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[
Methods Cell Biol,
1995]
Genetic balancers are genetic constructs or chromosomal rearrangements that allow lethal or sterile mutations to be stably maintained in heterozygotes. In this chapter we use the term balancer primarily to refer to chromosomal duplications or rearrangements that suppress crossing over. In addition, we define lethal as any mutation that blocks survival or reproduction. Phenotypes associated with lethal mutations in Caenorhabditis elegans range from egg or larval lethality to adult sterility and maternal effect lethality, and can include conditional effects such as temperature sensitivity. The number of essential genes in C. elegans (those identified by lethal mutations) may range as high as 7000 according to genetic estimates. Thus, lethal mutations constitute a rich source of information about basic biological processes in this nematode.
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[
1981]
A neuron can be characterized by its morphology, transmitter (s?), receptor(s) and the nature of its synaptic contacts (chemical or electrical; excitatory or inhibitory; number and distribution of synapses; identity of the cells to which it is presynaptic or postsynaptic). It is clear that according to such criteria nervous sytems consist of neurons of many distinct types. The origin of neuronal diversity is unknown. Both how such diversity is generated during development and how the relevant developmental programme is encoded in the genome remain to
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[
1992]
Nematodes are generally small animals that superficially resemble miniature earthworms in overall shape. Although the morphology of Caenorhabditis elegans is very simple, the establishment or maintenance of this shape involves a large number of genes. Mutant C. elegans strains have been isolated in which worms are short and fat, abnormally long and thin, twisted into a left or right helix, or covered with irregular lumps. This chapter deals with experiments and observations that suggest how the basic shape of the nematode is first established during embryogenesis and why certain genes may be essential for normal morphogenesis.
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[
1960]
For the purpose of the present chapter the noun 'cultivation' is to be taken as the maintenance, in the laboratory, of a population of organisms belonging to a desired species through successive generations and subcultures over a prolonged period of time (weeks, months, or years). This is a deliberate restriction of the term. The noun 'culture' is most aptly used for a population within a circumscribed vessel or container (test-tube, Petri dish, U.S. Bureau of Plant Industry watch glass, etc.); it is also used in a looser, more general way (as "in culture") to cover conditions of substantial growth whether or not leading to cultivation in the strict sense
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[
1983]
Most multicellular eukaryotes posses a distinct group of germ-line cells that produces oocytes in one sex and sperm in the other. The production of adult germ cells appears to involve several developmental steps. First, during early embryogenesis, one or a few cells are committd to become germ precursor cells. Secondly, after a period of proliferation, some or all germ line descendants of the germ precursor cell leave the mitotic cell cycle and enter meiotic prophase. Thirdly, the meiotic germ cell matures as either a sperm or an oocyte. In this paper, I will review our knowledge of how each of these steps might be controlled in the small non-parasitic soil nematode, Caenorhabditis elegans.
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[
Methods Mol Biol,
2011]
Quantitative proteomics aims to identify and quantify proteins in cells or organisms that have been obtained from different biological origin (e.g., "healthy vs. diseased"), that have received different treatments, or that have different genetic backgrounds. Protein expression levels can be quantified by labeling proteins with stable isotopes, followed by mass spectrometric analysis. Stable isotopes can be introduced in vitro by reacting proteins or peptides with isotope-coded reagents (e.g., iTRAQ, reductive methylation). A preferred way, however, is the metabolic incorporation of heavy isotopes into cells or organisms by providing the label, in the form of amino acids (such as in SILAC) or salts, in the growth media. The advantage of in vivo labeling is that it does not suffer from side reactions or incomplete labeling that might occur in chemical derivatization. In addition, metabolic labeling occurs at the earliest possible moment in the sample preparation process, thereby minimizing the error in quantitation. Labeling with the heavy stable isotope of nitrogen (i.e., (15)N) provides an efficient way for accurate protein quantitation. Where the application of SILAC is mostly restricted to cell culture, (15)N labeling can be used for micro-organisms as well as a number of higher (multicellular) organisms. The most prominent examples of the latter are Caenorhabditis elegans and Drosophila (fruit fly), two important model organisms for a range of regulatory processes underlying developmental biology. Here we describe in detail the labeling with (15)N atoms, with a particular focus on fruit flies and C. elegans. We also describe methods for the identification and quantitation of (15)N-labeled proteins by mass spectrometry and bioinformatic analysis.
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[
WormBook,
2005]
This chapter reviews analytical tools currently in use for protein classification, and gives an overview of the C. elegans proteome. Computational analysis of proteins relies heavily on hidden Markov models of protein families. Proteins can also be classified by predicted secondary or tertiary structures, hydrophobic profiles, compositional biases, or size ranges. Strictly orthologous protein families remain difficult to identify, except by skilled human labor. The InterPro and NCBI KOG classifications encompass 79% of C. elegans protein-coding genes; in both classifications, a small number of protein families account for a disproportionately large number of genes. C. elegans protein-coding genes include at least ~12,000 orthologs of C. briggsae genes, and at least ~4,400 orthologs of non-nematode eukaryotic genes. Some metazoan proteins conserved in other nematodes are absent from C. elegans. Conversely, 9% of C. elegans protein-coding genes are conserved among all metazoa or eukaryotes, yet have no known functions.
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[
Methods Cell Biol,
1995]
This chapter is devoted to providing information on techniques applicable to studying transcription and translation in Caenorhabditis elegans. These techniques are constantly evolving and being passed among workers, each making improvements or adaptations. None of the techniques discussed below are original, but, rather, have emerged from a variety of sources over the years, making it difficult to trace their origin or give credit to the originators. Although each technique has been used successfully, for each there are alternative methods available in the literature that work equally well. In fact, depending on the available resources, you might find that an alternative technique suits your needs and facilities better than the one described below. For this reason, the procedures discussed below are usually accompanied by one or more references that will allow you to look at other, related methods. Where appropriate, there will also be a discussion of factors to consider when
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[
1987]
Each year thousands of new chemicals are developed but the potential societal benefits are often unrealized or delayed due to the lack of toxicological data. In the past, chemicals were introduced into the environment with little or no toxicological testing. This has resulted in many examples where adverse effects to humans were seen only after years of exposure (e.g., asbestos, benzene, vinyl chloride). Because few chemicals are used as pure substances, the toxicity of mixtures is another problem. However, these potential chemical interactions are seldom evaluated. All of the above have increased the need for toxicological testing.
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[
Methods Cell Biol,
1995]
In studying embryos of many species, methods of fragmenting and culturing embryonic tissues or cells have been useful for addressing questions of blastomere autonomy in early and later embryogenesis, for exposure to drugs or other agents that perturb specific processes, and for direct labeling of DNA or RNA. For Caenorhabditis elegans workers, the small size of the embryo and the impermeability of the chitinous eggshell and inner vitelline membrane have made such experiments difficult. A method of permeabilization and blastomere isolation, a culture system that will support further cellular development and differentiation, and assay methods for assaying the degree of development and its relative normality after experimental manipulation are minimal requirements for a satisfactory C. elegans embryonic culture system. Methods of isolating early blastomeres have included crushing of the eggshell and extrusion, laser ablation of neighboring blastomeres within an itact eggshell, laser puncturing of the eggshell producing extrusion, and digestion of the eggshell followed by shearing or manual stripping of the vitelline membrane. This last method is described in detail below. Permeabilization of complete embryos can be achieved by the same methods; in addition, one-cell embryos within the shell can be permeabilized to certain drugs such as cytochalasin D by gentle pressure on an overlying