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PubMed2003

The origins and genetic structure of three co-resident Chinese Muslim populations: the Salar, Bo'an and Dongxiang.

A genome-based investigation of three Muslim populations, the Salar, Bo'an, and Dongxiang, was conducted on 212 individuals (148 males, 64 females) co-resident in Jishisan County, a minority autonomous region located in the province of Gansu, PR China. The Salar are believed to be of Turkic origin, whereas the Bo'an and Dongxiang both speak Mongolian. Biparental dinucleotide markers on chromosomes 13 and 15 indicated elevated mean homozygosity in the Salar (0.32), Bo'an (0.32), and Dongxiang (0.27), equivalent to inbreeding coefficients ( F(is) ) of 0.16; 0.12; 0.01, confirming varying levels of endogamous and consanguineous marriage in all three communities. Y-chromosome unique event polymorphisms (UEPs) showed that males in the three communities shared common ancient origins, with 80-90% of haplotypes in common. However, the high levels of community-specific Y-chromosome STR haplotypes strongly suggested the action(s) of founder effect, genetic drift and preferential consanguinity during more recent historical time. By comparison with the marked inter-community differentiation revealed by the Y-chromosome STRs (29.4%), the mtDNA data indicated similarity between the female lineages of each community with just 1.2% inter-community variation. The combined use of these different marker systems gives an in-depth historical perspective, and provides evidence of past inter-marriage between genetically diverse male founders of each community and Han Chinese females with subsequent community endogamy.

Adolescent↗
PubMed2005

[The effect of marriage migration on the genetic structure of the Taimyr Nganasan population: genealogical analysis inferred from MtDNA markers].

The marriage structure of Nganasans during the time period from 1796 to 1991 and genealogy of carriers of mitochondrial DNA haplotypes was studied in a sample of 280 individuals. It was shown that, from the beginning of its formation to the late 1970s, the population exhibited high endogamy (1976, 83.8%; 1926, 88.4%; 1976, 74.3%). The main source of traditional marriage migration (preferentially female) was populations of Entsy and, indirectly, Nentsy. Intense assimilation of Nganasans by the immigrant population, and to a lesser extent, by Dolgans, in the second half of the 20th century resulted in a reduction of endogamy index in Avam Nganasans to 42.5% by 1991. Assimilation by the immigrants was predominantly paternal, promoting preservation of the historically formed genetic diversity of the Nganasan mitochondrial gene pool. Genealogical analysis of mtDNA haplotypes showed that a relatively high total frequency of Western Eurasian mtDNA haplogroups (20.4%) in the Mongoloid (according to anthropological type) Nganasan population is explained not only by the common ethnic origin with Entsy and Nentsy, but also by direct marriage migration from the Entsy population and indirect marriage migration, from the Nentsy population. This migration led to accumulation of Entsy-Nentsy maternal lineages in the genealogy of Avam Nganasans (38.9% of the total number). Of all mtDNA haplotypes, 28.6% were introduced to Avam Nganasans by female Entsy and Nentsy, whereas the total frequency of these haplotypes was 0.204. Genetic diversity of mitochondrial DNA haplotypes was 0.935.

DNA, Mitochondrial↗
PubMed1980

OK10, an avian acute leukemia virus of the MC 29 subgroup with a unique genetic structure.

The RNA of defective avian acute leukemia virus OK10 was isolated from a defective virus particle, released by OK10-transformed nonproducer avian fibroblasts, as a 60S complex consisting of 8.6-kilobase subunits. Oligonucleotide fingerprinting and RNA.cDNA hybridization identified two sets of sequences in OK10 RNA: group-specific sequences, which are related to all nondefective members of the avian tumor virus group, and a sequence closely related to the subgroup-specific sequences (mcv) of the myelocytomatosis virus (MC29) subgroup of avian acute leukemia viruses. Hence, OK10 is classified as a member of the MC29 subgroup of avian tumor viruses, in agreement with classification based on its oncogenic spectrum. The group-specific sequences of OK10 RNA include partial (Delta) pol and env genes, a c-region, and, unlike those of all other members of the MC29 subgroup, a complete gag gene. Oligonucleotide mapping revealed 5'-gag-Deltapol-mcv-Deltaenv-c-3' as the order of the subgroup-specific and group-specific elements of OK10 RNA. The genetic unit gag-Deltapol-mcv, measuring approximately 6.4 kilobases, codes for the nonstructural, presumably transforming, 200,000-dalton OK10-specific protein and also includes the gag gene coding for the internal virion proteins. Because gag is the only intact virion gene shared in addition to regulatory RNA sequences between OK10 and nondefective avian tumor viruses, it is concluded that the gag gene is sufficient for the formation of a defective virus particle. Comparisons among the RNAs and gene products of different viruses of the MC29 subgroup show that they share 5'-terminal gag-related and internal mcv sequences but differ from each other in intervening gag-, pol-, and mcv-related sequences. It follows that the probable transforming genes and their protein products have two essential domains, one consisting of conserved 5' gag-related and the other of 3' mcv-related sequence elements. In the light of this and previous knowledge we can now distinguish two designs among five different transforming onc genes of avian tumor viruses: onc genes with coding sequences unrelated to virion genes, like those of Rous sarcoma virus and avian myeloblastosis virus, and onc genes with coding sequences that are hybrids of virion genes and specific sequences, like those of the MC29 subgroup viruses, of avian erythroblastosis virus, and of Fujinami sarcoma virus.

Animals↗
PubMed1977

[Role of the membranes in the regulation of the activity of genetic structures of bacteria and mitochondria].

The literature on DNA interaction with both the prokaryotic cell membranes and the mitochondria of the Eukaryota is surveyed. Data are presented in favour of membrane localization of DNA and of the regulatory role of membranes in genome expression. A possible "conformational" mechanism of the control of gene activity by conformational changes of membranes related to cell metabolism is discussed. The problems of protein-nucleic recognition are concerned.

Cell Membrane↗
PubMed1994

Genetic structure of the Enterococcus faecalis plasmid pAD1-encoded cytolytic toxin system and its relationship to lantibiotic determinants.

Pheromone-responsive conjugative plasmids are unique to the species Enterococcus faecalis. Many pheromone-responsive plasmids, including those frequently isolated from sites of infection, express a novel cytolysin that possesses both hemolytic and bacteriocin activities. Further, this cytolysin has been shown to be a toxin in several disease models. In the present study, nucleotide sequence determination, mutagenesis, and complementation analysis were used to determine the organization of the E. faecalis plasmid pAD1 cytolysin determinant. Four open reading frames are required for expression of the cytolysin precursor (cylLL, cylLS, cylM, and cylB). The inferred products of two of these open reading frames, CyILL and CyILS, constitute the cytolysin precursor and bear structural resemblance to posttranslationally modified bacteriocins termed lantibiotics. Similarities between the organization of the E. faecalis cytolysin determinant and expression units for lantibiotics exist, indicating that the E. faecalis cytolysin represents a new branch of this class and is the first known to possess toxin activity.

Adenosine Triphosphate↗
PubMed1977

Genetic structure of the replication origin of bacteriophage lambda.

A fragment of bacteriophage lambda DNA produced by the restriction endonuclease Eco RI and extending from the immunity region to a point inside gene O is found to have a fully functional origin of replication. Seven ori- mutations of lambda cluster in a small region just to the left of the Eco RI cleavage site which defines the right end of this fragment. These mutations lie within gene O.

Chromosome Mapping↗
PubMed2002

Investigation of the population genetic structure and mating system in the ant Pheidole pallidula.

The origin of eusociality in haplo-diploid organisms such as Hymenoptera has been mostly explained by kin selection. However, several studies have uncovered decreased relatedness values within colonies, resulting primarily from multiple queen matings (polyandry) and/or from the presence of more than one functional queen (polygyny). Here, we report on the use of microsatellite data for the investigation of sociogenetic parameters, such as relatedness, and levels of polygyny and polyandry, in the ant Pheidole pallidula. We demonstrate, through analysis of mother-offspring combinations and the use of direct sperm typing, that each queen is inseminated by a single male. The inbreeding coefficient within colonies and the levels of relatedness between the queens and their mate are not significantly different from zero, indicating that matings occur between unrelated individuals. Analyses of worker genotypes demonstrate that 38% of the colonies are polygynous with 2-4 functional queens, and suggest the existence of reproductive skew, i.e. unequal respective contribution of queens to reproduction. Finally, our analyses indicate that colonies are genetically differentiated and form a population exhibiting significant isolation-by-distance, suggesting that some colonies originate through budding.

Animals↗
PubMed1997

Isolation of the Bacillus subtilis cdd downstream region and analysis of genetic structure around the cdd vicinity.

A 310 bp EcoRI/HindIII fragment downstream of the Bacillus subtilis cdd gene was isolated from pSO52 which harbours the cdd gene and its vicinity, and was inserted into the pDIA5304. The hybrid vector pSO701 was integrated into the targeted locus of the B. subtilis chromosome and the cdd downstream region was rescued by furthermost BamHI walking toward the sigA locus. By sequencing and analyzing the intergenic region between the cdd and p23-dnaG-sigA operon from the selected clone pSO702, the era genes encoding glycyl tRNA synthetase alpha and beta chains with two unknown distal genes at both terminals were identified and mapped. The cdd was separated by 6,964 bp from the p23-dnaG-sigA operon. Combined data with an additional analysis of the cdd upstream from the sequenced 280 kb stretch in GenBank database (accession No. D84432) indicates that the revised gene order like hrcA-grpE-dnaK-dnaJ-phoH-dgk-cdd-era-tRNA( gly) synthetase alpha and beta-p23-dnaG-sigA-cccA with unidentified distal genes was established genetically on a counter clockwise orientation at 225 degrees of the linkage map.

Bacillus subtilis↗
PubMed2003

Y chromosome STR haplotypes and the genetic structure of U.S. populations of African, European, and Hispanic ancestry.

To investigate geographic structure within U.S. ethnic populations, we analyzed 1705 haplotypes on the basis of 9 short tandem repeat (STR) loci on the Y-chromosome from 9-11 groups each of African-Americans, European-Americans, and Hispanics. There were no significant differences in the distribution of Y-STR haplotypes among African-American groups, whereas European-American and Hispanic groups did exhibit significant geographic heterogeneity. However, the significant heterogeneity resulted from one sample; removal of that sample in each case eliminated the significant heterogeneity. Multidimensional scaling analysis of R(ST) values indicated that African-American groups formed a distinct cluster, whereas there was some intermingling of European-American and Hispanic groups. MtDNA data exist for many of these same groups; estimates of the European-American genetic contribution to the African-American gene pool were 27.5%-33.6% for the Y-STR haplotypes and 9%-15.4% for the mtDNA types. The lack of significant geographic heterogeneity among Y-STR and mtDNA haplotypes in U.S ethnic groups means that forensic DNA databases do not need to be constructed for separate geographic regions of the U.S. Moreover, absence of significant geographic heterogeneity for these two loci means that regional variation in disease susceptibility within ethnic groups is more likely to reflect cultural/environmental factors, rather than any underlying genetic heterogeneity.

Africa↗
PubMed1998

Genetic structure of the ancestral population of modern humans.

Neutral DNA polymorphisms from an 8-kb segment of the dystrophin gene, previously ascertained in a worldwide sample (n = 250 chromosomes), were used to characterize the population ancestral to the present-day human groups. The ancestral state of each polymorphic site was determined by comparing human variants with their orthologous sites in the great apes. The "age before fixation" of the underlying mutations was estimated from the frequencies of the new alleles and analyzed in the context of these polymorphisms' distribution among 13 populations from Africa, Europe, Asia, New Guinea, and the Americas (n = 860 chromosomes in total). Seventeen polymorphisms older tan 100,000-200,000 years, which contributed approximately 90% to the overall nucleotide diversity, were common to all human groups. Polymorphisms endemic to human groups or continentally restricted were younger than 100,000-200,000 years. Africans (six populations) with 13 such sites stood out from the rest of the world (seven populations), where only 2 population-specific variants were observed. The similarity of the frequencies of the old polymorphisms in Africans and non-Africans suggested a similar profile of genetic variability in the population before the modern human's divergence. This ancestral population was characterized by an effective size of about 10,000 as estimated from the nucleotide diversity; this size may describe the number of breeding individuals over a long time during the Middle Pleistocene or reflect a speciation bottleneck from an initially larger population at the end of this period.

Alleles↗
PubMed1991

Genetic structure of natural populations of Anopheles albimanus in Colombia.

Electrophoretic and cytogenetic studies were undertaken on the population structure of Anopheles albimanus from 11 localities in Colombia, 3 from northern (Atlantic coast) and 8 from southern (Pacific coast) regions. Of the 25 allozyme loci examined, significant allele frequency differences were observed at 4 loci: hydroxy acid dehydrogenase (Had-1) and 3 esterases (Est-2, Est-4 and Est-6). The northern populations had higher variability, with 55% polymorphic loci, a mean heterozygosity of 20.4% and a mean of 3.0 alleles per locus. These values for southern populations were 24%, 9.1% and 1.5%, respectively. There were neither diagnostic loci nor clinal effect on frequencies of allozymes. Except for a small inversion on the X chromosome in low frequency in certain populations, all populations were homosequential in chromosomal banding patterns. Hybrids from matings between natural populations and the Gainesville laboratory strain were fully fertile. Estimates of genetic similarities (0.95-0.97 among southern and 0.99-1.00 among northern populations) suggest a lack of significant genetic differentiation among distant populations in this species. Based on the chromosomal, hybridization and electrophoretic data, we concluded that mosquitoes from the 11 collections were conspecific populations of An. albimanus.

Alleles↗
PubMedDate not supplied

[Examination of genetic structures of sex cells of rats flown during their prenatal development on Cosmos-1514].

Male rats that were flown on Cosmos-1514 during their prenatal days 13 through 18 were investigated. The animals were sacrificed when they reached sexual maturity. Preparations were made of their testes for cytogenetic analysis: spermatocytes were at the stages of diakinesis--metaphase 1. The flown rats had 0.9% reciprocal translocations while the ground-based synchronous controls showed 0.5%. Exposure to space flight factors in combination had a mutagenic effect on gonocytes. However, the adverse effect of microgravity per se was not demonstrated unambiguously.

Animals↗
PubMed2005

Temporal variation of the population structure and genetic diversity of Farfantepenaeus notialis assessed by allozyme loci.

Population genetic studies carried out on penaeid shrimps have disclosed different patterns of population subdivision, revealing new aspects of shrimp biology as well as the effects of historical contingency molding those patterns. However, the stability of observed allele frequencies over time still remains untested. The objective of this article is to show the analysis of the temporal variation of allozymes in a shrimp species inhabiting Cuba which proves that the genetic structure of this species could significantly change in time. The study involves four populations of Farfantepenaeus notialis sampled in a period of 8 years. The significant statistics obtained from partitions observed in 1995 were not detected in 2003 (as suggested by AMOVA and F(ST)), whereas temporal genetic differentiation and heterozygosity became highly significant. The results strongly suggest that the effect of migrations could be the cause for the loss of F. notialis genetic structure in 2003. It is therefore imperative to call attention on the vulnerability of these populations when facing unstable environmental and habitat conditions.

Alleles↗
PubMed1995

Mitochondrial DNA variation and population genetic structure of the northern redbelly dace (Phoxinus eos).

Two sections of the control region and the genes coding for NADH dehydrogenase subunits 5 and 6 (ND-5/6) of mitochondrial DNA (mtDNA) were amplified from Phoxinus eos with the polymerase chain reaction. Both sections of the control region were sequenced directly while the ND-5/6 fragment was sequenced in from each end only. Additionally, the entire ND-5/6 fragment was examined for sequence variation using RFLP analysis. No sequence variation was detected in the control region among 70 individuals sampled from 18 populations across three Ontario regions (Spanish River, Madawaska R. and Cataraqui R.). To examine ND-5/6 variation, a total of 75 individuals were sampled from five populations representing two of the three regions (Madawaska River and Cataraqui R.). Six haplotypes were detected by direct sequencing and four by RFLP analysis. Estimates of population subdivision from RFLP data, sequence analysis, and the two data sets combined for the ND-5/6 fragment, suggest that gene flow is restricted within and between regions. However, estimates of sequence divergence for both sequence and RFLP analysis of this fragment suggested that populations were either founded by already differentiated populations or that populations were founded by a single stock and divergence between regions occurred prior to isolation of populations within regions. These estimates of population structure are much greater than those obtained from allozyme analysis. Additionally, high levels of heterozygosity in nuclear DNA, but low mtDNA diversity suggests that populations have experienced reductions in population size sufficient to reduce only mtDNA variation. Random lineage extinction and limited time for the accumulation of new mutations are likely responsible for low levels of mtDNA variation in ND-5/6 and the control region, while functional constraints may limit variation more than expected in the control region in dace and other fishes.

Animals↗
PubMed2000

Biochemical, structural, genetic, physiological, and pathophysiological features of lipocalin-type prostaglandin D synthase.

Lipocalin-type prostaglandin (PG) D synthase (PGDS) catalyzes the isomerization of PGH(2), a common precursor of various prostanoids, to produce PGD(2), a potent endogenous somnogen and nociceptive modulator, in the presence of sulfhydryl compounds. PGDS is an N-glycosylated monomeric protein with an M(r) of 20000-31000 depending on the size of the glycosyl moiety. PGDS is localized in the central nervous system and male genital organs of various mammals and in the human heart and is secreted into the cerebrospinal fluid, seminal plasma, and plasma, respectively, as beta-trace. The PGDS concentrations in these body fluids are useful for the diagnosis of several neurological disorders, dysfunction of sperm formation, and cardiovascular and renal diseases. The cDNA and gene for PGDS have been isolated from several animal species, and the tissue distribution and cellular localization have also been determined. This enzyme is considered to be a dual functional protein; i.e. it acts as a PGD(2)-producing enzyme and also as a lipophilic ligand-binding protein, because the enzyme binds biliverdin, bilirubin (K(d)=30 nM), retinaldehyde, retinoic acid (K(d)=80 nM) with high affinities. X-ray crystallographic analyses revealed that PGDS possesses a beta-barrel structure with a hydrophobic pocket in which an active thiol, Cys(65), the active center for the catalytic reaction, was located facing to the inside of the pocket. Gene-knockout and transgenic mice for PGDS were generated and found to have abnormalities in the regulation of nociception and sleep.

Amino Acid Sequence↗
PubMed1987

[Inversion polymorphism in the malaria mosquito Anopheles messeae. VII. Fertility and the population genetics structure of the species].

The role of chromosomal inversional complexes of different fecundity has been studied in the process of formation of karyotypic populational structure. Females with homozygotes 2R11 and "north-est" inversional combinations are shown to have maximal total egg production, while females with three or four inversional heterozygotes from XL01, XL12, 2R01, 3R01 and 3L01 demonstrated lower level of fecundity. It is found that the seasonal conversion from r-selection to K-selection occurs in the period of population "prosperity" (July). The results of such conversion are destruction of "northest" genocomplexes and reduction of relative fecundity of inversional homozygotes 2R11-Alternative tendencies take place at the beginning of the reproductive period.

Animals↗
PubMed2006

Genetic structure in aquatic bladderworts: clonal propagation and hybrid perpetuation.

BACKGROUND AND AIMS: The free-floating aquatic bladderwort Utricularia australis f. australis is a sterile F(1) hybrid of U. australis f. tenuicaulis and U. macrorhiza. However, co-existence of the hybrids and parental species has not been observed. In the present study, the following questions are addressed. (a) Does the capacity of the two parental species to reproduce sexually contribute to higher genotypic diversity than that of sterile F(1) hybrid? (b) Are there any populations where two parental species and their hybrid co-exist? (c) If not, where and how do hybrids originate? METHODS: The presence and absence of Utricularia was thoroughly investigated in two regions in Japan. An amplified fragment length polymorphism (AFLP) analysis was conducted for 397 individuals collected from all populations (33 in total) where Utricularia was observed. KEY RESULTS: The mean number of genotypes per population (G) and genotypic diversity (D) were extremely low irrespective of the capacity to reproduce sexually: G was 1.1-1.2 and D was 0.02-0.04. The hybrid rarely co-existed with either parental species, and the co-existence of two parental species was not observed. Several AFLP bands observed in the hybrid are absent in both parental genotypes, and parent and hybrid genotypes in the same region do not show greater genetic similarity than those in distant regions. CONCLUSIONS: The capacity to reproduce sexually in parental species plays no role in increasing genotypic diversity within populations. The observed genotypes of the hybrid could not have originated from hybridization between the extant parental genotypes within the study regions. Considering the distribution ranges of three investigated taxa, it is clear that the hybrid originated in the past, and hybrid populations have been maintained exclusively by clonal propagation, which may be ensured by both hybrid vigor and long-distance dispersal of clonal offspring.

Genotype↗
PubMedDate not supplied

Genetic structure of susceptibility traits for hip dysplasia and microsatellite informativeness of an outcrossed canine pedigree.

An outcrossed canine pedigree was developed for quantitative trait locus (QTL) mapping of hip dysplasia by breeding dysplastic Labrador retrievers to trait-free greyhounds. Measured susceptibility traits included age at onset of femoral capital chondroepiphyseal ossification (OSS), maximum hip distraction (laxity) index (DI), and the dorsolateral subluxation (DLS) score. The pedigrees consisted of 147 dogs representing four generations. For 59 dogs genotyped with 65 microsatellites, the median heterozygosity and polymorphic information content (PIC) values of the F(1) generation were 0.82 and 0.68, respectively. Seventy-seven percent of microsatellites had a PIC greater than 0.59 in the F(1)s. Ninety-six percent of alleles showed Mendelian inheritance. Based on marker informativeness, approximately 350 randomly selected markers would be required for genome-wide screening to obtain an average interval between informative markers of 10 cM. Heritability was estimated as 0.43, 0.5, and 0.61 for OSS, DI, and the DLS score, respectively. Biometric estimates of the mean (+/- variance) effective number of segregating QTLs was 1.2 (+/- 0.05), 0.8 (+/- 0.02), and 1.0 (+/- 0.03) for OSS, DI, and the DLS score, respectively. The distributions of simulated backcross trait data suggested that the loci controlling these traits acted additively and that the DI may be controlled by a major locus. When combined with previous power and quantitative genetic analyses, these estimates indicate that this pedigree is informative for QTL mapping of hip dysplasia traits.

Animals↗