scholarly journals NOVEL BIOINFORMATICS APPROACH DETECTS HUNDREDS OF PREVIOUSLY UNDETECTED SPLICED TRANSCRIPTS DISCOVERED FROM CAENORHABDITIS ELEGANS GENOME

2016 ◽  
Vol 68 (1) ◽  
pp. 49
Author(s):  
Kashyap Luv ◽  
Kriti Shrivastava ◽  
Aakriti Shrivastava ◽  
Ugam Kumari Chauhan
Keyword(s):  
Caenorhabditis Elegans ◽  
Genomic Sequence ◽  
Single Gene ◽  
Genome Structure ◽  
Chromosome 1 ◽  
Soil Nematode ◽  
C Elegans ◽  
Full Genomic Sequence ◽  
Depth Analysis ◽  
Alternatively Spliced

<p><strong>CONTEXT:</strong> With the completion of genome sequence of several organisms including free-living soil nematode Caenorhabditis elegans, precise genome annotations of this sea of raw information are now of prime importance, as they allow the accurate definition of generic regions. Alternative splicing is seen in nearly all metazoan organisms as a means for producing functionally diverse polypeptides from a single gene. <strong>AIM:</strong> In this study, we performed a detailed and in-depth analysis of the full genomic sequence of one of the six chromosomes of C. elegans. <strong>MATERIALS AND METHODS:</strong> In this study, several bioinformatics tools including gene/exon prediction programs, ORF finders, blast analysis tools, and alignment programs were used to analyze the genes/exons encoded by chromosome 1 of C. elegans with special reference to alternatively spliced transcripts. <strong>CONCLUSION:</strong> Using these tools, we have predicted &gt;200 new alternatively spliced hypothetical transcripts from the genes encoded by chromosome 1 in C. elegans. These new spliced transcripts were identified from unusually large untranslated (UTR) regions and large introns present at the 3’ and 5’ ends of the genes with a maximum number of transcripts predicted from 5’ UTR analysis. Further studies and subsequent confirmation of these alternatively spliced transcripts will enhance our understanding of the genome structure, expression, and in elucidating their role during the development of C. elegans.</p>

Broad oxygen tolerance in the nematode Caenorhabditis elegans

2000 ◽  
Vol 203 (16) ◽  
pp. 2467-2478 ◽  
Author(s):  
W.A. Van Voorhies ◽  
S. Ward
Keyword(s):  
Caenorhabditis Elegans ◽  
Metabolic Rate ◽  
Developmental Stages ◽  
Small Body ◽  
Metabolic Cost ◽  
Soil Nematode ◽  
Nematode Caenorhabditis Elegans ◽  
Oxygen Levels ◽  
C Elegans ◽  
Short Period

This study examined the effects of oxygen tensions ranging from 0 to 90 kPa on the metabolic rate (rate of carbon dioxide production), movement and survivorship of the free-living soil nematode Caenorhabditis elegans. C. elegans requires oxygen to develop and survive. However, it can maintain a normal metabolic rate at oxygen levels of 3.6 kPa and has near-normal metabolic rates at oxygen levels as low as 2 kPa. The ability to withstand low ambient oxygen levels appears to be a consequence of the small body size of C. elegans, which allows diffusion to supply oxygen readily to the cells without requiring any specialized respiratory or metabolic adaptations. Thus, the small size of this organism pre-adapts C. elegans to living in soil environments that commonly become hypoxic. Movement in C. elegans appears to have a relatively minor metabolic cost. Several developmental stages of C. elegans were able to withstand up to 24 h of anoxia without major mortality. Longer periods of anoxia significantly increased mortality, particularly for eggs. Remarkably, long-term exposure to 100 % oxygen had no effect on the metabolic rate of C. elegans, and populations were able to survive for a least 50 generations in 100 % (90 kPa) oxygen. Such hyperoxic conditions are fatal to most organisms within a short period.

Reporter gene constructs suggest that the Caenorhabditis elegans avermectin receptor beta-subunit is expressed solely in the pharynx.

1997 ◽  
Vol 200 (10) ◽  
pp. 1509-1514 ◽  
Author(s):  
D L Laughton ◽  
G G Lunt ◽  
A J Wolstenholme
Keyword(s):  
Caenorhabditis Elegans ◽  
Genomic Sequence ◽  
Gene Promoter ◽  
Pcr Amplification ◽  
Beta Subunit ◽  
Amino Acid Residues ◽  
C Elegans ◽  
Larval Stages ◽  
Major Mode ◽  
Flanking Sequences

Gene promoter/LacZ reporter constructs were made in order to analyse the expression of the beta-subunit of the Caenorhabditis elegans glutamate-gated Cl- channel (Glu-Cl) receptor. Southern blot analysis of the C. elegans cosmid C35E8 identified a 4kbp EcoRI fragment which contained the 5' portion of the Glu-Cl beta coding sequence together with 5' flanking sequences. This was subcloned and used as the template for polymerase chain reaction (PCR) amplification of a DNA fragment encoding the first 24 amino acid residues of Glu-Cl beta together with 1.4 kbp of 5' genomic sequence. The fragment was subcloned into the LacZ expression vector pPD22.11 to form a translational reporter fusion. After injection of the construct into worms, six stably transformed lines were established and assayed for beta-galactosidase activity. Stained nuclei were observed in the pharyngeal metacorpus in adults and in all larval stages, and stained nuclei were seen in many embryos undergoing morphogenesis. Additional stained nuclei towards the terminal bulb of the pharynx were observed in larval stages. These results provide further evidence that the Glu-Cl receptor mediates the glutamatergic inhibition of pharyngeal muscle via the M3 motor neurone and point to inhibition of pharyngeal pumping as a major mode of action for avermectins.

scholarly journals The Caenorhabditis elegans muscle-affecting gene unc-87 encodes a novel thin filament-associated protein.

1994 ◽  
Vol 127 (1) ◽  
pp. 79-93 ◽  
Author(s):  
S Goetinck ◽  
R H Waterston
Keyword(s):  
Caenorhabditis Elegans ◽  
Gene Product ◽  
Thin Filament ◽  
Genomic Sequence ◽  
Muscle Protein ◽  
Thin Filaments ◽  
C Elegans ◽  
Neuronal Protein ◽  
And Function ◽  
Filament Protein

Mutations in the unc-87 gene of Caenorhabditis elegans affect the structure and function of bodywall muscle, resulting in variable paralysis. We cloned the unc-87 gene by taking advantage of a transposon-induced allele of unc-87 and the correspondence of the genetic and physical maps in C. elegans. A genomic clone was isolated that alleviates the mutant phenotype when introduced into unc-87 mutants. Sequence analysis of a corresponding cDNA clone predicts a 357-amino acid, 40-kD protein that is similar to portions of the vertebrate smooth muscle proteins calponin and SM22 alpha, the Drosophila muscle protein mp20, the deduced product of the C. elegans cDNA cm7g3, and the rat neuronal protein np25. Analysis of the genomic sequence and of various transcripts represented in a cDNA library suggest that unc-87 mRNAs are subject to alternative splicing. Immunohistochemistry of wildtype and mutant animals with antibodies to an unc-87 fusion protein indicates that the gene product is localized to the I-band of bodywall muscle. Studies of the UNC-87 protein in other muscle mutants suggest that the unc-87 gene product associates with thin filaments, in a manner that does not depend on the presence of the thin filament protein tropomyosin.

scholarly journals Genetic Analysis of Adult-Specific Surface Antigenic Differences Between Varieties of the Nematode Caenorhabditis elegans

Genetics ◽  
1987 ◽  
Vol 117 (3) ◽  
pp. 467-476
Author(s):  
Samuel M Politz ◽  
Karl J Chin ◽  
Daniel L Herman
Keyword(s):  
Caenorhabditis Elegans ◽  
Linkage Group ◽  
Genetic Analysis ◽  
Surface Antigen ◽  
Single Gene ◽  
Surface Antigens ◽  
Nematode Caenorhabditis Elegans ◽  
Specific Antibodies ◽  
C Elegans ◽  
Stage Specificity

ABSTRACT We have studied developmental stage-specificity and genetic specification of surface antigens in the nematode Caenorhabditis elegans. Rabbit antisera directed against the adult C. elegans cuticle were used in conjunction with antiserum adsorption experiments to obtain antibody reagents with specificity for the adult surface. Adult-specific antibodies were used to identify several varietal strains of C. elegans that display antigen-negative phenotypes as adults. Genetic mapping results using the surface antigen phenotype as a marker indicated that a single gene (designated srf-1) or cluster of genes on linkage group II determines the adult surface antigen phenotype.

Sodium–hydrogen exchangers in the nematode Caenorhabditis elegans: investigations towards their potential role in hypodermal H+ excretion, Na+ uptake, and ammonia excretion, as well as acid–base balance

2017 ◽  
Vol 95 (9) ◽  
pp. 623-632 ◽  
Author(s):  
Aida Adlimoghaddam ◽  
Michael J. O’Donnell ◽  
Alex Quijada-Rodriguez ◽  
Dirk Weihrauch
Keyword(s):  
Caenorhabditis Elegans ◽  
Cell Volume Regulation ◽  
Ammonia Excretion ◽  
Transport Processes ◽  
Soil Nematode ◽  
Acid Base Balance ◽  
Nematode Caenorhabditis Elegans ◽  
Acid Base ◽  
C Elegans ◽  
Base Balance

Cation/proton exchangers of the cation proton antiporter 1 (CPA1) subfamily (NHEs, SLC 9) play an important role in many physiological processes, including cell volume regulation, acid–base homeostasis, and ammonia excretion. The soil nematode Caenorhabditis elegans (Maupas, 1900) (N2, 1968) expresses nine paralogues (NHX-1 to NHX-9). The current study was undertaken to investigate the role of the cation/proton exchanger in hypodermal Na+ and H+ fluxes, as well in ammonia excretion processes. Measurements using SIET (scanning ion-selective electrode technique) showed that the hypodermis promotes H+ secretion and Na+ uptake. Inhibitory effects on fluxes were observed upon application of amiloride but not EIPA, suggesting that NHXs are not involved in the transport processes. In response to stress induced by starvation or exposure to 1 mmol·L−1 NH4Cl, pH 5.5, or pH 8.0, body pH stayed fairly constant, with changes in mRNA expression levels detected in intestinal NHX-2 and hypodermal NHX-3. In conclusion, the study suggest that hypodermal apically localized EIPA-sensitive Na+/H+ exchangers do not likely play a role in ammonia excretion and Na+ uptake in the hypodermis of C. elegans, whereas apical amiloride-sensitive Na+ channels seem to be involved not just in hypodermal Na+ uptake but indirectly also in NH4+ and H+ excretion.

Behavioural phenotyping of C. elegans on UV-killed E. coli mutants v1

2021 ◽  
Author(s):  
Saul Moore
Keyword(s):  
Caenorhabditis Elegans ◽  
Gene Deletion ◽  
Uv Light ◽  
Single Gene ◽  
Deletion Mutants ◽  
E Coli ◽  
C Elegans ◽  
Behavioural Phenotyping ◽  
Keio Collection ◽  
Single Gene Deletion

Protocol for screening candidate behaviour-modifying E. coli BW25113 single-gene deletion mutants from the 'Keio Collection', to investigate their effects on Caenorhabditis elegans behaviour when killed by ultraviolet (UV) light

Developmental strategies during early embryogenesis of Caenorhabditis elegans

Development ◽  
1986 ◽  
Vol 97 (Supplement) ◽  
pp. 31-44
Author(s):  
Einhard Schierenberg
Keyword(s):  
Caenorhabditis Elegans ◽  
Parasitic Nematode ◽  
Soil Nematode ◽  
Developmental Studies ◽  
Central Question ◽  
Unique Combination ◽  
Nematode Caenorhabditis Elegans ◽  
Free Living ◽  
C Elegans ◽  
Multicellular Structure

How the complex, multicellular structure of an organism is generated from the information contained in the uncleaved egg is a central question in developmental studies. Nematodes are particularly suitable for studying this question. A unique combination of favourable properties, including transparent eggshell, normal embryogenesis under the microscope outside the mother, small number of cells and rapid, reproducible development made nematodes classic models for developmental biologists (for reviews see Chitwood & Chitwood, 1974; von Ehrenstein & Schierenberg, 1980). In addition to the attractive features mentioned above, the free-living soil nematode Caenorhabditis elegans (Fig. 1) is also well suited for analysis of the genetic control of development (Brenner, 1974) unlike the classically studied parasitic nematode Parascaris equorum (Ascaris megalocephala). Recently cellular (e.g. Sulston, Schierenberg, White & Thomson, 1983) and genetic (e.g. Sternberg & Horvitz, 1984) aspects of development have been studied extensively in C. elegans.

scholarly journals Degrading intestinal DAF-2 nearly doubles Caenorhabditis elegans lifespan without affecting development or reproduction

2021 ◽  
Author(s):  
Yan-Ping Zhang ◽  
Wen-Hong Zhang ◽  
Pan Zhang ◽  
Qi Li ◽  
Yue Sun ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Caenorhabditis Elegans ◽  
Dna Sequences ◽  
Single Gene ◽  
Nutrient Supply ◽  
Genomic Locus ◽  
Aging Research ◽  
C Elegans ◽  
Fluorescent Tags ◽  
Lifespan Regulation

Twenty-eight years following the breakthrough discovery that a single-gene mutation of daf-2 can double the lifespan of Caenorhabditis elegans, it remains unclear where this gene, which encodes an insulin/IGF-1 receptor, is expressed and where it acts to regulate aging. Here, by inserting DNA sequences of fluorescent tags into the genomic locus of daf-2 and that of its downstream transcription factor daf-16, we determined that both genes are expressed in most or all tissues from embryos through adulthood, in line with their diverse functions. Using tissue-specific auxin-induced protein degradation, we determined that both DAF-2 and DAF-16 act in the intestine to regulate organismal aging. Strikingly, loss of DAF-2 in the intestine nearly doubled C. elegans lifespan but did not produce the adverse developmental or reproductive phenotypes associated with genetic daf-2 mutants. These findings unify the mechanism of lifespan regulation by genes and that by dietary restriction, and begin to focus anti-aging research on nutrient supply.

scholarly journals Adherent-Invasive and Non-Invasive Escherichia coli Isolates Differ in Their Effects on Caenorhabditis elegans’ Lifespan

2021 ◽  
Vol 9 (9) ◽  
pp. 1823
Author(s):  
Maria Beatriz de Sousa de Sousa Figueiredo ◽  
Elizabeth Pradel ◽  
Fanny George ◽  
Séverine Mahieux ◽  
Isabelle Houcke ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Caenorhabditis Elegans ◽  
Epithelial Cells ◽  
Intestinal Epithelial Cells ◽  
Host Bacterium ◽  
Soil Nematode ◽  
Intestinal Epithelial ◽  
Barrier Dysfunction ◽  
E Coli ◽  
C Elegans

The adherent-invasive Escherichia coli (AIEC) pathotype has been implicated in the pathogenesis of inflammatory bowel diseases in general and in Crohn’s disease (CD) in particular. AIEC strains are primarily characterized by their ability to adhere to and invade intestinal epithelial cells. However, the genetic and phenotypic features of AIEC isolates vary greatly as a function of the strain’s clonality, host factors, and the gut microenvironment. It is thus essential to identify the determinants of AIEC pathogenicity and understand their role in intestinal epithelial barrier dysfunction and inflammation. We reasoned that soil nematode Caenorhabditis elegans (a simple but powerful model of host-bacterium interactions) could be used to study the virulence of AIEC vs. non- AIEC E. coli strains. Indeed, we found that the colonization of C. elegans (strain N2) by E. coli impacted survival in a strain-specific manner. Moreover, the AIEC strains’ ability to invade cells in vitro was linked to the median lifespan in C. elegans (strain PX627). However, neither the E. coli intrinsic invasiveness (i.e., the fact for an individual strain to be characterized as invasive or not) nor AIEC’s virulence levels (i.e., the intensity of invasion, established in % from the infectious inoculum) in intestinal epithelial cells was correlated with C. elegans’ lifespan in the killing assay. Nevertheless, AIEC longevity of C. elegans might be a relevant model for screening anti-adhesion drugs and anti-invasive probiotics.

The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation

Genetics ◽  
2021 ◽  
Author(s):  
Kimberly J Gilbert ◽  
Stefan Zdraljevic ◽  
Daniel E Cook ◽  
Asher D Cutter ◽  
Erik C Andersen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Caenorhabditis Elegans ◽  
Population Size ◽  
Random Mating ◽  
Genome Structure ◽  
Population Substructure ◽  
C Elegans ◽  
Fitness Effects ◽  
Self Fertilization ◽  
New Mutations

Abstract The distribution of fitness effects for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the distribution of fitness effects (DFE) from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, genome structure, and non-random mating. Although inference methods aim to control for population size changes, the influence of non-random mating remains incompletely understood, despite being a common feature of many species. We report the distribution of fitness effects estimated from 326 genomes of Caenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history of C. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection on linked sites can conspire to compromise estimates of the DFE from extant polymorphisms with existing methods. These factors together tend to bias inferences towards weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species like C. elegans. Improved methods for inferring the distribution of fitness effects are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.

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