C. elegans characterized thus far and discuss resources available to study them, including experimental (co)evolution, cryopreservation, behavioral assays, and genomic tools. Throughout, we present avenues of research that are interesting and feasible to address with caenorhabditid nematodes and their natural parasites, ranging from the maintenance of outcrossing to the community dynamics of host-associated microbes. In combining natural relevance with the experimental power of a laboratory supermodel, these fledgling host–parasite systems can take on fundamental questions in evolutionary ecology of disease. Key words: bacteria, Caenorhabditis, coevolution, evolution and ecology of infectious disease, experimental evolution, fungi, host–parasite interactions, immunology, microbiome, microsporidia, virus. -
S41467-018-05712-5.Pdf
ARTICLE DOI: 10.1038/s41467-018-05712-5 OPEN Biology and genome of a newly discovered sibling species of Caenorhabditis elegans Natsumi Kanzaki 1,8, Isheng J. Tsai 2, Ryusei Tanaka3, Vicky L. Hunt3, Dang Liu 2, Kenji Tsuyama 4, Yasunobu Maeda3, Satoshi Namai4, Ryohei Kumagai4, Alan Tracey5, Nancy Holroyd5, Stephen R. Doyle 5, Gavin C. Woodruff1,9, Kazunori Murase3, Hiromi Kitazume3, Cynthia Chai6, Allison Akagi6, Oishika Panda 7, Huei-Mien Ke2, Frank C. Schroeder7, John Wang2, Matthew Berriman 5, Paul W. Sternberg 6, Asako Sugimoto 4 & Taisei Kikuchi 3 1234567890():,; A ‘sibling’ species of the model organism Caenorhabditis elegans has long been sought for use in comparative analyses that would enable deep evolutionary interpretations of biological phenomena. Here, we describe the first sibling species of C. elegans, C. inopinata n. sp., isolated from fig syconia in Okinawa, Japan. We investigate the morphology, developmental processes and behaviour of C. inopinata, which differ significantly from those of C. elegans. The 123-Mb C. inopinata genome was sequenced and assembled into six nuclear chromo- somes, allowing delineation of Caenorhabditis genome evolution and revealing unique char- acteristics, such as highly expanded transposable elements that might have contributed to the genome evolution of C. inopinata. In addition, C. inopinata exhibits massive gene losses in chemoreceptor gene families, which could be correlated with its limited habitat area. We have developed genetic and molecular techniques for C. inopinata; thus C. inopinata provides an exciting new platform for comparative evolutionary studies. 1 Forestry and Forest Products Research Institute, Tsukuba 305-8687, Japan. 2 Biodiversity Research Center, Academia Sinica, Taipei city 11529, Taiwan.