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Biochemical Genetics (v.44, #7-8)

Phylogenetic Relationships among Indigenous Sheep Populations in East Asia based on Five Informative Blood Protein and Nonprotein Polymorphisms by Kenji Tsunoda; Chang Hong; Sun Wei; M. A. Hasnath; Maung Maung Nyunt; Heramba B. Rajbhandary; Tashi Dorji; Horloojau Tumennasan; Keizo Sato (pp. 287-306).

The phylogenetic relationships among 23 local sheep breeds and varieties in East Asia were determined based on allele frequency data for five informative and polymorphic blood protein and nonprotein loci (transferrin, arylesterase, hemoglobin-β, X-protein, and potassium transport) using electrophoresis and ion-densitometric techniques. Comparatively striking differences in the frequency distributions, especially of hemoglobin-β and X-protein alleles, were seen between the northern population of the Khalkhas, Bhyanglung, Baruwal, Jakar, Sakten, and five Chinese breeds and the southern population of the Bengal, Kagi, Lampuchhre, Myanmar, and Sipsu breeds. Clustering analyses using UPGMA and NJ methods and principal component analysis, using the data of all populations and loci tested, clearly demonstrated the difference. The two population groups are divided by the boundary of the Himalayas, and each diverged into three subgroups: Mongolian, Tibetan, and Himalayan groups in the north and Indian groups I, II, and III in the south. It was noted that the genetic differentiation of populations was more distinct in the northern group. These findings strongly suggest the existence of at least two large and phylogenetically different gene pools of sheep in East Asia.

Keywords: phylogenetic relationship; genetic distance; indigenous East Asian sheep; dendrogram; blood protein polymorphism

The Association Between Polymorphic Genotypes of Glutathione S-Transferases and COPD in the Turkish Population by Mukadder Çalıkoglu; Lülüfer Tamer; Nurcan Ates Aras; Sevim Karakaş; Bahadır Ercan (pp. 307-319).

Although smoking is regarded as the most important causal factor in chronic obstructive pulmonary disease (COPD), only 10–20% of smokers develop symptomatic COPD, which indicates the presence of genetic predisposing factors in its pathogenesis. This study investigates the association between gene polymorphysims of glutathione S-transferases (GSTs) and COPD. Blood samples were taken from 149 patients and 150 healthy controls. Polymorphisms of GSTT1, GSTM1, and GSTP1 were genotyped using Real-Time PCR. Multivariate logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals between specific genotypes and COPD. There was no difference in the frequencies of the genotypes of GSTM1 and GSTT1 between the groups, but the GSTP1 Ile/Ile genotype was significantly higher in the patients than in the controls (61.1% vs. 38%). GSTP1 Ile/Val and Val/Val genotypes were associated with a decreased risk of COPD when compared to the Ile/Ile genotype (2.12-fold and 4-fold, respectively). Thus we suggest that the Val allele of GSTP1 may have a protective effect for development of COPD. Furthermore, when we evaluated the association between GSTP1 genes and smoking status, smokers with the GSTP1 Ile allele had an increased risk for the development of COPD. Among the combinations of the genotypes, the combination of GSTM1, GSTT1 null, and GSTP1 Val/Val was associated with the maximal increased risk (12-fold) of COPD. Thus to explain the ethiopathogenesis of COPD, investigation of a single gene family is inadequate. Based on our results and the previous data, further studies should be focused on the GSTP1 gene and the interactions with other genes such as polymorphisms of N-acetyltransferases, GSTM1 and GSTT1, microsomal epoxide hydrolase, and allelic variants of cytochrome P450.

Keywords: glutathione S-transferase; chronic obstructive pulmonary disease; smoking

Mitochondrial DNA Restriction Map and Cytochrome c Oxidase Subunits I and II Sequence Divergence of Corn Stalk Borer Sesamia nonagrioides (Lepidoptera: Noctuidae) by Anna Kourti (pp. 320-331).

Corn stalk borer Sesamia nonagrioides (Lefebvre) (Lepidoptera: Noctuidae) is among the most important insect pests of corn in the Mediterranean basin. The mitochondrial DNA of this insect was purified and a restriction map was constructed. The size of the mtDNA genome is 16.3 kb. Genetic analysis of four corn stalk borer populations, collected from Greece (three populations) and Spain (one population), was undertaken using DNA sequences of the mtDNA cytochrome oxidase (CO) I and II genes. Sequencing of a 2079 bp region of these genes revealed 25 polymorphic sites among the populations. Five molecular RFLP markers, located in the mtDNA COI and COII genes, were surveyed, and two different haplotypes were detected. Phylogenetic analysis based on COI/COII nucleotide sequences revealed genetic differentiation between samples, and the results are discussed in relation to the geographic distribution of the corn stalk borer in two Mediterranean countries.

Keywords: corn stalk borer; mtDNA restriction map; cytochrome I and II (COI/COII); molecular diagnostics

Genetic Variation and Population Structure of Oriental Migratory Locust, Locusta migratoria manilensis, in China by Allozyme, SSRP-PCR, and AFLP Markers by Xianyun Zheng; Yang Zhong; Yihao Duan; Chunxuan Li; Li Dang; Yaping Guo; Enbo Ma (pp. 332-346).

Allozyme analysis, microsatellite primer PCR (SSRP-PCR), and amplified fragment length polymorphism (AFLP) techniques were used to assess genetic diversity and population structure of the Chinese oriental migratory locust, Locusta migratoria manilensis. A total of 299 PCR markers (67 SSRPs and 232 AFLPs) were detected in eight populations, of which 98.7% were polymorphic markers. The proportion of polymorphic loci (95.5–98.8%) by SSRP+AFLP markers indicated no significant differences between populations, and all populations exhibited a similar level of variability; results of the allozyme analysis demonstrated that 19 loci gave rise to a lower level of polymorphism (55.6–66.7%). The genetic distances between the populations were relatively low. Shannon’s index and Nei’s gene diversity showed low differentiation among the populations. Allozyme analysis, however, reflected greater similarity and smaller differentiation between the populations than those shown by SSRP and AFLP markers. Neighbor-joining dendrograms derived from both the allozyme and SSRP+AFLP markers showed that the genetic distances among Chinese oriental migratory locust populations were not greatly influenced by geographic distance and breeding habitats.

Keywords: Locusta migratoria manilensis ; population; allozyme; SSRP-PCR; AFLP; China

Transgenic Mice Can Express Mutant Human Coagulation Factor IX with Higher Level of Clotting Activity by Jing-Bin Yan; Shu Wang; Wen-Ying Huang; Yan-Ping Xiao; Zhao-Rui Ren; Shu-Zheng Huang; Yi-Tao Zeng (pp. 347-358).

To improve the available values of transgenic animals, we produced a mutant human coagulation factor IX minigene (including cDNA and intron I) with arginine at 338 changed to alanine (R338A-hFIX) by using a direct mutation technique. The R338A-hFIX minigene was then cloned into a plasmid carrying the goat β-casein promoter to get a mammary gland-specific expression vector. The clotting activity in the supernatant of the transfected HC-11 cells increased to approximately three times more than that of wild-type hFIX. Nine transgenic mice (three females and six males) were produced, and the copy number of the foreign gene was very different, ranging from 1 to 43 in different lines. ELISA, Western blot, and clotting assay experiments showed that the transgenic mice could express R338A-hFIX, showing higher average levels of clotting activity than wild-type hFIX in the milk (103.76% vs. 49.95%). The highest concentration and clotting activity of hFIX reached 26 μg/mL and 1287% in one founder (F₀-7), which was over 10 times higher than that in human plasma. Furthermore, RT-PCR, APTT assay, and histological analysis indicated that hFIX was expressed specifically in the mammary gland without affecting the intrinsic coagulation pathway and physiologic performance of the local tissue.

Keywords: mutant; human coagulation factor IX; transgenic mouse; expression

Glacial Effects on Sequence Divergence of Mitochondrial COII of Polyura eudamippus (Lepidoptera: Nymphalidae) in China by Yu Long; Hong Wan; Fengming Yan; Chongren Xu; Guangchun Lei; Shaowen Li; Rongjiang Wang (pp. 359-375).

Sequence divergence of mitochondrial COII was analyzed in 50 specimens belonging to five subspecies of Polyura eudamippus (Lepidoptera: Nymphalidae) collected from southern China. There were nine haplotypes in the 405 bp of partial COII sequence. Distribution of the five subspecies was primarily consistent with the spatial distribution of haplotypes. The K _st statistic showed genetic differentiation among these subspecies, except between the pair of P. e. kuangtungensis and P. e. formosana, which were separated by the Taiwan Strait. This is consistent with the 10,000-year history of the Taiwan Strait, not long enough for detectable differentiation. The present distribution pattern of COII haplotypes of P. eudamippus should be shaped by the alteration of Pleistocene glaciations, and Yunnan might be the refugium of P. eudamippus in the ice age, judging from the abundant haplotypes remaining. There were two routes for P. eudamippus in the postglacial expansion, one northward to Sichuan, Chongqing, and Hubei and another eastward to the southeastern coast of mainland China and Taiwan Island. Because the haplotype of butterflies on Hainan Island (P. e. whiteheadi) was completely different from that of mainland China, it was estimated that butterflies on Hainan Island might be from the Indo-China Peninsula rather than from mainland China.

Keywords: Polyura eudamippus ; subspecies; biogeography; COII; glaciation

Genetic Polymorphism of β-Lactoglobulin Gene in Native Turkish Sheep Breeds by Cengiz Elmaci; Yasemin Oner; M. Soner Balcioglu (pp. 376-381).

The genetic polymorphism of the β-lactoglobulin gene was investigated in three native Turkish sheep breeds. The study was carried out on 108 sheep (29 Kıvırcık, 38 Gökçeada, and 41 Sakız) by means of PCR-RFLP methods. Two genetic variants (A and B) and three genotypes (AA, AB, and BB) of β-lactoglobulin have been identified. The gene frequencies of β-LG A and B were 0.7759 and 0.2241 in Kıvırcık, 0.7632 and 0.2368 in Gökçeada, and 0.9756 and 0.0244 in Sakız breeds, respectively. The populations were in Hardy–Weinberg equilibrium in all samples from the three breeds.

Keywords: Turkish sheep breeds; genetic polymorphism; β-lactoglobulin gene; PCR-RFLP

Deleterious Pleiotropic Effects of the Atypical Aldehyde Dehydrogenase 2 (ALDH2) Allele: Comment on Luo et al., 2005 by David Sinclair (pp. 382-387).

Luo [Biochem. Genet. 43:223–227] concluded, “The mutation ALDH2⁽ 487Lys allele is not deleterious but is of great benefit to human health.” This statement is easily subject to misinterpretation and needs to be clarified. Their results actually show there is a pleiotropic effect associated with the mutation ALDH2⁽ 487Lys allele that is as deleterious as the risk of alcoholism for which it offers protection, and thus there is no net benefit from having the mutation. A clarification is needed because this statement and others in the paper might be used inappropriately as an endorsement of practices that are in fact worthless, because it masks the need to find what the pleiotropic effect is, and because it seems to contradict what otherwise seems to be a general rule of evolution.

Keywords: ALDH2; alcoholism; pleiotropic effect; eugenics

Haplotype Frequency Distribution and Linkage Disequilibrium Analysis of Single Nucleotide Polymorphisms at the Human FMO3 Gene Locus by Da-Cheng Hao; Jie Sun; Bjarte Furnes; Daniel Schlenk; Zhen-Fang Hou; Ya-Ping Zhang; Sheng-Li Yang; Ling Yang (pp. 388-404).

We analyzed flavin-containing monooxygenase 3 (FMO3) polymorphisms, haplotype structure, and linkage disequilibrium (LD) in 256 Han Chinese and 50 African-American individuals to compare their haplotype frequencies and LD with other world populations. For the Han Chinese, genotyping of three haplotype tag single nucleotide polymorphisms (E158K, V257M, and E308G) was performed by polymerase chain reaction (PCR)-restriction fragment length polymorphism. For the African-Americans, genotyping of all coding exons was performed by modified PCR-single strand conformational polymorphism. Haplotype frequencies, LD, and evolutionary rates were inferred and estimated computationally. There were significant differences in haplotype frequency distribution and LD pattern among Han Chinese, African-Americans, and other world populations. Four major haplotypes of Han Chinese were EVE, KVE, EME, and EVG. Two major haplotypes of African-Americans were EVE and KVE. We found that sites 158 and 257 are in significant LD in both populations. This is the first report comparing FMO haplotypes and LD of Han Chinese with African-Americans. The data presented here justify further pharmacogenetic studies for potentially optimizing recommended drug dosages and evaluating relationships with disease processes.

Keywords: FMO3; polymorphism; haplotype frequency; linkage; evolution

NYD-SP15: A Novel Gene Potentially Involved in Regulating Testicular Development and Spermatogenesis by Qinghuai Liu; Jin Liu; Qinhong Cao; Jiahao Sha; Zuomin Zhou; Hui Wang; Jianmin Li (pp. 405-419).

By hybridizing human adult testis cDNA microarrays with human adult and embryo testis cDNA probes, we identified a novel human testis gene, NYD-SP15. NYD-SP15 expression was 3.26-fold higher in adult than in fetal testis; however, there was almost no NYD-SP15 expression in the sperm. NYD-SP15 comprises 3364 base pairs, including a 1545 bp open reading frame encoding a 514 amino acid protein possessing 89% sequence identity with the mouse testis homologous protein. NYD-SP15 is located on human chromosome 13q14.2. The deduced structure of the protein contains two dCMP_cyt_deam domains, indicating a potential functional role for zinc ion binding. The gene is expressed variably in a wide range of tissues, with high expression levels in the testis. Sequence analysis revealed that NYD-SP15 is not a highly conserved protein, with its distribution in high-level species such as vertebrates including Homo, Mus, Rattus, and Canis. The results of semiquantitative polymerase chain reaction in mouse testis representing different developmental stages indicate that NYD-SP15 expression was developmentally regulated. These results suggest the putative NYD-SP15 protein may play an important role in testicular development and spermatogenesis and may be an important factor governing male infertility.

Keywords: gene; NYD-SP15 ; dCMP_cyt_deam domain; testis; spermatogenesis

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