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Biochemical Genetics (v.50, #5-6)

Gene Variation, Population Differentiation, and Sociogenetic Structure of Nests of Partamona seridoensis (Hymenoptera: Apidae, Meliponini) by Carlo Rivero Moura Fernandes; Celso Feitosa Martins; Kátia Maria Ferreira; Marco Antonio Del Lama (pp. 325-335).

Gene variation and the differentiation of two populations of Partamona seridoensis (Hymenoptera: Apidae: Meliponini) from the Caatinga biome, a semiarid ecosystem unique to Brazil, were estimated through allozymic and microsatellite analyses. These populations exhibited similar low degrees of enzyme gene variation. Observed genotype frequencies at the allozyme and microsatellite loci were in accordance with Hardy–Weinberg equilibrium in the two populations. Both markers demonstrated that the two populations are not genetically homogeneous and must be considered distinct populations. The occurrence of private alleles at the allozyme and microsatellite loci corroborates this differentiation, sustaining the hypothesis of a low level of interpopulation gene flow. The phenotypic segregations clearly demonstrated that the progeny inside each nest were the result of mating between the queen of the colony and only one male.

Keywords: Genetic variability; Interpopulation differentiation; Sociogenetic structure; Partamona seridoensis ; Brazilian Caatinga

Investigation of the Relationship Between Oxidative Stress and Glucose Signaling in Schizosaccharomyces pombe by Bedia Palabiyik; Cenk Kig; Murat Pekmez; Levent Dalyan; Nazli Arda; Guler Temizkan (pp. 336-349).

The invertase mutant defective in the glucose signaling pathway of Schizosaccharomyces pombe (ird11) is resistant to glucose repression. This mutant is able to consume sucrose alongside glucose and grows in glucose-containing media with a generation time close to that of the wild type. Intracellular oxidation, protein carbonyl, and reduced glutathione levels and catalase, superoxide dismutase, and glutathione peroxidase activity were investigated in ird11, to determine the relationship between oxidative stress response and glucose signaling. The expression profiles of some genes involved in regulation of glucose repression (fbp1, fructose-1,6-bis-phosphatase; hxk2, hexokinase) and stress response (atf1 and pap1 transcription factors; ctt1, catalase; sod1, Cu,Zn superoxide dismutase) were analyzed using the quantitative real-time PCR technique. Oxidative stress response in ird11 seems to be affected by glucose signaling in a manner different from that caused by glucose deprivation.

Keywords: Schizosaccharomyces pombe ; Glucose signaling; Oxidative stress response; Glucose repression; Fission yeast

Seasonal Changes in the Genetic Diversity of Two Rodent Populations, Midday Gerbil (Meriones meridianus) and Northern Three-Toed Jerboa (Dipus sagitta), Detected by ISSR by Rong Zhou; You Li; Jia-Qi Li; Nai-Fa Liu (pp. 350-371).

Seasonal changes in genetic diversity of Meriones meridianus and Dipus sagitta populations in the Ningxia Hui Autonomous Region were monitored using inter-simple sequence repeats. There were 45 discernible DNA fragments isolated from 33 samples of M. meridianus, and 25 from 40 samples of D. sagitta. The differences in gene frequencies are statistically significant for some alleles. Nei’s index revealed that the greatest genetic differentiation was distributed within the seasonal groups. Nei’s and Shannon’s indexes exhibited similar seasonal trends, indicating that the spring group has the highest level of genetic diversity and that genetic diversity changes with the seasons. Correlation analysis found no statistically significant correlation between genetic diversity and population density. The results suggest that the seasonal changes in genetic diversity of the two species depend mainly on reproduction and dispersal.

Keywords: ISSR; Genetic diversity; Reproduction; Immigration

Vicilin Genes of Vigna luteola: Structure, Organization, Expression, and Variation by Zhongyu Xie; Joseph Neigel; Caryl Chlan (pp. 372-388).

Two different but related sequences that encode Vigna luteola 7S vicilins were isolated and characterized. The sequences differ by two nucleotide substitutions, each of which results in an amino acid replacement. This low level of divergence suggests that a recent gene duplication has occurred. Both variants are expressed in cDNA populations; therefore, neither gene is a pseudogene. Both copies were present in all individuals (72) analyzed using real-time PCR and TaqMan probes. Segregation was not observed. The two sequences are not independent alleles. Vicilin genomic sequences of 11 specimens from six geographic locations were determined. No polymorphic sites were identified in either of the two gene copies. This lack of polymorphism suggests that either a population bottleneck or selection has occurred. The genetic structure, expression patterns, and protein composition of the V. luteola vicilins were compared to those of other legume vicilins.

Keywords: Vicilin; Storage protein; Gene duplication; Polymorphism; Vigna luteola

Association of CYP19 Gene Polymorphism with Vertebral Fractures in Japanese Postmenopausal Women by Yasuko Koudu; Tsuneko Onouchi; Takayuki Hosoi; Toshiyuki Horiuchi (pp. 389-396).

This study investigates aromatase gene polymorphism, which might influence bone strength in terms of mineral density and quality. We explored the relationship between CYP19 polymorphisms and vertebral fractures in postmenopausal Japanese women. In addition, we compared estrogen and testosterone levels in Japanese postmenopausal women with and without fractures. Osteoporotic postmenopausal women showed higher incidences of vertebral fractures than osteopenic women or women with normal lumbar bone mineral density (L2-4 BMD). Estrogen concentrations in postmenopausal women were associated with BMD; however, no association was found between sex hormone levels and the presence of fractures. The C allele rs2470152 was significantly associated with increased risk of vertebral fractures (P = 0.04), whereas none of the CYP19 polymorphisms showed differences in sex steroid levels between subjects with and without fractures. Allelic variants of aromatase genes appear to interact to influence the risk of vertebral fractures in postmenopausal Japanese women.

Keywords: Aromatase gene polymorphisms; Vertebral fractures; Postmenopausal women

Isolation of Microsatellite Markers and Analysis of Genetic Diversity Among East Atlantic Populations of the Sword Razor Shell Ensis siliqua: A Tool for Population Management by Alberto Arias-Pérez; Juan Fernández-Tajes; Miguel B. Gaspar; Josefina Méndez (pp. 397-415).

The sword razor shell Ensis siliqua (Linnaeus, 1758) is found mainly from Norway to the Atlantic coast of the Iberian Peninsula. It is intensively caught in Europe, being highly appreciated as seafood. To help in its conservation and management, five microsatellite markers were isolated and genetic variation was analyzed in samples from Ireland, Spain, and Portugal. The highly significant differentiation (θ = 0.287, P < 0.001) observed was mainly due to differences between samples from Irish and Iberian Peninsula localities, except Aveiro (its sample resembled the Irish samples, and it may be predominantly self-recruiting). These groups of samples showed significant differences in allelic richness that could be related to harvesting intensity. Moreover, microsatellites detected low but significant differentiation between Iberian localities (Celeiro and Olhão), and Aveiro differed significantly from Strangford Lough. Overall, results suggest that two independently evolving regions exist and that management strategies should be designed for each region.

Keywords: Ensis siliqua ; Genetic differentiation; Genetic variation; Management; Microsatellite markers; Sword razor shell

Genetic Structure of the Carnivorous Plant Pinguicula moranensis (Lentibulariaceae) on the Transvolcanic Mexican Belt by Raúl E. Alcalá; César A. Domínguez (pp. 416-427).

Most species of Pinguicula present a montane distribution with populations located at high altitudes. In this context, we proposed that populations of Pinguicula species could be genetically differentiated even at a local scale. This study supported that prediction, as a RAPD-based analysis of molecular variance revealed a high degree of genetic structure (Φ _st = 0.157, P = 0.001) and low gene flow (N _m = 1.0) among four central populations of Pinguicula moranensis in Mexico, with a maximum geographic separation of about 140 km. The four populations also exhibited high levels of genetic diversity (mean Nei’s genetic diversity = 0.3716; % polymorphism = 95.45%). The evolutionary implications of the genetic structure found in P. moranensis for other species in the genus are discussed in the context of the naturally fragmented distribution and a set of life history traits shared by most Pinguicula species that could promote geographic isolation and limited gene flow.

Keywords: AMOVA; Genetic differentiation; Gene flow; Life history traits; Geographic distribution; Pinguicula moranensis ; RAPD markers

Porcine Single Nucleotide Polymorphism (SNP) Development and Population Structure of Pigs Assessed by Validated SNPs by Toshimi Matsumoto; Naohiko Okumura; Hirohide Uenishi; Takeshi Hayashi; Noriyuki Hamasima; Takashi Awata (pp. 428-439).

In this study, we identified porcine single nucleotide polymorphisms (SNPs) by aligning eight sequences generated with two approaches: amplification of 665 intronic regions using one sample from each of eight breeds, including three East Asian pigs, and amplification of 289 3′-UTR regions using two samples from each of four major commercial breeds. The 1,760 and 599 SNPs were validated using two 384-sample DNA panels by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The phylogenetic tree and Structure analyses classified the pigs into two large clusters: Euro-American and East Asian populations. The membership proportions, however, differed between inferred clusters for K = 2 generated by the two approaches. With intronic SNPs, Euro-American breeds constituted about 100% of the Euro-American cluster, but with 3′-UTR SNPs, about 17% of the East Asian cluster comprised five Euro-American breeds. The differences in the SNP discovery panels may affect population structure found in study panels of large samples.

Keywords: SNP; Pig; Genetic diversity; Population structure; Ascertainment bias

Molecular Identification of Small Mammal Species Using Novel Cytochrome b Gene-Derived Degenerated Primers by Mathias Schlegel; Hanan Sheikh Ali; Nicole Stieger; Martin H. Groschup; Ronny Wolf; Rainer G. Ulrich (pp. 440-447).

Analysis of p15 INK4b and p16 INK4a Gene Methylation in Patients with Oral Squamous Cell Carcinoma by Dor Mohammad Kordi-Tamandani; Mohammad Ayub Rigi Ladies; Mohammad Hashemi; Abdul-Karim Moazeni-Roodi; Smriti Krishna; Adam Torkamanzehi (pp. 448-453).

Differences in Salinity Tolerance and Gene Expression Between Two Populations of Atlantic Cod (Gadus morhua) in Response to Salinity Stress by P. F. Larsen; E. E. Nielsen; K. Meier; P. A. Olsvik; M. M. Hansen; V. Loeschcke (pp. 454-466).

Populations of marine fish, even from contrasting habitats, generally show low genetic differentiation at neutral genetic markers. Nevertheless, there is increasing evidence for differences in gene expression among populations that may be ascribed to adaptive divergence. Studying variation in salinity tolerance and gene expression among Atlantic cod (Gadus morhua) from two populations distributed across a steep salinity gradient, we observed high mortality (45% North Sea cod and 80% Baltic Sea cod) in a reciprocal common garden setup. Quantitative RT-PCR assays for expression of hsp70 and Na/K-ATPase α genes demonstrated significant differences in gene regulation within and between populations and treatment groups despite low sample sizes. Most interesting are the significant differences observed in expression of the Na/K-ATPase α gene in gill tissue between North Sea and Baltic cod. The findings strongly suggest that Atlantic cod are adapted to local saline conditions, despite relatively low levels of neutral genetic divergence between populations.

Keywords: Gene expression variation; Population structure; Salinity gradient; Salinity tolerance

Isolation and Gene Expression of Yellow Grouper Ferritin Heavy Chain Subunit After Lipopolysaccharide Treatment by Li Wang; Yong Wei (pp. 467-475).

Ferritin is a ubiquitous and conserved iron storage protein that plays a central role in iron metabolism. The ferritin heavy chain subunit (FerH) homolog was isolated from yellow grouper (Epinephelus awoara) spleen using suppression subtractive hybridization and RACE-PCR. The nucleotide sequence of FerH full-length cDNA was 1173 bp and contained an open reading frame of 534 bp, encoding a putative protein of 177 amino acids. The encoded protein shows 78–94% identity with homologs. Based on phylogenetic analysis, yellow grouper FerH is highly conserved throughout evolution and is closer to European seabass than to other species. RT-PCR analysis demonstrated that FerH was widely expressed in various healthy tissues and significantly up-regulated in liver, spleen, and anterior kidney by lipopolysaccharide. The results suggest that yellow grouper FerH may play a role in immune response.

Keywords: Ferritin heavy chain subunit; Characterization; Gene expression; Lipopolysaccharide; Epinephelus awoara

Determination of Genetic Diversity of Vitis vinifera cv. Kabarcik Populations from the Coruh Valley Using SSR Markers by Guleray Agar; Nalan Yildirim; Sezai Ercisli; Ali Ergul; Canan Yuksel (pp. 476-483).

Northeastern Turkey is recognized as one of the most important germplasm centers for the grape in the world. In the present study, simple sequence repeat markers were used to investigate the genetic diversity between four Vitis vinifera cv. Kabarcik populations sampled from the Coruh Valley in Turkey, at altitudes of 800–1,150 m. The mean observed number of alleles per locus varied from 2 (loci VVMD7 and VVMD24) to 6 (VVS2) among populations. The population from the highest altitude showed the greatest average number of alleles, 4.5. With regard to the six loci examined in all populations, the mean observed heterozygosity was higher than the expected heterozygosity. Among the loci, VVS2 (probability of identity = 0.137) was found to be the most informative among populations. Genetic distances between populations ranged from 0.072 to 0.216. Genetic differentiation among populations was strongly related to geographic distances in all populations.

Keywords: SSR; Vitis vinifera ; Population; Genetic distance; Altitude

Increase in UV Mutagenesis by Heat Stress on UV-Irradiated E. coli Cells by Swati Saha; Tarakdas Basu (pp. 484-493).

When leu ⁻ auxotrophs of Escherichia coli, after UV irradiation, were grown at temperatures between 30 and 47°C, the frequency of UV-induced mutation from leu ⁻ to leu ⁺ revertant increased as the UV dose and the temperature increased. For cells exposed to a UV dose of 45 J/m², the mutation frequency at 47°C was 1.9 times that at 30°C; for a dose of 90 J/m², it was 3.25 times; and for 135 J/m², it was 4.8 times. Similar enhancement of reversion frequency was observed when the irradiated cells were grown at 30°C in the presence of a heat shock inducer, ethanol (8% v/v). Heat shock-mediated enhancement of UV mutagenesis did not occur in an E. coli mutant sigma 32 (heat shock regulator protein), but sigma 32 overexpression in the mutant strain (transformed with a sigma 32-bearing plasmid) increased the UV-induced mutation frequency. These results suggest that heat stress alone has no mutagenic property, but when applied to UV-damaged cells, it enhances the UV-induced frequency of cell mutation.

Keywords: Escherichia coli ; Mutation; UV radiation; Heat shock; Sigma 32; Ethanol

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Biochemical Genetics (v.50, #5-6)

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Biochemical Genetics (v.50, #5-6)