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[
Curr Top Dev Biol,
2012]
Noncoding RNAs have emerged as an integral part of posttranscriptional gene regulation. Among that class of RNAs are the microRNAs (miRNAs), which posttranscriptionally regulate target mRNAs containing complementary sequences. The broad presence of miRNAs in lower eukaryotes, plants, and mammals highlights their importance throughout evolution. MiRNAs have been shown to regulate many pathways, including development, and disruption of miRNA function can lead to disease (Ivey and Srivastava, 2010; Jiang et al., 2009). Although the first miRNA genes were discovered in the nematode, Caenorhabditis elegans, almost 20 years ago, the field of miRNA research began when they were found in multiple organisms a little over a decade ago (Lagos-Quintana et al., 2001; Lau et al., 2001; Lee and Ambros, 2001; Lee et al., 1993; Pasquinelli et al., 2000; Wightman et al., 1993). Here, we review one of the first characterized miRNAs,
let-7, and describe its role in development and the intricacies of its biogenesis and function.
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[
2005]
RNA interference (RNAi) is a recently discovered phenomenon in which doublestranded RNA (dsRNA) silences endogenous gene expression in a sequencespecific manner (Fire et al., 1998). Since its discovery, the use of RNAi has become widely employed in many organisms to specifically knock down gene function. RNAi shares a remarkable degree of similarity with silencing phenomena in other organisms (Cogoni et al., 1999a; Sharp, 1999). For instance, RNAi, posttranscriptional gene silencing in plants and cosuppression in fungi can all be activated by the presence of aberrant RNAs (Maine, 2000; Tijsterman et al., 2002a). Additionally, plant, worm, and fly cells or extracts undergoing RNA-mediated interference all contain small dsRNAs, around 25 nucleotides in length, identical to the sequences present in the silenced gene (Baulcombe, 1996; Hammond et al., 2000; Zamore et al., 2000; Catalanotto et al., 2000). The high degree of similarity between these RNA-mediated silencing phenomena supports the notion that they were derived from an ancient and conserved pathway used to regulate gene expression, presumably to eliminate defective RNAs and to defend against viral infections and transposons. (Zamore, 2002). Components of RNAi have also been implicated in developmental processes, suggesting that RNAi may play a broader role in regulating gene expression (Smardon et al., 2000; Knight et al., 2001; et al., Ketting et al., 2001). Although we have learned much about the general mechanisms underlying RNAi, a detailed understanding of how RNAi works remains to be elucidated. In this chapter we will discuss first the biology of RNAi, then the genes required for its function, and we will end with a discussion on recent findings that have implicated chromatin silencing in the mechanism of RNAi.
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[
Methods Cell Biol,
1995]
DNA transformation assays in a whole organism provide experimental links between molecular structure and phenotype. Experiments with transgenic Caenorhabditis elegans start in general with the injection of DNA into the adult gonad. Effects on phenotype or gene expression patterns can be analyzed either in F1 progeny derived from the injected animals or in derived transgenic lines. Microinjection of C. elegans was first carried out by Kimble et al. (1982). Stinchcomb et al. (1985) then showed that injected DNA could be maintained for several generations in transgenic lines. The first selective methods for producing and maintaining transgenic lines were reported in 1986 (Fire, 1986). These methods have been considerably improved since then (Mello et al., 1991) , so that assays involving DNA transformation are now a standard part of the experimental repertoire for C. elegans.
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[
2017]
Since their discovery in late 1970, transient receptor potential (TRP) channels have been implicated in a variety of cellular and physiological functions (Minke, 2010). The superfamily of TRP channels consists of nearly 30 members that are organized into seven major subgroups based on their specific function and sequence similarities (Owsianik et al., 2006; Ramsey et al., 2006). With the exception of TRPN channels that are only found in invertebrates and fish, mammalian genomes contain representatives of all six subfamilies: (1) TRPV (vanilloid); (2) TRPC (canonical); (3) TRPM (melastatin); (4) TRPA (ankyrin); (5) TRPML (mucolipin); and (6) TRPP (polycystin). TRP channels play crucial regulatory roles in many physiological processes, including those associated with reproductive tissues. As calcium-permeable cation channels that respond to a variety of signals (Clapham et al., 2003; Wu et al., 2010), TRP channels exert their role as sensory detectors in both male and female gametes, and play regulatory functions in germ cell development and maturation. Recent evidence obtained from Caenorhabditis elegans studies point to the importance of these proteins during fertilization where certain sperm TRP channels could migrate from a spermatozoon into an egg to ensure successful fertilization and embryo development. In this chapter we discuss how TRP channels can regulate both female and male fertility in different species and their specific roles.
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[
1969]
In order to study properly the nutrition and culture of nematodes, it is desirable to establish the organisms in axenic culture. Only in this way can the metabolic abilities of the nematodes be separated from those of coexisting and interacting organisms. One may settle for a mono-axenic culture, but the best way to attain this is to obtain axenic nematodes and then add the second organism or tissue, for example, alfalfa callus tissue for plant parasitic nematodes (Krusberg, 1961). This chapter will devote itself, in the main, to recent work on the culture and nutrition of nematodes, free-living and parasitic, and will refer only in passing to work already thoroughly reviewed (Dougherty et al., 1959; Nicholas, et al., 1959; Dougherty, 1960).
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[
1984]
Developmental fates of blastomeres in early C. elegans embryos appear to be governed by internally segregating, cell-autonomous determinants. To ascertain whether previously described gut-lineage dterminants are nuclear or cytoplasmic, laser microsurgery was used to show that exposing the nucleus of a non-gut-precursor cell to gut-precursor cytoplasm can cause the progeny of the resulting hybrid cell to express gut-specific differentiation markers, supporting the view that the determinants are cytoplasmic. In attempts to obtain molecular probes for such determinants, a library of monoclonal antibodies to early embryonic antigens was generated and screened by immunofluorescence microscopy for antibodies reacting with lineage-specific components. Three of the antibodies react with cytoplasmic granules (P granules) that segregate specifically with the germ line in early cleavages and are found uniquely in germ-line cells throughout the life cycle. Experiments on unfertilized eggs, on mutant embryos with defects in early cleavage, and on normal embryos treated with various cytoskeletal inhibitors indicate that P-granule segregation depends upon fertilization and requires the function of actin microfilaments, but is independent of spindle and microtubule functions. Work on the biochemical nature and function of the P granules is in progress.
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[
WormBook,
2005]
Asymmetric cell divisions play an important role in generating diversity during metazoan development. In the early C. elegans embryo, a series of asymmetric divisions are crucial for establishing the three principal axes of the body plan (AP, DV, LR) and for segregating determinants that specify cell fates. In this review, we focus on events in the one-cell embryo that result in the establishment of the AP axis and the first asymmetric division. We first describe how the sperm-derived centrosome initiates movements of the cortical actomyosin network that result in the polarized distribution of PAR proteins. We then briefly discuss how components acting downstream of the PAR proteins mediate unequal segregation of cell fate determinants to the anterior blastomere AB and the posterior blastomere P 1 . We also review how a heterotrimeric G protein pathway generates cortically based pulling forces acting on astral microtubules, thus mediating centrosome and spindle positioning in response to AP polarity cues. In addition, we briefly highlight events involved in establishing the DV and LR axes. The DV axis is established at the four-cell stage, following specific cell-cell interactions that occur between P 2 and EMS , the two daughters of P 1 , as well as between P 2 and ABp , a daughter of AB . The LR axis is established shortly thereafter by the division pattern of ABa and ABp . We conclude by mentioning how findings made in early C. elegans embryos are relevant to understanding asymmetric cell division and pattern formation across metazoan evolution.
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[
WormBook,
2006]
In the last decade, nematodes other than C. elegans have been studied intensively in evolutionary developmental biology. A few species have been developed as satellite systems for more detailed genetic and molecular studies. One such satellite species is the diplogastrid nematode Pristionchus pacificus. Here, I provide an overview about the biology, phylogeny, ecology, genetics and genomics of P. pacificus.
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[
1984]
Germ cells in a wide variety of invertebrate and vertebrate species contain distinctive cytoplasmic organelles that have been visualized by electron microscopy. The ubiliquity of such structures suggests that they play some role in germ-line determination or differentiation, or both. However, the nature and function of these structures remain unknown. We describe experiments with two types of immunologic probes, rabbit sera and mouse monoclonal antibodies, directed against ctyoplamsic granules that are unique to germ-line cells in the nematode, Caenorhabditis elegans, and that may correspond to the germ-line-specific structures seen by electron microscopy in C. elegans embryos. The antibodies have been used to follow the granules, termed P granules, during early embryonic cleavage stages and throughout larval and adult development. P granules become progressively localized to the germ-line precursor cells during early embryogenesis. We are using conditionally lethal maternal-effect mutations to study this localization process. In addition to providing a rapid assay for P granules in wild-type, mutant, and experimentally maipulated embryos, the antibodies also promise to be useful in biochemically characterizing the granules and in investigating their
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[
Methods Cell Biol,
1995]
Complementary DNA libraries are useful tools for uncovering genes of interest in C. elegans and finding specific homologies to genes in other organisms (Waterston et al., 1992; McCombie et al., 1992). When working with existing cDNA libraries, be sure to carefully choose which libraries would be most beneficial to the type of research being done. Some libraries may be specific for genes that are present in lower copy numbers, whereas others may be of a more general nature. It is important to fully understand the source and construction of the library you will be working with. Once an appropriate library has been chosen, work may begin to isolate a specific cDNA and sequence it completely or to survey many cDNAs by single-pass DNA sequencing. Whatever the project, it is important to develop a specific strategy for both the sequencing and the organization of the clones being characterized. The strategies and procedures we have outlined in this chapter have proven effective for rapid and comprehensive cDNA characterization.