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Biochemical Genetics (v.45, #9-10)
Population Genetic Structure of Endemic and Endangered Yellow Catfish, Horabagrus brachysoma, Using Allozyme Markers by P. M. Abdul Muneer; A. Gopalakrishnan; K. K. Lal; V. Mohindra (pp. 637-645).
The allozyme variation and population genetic structure of Horabagrus brachysoma in three natural populations from the southern part of the Western Ghats region, India, were investigated by polyacrylamide gel electrophoresis. Variations at 14 loci from 14 enzyme systems were analyzed. The allozyme analysis revealed a high level of genetic variation in this species, with an average of observed alleles per locus of 2.357 and observed heterozygosity of 0.178. The positive value of the fixation index (F IS = 0.507) implied a significant deficiency of heterozygosity at the population level. The highly significant probability (P < 0.0001) for the overall loci suggested that the three sample sets were not part of the same gene pool.
Keywords: allozyme; polymorphism; heterozygosity; Horabagrus brachysoma ; genetic variation
Genetic Structure of Different Populations of Walking Catfish (Clarias batrachus L.) in Bangladesh by Mohammad Nazrul Islam; Md. Shahidul Islam; Md. Samsul Alam (pp. 647-662).
Information on genetic variation is essential for conservation and stock improvement programs. Seven dinucleotide microsatellite loci were analyzed to reveal genetic variability in three wild populations (Kella beel, Hakaluki haor, and Shobornokhali beel) and one hatchery population of the freshwater walking catfish, Clarias batrachus, in Bangladesh. Upon PCR amplification, the alleles were separated on polyacrylamide gel using a sequencing gel electrophoresis system and visualized by the silver-staining method. The loci were polymorphic (P 95) in all the populations. Differences were observed in number and frequency of alleles as well as heterozygosity in the studied populations. Current gene diversity (H e ) was higher than expected under mutation-drift equilibrium, significantly in the Hakaluki haor and Shobornokhali beel populations, indicating a recent genetic bottleneck. Population differentiation (F ST) values were significant (P < 0.05) in all the population pairs. A relatively high level of gene flow and a low level of F ST values were found between wild population pairs compared to hatchery-wild pairs. The unweighted pair group method with averages dendrogram based on genetic distance resulted in two major clusters: the hatchery population was alone in one cluster whereas the three wild populations made another cluster. The results reflect some degree of genetic variability in C. batrachus populations indicating potentialities for improving this species through a selective breeding program. The results revealed a recent bottleneck in some wild populations of C. batrachus. Protection of habitat may help increase the population size and lower the risk of vulnerability of the species in the future.
Keywords: Population structure; Bottleneck; Polymorphism; Microsatellites; Clarias batrachus
Biochemical and Genetic Polymorphisms for Carboxylesterase and Acetylesterase in Grape Clones of Vitis vinifera L. (Vitaceae) Cultivars by Gleice Ribeiro Orasmo; Sandra A. Oliveira-Collet; Ana Sílvia Lapenta; Maria de Fátima P. S. Machado (pp. 663-670).
Native polyacrylamide gel electrophoresis (PAGE) was employed to show the highest number of esterase loci and to detect α- and β-esterase polymorphisms in leaf buds of Vitis vinifera cultivars. A total of 16 esterase isozymes were detected in leaf buds from 235 plants including Italia, Rubi, Benitaka, and Brasil cultivars. Biochemical characterization of the grape esterases using ester substrates revealed α-, β-, and α/β-esterases with inhibitor tests distinguishing both carboxylesterases (EST-2, EST-3, EST-5, EST-6, EST-7, EST-8, EST-9, EST-10, and EST-16 isozymes) and acetylesterases (EST-4, EST-11, EST-12, EST-13, EST-14, EST-15 isozymes). No allele variation for α-, β-, and α/β-esterases was detected; however, EST-3 α-carboxylesterase was absent in 61.7% of vines, and EST-4 α/β-acetylesterase was absent in one vine of Rubi cv. Null EST-3 carboxylesterase phenotype (61.7%) cannot be explained in this article, but the high genetic polymorphism in four V. vinifera clones is a positive aspect for genetic selection and development of new clones with different characteristics.
Keywords: Grapes; Esterase; Somatic mutations; Polymorphism
A Single Nucleotide Substitution (−107C → G) in the hMLH1 Promoter Found in Colorectal Cancer Population Reduces Transcriptional Activity by Xiaoling Zhong; Michitsune Arita; Kanae Yamada; Hisahiko Sugiyama; Ke Tan; Shinsaku Kanazawa; Junichi Koike; Tatsuo Teramoto; Hiromichi Hemmi (pp. 671-681).
Inactivation of the DNA mismatch repair gene hMLH1 predisposes one to colorectal cancer. We have identified a C to G nucleotide substitution at position –107 relative to the hMLH1 gene translation initiation site in three of 163 colorectal cancer patients with an allele frequency of 0.0092 (3/326). One of the three −107G alleles occurred in one patient out of five with reduced hMLH1 expression in the tumor tissue. The −107G was not found in 63 healthy individuals. This substitution reduced transcriptional activity by 51% compared with −107C (P < 0.01) and impeded the promoter-binding capacity of nuclear proteins. Although the small number of identified −107G alleles is insufficient to evaluate the contribution to the carcinogenesis and clinicopathological properties of the tumors, the effects of −107G on hMLH1 gene transcription and nuclear protein binding to the promoter sequence implicate the site, including −107C, as a crucial element interacting with the activator that maintains hMLH1 gene expression.
Keywords: hMLH1 ; Single nucleotide substitution; Promoter; Transcriptional activity; Colorectal cancer
Number of STR Repeats as a Potential New Quantitative Genetic Marker for Complex Diseases, Illustrated by Schizophrenia by Hui Liu; Weijian Yu; Xuebin Wang; Fang Fang; Guang Yang; Jie Zhou; Xiaohua Liang; Wanxin An (pp. 683-689).
It has proved difficult to find strong and replicable genetic linkages for complex diseases, since each susceptibility gene makes only a modest contribution to onset. This is partly because high-efficacy genetic markers are not usually available. The aim of this article is to explore the possibility that the total number of tandem repeats in one STR locus, rather than the frequencies of different alleles, is a higher efficacy quantitative genetic marker. DNA samples were collected from schizophrenic patients and from a control population. Alleles of the short tandem repeats (STR) loci D3S1358, vWA, and FGA were determined using the STR Profiler Plus PCR amplification kit. The two groups did not differ statistically in the frequencies of alleles at the D3S1358, vWA, or FGA loci. However, a significant difference was obtained in the vWA locus when the total number of core unit repeats was compared between the schizophrenia and control groups (33.28 ± 2.61 vs. 32.35 ± 2.58, P < 0.05). It seems that the number of STR repeats may be a new, quantitative, and higher efficacy genetic marker for directly indicating genetic predisposition to complex hereditary diseases such as schizophrenia.
Keywords: Genetics; Genetic marker; Short tandem repeats; Quantitative STR; Schizophrenia
RAPD Analysis of DNA Polymorphism in Turkish Sheep Breeds by Cengiz Elmaci; Yasemin Oner; Seniz Ozis; Erdogan Tuncel (pp. 691-696).
The genetic diversity and phylogenetic relationships of 108 individual sheep from three Turkish sheep breeds (Kıvırcık, Gökçeada, and Sakız) were studied using RAPD analysis. Polymorphisms within and between populations were assayed using 15 random primers, and 82 loci were amplified ranging from 250 to 2,500 bp. The percentage of polymorphic loci was found to be 80.49, 78.05, and 73.17%, for Kıvırcık, Gökçeada, and Sakız sheep breeds, respectively. Total genetic diversity was 0.2265, and the average coefficient of genetic differentiation was 0.1181. Genetically, the Gökçeada breed was more closely related to the Sakız breed than to the Kıvırcık breed.
Keywords: Sheep; DNA; Polymorphism; RAPD; PCR
Population Genetics and Phylogeography of Bufo gargarizans in China by Yu-Ling Hu; Xiao-Bing Wu; Zhi-Gang Jiang; Peng Yan; Xia Su; Sen-Yang Cao (pp. 697-711).
The Chinese toad Bufo gargarizans has an extensive range, covering nearly all of China. This study addresses the population genetic structure of this toad and the relation to geographic location. Partial sequences of the mtDNA control region were obtained from 14 populations, 29 haplotypes were defined, and 73 variable sites were found, including 66 parsimony informative sites. All population genetic analyses indicated no clear geographic pattern in the distribution of haplotypes. The genetic divergence between the populations was significant. Phylogeographic analyses suggested that past fragmentation and/or long-distance colonization seemed to have shaped the present-day distribution of the haplotypes of B. gargarizans.
Keywords: Bufo gargarizans ; Control region; Genetic structure; Phylogeographic
SSCP Screening of the Dihydropyrimidine Dehydrogenase Gene Polymorphisms of the Japanese Population Using a Semi-automated Electrophoresis Unit by Yoshihiro Okamoto; Akihito Ueta; Satoshi Sumi; Tetsuya Ito; Yumiko Okubo; Yuki Jose; Akiko Ninomiya; Hajime Togari; Mikio Nishida (pp. 713-724).
The single-strand conformation polymorphism (SSCP) procedure has been applied in routine testing for hereditary diseases. Temperature, running buffer, gel composition, and fragment length can influence its sensitivity. Mutation detection in the clinical setting depends on the development of automated technology, especially for large genes, such as the dihydropyrimidine dehydrogenase (DPYD) gene, which codes the initial, rate-limiting enzyme in the catabolism of 5-fluorouracil (5FU). The authors have optimized the condition of SSCP with an automated system (GenePhor system, GE Healthcare UK Ltd.) to screen genetic polymorphisms in the DPYD gene. The efficiency of the method was evaluated using 21 positive controls (DNA samples with polymorphisms in the DPYD gene, previously characterized) and DNA samples from 35 Japanese. Results showed that the use of three different running buffers (pH 7.4, 8.3, and 9.0) in combination with other optimized conditions (10% polyacrylamide gel, 60–90 min at constant 900 V at 5°C) resulted in a high polymorphism detection rate (95.3%), which was considered appropriate for routine screening. Therefore, this strategy could be useful for pharmacogenetic studies on 5FU.
Keywords: DPYD gene; Polymorphism; 5-fluorouracil (5FU); SSCP
Genetic Heterogeneity of the Blue Swimming Crab (Portunus pelagicus) in Thailand Determined by AFLP Analysis by Sirawut Klinbunga; Kannika Khetpu; Bavornlak Khamnamtong; Piamsak Menasveta (pp. 725-736).
Genetic diversity and population differentiation of the blue swimming crab (Portunus pelagicus) in Thailand, originating from Ranong and Krabi located in the Andaman Sea (west) and Chanthaburi, Prachuap Khiri Khan, and Suratthani located in the Gulf of Thailand (east), were examined by AFLP analysis. High genetic diversity of P. pelagicus in Thai waters was found (N = 72). The four primer combinations generated 227 AFLP fragments, and the percentage of polymorphic bands in each geographic sample was 66.19–94.38%. The mean genetic distance between pairs of samples was 0.1151–0.2440. Geographic heterogeneity analyses using the exact test and F ST-based statistics between all pairwise comparisons were statistically significant (P < 0.01), indicating a fine-scale level of intraspecific population differentiation of Thai P. pelagicus. The estimated number of migrants per generation (N e m) was 0.26–0.76, suggesting restricted gene flow levels of P. pelagicus in Thai waters.
Keywords: Genetic diversity; Population differentiation; Portunus pelagicus ; Amplified fragment length polymorphism (AFLP)
A Novel PCR-RFLP Assay for the Detection of the Single Nucleotide Polymorphism at Position +1440 in the Human CXCR2 gene by Aline C. Viana; Yeon J. Kim; Joni A. Cirelli; Silvana R. P. Orrico; Karen C. Curtis; Veridiana S. P. Cano; Sandro R. Valentini; Raquel Mantuaneli Scarel-Caminaga (pp. 737-741).
We designed a novel PCR-RFLP assay to genotype for the CXCR2 +1440 (G/A) single nucleotide polymorphism, which provides a simple, low-cost, practical, and reproducible method. Allele frequencies in healthy Brazilian individuals were found to be 0.65% for allele A and 0.35% for allele G.
Keywords: PCR-RFLP; Polymorphism; CXCR2; Human
Effect of New SNP Within Bovine Prolactin Gene Enhancer Region on Expression in the Pituitary Gland by P. Brym; T. Malewski; R. Starzyński; K. Flisikowski; E. Wójcik; A. Ruść; L. Zwierzchowski; S. Kamiński (pp. 743-754).
A new single nucleotide polymorphism was revealed using PCR–SSCP and sequencing methods within the bovine prolactin distal promoter region described as a functional enhancer. The A→G transition at position −1043 abolishes the recognition site for Hsp92II restriction endonuclease, allowing for PCR–RFLP genotyping. The application of real-time PCR revealed that the prolactin gene expression level in the pituitary was higher in cattle with the AA genotype than in those with the GG genotype. EMSA analysis, however, showed increased nuclear protein binding to the sequence variant with G, suggesting a possible inhibition event, in which the transcription factors Pit1, Oct1, and YY1 could be involved.
Keywords: Bovine prolactin; SNP; Promoter; Gene expression