Farrer T et al. (2002) Nucleic Acids Res "Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing."

Farrer T, Kent WJ, Roller AB, Zahler AM

[Nucleic Acids Res, 2002]

GC-AG introns represent 0.7% of total human pre-mRNA introns. To study the function of GC-AG introns in splicing regulation, 196 cDNA-confirmed GC-AG introns were identified in Caenorhabditis elegans. These represent 0.6% of the cDNA- confirmed intron data set for this organism. Eleven of these GC-AG introns are involved in alternative splicing. In a comparison of the genomic sequences of homologous genes between C.elegans and Caenorhabditis briggsae for 26 GC-AG introns, the C at the +2 position is conserved in only five of these introns. A system to experimentally test the function of GC-AG introns in alternative splicing was developed. Results from these experiments indicate that the conserved C at the +2 position of the tenth intron of the let-2 gene is essential for developmentally regulated alternative splicing. This C allows the splice donor to function as a very weak splice site that works in balance with an alternative GT splice donor. A weak GT splice donor can functionally replace the GC splice donor and allow for splicing regulation. These results indicate that while the majority of GC-AG introns appear to be constitutively spliced and have no evolutionary constraints to prevent them from being GT-AG introns, a subset of GC-AG introns is involved in alternative splicing and the C at the +2 position of these introns can have an important role in splicing regulation.

Zhang J et al. (2011) BMC Genomics "GC content around splice sites affects splicing through pre-mRNA secondary structures."

Zhang J, Chen L, Kuo CC

[BMC Genomics, 2011]

BACKGROUND: Alternative splicing increases protein diversity by generating multiple transcript isoforms from a single gene through different combinations of exons or through different selections of splice sites. It has been reported that RNA secondary structures are involved in alternative splicing. Here we perform a genomic study of RNA secondary structures around splice sites in humans (Homo sapiens), mice (Mus musculus), fruit flies (Drosophila melanogaster), and nematodes (Caenorhabditis elegans) to further investigate this phenomenon. RESULTS: We observe that GC content around splice sites is closely associated with the splice site usage in multiple species. RNA secondary structure is the possible explanation, because the structural stability difference among alternative splice sites, constitutive splice sites, and skipped splice sites can be explained by the GC content difference. Alternative splice sites tend to be GC-enriched and exhibit more stable RNA secondary structures in all of the considered species. In humans and mice, splice sites of first exons and long exons tend to be GC-enriched and hence form more stable structures, indicating the special role of RNA secondary structures in promoter proximal splicing events and the splicing of long exons. In addition, GC-enriched exon-intron junctions tend to be overrepresented in tissue-specific alternative splice sites, indicating the functional consequence of the GC effect. Compared with regions far from splice sites and decoy splice sites, real splice sites are GC-enriched. We also found that the GC-content effect is much stronger than the nucleotide-order effect to form stable secondary structures. CONCLUSION: All of these results indicate that GC content is related to splice site usage and it may mediate the splicing process through RNA secondary structures.

Rivas Alcala AR et al. Salud Publica Mex "[The correlation between onchocercomas and positivity for microfilaria in onchocerciasis]."

Villafuerte Martinez E, Alvarez Gordillo GC, Rivas Alcala AR, Vazquez Perez E

[Salud Publica Mex]

The objective of this work is to evaluate the palpation sensitivity of onchocercomata for the diagnosis of onchocerciasis in individuals residents of the locality of Nueva Costa Rica, Mapastepec, in the south endemic area of the state of Chiapas, Mexico. Every one of the 243 individuals who voluntarily participate in this study was interrogated and physical examined for the detection of nodules. The positivity and the worm burden to the Onchocerca volvulus infections was estimated by the presence of one or more microfilariae in any of the for skin snips taken from both suprascapular and gluteal regions, and by the mean of the Dmf/mg of each skin snip. From the total number of individual studied, 131 (53.9%) were positives to microfilariae and 37 (15.2%) to onchocercomata. Only 23 (17.6%) of the microfilariae positive individuals carried nodules. The distribution of positive individuals to nodules in relation to age, was similar in all the age groups. In relation to the intensity of the infection was found that, the mean of the Dmf/mg of all individuals was 6.67, there was not significant differences (p greater than 0.001) between males and females; being the Dmf/mg of 6.35 and 6.99, respectively. The age group between 21 and 30 years old showed the higher mean of Dmf/mg than the rest of the groups (p greater than 0.001). However, there was a high microfilariae positivity in the oldest groups than in the young. The prevalence for onchocerciasis in this locality, estimated by the positivity to either microfilariae or nodules, was 59.9 per cent. It is concluded that, the onchocercomata detection sensitivity for the diagnosis of onchocerciasis was very low, probably due to the nodulectomy activity of the onchocerciasis control program, which has been operating since 1930 and therefore, there are an important number of individuals positive to microfilariae without detectable nodules.

Hamelin M et al. (1993) Journal of Neurochemistry "unc-5 and unc-6, proteins that steers migrating growth cones in C. elegans."

Hamelin M, Su M-W, Culotti JG, Zhou YW, Scott IM

[Journal of Neurochemistry, 1993]

The unc-5 and unc-6 genes of C. elegans are required to guide pioneer axon growth cone (GC) and mesodermal cell migrations in a dorsal direction on the epidermis.

Ahn IY et al. (2005) J Biochem Biophys Methods "Determination of DNA base composition by small scale acrylamide-CsCl gradient centrifugation."

Winter CE, Ahn IY

[J Biochem Biophys Methods, 2005]

In this paper we describe a simple and rapid protocol for DNA base composition determination by CsCl gradient in the presence of acrylamide. This method permits the determination of GC content in microgram amounts of DNA, and results are easily documented in photographs or graphs. The protocol was applied to the characterization of nematode DNA, but can be used for other organisms. Analyzing several experiments the mean standard deviation observed in the calculated GC content is near 1.3%.

Rothstein N et al. (1988) Parasitology "DNA base composition of filarial nematodes."

Rothstein N, Rajan TV, Stoller TJ

[Parasitology, 1988]

We have determined the molar content of guanine + cytosine (GC content) of DNA of the filarial nematode (Brugia malayi, Brugia pahangi and Dirofilaria imitis) and of the free-living soil nematodes Caenorhabditis elegans and have analysed the DNA for the presence of methylcytosine. Two independent methods, thermal denaturation and direct analysis of base content by HPLC following enzymatic hydrolysis, reveal that the GC content of filarial nematodes is 26-28%. We have been unable to find methylcytosine in the DNA of B. malayi.

Sulston JE et al. (1974) Genetics "The DNA of Caenorhabditis elegans."

Brenner S, Sulston JE

[Genetics, 1974]

Chemical analysis and a study of renaturation kinetics show that the nematode, Caenorhabditis elegans, has a haploid DNA content of 8 X 10(7) base pairs (20 times the genome of E. coli). Eighty-three percent of the DNA sequences are unique. The mean base composition is 36% GC; a small component, containing the rRNA cistrons, has a base composition of 51% GC. The haploid genome contains about 300 genes for 4S RNA, 110 for 5S RNA, and 55 for (18 + 28)S RNA.

Piovesan A et al. (2019) BMC Res Notes "On the length, weight and GC content of the human genome."

Pelleri MC, Vitale L, Antonaros F, Strippoli P, Caracausi M, Piovesan A

[BMC Res Notes, 2019]

OBJECTIVE: Basic parameters commonly used to describe genomes including length, weight and relative guanine-cytosine (GC) content are widely cited in absence of a primary source. By using updated data and original software we determined these values to the best of our knowledge as standard reference for the whole human nuclear genome, for each chromosome and for mitochondrial DNA. We also devised a method to calculate the relative GC content in the whole messenger RNA sequence set and in transcriptomes by multiplying the GC content of each gene by its mean expression level. RESULTS: The male nuclear diploid genome extends for 6.27 Gigabase pairs (Gbp), is 205.00cm (cm) long and weighs 6.41 picograms (pg). Female values are 6.37 Gbp, 208.23cm, 6.51pg. The individual variability and the implication for the DNA informational density in terms of bits/volume were discussed. The genomic GC content is 40.9%. Following analysis in different transcriptomes and species, we showed that the greatest deviation was observed in the pathological condition analysed (trisomy 21 leukaemic cells) and in Caenorhabditis elegans. Our results may represent a solid basis for further investigation on human structural and functional genomics while also providing a framework for other genome comparative analysis.

Mitreva M et al. (2006) Genome Biol "Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species."

Wendl MC, Larson A, Parkinson J, McCarter JP, Waterston RH, Wylie T, Mitreva M, Yin Y, Martin J

[Genome Biol, 2006]

BACKGROUND: Codon usage has direct utility in molecular characterization of species and is also a arker for molecular evolution. To understand codon usage within the diverse phylum Nematoda,we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons ere analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms. RESULTS: Codon usage similarity in Nematoda usually persists over the breadth of a genus but thenrapidly diminishes even within each clade. Globodera, Meloidogyne, Pristionchus, and Strongyloides have the most highly derived patterns of codon usage. The major factor affecting differences in codon usage between species is the coding sequence GC content, which varies in nematodes from 32%to 51%. Coding GC content (measured as GC3) also explains much of the observed variation in the effective number of codons (R = 0.70), which is a measure of codon bias, and it even accounts for differences in amino acid frequency. Codon usage is also affected by neighboring nucleotides(N1 context). Coding GC content correlates strongly with estimated noncoding genomic GC content (R = 0.92). On examining abundant clusters in five species, candidate optimal codons were identified that may be preferred in highly expressed transcripts. CONCLUSION: Evolutionary models indicate that total genomic GC content, probably the product of directional mutation pressure, drives codon usage rather than the converse, a conclusion that is supported by examination of nematode genomes.

Pino EC et al. (2020) Methods Mol Biol "Quantitative Profiling of Lipid Species in Caenorhabditis elegans with Gas Chromatography-Mass Spectrometry."

Soukas AA, Pino EC

[Methods Mol Biol, 2020]

Gas chromatography-mass spectrometry (GC-MS) enables sensitive detection and relative quantification of fatty acids. In Caenorhabditis elegans, the use of GC-MS can corroborate findings from common staining methodologies, providing great resolution on the lipid species altered in abundance in aging, genetic mutants, or with dietary or pharmacologic manipulation. Here we describe a method to quantitate relative abundance of fatty acids in total worm lipid extracts, as well as a method that quantitates fatty acids following separation into neutral lipid pools (triacylglycerols and cholesteryl esters) versus more polar lipids (phospholipids) by solid-phase extraction (SPE).