Association of genetic variants in the HNF4A and HNF1B genes with early onset Type 2 diabetes mellitus in the Indo and Afro-Trinidadian populations

OBJECTIVE: To determine if variation in HNF4A, HNF1B and PAX4 genes is associated with increased risk of early onset Type 2 diabetes mellitus (T2DM) in Indo and Afro-Trinidadians. DESIGN AND METHODS: The promoter, exons and flanking intronic regions of the HFN4A, HNF1B and PAX4 genes were sequenced in 167 T2DM and 61 non-diabetic subjects of South Asian Indian ancestry, and 66 T2DM and 59 non- diabetic subjects of African ancestry. Differences in SNP allele and haplotype frequency between T2DM patients and non-diabetic subjects were calculated, and pairwise linkage disequilibrium was also assessed for regions within these genes. RESULTS: Three variants identified in intron 4 of the HNF4A gene, demonstrated association with early onset T2DM in the Indo-Trinidadian population, rs11574739, P = 0.0032, OR 2.99 (95% CI 1.44-6.22), rs3212194, P = 0.02, OR 2.57 (95% CI 1.17-5.65), rs321219, P = 0.0083, OR 2.72 (95% CI 1.29-5.71). In the HNF1B gene, an intron 7 SNP, rs2269842, was associated with early onset T2DM in both the Indo and Afro-Trinidadian groups, P = 0.012, OR 0.42 (95% CI 0.20-0.87) and, P = 0.012, OR 0.44(95% CI 0.23-0.86) respectively. Both findings are previously unreported. No association was demonstrated with variants typed within the PAX4 gene. CONCLUSIONS: Variants in the HNF4A and HNF1B genes may contribute to increased risk of early onset T2DM in Indo-Trinidadians. HNF1B variants may similarly influence diabetes susceptibility in Afro-Trinidadians. However, further studies are required to fully elucidate the contribution of such variants to the prevalence of diabetes in the Trinidadian population.

Genetic diversity and relatedness of uropathogenic Escherichia Coli with non-clinical isolates in Grenada

OBJECTIVE: To compare genetic profiles of uropathogenic E.coli (UPEC) to strains isolated from freshwater, seawater and iguanas in Grenada. DESIGN AND METHODS: Eighty-five E. coli strains were isolated using double streak-plating on eosin methylene blue (EMB) and MacConkey agar from human urine, iguanas, fresh and marine water. Species identification was confirmed using API20E. Genomic DNA was extracted from individual pure cultures of E. coli and amplified using the oligonucleotide (GTG5) and BOX primers. The DNA fingerprints were separated by electrophoresis, normalized using reference American Test Culture collection (ATCC) E.coli and compared using DendroUPGMA, the FigTree™, dominance and co-clustering analyses. RESULTS: Both DNA fingerprinting methods targeted extragenic DNA and demonstrated enormous intra-species diversity within the population of studied 85 E. coli isolated from four major eco-habitats. DNA fingerprinting based on BOX-PCR was less discriminating than the (GTG)5-PCR. The BOX analysis correlated better with the ecotype distribution. The combination of dominance and co-clustering analyses allowed us to trace the relatedness of strains among and between the four different ecotypes. CONCLUSIONS: The (GTG5) PCR based co-clustering analysis indicated that the clinical isolates had a closer relationship to iguana E. coli isolates than to fresh and marine water isolates. However, in accordance with the BOX analysis, clinical isolates were most similar to marine, followed by freshwater and iguanas.

First insight into Mycobacterium tuberculosis epidemiology and genetic diversity in Trinidad and Tobago.

This report is based on a 1-year recruitment of all of the culture-positive Mycobacterium tuberculosis cases in Trinidad and Tobago (n = 132). The study population was characterized by a high male-to-female sex ratio of 4 and a human immunodeficiency virus-tuberculosis (TB) coinfection rate of 30 per cent. It mainly occurred among African descendants, who represent 37.5 per cent of the total population but 69.7 per cent of all TB cases (P < 0.001). Spoligotyping resulted in 25 different patterns and 12 clusters (2 to 74 strains per cluster), with the predominance of a highly conserved spoligotype international type clone, SIT566.

Size heterogeneity in the 3' noncoding region of South American isolates of yellow fever virus

The 3' noncoding region (3' NCR) of flaviviruses contains secondary and tertiary structures essential for virus replication. Previous studies of yellow fever virus (YFV) and dengue virus have found that modifications to the 3' NCR are sometimes associated with attenuation in vertebrate and/or mosquito hosts. The 3' NCRs of 117 isolates of South American YFV have been examined, and major deletions and/or duplications of conserved RNA structures have been identified in several wild-type isolates. Nineteen isolates (designated YF-XL isolates) from Brazil, Trinidad, and Venezuela, dating from 1973 to 2001, exhibited a 216-nucleotide (nt) duplication, yielding a tandem repeat of conserved hairpin, stem-loop, dumbbell, and pseudoknot structures. YF-XL isolates were found exclusively within one subclade of South American genotype I YFV. One Brazilian isolate exhibited, in addition to the 216-nt duplication, a deletion of a 40-nt repeated hairpin (RYF) motif (YF-XL-DeltaRYF). To investigate the biological significance of these 3' NCR rearrangements, YF-XL-DeltaRYF and YF-XL isolates, as well as other South American YFV isolates, were evaluated for three phenotypes: growth kinetics in cell culture, neuroinvasiveness in suckling mice, and ability to replicate and produce disseminated infections in Aedes aegypti mosquitoes. YF-XL-DeltaRYF and YF-XL isolates showed growth kinetics and neuroinvasive characteristics comparable to those of typical South American YFV isolates, and mosquito infectivity trials demonstrated that both types of 3' NCR variants were capable of replication and dissemination in a laboratory-adapted colony of A. aegypti.

Multiple mating and reproductive skew in Trinidadian guppies

Male offspring production in promiscuously mating species is typically more skewed than female offspring production. It is therefore advantageous for males to seek as many mating partners as possible. However, given the documented benefits of polyandry we expect females, as well as males, to mate multiply. We tested these ideas using Trinidadian guppies, Poecilia reticulata. Fishes were collected from the wild, housed in groups of 10 males and 10 females and allowed to reproduce freely over a period of three months. We used hypervariable microsatellite loci to identify the parents of 840 offspring and to quantify the variance in mating success. As anticipated, and in line with the Bateman gradient, there was greater skew in the number of progeny produced by males. By contrast, we found no sex difference in mating partner number over the duration of the experiment. A median of two males fathered each brood and there was marked turnover in the identities of the sires of successive broods. Female partner turnover was, however, less than expected under random mating. We suggest that partner switching over time, as well as polyandry within broods, could contribute to the maintenance of genetic diversity in guppy populations.

Cacao domestication II: progenitor germplasm of the Trinitario cacao cultivar

Cacao (Theobroma cacao L.) has been cultivated in Central America since pre-Columbian times. The type of cacao cultivated in this region was called Criollo; cacao populations from the Amazon basin were called Forastero. The type of Forastero most commonly cultivated until 1950 was named Amelonado. Historical data show Trinitario cacao to have originated in Trinidad, resulting from natural hybridisation between Criollo and Amelonado Forastero. Doubts persist on the source of the Amelonado Forastero involved in the origin of Trinitario; the Amelonado parent may have come from the Lower Amazon, the Orinoco or the Guyanas. Most of the cacao cultivated worldwide until 1950 consisted of Criollo, Trinitario and Amelonado. From the early 1950s, Forastero material collected in the Upper Amazon region during the 1930s and 1940s began to be employed in breeding programmes. To gain a better understanding of the origin and the genetic basis of the cacao cultivars exploited before the utilisation of germplasm collected in the Upper Amazon, a study was carried out using restriction fragment length polymorphism and microsatellite markers. Trinitario samples from 17 countries were analysed. With molecular markers, it was possible to clearly identify three main genotypes (represented by clones SP1, MAT1-6 and SIAL70) implicated in the origin of most Trinitario clones.

Genetic diversity in mesoamerican populations of mahogany (Swietenia macrophylla), assessed using RAPDs

Swietenia macrophylla King, a timber species native to tropical America, is threatened by selective logging and deforestation. To quantify diversity within the species and monitor the impact of selective logging, populations were sampled across Mesoamerica, from Mexico to Panama, and analysed for RAPD DNA variation. Ten decamer primers generated 102 polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei, then used to construct a radial neighbour-joining dendrogram and examine intra- and interpopulation variance coefficients, by analysis of molecular variation (AMOVA). Populations from Mexico clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Belize also clustered closely together. Populations from Panama, Guatemala, Costa Rica, Nicaragua and Honduras, however, did not cluster closely by country but were more widely scattered throughout the dendrogram. This result was also reflected by an autocorrelation analysis of genetic and geographical distance. Genetic diversity estimates indicated that 80 percent of detected variation was maintained within populations and regression analysis demonstrated that logging significantly decreased population diversity (P=0.034). This study represents one of the most wide-ranging surveys of molecular variation within a tropical tree species to date. It offers practical information for the future conservation of mahogany and highlights some factors that may have influenced the partitioning of genetic diversity in this species across Mesoamerica.(Au)

Lipoprotein-genotype associations in Trinidadian neonates

OBJECTIVES: We hypothesized that common variation in the angiotensinogen (AGT), beta-3-adrenergic receptor. intestinal fatty acid-binding protein, serum paraoxonase, paraoxonase-2, hepatic lipase, apolipoprotein E (APOE), and Werner helicase (WRN) genes would be associated with variation in biochemical phenotypes in a previously unstudied neonatal sample. DESIGN AND METHODS: We examined associations of both nongenetic and genetic variables with plasma lipoprotein traits in neonates from Trinidad. RESULTS: Among nongenetic variables, we found significant associations between plasma concentrations of 1.) lipoprotein (a) [Lp(a)] and both ethnicity (p=0.037) and birth weight (p=0.001); 2)total cholesterol and gender (p=0.010); 3)triglyceride and birth weight (p=0.035); and 4)apolipoprotein A1 and gender (p=0.016). Among genetic variables, we found that: 1)common variation on chromosome 1q in AGT codon 235 was significantly associated with variation in plasma apolipoproteins Al (p<0.0001); and 3)common variation in APOE at codons 112 and 158 was significantly associated with variation in plasma triglycerides (p=0.013). CONCLUSIONS: The associations with AGT and WRN are novel and may have resulted either from direct influence of the genetic variants or through linkage disequilibrium with other functional loci, such as the familial combined hyperlipidemia locus on chromosome 1q in the case of AGT. Despite the fact that there are some limitations in making determinations from cord blood, the results suggest that there may be genetic determinants of plasma lipoproteins in neonates. (AU)

Ancestral origin of variation in the triosephosphate isomerase gene promoter

A high frequency of nucleotide substitutions -5A/G, -8G/A, -24T/G in the triosephosphate isomerase (TPI) gene promoter has been demonstrated in African-Americans. The biological significance of these promoter variants, two of which, -8G/A and -24T/G, occur within regulatory elements essential for transcription, is controversial. The geographical distribution and frequency of allelic variation in the TPI promoter was determined in 378 unrelated normal subjects from Sub-Saharan African (n = 103), Caribbean (n = 26), Northern European (n = 57), Mediterranean (n = 55), Middle Eastern (n = 42), Asian Indian (n = 48) and Oriental (n = 47) populations. Five haplotypes were identified: the common haplotype, -5A-8G-24T, -5G, -8A, -5G-8A, and -5G-8A-24G. All, with the exception of the -8A haplotype, were present in geographically dispersed populations. The -5G allele, which was found at varying frequency in the African, Caribbean and Oriental populations. Phylogenetic comparison suggests this may represent the ancestral promoter haplotype. Homozygosity for the -5G-8A haplotype identified in four subjects confirms that these variants are not responsible for a null allele as formerly postulated. Linkage disequilibrium between related TPI promoter haplotypes, -5G, -5G-8A and -5G-8A-24G, and a single nucleotide polymorphism at nt2262 of the TPI gene supports a single ancestral origin for these mutations which preceeds the separation of African populations.(Au)

Jamaican symmetry project: long-term study of fluctuating asymmetry in rural Jamaican children

Fluctuating asymmetry, small deviations from perfect bilateral symmetry, is negatively correlated with health and positively correlated with sexual selection in human adults, but the accumulation, persistence, and fitness implications of asymmetries during childhood are largely unknown. Here, we introduce the Jamaican Symmetry Project, a long-term study of fluctuating asymmetry and its physical and behavioral correlates in rural Jamaican children. The project is based on an initial sample of 285 children (156 boys and 129 girls), aged 5 to 11 years. We describe the design of the project and the methodology of measuring 10 paired morphometric traits. All traits except hand width showed fluctuating asymmetry. Fluctuating asymmetries of the legs tended to be related and were less than half as great as fluctuating asymmetries of the arms and ears. Therefore the legs may show high developmental stability resulting from selection for mechanical efficiency. A fluctuating asymmetry composite score revealed that boys have significantly lower fluctuating asymmetry than girls and that this effect resides mainly in the elbows. There were significant positive relationships between composite fluctuating asymmetry and age, height, and weight, but multiple regression analyses showed that age was negatively related to fluctuating asymmetry, whereas body size was positively correlated. These findings are compared with results from recent English studies (Au)

The map1 gene of Cowdria ruminantium is a member of a multigene family containing both conserved and variable genes

Heartwater is an economically important disease of ruminants caused by the tick-transmitted rickettsia Cowdria ruminantium. The disease is present in Africa and the Caribbean and there is a risk of spread to the Americas, particularly because of a clinically asymptomatic carrier state in infected livestock and imported wild animals. The causative agent is closely related taxonomically to the human and animal pathogens Ehrlichia chaffeensis and Ehrlichia canis. A dominant immune response of infected animals or people is directed against variable outer membrane proteins of these agents known, in E. chaffeensis and E. canis, to be encoded by polymorphic multigene families. We demonstrate, by sequence analysis, the map1 encoding the major outer membrane protein of C. ruminantium is also encoded by a polymorphic multigene family. Two members of the gene family are located in tandem in the genome. The upstream member, orf2, is conserved, encoding only 2 amino acid substitution among six different rickettsial strains from diverse locations in Africa and the Caribbean. In contrast, the downstream member, map1, contains variable and conserved regions between strains. Interestingly, orf2 is more closely related in sequence to omplb of E. chaffeensis than to map1 of C. ruminantium. The regions that differ among orf2, map1, and omp1b correspond to previously identified variable sequences in outer membrane protein genes of E. chaffeensis and E. canis. These data suggest that diversity in these outer membrane proteins may arise by recombination among gene family members and offer a potential mechanism for persistence of infection in carrier animals.(AU)

An analysis of fetal hemoglobin variation in sickle cell disease: the relative contributions of the x-linked factor, á-Globin haplotypes, O-globin gene number, gender, and age

Five factors have been shown to influence the 20-fold variation of fetal hemoglobin (Hb F) levels in sickle cell anemia (SS): age, sex, the O-globin gene number, á-globin haplotypes, and an X-linked locus that regulates the production of Hb F-containing erythrocytes (F cells), i.e., the F-cell production (FCP) locus. To determine the relative importance of these factors, we studied 257 Jamaican SS subjects from a cohort group identified by newborn screening and from a sib pair study. Linear regression analyses showed that each variable, when analyzed alone, had a significant association with Hb F levels (P < 0.05). Multiple regression analysis, including all variables, showed that the FCP locus is the strongest predictor, accounting for 40 percent of Hb F variation. á-Globin haplotypes, O-globin genes, and age accounted for less than 10 percent of the variation. The association between the á-globin haplotypes and Hb F levels becomes apparent if the influence of the FCP locus is removed by analyzing only individuals with the same FCP phenotype. Thus, the FCP locus is the most important factor identified to date in determining Hb F levels. The variation within each FCP phenotype is modulated by factors associated with the three common á-globin haplotypes and other as yet unidentified factor(s).(AU)

Sequence variation in the capsid protein genes of human papillomavirus type 16

We have cloned and sequenced the L1 and L2 genes from human papillomavirus type 16 (HPV16) DNA-containing cervical cytology samples collected from the U.K. and Trinidad. Samples containing high copy numbers of HPV16 DNA were selected as being likely to contain fully functional virus DNA molecules in an episomal state, rather than in an integrated and possibly altered state. In comparison with the perviously published sequence of HPV16 isolated from an invasive cancer a variety of differences were detected in both L1 and L2. The pattern of changes appears to be different in samples from the two geographic regions. One of the differences (resulting in D at position 202 of the L1 protein) reported recently to be functionally important for virus particle assembly was found to occur in all the samples examined. Variations in L1 found within known immunoreactive regions or hydrophobic domains should be taken into account in design of prophylactic vaccines for HPV16 based on virus-like particles. All variations within L2 protein were found in hydrophilic domains in the carboxy-terminal half of L2. These positions were highly variable among other types of papillomavirus and are located outside the known L2 immunoreactive region. (AU)

Genetic variation at the immunoglobulin allotype loci in Creoles of Trinidad

The sera of a sample of 204 Creoles from Trinidad were tested for the presence of polmorphic gene complexes occurring on immunoglobulin light and heavy-chain molecules including the allotypic markers IGKC 1, IGHA2 1 and 2, IGHG1 A, X, F, and Z, and IGHG3 G, G5, B0, B1, B3, B4, B5, C3, C5, S, and T. Nine IGHG (GM) haplotypes occur in polymorphic frequencies (greater than .01) in this population, including known African, Asian, Caucasian, and Amerindian marker haplotypes. Significant differences (P less than .01) were found in the frequency distributions of three IGHI (GM) haplotypes and the frequency of IGKC*1 in these data and data from Creole populations of Belize and St. Vincent. The Creoles of Trinidad and St. Vincent are more similar in IGHG (GM) haplotype distributions than are Trinidad and Belize populations. Previous testing has revealed no significant differences between St. Vincent and Belize Creoles at the Ig allotypic loci. Analysis of migration patterns in the Caribbean suggests that different rates of Asian migration have maintained regional diversity at these loci, while continuous gene flow from the eastern Caribbean to Trinidad has had a relative homogenising effect on the gene pools of this area. (AU)

Mitochondrial DNA polymorphis in three Antillean island populations of the fruit bat, Artibeus jamaicensis

The Neotropical fruit bat, Artibeus jamaicensis, occurs throughout Latin America and on many islands in the Caribbean. Populations from Jamaica (in the Greater Antilles) to Barbados (in the Lesser Antilles) have been classified as a subspecies (A. J. jamaicensis) separate from that on the Lesser Antillean island of St. Vincent (A. j. schwartz). Mitochondrial DNA (mtDNA) was isolated from 54 individuals collected on these islands, analyzed by digestion with restriction endonucleases, and the restriction sites were mapped. Three different mtDNA genotypes (16,000 ñ 200 bp) were identified: J-i (16 animals from Jamaica, one from St. Vincent, 15 from Barbados), 1-2 (two animals from Jamaica), and SV -1 (18 animals from St. Vincent, two from Barbdos). The J-1 and J-2 genotypes were estimated to differ from each other by only 0.4 percent, but the SV-1 genotype differ from J-1 and J-2 by 8.1 percent-10.5 percent. The estimated sequence divergence between SV-1 and J-1 unusually large for mammals that are regarded as conspecific. Restriction mapping showed that the differences among the genotypes (presence or abscence of particular restriction site) were located throughout the genome. The presence of the J-1 mtDNA genotype on Jamaica and on St. Vincent and Barbados (1,400 km away) demonstrates that maternal lineages in these bats are not necessarily confined to single islands or limited geographic regions. The presence of the J-1 mt DNA genotype within the A. j. schwartzi population on St. Vincent and the presence of the SV-1 genotype in two specimens of A. j. jamaicensis from Barbados document genetic exchange between subspecific populations on these islands, which are separated by 180 km of open water (AU)

Oral infection of Aedes aegypti with yellow fever virus: geographic variation and genetic consideration

Twenty-eight populations representing a worldwide distribution of Aedes aegypti were tested for their ability to become orally infected with yellow fever virus (YFV). Populations had been analyzed for genetic variations at 11 isozyme loci and assigned to one of 8 genetic geographic groups of Ae. aegypti. Infection rates suggest that populations showing isozyme genetic relatedness also demonstrate similarity to oral infection rates with YFV. The findings support the hypothesis that genetic variation exists for oral susceptibility to YFV in Ae. aegypti.(AU)

Mapping of antigenic sites on human haemoglobin by means of monoclonal antibodies and haemoglobin variants

Monoclonal antibodies specific for human globin chains have been prepared and the following strategy has been applied in delimiting the antigenic sites involved in antibody binding. The structural sites of the human globin subunit that might be recognised by the monoclonal antibody were deduced from comparisons of the primary structures of mamalian globin chains that did or did not react with the antibody. The involvement of individual residues at these specific sites was subsequently tested by reacting the antibody with abnormal human haemoglobins in which there was either a substitution or a structural site recognised by monoclonal antibody HuHb á 3-2 (an antibody that reacts with the adult haemoglobins from man and macaque monkey, but not with those from baboon and mouse) includes the aspartic acid residue at position 52 of the á-globin subunit.(AU)

Beta-chain variants in Jamaica newborns

In an electrophoretic study of 15,661 Jamaican cord bloods, 8 rare beta-chain variants were found in 18 subjects in addition to the common beta-chain variants, Hb S and Hb C. The heterozygote frequencies for Hb S and Hb C were 10.1 percent and 3.7 percent respectively. The most frequent of the rare beta-chain variants were Hb Korle Bu (beta 73 Asp leads to Asn) (7 cases) and Hb O su-Christiansborg (beta 52 Asp leads to Asn) (3 cases). One new beta-chain variant, Hb Caribbean (beta 91 Leu leads to Arg) was found. (AU)

Gamma chain variants in Jamaica newborns

15,661 cord bloods from Jamaican infants were examined for abnormal hemoglobins using alkaline cellulose acetate electrophoresis for the initial screening, supplemented by acid agar gel electrophoresis for samples exhibiting abnormal hemoglobin bands. Of the 16 electrophoretic variants which were detected, six were fully characterized and found to be: four Hb F Port Royal (alpha2 Ggamma2 125 Glu replaced by Ala) and two Hb F Victoria Jubilee (alpha2Agamma2 80 Asp replaced by Tyr). The Hb F Port Royal samples each constituted about one eighth of the total Hb F as did seven additional samples presumed to be Hb F Port Royal. The infants with this variant exhibited no special hematological characteristics or other consistent associations. Both Hb F Victoria Jubilee samples ocurred in somewhat lower proportions of the total Hb F compared with Hb F Port Royal and exhibited an apparent increase of free alpha chains in the whole hemolysate. The data available on detectable gamma chain variants suggest that a specific point mutation may occur in either a HbGgamma or a HbAgamma locus. (AU)

A theoretical note on sex linkage and race differences in spatial visualization ability

Evidence on the poorer spatial visualization ability in various Negro populations compared to the white populations and the direction and magnitude of sex differences in spatial ability relative to other abilities suggests the genetic hypothesis that spatial ability is enhanced by a sex-linked recessive gene and that, since the 20-30 percent admixture of Caucasian genes in American Negroes came mostly from male white ancestors, relatively fewer X-linked than autosomal Caucasian genes were transmitted to the American Negro gene pool. The genetic model as explicitly formulated indicates the kinds of data which could substantiate or disprove the theory, but which do not now exist (AU)