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PubMed2000

Genetic variation at position -1082 of the interleukin 10 (IL10) promotor and the outcome of multiple sclerosis.

Interleukin-10 is a potent immunomodulatory cytokine with possible implications for the pathogenesis of multiple sclerosis. Increased IL10 mRNA expression is associated with stable disease. The interleukin 10 gene is highly polymorphic and certain haplotypes result in differential interleukin-10 expression. The presence of guanine instead of adenine at position -1082 in the IL10 promotor was shown to result in a higher IL10 production. We analysed this diallelic polymorphism in patients with multiple sclerosis but did not find any association between a certain -1082 IL10 genotype and susceptibility to or severity of multiple sclerosis.

Alleles↗
PubMed2001

Common genetic variation in ABCA1 is associated with altered lipoprotein levels and a modified risk for coronary artery disease.

BACKGROUND: Low plasma HDL cholesterol (HDL-C) is associated with an increased risk of coronary artery disease (CAD). We recently identified the ATP-binding cassette transporter 1 (ABCA1) as the major gene underlying the HDL deficiency associated with reduced cholesterol efflux. Mutations within the ABCA1 gene are associated with decreased HDL-C, increased triglycerides, and an increased risk of CAD. However, the extent to which common variation within this gene influences plasma lipid levels and CAD in the general population is unknown. METHODS AND RESULTS: We examined the phenotypic effects of single nucleotide polymorphisms in the coding region of ABCA1. The R219K variant has a carrier frequency of 46% in Europeans. Carriers have a reduced severity of CAD, decreased focal (minimum obstruction diameter 1.81+/-0.35 versus 1.73+/-0.35 mm in noncarriers, P:=0.001) and diffuse atherosclerosis (mean segment diameter 2.77+/-0.37 versus 2.70+/-0.37 mm, P:=0.005), and fewer coronary events (50% versus 59%, P:=0.02). Atherosclerosis progresses more slowly in carriers of R219K than in noncarriers. Carriers have decreased triglyceride levels (1.42+/-0.49 versus 1.84+/-0.77 mmol/L, P:=0.001) and a trend toward increased HDL-C (0.91+/-0.22 versus 0.88+/-0.20 mmol/L, P:=0.12). Other single nucleotide polymorphisms in the coding region had milder effects on plasma lipids and atherosclerosis. CONCLUSIONS: These data suggest that common variation in ABCA1 significantly influences plasma lipid levels and the severity of CAD.

ATP Binding Cassette Transporter 1↗
PubMed1997

Genetic variation in two cultures of Bradyrhizobium japonicum 110 differing in their ability to impart drought tolerance to soybean.

The polymerase chain reaction with arbitrary primers (RAPD) discriminated between two separately maintained cultures of Bradyrhizobium japonicum USDA 110 differing in symbiotic performance under drought conditions. Since strain 110 is used in inoculum production, the use of RAPD to monitor inoculum cultures could help to preserve their genetic composition and prevent the loss of important symbiotic properties. The use of RAPD could also be extended to other B. japonicum strains currently used in inoculum production.

Genetic Variation↗
PubMed2003

Palaeoceanographic implications of genetic variation in living North Atlantic Neogloboquadrina pachyderma.

The shells of the planktonic foraminifer Neogloboquadrina pachyderma have become a classical tool for reconstructing glacial-interglacial climate conditions in the North Atlantic Ocean. Palaeoceanographers utilize its left- and right-coiling variants, which exhibit a distinctive reciprocal temperature and water mass related shift in faunal abundance both at present and in late Quaternary sediments. Recently discovered cryptic genetic diversity in planktonic foraminifers now poses significant questions for these studies. Here we report genetic evidence demonstrating that the apparent 'single species' shell-based records of right-coiling N. pachyderma used in palaeoceanographic reconstructions contain an alternation in species as environmental factors change. This is reflected in a species-dependent incremental shift in right-coiling N. pachyderma shell calcite delta18O between the Last Glacial Maximum and full Holocene conditions. Guided by the percentage dextral coiling ratio, our findings enhance the use of delta18O records of right-coiling N. pachyderma for future study. They also highlight the need to genetically investigate other important morphospecies to refine their accuracy and reliability as palaeoceanographic proxies.

Animals↗
PubMedDate not supplied

Genetic variation in ABCB1 influences paclitaxel pharmacokinetics in Japanese patients with ovarian cancer.

Paclitaxel, an antineoplastic agent used for the treatment of ovarian cancer, is metabolized by cytochrome P450 (CYP)3A4 and CYP2C8 and is excreted from cells by ATP-binding cassette (ABCB1) (multi-drug resistance [MDR1], P-glycoprotein). Expression of these proteins is regulated by pregnane X receptor (PXR). Although there are common genetic polymorphisms in the genes encoding these proteins, their effect on the clinical efficacy of paclitaxel is unclear. We therefore examined the relationship of the paclitaxel pharmacokinetics in 13 patients with ovarian cancer to polymorphisms in CYP2C8, CYP3A5, ABCB1, and PXR. We found high interindividual variability in the plasma concentrations of two metabolites, 6alpha-hydroxypaclitaxel and p-3'-hydroxypaclitaxel. All the patients were genotyped as CYP2C8*1/*1. Neither the CYP3A5 A6986G (CYP3A5*3) nor the PXR C-25385T alleles were associated with altered plasma concentrations of paclitaxel and its metabolites. ABCB1 T-129C, T1236C, and G2677(A,T), however, was associated with lower area under the plasma concentration-time curve (AUC) of paclitaxel. We also observed a significant correlation between the AUC (r=-0.721) or the total clearance of paclitaxel (CL(tot)) (r= 0.673) and the ABCB1 mutant allele dosage in each patient. Taken together, our findings suggest that interindividual variability in paclitaxel pharmacokinetics could be predicted by ABCB1 genotyping.

ATP Binding Cassette Transporter, Subfamily B↗
PubMed2002

Genetic variation at the O-antigen biosynthetic locus in Pseudomonas aeruginosa.

The outer carbohydrate layer, or O antigen, of Pseudomonas aeruginosa varies markedly in different isolates of these bacteria, and at least 20 distinct O-antigen serotypes have been described. Previous studies have indicated that the major enzymes responsible for O-antigen synthesis are encoded in a cluster of genes that occupy a common genetic locus. We used targeted yeast recombinational cloning to isolate this locus from the 20 internationally recognized serotype strains. DNA sequencing of these isolated segments revealed that at least 11 highly divergent gene clusters occupy this region. Homology searches of the encoded protein products indicated that these gene clusters are likely to direct O-antigen biosynthesis. The O15 serotype strains lack functional gene clusters in the region analyzed, suggesting that O-antigen biosynthesis genes for this serotype are harbored in a different portion of the genome. The overall pattern underscores the plasticity of the P. aeruginosa genome, in which a specific site in a well-conserved genomic region can be occupied by any of numerous islands of functionally related DNA with diverse sequences.

Amino Acid Sequence↗
PubMed1999

Limited genetic variation in Lacerta mixta and its parthenogenetic daughter species: evidence from cytochrome b and ATPase 6 gene DNA sequences.

Little mtDNA variation was observed among populations of the bisexual Caucasian rock lizard Lacerta mixta and unisexual L. dahli and L. armeniaca. Three haplotypes were detected in L. mixta and the maximum pairwise difference among the samples was 0.67%. No intra- and interspecific variation was found among populations of either L. armeniaca or L. dahli. Moreover, both unisexual species were identical to one of the three haplotypes of L. mixta. The limited variation in L. mixta is likely the result of bottleneck effect, although the small sample size may also be responsible. The lack of variation in the unisexual was attributed to the restricted variation among the maternal parents, limited involvement of females in the hybridization, and recent origin.

Adenosine Triphosphatases↗
PubMed1996

Association of genetic variation at the beta-fibrinogen gene locus and plasma fibrinogen levels; interaction between allele frequency of the G/A-455 polymorphism, age and smoking.

The beta-fibrinogen G/A-455 polymorphism genotype along with plasma fibrinogen levels was determined in 482 healthy middle-aged men, of whom 231 were smokers. Smokers had the highest plasma fibrinogen levels (2.92 g/l), ex-smokers the next (2.73 g/l), and never-smokers the lowest levels (2.66 g/l, P < 0.001). Those with one or two A-455 alleles had significantly higher plasma fibrinogen levels in never-smokers and ex-smokers (8.2% and 9.0%, respectively, P < 0.05), and the effect was larger in younger men (45 < 55 years, 11.6%, P = 0.002) than older men (> 65 years, 4.5%, NS), and was not significant in smokers (2.4%, P > 0.05). Allele frequencies were calculated and compared across age groups and between smokers and non-smokers. The difference in frequency of the A-455 allele between smokers and non-smokers varied significantly with age (P < 0.01), with the frequency of the A-455 allele being significantly lower in smokers than in non-smokers in subjects aged > 65 years (P < 0.05), but not in younger men. This demonstrates an interaction between age, smoking and allele frequency of the G/A-455 polymorphism in this population-based sample.

Age Factors↗
PubMed1995

Genetic variation and geographic distribution on the mitochondrial DNA in local populations of the musk shrew, Suncus murinus.

The musk shrew (Suncus Murinus) is widely distributed throughout Asia and East Africa. The mitochondrial DNA (mtDNA) of this species was analyzed in individuals from 31 local populations in nine Asian countries and Mauritius, using 17 restriction endonucleases. Although fourteen and nine mtDNA haplotypes were detected from Bangladesh and Nepal, respectively, one to four haplotypes were found in each Southeast Asian country, and one common haplotype existed in Japan, Philippines, Vietnam, Thailand and Indonesia. Clustering analysis of mtDNA haplotypes classified shrew populations to three groups--continental group (Bangladesh and Nepal), islands' group (insular countries and Vietnam) and Malay group. The average nucleotide diversity among these three groups was calculated to be about 3.5%. These results indicate that the origin of feral populations in this species might be old and their population sizes are extremely large in the continent, and suggest a rapid spread of this animal throughout the islands. Although we have not shown yet an evidence of close relationships between islands' and continental mtDNA haplotypes, it is likely that the musk shrew had migrated from the continent in South Asia to the islands in Southeast Asia recently.

Animals↗
PubMed2006

Genetic variation of the prevailing porcine respiratory and reproductive syndrome viruses occurring on a pig farm upon vaccination.

Recurrence of porcine respiratory and reproductive syndrome (PRRS) was observed on a pig farm after introducing two PRRS live virus vaccines to combat preceding outbreaks. The phylogenetic analysis of the nucleotide sequence encoding the GP5 envelope glycoprotein and the nucleocapsid protein coding sequences (ORF5 and ORF7, respectively) showed a close genetic relationship between the new outbreak-related and one of the vaccine viruses, while the prevailing PRRS virus genetic variants disappeared from the farm. These findings, supported by the epidemiological data, indicate that the new variant PRRS viruses might originate from a vaccine virus and demonstrate the limited efficacy of modified live vaccines against heterologous PRRS virus strains.

Animal Husbandry↗
PubMed2005

Genetic variation and population structure in remnant populations of black rhinoceros, Diceros bicornis, in Africa.

Black rhinoceros (Diceros bicornis) are one of the most endangered mammal species in Africa, with a population decline of more than 96% by the end of the last century. Habitat destruction and encroachment has resulted in fragmentation of the remaining populations. To assist in conservation management, baseline information is provided here on relative genetic diversity and population differentiation among the four remaining recognized subspecies. Using microsatellite data from nine loci and 121 black rhinoceros individuals, and comparing the results with those of other African species affected in similar ways, Diceros bicornis michaeli retained the most genetic diversity (heterozygosity 0.675) compared with Diceros bicornis minor (0.459) and Diceros bicornis bicornis (0.505), suggesting that the duration of the known bottlenecks in these populations has only had a limited impact on diversity. Comparable and moderate degrees of population differentiation were found between D. b. minor, D. b. bicornis and D. b. michaeli. Results from the single sample available of the most endangered subspecies, Diceros bicornis longipes, showed the least diversity of all individuals examined. This information should assist conservation management decisions, especially those affecting population viability assessments and selection of individuals for translocations, and will also facilitate subspecies identification for ex situ individuals of uncertain origin.

Africa, Eastern↗
PubMed1985

Analysis of genetic variation in two human thyroxine-binding plasma proteins by immunodetection after isoelectric focusing.

An immunological method for the detection of two thyroxine-binding plasma proteins, thyroxine-binding globulin (TBG) and thyroxine-binding prealbumin (TBPA), following polyacrylamide gel isoelectric focusing is described. Both proteins show complex electrophoretic patterns, attributable to post-translational glycosylation, which are affected by unfavourable conditions of sample storage. No genetic variants of TBG or TBPA were encountered in a study of N. European individuals (n = 50). The X-linked TBG polymorphism, previously detected using a radiolabelled ligand binding technique in Pacific Islanders, was, however, demonstrable by our new immunological method in a previously untested population (n = 139) from the island of Maewo in Vanuatu.

Gene Frequency↗
PubMed1994

An investigation of natural genetic variation in the circadian system of Drosophila melanogaster: rhythm characteristics and methods of quantification.

Variation in four characteristics of the circadian locomotor activity rhythm was investigated in 24 true-breeding strains of Drosophila melanogaster with a view to establishing methods of phenotypic measurement sufficiently robust to allow subsequent biometric analysis. Between them, these strains formed a representative sample of the genetic variability of a natural population. Period, phase, definition (the degree to which a rhythmic signal was obscured by noise), and rhythm waveform were all found to vary continuously among the strains, although within each strain the rhythm phenotype was remarkably consistent. Each characteristic was found to be sufficiently robust to permit objective measurement using several different methods of quantification, which were then compared.

Animals↗
PubMed1992

Genetic variation in total plasma and high density lipoprotein cholesterol and body weight in medium white turkeys.

Plasma total cholesterol (PC) and its high density lipoprotein cholesterol (HDLC) fraction were determined in 700 16-wk-old Medium White turkeys in Generation 15 of selection for low and high semen ejaculate volumes (SEV). The birds examined were from pedigree matings involving 10 sires mated to 100 dams in each line. Mean PC and HDLC were not different between lines and between sexes within lines. Genetic parameters were estimated for PC, HDLC, and BW. Sire component heritabilities estimated based on pooled data from low and high SEV lines for PC and HDLC were -.03 and .26, respectively. Genetic correlations were .05 between PC and HDLC; .13 between PC and BW; and -.34 between HDLC and BW. It was concluded that variation in PC in 16-wk-old Medium White turkeys is largely due to environmental variation and that the genetic component is largely nonadditive. However, a moderate additive genetic component was observed for HDLC. Further, determination of total PC and HDLC at 16 wk of age does not exhibit a potential value as an indicator of future SEV potential.

Animals↗