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PubMed1999

Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow.

A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations.

Animals↗
PubMed1999

Genetic divergence and phylogeographic relationships among european perch (Perca fluviatilis) populations reflect glacial refugia and postglacial colonization.

We used the widely distributed freshwater fish, perch (Perca fluviatilis), to investigate the postglacial colonization routes of freshwater fishes in Europe. Genetic variability within and among drainages was assessed using mitochondrial DNA (mtDNA) D-loop sequencing and RAPD markers from 55 populations all over Europe as well as one Siberian population. High level of structuring for both markers was observed among drainages and regions, while little differentiation was seen within drainages and regions. Phylogeographic relationships among European perch were determined from the distribution of 35 mtDNA haplotypes detected in the samples. In addition to a distinct southern European group, which includes a Greek and a southern Danubian population, three major groups of perch are observed: the western European drainages, the eastern European drainages including the Siberian population, and Norwegian populations from northern Norway, and western side of Oslofjord. Our data suggest that present perch populations in western and northern Europe were colonized from three main refugia, located in southeastern, northeastern and western Europe. In support of this, nested cladistic analysis of mtDNA clade and nested clade distances suggested historical range expansion as the main factor determining geographical distribution of haplotypes. The Baltic Sea has been colonized from all three refugia, and northeastern Europe harbours descendants from both eastern European refugia. In the upper part of the Danube lineages from the western European and the southern European refugia meet. The southern European refugium probably did not contribute to the recolonization of other western and northern European drainages after the last glaciation. However, phylogenetic analyses suggest that the southern European mtDNA lineage is the most ancient, and therefore likely to be the founder of all present perch lineages. The colonization routes used by perch probably also apply to other freshwater species with similar distribution patterns.

Animals↗
PubMed2003

A morphological cline in Eucalyptus: a genetic perspective.

The putative hybrid zone between Eucalyptus populnea and E. brownii is examined using morphological and molecular techniques. This species complex displays continuous morphological variation across the study area, which has been previously interpreted as the product of hybridization between allopatric species. A microsatellite analysis indicates that there was little genetic structuring across the morphological cline and only low levels of population differentiation. The nested clade analysis of the JLA+ region of the chloroplast DNA (cpDNA) indicates that the geographical distribution of cpDNA haplotypes is unlikely to be the result of historical hybridization events, and that restricted seed-mediated gene flow with isolation by distance is responsible for the phylogeographical distribution. A more plausible explanation for the origin and persistence of the morphological cline is that the process of continuous morphological diversification has been promoted by a directional selection gradient. This study addresses species status within Eucalyptus and the belief that hybridization is widespread and is an important process in the group's evolution.

Analysis of Variance↗
PubMed2003

Mutations of the Uromodulin gene in MCKD type 2 patients cluster in exon 4, which encodes three EGF-like domains.

BACKGROUND: Autosomal-dominant medullary cystic kidney disease type 2 (MCKD2) is a tubulointerstitial nephropathy that causes renal salt wasting, hyperuricemia, gout, and end-stage renal failure in the fifth decade of life. The chromosomal locus for MCKD2 was localized on chromosome 16p12. Within this chromosomal region, Uromodulin (UMOD) was located as a candidate gene. UMOD encodes the Tamm-Horsfall protein. By sequence analysis, one group formerly excluded UMOD as the disease-causing gene. In contrast, recently, another group described mutations in the UMOD gene as responsible for MCKD2 and familial juvenile hyperuricemic nephropathy (FJHN). METHODS: Haplotype analysis for linkage to MCKD2 was performed in 25 MCKD families. In the kindreds showing linkage to the MCKD2 locus on chromosome 16p12, mutational analysis of the UMOD gene was performed by exon polymerase chain reaction (PCR) and direct sequencing. RESULTS: In 19 families, haplotype analysis was compatible with linkage to the MCKD2 locus. All these kindreds were examined for mutations in the UMOD gene. In three different families, three novel heterozygous mutations in the UMOD gene were found and segregated with the phenotype in affected individuals. Mutations were found only in exon 4. CONCLUSION: We confirm the UMOD gene as the disease-causing gene for MCKD2. All three novel mutations were found in the fourth exon of UMOD, in which all mutations except one (this is located in the neighboring exon 5) published so far are located. These data point to a specific role of exon 4 encoded sequence of UMOD in the generation of the MCKD2 renal phenotype.

Adolescent↗
PubMed2003

Sequence variation of alcohol dehydrogenase (Adh) paralogs in cactophilic Drosophila.

This study focuses on the population genetics of alcohol dehydrogenase (Adh) in cactophilic Drosophila. Drosophila mojavensis and D. arizonae utilize cactus hosts, and each host contains a characteristic mixture of alcohol compounds. In these Drosophila species there are two functional Adh loci, an adult form (Adh-2) and a larval and ovarian form (Adh-1). Overall, the greater level of variation segregating in D. arizonae than in D. mojavensis suggests a larger population size for D. arizonae. There are markedly different patterns of variation between the paralogs across both species. A 16-bp intron haplotype segregates in both species at Adh-2, apparently the product of an ancient gene conversion event between the paralogs, which suggests that there is selection for the maintenance of the intron structure possibly for the maintenance of pre-mRNA structure. We observe a pattern of variation consistent with adaptive protein evolution in the D. mojavensis lineage at Adh-1, suggesting that the cactus host shift that occurred in the divergence of D. mojavensis from D. arizonae had an effect on the evolution of the larval expressed paralog. Contrary to previous work we estimate a recent time for both the divergence of D. mojavensis and D. arizonae (2.4 +/- 0.7 MY) and the age of the gene duplication (3.95 +/- 0.45 MY).

Alcohol Dehydrogenase↗
PubMed2006

Bone morphogenetic protein 15 (BMP15) alleles predict over-response to recombinant follicle stimulation hormone and iatrogenic ovarian hyperstimulation syndrome (OHSS).

OBJECTIVE: Controlled ovarian stimulation (COS) using recombinant follicle-stimulating hormone (rFSH) is the main treatment in assisted reproduction. We performed a pharmacogenetic analysis of bone morphogenetic protein 15 (BMP15) gene using single nucleotide polymorphisms (SNPs) in COS. We also investigated the role of the BMP15 gene in ovarian hyperstimulation syndrome (OHSS). METHODS: We analysed different intragenic SNPs located within the BMP15 gene in 307 women treated with rFSH, evaluating its involvement in COS outcome. RESULTS: First, we analysed two polymorphisms, by applying different tests for genetic association, and we found a minimum P-value in patients producing > or =12 follicles in COS (high responders) in both polymorphisms of the BMP15 gene. Using bi-directional DNA sequencing, we identified two additional single nucleotide DNA variants. Second, we conducted association studies with all polymorphisms together, and noticed that none of them seemed to fully explain the association of the BMP15 gene with over-response to rFSH. However, N103S missense mutation is predicted to disrupt the secondary structure of human BMP15 protein and is weakly associated with OHSS. This coding mutation of the BMP15 gene may partially explain the results obtained during our research. Using Thesias software, we reconstructed haplotypes with the four intragenic variants and calculated their frequencies in normal and over-responders to rFSH. The haplotype TGGA was over-represented in high responders when compared with the rest of patients. Moreover, this association was higher in patients with OHSS, with a significant global haplotypic effect of the BMP15 gene. CONCLUSION: Our results suggest a direct relationship between increased follicle production during COS and BMP15 alleles in response to rFSH in humans. The use of BMP15 markers to prevent OHSS is also a possibility that requires thorough evaluation.

Adult↗
PubMed1996

Immunogenicity and antigenicity of the ATPase/helicase domain of the hepatitis C virus non-structural 3 protein.

The immunogenicity and antigenicity of an enzymatically functional (ATPase/helicase) recombinant protein encompassing residues 1207-1612 of the hepatitis C virus (HCV) non-structural 3 (NS3) protein was characterized using B10 congenic mice. Previous studies have indicated a high frequency of NS3-specific antibodies in HCV-infected humans. Similarly, all six immunized murine haplotypes were antibody responders to the NS3 ATPase/helicase domain, with the H-2k and H-2s haplotypes as high responders. As also observed in HCV-infected humans, the murine NS3 antibodies were predominantly directed to conformational determinants. Irrespective of the murine haplotype, IgG1 predominated in the primary anti-NS3 response, whereas IgG1 and IgG2b predominated in the secondary response. The antibody responder hierarchy was reiterated at the T cell level, with the H-2k and the H-2s haplotypes as the best responders. In both the H-2d and H-2k haplotypes ATPase/helicase-primed T cells secreted interleukin 2 and interferon gamma, corroborating observations from HCV-infected humans. In the H-2d, H-2k and H-2s haplotypes the fine specificity of the T cell recognition of the ATPase/helicase domain was further characterized. Multiple, although generally weak, T cell recognition sites were found for all three haplotypes. The large size of the NS3 protein together with the presence of multiple class II binding motifs explain the high prevalence of NS3 antibodies in immunized mice and predict a similar explanation for the observed high frequency of NS3-specific antibodies in HCV-infected humans.

Adenosine Triphosphatases↗
PubMed1980

The HLA system in the Campania region: a genetic study.

The HLA-A, -B and -C locus gene frequencies and the significant A, B and B, C haplotypes of the population of Campania (Southern Italy) are reported. From a comparison of gene frequencies and from an overall genetic distance evaluation with other European and Mediterranean populations the typical Mediterranean structure of the Campanian population is confirmed. While keeping several Middle Eastern features, it places itself as far from Northern Italy (Bergamo) as from the Spanish and the French populations. Among all the groups compared, including Turkish and Lebanese, the largest distance is measured from the English, the Danish and the German populations.

Chromosome Mapping↗
PubMed1993

Gastric chief cell-specific transcription of the pepsinogen A gene.

The molecular mechanisms underlying the regulation of pepsinogen A (PGA) gene expression in mammalian cells are poorly understood. In this paper we describe the structural and functional analysis of the pepsinogen A gene promoter in the pig. By genomic Southern analyses we demonstrate that, in contrast with human PGA genes which are amplified and organized in haplotypes, only a single PGA gene is present per haploid porcine genome. With the aim of identifying promoter elements mediating the gastric mucosa cell-specific transcription of the PGA gene in pig, we isolated a PGA gene from a porcine genomic library. The nucleotide sequence of the first exon and 1.7 kb of the upstream DNA region were determined and compared with the corresponding regions of the human PGA gene encoding isozymogen Pg5. In order to study the promoter activity of the PGA gene a functional assay was developed: we succeeded in obtaining primary monolayer cultures of porcine gastric mucosal chief cells, suitable for transfection. Fragments of 5'-flanking and noncoding first exon sequences of the porcine and human PGA genes were linked to the chloramphenicol acetyltransferase (CAT) gene. The transcriptional activity of these hybrid genes was assessed in transient expression assays upon transfection (lipofection) of gastric and nongastric cells. Whereas PGA 5'-flanking sequences showed no promoter activity in nongastric cell types, the DNA region from -205 to +21 was found to be sufficient to direct expression of the porcine PGA constructs in a cell-specific manner. Further deletion analysis of the proximal promoter fragment identified several regions (-205 to -167, -127 to -67 and +2 to +21) acting synergistically in the transcriptional regulation of the PGA gene. In contrast, all human PGA-CAT constructs used failed to show promoter activity in porcine gastric chief cells, indicating species-specific control of PGA gene expression. In addition, the transcriptional activity of the porcine PGA promoter in chief cells from pig was completely abolished by in vitro CpG methylation. Footprint analyses of the proximal promoter fragment using nuclear extracts from either porcine gastric mucosal chief cells or liver revealed some notable differences between both extracts, which might reflect the interaction with (a) cell-specific factor(s).

Animals↗
PubMed2002

Candidate gene analysis of KIAA0678 encoding a DnaJ-like protein for adolescent nephronophthisis and Senior-Løken syndrome type 3.

Nephronophthisis (NPH), an autosomal recessive cystic kidney disease, causes progressive renal failure. The gene for adolescent nephronophthisis (NPHP3) has been mapped to chromosome 3q21-->q22. Senior-Løken syndrome (SLS) describes the association of NPH and Leber congenital amaurosis. Recently a locus for Senior-Løken syndrome (SLSN3) has been localized on chromosome 3q21-->q22 containing the whole critical NPHP3 region. Within the critical NPHP3/SLSN3 region we identified the gene KIAA0678 encoding a DnaJ-like protein. KIAA0678 was considered a good functional candidate gene for NPH3 and SLS3, because molecular cha- perones are involved in the etiology of renal and retinal diseases. Analysis of the genomic structure of KIAA0678 identified 25 exons. For mutational analysis all exons and intron-exon boundaries were amplified and directly sequenced. Affected individuals of two NPH3 families and one SLS family with haplotypes indicative for homozygosity by descent for the NPHP3/SLSN3 locus were studied. No mutation in KIAA0678 was detected. We conclude, KIAA0678 most likely is not responsible for NPH and SLS in the patients studied.

Adolescent↗
PubMed2003

Modulation of factor V levels in plasma by polymorphisms in the C2 domain.

OBJECTIVE: Functional polymorphisms contributing to coagulation factor levels are preferential markers for association studies aimed at identifying prothrombic genetic components. METHODS AND RESULTS: Factor V (FV) microsatellite genotypes were found to be associated with FV levels (P=0.003). Single nucleotide polymorphisms analysis and sequencing of the promoter and of coding regions identified two polymorphisms (Met2120Thr, Asp2194Gly) present in 20% of the population (n=1013) that are responsible for genotype-phenotype associations. The effect of the Met2120Thr polymorphism, both in plasma (mean reduction of FV level in the heterozygous condition: 25%) and in recombinant FV studies (34% reduction), was comparable to that of the Asp2194Gly change (20% and 34%, respectively). The study of 10 subjects with a rare genotype indicated that the Asp2194Gly substitution is the functional determinant of the reduced FV levels associated with the FVHR2 haplotype. Among Leiden carriers, the doubly heterozygous condition for FV2120Thr was found to be associated with a significantly increased activated protein-C resistance (APCR) (P<0.05), and the doubly heterozygous condition for FV2194Gly was found to be more frequent (P=0.009) in symptomatic than in asymptomatic subjects. CONCLUSIONS: Extensive analysis of FV polymorphisms indicated that changes in the C2 domain modulate FV levels and might increase APCR and thrombotic risk in FV Leiden carriers through a pseudohomozygous mechanism.

Activated Protein C Resistance↗
PubMed1995

Genetic markers on chromosome 19p and prenatal diagnosis of HLA class II-deficient combined immunodeficiency.

HLA class II-deficient combined immunodeficiency (CID) is an inherited disease characterized by a total lack of HLA class II gene expression, due to a regulatory defect affecting these genes. In the family investigated the disease phenotype occurs parallel to an abnormal structural feature of the CD23 antigen. We sequenced parts of the FCER2 gene coding for CD23 and found a restriction fragment length polymorphism (RFLP) that cosegregates with the disease. Analysis of recombinant haplotypes by microsatellites mapping to the chromosomal region 19p13.3 suggests that the disease locus maps between FCER2 and the microsatellite marker D19S424, probably close to D19S216 and D19S177. These data may offer the possibility of a rapid and early prenatal diagnosis of a subgroup of patients with HLA class II-deficient CID.

Amino Acid Sequence↗
PubMed2006

A quantitative trait loci analysis to map genes involved in lipopolysaccharide-induced inflammatory response: identification of macrophage scavenger receptor 1 as a candidate gene.

Septic shock, which is a major complication observed after trauma and other human diseases, is likely the product of a prolonged and poorly controlled systemic inflammatory response. Symptoms of sepsis can be partially reproduced by injection of bacterial LPS in mice. Differences in mortality between C57BL/6J(high) and A/J(low) mice after LPS injection have been previously observed and correlated with differences in the inflammatory response between these two inbred strains. In the present study, we have mapped four loci responsible for differences in levels of LPS-induced IL-10, named modifier of IL-10, between the two strains. A locus within mouse chromosome 8 was confirmed using chromosome 8 consomic mice. This locus was further reduced in size by haplotype analysis and evaluated by the presence of potential candidate genes. The macrophage scavenger receptor 1 (Msr1) within this locus emerged as a candidate gene based on differences at the expression and structural levels between C57BL/6J and A/J mice. In comparison with wild-type (C57BL/6J) mice, Msr1 knockout mice displayed reduced levels of LPS-induced IL-10, but not of TNF-alpha or IL-6, confirming a specific role for this gene in the regulation of IL-10. These results suggest that Msr1 is involved in the regulation of the anti-inflammatory process, thus offering a new perspective on the molecular mechanisms involved in endotoxemia and sepsis.

Animals↗
PubMed2003

[Observation on gene polymorphism of Rh blood group in Chinese Han nationality].

To observe the gene polymorphism of Rh blood group in unrelated random individuals and families for Chinese Han nationality, polymerase chain reaction-sequence specific primer (PCR-SSP) was used to amplify the Rh C/E gene, RhD gene, exons, intron 2 and 10, insert and Rh Box in 160 blood samples of RhD positive unrelated individuals and 71 samples of RhD negative unrelated individuals and 7 samples of families whose probands were RhD-negative. The results showed that RhD genes of RhD-negative individuals with C antigens were polymorphism, three forms were found for D exon including intact, partial deletion and complete deletion exons. Insert fragments and Rh Box were found in most cases of families whose probands were RhD-negative and its inheritance accorded with the Mendel's Law, and it did not affect the expression of RhD gene. "Normal" RhD exon 4 amplifying product was not found in all of the samples. It was concluded that gene structure of the RhD-negative in Chinese was polymorphism, intact, partial deletion and complete deletion exons were found in the individuals with C antigen and probably existed specific D (nf) Ce haplotype. The function of insert was uncertain. The Rh gene sequences of Chinese Han nationality are different from those of Caucasian and the Rh gene library based on Han nationality should be established.

Asian People↗
PubMedDate not supplied

Sequential order of T and B cell epitopes affects immunogenicity but not antibody recognition of the B cell epitope.

Synthetic peptide constructs, co-linearly linking a MUC1 mucin B cell epitope peptide to a known murine T cell epitope, both in T-B and B-T orientations, show that induction of high murine anti-MUC1 antibody titers is dependent on the presence and orientation of the T cell determinant. However, the sequential order of the epitopes does not affect binding of anti-B cell epitope antibodies to the constructs. Haplotype mismatching leads to a significant lowering of the anti-MUC1 antibody responses, implicating a central role for the T cell epitope in eliciting anti-B cell epitope responses. Secondary structure analysis by circular dichroism spectroscopy reveals the T-B construct to be partially ordered, while the B-T peptide adopts a highly ordered conformation in trifluoroethanol. These studies suggest that the sequential order of epitopes may significantly alter the immunogenicity of the peptide but may not necessarily affect its antigenicity. Immunogenicity of the peptide constructs may be governed by subtle differences in secondary structure, leading to variation in the way peptides are presented or processed within cells governing immune responses. These findings have relevance for the construction of peptides to be utilized as potential synthetic vaccines and for the design of peptide immunogens.

Amino Acid Sequence↗
PubMed1993

Independent mutation of arginine(3500)-->glutamine associated with familial defective apolipoprotein B-100.

Familial defective apolipoprotein B-100 (FDB) is characterized by a decreased affinity of low density lipoprotein (LDL) to the LDL receptor resulting in a dominantly inherited increase of plasma LDL. It is postulated that FDB is caused by a G to A mutation at nucleotide 10,708 in exon 26 of the apoB gene creating a substitution of glutamine for arginine in amino acid 3500. The arginine(3500)-->glutamine mutation has been identified on the same haplotype of the apoB gene in several populations from North America and Europe, suggesting that it occurred on a single ancestral gene. Independent mutations were not observed. The purpose of this paper is to report on a family where individuals show a dominantly inherited increase of plasma LDL associated with an independent arginine(3500)-->glutamine mutation as determined by haplotype analysis using polymorphic markers of the apoB gene. The identification of these individuals is strong evidence that the arginine(3500)-->glutamine mutation is causative for the defective binding of apoB-100.

Adult↗
PubMed1998

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.

Animals↗