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PubMed2006

Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1.

BACKGROUND: Genetic diversity of the human immunodeficiency virus type 1 (HIV-1) population within an individual is lost during transmission to a new host. The demography of transmission is an important determinant of evolutionary dynamics, particularly the relative impact of natural selection and genetic drift immediately following HIV-1 infection. Despite this, the magnitude of this population bottleneck is unclear. RESULTS: We use coalescent methods to quantify the bottleneck in a single case of homosexual transmission and find that over 99% of the env and gag diversity present in the donor is lost. This was consistent with the diversity present at seroconversion in nine other horizontally infected individuals. Furthermore, we estimated viral diversity at birth in 27 infants infected through vertical transmission and found there to be no difference between the two modes of transmission. CONCLUSION: Assuming the bottleneck at transmission is selectively neutral, such a severe reduction in genetic diversity has important implications for adaptation in HIV-1, since beneficial mutations have a reduced chance of transmission.

Bayes Theorem↗
PubMed2006

Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps.

Microsatellites are tandemly repeated short DNA sequences that are favored as molecular-genetic markers due to their high polymorphism index. Plant genomes characterized to date exhibit taxon-specific differences in frequency, genomic location, and motif structure of microsatellites, indicating that extant microsatellites originated recently and turn over quickly. With the goal of using microsatellite markers to integrate the physical and genetic maps of Medicago truncatula, we surveyed the frequency and distribution of perfect microsatellites in 77 Mbp of gene-rich BAC sequences, 27 Mbp of nonredundant transcript sequences, 20 Mbp of random whole genome shotgun sequences, and 49 Mbp of BAC-end sequences. Microsatellites are predominantly located in gene-rich regions of the genome, with a density of one long (i.e., > or = 20 nt) microsatellite every 12 kbp, while the frequency of individual motifs varied according to the genome fraction under analysis. A total of 1,236 microsatellites were analyzed for polymorphism between parents of our reference intraspecific mapping population, revealing that motifs (AT)n, (AG)n, (AC)n, and (AAT)n exhibit the highest allelic diversity. A total of 378 genetic markers could be integrated with sequenced BAC clones, anchoring 274 physical contigs that represent 174 Mbp of the genome and composing an estimated 70% of the euchromatic gene space.

Alleles↗
PubMed2004

Trypanosoma cruzi: genetic structure of populations and relevance of genetic variability to the pathogenesis of chagas disease.

Chagas disease, caused by the protozoan Trypanosoma cruzi, has a variable clinical course, ranging from symptomless infection to severe chronic disease with cardiovascular or gastrointestinal involvement or, occasionally, overwhelming acute episodes. The factors influencing this clinical variability have not been elucidated, but it is likely that the genetic variability of both the host and the parasite are of importance. In this work we review the the genetic structure of T. cruzi populations and analyze the importance of genetic variation of the parasite in the pathogenesis of the disease under the light of the histotropic-clonal model.

Animals↗
PubMed2004

Regulation of the activity of the human drug metabolizing enzyme arylamine N-acetyltransferase 1: role of genetic and non genetic factors.

Human arylamine N-acetyltransferases 1 and 2 (NAT1 and NAT2) are polymorphic phase II xenobiotic-metabolising enzymes (XME) that acetylate arylamine compounds. They therefore play an important role in the detoxication and/or metabolic activation of certain therapeutic drugs, occupational chemicals and carcinogens. Although the use of the term "xenobiotic" implies that XME form a separate and distinct class of enzymes, possible endogenous substrates may exist. Unlike NAT2, NAT1 is produced in most tissues. Polymorphism at the NAT1 locus has been associated with the existence of at least 26 allelic variants, generating phenotypic variations in terms of NAT1 catalytic activity. This genetic variation affects the acetylator status of individuals, leading to interindividual differences in drug response and predisposition to disease in humans. Recent studies have shown that non-genetic factors may also regulate NAT1 activity at the posttranslational level, with potentially important consequences for drug toxicity. In this mini-review, we summarise what is currently known about the regulation of NAT1 activity by non-genetic factors, including substrates and oxidative stress. Recent findings presented here may account for the genotype/phenotype relationship for the NAT1 locus being less clear-cut than that for human NAT2.

Alleles↗
PubMed1987

Simulation of genetic control of reproduction in beef cows. II. Derived genetic parameters.

A stochastic computer simulation model was used to predict heritability (h2) and repeatability (t) of derived reproductive traits in beef cattle as a function of underlying, normally-distributed genetic variation in interval from calving to first estrus (postpartum interval) and single-service conception rate. Traits simulated were mating rate, first-service conception rate, overall conception rate, date of first service, number of services during a 63-d breeding season, calving date and postpartum interval. Weight of calf weaned was also simulated on a per-cow-exposed, per-cow-mating, per-cow-calving, per-calf-weaned or adjusted 205-d basis. Derived estimates of h2 for mating rate and date of first service were not significantly different from 0, reflecting the high proportion of cows that were predicted to cycle within the first 21 d of breeding. Estimates of h2 were significant and approached the level of input h2 for overall and first-service conception rate and number of services, suggesting that these traits may be potential selection criteria. Values of h2 for calving date were significant but considerably smaller than input h2. Estimates of t were much larger than h2 for date of first service and calving date, even when no nonadditive genetic or permanent environmental effects were explicitly simulated. Estimates of h2 for weaning weight per cow exposed and especially for weaning weight per cow calving (in the presence of random calf death losses) were much lower than underlying h2 values. Culling of open cows generally reduced genetic variances of derived reproductive traits to negligible levels within three calf crops.

Animals↗
PubMed1987

Genetic relationships and additive genetic variation of productive and reproductive traits in Guernsey dairy cattle.

Data were first lactation production and reproduction records initiated from 1958 to 1981 in two experiment station Guernsey herds. Heritability estimates using paternal half sib groups were .24 +/- .12 for milk yield, .27 +/- .12 for fat yield, and .77 +/- .15 for fat percentage. Heritability estimates for reproductive traits ranged from .01 to .04 for number of services, service period, conception rate, and days open, but were higher for days in milk at first breeding (.12) and age at first calving (.13). Except for age at first calving, coefficients of additive genetic variation were larger for reproductive traits than for productive traits. Genetic correlations between measures of production and reproduction were moderate to large and antagonistic, except that the relationship between production and age at first calving was favorable. Breeding value estimates for milk yield and reproduction were negatively correlated for sires with above average breeding values for milk yield. Huge phenotypic variances for reproductive traits masked substantial additive genetic variation for these traits. When all things are considered it seems unwise to ignore reproductive performance in selection programs for dairy cattle.

Animals↗
PubMed1993

Clinical and genetic studies of renal cell carcinomas in a family with a constitutional chromosome 3;8 translocation. Genetics of familial renal carcinoma.

OBJECTIVE: To describe the clinical course and genetic studies of renal carcinoma in members of a family with the constitutional chromosome translocation, t(3;8) (p14;q24). DESIGN: A follow-up study that updates our 1979 report of renal carcinoma in 10 of these relatives. SETTING: A cancer center and university hospital. PATIENTS: Members of the family, including five carriers of the 3;8 translocation who were in remission of renal cancer. MEASUREMENTS: Clinical follow-up of the family and genetic analyses of the renal cancer specimens of three patients. RESULTS: Renal carcinoma recurred in all five patients in the family at 1 to 16 years of follow-up. Three patients have died of renal cancer, and two are in a second remission. The renal cancers from three family members consistently reveal loss of the entire derivative chromosome 8, which bears the chromosome 3p segment spanning band p14 to the telomere. In contrast, no genetic change was detected in the derivative chromosome 3 or in normal chromosomes 3 and 8. CONCLUSIONS: This family illustrates the importance of clinical follow-up of patients with a hereditary cancer that can develop at multiple foci and recur over time. The inherited 3;8 translocation and loss of the translocated distal chromosome 3p in tumor specimens of family members may help localize the gene or genes involved in the pathogenesis of both familial and sporadic renal carcinoma.

Adult↗
PubMed1976

[Relationship between genetic differentiation of the thymus in mice of different strains and malignant growth. IV. Genetic analysis of the thymic index in mice].

Relative thymus weight was estimated in C3H/He, C57BL/6 mice, their F1 and backcross hybrids, as well as in the progeny of complete diallel crosses between the BALB/c, C3H/He, C57BL/6 and AKR/J strains. On the basis of the analysis of these measurements, a conclusion is drawn that this character is inherited with incomplete dominance of smaller relative weight. The genes determining greater thymus weight are concentrated in the genetic pool of AKR/J and C57BL/6 strains. These genes are characterized by some degree of recessivity with respect to the genes determining smaller thymus weight which are concentrated in the genetic pool of C3H/He and BALB/c strains. The highest concentration of the "plus" and "minus" genes is found in the genetic pools of AKR/J and C3H/He strains respectively.

Animals↗
PubMedDate not supplied

[The genetic contribution to coronary disease. The genetic factors related to lipid metabolism].

The increasing development of molecular genetics, the progress of the Human Genome Project, and the widespread application of its new methods and molecular techniques provide a new perception of coronary heart disease and a better recognition of genetic markers (mutations and polymorphism) related to new or traditional cardiovascular risk factors. An example of this has been the major effort made over the last years to evaluate and establish the genetic molecular mechanisms that are the basis of the synthesis of apolipoproteins, lipoprotein processing enzymes and lipoprotein receptors. These are some of the subjects discussed in this review [apoB, apoE, atherogenic lipid profile and CETP, and Lp(a)], in which the role of polymorphic alleles and isoforms in cardiovascular risk and coronary heart disease is stressed.

Apolipoproteins↗
PubMed2002

Genetic basis of systemic lupus erythematosus: a review of the unique genetic contributions in African Americans.

Systemic lupus erythematosus (SLE) is a complex autoimmune disease involving critical genetic and environmental risk factors. SLE is a relatively common disease among African American women, affecting as many as one in 250. A collection of more than 250 African American and European American pedigrees multiplex for SLE have been collected in Oklahoma over the past decade for the purpose of identifying the genetic risk factors involved in the pathogenesis of SLE. A genome scan has been performed, and interestingly, the linkage results usually dominate in families from one or the other of these ethnicities. For example, the linkage effect at 1q21-22 near FcgammaRIIA is much stronger in the African American pedigrees than in the European American pedigrees. On the other hand, a gene near the top of chromosome4 (at 4p l6-15) contributes to SLE in the European American pedigrees, but not in the African American pedigrees. The racially-specific results lead to the tentative conclusion of genetic differences associated with SLE in African Americans and European Americans. The identification of the genes responsible for the observed linkage effects will provide fundamental knowledge concerning SLE and may even provide new targets for therapy and strategies to defeat this enigmatic and difficult disease.

Black People↗
PubMed2002

[Detection of the genetically modified organisms in genetically modified soybean and maize by polymerase chain reaction method].

A method for the detection of the (genetically modified organism GMOs) in genetically modified soybean (Round-up Ready soybean, RR soybean) and maize(Bt-176 maize) is described. The polymerase chain reaction (PCR) method is discussed with the genetically modified soybean and maize whose contents are known. The detection limit can be 0.1%, that is to say, we can detect the GMO in the food whose content is only 0.1%, the detection method is just a screening method. The procedure includes: (1) extraction of genomic DNA of maize and soybean, (2) amplification of the inserted genes, CaMV35S promoter and the NOS terminator inserted by means of the polymerase chain reaction (PCR) method, (3) amplification of the specific genes of maize and soybean in order to determine that the samples are maize and soybean, (4) characterization and confirmation of the PCR products by restriction enzyme analysis and the electrophoresis on agarose gel. The RR soybean contains CaMV35S promoter and NOS terminator, and the Bt-176 maize contains only CaMV35S promoter. Due to the high content of the starch in maize, the effect of the electrophororesis is not so good as of the soybean's.

DNA, Plant↗
PubMed2004

[Genetics of preeclampsia: an approach to genetic linkage studies].

Due to its high prevalence during pregnancies, preeclampsia is considered an important public health problem. Many investigators agree in that its expression is related to the interaction between genetic and environmental factors. Many studies have searched for genetic factors, attempting to identify chromosomal regions or candidate genes whose variants may be related to high preeclampsia susceptibility. Several studies have associated a number of susceptibility genes to preeclampsia, but the results have not been replicated consistently in all populations. Mapping of genes and chromosomal regions by linkage analysis has located potential markers on chromosomes 2 and 4. Identification of the genes located in these candidate regions will pinpoint the genetic risk factors, will lead to a better understanding of the syndrome, and will provide clues for its prevention and treatment.

Female↗
PubMed2005

[The "horse-shoe effect"of correspondence analysis for human population genetic structure and its population genetic explanation].

At present study, the reasons of "horse-shoe effect" in correspondence analysis for analyzing human population genetic structure was explained. Based on the structure of gene frequency matrix, we displaye the different patterns of Scallergram of correspondent analysis from different types of loci (HLA-A locus, and STR- CSF1PO locus in Chinese Han populations). The results indicate that different types of loci showed different patterns of Scallergram of correspondent analysis. When some alleles have very low frequency in the gene frequency matrix, there would be "horse-shoe effect" in the Scallergram of correspondent analysis. The reason is that the c2 distance measurement in correspondent analysis usually overrates the effect of the genes with low frequencies. To carry out the correspondent analysis of human population genetic structure, when the Scallergram presents "horse-shoe effect", one should examine the structure of gene frequency matrix, and confirm whether the "horse-shoe effect" shows the real pattern of population genetic structure. Only in this way, one can explain the "horse-shoe effect" correctly.

Alleles↗
PubMed2006

Testing the limits of care. Concern about 'genetic discrimination' from employers and insurers trying to keep costs down casts a pall on genetic testing.

The specter of "genetic discrimination" casts a long shadow over the breakthroughs and the promise of advances in genetic testing. Nearly 70% of respondents in a recent survey said they are concerned about who would have access to genetic data. But scientists say the tests can offer real benefits. Paul Femhoff, left, says a child identified with fragile X syndrome, for example, could benefit from early treatment.

Cost Control↗
PubMed1989

Genetic studies of low-abundance human plasma proteins. XIII. Population genetics of C1R complement subcomponent and description of new variants.

Isoelectric focusing and immunoblotting reveals considerable biochemical and genetic variation in the C1R subcomponent of the first complement component. The nature of the intraindividual biochemical variation can be explained by differences in sialic acid content because after digestion with neuraminidase the terminal sialic acids are removed to yield a single major band corresponding to the C1R polypeptide. Plasma samples from a large number of different ethnic groups, consisting of U.S. whites, U.S. blacks, Nigerian blacks, and Inuit, Aleut, and Amerindian populations from the Western Hemisphere have revealed genetically determined charge variation with heterozygous phenotypes consisting of two major asialo bands, indicating that the underlying variation is not due to variation in sialic acid content. Two previously reported common alleles, C1R*1 and CIR*2, have been observed in all studied populations, the notable exception being the Dogrib Indian population, which is devoid of the C1R*2 allele. Several new alleles--designated C1R*3, C1R*4, C1R*5, C1R*6, and C1R*7-have been observed, with variable frequencies ranging from the occurrence in a single individual and related family members to the polymorphic occurrence of certain alleles in several populations. Of these new alleles, the C1R*5 is of considerable interest in population and anthropological genetics studies. The C1R*5 allele is widely distributed, at a frequency of .03 to .17, in all of the North American aboriginal populations screened. This allele is not present in U.S. whites but is present at a polymorphic frequency in U.S. and Nigerian blacks.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗
PubMed1989

[Genetic linkage of the autosomal dominant form of Charcot-Marie-Tooth amyotrophy and 3 genetic markers on chromosome 1].

In a large pedigree with the autosomal dominant form of Charcot-Marie-Tooth neuropathy type I (CMT 1) segregating in four generations, genetic linkage was studied between this disease and three genetic markers from the centromere region of chromosome 1: Duffy blood group (Fy), salivary and pancreatic isoamylases (AMY 1, AMY 2), and DNA polymorphism at the antithrombin III locus, detected with the probe pAT3c. The lod-scores found do not support linkage between CMT 1 and both Fy and AT 3, since they are negative for all recombination frequencies. Very close linkage could have been excluded. For the AMY polymorphism, the pedigree was not linkage-informative. In agreement with the data from literature, these results support the notion of genetic heterogeneity of CMT 1: in the pedigree under study, the responsible locus is probably not in the centromeric region of the chromosome 1, where it was shown to map to in several other pedigrees. Thus, there seem to exist at least two loci responsible for this type of CMT disease.

Antithrombin III↗
PubMed1987

[Genetics and evolution of the Lpm-system in American mink. VI. Identification, genetic control and phylogenesis of the new allotype Lpm13].

Data on immuno- and biochemical identification, genetic control and phylogenesis of new allotype Lpm13 of the Lpm system in domestic mink are presented. This allotype is encountered in mink populations with the frequency 0.9 and higher. The availability of Lpm13 genetic marker permitted another haplotype to be revealed, in addition to the eight known Lpm haplotypes by means of genetic analysis. It was established that, alongside with the earlier described haplotype Lpm3,4,6,8,9,10,11 (abbreviation H3), there exists a similar haplotype, Lpm3,4,6,8,9,10,11,13 (abbreviation H3.13), containing the Lpm13 gene. Of the rest seven haplotypes, five have the Lpm13 gene and two do not. Taking into account this gene and corresponding antigenic marker, the differentiation of 28, instead of 25, phenotypes and 45, instead of 36, genotypes for the Lpm system became possible. Lpm13 antigenic specificity was found with no exception in all individual serum samples taken from ten species and interspecific hybrids of Mustelidae which are closely related to domestic mink. The data obtained give grounds to refer the newly identified Lpm13 gene to the first evolutionary conservative category of genes of the multigenic Lpm system which is also represented by the Lpm6, Lpm9, Lpm10 and Lpm11 genes. The hypotheses of instantaneous formation of polymorphism of the Lpm system in domestic mink are briefly regarded.

Animals↗
PubMed1973

Genetic manipulation of Aedes aegypti: incorporation and maintenance of a genetic marker and a chromosomal translocation in natural populations.

Studies with Aedes aegypti were undertaken to determine if an alien genotype can be (1) incorporated into a natural population and (2) maintained for several generations on its own without any subsequent introductions. Such information is an essential prerequisite for successful application of any genetic control method. Data from a walk-in, field population cage and from field releases of a genetic marker and a chromosomal translocation have demonstrated both genetic incorporation and persistence for at least three successive generations. This is the first demonstration of its type with any vector species.

Aedes↗