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Biochemical Genetics (v.47, #9-10)

Opossum Aldehyde Dehydrogenases: Evidence for Four ALDH1A1-like Genes on Chromosome 6 and ALDH1A2 and ALDH1A3 Genes on Chromosome 1 by Roger S. Holmes (pp. 609-624).

Evidence is presented for six opossum ALDH1A genes, including four ALDH1A1-like genes on chromosome 6 and ALDH1A2- and ALDH1A3-like genes on chromosome 1. Predicted structures for the opossum aldehyde dehydrogenase (ALDH) subunits and the intron–exon boundaries for opossum ALDH genes showed a high degree of similarity with other mammalian ALDHs. Phylogenetic analyses supported the proposed designation of these opossum class 1 ALDHs as ALDH1A-like, ALDH1A2-like, and ALDH1A3-like and are therefore likely to play important roles in retinal and peroxidic aldehyde metabolism. Alignments of predicted opossum ALDH1A amino acid sequences with sheep ALDH1A1 and rat ALDH1A2 sequences demonstrated conservation of key residues previously shown to participate in catalysis and coenzyme binding. Amino acid substitution rates observed for family 1A ALDHs during vertebrate evolution indicated that ALDH1A2-like genes are evolving slower than ALDH1A1- and ALDH1A3-like genes. It is proposed that the common ancestor for ALDH1A genes predates the appearance of birds during vertebrate evolution.

Keywords: Aldehyde dehydrogenase; Opossum; Genetics; Evolution

Association of the Hypoxia Inducible Factor-1α Gene Polymorphisms with Gastric Cancer in Tibetans by Kang Li; Yali Zhang; Zeng Dan; Yi Wang; Zhuoma Ci Ren (pp. 625-634).

To determine how single nucleotide polymorphisms (SNPs) in the hypoxia inducible factor-1α (HIF-1α) gene coding regions affect gastric cancer, the authors conducted an association study of the HIF-1α polymorphisms C1772T and G1790A for a Tibet population. DNA was extracted from peripheral blood of 87 gastric cancer patients and 106 controls and analyzed using the polymerase chain reaction/ligase detection reaction test for HIF-1α polymorphisms. There was a significant increase in the frequency of the GA 1790 genotype in patients with gastric cancer compared with healthy controls (OR 2.93; 95% CI 1.06–8.06). The genotype frequency of the HIF-1α G1790A allele A is higher in gastric cancer groups than in controls (OR 2.78; 95% CI 1.03–7.45). As for the C1772T polymorphism, no positive correlation was found between gastric cancer patients and controls (P = 0.06). Our results suggest that the HIF-1α G1790A polymorphism may be associated with gastric cancer in Tibetans.

Keywords: Hypoxia inducible factor-1α; Polymorphism; Stomach neoplasms; Tibetan

Long-Term Evolution of 5S Ribosomal DNA Seems to Be Driven by Birth-and-Death Processes and Selection in Ensis Razor Shells (Mollusca: Bivalvia) by Joaquín Vierna; Ana M. González-Tizón; Andrés Martínez-Lage (pp. 635-644).

A study of nucleotide sequence variation of 5S ribosomal DNA from six Ensis species revealed that several 5S ribosomal DNA variants, based on differences in their nontranscribed spacers (NTS), occur in Ensis genomes. The 5S rRNA gene was not very polymorphic, compared with the NTS region. The phylogenetic analyses performed showed a between-species clustering of 5S ribosomal DNA variants. Sequence divergence levels between variants were very large, revealing a lack of sequence homogenization. These results strongly suggest that the long-term evolution of Ensis 5S ribosomal DNA is driven by birth-and-death processes and selection.

Keywords: 5S ribosomal DNA; Birth-and-death evolution; Ensis ; Mollusca; Bivalvia

MTHFR Polymorphisms Involved in Vitamin B₁₂ Deficiency Associated with Atrophic Gastritis by Mariangela Palladino; Patrizia Chiusolo; Giovanni Reddiconto; Sara Marietti; Daniela De Ritis; Giuseppe Leone; Simona Sica (pp. 645-650).

Genetic polymorphisms affecting methylentetrahydrofolate reductase (MTHFR) activity may influence hematological and neurological dysfunction in cobalamin-deficient patients. We studied the prevalence of C677T and A1298C polymorphisms by analyzing genomic DNA in 30 cobalamin-deficient patients. No significant difference was found in 677 and 1298 genotype distribution with respect to hematological parameters, B₁₂ and folate levels, and neurological symptoms. The two MTHFR polymorphisms were not protective against anemia or neurological dysfunction in patients with cobalamin deficiency; however, we found evidence of a significant increase in atrophic gastritis in the 677TT group (P = 0.009) but not for the 1298CC genotype. Based on observations that inadequate cobalamin intake and reduced MTHFR activity might be significant risk factors for gastric cancer, and the increased risk of gastric cancer shown in patients affected by atrophic gastritis, we speculate that concomitant atrophic gastritis and impaired MTHFR function could have a role in the development of gastric cancer.

Keywords: Genetic polymorphisms; Folate metabolism; Anemia; Gastric cancer

Molecular Evolution of TEPP Protein Genes in Metazoans by Yoonsoo Hahn (pp. 651-664).

TEPP is a gene expressed in human reproductive organs such as testis, prostate, and placenta. Here, identification and molecular evolutionary analysis of TEPP proteins in various metazoan animals including deuterostomes (chordates, hemichordates, and echinoderms), lophotrochozoans (mollusks and annelids), and cnidarians (sea anemone and coral) are reported. A multiple sequence alignment revealed two highly conserved regions in TEPP proteins that had no similarity to any other known domains or proteins. Genomic sequence analysis showed frequent shifting of the splice sites of intron 1 in mammalian TEPP genes. A comparison of the intron positions in the coding region showed that the exon/intron structure of the TEPP gene was established in an early metazoan ancestor and that independent loss of a single intron occurred in echinoderms and in vertebrates. The urochordate tunicate TEPP genes are intronless, possibly due to replacement of the original gene by a retrogene. No homolog was detected in birds, insects, nematodes, and teleost fishes despite the extensive sequence data of these species, implying that the TEPP gene might be lost in these lineages.

Keywords: Molecular evolution; Metazoan; Intron loss; Gene loss

A 2.7-kb Deletion in the Human NLRP10 Gene Exon 2 Occurred After the Human–Chimpanzee Divergence by Hye Jeong Ha; Dong Seon Kim; Yoonsoo Hahn (pp. 665-670).

NLRP10 is a member of the NLRP protein family, which is involved in inflammation and apoptosis. Genome sequence comparisons revealed that a 2.7-kb deletion occurred in the human NLRP10 gene exon 2 after the divergence of humans and chimpanzees, resulting in replacement of the entire 3′ untranslated region with the flanking LINE-1 element. The human NLRP10 protein lost 30 or more amino acids that are conserved in primates at its carboxy-terminus. The structural modification of the NLRP10 gene might have played a role in development or enhancement of human-specific traits during evolution.

Keywords: Human; Chimpanzee; NLRP10; Molecular evolution; LINE-1

Analysis of STAT5A/AvaI Gene Polymorphism in Four Italian Cattle Breeds by C. Dario; M. Dario; F. Ciotola; V. Peretti; D. Carnicella; M. Selvaggi (pp. 671-679).

The STAT5A/AvaI polymorphism was investigated with PCR-RFLP in a sample of 339 cattle belonging to four breeds: Italian Friesian, Jersey, Italian Brown, and Podolica reared in south Italy. All three possible genotypes for the C/T polymorphism were identified. In these breeds, PCR-RFLP showed the predominance of the TT genotype in Italian Brown and Jersey cows; in Podolica and Italian Friesian CT is the most frequent genotype. The frequency of the T allele ranged from 0.55 to 0.81 in the analyzed populations. The distribution of genotypic and allelic frequencies at this locus was significantly different among the four populations based on a χ² test (P < 0.001), suggesting that the molecular characteristics of the STAT5A gene could be significantly affected by the breed selection. Gene heterozygosity, gene homozygosity, effective allele number, fixation index, and polymorphism information content (PIC) were calculated. The observed heterozygosity, as well as the N _e and PIC values, indicates high genetic variability in the Podolica breed. Podolica could be considered an interesting reservoir of genetic diversity for a species under high selective pressure elsewhere.

Keywords: STAT5A; Cattle; Gene polymorphism; PCR-RFLP

Allele Frequency Distribution Data for D8S1132, D8S1779, D8S514, and D8S1743 in Four Ethnic Groups in Relation to Metabolic Syndrome: Tehran Lipid and Glucose Study by Maryam Sadat Daneshpour; Suad Alfadhli; Massoud Houshmand; Sirous Zeinali; Mehdi Hedayati; Maryam Zarkesh; Amir Abbas Momenan; Fereidoun Azizi (pp. 680-687).

Apolipoprotein E Polymorphism in Hemodialyzed Patients and Healthy Controls by Jaroslav A. Hubacek; Silvie Bloudickova; Ruzena Kubinova; Hynek Pikhart; Ondrej Viklicky; Martin Bobak (pp. 688-693).

A possible association between end-stage renal disease (ESRD) and apolipoprotein E (APOE) polymorphism was found in some but not all studies. We have analyzed the APOE genotypes in 995 hemodialyzed patients (cases) and a sample of 6242 healthy individuals (controls) in the Czech Republic. There was a statistically significant difference in the frequency of APOE alleles between cases and controls, with more carriers of the APOE2 allele in ESRD patients (15.9%) than in controls (12.2%) (P = 0.005). The odds ratio of ESRD for the APOE2 allele, compared with APOE3E3 homozygotes, was 1.37 (95% confidence interval 1.13–1.67). The strength of the association increased with the time spent on hemodialysis: the odds ratio of all-cause ESRD in patients dialyzed for eight or more years was 1.27 (0.94–1.71), for 1–8 years 1.41 (1.09–1.81), and less than 1 year (nonsurvivors) 1.94 (0.88–4.18). This study suggests that the APOE2 allele is a possible genetic risk factor for all-cause ESRD in Caucasians.

Keywords: Apolipoprotein E; End-stage renal disease; Polymorphism

A Genomic Insight into Diversity Among Tribal and Nontribal Population Groups of Manipur, India by K. N. Saraswathy; Naorem Kiranmala; Benrithung Murry; Ekata Sinha; Deepti Saksena; Harpreet Kaur; M. P. Sachdeva; A. K. Kalla (pp. 694-706).

Twenty autosomal markers, including linked markers at two gene markers, are used to understand the genomic similarity and diversity among three tribal (Paite, Thadou, and Kom) and one nontribal communities of Manipur (Northeast India). Two of the markers (CD4 and HB9) are monomorphic in Paite and one (the CD4 marker) in Kom. Data suggest the Meitei (nontribal groups) stand apart from the three tribal groups with respect to higher heterozygosity (0.366) and presence of the highest ancestor haplotypes of DRD2 markers (0.228); this is also supported by principal co-ordinate analysis. These populations are found to be genomically closer to the Chinese population than to other Indian populations.

Keywords: Northeast India; Manipur; Autosomal marker; Tribal population; Nontribal population

Tumor Necrosis Factor Alpha and Interleukin 10 Promoter Polymorphisms in Mexican Patients with Restenosis After Coronary Stenting by Marco Antonio Martínez-Ríos; Marco Antonio Peña-Duque; José Manuel Fragoso; Hilda Delgadillo-Rodríguez; José Manuel Rodríguez-Pérez; Emma Miranda-Malpica; David Cruz-Robles; María Magdalena Cavazos-Quero; Luis Gerardo Rodríguez-Lobato; Gilberto Vargas-Alarcón (pp. 707-716).

To test for an association with risk for restenosis after coronary stent placement, the TNF-α and IL-10 polymorphisms were analyzed by 5′ exonuclease TaqMan assays in 162 patients who initially underwent coronary stenting. Analysis of basal and procedure coronary angiographies revealed a higher proportion of restenosis in lesions treated with bare metal stents compared with those treated with drug-eluting stents (P < 0.001). Distribution of TNF-α genotypes was similar in patients with and without restenosis. The IL-10 polymorphisms showed a moderate protective trend of the −819 TT genotype against restenosis when the lesions were analyzed (P = 0.071, OR = 0.471). Multivariate analysis confirmed a protective role for drug-eluting stents (P < 0.001, OR = 0.199) and the −819 TT genotype (P = 0.037, OR = 0.391). These results suggest the IL-10 −819 TT genotype has a protective role against in-stent restenosis.

Keywords: Coronary stenting; Interleukin 10; Polymorphisms; Restenosis; Tumor necrosis factor alpha

Mitochondrial DNA Variation in the CoxI–CoxII Intergenic Region among Turkish and Iranian Honey Bees (Apis mellifera L.) by Fulya Özdil; Bahman Fakhri; Hasan Meydan; Mehmet Ali Yıldız; H. Glenn Hall (pp. 717-721).

Development of Microsatellite Markers from an Enriched Genomic Library for the Genetic Analysis of the Malaysian Giant Freshwater Prawn, Macrobrachium rosenbergii by L. Min See; Soon Guan Tan; Rosly Hassan; Siti Shapor Siraj; Subha Bhassu (pp. 722-726).

MLPA Subtelomere Analysis in Tunisian Mentally Retarded Patients by Lamia Hila; Hédia Tébourbi; Leila Abaied; Imène Rejeb; Lamia Ben Jemaa; Habiba Chaabouni (pp. 727-733).

Subtelomeric rearrangements significantly contribute to idiopathic mental retardation and result in several mental retardation syndromes; however, most subtelomeric defects lack a characteristic phenotype. Thirty patients with unexplained mental retardation, a normal R banded karyotype at the 550 band, and no clinically recognizable syndrome were screened by Multiplex ligation-dependent probe amplification (MLPA). Four anomalies were identified: deletion 17q, duplications (4q), and associated duplications 15q and Xq. This duplication was found in two sisters of the proband. Anomalies were unidentified by the conventional technique. The prevalence of subtelomeric imbalances in our cohort of moderate to severe mental retardation is around 13% and is consistent with the literature. The sensitivity of the MLPA technique was characterized on cytogenetically verified positive and negative controls. MLPA is a fast, reliable, and relatively inexpensive technique to detect subtelomeric rearrangement in comparison with the fluorescence in situ hybridization (FISH) technique.

Keywords: Deletion; Duplication; Mental retardation; MLPA; Subtelomeric rearrangements

Low Genetic Variability of Domestic Muscovy Duck (Cairina moschata) in China Revealed by Mitochondrial DNA Control Region Sequences by Shi-Yi Chen; Da-Qian He; Yi-Ping Liu (pp. 734-738).

Comparative Analyses of Disease Risk Genes Belonging to the Acyl-CoA Synthetase Medium-Chain (ACSM) Family in Human Liver and Cell Lines by Inka Boomgaarden; Christina Vock; Maja Klapper; Frank Döring (pp. 739-748).

The human ACSM1, 2A and B, 3, and 5 genes, located on chromosome 16p12-13, encode for enzymes catalyzing the activation of medium-chain length fatty acids. Association studies have linked several polymorphisms of these genes to traits of insulin resistance syndrome. In our study, ACSM transcripts showed 3 to >400-fold higher expression levels in human liver when compared to cell lines by qRT-PCR. This difference was also evident at the protein level, as shown for ACSM2. In liver, ACSM2 was the most abundant transcript, showing sixfold (vs. ACSM3) to >300-fold higher expression levels (vs. ACSM1). Mitochondrial localization of the ACSM2 protein and the presence of an N-terminal targeting sequence were shown by GFP-tagging. We have shown ACSM2B to be the predominant transcript in human liver, and genetic variations of this gene could therefore play an important role in disease susceptibility.

Keywords: Acyl-CoA synthetase medium-chain (ACSM); Medium-chain fatty acid; Liver; HuH-7; HepG2

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Biochemical Genetics (v.47, #9-10)

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Biochemical Genetics (v.47, #9-10)