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Biochemical Genetics (v.46, #9-10)
Genetic Structure of the Veined Rapa Whelk (Rapana venosa) Populations Along the Coast of China by Jianmin Yang; Qi Li; Lingfeng Kong; Xiaodong Zheng; Rucai Wang (pp. 539-548).
The veined rapa whelk (Rapana venosa) is a valuable and important fishery resource in China. In order to provide guidelines for fisheries management, the genetics population structure was assessed using 10 polymorphic allozyme loci from seven populations of R. venosa across the species’ range on the Chinese coast. The mean allele richness ranged from 1.65 to 2.13, and the mean heterozygosity ranged from 0.086 to 0.149. Significant genetic differentiation was present, and the θ value was 0.016 across all populations. The nMDS plot of pairwise θ values, UPGMA dendrogram, and AMOVA analysis were in good agreement and identified three geographic subdivision groups. We propose that the genetic structure may be due to larval dispersal barriers and localized adaptation or a combination thereof. The implications of these results for the management of R. venosa populations are discussed.
Keywords: Rapana venosa ; Allozyme; Fisheries management; Genetic structure
Genetic Polymorphism of Type 1 Intermediate Filament Wool Keratin Gene in Native Indian Sheep Breeds by R. Arora; S. Bhatia; A. Sehrawat; A. K. Pandey; R. Sharma; B. P. Mishra; A. Jain; B. Prakash (pp. 549-556).
Information is presented on the genetic polymorphism of the Type 1 intermediate filament wool keratin gene in 15 native Indian sheep breeds belonging to different agro-ecological regions of India. The study analyzed random blood samples of the 638 sheep by the PCR-RFLP technique. Restriction digestion analysis of a 480 bp PCR fragment of the first exon region with MspI revealed two allelic variants (M = 0.748 and N = 0.252) and three genotypes (MM = 0.543, MN = 0.410, and NN = 0.047) across the 15 sheep breeds. The allelic frequency differences for both alleles across the Indian breeds, irrespective of their geographic distribution, color pattern, and utility traits, were observed to be statistically insignificant by a chi-square test (P > 0.05). According to the pattern of occurrence of allelic variants (M > N), the Indian breeds exhibited similarity to some of the reported European sheep breeds. The average heterozygosity was 0.420, and none of the breeds deviated from Hardy-Weinberg equilibrium. The predominance of the M over the N allele supported its ancestry in Indian sheep too.
Keywords: Indian sheep breeds; Type 1 intermediate filament wool keratin gene; Genetic polymorphism; PCR-RFLP
A Single Amino Acid Substitution in One of the Lipases of Aspergillus nidulans Confers Resistance to the Antimycotic Drug Undecanoic Acid by Ana G. Brito-Madurro; Rolf A. Prade; João M. Madurro; Mário A. Santos; Nalu T. A. Peres; Jeny R. Cursino-Santos; Nilce M. Martinez-Rossi; Antonio Rossi (pp. 557-565).
A plausible approach to evaluate the inhibitory action of antifungals is through the investigation of the fungal resistance to these drugs. We describe here the molecular cloning and initial characterization of the A. nidulans lipA gene, where mutation (lipA1) conferred resistance to undecanoic acid, the most fungitoxic fatty acid in the C7:0–C18:0 series. The lipA gene codes for a putative lipase with the sequence consensus GVSIS and WIFGGG as the catalytic signature. Comparison of the wild-type and LIP1 mutant strain nucleotide sequences showed a G → A change in lipA1 allele, which results in a Glu214 → Lys substitution in LipA protein. This ionic charge change in a conserved LipA region, next to its catalytic site, may have altered the catalytic properties of this enzyme resulting in resistance to undecanoic acid.
Keywords: Aspergillus nidulans ; Undecanoic acid; Antifungal resistance; lipA gene; Lipase
Characteristics of the β-Globin Gene Cluster Haplotypes of Three Han Chinese Populations at Beijing, Xi’an, and Kunming as Compared with Those of Other Asian Populations by Koji Shimizu; Erika Nagaoka; Yusuke Okada; Yukiko Takeuchi; Shinji Harihara; Keiichi Omoto; Tadashi Imanishi; Wook Kim; Dong-Jik Shin; Luping Hao; Feng Jin (pp. 566-582).
Haplotype frequencies of the β-globin gene cluster of Han Chinese at Beijing, Xi’an, and Kunming were estimated, and their mutual genetic relationships were examined and compared to those of Buryats, Khalkhs, Evenkis, Oroqens, Koreans, and Colombian Amerindians. A major 5′ subhaplotype (5′ to the δ-globin gene), a major 3′ subhaplotype (in and 3′ to the β-globin gene), and a major haplotype (combination of 5′ and 3′ subhaplotypes) are represented as + − − − −, − +, and + − − − − − +, respectively, and found in all three Han Chinese. A rare 5′ subhaplotype, − − − − −, which is one of the possible ancestral types, was found only in Han Chinese at Kunming at low frequency (0.013), and a rare 3′ subhaplotype, − −, was also observed in all three Han Chinese at low frequencies (0.009–0.014). The present haplotype frequency study suggested that the highest genetic affinity was found between Han Chinese at Beijing and those at Xi’an; the next highest was between Han Chinese at Beijing and Koreans, followed by that between Han Chinese at Beijing and Khalkhs, then that between Han Chinese at Xi’an and those at Kunming or Khalkhs, and finally that between Han Chinese at Beijing and those at Kunming. A genetic boundary between northern and southern Han Chinese was not evident in the present study.
Keywords: β-Globin gene cluster haplotype; Han Chinese; Asian populations
Mitochondrial DNA Diversity of Monopterus albus from the Sichuan Basin of China by Xin Cai; Xingneng Gou; Fankun Zeng; Tinghua Zhang; Li Jiang; Ding Fan; Daifang Pu; Xuemei Zeng (pp. 583-589).
Genetic diversity of Monopterus albus in a wild population in the Sichuan Basin was investigated by employing mtDNA polymorphisms. The mitochondrial control region was sequenced for a total of 59 individuals collected from four localities. These sequences (553 bp) belonged to 13 haplotypes defined by eight polymorphic sites. The haplotypes were clustered into one lineage, suggesting that Monopterus albus from the Sichuan Basin might originate from a single ancestor in maternal lineages. The genetic differentiation between the population from Zhongxian in Chongqing city and the other three populations, from Mianyang, Longchang, and Ya’an in Sichuan province (F ST: 0.29167–0.55126), was higher than that among the latter three (F ST: −0.04196 to 0.05984). Little genetic differentiation was found in the three populations from Sichuan province (Nm: −6.21 to 3.93), and the Zhongxian population also showed lower genetic heterogeneity (P i: 0.00077 ± 0.00027; H d: 0.404 ± 0.130). The combination of limited variation and weak phylogenetic structure revealed that the Monopterus albus from the Sichuan Basin exhibited lower mtDNA diversity and should probably be treated as a monogroup genetically.
Keywords: mtDNA D-loop; Genetic diversity; Monopterus albus ; Sichuan Basin
Genetic Diversity in Grapevine Germplasm Resources in the Coruh Valley Revealed by RAPD Markers by Sezai Ercisli; Emine Orhan; Yasemin Hizarci; Nalan Yildirim; Guleray Agar (pp. 590-597).
Random amplified polymorphic DNA analysis was carried out in 35 autochthonous table grapevine cultivars grown in Coruh valley. Fifty-five oligonucleotide primers were screened on cultivars, and among them, 12 primers showed clear polymorphic patterns. PCR amplification with 12 primers generated a total of 157 polymorphic bands. There was genetic variation among the cultivars with values of genetic diversity ranging from 0.19 to 0.72 using the Jaccard coefficient. UPGMA analysis of the distance matrix resulted in a dendrogram with two main clusters. The first cluster included 28 cultivars and the second 7 cultivars. The greatest genetic similarity was observed between cultivars Gah and Kolik, while the greatest dissimilarity was observed between cultivars Gah and Siyah Kus Uzumu. The dendrogram revealed that the cultivars present in Coruh valley can be distinguished to a relatively high degree.
Keywords: Vitis vinifera ; RAPD (random amplified polymorphic DNA); Genetic diversity
Ecological Genetics of Phrynocephalus vlangalii on the North Tibetan (Qinghai) Plateau: Correlation between Environmental Factors and Population Genetic Variability
by Yuan-Ting Jin; Nai-Fa Liu (pp. 598-604).
Phylogenetic Analysis of Leymus (Poaceae: Triticeae) Inferred from Nuclear rDNA ITS Sequences by Li-na Sha; Rui-wu Yang; Xing Fan; Xiao-li Wang; Yong-hong Zhou (pp. 605-619).
To investigate the phylogenetic relationships of polyploid Leymus (Poaceae: Triticeae), sequences of the nuclear rDNA internal transcribed spacer region (ITS) were analyzed for 34 Leymus accessions representing 25 species, together with three Psathyrostachys species (Ns genome), two Pseudoroegneria (St genome) species, Lophopyrum elongatum (Ee genome), and Thinopyrum bessarabicum (Eb genome). The phylogenetic analyses (maximum likelihood and Bayesian inference) supported two major clades, one including 21 Leymus species and three Psathyrostachys species, the other with nine Leymus species and four diploid species. The ITS RNA secondary structure of the Leymus species was compared with that of their putative diploid donor. It is suggested that (1) the species from the same areas or neighboring geographic regions are closely related to each other; (2) L. coreanus, L. duthiei, L. duthiei var. longearistatus, and L. komarovii are closely related to other Leymus species, and it is reasonable to transfer these species from the genus Hystrix to Leymus; (3) the ITS sequences of Leymus are evolutionarily distinct; (4) the different Leymus species and different distribution of a species derived their Ns genome from different Psathyrostachys species; and (5) there is a close relationship among Leymus, Pseudoroegneria, Lophopyrum, and Thinopyrum, but it is difficult to presume that the St, Ee, and Eb genome may be the Xm genome donor of the Leymus species.
Keywords: Leymus ; Internal transcribed spacer (ITS); Phylogeny; RNA secondary structure
Molecular Characterization and Expression Pattern of Fetuin-B in Gibel Carp (Carassius auratus gibelio) by Jing-Xia Liu; Yan-Hua Zhai; Fan-Suo Geng; Jian-Hong Xia; Jian-Fang Gui (pp. 620-633).
Fetuin-B has recently been cloned and identified from rats, mice, and humans; their expression patterns, however, have not been elucidated yet. In this study, Cagfetuin-B has been cloned in gibel carp. RT-PCR and Western blot detection revealed that Cagfetuin-B is first transcribed from the blastula stage and at a relatively stable level afterward during embryogenesis and the larval stage. Cagfetuin-B transcripts are predominantly distributed over the yolk syncytial layer in the early embryos and later restricted to the cells of liver and brain in newly hatched larvae. Moreover, a dynamic distribution of Cagfetuin-B protein was observed in brain, kidney, liver, and skin during morphogenesis. In adult fish, Cagfetuin-B transcripts are restricted in liver and ovary. Our work, for the first time, revealed the extra-hepatic transcription and a dynamic distribution of fetuin-B during embryogenesis and in adults, which indicates the potential roles of fetuin-B in fish organogenesis.
Keywords: Fetuin-B; Embryogenesis; Organogenesis; Extra-hepatic transcription; Gibel carp
Polymorphic Variants of Extracellular Superoxide Dismutase Gene in a Romanian Population with Atheroma by Olguta C. Samoila; Angela M. Carter; Simon T. Futers; Gabriela Otiman; Andrei Anghel; Liviu Tamas; Edward Seclaman (pp. 634-643).
Extracellular superoxide dismutase (EC-SOD) is the main SOD isoform in the arterial wall contributing to cardiovascular defense against oxidative stress by removing the superoxide anion. In our study, the Thr40Ala and Arg213Gly polymorphic variants of the EC-SOD gene (SOD 3 ) were investigated for associations with atherosclerosis and other related factors in 144 subjects with significant atheroma (having one, two, or three major coronary arteries with >50% obstruction, and/or peripheral artery lesions, and/or carotid artery stenosis demonstrated by angiography and echography) and in 150 subjects with no significant atheroma. For the Arg213Gly polymorphism, only five heterozygous subjects were found. Although the difference in the genotype distribution for the Thr40Ala polymorphism was not statistically significant between patients with atheroma (AA 49.3%, AG 34.7%, GG 16.0%) and those without significant atheroma (AA 41.3%, AG 43.3%, GG 15.3%), there was an association of the Thr40 allele with diabetes (P = 0.03) and hypertension (P = 0.04).
Keywords: Extracellular superoxide dismutase polymorphism; Atherosclerosis; Diabetes; Hypertension; Association study
Molecular Characterization and Expression Pattern of the Porcine STARS, a Striated Muscle-Specific Expressed Gene by Y. B. Peng; H. P. Guan; B. Fan; S. H. Zhao; X. W. Xu; K. Li; M. J. Zhu; M. Yerle; B. Liu (pp. 644-651).
STARS (striated muscle activator of Rho signaling) promotes the nuclear localization of MRTFs and mediates SRF transcription, which provides a potential muscle-specific mechanism for linking changes in the actin cytoskeleton structure with muscle gene expression. In this study, the full-length cDNA of the porcine STARS was cloned. The open reading frame of this gene contains 1,155 bp and encodes a protein of 384 amino acids, which is 79, 73, and 77% identical with human, mouse, and rat STARS genes, respectively. RT-PCR revealed that STARS is specifically expressed in heart and skeletal muscles. STARS is also distinctly different in different muscle developmental stages. The result indicates that its expression increased gradually from 33 dpc (days postcoitum) to postnatal muscles, and peaked 28 days postnatal. The porcine STARS was mapped to SSC4p13 using the somatic cell hybrid panel and the radiation hybrid panel IMpRH (LOD score 11.98). The data show that STARS is closely linked to marker SW871. A T/G single nucleotide polymorphism in the coding sequence, detected as Bsh1236I PCR-RFLP, displays allele frequency differences in six pig breeds.
Keywords: Sequence analysis; Physical mapping; Polymorphism; Pig; STARS
Isolation and Characterization of the Cetn1 Gene from Tufted Deer (Elaphodus cephalophus) by Wen Zhang; Xiangrong Cao; Quan Shen; Wei Liu; Siyang Ni; Xiuguo Hua; Xiran Zhang (pp. 652-662).
The tufted deer, a species found only in China, has polymorphic sex chromosomes (2n = 46, 47, 48). Centrins are centrosome components in species from yeast to humans. Here, the Cetn1 gene was isolated from the testis cDNA library of tufted deer, and its expression pattern, number of gene copies, and gene structure were studied. To date, for unknown reasons, satisfactory genomic DNA of the tufted deer has not been obtained. In the present study, we extracted high molecular weight genomic DNA from tissues of the tufted deer. Results showed that genomic DNA was isolated successfully and could be used for Southern blotting of the Cetn1 gene. Centrin 1 transcripts were shown to exist in testis and the retina. It has no intron and only a single copy in the genome. Protein sequence analyses indicate that the C-terminal Ser-170, which was shown to be phosphorylated in human centrin, is not conserved except in sequences from the human, chimpanzee, and tufted deer.
Keywords: cDNA library; Genomic DNA; Cetn1 ; Southern blot
Analysis of Expressed Sequence Tags (ESTs) from Agrostis Species Obtained Using Sequence Related Amplified Polymorphism by Gizem Dinler; Hikmet Budak (pp. 663-676).
Bentgrass (Agrostis spp.), a genus of the Poaceae family, consists of more than 200 species and is mainly used in athletic fields and golf courses. Creeping bentgrass (A. stolonifera L.) is the most commonly used species in maintaining golf courses, followed by colonial bentgrass (A. capillaris L.) and velvet bentgrass (A. canina L.). The presence and nature of sequence related amplified polymorphism (SRAP) at the cDNA level were investigated. We isolated 80 unique cDNA fragment bands from these species using 56 SRAP primer combinations. Sequence analysis of cDNA clones and analysis of putative translation products revealed that some encoded amino acid sequences were similar to proteins involved in DNA synthesis, transcription, and signal transduction. The cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene (GenBank accession no. EB812822) was also identified from velvet bentgrass, and the corresponding protein sequence is further analyzed due to its critical role in many cellular processes. The partial peptide sequence obtained was 112 amino acids long, presenting a high degree of homology to parts of the N-terminal and C-terminal regions of cytosolic phosphorylating GAPDH (GapC). The existence of common expressed sequence tags (ESTs) revealed by a minimum evolutionary dendrogram among the Agrostis ESTs indicated the usefulness of SRAP for comparative genome analysis of transcribed genes in the grass species.
Keywords: Bentgrass species; Expressed sequence tag (EST); Sequence related amplified polymorphism
Mapping and Expression Analysis of Chicken NDRG1 and NDRG3 Genes by Yong Tian; Minlin Xu; Yan Fu; Aiping Yuan; Deqian Wang; Guoqin Li; Gentao Liu; Lizhi Lu (pp. 677-684).
N-myc downstream-regulated genes 1 and 3 (NDRG1 and NDRG3) are members of the alpha/beta hydrolase superfamily. Phylogenetic analysis of the family demonstrated that human NDRG1 and 3 belong to a subfamily. The mapping and gene expression patterns of these genes represent one step toward further investigation into their possible roles in the chicken (Gallus gallus). To map these genes in the chicken chromosome, a 6000 rads chicken-hamster radiation hybrid panel (ChickRH6) was used. Primers were designed according to the published human sequences for amplification of those two genes. We compared the corresponding human mRNA sequences with the predicted coding sequences of the chicken NDRG1 and 3 genes and found that the assembled contigs shared a high percentage of similarity with the human genes. PCR of samples from ChickRH6 revealed that the locations of NDRG1 and 3 are linked to the markers MYC (58 cRs away, LOD score 4.52) and SEQ0265 (10 cRs away, LOD score 17.81), respectively. This result adds two new markers to the chicken RH map, and it reinforces that the RH technique is indeed a powerful tool for mapping genes due to its rapidity, precision, convenience, and reproducibility. In addition, we detected the gene expression and distribution of chicken NDRG1 and 3 in seven tissues, including heart, liver, spleen, lung, muscle, brain, and thymus, by RT-PCR, and found that NDRG1 is relatively ubiquitously expressed in all the tested tissues and highly expressed in heart and liver, whereas NDRG3 is high in heart, muscle, and brain.
Keywords: RH panel; Mapping; Genetic marker; NDRG1 gene; NDRG3 gene; Chicken