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There is a large variation in divergence times across genomic regions between human and chimpanzee. It has been suggested that this could partly result from selection against ancestral gene flow between incipient species in regions of the genome containing genetic incompatibilities. It is possible that such barriers to gene flow could arise in specific genes or in chromosomal inversions. I analysed...
Nebulin family genes are believed to have diverged from a single gene during the evolution of vertebrates. We determined the structure of the amphioxus nebulin gene and showed that in addition to the features of the human nebulin gene, this gene had a LIM domain, secondary super repeats and a giant exon with 98 nebulin repeats containing unique sequences. A transcript of this gene amplified by reverse...
Streptococcus pneumoniae, a facultative human pathogen associated with wide variety of diseases, such as pneumonia, meningitis, sepsis and otitis media. Factors involved in the initial colonization, survival and etiology of this commensal bacteria in the human host from the ex vivo environment is still not clearly understood. Here, we report alterations in global transcriptional profiles of S. pneumoniae...
Although great progress has been made in identifying microRNAs (miRNAs) and their functions, their essential functional features remain largely unknown. In this study, we systemically investigated the nucleotide and thermodynamic folding distribution characteristics of 3853 miRNAs currently reported for metazoans. We determined that uracil is the dominant nucleotide in both mature and precursor sequences,...
Selection at the DNA level is usually detected by analysing substitution rates from multiple-species comparisons. It has been suggested that measures of genetic robustness at the codon level, which can be measured by analysing a single coding sequence, can be used to estimate selection, but the validity of these measures has been questioned. Here I test the efficiency of different measures of genetic...
The paraoxonase (PON) gene family has 3 members, PON1, PON2 and PON3, which are known to be involved in oxidative stress-associated processes such as dyslipidemia, diabetes and coronary heart disease. Although PON3 is the least studied paraoxonase, recent findings have shown that it can significantly reduce atherosclerotic lesion formation and obesity in PON3 transgenic mice. Here, we describe the...
Glutathione S-transferases (GSTs) represent a multifunctional family of enzymes grouped into four main classes (tau, phi, theta, and zeta) conjugating endobiotic and xenobiotic compounds to glutathione. In plants, this is considered to be a crucial step in the detoxification process as the S-glutathionylated metabolites are tagged for vacuolar sequestration. In this work, we have isolated two glutathione...
Based on the hypothesis that highly expressed genes are often characterized by strong compositional bias in terms of codon usage, there are a number of measures currently in use that quantify codon usage bias in genes, and hence provide numerical indices to predict the expression levels of genes. With the recent advent of expression measure from the score of the relative codon usage bias (RCBS), we...
Glycine N-methyltransferase (GNMT) is a tumor susceptibility gene for both hepatocellular carcinoma and prostate cancer. We have previously characterized GNMT genomic structure and mapped its chromosomal localization to 6p12. For this study we identified a GNMT transcriptional start site at the 14th position upstream of the ATG codon. Electrophoretic mobility shift assay results indicate binding of...
It has been reported that components of Cinnamomi Ramulus (CR) demonstrate an anti-inflammatory effect by inhibiting the expression of inducible nitric oxide synthesis (iNOS) and cyclooxygenase-2 (COX-2) and by suppressing nitric oxide (NO) production in the central nervous system (CNS) as well as in the periphery. In this study, microarray analysis was performed to investigate the effect of CR on...
The generation of unmarked deletion mutants free from polar effects on downstream genes is typically a lengthy and arduous process in Streptomyces spp. The use of FLP recombinase can greatly facilitate this process when combined with established polymerase chain reaction (PCR)-targeting techniques. In vivo production of FLP within Streptomyces cells would streamline the process further, but expression...
Immune evasion by Plasmodium falciparum is favored by extensive allelic diversity of surface antigens. Some of them, most notably the vaccine-candidate merozoite surface protein (MSP)-1, exhibit a poorly understood pattern of allelic dimorphism, in which all observed alleles group into two highly diverged allelic families with few or no inter-family recombinants. Here we describe contrasting levels...
RASSF1A, which is frequently found inactivated in human cancers, is revealed as a tumor suppressor gene in nasopharyngeal carcinoma (NPC). Using RASSF1A-expressing (NP69 and HK-1) and non-RASSF1A-expressing (C666-1) cell models, the transcriptional regulation of RASSF1A was studied. By deletion analysis of 3.1 kb of 5′ flanking region, the core promoter of RASSF1A was identified in the region between...
The activation of plasminogen plays a crucial role in a variety of extracellular proteolytic events such as, fibrinolysis, cell migration, ovulation, involution of the mammary gland and the activation of other protease classes and growth factors. In this paper we describe the isolation of the full-length cDNAs of ovine urokinase plasminogen activator (u-PA) and its receptor (u-PAR) using a polymerase...
Staphylococcal peptidoglycan hydrolases are a potential new source of antimicrobials. A large subset harbors C-terminal SH3b_5 cell wall binding domains. These C-terminal domains have been shown to be necessary for accurate cell wall recognition and subsequent staphylolytic activity for some endolysins. Over fifty proteins of staphylococcal or phage origin containing SH3b domains were aligned, yielding...
The medaka (Oryzias latipes), a tiny fish, has been an excellent experimental model for molecular and developmental genetics, and is expected for being a “vertebrate” model animal for population genetics, because 1) there is abundant within-species variation, and 2) the whole genome sequence has been determined for one of the inbred strains. In spite of its potential usefulness, there is no comprehensive...
Due to the ability to respond after exposure to organic toxic compounds, peroxisome proliferation is used as biomarker of exposure to organic pollutants in mussels and in fish. Mussels are worldwide studied as sentinels of pollution in marine environments while mullets such as the thicklip grey mullet Chelon labrosus have been proposed as appropriate sentinel species since they inhabit highly polluted...
Searching for hsp70 genes in Echinococcus granulosus, a divergent cytoplasmic hsp70-like sequence (EgψHsp70) was isolated, possessing a small truncation in the region coding for the C-terminal glycine-rich linker and EEVD-Ct motif. Southern Blot analyses of E. granulosus, and in silico analyses of E. multilocularis indicate that this truncated sequence is repeated several times in both genomes, in...
Aggregatibacter actinomycetemcomitans is a human pathogen that produces the RTX toxin (repeats in toxin), leukotoxin (LtxA). Based on other RTX toxin systems, the product of ltxC, the first gene of the ltx operon, is predicted to be involved in fatty acid modification of LtxA. To determine the function of ltxC in A. actinomycetemcomitans, we generated an ltxC mutation in the highly leukotoxic strain...
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