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Biochemical Genetics (v.50, #3-4)

Worldwide Distribution of Type II Diabetes-Associated TCF7L2 SNPs: Evidence for Stratification in Europe by Kieran J. Guinan (pp. 159-179).

Type II diabetes is a multifactorial disease with a complex etiology. Numerous genes have been implicated in disease pathogenesis. In particular, SNPs at the TCF7L2 locus have consistently shown strong associations with type II diabetes. This study characterizes the global distribution of type II diabetes-associated TCF7L2 SNPs utilizing HapMap, HGDP–CEPH, and Alfred databases and the literature. High frequencies of rs7903146(T), rs12255372(T), and rs7901695(C) SNPs are observed in Africa, Europe, and the Middle East, but they are reduced and almost absent in Southeast Asian and Native American populations. In contrast, rs11196218(A) has the highest frequency in Eurasia but is reduced in sub-Saharan African and Native American populations. Regional variations in rs7903146(T) follow a gradient of decreasing frequency from southern into northeastern Europe. These findings demonstrate extensive global and regional variations in the frequencies of TCF7L2 SNPs, which may contribute to differences in the incidence of type II diabetes worldwide.

Keywords: Diabetes; TCF7L2 gene; Europe; Genetic gradient; Natural selection

Genetic Variation Analysis of Mugil cephalus in China Sea Based on Mitochondrial COI Gene Sequences by Peng Sun; Zhao-hong Shi; Fei Yin; Shi-ming Peng (pp. 180-191).

In this study, genetic diversity and population genetic structure of flathead grey mullet, Mugil cephalus, among four China Sea populations were investigated by COI sequences. All the populations studied had high values of haplotype and nucleotide diversity, except for the Yellow Sea population. In the phylogenetic tree, these haplotypes clustered in two groups, one for the populations from the Bohai and East China seas, and the other from the Yellow and South China seas. Analysis of molecular variance indicated that the northern populations (Bohai and East China) had lower genetic divergence (0.0725, P > 0.05) than that of the southern population (South China) (0.4530–0.6827, P < 0.001), suggesting that two distinct genetic groups exist in Chinese waters. Tests of neutral evolution and mismatch distribution indicated that no historical demographic expansion occurred in these populations. The results provide new information for genetic assessment, fishery management, and conservation of this species.

Keywords: Mitochondrial DNA; Cytochrome c oxidase subunit I; Genetic diversity; Population genetic structure

Comparative Assessment of Genetic Variability in the Populations of Endemic and Endangered Yellow Catfish, Horabagrus brachysoma (Teleostei: Horabagridae), Based on Allozyme, RAPD, and Microsatellite Markers by P. M. Abdul Muneer; A. Gopalakrishnan; K. K. Musammilu; V. S. Basheer; V. Mohindra; K. K. Lal; K. G. Padmakumar; A. G. Ponniah (pp. 192-212).

The comparative assessment of genetic diversity using allozymes, random amplified polymorphic DNA (RAPD), and microsatellite markers was conducted in endemic and endangered yellow catfish (Horabagrus brachysoma) sampled from three locations in Western Ghats river systems of India. Among the three markers, microsatellites show more polymorphism, having 100% polymorphic loci, whereas allozymes show the least (56%). In RAPD, 60.5% of fragments were polymorphic. Observed heterozygosity and F _ST values were very high in microsatellites, compared with the other markers. Microsatellite and RAPD markers reported a higher degree of genetic differentiation than allozymes among the populations depicted by pairwise F _ST/G _ST, AMOVA, Nei’s genetic distance, and UPGMA dendrogram. The three classes of markers demonstrated striking genetic differentiation between pairs of H. brachysoma populations. The data emphasize the need for fishery management, conservation, and rehabilitation of this species.

Keywords: Horabagrus brachysoma ; Allozymes; RAPD; Genetic variation; Microsatellites; PCR; Polymorphism

Molecular Cloning and Evolutionary Analysis of GJB6 in Mammals by Binghua Ru; Naijian Han; Guimei He; Kathryn Brayer; Shuyi Zhang; Zhe Wang (pp. 213-226).

GJB6 plays a crucial role in hearing. In mammals, bats use ultrasonic echolocation for orientation and locating prey. To investigate the evolution of GJB6 in mammals, we cloned the full-length coding region of GJB6 from 16 species of bats and 4 other mammal species and compared them with orthologous sequences in 11 other mammals. The results show purifying selection on GJB6 in mammals, as well as in the bat lineage, which indicates an important role for GJB6 in mammal hearing. We also found one unique amino acid substitution shared by 16 species of bats and 10 shared by two species of artiodactyls. This positioned the artiodactyls at an abnormal location in the gene tree. In addition, the cytoplasmic loop and carboxy terminus were more variable than other domains in all the mammals. These results demonstrate that GJB6 is basically conserved in mammals but has undergone relatively rapid evolution in particular lineages and domains.

Keywords: Evolution; GJB6 ; Mammals; Molecular cloning

Na⁺/H⁺ Exchanger 1 Gene Expression in Tissues of Yellow Chicken by Zhang-yong Ning; Yu-fu An; Wen-bao Qi; Heng Wang; Jia-qiang Pan; Xin-tao Wu; Ming Liao (pp. 227-234).

The Na⁺/H⁺ exchanger 1 (NHE1) transmembrane protein regulates intracellular pH, cell survival, cell growth, cell differentiation and plays a critical role in the progression of some diseases, including the pathogenesis of J avian leukosis. The chicken is an ideal model to study the function of NHE1 because it has developed highly efficient Na⁺-absorptive mechanisms in its small and large intestines. To date, there has been no detailed expression analysis to determine NHE1 expression in various tissues of the chicken. We determined the mRNA and protein expression levels of avian NHE1 by real-time quantitative PCR and immunohistochemical analysis. NHE1 mRNA was detected in all chicken tissues examined. Protein expression levels varied widely among tissues and did not always correlate with mRNA expression. Determining the mRNA and protein of NHE1 expression patterns in chicken should help to delineate the NHE1 role in different tissues and its contribution to physiological and pathological processes. These data provide the basis for examining the distinct function of chicken NHE1 compared with its mammalian counterpart.

Keywords: Na⁺/H⁺ exchanger 1 (NHE1); Chicken; Tissues; Expression; Distribution

Positive Selection and Functional Divergence After Melanopsin Gene Duplication by Changgui Dong; Junpeng Zhang; Jian Qiao; Guimei He (pp. 235-248).

A newly discovered melanopsin gene (Opn4) encodes a member of the opsins, melanopsin. Two melanopsin genes, mammalian-like Opn4m and Xenopus-like Opn4x, have been described in nonmammalian vertebrates, but the underlying evolutionary mechanisms behind the duplication of melanopsin genes remain unclear. We conducted a comprehensive evolutionary analysis within a phylogenetic framework. In our phylogenetic tree, the duplication of Opn4m and Opn4x probably occurred prior to the emergence of vertebrates, and subsequently Opn4x disappeared in the lineages leading to mammalian species. Evolutionary analyses show strong purifying selection during melanopsin evolution. We also provide evidence that Opn4x underwent positive selection after the early gene duplication events. It has been indicated that functional divergence and altered functional constraints occurred between Opn4m and Opn4x duplicates with the identification of positively selected amino acids. Our findings highlight the evolutionary malleability in vertebrate melanopsin genes and provide a genetic basis for comparative studies of functional properties of these two melanopsins.

Keywords: Melanopsin; Duplication; Positive selection; Functional divergence; Vertebrates

Polymorphism of the Apolipoprotein B Gene and Association with Plasma Lipid and Lipoprotein Levels in the Mongolian Buryat by Kenji Tsunoda; Shinji Harihara; Yuichi Tanabe; Bumbein Dashnyam (pp. 249-268).

Allele frequencies at six RFLP sites (Ins/Del, ApaLI, AluI, XbaI, MspI, and EcoRI) of the apolipoprotein B gene (APOB) and the relationship of genotypes with plasma lipid and lipoprotein levels in the Mongolian Buryat were investigated. Common alleles at these sites in 110 Buryat subjects were I, G, A−, X−, M+, and E+; the frequencies of 0.809–0.991 differed strikingly from those of a few Asians and most Europeans. Five unambiguous haplotypes of all sites were revealed at 74%; haplotype IGA−X−M+E+ (000000) was the most frequent (67%), followed by IGA+X−M+E+ (001000) (19%). The frequency constitution differed significantly from the Chinese, Malaysians, and Caucasians but resembled the Indians. No APOB polymorphisms were associated with cholesterol levels (total, HDL and LDL). Significant associations of genotypes were shown with the triglyceride level only at the AluI and XbaI sites. The lipid level of A−A+ females or X−X+ males was higher than that of A−A− females or X−X− males, respectively.

Keywords: Apolipoprotein B; DNA polymorphism; Plasma lipid and lipoprotein; Haplotype; Mongolian Buryat

Sequence of the Pearl Oyster Carbonic Anhydrase-Related Protein and Its Evolutionary Implications by Hiroshi Miyamoto (pp. 269-276).

Carbonic anhydrases are conserved in vertebrates and invertebrates, and a noncatalytic carbonic anhydrase-related protein VIII (CARP VIII) has been found in deuterostomes and the phylum Placozoa. I isolated a cDNA encoding a noncatalytic CARP from the mantle of the pearl oyster Pinctada fucata. The polypeptide (CARP-1) predicted from the nucleotide sequence shares 44–60% identity with known CARP VIII sequences, and its phylogenetic analysis showed that P. fucata formed a single group with deuterostome invertebrates. However, since CARP VIII sequences are not identified in protostomes, these results suggest that CARP-1 may have originated in molluscs independently from deuterostome CARP VIII sequences.

Keywords: Pearl oyster; Carbonic anhydrase-related protein; Sequence; Mantle

Prion Protein Coding Gene (PRNP) Variability in Sheep from Turkey and Iran by Fateme Frootan; Gholamreza Nikbakht; Nehir Özdemir Özgentürk; Cemal Ün (pp. 277-284).

This study was designed to analyze variation of ovine prion protein in sheep breeds in Iran and Turkey. A competitive approach was used to analyze the open reading frame (ORF) of the ovine PRNP gene using a total of 186 samples from five indigenous sheep breeds. The ARQ allele was found to be the predominant allele in five breeds. The ARR allele was not observed in homozygous combination among the 11 genotypes found in the study. In addition, six other polymorphisms were indicated. These findings have great significance for estimating genetic variability in the PRNP gene with regard to Iranian and Turkish sheep. Since no information on the susceptibility of some genotypes identified in this study has been reported, no grouping was made on the basis of susceptibility.

Keywords: Gene variation; Prion gene; Iranian sheep; Turkish sheep

Camelus dromedarius Putative Cytochrome P450 Enzyme CYP2E1: Complete Coding Sequence and Phylogenetic Tree by Mohammad Saud Alanazi; Hesham Mahmoud Saeed; Zainul Ariffen Abduljaleel (pp. 285-297).

This study determined the full-length sequence of CYP2E1, one of six cytochrome P450 genes previously examined in camel tissues by western blotting and semi-quantitative PCR. The Camelus dromedarius CYP2E1 has an open reading frame of 1,473 bp, and the cDNA encodes a protein of 490 amino acid residues with a molecular weight of 54.8 kDa. The deduced amino acid sequence showed the highest identity with Bos taurus (88%), Sus scrofa (87%), and Homo sapiens (83%). In a phylogenetic analysis, the C. dromedarius CYP2E1 isoform was located beside cattle and pigs. The deduced amino acid sequence of camel CYP2E1 showed the conserved proline-rich amino terminus and the heme-binding signature localized near the carboxy terminus of the protein.

Keywords: Cytochrome P450; Monooxygenases; Xenobiotics; Degenerate primers; Camelus dromedarius

Association of Hepatocyte Nuclear Factor 4 Alpha Polymorphisms with Type 2 Diabetes With or Without Metabolic Syndrome in Malaysia by Riyadh Saif-Ali; Roslan Harun; Nor Azmi Kamaruddin; Saad Al-Jassabi; Wan Zurinah Wan Ngah (pp. 298-308).

This study investigated the association of hepatocyte nuclear factor 4 (HNF4) alpha single nucleotide polymorphisms (SNPs) with type 2 diabetes with or without metabolic syndrome in Malaysia. Nine HNF4 alpha SNPs were genotyped in 390 type 2 diabetic subjects with metabolic syndrome, 135 type 2 diabetic subjects without metabolic syndrome, and 160 control subjects. The SNPs rs4810424, rs1884613, and rs2144908 were associated with protection against type 2 diabetes without metabolic syndrome (recessive P = 0.018, OR 0.32; P = 0.004, OR 0.25; P = 0.005, OR 0.24, respectively). The 6-SNP haplotype2 CCCGTC containing the risk genotype of these SNPs was associated with higher risk for type 2 diabetes with or without metabolic syndrome (P = 0.002, OR 2.2; P = 0.004, OR 3.1). These data suggest that HNF4 alpha SNPs and haplotypes contributed to increased type 2 diabetes risk in the Malaysian population.

Keywords: Hepatocyte nuclear factor 4 alpha; Type 2 diabetes; Metabolic syndrome; Single nucleotide polymorphisms; Haplotype

Comparative Genetics of the Poly-Q Tract of Ataxin-1 and Its Binding Protein PQBP-1 by Tatsuaki Kurosaki; Jun Gojobori; Shintaroh Ueda (pp. 309-317).

Human PQBP-1 is known to interact with triplet repeat disease gene products such as ataxin and huntingtin through their poly-glutamine (poly-Q) tracts. The poly-Q tracts show extensive variation in both the number and the configuration of repeats among species. A surface plasmon resonance assay showed clear interaction between human PQBP-1 and Q₁₁, representative of the poly-Q tract of the ataxin-1 of Old World monkeys. No response was observed using Q₂PQ₂P₄Q₂, representative of the poly-Q tract of the ataxin-1 of New World monkeys. This implies that the interaction of human PQBP-1 with ataxin-1 is limited to humans and closely related species. Comparison of the human and mouse PQBP-1 sequences showed an elevated amino acid substitution rate in the polar amino acid-rich domain of PQBP-1 that is responsible for binding to poly-Q tracts. This could have been advantageous to the new biological function of human PQBP-1 through poly-Q tracts.

Keywords: Poly-Q tract; Ataxin-1; PQBP-1; Nonsynonymous substitution; Intrinsically disordered

Molecular Cloning, Phylogenetic Analysis, Tissue Distribution, and Expression of the Cytokine TWEAK in Zebrafish (Danio rerio) by Mingxiang Du; Zhenning Liang; Xingzhou Xu; Jianfeng Li; Hongxin Ai; Jiaxin Zhang; Shuangquan Zhang (pp. 318-324).

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Biochemical Genetics (v.50, #3-4)