Check out our New Publishers' Select for Free Articles

Biochemical Genetics (v.50, #1-2)

Cloning and Identification of MicroRNAs in Earthworm (Eisenia fetida) by Xue-Mei Huang; Qing-Nan Tian; Zhen-Xia Bao; Yun-Fei Qin; San-Jun Chen; Ping Lu; Xiao-Ling Zhang; Yi-Zhe Zhang; Shou-Tao Zhang (pp. 1-11).

MicroRNAs (miRNAs) (noncoding RNAs of 20–25 nucleotides) play important roles in the post-transcriptional regulation of gene expression in various eukaryotes and prokaryotes. Piwi-interacting RNAs function by combining with PIWI proteins to regulate protein synthesis and to stabilize mRNA, the chromatin framework, and genome structure. This study investigates the role of miRNAs in regeneration. A scrDNA library was constructed, and 17 noncoding RNAs from Eisenia fetida (an optimal model for the study of earthworm regeneration) were cloned and characterized. In addition, reverse transcription polymerase chain reaction was performed to analyze the expression of four small RNAs during different developmental stages. The expression levels of these RNAs in regenerating tissue were higher than in normal tissue, and the expression patterns of these small RNAs were unique during development.

Keywords: miRNA; piRNA; Eisenia fetida ; Regeneration

Nucleotide Polymorphisms in the Canine Noggin Gene and Their Distribution Among Dog (Canis lupus familiaris) Breeds by Yuji Ishii; Tatsuya Takizawa; Hiroshi Iwasaki; Yukihiro Fujita; Masaru Murakami; Jay C. Groppe; Kazuaki Tanaka (pp. 12-18).

Noggin (NOG) is an important regulator for the signaling of bone morphogenetic proteins. In this study, we sequenced the complete coding sequence of the canine NOG gene and characterized the nucleotide polymorphisms. The sequence length varied from 717 to 729 bp, depending on the number of a 6-bp tandem repeat unit (GGCGCG), an insertion that has not been observed in other mammalian NOG genes investigated to date. It results in extensions of (Gly–Ala)_3–5 in the putative NOG protein. To survey the distribution of these tandem repeat polymorphisms, we analyzed 126 individuals in seven dog breeds. We identified only three alleles: (GGCGCG)₃, (GGCGCG)₄, and (GGCGCG)₅. Although the allele frequencies were remarkably different among the breeds, the three alleles were present in all seven of the breeds and did not show any deviation from Hardy–Weinberg equilibrium.

Keywords: Noggin; Dog; Canis lupus familiaris ; Polymorphisms; VNTR

Association of B3GNT5 Polymorphisms with Susceptibility to ETEC F4ab/ac in the White Duroc × Erhualian Intercross and 15 Outbred Pig Breeds by Jing Ouyang; Weihong Zeng; Jun Ren; Xueming Yan; Zhiyan Zhang; Ming Yang; Pengfei Han; Xiang Huang; Huashui Ai; Lusheng Huang (pp. 19-33).

The B3GNT5 gene is a candidate for the F4ab/ac receptor conferring susceptibility to enterotoxigenic Escherichia coli (ETEC) F4ab/ac in pigs. In this study, we screened mutations in the complete coding region of the porcine B3GNT5 gene and identified four SNPs in the 3′ untranslated regions. We genotyped the four SNPs across a large-scale White Duroc × Chinese Erhualian F ₂ resource population (total F ₂ = 755) and 292 purebred piglets representing 15 Chinese and Western breeds. We found that the g.1476G→A locus and haplotypes [A;T;G;T] and [A;G;G;T] had significant association with susceptibility to ETEC F4ac in the resource population. None of the B3GNT5 polymorphisms and haplotypes was associated with susceptibility to ETEC F4ab/ac in outbred piglets. This result, together with other reports, supports the conclusion that B3GNT5 is not the responsible gene encoding the ETEC F4ab/ac receptors.

Keywords: Association; B3GNT5 ; ETEC F4ab/ac; Pig; Susceptibility

G6PD Genotype and Its Associated Enzymatic Activity in a Chinese Population by Wei Ying Jiang; Bing Yi Zhou; Guo Long Yu; Han Liu; Jing Bo Zeng; Qun Di Lin; Hong Li Xi; Hua Liang (pp. 34-44).

Knowledge of the G6PD genotype and its associated enzyme activity is significant for population genetics, diagnosis of disease, and management of patients. We tested 2,872 unrelated subjects from a Hakka population in China for G6PD activity by the WHO standard method and for genotype by DHPLC and DNA sequencing. Among female heterozygotes, 78.5% had relatively normal enzyme activity. The phenotype frequency of G6PD deficiency is 0.028, and the causal allele frequency is 0.060 in females. The accuracy, sensitivity, and specificity of DHPLC are more than 98% for detecting G6PD-deficient hemizygotes, heterozygotes, and homozygotes. Measuring enzyme activity alone is not sufficient for the diagnosis of heterozygotes. A combination of enzyme activity and DNA analysis should be used.

Keywords: Denaturing high performance liquid chromatography; Enzymatic activity; Genotype; G6PD deficiency; Hakka

Very Low Mitochondrial Diversity and Genetic Homogeneity in the Starfish Echinaster sepositus Along the Tunisian Coast by Noureddine Chatti; Rym Zitari-Chatti; Mohamed Habib Attia; Yosra Ben Khadra; Khaled Said (pp. 45-51).

The 27-bp VNTR Polymorphism in Intron 4 of the Human eNOS Gene in Healthy Singaporean Chinese, Indians, and Malays by Yik Yuen Gan; Chuan Fei Chen (pp. 52-62).

Human endothelial nitric oxide synthase (eNOS) is one isoform of the nitric oxide synthases that are responsible for nitric oxide synthesis from l-arginine. The gene encoding eNOS contains a 27-bp VNTR polymorphism in intron 4. We report here for the first time the presence of a novel allele 3, which was absent in all other populations studied to date, in 1.7% each of Singaporean Indians and Malays. We also detected the presence of a novel genotype 3/5 in 3.4% each of Singaporean Indians and Malays. Allele 6, which was absent in Han Chinese from northern China and Taiwan and was also absent in Indians from the Indian subcontinent, was found in 2.1% of Singaporean Chinese and in 0.3% of Singaporean Indians.

Keywords: Endothelial nitric oxide synthase (eNOS); Variable number of tandem repeats (VNTR); Chinese; Indians; Malays

Hardy–Weinberg Disequilibrium of the IL-18 C−607A SNP Suggesting Selective Advantage of Heterozygotes by Chuan Fei Chen; Yik Yuen Gan (pp. 63-72).

Interleukin-18 (IL-18) plays a key role in autoimmune, inflammatory, and infectious diseases. The IL-18 gene contains a C to A single nucleotide polymorphism (SNP) at position −607 (C−607A) within the promoter region, which was found to affect the promoter activity and subsequently the protein level of IL-18. We investigated this SNP in a group of healthy Singaporeans and found that CA was the most common genotype and the C allele was more prevalent than the A allele, which was not always the case in other ethnic groups. In addition, Singaporean Chinese were significantly different from Singaporean Indians in both allelic and genotypic distributions. Furthermore, significant deviations from Hardy–Weinberg equilibrium of this SNP were found in all three ethnic groups studied (Chinese, Indians, and Malays) and also in other published literature, suggesting that heterozygotes of this IL-18 C−607A SNP may have certain selective advantages.

Keywords: Interleukin 18 (IL-18); Single nucleotide polymorphism (SNP); Hardy–Weinberg disequilibrium; Selective advantage of heterozygotes; Singaporeans

Identification of Single Nucleotide Polymorphisms in the Nicastrese Goat and Sardinia Sheep Mannose-Binding Lectin by Gianfranco Cosenza; Alfredo Pauciullo; Andrea Mancusi; Annalisa D’Avino; Letizia Colimoro; Dino Di Berardino; Luigi Ramunno (pp. 73-83).

This study was undertaken to detect polymorphisms in the goat and sheep mannose-binding lectin encoding gene (MBL2) and to explore allelic variability of this gene in these two species. The analysis and comparison of the sequences obtained from sheep showed 13 polymorphic sites, six in the promoter and seven in exon 1, four of which were of the missense type. In the goats, 12 polymorphic sites were detected, five intronic, five in the promoter, and one exonic. The exon site was responsible for an amino acid change. Mutations detected at the MBL2 locus in the sheep are of particular interest, being potentially responsible for the alterations of gene expression. A population survey involved 102 ewes of the Sardinian breed and 218 goats of the Nicastrese breed, all reared in southern Italy.

Keywords: MBL2; Goat; Sheep; Polymorphism; DNA

Influence of Eight Unclassified Missense Variants of the MLH1 Gene on Lynch Syndrome Susceptibility by Yimei Fan; Jinyun Chen; Wei Wang; Puyuan Wu; Wenxian Zhi; Binshuang Xue; Wanfen Zhang; Yaping Wang (pp. 84-93).

Missense mutations in MLH1 have frequently been detected in patients with Lynch syndrome, but their genetic significance has not been extensively assessed. In this study, we attempt to evaluate the etiological role of eight MLH1 missense variants. The variants were analyzed for their ability to affect MLH1 protein interaction with its partner PMS2 in vivo employing a yeast two-hybrid system. In addition, a SIFT (sorting intolerant from tolerant) algorithm was adopted to predict the effects of amino acid substitutions. Finally, scanning of mutations in a normal Chinese population and assay of the clinical characteristics have all been taken into account. Our results demonstrated that the MLH1 variants D485E and L653R cause functional alterations of the human MutLα complex significantly. The R265C, D304V, A586P, and R755S variants affect partial interaction. The remaining two variants, N38D and L559R, could be nonfunctional polymorphisms or might affect the mismatch repair system through other mechanisms.

Keywords: Lynch syndrome; MLH1 ; Missense mutations; Yeast two-hybrid analysis; SIFT

Identification of a Novel Mutation Within the Goat Adiponectin Gene and Its Effect on Body Weight in Chinese Indigenous Breeds by X. Y. Lan; J. B. Liu; J. L. Zhu; T. G. Liu; L. Z. Zhang; Y. Zhang; C. Z. Lei; H. Chen (pp. 94-102).

Polymorphism of the CD36 Gene and Cardiovascular Risk Factors in Patients with Coronary Artery Disease Manifested at a Young Age by Monika Ewa Rać; Janina Suchy; Grzegorz Kurzawski; Agnieszka Kurlapska; Krzysztof Safranow; Michał Rać; Dagmara Sagasz-Tysiewicz; Andrzej Krzystolik; Wojciech Poncyljusz; Katarzyna Jakubowska; Maria Olszewska; Beata Krupa; Dariusz Chlubek (pp. 103-111).

This study investigates potential associations between CD36 gene variants and the presence of risk factors in Caucasians with coronary artery disease (CAD) manifested at a young age. The study group consisted of 90 patients; the men were ≤ 50 years old and the women were ≤ 55 years old. Amplicons of exons 4 and 5 including fragments of introns were analyzed by DHPLC. Two polymorphisms were found: IVS3-6 T/C (rs3173798) and IVS4-10 G/A (rs3211892). The C allele of the IVS3-6 T/C polymorphism was associated with higher prevalence of obesity and diabetes, higher hsCRP, lower Lp(a) serum concentrations, and younger age at myocardial infarction. The A allele of the IVS4-10 G/A polymorphism was associated with older age of myocardial infarction and higher white blood cell count. The functional role of CD36 polymorphisms in CAD development needs further research.

Keywords: CD36 gene; Coronary artery disease; Genetic risk factors; Obesity; Myocardial infarction

Gene Silencing Efficiency and INF-β Induction Effects of Splicing miRNA 155-Based Artificial miRNA with Pre-miRNA Stem-Loop Structures by Onsam Sin; Prudence Mabiala; Ye Liu; Ying Sun; Tao Hu; Qingzhen Liu; Deyin Guo (pp. 112-121).

Artificial microRNA (miRNA) expression vectors have been developed and used for RNA interference. The secondary structure of artificial miRNA is important for RNA interference efficacy. We designed two groups of six artificial splicing miRNA 155-based miRNAs (SM155-based miRNAs) with the same target in the coding region or 3′ UTR of a target gene and studied their RNA silencing efficiency and interferon β (IFN-β) induction effects. SM155-based miRNA with a mismatch at the +1 position and a bulge at the +11, +12 positions in a miRNA precursor stem-loop structure showed the highest gene silencing efficiency and lowest IFN-β induction effect (increased IFN-β mRNA level by 10% in both target cases), regardless of the specificity of the target sequence, suggesting that pSM155-based miRNA with this design could be a valuable miRNA expression vector.

Keywords: Interferon β induction effect; Precursor miRNA stem-loop structure; Silencing effect; Splicing microRNA 155-based miRNA expression vector

Effect of CpG Island Methylation on MicroRNA Expression in the k-562 Cell Line by Yang Yang; Li-Li Wang; Yong-Hui Li; Xiao-Ning Gao; Yang Liu; Li Yu (pp. 122-134).

To test the hypothesis that methylation of a CpG island is associated with regulation of microRNA expression, we investigated CpG islands in the upstream sequences of microRNA precursors (pre-miRNAs) through bioinformatic analysis and determined whether the CpG islands were methylated by methylation-specific PCR in the k-562 cell line. We used 5-azacytidine for DNA demethylation, and changes in microRNA expression were detected by microarray assay, RT-PCR, and real-time PCR after 5-azacytidine induction. We showed that the CpG islands in the upstream regions of 18 pre-miRNAs were methylated, including miR-663, miR-369, miR-615, and miR-410, and promoter activity was detected in the upstream region of pre-miR-663. We found that a decrease in methylation of a CpG island could up-regulate the expression of miR-663, suggesting that miR-663 could be regulated by DNA methylation. Expression levels of miR-369, miR-615, and miR-410 were not regulated by DNA methylation in this cell line.

Keywords: MicroRNA; CpG island; Regulation; Expression

Genome Characterization of a Breeding Line Derived from a Cross Between Oryza sativa and Oryza rufipogon by B. P. Keong; J. A. Harikrishna (pp. 135-145).

A preliminary screening was conducted on BC₃F₁ and BC₄F₁ backcross families developed from crossing Oryza sativa (MR219) and O. rufipogon (IRGC105491). Despite earlier results showing that O. rufipogon alleles (wild introgression) contributed to both number of panicles (qPPL-2) and tillers (qTPL-2) at loci RM250, RM208, and RM48 in line A20 of the BC₂F₂ population, we observed that wild introgression was lost at loci RM250 and RM208 but retained at locus RM48 in BC₃F₁ and BC₄F₁. Progeny tests conducted utilizing genotype and phenotype data on both BC₄F₁ and a reference population, BC₂F₇ (A20 line), did not show significant differences between groups having the MR219 allele and wild introgression at locus RM48. This suggests that there is no additive and transgressive effect of wild introgression in the BC₃F₁ and BC₄F₁ generated. The presence of wild introgression was largely due to gene contamination by cross-pollination during field breeding practices.

Keywords: Oryza sativa ; Oryza rufipogon ; Advanced backcross; Microsatellite; Genetic contamination

Genetic Structure Within and Among Populations of Saruma henryi, an Endangered Plant Endemic to China by Tian-Hua Zhou; Shan-Shan Dong; Shan Li; Gui-Fang Zhao (pp. 146-158).

The endangered perennial plant Saruma henryi Oliv. is endemic to China and has phylogenetic, ecological, and medicinal value. We used 10 microsatellite (SSR) loci to investigate genetic diversity and differentiation in 16 natural populations. Genetic diversity was high at the species level (H _E = 0.9427, h = 0.9410, I = 3.0213) and low at the population level (H _E = 0.4441, h = 0.4307, I = 0.6822). Pronounced genetic differentiation was detected among populations (G _ST = 0.5428, F _ST = 0.5524), in line with the limited among-population gene flow (N _m = 0.21). The significant isolation-by-distance pattern revealed by a Mantel test (r = 0.311, P = 0.001) suggested a clear geographic tendency in the distribution of genetic variability. Bayesian assignment and principal coordinates analyses supported the clustering of 16 populations into three groups. The present SSR results were also compared with previously published ISSR results. These results have significant implications for conservation of the species.

Keywords: Saruma henryi Oliv.; Simple sequence repeats (SSRs); Endemic species; Genetic diversity; Genetic differentiation

Sections

Personal tools

Biochemical Genetics (v.50, #1-2)

Sections

Personal tools

Local resources

Biochemical Genetics (v.50, #1-2)