U6 snRNA variants isolated from the posterior silk gland of the silk moth Bombyx mori.

Five U6 small nuclear RNA (snRNA) isoforms were detected and characterized from the posterior silk gland (PSG) of the silk moth Bombyx mori (Nistari strain). Using the currently accepted U6 secondary structure model as a basis for comparison, the variants were analyzed for nucleotide differences across the sequence with a focus on known functional domains. Differences were observed primarily in single-stranded areas of which sixty percent were found in the highly conserved U4-U6 binding sites. In the Nistari strain, the U6A variant was found to be approximately four times more abundant as part of high molecular weight spliceosomal complexes when compared with U6A in the total unfractionated PSG cell lysate. Additionally, the European 703 B. mori strain total cell lysate U6 snRNA was analyzed and only the dominant U6A isoform initially identified in Nistari was found. Due to U6's essential role in pre-mRNA processing, variants may modulate assemblage of the catalytic core and in doing so potentially affect the rate of splicing. Phylogenetic analysis of the U6 snRNA sequences indicate an ancient divergence of U6 from the self-splicing group II intron module and a high degree of evolutionary conservation across species possibly due to functional constraints on the gene. Using in silico analysis, 35 full-length U6 variants were observed in the recently released Whole Genome Shotgun (WGS) database of the p50T strain. The consensus sequence of these U6 genes from p50T is identical to U6A identified in the Nistari strain. Furthermore p50T variant 1, which is represented in 14 genes, is equivalent to Nistari U6A.

Molecular identification of pathogenic house dust mites using 12S rRNA sequences.

House dust mites are microarthropods implicated in the cause of allergic diseases. Currently, there is no phylogenetic analysis of dust mites based on genomic or mitochondrial DNA (mtDNA) evidence. For the first time, we report evolutionary relationships based on partial mtDNA 12S rRNA sequences among the four dust mite families Pyroglyphidae (Dermatophagoides pteronyssinus), Glycyphagoidea (Glycyphagus privatus), Acaridae (Aleuroglyphus ovatus), and Echimyopodidae (Blomia tropicalis). Thirteen sequence variants were obtained and phylogenetic analysis showed two monophyletic clades composed of two species each. Contrary to current taxonomic classification, the Acaridae clustered in a monophyletic group with the Pyroglyphidae. Considering the current difficulties in identifying these medically important species for the purpose of eradication and treatment, it is significant that sequence data are capable of discriminating between species belonging to different families of dust mites.

The silk moth Bombyx mori U1 and U2 snRNA variants are differentially expressed.

Five U1 and eight U2 isoforms of the silk moth Bombyx mori exhibiting internal nucleotide differences have been previously identified and characterized in various tissues and developmental stages. In this investigation, it is demonstrated that the levels of some snRNA variants differ in egg and silk gland tissue and change during development. Qualitative and quantitative differences in the U1 and U2 variant populations were observed at three developmental points (early, middle and late) of the silk gland (SG) during the fifth instar larval stage of the silk moth. Statistical analyses of the various isoform populations across the fifth instar larval and egg stages show significant differences for some of the U1 and U2 variants. The representation of variant sequences in expressed U1 and U2 sequences (RT-PCR libraries) and in a whole-genome shotgun (WGS) assembly database was confirmed. In addition, conserved elements in the promoter 5'-flanking region of the U1 and U2 variants were identified in the WGS.

Superimposing polymorphism: the case of a point mutation within a polymorphic Alu insertion.

The COL3A1 Alu insertion is a member of the AluY subfamily. It has been found to be absent in non-human primates and polymorphic in worldwide human populations. The integration of the element into the human genome seems to have preceded the initial migration(s) of anatomically modern humans out of the African continent. Although the insertion has been detected in populations from all the continents, its highest frequency values are located within sub-Saharan Africa. The sequence alignment of the COL3A1 insertion from several African individuals revealed a bi-allelic single nucleotide polymorphism (SNP) at the downstream terminus of the element's poly-A tract. Once discovered, a selective PCR procedure was designed to determine the frequency of both alleles in 19 worldwide populations. The A-allele in this binary SNP experiences a clinal increase in the eastward direction from Africa to Southeast Asia and Mongolia, reaching fixation in the two latter regions. The T variant, on the other hand, exhibits a westward clinal increase outside of Africa, with its lowest frequency in Asia and achieving fixation in northern Europe. The presence of this internal SNP extends the usefulness provided by the polymorphic Alu insertion (PAI). It is possible that superimposing polymorphisms like this one found in the COL3A1 locus may accentuate signals from genetic drift events allowing for visualization of recent dispersal patterns.