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Biochemical Genetics (v.46, #11-12)

Tissue Expression Pattern of Class II and Class V Genes Found in the Adh Complex on Mouse Chromosome 3 by Gabor Szalai; Monika Veres; Gregg Duester; Robert Lawther; Marie Lockhart; Michael R. Felder (pp. 685-695).

The alcohol dehydrogenase enzymes in mice and humans are encoded by a linked group of genes in the same transcriptional orientation. The enzymes play important roles in alcohol metabolism and retinoid signaling and homeostasis. The expression patterns at the mRNA level of the mouse Adh4 (class II) gene and the recently identified Adh6a and Adh6b genes (class V) are now reported to complete this analysis for the entire family. Adh4 is expressed at high levels in liver and is detectable in small intestine and testes. Adh6b is expressed in liver but Adh6a is not. Adh6a is expressed at high levels in small intestine while Adh6b is not. Adh6a expression is detectable in the female adrenal and not at all in the male adrenal, but Adh6b is expressed at moderate levels in both sexes. Although Adh6a and Adh6b have expression patterns different from each other, neither expresses like any other gene in the complex, suggesting different control mechanisms and possibly different functions.

Keywords: Alcohol dehydrogenases; Gene expression; Mouse

Analysis of TNF Polymorphisms in Turkish Systemic Sclerosis Patients with Interstitial Lung Involvement by Ömer Ates; B. Müsellim; G. Öngen; A. Topal-Sarıkaya (pp. 696-701).

A Novel RUNX2 Mutation in Cleidocranial Dysplasia Patients by Dongying Xuan; Shi Li; Xiong Zhang; Lixin Lin; Chunxian Wang; Jincai Zhang (pp. 702-707).

Cleidocranial dysplasia (CCD) is an autosomal-dominant heritable skeletal disease caused by heterozygous mutations in the RUNX2 gene. Here, the RUNX2 gene was analyzed within a CCD family from China, and a novel missense mutation (c. 475G → C [p.G159R]) was identified. Normal and mutant RUNX2 expression vectors were then constructed and expressed transiently in NIH3T3 cells. Immunofluorescent staining and Western blotting showed that wild-type RUNX2 protein was localized exclusively in the nucleus; however, the mutant protein was found in both the nucleus and the cytoplasm, which demonstrated that transport of the RUNX2 mutant into the nucleus was disturbed by the G159R mutation. Therefore, we suggest that G159 is very important to promote RUNX2 nuclear localization. According to clinical analysis, the patient displays severe dysplasia of bones and relatively low-grade craniofacial abnormality, and we infer that G159 may be vital for normal skeletal development, other than control of tooth number. These findings confirm that mutations in the RUNX2 gene are associated with the pathogenesis of CCD across different ethnic backgrounds.

Keywords: Cleidocranial dysplasia; Mutation; RUNX2; Subcellular localization

Lack of Association of the HbE Variant with Protection from Cerebral Malaria in Thailand by Izumi Naka; Jun Ohashi; Pornlada Nuchnoi; Hathairad Hananantachai; Sornchai Looareesuwan; Katsushi Tokunaga; Jintana Patarapotikul (pp. 708-711).

Hemoglobin E (HbE; ^β26Glu → Lys) is the most common variant of the β-globin gene in Southeast Asia; it has been suggested that it confers resistance against Plasmodium falciparum malaria. In this study 306 adult patients with P. falciparum malaria (198 mild and 108 cerebral malaria patients) living in northwest Thailand were investigated to examine whether the HbE variant is associated with protection from cerebral malaria. Our results revealed that the sample allele frequency of HbE was not significantly different between mild (7.3%) and cerebral malaria (7.4%) patients. Thus, the HbA/HbE polymorphism would not be a major genetic factor influencing the onset of cerebral malaria in Thailand.

Keywords: Hemoglobin E; Cerebral malaria; Thai

HLA Typing of Patients with 21-Hydroxylase Deficiency in Iranian Children with Congenital Adrenal Hyperplasia by Mohammad Taghi Haghi Ashtiani; Ali Rabbani; Fereidoun Mostafavi; Maryam Monajemzadeh; Fahimeh Ranjbar Kermani; Jila Soltaninia (pp. 712-719).

Congenital adrenal hyperplasia (CAH) is a group of potentially life-threatening disorders, most often caused by deficiency of steroid 21-hydroxylase. Children with ambiguous genitalia, hermaphroditism, or signs and symptoms of CAH admitted to Children’s Medical Center were enrolled in the survey, and 101 patients were found. Karyotyping, clinical examination, and paraclinical tests were done. HLA typing was done in patients with proven classical CAH and their parents. HLA antigens were typed in children with CAH-type 21-hydroxylase deficiency. The antigen frequencies were compared with those of the control population. The studies revealed that two HLA antigens, HLA-B18 and HLA-B21, showed a significant increase in frequency. The calculated relative risk value was high, distinguishing the population of patients and their parents. The relative risk among patients was 11.82 for HLA-B18 and 1.75 for HLA-B21 antigens. There was no relationship between HLA-DR antigens and CAH. Studies on the correlation between HLA and CAH indicate an association with HLA-B18 and HLA-B21 antigens, and they can be used as genetic markers of the disorder in the Iranian population, if they are restricted to Iranian patients.

Keywords: Congenital adrenal hyperplasia; 21-Hydroxylase deficiency; HLA typing; Ambiguous genitalia; Hermaphroditism

Association of MYF5 and MYOD1 Gene Polymorphisms and Meat Quality Traits in Large White × Meishan F2 Pig Populations by Min Liu; Jian Peng; De-Quan Xu; Rong Zheng; Feng-E Li; Jia-Lian Li; Bo Zuo; Ming-Gang Lei; Yuan-Zhu Xiong; Chang-Yan Deng; Si-Wen Jiang (pp. 720-732).

MYF5 and MYOD1 belong to the myogenic regulatory factor (MRF) gene family. They code for the basic helix-loop-helix transcription factors that play key regulatory roles in the initiation and development of skeletal muscle and the maintenance of its phenotype. In this work three single nucleotide polymorphisms (SNPs) in porcine MYF5 and one in porcine MYOD1 were detected in three pig breeds (Large White, Landrace, and Meishan) by means of a PCR-RFLP protocol. Analysis of the association of meat quality traits with the four polymorphisms in a series of three Large White × Meishan F2 populations, totaling 399 pigs, found: (1) MYF5 exon 1 Hsp92II polymorphism causing a Met → Leu substitution was associated with intramuscular fat content (P = 0.04) and water moisture content (P = 0.0001) in the longissimus dorsi; (2) MYF5 exon 2 MspI polymorphism and an intron 1 HaeIII polymorphism, which were completely linked, were significantly associated with longissimus dorsi pH (P < 0.05); (3) MYOD1 intron 1 DdeI polymorphism was not significantly associated with any meat quality traits tested. Among these genetic variants (a novel SNP and three identified SNPs), our data suggested that the novel SNP of the MYF5 gene within exon 1 is valuable for pig breeding.

Keywords: MYF5 ; MYOD1 ; Polymorphism; Meat quality traits; Pigs

Different Allelic Distribution of a Single SNP Between Sexes in Humans by P. Tripputi; D. Cigognini; S. Bianchi; L. Fedele (pp. 733-736).

We searched for a difference in allele distribution between males and females of a single nucleotide polymorphism located in the human beta T-cell receptor, in 500 subjects (200 males and 300 females). Genotype analysis gave the following results: among the males, 114 (57%) were heterozygous for the T/C polymorphism, 52 (26%) were homozygous (T/T), and 34 (17%) were homozygous (C/C). Among the females, 142 (47.3%) were heterozygous, 73 (24.3%) were homozygous (T/T), and 85 (28.3%) were homozygous (C/C). The allele frequency was significantly different between sexes (χ² = 8.799, P = 0.012).

Keywords: T-cell receptor; Polymorphism; Linkage disequilibrium; Gender; DNA

Paired-Like Subclass Homeobox Genes from the Clitellate Annelid Perionyx excavatus by Sung-Jin Cho; Soon Cheol Park (pp. 737-743).

Detection of SNPs in Porcine Haptoglobin and Apolipoprotein Genes by H. Y. Chung; H. J. Park; S. H. Yoon; M. G. Baek; J. Y. Kim; M. J. Kim (pp. 744-754).

To find differentially expressed protein spots using two-dimensional electrophoresis proteomic analysis, we took blood serum samples from 40 purebred Yorkshire pigs at 12, 18, 24, and 30 weeks. Each growth stage contained 10 male pigs having half-sib pedigrees. With the pooled serum samples, two interesting spots, differentially expressed in the growth stages, were identified using MALDI-TOF-TOF MS/MS analysis as haptoglobin alpha 1S (Hp) and apolipoprotein A-IV (APOA4) gene products. The Hp was down-regulated from 12 to 30 weeks, and APOA4 was not expressed much before 18 weeks but was highly expressed in the late growth stages. There may be an inverse relationship between the Hp and APOA4 genes. Four segments for the Hp and APOA4 genes were successfully amplified with sizes around 500 bp. The porcine Hp and APOA4 genes were screened in the 40 purebred Yorkshire pigs and a random cross population (90 pigs), resulting in the location of 6 single nucleotide polymorphisms (SNPs) in the coding regions. The mutations resulted in amino acid changes in segments of Hp627, Hp742, and APOA41203. Further investigation of the function of the Hp and APOA4 genes with SNPs will be necessary to understand fully the different expression profiles and association studies.

Keywords: Haptoglobin; Apolipoprotein; Porcine; Proteomics; SNPs

Allozyme Analysis of Hypostomus (Teleostei: Loricariidae) from the Rio Corumbá, Upper Rio Paraná Basin, Brazil by Cláudio Henrique Zawadzki; Erasmo Renesto; Rogério Pincela Mateus (pp. 755-769).

The taxonomy of the genus Hypostomus in the upper Rio Paraná basin presents some very complex issues. For this reason, an allozyme electrophoresis survey of 10 populations of Hypostomus from the Rio Corumbá basin was performed, revealing 25 loci from 14 enzyme systems. Allozyme data revealed diagnostic genetic markers for the four nominal species analyzed (Hypostomus ancistroides, H. iheringi, H. margaritifer, and H. regani) and for six possible undescribed species. The mean expected heterozygosity of the populations ranged from 0.009 in H. iheringi to 0.099 in Hypostomus sp. 4. The genetically most similar populations (I = 0.954) were H. iheringi and Hypostomus sp. 2; the most divergent (D = 0.839) were H. iheringi and H. ancistroides.

Keywords: Genetic variability; Heterozygosity; Hypostominae; Neotropical fishes; Siluriformes

Variation of 423G>T in the Agouti Gene Exon 4 in Indigenous Chinese Goat Breeds by Chun-Juan Tang; Rong-Yan Zhou; Xiang-Long Li; Jing-Wen Zhao; Lan-Hui Li; Fu-Jun Feng; Dong-Feng Li; Jian-Tao Wang; Xiu-Li Guo; Jing-Fen Keng (pp. 770-780).

The Agouti gene plays an important role in pigment synthesis in domestic animals. A transversion of 423G>T recognized by BanII was found after a fragment (178 bp) of the goat Agouti gene exon 4 was amplified and sequenced. To investigate its genetic effect and diversity, 677 individuals from 12 indigenous Chinese goat breeds and one imported goat breed from South Africa (Boer goat) were analyzed by PCR-RFLP. Two alleles, T and G, and three genotypes, TT, TG, and GG, were detected. Allele T had a higher frequency in most goat breeds and, combined with the coat color phenotype, is believed to be responsible for the black phenotype or to be linked with the causative site in the goat. The results also indicate that the 423G>T transversion showed lower genetic diversity in goat breeds with black coat color in China. Genetic differentiation among the 13 goat populations was 0.2023. The clustering of populations based on the 423G>T site was basically consistent with the variation of coat color.

Keywords: Goat; Agouti ; 423G>T; Coat color; Genetic diversity

Genetic Divergence Among Marine and Lagoon Atherina boyeri Populations in Greece Using mtDNA Analysis by Spiridoula Kraitsek; Elena Klossa-Kilia; Vasilis Papasotiropoulos; Stamatis N. Alahiotis; George Kilias (pp. 781-798).

Genetic differentiation and phylogenetic relationships among 15 Atherina boyeri populations from several marine and lagoon or lake sites in Greece were investigated using mtDNA analysis. PCR-RFLP analysis of 12s, 16s rRNA genes and D-loop revealed 23 haplotypes. All the lake or lagoon populations, as well as the Kymi and Kalymnos populations that originated from sites with lagoonlike environmental conditions, showed haplotypes 1–6, clearly distinguishable from the marine populations, which exhibited types 7–23. The genetic divergence values estimated between the lagoon and the marine populations ranged from 5.55 to 10.45%. The high genetic differentiation observed between these two types of populations is also highlighted by the dendrograms obtained using UPGMA and maximum parsimony methods.

Keywords: Atherina boyeri ; mtDNA; RFLP analysis; Marine; Lagoon populations

The Risk of Coronary Artery Disease Associated with Cigarette Smoking and Hypercholesterolemia Is Additionally Increased by the Presence of the AT 1 R Gene 1166C Allele by Pawel Niemiec; Iwona Zak; Krystian Wita (pp. 799-809).

Cigarette smoking and hypercholesterolemia influence the renin-angiotensin system (RAS) functions, including increased RAS-mediated vasoconstriction, mitogenic signaling, and angiotensin II type 1 receptor (AT₁R) expression. We have explored the interactions of the AT 1 R gene 1166 A>C polymorphism and traditional risk factors using an epidemiological approach. The study cohort included 341 subjects; 172 were patients with angiographically confirmed coronary artery disease (CAD) and 169 were blood donors. The 1166 A>C polymorphism was genotyped using the PCR-RFLP method. We found a synergy of the 1166C allele with cigarette smoking (synergy indices: SI = 1.41, SIM = 1.33), LDL cholesterol levels ≥ 3 mmol/l (SI = 1.25, SIM = 1.19), and elevated total cholesterol (≥5 mmol/l) levels (SI = 1.15, SIM = 1.13). In each case, the estimated CAD risk was greater than that predicted by assuming the additivity and multiplication of effects. We conclude that the 1166C allele increases the risk of CAD associated with the presence of cigarette smoking and hypercholesterolemia.

Keywords: Gene–environment interactions; Polymorphism; AT₁ receptor

High Level of Genetic Diversity Among the Selected Accessions of Tea (Camellia sinensis) from Abandoned Tea Gardens in Western Himalaya by S. Karthigeyan; S. Rajkumar; R. K. Sharma; Ashu Gulati; R. K. Sud; P. S. Ahuja (pp. 810-819).

To revive cultivation of the tea unique to the western Himalayan region, it is important to evaluate the seed-derived bushes available in the area’s abandoned gardens. This study used quantitative leaf characters, catechin content, and AFLP markers to assess these China cultivar type bushes. Compared with other China cultivar germplasm, these accessions showed a higher level of diversity among themselves. Among the quantitative morphological characters, leaf length is important in distinguishing the accessions studied, with a high loading value in the principal component analysis. The catechins and AFLP markers displayed the genetic makeup of the accessions. Other than total catechins, the trihydroxylated catechins showed a high loading value in differentiating the accessions. The genetic control of the ratio of dihydroxylated and trihydroxylated catechins is found to be based on a correlation with AFLP markers. The genetic similarity between Kangra Asha and Kangra Jat suggests that Kangra Jat must be descended from Kangra Asha. Kangra Jat is well adapted to local environmental conditions, as is evident from its high catechin content.

Keywords: Tea germplasm; Western Himalaya; Catechin; AFLP; Leaf morphology; China cultivar type

Detection of Bovine Spongiform Encephalopathy-Related Prion Protein Gene Promoter Polymorphisms in Local Turkish Cattle by Cemal Ün; Kemal Oztabak; Nehir Özdemir; Dawit Tesfaye; Ahmet Mengi; Karl Schellander (pp. 820-827).

Polymorphisms in open reading frames of the prion protein gene (PRNP) have been shown to be associated with prion disease susceptibility in humans, sheep, and mice. Studies in recent years have demonstrated a similar effect of PRNP promoter and intron-1 polymorphisms on bovine spongiform encephalopathy (BSE) susceptibility in cattle. In this study, the deletion/insertion (indel) polymorphisms of the bovine PRNP gene within the promoter sequence (23 bp) and intron 1 (12 bp) were analyzed in local Turkish cattle. For this, 150 animals belonging to three different local breeds—the South Anatolian red, the East Anatolian red, and the Turkish gray—were tested using DNA purification and polymerase chain reaction. The ins allele in the 12 bp indel, which is associated with low susceptibility to BSE, showed a high frequency in all three breeds. The low-susceptibility allele of the 23-bp indel was identified in Turkish gray cattle with a frequency of 0.80. Results of the study have shown that local Turkish cattle might have an important genetic value for selection against BSE.

Keywords: Local Turkish cattle; PRNP ; Promoter; Indel polymorphism; Genotypes

Novel SNPs of the Bovine LEPR Gene and Their Association with Growth Traits by Yikun Guo; Hong Chen; Xianyong Lan; Bao Zhang; Chuanying Pan; Liangzhi Zhang; Cunfang Zhang; Miao Zhao (pp. 828-834).

In this study, polymorphism in the bovine LEPR gene exon 4 was detected by PCR-SSCP and DNA sequencing methods in 653 individuals from five Chinese cattle breeds. Two haplotypes (M and N), three observed genotypes (MM, MN, and NN), and five single nucleotide polymorphisms (SNPs) (NC_007301:g.26767T>C, NC_007301:g.26805C>T, NC_007301:g.27050A>G, NC_007301:g.27063G>A, NC_007301:g.27079G>A) were detected. The frequencies of haplotypes M and N in the five breeds were 0.661–0.747 and 0.253–0.339, respectively. The SNP locus was in Hardy–Weinberg equilibrium in Nanyang, Jiaxian red, Angus, and Jinnan cattle (P > 0.05) and was in Hardy–Weinberg disequilibrium in Qinchuan cattle (P < 0.05). Polymorphism of the LEPR gene was shown to be associated with growth traits in the Nanyang breed. The SNP in the bovine LEPR gene had significant effects on body height, body length, body weight, heart girth, and average daily gain at 6 and 12 months old (P < 0.01 or P < 0.05). Therefore, these results suggest that the LEPR gene is a strong candidate gene that affects growth traits in cattle.

Keywords: Bovine; LEPR gene; PCR-SSCP; Growth trait

Role of Genetic Recombination in the Molecular Architecture of Papaya ringspot virus by Satendra K. Mangrauthia; B. Parameswari; R. K. Jain; Shelly Praveen (pp. 835-846).

Papaya ringspot virus (PRSV) has a single-stranded RNA genome and causes severe economic losses both in cucurbits and papaya worldwide. The extent to which the genome of PRSV is shaped by recombination provides an understanding of the molecular evolution of PRSV and helps in studying features such as host specificity, geographic distribution, and its emergence as new epidemics. The PRSV-P-Indian isolate was completely sequenced and compared with 14 other isolates reported from the rest of the world for their phylogenetic survey of recombination events. Cistron-by-cistron sequence comparison and phylogenetic analysis based on full-genome polyprotein showed two distinct groupings of Asian and American isolates, although PRSV-P and W-India clustered along with the American isolates. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene. A significant proportion of recombination hotspots was found in the P1 gene, followed by P3, cylindrical inclusion (CI), and helper component proteinase (HcPro). Correlations between the presence of recombination sites, geographic distribution, and phylogenetic relationship provide an opportunity to establish the molecular evolution and geographic route of PRSV.

Keywords: Potyvirus; Genome diversity; P1; PRSV-P-India

Implication of the Cystic Fibrosis Transmembrane Conductance Regulator Gene in Infertile Family Members of Indian CF Patients by Neeraj Sharma; Meenu Singh; Naveen Acharya; Shrawan K. Singh; Babu R. Thapa; Gurjeet Kaur; Rajendra Prasad (pp. 847-856).

Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CFTR gene. Among males with CF, 95% are infertile due to congenital absence of the vas deferens. We investigated the role of family history of infertility among CF subjects and characterized mutations in them. Among 50 CF subjects, four had a family history of infertility. A homozygous c.1521_1523delCTT mutation was detected in one, two had a compound heterozygous genotype (c.1521_1523delCTT/c.3717 + 10 kbC>T), and c.1521_1523delCTT mutation was identified on one allele of fourth CF subject. Genetic analysis of each infertile family members of CF subjects revealed the c.1521_1523delCTT mutation on one allele; however, no mutation could be identified on other allele. Haplotype analysis of the infertile family members showed that at least one of the alleles shared the same haplotype as that of the index case. It is suggested that the CFTR gene is implicated in the infertile members of the CF families. Failure to detect mutations on the other allele by SSCP analysis demands direct gene sequencing to detect mutations in the intronic or promoter region.

Keywords: c.1521_1523delCTT mutation; Cystic fibrosis; CFTR gene; Male infertility; Genetic testing; ARMS PCR

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Biochemical Genetics (v.46, #11-12)