Y-chromosome STR haplotypes in an Italian population sample

A series of cloning vectors with conditional, temperature-sensitive replication that are selectable with ampicillin, chloramphenicol, and kanamycin has been constructed. These vectors are derivatives of a pSC101 mutant that can replicate only at low temperatures. The cloning vectors carry a number of unique restriction sites and provide for screening of recombinant plasmids by alpha complementation. These vectors have proven useful for a variety of applications where conditional replication of a recombinant plasmid is desired.     

Characterization of ancestral and derived Y-chromosome haplotypes of New World native populations

We analyze the allelic polymorphisms in seven Y-specific microsatellite loci and a Y-specific alphoid system with 27 variants (alphah I-XXVII), in a total of 89 Y chromosomes carrying the DYS199T allele and belonging to populations representing Amerindian and Na-Dene linguistic groups. Since there are no indications of recurrence for the DYS199C-->T transition, it is assumed that all DYS199T haplotypes derive from a single individual in whom the C-->T mutation occurred for the first time. We identified both the ancestral founder haplotype, 0A, of the DYS199T lineage and seven derived haplogroups diverging from the ancestral one by one to seven mutational steps. The 0A haplotype (5.7% of Native American chromosomes) had the following constitution: DYS199T, alphah II, DYS19/13, DYS389a/10, DYS389b/27, DYS390/24, DYS391/10, DYS392/14, and DYS393/13 (microsatellite alleles are indicated as number of repeats). We analyzed the Y-specific microsatellite mutation rate in 1,743 father-son transmissions, and we pooled our data with data in the literature, to obtain an average mutation rate of.0012. We estimated that the 0A haplotype has an average age of 22,770 years (minimum 13,500 years, maximum 58,700 years). Since the DYS199T allele is found with high frequency in Native American chromosomes, we propose that 0A is one of the most prevalent founder paternal lineages of New World aborigines.     

Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum

Nonrandom associations of alleles or haplotypes with geographical location can arise from restricted gene flow, historical events (fragmentation, range expansion, colonization), or any mixture of these factors. In this paper, we show how a nested cladistic analysis of geographical distances can be used to test the null hypothesis of no geographical association of haplotypes, test the hypothesis that significant associations are due to restricted gene flow, and identify patterns of significant association that are due to historical events. In this last case, criteria are given to discriminate among contiguous range expansion, long-distance colonization, and population fragmentation. The ability to make these discriminations depends critically upon an adequate geographical sampling design. These points are illustrated with a worked example: mitochondrial DNA haplotypes in the salamander Ambystoma tigrinum. For this example, prior information exists about restricted gene flow and likely historical events, and the nested cladistic analyses were completely concordant with this prior information. This concordance establishes the plausibility of this nested cladistic approach, but much future work will be necessary to demonstrate robustness and to explore the power and accuracy of this procedure.     

Bioelectrical impedance analysis and anthropometry in Ecuadorian children of African ancestry

In the city of Esmeraldas, north-western coast of Ecuador, height, weight, and body composition of 600 male and female schoolchildren of African ancestry in the age groups four, five and six years were investigated. All the children were apparently healthy without any obvious or reported pathologies and in accordance with data from personal information were assigned to one of two socio-economic classes. The greater values for weight and height shown by children in the higher socio-economic group than in the less well off are compatible with those for more fat and water as obtained by the BIA investigation. Additional information on nutritional, muscular and general health status was obtained from positioning and degree of dispersion of the 'Biagram' ellipses. It seems that both the anthropometric and the bioelectrical impedance methods provide useful information on the differences due to belonging to one or other of the socio-economic groups.     

Characterization of an African swine fever virus 20-kDa DNA polymerase involved in DNA repair

African swine fever virus (ASFV) encodes a novel DNA polymerase, constituted of only 174 amino acids, belonging to the polymerase (pol) X family of DNA polymerases. Biochemical analyses of the purified enzyme indicate that ASFV pol X is a monomeric DNA-directed DNA polymerase, highly distributive, lacking a proofreading 3'-5'-exonuclease, and with a poor discrimination against dideoxynucleotides. A multiple alignment of family X DNA polymerases, together with the extrapolation to the crystal structure of mammalian DNA polymerase beta (pol beta), showed the conservation in ASFV pol X of the most critical residues involved in DNA binding, nucleotide binding, and catalysis of the polymerization reaction. Therefore, the 20-kDa ASFV pol X most likely represents the minimal functional version of an evolutionarily conserved pol beta-type DNA polymerase core, constituted by only the "palm" and "thumb" subdomains. It is worth noting that such an "unfingered" DNA polymerase is able to handle templated DNA polymerization with a considerable high fidelity at the base discrimination level. Base excision repair is considered to be a cellular defense mechanism repairing modified bases in DNA. Interestingly, the fact that ASFV pol X is able to conduct filling of a single nucleotide gap points to a putative role in base excision repair during the ASFV life cycle.     

Multiple genotypes of mitochondrial DNA within a horse population from a small region in Yunnan Province of China

mtDNA genotypes of six domestic horses (three adult short horses whose heights are under 1 m and three common domestic horses) from a small region of 15 km2 in Malipo county of Yunnan province of China were investigated by the technique of restriction fragment length polymorphism (RFLP) with 16 restriction endonucleases which recognize 6-bp sequences. An average of 56 fragments for an individual was obtained. Unlike other domestic animals, this population of horses exhibits high mtDNA genetic diversity. Each of the six horses has a specific mtDNA genotype showing a pattern of multiple maternal origins, as suggested by fossil and literature records. We think the population of horses is an amazing seed-resource pool of horses and hence deserves to be paid more attention from the view of conservation genetics. However, it is also remarkable that we did not find any typical mtDNA genetic markers which would discriminate between short horses and common domestic horses.     

Human genetic affinities for Y-chromosome P49a,f/TaqI haplotypes show strong correspondence with linguistics

Numerous population samples from around the world have been tested for Y chromosome-specific p49a,f/TaqI restriction polymorphisms. Here we review the literature as well as unpublished data on Y-chromosome p49a,f/TaqI haplotypes and provide a new nomenclature unifying the notations used by different laboratories. We use this large data set to study worldwide genetic variability of human populations for this paternally transmitted chromosome segment. We observe, for the Y chromosome, an important level of population genetics structure among human populations (FST = .230, P < .001), mainly due to genetic differences among distinct linguistic groups of populations (FCT = .246, P < .001). A multivariate analysis based on genetic distances between populations shows that human population structure inferred from the Y chromosome corresponds broadly to language families (r = .567, P < .001), in agreement with autosomal and mitochondrial data. Times of divergence of linguistic families, estimated from their internal level of genetic differentiation, are fairly concordant with current archaeological and linguistic hypotheses. Variability of the p49a,f/TaqI polymorphic marker is also significantly correlated with the geographic location of the populations (r = .613, P < .001), reflecting the fact that distinct linguistic groups generally also occupy distinct geographic areas. Comparison of Y-chromosome and mtDNA RFLPs in a restricted set of populations shows a globally high level of congruence, but it also allows identification of unequal maternal and paternal contributions to the gene pool of several populations.     

Osteoarthrosis in a rural South African Negro population

The prevalence and distribution of osteoarthrosis has been studied in a South African Negro population. One or more joints were affected in 60% of the males and 48% of the females, compared with a prevalence of 55% in males and 63% in females in a comparable English population. Multiple osteoarthrosis was significantly less common in the African than in the English population, the difference here being greatest in females. Clinical Heberden's nodes were also very infrequent in the African population. However, the Tswana males had significantly more osteoarthrosis of the metacarpophalangeal and proximal interphalangeal joints than was encountered in English males. This is attributed to the traumatic effect of hard manual work which is carried on into old age among most African populations.     

Ethnicity and cardiovascular risk: variations in people of African ancestry and South Asian origin

Mortality from coronary heart disease (CHD), stroke and end-stage renal failure are high in South Asian migrants in the UK. This is associated with high prevalence of diabetes and hypertension. These seem to be manifestations of a metabolic syndrome with insulin resistance (hyperinsulinaemia) and central obesity (based on high waist-to-hip ratio rather than on conventional measures of body mass index). This is associated with sedentary lifestyle, high serum triglycerides and low HDL-cholesterol. Mortality from stroke and end-stage renal failure are high in black migrants to the UK (both Caribbeans and West Africans). However, CHD mortality is low in this group. This pattern of mortality is associated with high prevalence of hypertension and diabetes. This group tends to be obese (particularly women) according to conventional measures of body mass index and to have hyperinsulinaemia, low serum triglycerides and high HDL-cholesterol. Conventional risk factors such as cigarette smoking and hypercholesterolaemia are less prevalent in ethnic minority populations in the United Kingdom and unlikely to explain the differences seen between groups, although each risk factor is likely to contribute to the variation in vascular disease within each group. There is difficulty in reconciling the results of migration studies (eg, from rural to urban environments) pointing to major environmental influences on the changes in cardiovascular risk factors with the consistent pattern of disease of ethnic groups across the world and in subsequent generations, suggesting a certain degree of genetic susceptibility. Important environment-gene interplays might be underlying some of these processes. The detection and management of hypertension and diabetes are still unsatisfactory in inner city areas and show variations by ethnic origin. Strategies for the control of CHD and stroke adopted in European countries directed mostly to white populations may be inappropriate for ethnic minority populations.     

Global matrilineal population structure in sperm whales as indicated by mitochondrial DNA sequences

The genetic variability and population structure of worldwide populations of the sperm whale was investigated by sequence analysis of the first 5'L 330 base pairs in the mitochondrial DNA (mtDNA) control region. The study included a total of 231 individuals from three major oceanic regions, the North Atlantic, the North Pacific and the Southern Hemisphere. Fifteen segregating nucleotide sites defined 16 mtDNA haplotypes (lineages). The most common mtDNA types were present in more than one oceanic region, whereas ocean-specific types were rare. Analyses of heterogeneity of mtDNA type frequencies between oceans indicated moderate (GST = 0.03) but statistically significant (p = 0.0007) genetic differentiation on a global scale. In addition, strong genetic differentiation was found between potential social groups (GST = 0.03-0.6), indicating matrilineal relatedness within groups. The global nucleotide diversity was quite low (pi = 0.004) implying a recent common mtDNA ancestry (< 100,000) years ago) and a young global population structure. However, within this time period, female dispersal has apparently been limited enough to allow the development of global mtDNA differentiation. The results are consistent with those from observational studies and whaling data indicating stable social affiliations, some degree of area fidelity and latitudinal range limitations in groups of females and juveniles.     

Polymorphic sites in human mitochondrial DNA control region sequences: population data and maternal inheritance

Short-circuit current (Isc), transepithelial conductance (Gt), electrical capacitance (CT) and the fluctuation in Isc were analyzed in polarized epithelial cells from the distal nephron of Xenopus laevis (A6 cell line). Tissues were incubated with Na+- and Cl--free solutions on the apical surface. Basolateral perfusate was NaCl-Ringer. Agents that increase cellular cAMP evoked increases in Gt, CT, Isc and generated a Lorentzian Isc-noise. The responses could be related to active, electrogenic secretion of Cl-. Arginine-vasotocin and oxytocin caused a typical peak-plateau response pattern. Stimulation with a membrane-permeant nonhydrolyzable cAMP analogue or forskolin showed stable increases in Gt with only moderate peaking of Isc. Phosphodiesterase inhibitors also stimulated Cl- secretion with peaking responses in Gt and Isc. All stimulants elicited a spontaneous Lorentzian noise, originating from the activated apical Cl- channel, with almost identical corner frequency (40-50 Hz). Repetitive challenge with the hormones led to a refractory behavior of all parameters. Activation of the cAMP route could overcome this refractoriness. All agents caused CT, a measure of apical membrane area, to increase in a manner roughly synchronous with Gt. These results suggest that activation of the cAMP-messenger route may, at least partly, involve exocytosis of a vesicular Cl- channel pool. Apical flufenamate depressed Cl- current and conductance and apparently generated blocker-noise. However, blocking kinetics extracted from noise experiments could not be reconciled with those obtained from current inhibition, suggesting the drug does not act as simple open-channel inhibitor.     

Familial streptomycin ototoxicity in a South African family: a mitochondrial disorder

The vestibular and ototoxic effects of the aminoglycoside antibiotics (streptomycin, gentamycin, kanamycin, tobramycin, neomycin) are well known; streptomycin, in particular, has been found to cause irreversible, profound, high frequency sensorineural deafness in hypersensitive persons. Aminoglycoside ototoxicity occurs both sporadically and within families and has been associated with a mitochondrial DNA (mtDNA) 1555A to G point mutation in the 12S ribosomal RNA gene. We report on the molecular analysis of a South African family with streptomycin induced sensorineural deafness in which we have found transmission of this same predisposing mutation. It is now possible to identify people who are at risk of hearing loss if treated with aminoglycosides in the future and to counsel them accordingly. In view of the fact that aminoglycoside antibiotics remain in widespread use for the treatment of infections, in particular for tuberculosis, which is currently of epidemic proportions in South Africa, this finding has important implications for the family concerned. In addition, other South African families may potentially be at risk if they carry the same mutation.     

Cytosolic enzymes with a mitochondrial ancestry from the anaerobic chytrid Piromyces sp. E2

The anaerobic chytrid Piromyces sp. E2 lacks mitochondria, but contains hydrogen-producing organelles, the hydrogenosomes. We are interested in how the adaptation to anaerobiosis influenced enzyme compartmentalization in this organism. Random sequencing of a cDNA library from Piromyces sp. E2 resulted in the isolation of cDNAs encoding malate dehydrogenase, aconitase and acetohydroxyacid reductoisomerase. Phylogenetic analysis of the deduced amino acid sequences revealed that they are closely related to their mitochondrial homologues from aerobic eukaryotes. However, the deduced sequences lack N-terminal extensions, which function as mitochondrial leader sequences in the corresponding mitochondrial enzymes from aerobic eukaryotes. Subcellular fractionation and enzyme assays confirmed that the corresponding enzymes are located in the cytosol. As anaerobic chytrids evolved from aerobic, mitochondria-bearing ancestors, we suggest that, in the course of the adaptation from an aerobic to an anaerobic lifestyle, mitochondrial enzymes were retargeted to the cytosol with the concomitant loss of their N-terminal leader sequences.     

Different genetic components in the Ethiopian population, identified by mtDNA and Y-chromosome polymorphisms

Structural equation modeling procedures were used to examine relationships among several war zone stressor dimensions, resilience-recovery factors, and post-traumatic stress disorder symptoms in a national sample of 1,632 Vietnam veterans (26% women and 74% men). A 9-factor measurement model was specified on a mixed-gender subsample of the data and then replicated on separate subsamples of female and male veterans. For both genders, the structural models supported strong mediation effects for the intrapersonal resource characteristic of hardiness, postwar structural and functional social support, and additional negative life events in the postwar period. Support for moderator effects or buffering in terms of interactions between war zone stressor level and resilience-recovery factors was minimal.     

Content of mutant mitochondrial DNA and organ dysfunction in a patient with a MELAS subgroup of mitochondrial encephalomyopathies

A point mutation of mitochondrial tRNALeu(UUR) gene is responsible for a MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes) subgroup of mitochondrial encephalomyopathies. In most cases, the mutant mitochondrial DNA (mtDNA) coexists with normal mtDNA in a heteroplasmic manner. In order to quantify the content of mutant mtDNA, we developed a quantitative method of PCR. Using this method, the distribution of the mutant mtDNA was examined in 32 different tissues among 18 autopsied organs from a patient with MELAS, who had shown hypophyseal dysfunction. The percentage of the mutant mtDNA at nucleotide number 3243 in each tissue was ranged between 22% and 95%. The content of the mutant mtDNA was at the highest (95%) in the hypophysis and higher in the cerebral cortex than in the white matter. This study shows a possible correlation of tissue dysfunction with accumulation of the mutant mtDNA within the brain.     

Pesticides and the South African population

Legislation which has a bearing on pesticides, and its current implementation by the State departments of Agricultural Technical Services and Health, are discussed. Organophosphate compounds account for about 80% of all deaths from pesticides and for about 60% of non-fatal cases of intoxication. In South Africa, levels of lipophilic organochlorine compounds in human adipose tissue are generally well under the world average and are demonstrating a progressive downward trend.     

The sorting of mitochondrial DNA and mitochondrial proteins in zygotes: preferential transmission of mitochondrial DNA to the medial bud

Green fluorescent protein (GFP) was used to tag proteins of the mitochondrial matrix, inner, and outer membranes to examine their sorting patterns relative to mtDNA in zygotes of synchronously mated yeast cells in rho+ x rho0 crosses. When transiently expressed in one of the haploid parents, each of the marker proteins distributes throughout the fused mitochondrial reticulum of the zygote before equilibration of mtDNA, although the membrane markers equilibrate slower than the matrix marker. A GFP-tagged form of Abf2p, a mtDNA binding protein required for faithful transmission of rho+ mtDNA in vegetatively growing cells, colocalizes with mtDNA in situ. In zygotes of a rho+ x rho+ cross, in which there is little mixing of parental mtDNAs, Abf2p-GFP prelabeled in one parent rapidly equilibrates to most or all of the mtDNA, showing that the mtDNA compartment is accessible to exchange of proteins. In rho+ x rho0 crosses, mtDNA is preferentially transmitted to the medial diploid bud, whereas mitochondrial GFP marker proteins distribute throughout the zygote and the bud. In zygotes lacking Abf2p, mtDNA sorting is delayed and preferential sorting is reduced. These findings argue for the existence of a segregation apparatus that directs mtDNA to the emerging bud.     

DNA haplotypes in the G6PD gene cluster studied in the Chinese Li population and their relationship to G6PDCanton

In an effort to investigate the subtelomeric region of the X chromosome among Orientals, five DNA sites in the F8C and G6PD genes were analyzed in a sample of 46 chromosomes belonging to the Chinese Li population, an ethnic group characterized by a high prevalence of G6PD deficiency. The DNA sites analyzed, which are highly polymorphic in other populations, have a low degree of heterozygosity in the Li sample and, furthermore, the distribution of the corresponding haplotypes is very different from that previously observed in Italian populations. Interestingly, three unrelated Li G6PD-deficient variants analyzed at the DNA level have the 1376G-->T mutation characteristic of G6PDCanton and they share the same haplotype, including the sites mentioned above, as well as eight DNA polymorphisms in the red/green color vision pigment genes located proximal to G6PD on chromosome X.     

An evaluation of introgression of Atlantic coast striped bass mitochondrial DNA in a Gulf of Mexico population using formalin-preserved museum collections

Striped bass Morone saxatilis populations in drainages along the Gulf of Mexico coast (Gulf) were depleted in the 1950s and 1960s, probably because of anthropogenic influences. It is believed that only the Apalachicola-Chattahoochee-Flint (A-C-F) river system continually supported a naturally reproducing population of Gulf lineage. Striped bass juveniles of Atlantic coast (Atlantic) ancestry were introduced to restore population abundances in the A-C-F from the late 1960s to the mid 1970s and in many other Gulf rivers from the 1960s to the present. We previously identified mtDNA polymorphisms that were unique to approximately 60% of striped bass from the A-C-F and which confirmed the continued successful natural reproduction of striped bass of Gulf maternal ancestry within the system. However, the genetic relatedness of the extant A-C-F population to 'pure' Gulf striped bass was not addressed. In this study, we determined the frequency of a diagnostic mtDNA XbaI polymorphism in samples of 'pure' Gulf striped bass that were collected from the A-C-F prior to the introduction of Atlantic fish, that were obtained from museum collections, and that were originally preserved in formalin. PCR primers were developed that allowed for amplification of a 191-bp mtDNA fragment that contained the diagnostic XbaI restriction site. Using RFLP and direct sequence analyses of the PCR amplicons, we found no significant differences in mtDNA XbaI genotype frequencies between the archived samples and extant A-C-F samples collected over a 15-year period. This indicates that significant maternally mediated introgression of Atlantic mtDNA genomes into the A-C-F gene pool has not occurred. Additionally, we found no evidence of the unique Gulf mtDNA genotype in striped bass from extant populations in Texas, Louisiana and the Mississippi River. These results highlight the importance of the A-C-F as a repository of striped bass to restore extirpated Gulf populations and the potential use of museum collections in retrospective population studies.