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Biochemical Genetics (v.51, #1-2)

A Simple and Affordable Method of DNA Extraction from Fish Scales for Polymerase Chain Reaction by Yanhe Li; Yasmeen Gul; Zexia Gao; Wei Luo; Weimin Wang (pp. 1-6).

Cloning and Molecular Evolution of the Aldehyde Dehydrogenase 2 Gene (Aldh2) in Bats (Chiroptera) by Yao Chen; Bin Shen; Junpeng Zhang; Gareth Jones; Guimei He (pp. 7-19).

Old World fruit bats (Pteropodidae) and New World fruit bats (Phyllostomidae) ingest significant quantities of ethanol while foraging. Mitochondrial aldehyde dehydrogenase (ALDH2, encoded by the Aldh2 gene) plays an important role in ethanol metabolism. To test whether the Aldh2 gene has undergone adaptive evolution in frugivorous and nectarivorous bats in relation to ethanol elimination, we sequenced part of the coding region of the gene (1,143 bp, ~73 % coverage) in 14 bat species, including three Old World fruit bats and two New World fruit bats. Our results showed that the Aldh2 coding sequences are highly conserved across all bat species we examined, and no evidence of positive selection was detected in the ancestral branches leading to Old World fruit bats and New World fruit bats. Further research is needed to determine whether other genes involved in ethanol metabolism have been the targets of positive selection in frugivorous and nectarivorous bats.

Keywords: ALDH2; Ethanol oxidization; Fruit bats; Evolution

Transcriptome Analysis Reveals Genes Related to Floral Development in Chrysanthemum Responsive to Photoperiods by Hongyan Ren; Farong Zhu; Chengshu Zheng; Xia Sun; Wenli Wang; Huairui Shu (pp. 20-32).

This research used the cDNA-AFLP technique to identify differentially expressed transcript-derived fragments (TDFs) in the apical tips of chrysanthemum induced by different photoperiods. Of the 3,152 TDFs screened by 64 primer recombinations, 861 were found to be differentially expressed, with 597 up-regulated and 264 down-regulated. We successfully cloned, sequenced, and analyzed the homologies of 57 TDFs. We found homologies for 37 of them in the NCBI: 31 displayed homology to genes with known functions, 3 to genes with unknown function, and 3 showed no matches. Functional analysis indicated that 34 TDFs participated in seven processes: transcription regulation, signal transduction, substance and energy metabolism, differentiation and development, protein degradation and synthesis, stress responses, and unclassified protein. Semi-quantitative RT-PCR analysis with selected transcripts of four genes related to floral development indicated that they all were expressed or up-regulated under short-day conditions. This was supported by analysis of cDNA-AFLP.

Keywords: Chrysanthemum; Floral differentiation; Photoperiod; Transcript-derived fragments; Transcriptome

Analysis of Human Mitochondrial DNA Polymorphisms in the Japanese Population by Sayaka Maruyama; Toshinobu Komuro; Hikaru Izawa; Hirofumi Tsutsumi (pp. 33-70).

The highly polymorphic nature and high amplification efficiency of mitochondrial DNA (mtDNA) is valuable for the analysis of biological evidence in forensic casework, such as the identification of individuals and assignment of race/ethnicity. To be useful, a mtDNA polymorphism database for the Japanese population requires an understanding of the range of haplotype variation and phylogenies of mtDNA sequences. To extend current knowledge on the haplotypes in the Japanese population, this study defines new lineages and provides more detail about some of those previously described. We compared the hypervariable regions (HVRs) of 270 healthy, unrelated Japanese individuals and demonstrated 192 haplotypes. Combining HVR1 and HVR2, the genetic diversity was 0.9935, thus providing a high level of identification capability. Haplogroup status was defined for 160 individuals using HVR1, HVR2, and particular coding region polymorphisms; these individuals belonged to 94 haplotypes, four of which were new lineages. The complete mtDNA sequence was also determined from seven individuals.

Keywords: Mitochondrial DNA; Identification; Polymorphism; Haplogroup; Phylogenetic tree

Molecular Studies on the Origin of the Hb G-Coushatta Mutation in Denizli Province of Turkey by Aylin Köseler; Onur Öztürk; Ayfer Atalay; Erol Ö. Atalay (pp. 71-75).

Association of PON1 and PON2 Polymorphisms with PON1 Activity and Significant Coronary Stenosis in a Tunisian Population by Jihène Rejeb; Asma Omezzine; Lamia Rebhi; Imen Boumaiza; Hajer Mabrouk; Hamida Rhif; Nabila Ben Rejeb; Naoufel Nabli; Wahiba Douki; Ahmed Ben Abdelaziz; Essia Boughzala; Ali Bouslama (pp. 76-91).

PON1 and PON2 have attracted considerable attention as candidate genes for coronary heart disease because their enzymes function as key factors in lipoprotein catabolism pathways. We studied the distribution of PON1 and PON2 polymorphisms, including genotyping, lipid profile, and PON1 activity, and their association with PON1 activity and significant coronary stenosis (SCS) in a Tunisian population. PON1 activity was lower in patients with SCS than in controls. It increased with the R allele (QQ < QR < RR) in PON1-192 genotypes and with the L allele (MM < ML < LL) in PON1-55 genotypes. In the presence of metabolic syndrome and diabetes, PON1-192RR and PON2-311CC were associated with an increased risk of SCS and PON1-55MM seems to have lower risk. This association was evident among nonsmokers for PON1-55MM and among smokers for PON1-192RR and PON2-311CC. The GTGC haplotype seemed to increase the risk of SCS compared with the wild haplotype in a Tunisian population.

Keywords: PON1 and PON2 polymorphisms; PON1 activity; Significant coronary stenosis; Tunisian

Lack of Association of NOS3 and ACE Gene Polymorphisms with Coronary Artery Disease in Southern Tunisia by Rania Abdelhedi; Najla Kharrat; Nouha Abdelmoula Bouayed; Leila Abid; Wafa Abdelmouleh; Imen Trabelsi Sahnoun; Suad AlFadhli; Lobna Laroussi; Ahmed Rebai (pp. 92-100).

Sensitivity of Translation Initiation Factor eIF1 as a Molecular Target of Salt Toxicity to Sodic-Alkaline Stress in the Halophytic Grass Leymus chinensis by Yan-Lin Sun; Soon-Kwan Hong (pp. 101-118).

Eukaryotic translation initiation factors (eIFs) have been shown to be critical in the initiation of protein synthesis. Here, we report the cloning and characterization of a novel gene, LceIF1, from a potentially interesting forage grass, Leymus chinensis (Trin.). The expression results show that LceIF1 is expressed in most organisms under normal conditions, but the transcription patterns differ under sodic-saline and sodic-alkaline stresses. Sodic-saline stress induced a persistent decrease, and sodic-alkaline stress induced overexpression of LceIF1. Potassic-saline and alkaline stresses did not cause any changes in expression of eIF1. These results indicate that not only pH but also Na⁺ concentration affects overtranscription of LceIF1. The eIF1 transgenic lines showed relatively high eIF1 expression, resulting in potentially higher stress resistance. Combined with eIF1 transcription in transgenic lines, LceIF1 as a molecular target of salt toxicity is believed to help enhance salt tolerance.

Keywords: Leymus chinensis ; Eukaryotic translation initiation factors; Saline stress; Alkaline stress; eIF1; Transgenic plant

The Igf2as Transcript is Exported into Cytoplasm and Associated with Polysomes by Carolina Duart-Garcia; Martin H. Braunschweig (pp. 119-130).

Murine insulin-like growth factor 2 antisense (Igf2as) transcripts originate from the opposite strand of the same Igf2 locus as the Igf2 sense mRNA. The Igf2, insulin 2 (Ins2), and H19 genes form a cluster of imprinted genes on chromosome 7. Loss of imprinting of IGF2 in humans is associated with Beckwith–Wiedemann syndrome and Silver–Russell syndrome, as well as with Wilm’s tumor and colorectal cancer. We developed a RNA-FISH protocol to detect Igf2as and Igf2 transcripts. The results from the RNA-FISH were confirmed with quantitative real-time PCR and clearly indicate that the Igf2as transcripts are predominantly located in the cytoplasm of C2C12 cells. In a polysome association study, we showed that the Igf2as sedimented with polysomes in a sucrose gradient. The cellular localization of Igf2as transcripts together with polysome fractionation analysis provides compelling evidence that the Igf2as is protein coding.

Keywords: Igf2as ; RNA-FISH; C2C12 cells; Genomic imprinting; Polysome analysis

Prevalence and Molecular Identification of the Mediterranean Variant Among G6PD-Deficient Sistani and Balouch Males in Southeastern Iran by Ebrahim Miri-Moghaddam; Yousef Mortazavi; Alireza Nakhaee; Abdurrashid Khazaei Feizabad (pp. 131-138).

To determine the prevalence of G6PD deficiency and a Mediterranean mutation among males in southeastern Iran, we studied 1,097 Sistani and Balouch schoolboys. A questionnaire was used to collect demographic data and a history of malaria infection; blood samples were evaluated for G6PD deficiency and the G6PD Mediterranean mutation. Of the 1,097 boys screened, 175 were G6PD deficient (5.8 % of the Sistani boys and 19.3 % of the Balouch boys). The malaria survey indicated that among Balouch subjects, malaria infection was about 14 times that of Sistani subjects. Molecular characterization of G6PD-deficient samples revealed a general frequency of 85.1 % for the Mediterranean variant among all subjects (75 % among Sistani and 86.2 % among Balouch cases). The high prevalence of G6PD deficiency among Balouch populations confirms the hypothesis that the distribution of G6PD deficiency is concordant with the geographic distribution of malaria.

Keywords: G6PD deficiency; Mediterranean mutation; Prevalence; Malaria

Molecular Cloning and Polymorphism of the Major Histocompatibility Complex (MHC) Class IIB Gene of Grass Carp (Ctenopharyngodon idella) by Zhong-Dian Dong; Yan Zhao; Qi Fan Zeng; Yong Fu; Fen Na Zhou; Xiang Shan Ji; Hui Wang (pp. 139-146).

Plasma and Urinary Sulfate Determination in a Cohort with Autism by Francis G. Bowling; Helen S. Heussler; Avis McWhinney; Paul A. Dawson (pp. 147-153).

Sulfate is important for mammalian development but is not routinely measured in clinical settings. The renal NaS1 sulfate transporter maintains circulating sulfate levels and is linked to renal sulfate wasting in mice. Some autistic individuals exhibit renal sulfate wasting, but the etiology is yet unknown. We measured plasma and urinary sulfate levels, calculated the fractional excretion index (FEI) of sulfate, and screened for two loss-of-function NaS1 sequence variants (R12X and N174S) in 23 autistic individuals. The FEI sulfate values ranged from 0.13 to 0.50. NaS1 variants were detected in 18 of the 23 individuals (11 heterozygous N174S, four homozygous N174S, two heterozygous R12X, and one individual carried both R12X and N174S). Those individuals with neither sequence variant had FEI sulfate ≤ 0.34, whereas FEI sulfate ≥ 0.35 was found in about 60 % (11 of 18) of individuals that had R12X and/or N174S. This study links renal sulfate wasting with loss-of-function NaS1 sequence variants in humans.

Keywords: Sulfate; Renal sulfate wasting; Sulfate transporter

Phylogenetic Comparison of Opine Dehydrogenase Sequences from Marine Invertebrates by Sandra Vázquez-Dorado; Alejandro de Carlos; Ángel S. Comesaña; Andrés Sanjuán (pp. 154-165).

Three cDNA sequences encoding putative opine dehydrogenase (OpDH) enzymes from the mussel Mytilus galloprovincialis were obtained. The deduced amino acid sequences were clearly distinguishable from each other, showing that several OpDH transcripts could occur in the mussel tissues (p distance 0.46–0.55). When these sequences were aligned and compared with published databank proteins, the range of identity among the M. galloprovincialis OpDH and the strombine dehydrogenase from Ostrea edulis was 51–59 %, the best hit in the three comparisons, followed by OpDH enzymes from other marine invertebrates. Sequence alignment revealed structural motifs possibly related to the binding sites of the substrates. A phylogenetic analysis compared M. galloprovincialis OpDH and annotated sequences belonging to five phyla and seven taxonomic classes, including 19 species, representing the five OpDH protein family members. The phylogenetic tree clustered the OpDH enzymes according to the evolutionary relationships of the species and not to the biochemical reaction catalyzed.

Keywords: RT-PCR; cDNA cloning; Amino acid sequences; Bivalvia; Mollusca; Molecular evolution

Influence of Adiponectin and Resistin Gene Polymorphisms on Quantitative Traits Related to Metabolic Syndrome Among Malay, Chinese, and Indian Men in Malaysia by Cia-Hin Lau; Sekaran Muniandy (pp. 166-174).

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Biochemical Genetics (v.51, #1-2)