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Biochemical Genetics (v.47, #5-6)

Identification and Characteristics of Cattle MicroRNAs by Homology Searching and Small RNA Cloning by Jian-Er Long; Hai-Xuan Chen (pp. 329-343).

MicroRNAs (miRNA) are a class of noncoding RNA molecules that regulate gene expression by an RNA-interfering pathway through cleavage or inhibition of the translation of target mRNA. The 254 cattle miRNA candidates found by homology searching frequently clustered at certain chromosomes, and some are possibly expressed from more than one genomic locus. They were partially verified by cloning from a small cattle RNA library, where 31 distinct miRNAs were identified: 18 previously registered in the database of miRBase, 11 novel and homologous to known mammalian miRNAs, and 2 potentially novel without homology to any known miRNAs. Partial miRNA expression was detected by RT-PCR in cattle tissues, such as brain, liver, lung, and heart; some were expressed in all tissues and others in a specific tissue. Sequence alignments revealed that many had end variants, most of which differed in the 3′ end; a small number differed in the 5′ end. This indicates that the same miRNA gene can be individually modified in the process of miRNA biogenesis and could have a different role in regulating target gene expression.

Keywords: MicroRNA; Cattle; Homology searching; Small RNA cloning

Angiotensinogen T174M and M235T Variants and Hypertension in the Hani and Yi Minority Groups of China by Jiali Yuan; Wenru Tang; Yinan Chun; Hua Ying; Yang Yang; Chunjie Xiao (pp. 344-350).

A case–control study of 538 individuals investigated whether the angiotensinogen gene (AGT) might be implicated in the pathogenesis of essential hypertension in the Hani and Yi populations of China. Genotypes for two diallelic DNA polymorphisms observed at amino acid residues 174 (T174M) and 235 (M235T) within the coding sequence were determined. M235T and T174M genotyping with PCR-RFLP was performed in 267 normotensive subjects and 271 hypertensive subjects. No significant difference was found between normotensives and hypertensives in genotype distribution and allele frequency for either M235T or T174M in the Hani or the Yi populations (P > 0.05). Relative to carriers of the 235T/235T and 174T/174T combination, the others had a significantly elevated risk of hypertension (OR = 1.62, 95% CI 1.02–2.59; P = 0.043) in the Hani population. The AGT M235T and T174M variants in combination may play a role in the genetic predisposition to develop essential hypertension in the Hani minority of China.

Keywords: Angiotensinogen; Hypertension; Hani population; Yi population

Evolution of the Chloroplast trnL-trnF Region in the Gymnosperm Lineages Taxaceae and Cephalotaxaceae by Da Cheng Hao; Bei Li Huang; Shi Lin Chen; Jun Mu (pp. 351-369).

The trnL-trnF region is located in the large single-copy region of the chloroplast genome. It consists of the trnL gene, a group I intron, and the trnL-F intergenic spacer. We analyzed the evolution of the region in three gymnosperm families, Taxaceae, Cephalotaxaceae, and Podocarpaceae, with especially dense sampling in Taxaceae and Cephalotaxaceae, for which we sequenced 43 accessions, representing all species. The trnL intron has a conserved secondary structure and contains elements that are homologous across land plants, and the spacer is highly variable in length and composition. The spatial distribution of nucleotide diversity along the trnL-F region suggests that different portions of this region have different evolutionary patterns. Tandem repeats that form stem–loop structures were detected in both the trnL intron and the trnL-F spacer, and the spacer sequences contain promoter elements for the trnF gene. The presence of promoters and stem–loop structures in the trnL-F spacer and high sequence variation in this region suggest that trnL and trnF are independently transcribed. Stem–loop regions P6, P8, and P9 of the trnL intron and the trnL-F spacer (except the promoter elements) might undergo neutral evolution with respect to their escape from functional constraints.

Keywords: Taxaceae; Cephalotaxaceae; trnL Intron; Tandem repeat; trnL-F Intergenic spacer; Molecular evolution

Polymorphism at the Apical Membrane Antigen 1 Gene (AMA1) of the Malaria Parasite Plasmodium falciparum in a Vietnamese Population by Nguyen Duc Quang; Phan Thi Phuong Hoa; Mai Sy Tuan; Nguyen Xuan Viet; Amadu Jalloh; Hiroyuki Matsuoka (pp. 370-383).

The patterns of molecular evolution of the most diverse region of the apical membrane antigen 1 (AMA1) gene in Plasmodium falciparum from a Vietnamese subpopulation (Bao Loc) were investigated. Within the Bao Loc population, the sequenced gene region showed relatively high allelic and nucleotide diversity (0.985 and 0.02694, respectively). Further, the level of population recombination was substantial, resulting in a significant decay of linkage disequilibrium along the gene region. The results suggest that AMA1 is a useful genetic marker for studying the relationships between adaptation of parasite populations (to the human host immune system) and malaria epidemiology.

Keywords: Malaria; AMA1 ; Evolution; Vietnam

Molecular Characterization of the pina Gene in Einkorn Wheat by Qing Chen; Peng-Fei Qi; Yu-Ming Wei; Ji-Rui Wang; You-Liang Zheng (pp. 384-396).

Fifty-six sequences encoding the pina protein were characterized from three species or subspecies of einkorn wheat. These sequences contained 1,595 nucleotides, including 1,270 conserved sites, 21 single nucleotide polymorphisms (SNPs), and 16 indels. The average frequency of SNPs and indels was one out of 76.1 and 99.9 bases, respectively. Five SNPs and no indels were found in the translated sequences. Fourteen haplotypes were defined, and the accessions in each haplotype ranged from 1 to 18. There were nine haplotypes in Triticum monococcum ssp. aegilopoides, eight in T. monococcum ssp. monococcum, and two in T. urartu. Phylogenetic analysis showed that pina genes from different species or subspecies could be clearly differentiated based on the open reading frame. Genes from T. urartu grouped together, whereas genes from T. monococcum ssp. aegilopoides and T. monococcum ssp. monococcum were shared by three and two clusters, respectively. Both the haplotype and phylogenetic analyses indicated that T. monococcum ssp. aegilopoides was more diverse. These results would contribute to the understanding of functional aspects and efficient utilization of pina genes.

Keywords: Einkorn wheat; Pina ; SNP; Indel; Haplotype

Novel Mutations of the FASN Gene and Their Effect on Fatty Acid Composition in Japanese Black Beef by Tsuyoshi Abe; Junich Saburi; Hiroyuki Hasebe; Tetsuo Nakagawa; Satsuki Misumi; Toshihiro Nade; Hiroaki Nakajima; Noriaki Shoji; Masato Kobayashi; Eiji Kobayashi (pp. 397-411).

Eight novel and four known mutations were detected in the coding sequence of the bovine fatty acid synthase (FASN) gene of an F2 population from Japanese Black and Limousin cattle. Two mutations, g.16024A>G and g.16039T>C, detected in exon 34, which determine amino acid substitutions of threonine (T) to alanine (A) and tryptophan (W) to arginine (R), were clearly separated in the parental breeds. The haplotypes (TW and AR) segregated in F2 individuals and had a significant effect on the fatty acid composition of backfat, intermuscular fat, and intramuscular fat. The TW haplotype was associated with increasing C18:0 and C18:1 content and the ratio of monounsaturated to saturated fatty acids, and decreasing C14:0, C14:1, C16:0, and C16:1 content. The two mutations were screened in two commercial Japanese Black half-sibling populations and similarly determined the contribution to the fatty acid composition of intramuscular fat. The frequency of the TW haplotype was markedly higher in Japanese Black (0.67) than in Holstein (0.17), Angus (0.02), and Hereford (0.07). We conclude that these mutations may contribute to the characteristic fatty acid composition of Japanese Black beef.

Keywords: Bovine; Fatty acid composition; Fatty acid synthase; Japanese Black beef

Prevalence of the Angiotensin I Converting Enzyme Gene Insertion/Deletion Polymorphism in a Healthy Turkish Population by Afig Berdeli; F. Sirri Cam (pp. 412-420).

Angiotensin converting enzyme (ACE) plays an essential role in the renin–angiotensin system. It converts angiotensin I to angiotensin II and inactivates bradykinin and tachykinins. Numerous studies have been published investigating associations of the ACE gene I/D polymorphism with various pathophysiological conditions. We examined the prevalence of the ACE I/D polymorphism in a sample of healthy volunteers from western Turkey, including 1063 healthy Turkish controls. Analysis of the ACE I/D gene polymorphisms by polymerase chain reaction found frequencies of 16.1% for the II genotype, 47.7% for the ID genotype, and 36.2% for the DD genotype. The allele frequency was 39.9% for the I alleles and 60.1% for the D allele. This study demonstrates that the allele and genotype frequency values for the Turkish population are similar to previously published frequencies for Caucasian populations.

Keywords: ACE I/D; Allele; Frequency; Healthy volunteers; Turkish

Genetic Diversity in Metapenaeus dobsoni using RAPD Analysis by Prem Sagar Mishra; Aparna Chaudhari; Gopal Krishna; Dilip Kumar; W. S. Lakra (pp. 421-426).

Cloning and Characterization of the Promoter of the Human AHI1 Gene by Xian-Fang Meng; Yi Luo; Wei Xiao; Man Li; Jing Shi (pp. 427-438).

The AHI1 gene is involved in axons crossing the midline during development, and its mutation can cause Joubert syndrome and other related neurological system diseases. Its transcriptional regulation mechanism is still unknown. Here we cloned and characterized the upstream 5′ region of the gene. It was shown that 1.3 kb upstream of ATG had the transcription activity. Progressive deletion analysis was done, and all the constructs were transfected into COS7 cells. The promoter activity was determined by fluorescence microscopy, flow cytometry, and reverse transcription polymerase chain reaction. Our results showed that all the constructs had transcription activity. The highest promoter activity was 30 bp upstream of ATG, which included a transcription factor-binding site for Oct-1. Our research provides an important basis for further investigations on the transcriptional regulation of the human AHI1 gene.

Keywords: Promoter; Human AHI1 gene; Joubert syndrome

A Novel Ankyrin Repeat-rich Gene in Potato, Star, Involved in Response to Late Blight by Tian Wu; Zhendong Tian; Jun Liu; Chunguang Yao; Conghua Xie (pp. 439-450).

The Solanum tuberosum ankyrin repeat gene (Star) is a novel gene from potato leaves challenged by Phytophthora infestans, a pathogen causing late blight disease. The gene was isolated, based on the reported expressed sequence tag, by the rapid amplification of cDNA ends. Star contains a maximum open reading frame of 1542 bp encoding a peptide with 514 amino acids, and it encodes a RING finger ankyrin repeat protein, a putative E3 ubiquitin ligase. To the authors’ knowledge, it is the first RING finger ankyrin repeat gene isolated from the potato. The gene is highly expressed in roots, stems, and flowers at the transcript level. Star mRNA was strongly expressed from 24 to 72 h in potato leaves inoculated with P. infestans. The results suggested that Star may be involved in the development of organs and may play a role in late blight resistance.

Keywords: Star ; Ankyrin repeat; RING finger; Solanum tuberosum L.; Late blight resistance

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Biochemical Genetics (v.47, #5-6)

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Biochemical Genetics (v.47, #5-6)