Biological Sciences
C Elegans
C. elegans is a species of roundworm commonly used as a model organism in biological research. It has a simple and well-defined anatomy, a short lifespan, and a fully sequenced genome, making it an ideal subject for studying various biological processes. Its transparency allows for easy observation of internal structures, and its genetic makeup shares similarities with higher organisms, making it a valuable tool for understanding fundamental biological principles.
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eBook - PDFNeurobehavioral Genetics
Methods and Applications, Second Edition
- Byron C. Jones, Pierre Mormede, Byron C. Jones, Pierre Mormede(Authors)
- 2006(Publication Date)
- CRC Press(Publisher)
First, we will briefly describe this animal model, which has become increasingly popular for molecular and cellular biology studies, and then we will present a few examples of behavioral studies that are conducted on this organism. We aim to show that this model provides paradigms for questions central to many behaviors, and that they can be addressed at a single cell/single gene resolution. 24.2 C. ELEGANS AS A MODEL ORGANISM 24.2.1 C. ELEGANS H AS A V ERY S IMPLE N ERVOUS S YSTEM The nematode Caenorhabditis elegans is a free-living round worm present in the soils of temperate climates (Wood, 1988; Riddle et al., 1997). For laboratory use, it 354 Neurobehavioral Genetics can be grown easily on petri dishes seeded with Escherichia coli (Figure 24.1). Its length is about 1 mm as an adult and it has 959 somatic cells. Among those, 302 of them are neurons, which can be divided into 116 classes on the basis of their morphology (Figure 24.2). With a laser beam, it is possible to destroy a given neuron in an anaesthetized animal to assess the involvement of this neuron in a behavior or a function. Moreover, the—almost invariant—connectivity of all neurons has been established by 3D reconstruction of serially sectioned animals. At the molecular level, the nervous system of C. elegans shares a common organization with the far-distant vertebrates: its main excitatory transmitter is FIGURE 24.1 C. elegans on a culture plate. Worms of various stages can be seen, including eggs, larvae and adults. Adults are approximately 1 mm long. FIGURE 24.2 The nervous system of C. elegans . Most or all neurons of C. elegans are visualized by expressing a gpc-2::GFP construct. Weakly, staining of muscle cells can be seen. Arrows indicate the ventral nerve cord, a triangle indicates staining in the anterior ganglia, an asterisk indicates the posterior ganglia.
eBook - PDFGenes in Development
Re-reading the Molecular Paradigm
- Eva M. Neumann-Held, Christoph Rehmann-Sutter, Eva M. Neumann-Held, Christoph Rehmann-Sutter, Barbara Herrnstein Smith, E. Roy Weintraub(Authors)
- 2006(Publication Date)
- Duke University Press Books(Publisher)
I EMPIRICAL APPROACHES 1 GENOME ANALYSIS AND DEVELOPMENTAL BIOLOGY The Nematode Caenorhabditis elegans as a Model System thomas r. bürglin A general and basic tenet of scientific research is to simplify a complex prob-lem to smaller, more tractable units that can be studied and unraveled. De-pending on the biological question, scientists choose particular organisms as model systems. Each model provides researchers with particular biological or experimental advantages that help them in their quest to understand fun-damental biological principles and problems. In 1963 Sydney Brenner wanted to proceed from bacterial and viral genetics to a more complex, multicellu-lar animal. He proposed studying a small nematode that he thought would be eminently suitable for investigating many aspects of cell and nervous sys-tem development. After careful deliberation he chose Caenorhabditis elegans , and with this model he succeeded in establishing a whole new research field. As a result, ‘‘founding father’’ Sydney Brenner and two other C. elegans re-searchers, John Sulston and Bob Horvitz, were awarded the Nobel Prize in Physiology or Medicine in 2002. John Sulston made key contributions to elu-cidating the C. elegans cell lineage as well as to its genome project, and Bob Horvitz contributed significantly to the understanding of programmed cell death. I became attracted to this model system because of its elegance and other advantages I will outline below. The little worm will serve here as an introduction to how researchers study genes and understand their function in the context of a living organism. This chapter will first introduce the advantages of the C. elegans model system (see also the key textbooks by Wood [1988] and Riddle et al. [1997]), and then will proceed to the C. elegans genome, where the principle of gene function via Thomas R. Bu ¨rglin proteins is introduced (for a key textbook on molecular biology, see Alberts et al. 2002).
eBook - ePubMovement Disorders
Genetics and Models
- Mark S. LeDoux(Author)
- 2014(Publication Date)
- Academic Press(Publisher)
Caenorhabditis elegans , toward the investigation of evolutionarily conserved functional relationships among organisms represents a rapid route toward a comprehensive understanding of cellular malfunction.6.1. Caenorhabditis elegans : Why the Worm?
Starting in the early 1960s, Sydney Brenner championed the establishment of the nematode C. elegans as a model system for the investigation of embryonic and neuronal development (Wood, 1988 ). Brenner’s vision was centered on the premise that the simplicity of C. elegans anatomy and genetics, coupled with an ease of culturing, manipulation, and rapid generation time (3 days from fertilized egg to adult), would render it experimentally accessible for discerning more-complex issues of development (Brenner, 1974 ). Notably, although males can result from rare chromosomal nondisjunction events, C. elegans is primarily found as a hermaphrodite. The ability of this animal to self-fertilize is especially advantageous for purposes of laboratory propagation and in designing genetic crosses. Literally hundreds of isogenic animals can be obtained from a single worm in the course of several days, making expansion of stocks simple. Moreover, these microscopic worms (∼1 mm as an adult) can be stored frozen, much like bacterial and yeast cultures, and revived to replenish stocks even after several years in storage.In late 1998, C. elegans ushered in the genomic era for metazoan species, as it became the first animal to have its complete genome sequence released (The C. elegans Sequencing Consortium, 1998). This milestone enabled rapid and comprehensive molecular analyses to be coupled to powerful traditional genetic resources within the context of a multicellular organism. These collectively augment existing and unique resources for this animal, such as a defined neuronal connectivity and fully mapped cell lineage (Bargmann, 1998
eBook - ePub- William Slikker Jr., Merle G. Paule, Cheng Wang, William Slikker, Jr.(Authors)
- 2018(Publication Date)
- Academic Press(Publisher)
9Historically the nematode was exploited for its short generation time, straight-forward Mendelian genetics, and simple anatomy. It possesses nerves, muscles, gut, gonad, and a cuticle. The adult is about a millimeter long, and in the laboratory feeds on bacteria either in liquid or, more commonly, on agar plates. Adults are either self-fertilizing XX hermaphrodites (which allows propagation of severely defective strains) or XO males (which allows mating and genetic manipulation). At any given temperature, wild-type development is invariant. At 20°C the wild-type animal has a 3-day generation time; each hermaphrodite can produce 300 isogenic offspring. The excellent genetics,2 superb catalogue of known neuronal/muscular mutations, well-defined behaviors, characterized cell lineage, and neural anatomy,1 contributed to its early success as a model organism. C. elegans is transparent, which allowed for the construction of its entire cell lineage, and also led to the productive use of fluorescent markers as reporters for gene expression.10 A wiring diagram of every synapse of the hermaphrodite’s 302 neurons is known, and a huge catalog of data has been shared online for decades. The advent of fluorescent markers for specific cells has only increased the importance of this transparency.10Two additional tools have greatly added to the utility of this model organism. The entire C. elegans genome was sequenced in 1998.11 When the human genome was eventually sequenced, it was somewhat surprising to discover that 60%–80% of the nematode genes have homologues in humans.11 , 12 This strongly supported the use of C. elegans as a model for mammalian development for a wide range of genetic studies. Second, RNA interference (RNAi), discovered in the nematode, was developed as a successful way to knockdown expression of essentially any gene in the organism.13 , 14 Coupled with the known sequence of the genome, an RNAi library has been constructed and made available to all laboratories working on C. elegans. Mutants, either classically generated or achieved via RNAi, can interrogate the function of almost every gene in the worm’s genome. This technique is quite straightforward in C. elegans
eBook - PDF- Edward J. Masoro, Steven N. Austad(Authors)
- 2011(Publication Date)
- Academic Press(Publisher)
Section II: Non-Mammalian Models Handbook of the Biology of Aging, Sixth Edition Copyright © 2006 by Academic Press. All rights of reproduction in any form reserved. 360 I. Introduction A. Caenorhabditis elegans as a Model System for the Analysis of Biological Function Genetic analysis of C. elegans was initiated by the epic paper of Sydney Brenner (Brenner, 1974) in which the entire genetic map of “the worm” was first pub-lished. This paper also set the “style” for C. elegans research and described about 30 years of work, much of it from the hands of the author himself. Similar semi-nal papers described the cell lineage of all 959 cells making up the soma and repro-ductive system (Kimble & Hirsh, 1979; Sulston & Horvitz, 1977), the systematic cloning of the genome (Coulson et al. , 1988), the entire DNA sequence ( C. ele-gans Sequencing Consortium, 1998), a description of a gene expression “map” using microarrays (Kim et al ., 2001), and an analysis of gene function using whole-genome RNAi libraries (Kamath & Ahringer, 2003). In little more than 30 years, this lowly round worm has become, arguably, the best genetic model system among metazoa, and certainly the best species in which to study the genetics of aging. Soon after the founding of the National Institute on Aging in 1974, a Request for Applications (RFA) was issued stating that “Applications for work on genetic analyses of aging in C. elegans . . . . are welcome.” This RFA was a harbinger of the future impact of this species on the understanding of the processes of aging, the subject of this chap-ter. Throughout its relatively brief history, the study of C. elegans has relied on cur-rent methodology in both molecular genet-ics and in computer sciences, the first allowing the breakthroughs and the second allowing the wide dissemination of Chapter 13 Dissecting the Processes of Aging Using the Nematode Caenorhabditis elegans Samuel T.
eBook - PDFParkinson's Disease
Genetics and Pathogenesis
- Ted M. Dawson(Author)
- 2007(Publication Date)
- CRC Press(Publisher)
311 Caenorhabditis elegans Models of Parkinson’s Disease Garry Wong Department of Neurobiology, A.I. Virtanen Institute and Department of Biochemistry, Kuopio University, Kuopio, Finland INTRODUCTION The use of Caenorhabditis elegans as an animal model has its historical roots in the laboratory of Sydney Brenner during the early 1960s. Together with members of his laboratory, which included John Sulston and Robert Horvitz, these pioneers found and exploited the many advantageous features of the nematode as a model system. Initially, the idea was to find a system suitable for studying the fields of develop-ment and neuroscience. The model needed to be simple enough to manipulate genetically, yet sufficiently complex to probe deep questions relevant to higher organisms. Later, a few features of the nematode, which now seem obvious in hind-sight, proved to be critical. First, the organism was transparent, which was essential to study cell-division, -proliferation, and -death within a living animal. Second, the organism had a reproductive cycle of three days, which allowed for extremely fast and convenient genetic analysis. Third, a point which is often overlooked by the sci-entific community, is that Sydney Brenner and his early colleagues encouraged a culture of sharing resources and information that has benefited not only the worm research community, but also has served as a model for many later, large scale sci-entific efforts, including the human genome sequencing project. These efforts culmi-nated in the Nobel prize being awarded to these three early pioneers. Their legacy, however, may be better signified by the enormous collection of worm mutants, clones, sequences, and techniques that are utilized and shared by the worm research community which will be described in the following section. CAENORHABDITIS ELEGANS GENETICS Genomics The entire C. elegans genome was sequenced and reported in 1998 (1).
eBook - PDF- J. Eric McDuffie(Author)
- 2018(Publication Date)
- IntechOpen(Publisher)
However, this organism lacks the ease of cultivation and powerful genetics of the model organism, C. elegans . The soil nematode , C. elegans , is an excellent model organism for neurotoxicology study of fungicides [ 31 ]. C. elegans is an important mesofaunal soil nematode that consumes bacteria and is pre-dated by fungi, other nematodes and a host of other soil organisms [ 32 ]. C. elegans is a free-living, non-parasitic nematode that grows from egg to adult in about 3.5 days at 20°C, with a lifespan of about 18 days at that temperature. The nematode is transparent, 1 mm in length as an adult and is easily grown on agar plates with small patches of Escherichia coli as food. Hermaphroditic with the possibility of sexual mating with a low frequency male phenotype, the nematodes each produce 300 progeny through self-fertilization and up to 1000 progeny if mated with a male. The genome has been fully sequenced and a number of laboratories have generated a rich variety of mutants, including strains that express green fluorescent protein under different promoters. The GFP strains allow researchers to examine particular cell types or tissues using fluorescence microscopy. While a simple organism with only 302 neurons and a total of 959 cells, C. elegans nonetheless exhibits numerous behaviors and sensory func -tions, including associative and non-associative learning. It uses all the major neurotransmit -ters found in other invertebrates and shares at least 60% genes with mammals. C. elegans can self-fertilize or reproduce sexually, making genetic-level studies straightforward. Its short life span, transparent body and ease of cultivation have made C. elegans a key model for neuro-toxicological study [ 33 ]. 3.1. C. elegans dopamine neurons Fungicides can have long-term effects on soil organisms, including nematodes [ 34 ].
eBook - PDFChromosomal Instability and Aging
Basic Science and Clinical Implications
- Fuki Hisama, Sherman M. Weissman, George M. Martin(Authors)
- 2003(Publication Date)
- CRC Press(Publisher)
20 Genetics of Aging in the Nematode Caenorhabditis elegans Philip S. Hartman Texas Christian University, Fort Worth, Texas, U.S.A. Naoaki Ishii Tokai University School of Medicine, Isehara, Kanagawa, Japan Thomas E. Johnson University of Colorado at Boulder, Boulder, Colorado, U.S.A. I. CAENORHABDITIS ELEGANS AS A MODEL SYSTEM FOR AGING RESEARCH Caenorhabditis elegans is a small nematode worm containing somewhat less than 1000 postmitotic, somatic cells at adulthood. Its invariant, mosaic pattern of de- velopment and self-fertilizing hermaphroditic life style have made it favorite of developmental biologists second only to Drosophila. Details on numerous aspects of its development and other aspects of current studies have been compiled in two books (1,2), and detailed methodologies can be found in the journal Methods in Cell Biology, Vol. 48 (3). Several online sources of information are available, including an informal newsletter, published by the C. elegans Stock Center (http://elegans.swmed.edu/), which also includes access to all nematode publica- tions (4654 at the time of this writing, including 146 cross referenced to aging). Numerous bioinformatics resources are available and can be accessed through the same URL or at http://www.wormbase.org/ and other sites. Biologists identified C. elegans as a good model for studying aging in the 1970s (reviewed in refs. 4–6). However, studies on aging were galvanized with the recognition that a lack of inbreeding depression and significant heritabil- ities makes it possible to identify genetic variants affecting the processes of 493 aging (7). Soon the first single-gene mutation (age-1) leading to longer-than- normal life span was identified (8) and subsequently mapped and shown to behave as a single gene (9). Mutations in age-1 are recessive to the wild type and dramatically lengthen life expectancy by an average of about 40% and maximum life span by about 70% (10).
eBook - ePub- Dr Richard Twyman(Author)
- 2023(Publication Date)
- Taylor & Francis(Publisher)
fruiting body from which spores are released. Unicellular developmental models are discussed in more detail in Section D.Model invertebrates
The two major invertebrate developmental models are the fruit fly Drosophilamelanogaster and the nematode worm Caenorhabditis elegans. Drosophila was chosen because of its early pivotal role in the study of genetics. Saturation mutagenesis screens are relatively straightforward, allowing mutants for any system of biological interest to be isolated. It has become established as a developmental model over the last 20 years through the identification and cataloging of many hundreds of developmentally important genes. Genetic manipulation in Drosophila is also a simple procedure, involving the injection of recombinant P-elements (Drosophila transposons; see Topic B3) into the egg. Early Drosophila development is described in Topics Fl and F2. The molecular basis of axis specification and patterning in Drosophila is the subject of Section H (also see Topics J5, L2 and L3).C. elegans is a remarkably simple organism, containing approximately 1000 somatic cells and a similar number of germ cells. Like Drosophila, C. elegans is amenable to genetic analysis and modification, and the embryos are transparent. Further advantages of C. elegans include the fact that adults can be stored as frozen stocks and recovered later by thawing, and that the species is hermaphrodite, so that one individual can seed an entire population. One remarkable feature of C. elegans is that the somatic cell lineage is invariant, i.e. every cell division and inductive interaction between cells is programmed and predictable. This has allowed the entire somatic cell lineage from egg to adult to be mapped out. There is also a complete wiring diagram of the C. elegans nervous system. C. elegans
eBook - PDFSystems Genetics
Linking Genotypes and Phenotypes
- Florian Markowetz, Michael Boutros(Authors)
- 2015(Publication Date)
- Cambridge University Press(Publisher)
elegans locomotive behavior’, Journal of the Association for Laboratory Automation 14, 269–276. White, J. G., Southgate, E., Thomson, J. N. & Brenner, S. (1986), ‘The structure of the ner- vous system of the nematode Caenorhabditis elegans’, Philosophical Transactions of the Royal Society B: Biological Sciences 314(1165), 1–340. Williams, P. L. & Dusenbery, D. B. (1990), ‘A promising indicator of neurobehavioral toxicity using the nematode Caenorhabditis elegans and computer tracking’, Toxicology and Industrial Health 6(3–4), 425–440. Yanik, M. F., Cinar, H., Cinar, H. N., Chisholm, A. D., Jin, Y. et al. (2004), ‘Neurosurgery: Functional regeneration after laser axotomy’, Nature 432(7019), 822. Yemini, E., Kerr, R. A. & Schafer, W. R. (2011a), ‘Illumination for worm tracking and behavioral imaging’, Cold Spring Harbor Protocols 2011(12), pdb.prot067009–pdb.prot067009. Yemini, E., Kerr, R. A. & Schafer, W. R. (2011b), ‘Preparation of samples for single-worm tracking’, Cold Spring Harbor Protocols 2011(12), pdb.prot066993–pdb.prot066993. Yook, K., Harris, T. W., Bieri, T., Cabunoc, A., Chan, J. et al. (2012), ‘WormBase 2012: More genomes, more data, new website’, Nucleic Acids Research 40, D735–741.
eBook - PDF- Peter Machamer, Rick Grush, Peter McLaughlin, Peter Machamer, Rick Grush, Peter McLaughlin, Rick Grush(Authors)
- 2017(Publication Date)
- University of Pittsburgh Press(Publisher)
(1994), and Thomas (1994) develop the details supporting these claims. The importance of animal models in behavioral genetics as it relates to neuroscience is underscored in a chapter on "Genes and Behavior" in the textbook Essentials of Neural Science and Behavior by Kandel et aI. (1995). This chapter, written by Greenspan et aI., summarizes much of the recent research in comparative behavioral genetics. They write that "Extensive efforts are being made to understand the connections between genes and behavior in four organisms: the nematode Caenorhabditis eiegans, the fruit fly Drosophila melanogaster, the lab- oratory mouse Mus musculus, and ourselves, Homo sapiens. Each has unique behavioral characteristics and each offers a different set of advantages and disadvantages for pursuing the study of genes and behavior" (1995, 556). In the remainder of this chapter, I discuss recent work involving these four organisms and the extrapolation issue, not only among the three model organisms on which I draw, but also to human beings. First, the Worm Caenorhabditis elegans is a tiny worm that has become the focus of a large number of research projects in many countries: projects that 202 Kenneth F. Schaffner examine its genetics, development, nervous system, and behavior. In connection with the latter two areas, several groups of investigators (among them the laboratories of Avery, Bargmann, Chalfie, Horvitz, Lockery, Rankin, and Thomas) have worked to tie together the be- havior of the organism and the underlying neural circuits and molecu- lar processes implemented in those circuits. (Two other recent papers describe the early to middle years of worm research, essentially the period 1970-84; see de Chadarevian 1998; Ankeny 2000.) Here I concentrate on work done mostly in the 1990s, but I also provide some relevant background.
eBook - PDF- Marty Shankland(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
I. C. elegans Neura l Developmen t 5 development in this animal is mostly mosaic, that is, the fate of most cells is based solely on their lineal history (by factors that are segregated in their precursors) rather than on environmental cues. This would seem to contrast with vertebrate development in which intercellular signalling is known to play a dominant role (see Chapter 11). However, a variety of cell ablation studies and other experiments, discussed in detail in this chapter, have revealed many examples of cell interactions that are critical to cell fate determination in the nematode. The invariant lineage is as much caused by highly reproducible cell interactions as by mosaic development. The position of each cell with respect to its neighbors is invariant; consequently, the positional cues and intercellular signals are invariant. The invariance of C Elegans development, rather than being unique, makes the nematode a useful experimental system in which to study how cell interactions specify cell fate. Considering the importance of cell interactions, the relative positions of cells in the developing animal become as important as their lineage histories. Neuronal precursors, when viewed in the context of the cell lineage, arise from divergent locations; however, when viewed anatomically, they occupy a common position in the animal. For example, the Pn.a cells that generate the postembryonic motor neurons sit evenly spaced along the anterior-posterior axis at the most ventral part of the animal. In fact, most neuronal precursor cells occupy the position of the ventral ectoderm. Anatomically, neuroblasts are segregated in the same manner as their counterparts in other animals are (see Hedgecock and Hall, 1990, for a discussion of comparative neurogen-esis). These unrelated neuroblasts then generate neurons via similar patterns of cell divisions or sublineages (see subsequent text).
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