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Prior analysis on human protein-coding DNA sequences has identified local base composition as the primary predictor of synonymous codon usage. However, in many organisms, codon usage is influenced by natural selection, particularly for efficient expression of functional gene products. Because viruses are expected to evolve codon usage in the context of their host's molecular machinery, their genomes...
In order to investigate heterosis on a molecular basis, suppression subtractive hybridization was used to analyze the differences in gene expression between porcine F1 hybrids Landrace × Yorkshire and their female parents Yorkshire. From two specific subtractive cDNA libraries, the clones screened out by reverse Northern high-density blots screening were chosen to clone full-length cDNA by RACE. An...
The spliced leader RNA gene (SL RNA) repeat is present in large multicopy arrays and has been used as a marker for the diversity of kinetoplastid protozoans. Intra-array variation could affect conclusions made using a randomly isolated repeat as a marker. We examined the Leishmania major (Friedlin) and Trypanosoma cruzi (CL Brener) genome projects for SL RNA repeat sequences in order to assess their...
Spermadhesins belong to a novel family of secretory proteins of the male genital tract. They are major proteins of the seminal plasma and have been found peripherally associated to the sperm surface. So far, they have only been detected in ungulates, specifically in pig, cattle, and horse, respectively. Spermadhesins form a subgroup of the superfamily of proteins with a CUB-domain that has been found...
Hlx is a homeobox transcription factor gene that is expressed in intestinal and hepatic mesenchyme of the developing mouse embryo and is essential for normal intestinal and hepatic development. Because of the morphological and molecular similarities in the development of the digestive system across species, we hypothesized that the Hlx gene and protein sequences and expression patterns would be conserved...
Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported findings about preferential positioning of splice junctions within the nucleosomes. The RR and YY dinucleotides oscillate counter-phase, i.e., their respective preferred positions are shifted about...
Prophenin-2 (PF-2) is a cathelicidin, 97-amino-acid antimicrobial protein stored in neutrophil secondary granules. PF-2 is expressed specifically in porcine immature myeloid cells; however, little is known about its regulation. In this study, we characterized the 5′ regulatory regions of the PF-2 gene to understand the molecular mechanisms regulating its expression. Using bioinformatic approaches,...
The first autosomal dominant high-grade myopia locus has been mapped to chromosome 18p11.31 between markers D18S59 and D18S1138 by haplotype analysis. Refinement of the region by transmission disequilibrium testing suggests that a candidate gene (or genes) for this locus named myopia 2 (MYP2) is likely in an interval between markers D18S63 and D18S52. Lipin 2 (LPIN2), a candidate gene for lipodystrophy,...
We previously discovered Y-chromosomal red-green opsin genes in two types of owl monkeys with different chromosomal characteristics. In one type, the Y-linked opsin gene is a single-copy intact gene and in the other, the genes exist as multiple pseudogenes on a Y/autosome fusion chromosome. In the present study, we first distinguished the two types of monkeys as distinct allopatric species on the...
MRGX2, a G-protein-coupled receptor, is specifically expressed in the sensory neurons of the human peripheral nervous system and involved in nociception. Here, we studied DNA polymorphism patterns and evolution of the MRGX2 gene in world-wide human populations and the representative nonhuman primate species. Our results demonstrated that MRGX2 had undergone adaptive changes in the path of human evolution,...
In this work we identify an intronless open reading frame encoding an RNase A ribonuclease from genomic DNA from the Iguana iguana IgH2 cell line. The iguana RNase is expressed primarily in pancreas, and represents the majority of the specific enzymatic activity in this tissue. The encoded sequence shares many features with its better-known mammalian counterparts including the crucial His 12 ...
Previous studies on computational gene functional prediction have not fully exploited the taxonomy structure of Gene Ontology (GO). They just select a few classes from GO into a set, and conduct classwise learning of these classes. The pre-selection of learning classes, often done according to the annotation sizes, limits the prediction breadth and depth. This way of pre-selecting learning classes...
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...
Trypsins constitute a subclass of the S1A family of serine peptidases found in all groups of animal and some bacteria. At present, no information about the genomic organisation of trypsins is available for copepods. The only data of copepod trypsins indicate several different trypsins in the marine parasitic copepod Lepeophtheirus salmonis. In the present study, 31.7 kbp of genomic DNA surrounding...
Most endosymbiotic bacteria have extremely reduced genomes, accelerated evolutionary rates, and strong AT base compositional bias thought to reflect reduced efficacy of selection and increased mutational pressure. Here, we present a comparative study of evolutionary forces shaping five fully sequenced bacterial endosymbionts of insects. The results of this study were three-fold: (i) Stronger conservation...
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