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Biochemical Genetics (v.48, #3-4)

Cloning and Characterization of Novel Isoforms of the BOULE Gene in Bats by Lihong Yuan; Xueguo Zuo; Lingjiang He; Paul Racey; Eran Levin; Shuyi Zhang (pp. 173-180).

Development of a Species-Diagnostic Marker for Identification of the Stingless Bee Trigona pagdeni in Thailand by Sirikul Thummajitsakul; Sirawut Klinbunga; Siriporn Sittipraneed (pp. 181-192).

A species-diagnostic SCAR marker for identification of the stingless bee (Trigona pagdeni Schwarz) was successfully developed. Initially, amplified fragment length polymorphism analysis was carried out across representatives of 12 stingless bee species using 64 primer combinations. A 284 bp band restrictively found in T. pagdeni was cloned and sequenced. A primer pair (CUTP1-F/R) was designed and tested for species-specificity in 15 stingless bees. The expected 163 bp fragment was successfully amplified in all examined individuals of T. pagdeni (129/129). Nevertheless, cross-species amplification was also observed in T. fimbriata (1/3), T. collina (11/112), T. laeviceps (1/12), and T. fuscobalteata (15/15), but not in other species. SSCP analysis of CUTP1 further differentiated T. fuscobalteata and T. collina from T. pagdeni. Although T. laeviceps, T. fimbriata, and T. pagdeni shared an identical SSCP genotype, they are not taxonomically problematic species.

Keywords: Stingless bees; Trigona pagdeni ; AFLP; SSCP; Species-specific marker

Replacement of C305 in Heart/Muscle-Type Isozyme of Human Carnitine Palmitoyltransferase I with Aspartic Acid and Other Amino Acids by Taisuke Matsuo; Atsushi Yamamoto; Takenori Yamamoto; Kaoru Otsuki; Naoshi Yamazaki; Masatoshi Kataoka; Hiroshi Terada; Yasuo Shinohara (pp. 193-201).

Liver- and heart/muscle-type isozymes of human carnitine palmitoyltransferase I (L- and M-CPTI, respectively) show a certain similarity in their amino acid sequences, and mutation studies on the conserved amino acids between these two isozymes often show essentially the same effects on their enzymatic properties. Earlier mutation studies on C305 in human M-CPTI and its counterpart residue, C304, in human L-CPTI showed distinct effects of the mutations, especially in the aspect of enzyme stability; however, simple comparison of these effects on the conserved Cys residue between L- and M-CPTI was difficult, because these studies were carried out using different expression systems and distinct amino acids as replacements. In the present study, we carried out mutation studies on the C305 in human M-CPTI using COS cells for the expression system. Our results showed that C305 was replaceable with aspartic acid but that substitution with other amino acids caused both loss of function and reduced expression.

Keywords: Carnitine palmitoyltransferase; Mutants; Cysteine residue; Expression

Nucleotide Sequence of Canine Smad3 by Kazutoshi Sugiyama; Ryo Ooishi; Yoshii Nishino; Masayuki Funaba; Masaru Murakami (pp. 202-207).

The whole genome sequence of a Boxer dog suggested that the amino acid sequence of the carboxyl terminus of a putative Smad3 is SSVF-_COOH, not SSVS-_COOH as in all Smad3 sequences identified in many species. Because phosphorylation of the last two serines at the carboxyl terminus is generally indispensable for Smad3-mediated signaling, the role of Smad3 may be unique in dogs. The present study determines the nucleotide sequence of the coding region of canine Smad3 and deduces the carboxyl terminal amino acids of Smad3 in several breeds. Except for the Boxer, the deduced amino acid sequence was SSVS-_COOH in all dogs examined. In addition, the nucleotide at position 1204 in the Boxer was different from that of the other dogs. Furthermore, there was a SNP at nt 240. The present study indicates that the carboxyl terminal amino acid of canine Smad3 is not unique, although it is unknown in the Boxer breed.

Keywords: Smad3; Dog; Nucleotide sequence; TGF-β

Polymorphic Analysis of the Human Phosphoglucomutase-3 Gene Based on Mismatched PCR–RFLP Technique by Hao Pang; Zhongjie Li; Baojie Wang; Mei Ding (pp. 208-214).

Polymorphic analysis of human phosphoglucomutase-3 (PGM₃) has been carried out from the level of the gene product. Due to a weak zymogram, leading to ambiguity in phenotyping, information on the PGM 3 locus has rarely been reported. In this study, the missense mutation G1396A, confirmed to underlie common phenotypes of PGM₃, was identified by performing mismatched PCR–RFLP. Population data on the PGM 3 locus was also obtained for the first time in China. The allele frequency distribution was PGM 3 *1 = 0.625, PGM 3 * 2 = 0.375, and no deviation from Hardy–Weinberg equilibrium was observed. The application of the information in both genetics and forensic medicine demonstrated that the polymorphism information content was 0.5163, heterozygosity 0.4872, power of discrimination 0.5986, and probability of paternity exclusion 0.1794. Polymorphic analysis of the locus at the DNA level will also provide significant data for disease susceptibility and linkage analysis.

Keywords: PGM₃ ; AGM₁ ; Genetic polymorphisms; Mismatched PCR

Genetic Structure of Tree and Shrubby Species Among Anthropogenic Edges, Natural Edges, and Interior of an Atlantic Forest Fragment by Flavio Nunes Ramos; Paula Feliciano de Lima; Maria Imaculada Zucchi; Carlos Augusto Colombo; Vera Nisaka Solferini (pp. 215-228).

Two species, Psychotria tenuinervis (shrub, Rubiaceae) and Guarea guidonia (tree, Meliaceae), were used as models to compare the genetic structure of tree and shrubby species among natural edges, anthropogenic edges, and a fragment interior. There were significant differences between two genetic markers. For isozymes, P. tenuinervis presented greater heterozygosity (expected and observed) and a higher percentage of polymorphic loci and median number of alleles than G. guidonia. For microsatellites, there was no difference in genetic variability between the species. Only P. tenuinervis, for isozymes, showed differences in genetic variability among the three habitats. There was no genetic structure (F _ST < 0.05) among habitats in both plant species for both genetic markers. Isozymes showed great endogamy for both plant species, but not microsatellites. The forest fragmentation may have negative effects on both spatial (among edges and interior) and temporal genetic variability.

Keywords: Atlantic forest; Forest fragmentation; Genetic structure; Isozyme; Microsatellites

MTHFR Gene Polymorphism and Its Relationship with Plasma Homocysteine and Folate in a North Indian Population by Usha Kant Misra; Jayantee Kalita; Amit Kumar Srivastava; Suraksha Agarwal (pp. 229-235).

There is a paucity of data on the prevalence of elevated homocysteine and its relation with plasma folate and the methylenetetrahydrofolate reductase (MTHFR) gene in the population of North India. This study evaluates MTHFR gene polymorphism and its relationship with plasma homocysteine and folate levels in a healthy North Indian population. The age of the 200 subjects included in this study was in the range 18–73 (mean 39.4) years. The plasma homocysteine level was elevated in 56.5%, and the plasma folate level was low in 49.5% of the subjects. Heterozygous MTHFR gene polymorphism (CT) was present in 15.5%, and homozygous (TT) in 3.5% of the subjects. Age, diet, and MTHFR gene polymorphisms were related to homocysteine level. All the subjects with the TT and 79% with the CT genotype had a high level of plasma homocysteine, whereas 51% with the CC genotype had a high homocysteine level. After adjustment for the effect of covariates, however, homocysteine was not related to MTHFR gene polymorphism.

Keywords: MTHFR gene polymorphism; Homocysteine; Folate; Dietary habit; Healthy population; Indian population

Adaptive Evolution in the GAF Domain of Phytochromes in Gymnosperms by Jing Wang; Boqian Yan; Guopei Chen; Yingjuan Su; Ting Wang (pp. 236-247).

The GAF domain of phytochrome is essential for photoconversion and signal transduction. In gymnosperms, it exists in all members of the phytochrome family that experience gene duplication. Maximum-likelihood models of codon substitution can provide a framework for constructing likelihood ratio tests of changes in selective pressure and make clear predictions about patterns of genetic change following gene duplication. In this study, 68 gymnosperm GAF sequences were analyzed to identify lineages and sites under positive selection. Our results indicate that (1) positive selection at a few sites (3.6%), rather than relaxation of selective constraints, has played a major role in the evolution of the gymnosperm GAF domain; (2) strong positive selective pressure tends to occur in the recent PHYP lineages of cogeneric species, but is absent in old lineages consisting of distantly related species; and (3) the selective pressure indicated by the ω ratio varies greatly among lineages and sites in the GAF domain.

Keywords: Adaptive evolution; GAF domain; Phytochrome; Gymnosperm

Two Novel Missense Mutations in the Connexin 26 Gene in Turkish Patients with Nonsyndromic Hearing Loss by Akin Yilmaz; Sevda Menevse; Yildirim Bayazit; Recep Karamert; Volkan Ergin; Adnan Menevse (pp. 248-256).

Most nonsyndromic hearing losses are caused by mutations in the GJB2 gene, and studies have revealed that the forms and frequencies of these mutations are largely dependent on ethnic origin. In the present study, we aimed to characterize the mutation profiles of 151 patients with hearing loss in Turkey. The entire coding region of the GJB2 was directly sequenced in all patients. We found 35 (23.2%) individuals carrying GJB2 mutations. Seven different mutations were identified, five of which were previously known (35delG, delE120, R184P, M163V, L90P), the remaining two being novel variants (M34V, L205V). The most common mutation was 35delG followed by delE120. The 35delG mutation was homozygous in 22 cases (14.5%) and heterozygous in 4 cases (2.6%). Compound heterozygosity for 35delG was also observed. The delE120 mutation was found in three patients in homozygous form. A homozygous L90P and heterozygous mutations M163V and M34V were found in single cases.

Keywords: Connexin 26; Mutation; Hearing loss; Turkish

Association of Porcine IGF Binding Protein-5 Gene with Meat Quality by Wenjun Wang; Kehui Ouyang; Xinchen Shangguan; Mingsheng Xu (pp. 257-265).

IGFBP-5 is a member of the IGF families. Using PCR-SSCP, genotypic and allelic frequencies were analyzed in 18 pig breeds (n = 600). The association between haplotypes and production performance was analyzed in a Jinhua × Pietrain population family (n = 212, total 24 traits). Two SNPs (T199C and G485A) within the gene were analyzed. The breeds had different genotypic and allelic frequencies. Typically, the Chinese native pig breeds carried a higher allele C and G frequency (over 50%) than those of the European pigs, and only Guangdong Large White and wild boar were at Hardy–Weinberg equilibrium. The pigs carrying the CG haplotype had higher hue, loin, and thigh pH1 values than pigs with the TA haplotype, and pigs with the TA haplotype had the lowest loin pH2 value and highest color-a value among the haplotypes. It is proposed that the IGFBP-5 gene is associated with the variation in meat quality, especially in pH value together with other QTLs on chromosome 15.

Keywords: Insulin-like growth factor binding protein-5; Haplotype; Production performance; Association; Swine

Interpopulation Crosses, Inheritance Study, and Genetic Variability in the Brown Planthopper Complex, Nilaparvata lugens (Homoptera: Delphacidae) by M. A. Latif; Mohd. Yosuh Omar; Soon Guan Tan; Siti Shapor Siraj; Abdul Rahim Ismail (pp. 266-286).

Studies on hybridization, inheritance, and population genetics of brown planthoppers that infest rice and weeds were undertaken using starch gel electrophoresis to determine whether the weed-infesting population represents a biological race or a species. F₁ and F₂ generations were produced by crosses between parental insects from the two populations with little indication of hybrid sterility. Gpi, Mdh, and Idh loci were inherited in a simple Mendelian fashion in families of two sympatric populations. Sixteen populations of Nilaparvata spp. from eight locations were collected. The Mdh, Idh, Pgm, Gpi, 6Pgd, and Acp loci were polymorphic. The N. lugens of rice with high esterase activity were clustered into a group and characterized by the presence of alleles Gpi 110 and Gpi 120, whereas N. lugens from weeds with low esterase activity were clustered into another group and characterized by Gpi 100 and Gpi 90 . There was a lack of heterozygotes between the common alleles of the two populations. This means that the two groups of individuals belong to different gene pools.

Keywords: Hybridization; Allozymes; Inheritance study; Genetic variability; Brown planthopper complex

Biochemical Genetics of Opossum Aldehyde Dehydrogenase 3: Evidence for Three ALDH3A-Like Genes and an ALDH3B-Like Gene by Roger S. Holmes (pp. 287-303).

Mammalian ALDH3 isozymes participate in peroxidic and fatty aldehyde metabolism, and in anterior eye tissue UV-filtration. BLAT analyses were undertaken of the opossum genome using rat ALDH3A1, ALDH3A2, ALDH3B1, and ALDH3B2 amino acid sequences. Two predicted opossum ALDH3A1-like genes and an ALDH3A2-like gene were observed on chromosome 2, as well as an ALDH3B-like gene, which showed similar intron–exon boundaries with other mammalian ALDH3-like genes. Opossum ALDH3 subunit sequences and structures were highly conserved, including residues previously shown to be involved in catalysis and coenzyme binding for rat ALDH3A1. Eleven glycine residues were conserved for all of the opossum ALDH3-like sequences examined, including two glycine residues previously located within the stem of the rat ALDH3A1 active site funnel. Phylogeny studies of human, rat, opossum, and chicken ALDH3-like sequences indicated that the common ancestor for ALDH3A- and ALDH3B-like genes predates the appearance of birds during vertebrate evolution.

Keywords: Aldehyde dehydrogenase; Opossum; Genetics; ALDH; Evolution; Mammal; Gene mapping

Genetic Polymorphism of the β-Lactoglobulin Gene in Native Sheep from India by R. Arora; S. Bhatia; B. P. Mishra; R. Sharma; A. K. Pandey; B. Prakash; A. Jain (pp. 304-311).

The genetic polymorphism of the β-lactoglobulin (β-LG) gene was determined in 638 animals belonging to 15 native Indian sheep breeds reared in different agroecological regions for various production traits. Variants of β-LG were found using PCR–RFLP of genomic DNA. Rsa1 restriction enzyme digestion of a 120-bp PCR fragment of exon 2 of β-LG revealed two genetic variants, A (0.37) and B (0.63), and the three genotypes AA (0.175), AB (0.389), and BB (0.436). The differences in allelic frequency were not significant across the breeds, irrespective of their geographic origin and utility (χ² test, P > 0.05). The pattern of occurrence of allelic variants revealed that the B allele was more frequent in the majority of the Indian breeds than in breeds reported from countries of Southwest Asia, Eastern and Central Europe, and the Mediterranean. A higher level of heterozygosity (0.422) was discerned, despite the declining status of several of the Indian breeds. These findings revealed that Indian sheep are predominantly of the β-LG B type.

Keywords: Indian sheep breeds; β-Lactoglobulin gene; Genetic polymorphism; Rsa1 allele; PCR–RFLP

Temporal Variation in Genetic Structure of the Chinese Rare Minnow (Gobiocypris rarus) in Its Type Locality Revealed by Microsatellite Markers by Yongfeng He; Jianwei Wang (pp. 312-325).

Gobiocypris rarus, an endemic cyprinid fish with high fecundity, lives mainly in small water systems easily influenced by changes in natural surroundings. This study used 11 polymorphic microsatellite primers to identify the temporal variation of its topotype population. Moderate genetic diversity, inbreeding phenomena, and limited temporal variation between 1997 and 2006 were revealed in the topotype population. The main temporal fluctuations involved only the change of allelic frequencies over two loci and allelic richness. The effective population size was estimated to be 645. The authors argue that inbreeding did not induce dramatic depression effects on the topotype population, and the forces to maintain genetic diversity were mainly from environmental fluctuations and life history traits. Considering that the topotype population is facing increased habitat loss, destruction, and disturbance due to human activities, the authors suggest that a habitat and species management area be established in the type locality.

Keywords: Gobiocypris rarus ; Genetic diversity; Temporal variation; Microsatellite

Mitochondrial DNA Diversity of Orchid Bee Euglossa fimbriata (Hymenoptera: Apidae) Populations Assessed by PCR-RFLP by Karen M. Suzuki; Maria C. Arias; Douglas C. Giangarelli; Gabriele A. Freiria; Silvia H. Sofia (pp. 326-341).

Euglossa fimbriata is a euglossine species widely distributed in Brazil and occurring primarily in Atlantic Forest remnants. In this study, the genetic mitochondrial structure of E. fimbriata from six Atlantic Forest fragments was studied by RFLP analysis of three PCR-amplified mtDNA gene segments (16S, COI-COII, and cyt b). Ten composite haplotypes were identified, six of which were exclusive and represented singleton mitotypes. Low haplotype diversity (0.085–0.289) and nucleotide diversity (0.000–0.002) were detected within samples. AMOVA partitioned 91.13% of the overall genetic variation within samples and 8.87% (ϕ_st = 0.089; P < 0.05) among samples. Pairwise comparisons indicated high levels of differentiation among some pairs of samples (ϕ_st = 0.161–0.218; P < 0.05). These high levels indicate that these populations of E. fimbriata, despite their highly fragmented landscape, apparently have not suffered loss of genetic variation, suggesting that this particular population is not currently endangered.

Keywords: Euglossini; Euglossine bees; Genetic structure; mtDNA; PCR-RFLP

The Influence of Nutrigenetics on the Lipid Profile: Interaction Between Genes and Dietary Habits by Fabiana M. de Andrade; Andréa C. Bulhões; Sharbel W. Maluf; Jaqueline B. Schuch; Francine Voigt; Juliana F. Lucatelli; Alessandra C. Barros; Mara H. Hutz (pp. 342-355).

Nutrigenetics is a new field with few studies in Latin America. Our aim is to investigate the way in which different genes related to the lipid profile influence the response to specific dietary habits. Eight polymorphisms on seven genes were investigated in a sample (n = 567) from Porto Alegre, RS, Brazil. All the volunteers completed a food diary that was then assessed and classified into nine food groups. A number of nutrigenetic interactions were detected primarily related to the apolipoprotein E (apoE) gene. For example, frequent consumption of foods rich in polyunsaturated fat resulted in the beneficial effect of increasing HDL-C only in individuals who were not carriers of the E*4 allele of the APOE gene, whereas variations in eating habits of E*4 carriers did not affect their HDL-C (P = 0.018). Our data demonstrate for the first time nutrigenetic interactions in a Brazilian population.

Keywords: Nutrigenetics; Lipid profile; Apolipoprotein E; Hepatic lipase

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Biochemical Genetics (v.48, #3-4)

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Biochemical Genetics (v.48, #3-4)