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Biochemical Genetics (v.42, #11-12)
Geographic Distribution of Pelteobagrus fulvidraco and Pelteobagrus vachelli in the Yangtze River Based on Mitochondrial DNA Markers by Zhongwei Wang; Qingjiang Wu; Jianfeng Zhou; Yuzhen Ye (pp. 391-400).
Three populations of Pelteobagrus vachelli and Pelteobagrus fulvidraco of the Yangtze River were examined by PCR-RFLP analysis of mitochondrial DNA fragments. ND5/6 and D-loop fragments were digested by 10 restriction endonucleases. Significant geographic variations between upstream and mid-downstream populations in the haplotype frequencies and restriction patterns were revealed. This suggested that the diversity of P. vachelli was high; 11 haplotypes were obtained from all the samples. The upstream population shared seven haplotypes and the middle and downstream populations shared another four haplotypes. Among all of the haplotypes, one haplotype was shared in 30 samples of the populations from middle and downstream, but it was not found in the upstream population. Any haplotype found in the upstream population was not detected in the middle and downstream populations. Genetic diversity of P. fulvidraco was low and only five haplotyes were detected from all 60 samples. Phylogenic relationships also indicated that the fishes from upstream and mid-downstream were apparently divided into two populations.
Keywords: Pelteobagrus vachelli ; Pelteobagrus fulvidraco ; mtDNA; PCR-RFLP; genetic diversity
A Simple and Highly Efficient Cloning Method That Employs PCR to Directly Create a Fusion Between Insert and Vector by Vincent Su; Ban-Dar Hsu (pp. 401-409).
We have developed a very simple procedure for gene cloning using compound primers. This approach permits the insertion of a DNA fragment in a single step using a PCR-based cloning protocol, which employs annealing rather than ligation to create the recombinant in the plasmid. This method has been tested successfully to clone a Phalaenopsis gene coding for P450. A potential application of this protocol for constructing a cDNA library is also proposed.
Keywords: PCR; gene cloning; compound primer; cDNA library
Note: Partial Sequence of Porcine MYF6 Gene, Its Comparative Analysis and a Novel Polymorphism of the Region Coding for the Basic Domain
by J. Wyszyńska-Koko; J. Kurył; K. Flisikowski (pp. 411-418).
A Novel Human Gene (WDR25) Encoding a 7-WD40-Containing Protein Maps on 14q32 by Feng Jin; Jianfeng Dai; Chaoneng Ji; Shaohua Gu; Maoqing Wu; Ji Qian; Yi Xie; Yumin Mao (pp. 419-427).
Members of the large family of WD-repeat proteins are involved in diverse functions such as RNA-procession, signal transduction, vesicular trafficking, cytoskeletal assembly, and cell cycle control. By large-scale-sequencing analysis of a human fetal brain cDNA library, we isolated a novel human cDNA encoding a 7-WD40-repeat protein. This cDNA is 2004 bp in length and it codes for a 544-amino-acid protein. We term it human WD40-repeat-containing gene 25 (WDR25) and this gene shows significant similarity with human pre-mRNA splicing factor 17. The WDR25 gene is mapped to chromosome 14q32 and contains seven exons. RT-PCR analysis shows that the WDR25 gene is widely expressed in human tissues and the expression levers in heart, muscle, testis, ovary, uterus, and prostate are relatively high.
Keywords: WDR25 ; WD40 repeat; RT-PCR
Molecular Cloning and Evolution of the Genes Encoding the Precursors of Taiwan Cobra Cardiotoxin and Cardiotoxin-Like Basic Protein by Long-Sen Chang; Shu-Kai Lin; Charling Chung (pp. 429-440).
Genomic DNAs encoding the precursors of eight cardiotoxins and two cardiotoxin-like basic proteins (CLBP) were isolated from the liver of Naja naja atra (Taiwan cobra). The cardiotoxin and CLBP genes have three exons like α-neurotoxin precursors. The promoter regions of these genes are highly conserved and contain the consensus transcriptional factor-binding sites for TBP, NF-1, CACCC-binding site, Spl and EFII, suggesting that these genes are regulated using similar transcriptional mechanisms. The introns and flanking regions of these genes share a high degree of nucleotide sequence identity, but except for the signal peptide domain the protein-coding regions are much more diversified than introns. The ratio of nonsynonymous to synonymous substitution is higher than one, reflecting that adaptive selection occurred during the evolution of cardiotoxin and CLBP proteins. Phylogenetic trees separate CLBPs and cardiotoxins into two clusters, suggesting that the CLBP gene and the cardiotoxin gene diverged earlier before the appearance of numerous cardiotoxins and CLBP.
Keywords: cardiotoxin; cardiotoxin-like basic protein; genomic structure; evolution; phylogenetic analysis
A Functional Truncated Form of c-kit Tyrosine Kinase Is Produced Specifically in the Testis of the Mouse But Not the Rat, Pig, or Human by Akiko Sakamoto; Akihiro Yoneda; Kei Terada; Yuka Namiki; Keita Suzuki; Tadashi Mori; Junji Ueda; Tomomasa Watanabe (pp. 441-451).
The complete nucleotide sequence of mouse-truncated mRNA of c-kit, tr-kit, has been determined using the CD1 strain. In this study, the nucleotide sequences of tr-kit from AKR/N, C57BL/6, and ICR strains of mice were determined and found to be identical, although many silent variations were found compared with the sequence in a database for CD1. Tr-kit protein consists of 12 amino acids encoded by the 16th intron and the following 190 amino acids of c-kit. In the sequences of tr-kit encoding 12 specific amino acids, no substitution was detected among the three strains and CD1. Furthermore, RT-PCR analysis clearly showed that tr-kit mRNA expression was present only in testis. No nucleotide mutation in two important regions of the presumptive promoter for tr-kit mRNA was detected within the 16th intron of the mouse strains examined. However, no functional form of tr-kit was found in the rat, pig, or human by sequence analysis and homology testing.
Keywords: tr-kit ; testis; nucleotide sequence; mouse; rat; pig
No Association Between Base Excision Repair Gene Polymorphisms and Risk of Lung Cancer by Ulla Vogel; Bjørn A. Nexø; Håkan Wallin; Kim Overvad; Anne Tjønneland; Ole Raaschou-Nielsen (pp. 453-460).
In a nested case–cohort study, we have investigated the occurrence of lung cancer in relation to polymorphisms in base excision repair genes XRCC1 and OGG1. Among 54,220 members of a Danish prospective cohort study, aged 50–65 years at entry, 265 lung cancer cases were identified and a subcohort comprising 272 individuals was used for comparison. No associations were found between the polymorphisms OGG1 Ser326Cys, XRCC1Arg280His, and XRCC1 Arg399Gln and risk of lung cancer. This is the first study of polymorphisms in base excision repair genes in relation to lung cancer among Danes.
Keywords: OGG1; XRCC1; base excision; polymorphisms; lung cancer
Molecular Analysis of δ-Aminolevulinic Acid Dehydratase (ALAD) Gene Polymorphism in a Turkish Population by Halit Sinan Süzen; Yalçın Duydu; Ahmet Aydın (pp. 461-467).
δ-Aminolevulinic acid dehydratase (ALAD) is a cytosolic enzyme in the heme biosynthetic pathway. ALAD is a polymorphic enzyme showing marked ethnic group differences. In this study, ALAD polymorphism is studied in a Turkish population. Genomic DNA extracted from 230 individuals and polymerase chain reaction (PCR) coupled with the restriction fragment length polymorphism (RFLP) technique were used to identify variants. The frequencies of the alleles ALAD1 and ALAD2 in Turkey were 0.887 and 0.113, respectively. This study provides the first analysis of the allele frequency distribution of the ALAD gene in a Turkish population. The results are compared with other world populations.
Keywords: ALAD polymorphism; Turkish population; PCR–RFLP