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New Window Opens on the Secret Life of Microbes: Scientists Develop First Microbial Profiles of Ecosystems
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Biochemical Genetics (v.45, #1-2)
The Relationship between Gene Polymorphism and CRP Level in a Chinese Han Population by Ming Yan; Lei Zhao; Fang Zheng; Xiaobo Sun; Ying Zhang; Chunhong Wang (pp. 1-9).
We investigated the relationships among the +1444C/T polymorphism in the C-reactive protein (CRP) gene and the concentration of CRP and the risk of coronary heart disease. Using polymerase chain reaction-restriction fragment length polymorphism, we analyzed the frequency distribution of genotypes and alleles of the +1444C/T polymorphism in samples from 128 patients with coronary heart disease (coronary stenosis more than 50%) and 119 unrelated normal individuals. The plasma levels of CRP and lipids in the subjects were also measured. The frequencies of the genotypes were CC 89.1%, CT 10.9%, and TT 0% in patients and CC 89.9%, CT 10.1%, and TT 0% in controls. The frequency of allele C was 94.5% in patients and 95.0% in controls, and allele T was 5.5% in patients and 5.1% in controls. The distribution of genotypes and alleles in the Chinese Han population was significantly different from that of the Caucasian population. There were no significant differences between frequencies of genotype and allele of controls and those of patients (P>0.05), but in controls the concentrations of CRP in the CC genotype subgroup were significantly higher than those in the CT genotype subgroup (P<0.05). This suggests that the +1444C/T variant in the CRP gene influences the basal CRP level in normal people. These findings imply that there may eventually be a need to establish genotype-specific risk thresholds of the CRP level.
Keywords: C-reactive protein; coronary heart disease; gene polymorphism; atherosclerosis
A Naturally Occurring Variant of Porcine Mx1 Associated with Increased Susceptibility to Influenza Virus In Vitro by Emiko Nakajima; Takeya Morozumi; Kenji Tsukamoto; Tomomasa Watanabe; Graham Plastow; Tadayoshi Mitsuhashi (pp. 11-24).
Mx1 has been implicated in resistance to the influenza virus. We have now identified four alleles of the Mxl gene in domesticated breeds of pigs. Two of the alleles encode deletion variants (a 3-bp deletion in exon 13 and an 11-bp deletion in exon 14), which might be expected to interfere with Mx activity. The porcine Mxl genes corresponding to wild type, the 3-bp deletion mutant, and the 11-bp deletion mutant were cloned and expressed in NIH3T3 cells, and the antiviral activity for influenza virus was assayed. Virus yield was observed to be 10–100-fold greater with the 11-bp deletion allele than that for wild type and the 3-bp deletion alleles. The results suggest that the 11-bp deletion type is lacking antiviral activity able to contribute to the interference of influenza virus replication.
Keywords: porcine Mx1 ; influenza virus; deletion allele
Evolution of the Spiroplasma P58 Multigene Family
by Jana Comer; Jacqueline Fletcher; Robert E. Davis; Ulrich Melcher (pp. 25-32).
Patterns of Genetic Variation in Swertia przewalskii, an Endangered Endemic Species of the Qinghai-Tibet Plateau by Defang Zhang; Shilong Chen; Shengyun Chen; Dejun Zhang; Qingbo Gao (pp. 33-50).
Swertia przewalskii Pissjauk. (Gentianaceae) is a critically endangered and endemic plant of the Qinghai-Tibet Plateau in China. RAPD and ISSR analyses were carried out on a total of 63 individuals to assess the extent of genetic variation in the remaining three populations. Percentage of polymorphic bands was 94% (156 bands) for RAPD and 96% (222 bands) for ISSR. A pairwise distance measure calculated from the RAPD and ISSR data was used as input for analysis of molecular variance (AMOVA). AMOVA indicated that a high proportion of the total genetic variation (52% for RAPD and 56% for ISSR) was found among populations; pairwise Φ ST comparisons showed that the three populations examined were significantly different (p < 0.001). Significant genetic differentiation was found based on different measures (AMOVA and Hickory θB) in S. przewalskii (0.52 on RAPD and 0.56 on ISSR; 0.46 on RAPD and 0.45 on ISSR). The differentiation of the populations corresponded to low average gene flow (0.28 based on RAPD and 0.31 based on ISSR), whereas genetic distance-based clustering and coalescent-based assignment analyses revealed significant genetic isolation among populations. Our results indicate that genetic diversity is independent of population size. We conclude that although sexual reproduction and gene flow between populations of S. przewalskii are very limited, they have preserved high levels of genetic diversity. The main factors responsible for the high level of difference among populations are the isolation and recent fragmentation under human disturbance.
Keywords: Swertia przewalskii ; genetic variation; RAPD; ISSR; endemic plant; Qinghai-Tibet Plateau
Molecular Cloning, Mapping, and Expression Analysis of the EIF4A2 Gene in Pig by Heng Wang; Huanling Wang; Zhengmao Zhu; Shulin Yang; Kui Li (pp. 51-62).
A full-length cDNA clone encoding the eukaryotic translation initiation factor 4A, isoform 2 (EIF4A2), was cloned from the fetal skeletal cDNA library from the pig (Sus scrofa). EIF4A2 is a highly conserved gene for one of the protein-synthesis initiation factors involved in the binding of mRNA to the ribosome. Based on this cDNA sequence, the deduced protein of 407 amino acids contains the characteristic motifs shared by the DEAD-box supergene family. The genomic nucleotide sequence of this gene was determined and a single nucleotide polymorphism located in the 5′ untranslated region was genotyped. The porcine EIF4A2 was expressed in all tissues examined but in variable amounts. The EIF4A2 expression level in muscle was upregulated through embryonic and neonatal development until adult, suggesting that porcine EIF4A2 was possibly involved in translation regulation of other muscle-related genes in muscle formation and development. In addition, we mapped porcine EIF4A2 to q4.1 of SSC13, in agreement with comparative mapping data.
Keywords: chromosome location; EIF4A2; expression pattern; polymorphism; porcine
Genetic Diversity in Five Iranian Native Chicken Populations Estimated by Microsatellite Markers by Saleh Shahbazi; Seyed Z. Mirhosseini; Michael N. Romanov (pp. 63-75).
Iranian chicken genetic resources are characterized by a long history and a vast diversity. This study represents the first results from the selection and evaluation of five polymorphic microsatellite markers for the genetic assessment of five native chicken populations located in the northwestern (West Azerbaijan), northern (Mazandaran), central (Isfahan, Yazd), and southern (Fars) provinces of Iran. The number of alleles ranged from three to six per microsatellite locus. All populations were characterized by a high degree of genetic diversity, with the lowest heterozygosity found in the Isfahan population (62%) and the greatest in the populations from West Azerbaijan and Mazandaran (79%). The largest Nei’s unbiased genetic distance was found between the Isfahan and Fars populations (0.696) and the smallest between the Mazandaran and Yazd populations (0.097). The Isfahan population was found to be the most genetically distant among all populations studied. These results serve as an initial step in the plan for genetic characterization and conservation of Iranian native chickens.
Keywords: Iranian native chickens; genetic diversity; microsatellites
DNA Fingerprinting and Phylogenetic Analysis of WNIN Rat Strain and Its Obese Mutants Using Microsatellite Markers by Kumar B. Kiran; Bhanu N. Vijaya; Rao M. Vishnuvardhan; Nappanveettil Giridharan (pp. 77-91).
Wistar is the oldest rat strain to be introduced in biomedical research, and various stocks of this strain are maintained in laboratories across the globe. The Wistar strain maintained in our facilities is 85 years old and is not typed genetically so far. Recently, two obese mutant rat strains evolved from this stock, one with euglycemia and the other with impaired glucose tolerance. These mutant rat strains, along with the parental Wistar stock and two other rat strains maintained in our facilities (WKY and F-344), were subjected to PCR-based DNA fingerprinting using microsatellite markers to evolve molecular signatures unique to them. Of the 96 markers screened, we identified a marker, leukosianin, that shows polymorphism between the strains tested and thus appears to be quite useful for rat strain identification. Also, the microsatellite data generated were subjected to hierarchical cluster analysis to generate a dendrogram and to estimate the phylogenetic closeness and distance between the rat strains tested. It was observed that the Wistar strain and its mutants maintained in our facility are genetically distinct and phylogenetically separate from the other two standard strains WKY and F-344.
Keywords: rat strains; obese mutants; microsatellite markers; phylogenetic analysis
Mitochondrial DNA Distinction of Northeastern China Roe Deer, Siberian Roe Deer, and European Roe Deer, to Clarify the Taxonomic Status of Northeastern China Roe Deer by Chao-Ting Xiao; Ming-Hai Zhang; Yan Fu; Hung-Son Koh (pp. 93-102).
Partial sequences of the mitochondrial control region of northeastern China roe deer were analyzed to determine the degree of genetic diversity. Fourteen haplotypes were observed. The haplotype diversity was high (h = 0.872), nucleotide diversity was medium (p i = 0.0108), and the average Tamura–Nei nucleotide distance among them was 1.9%, indicating that genetic diversity of roe deer from northeastern China was relatively high and that the effective population size was large historically. To clarify the northeastern China roe deer's taxonomic status, these 14 haplotypes were compared with 31 haplotypes published in Genbank from Europe, Siberia, and Korea. The average genetic distance between haplogroups of northeastern China and European roe deer (5.8%) was more than twice that between northeastern China and Siberian roe deer (2.7%), indicating sufficient variation to consider roe deer of northeastern China and Siberia as a single species (Capreolus pygargus), distinct from European roe deer (Capreolus capreolus). This is the first presentation of mtDNA data for roe deer in northeastern China, which will be helpful in investigations of genetic diversity and clarifications of the taxonomic status of roe deer in the whole of China.
Keywords: Capreolus pygargus ; taxonomic status; northeastern China roe deer; European roe deer; mitochondrial DNA
UCP2 and 3 Deletion Screening and Distribution in 15 Pig Breeds by Yanhua Li; Hanjie Li; Xingbo Zhao; Ning Li; Changxin Wu (pp. 103-111).
The uncoupling protein family is a mitochondrial anion carrier family. It plays an important role in the biological traits of animal body weight, basal metabolic rate and energy conversion. Using PCR and PCR-SSCP, we scanned the porcine uncoupling protein 2 gene (UCP2) and uncoupling protein 3 gene (UCP3) and found seven deletion sites, three in UCP2 and four in UCP3. The deletions in 15 pig breeds showed that deletion influenced weight. The genotype compounding of seven deletion sites in 15 pig breeds had significant effects on performance traits of the pig, such as body weight. We predicted the potential protein factor binding sites using the transcription factor analysis tool TFSearch version 1.3 online. Two deletions (1830 nt and 3219 nt) in UCP3 were found to change the transcriptional factor sites. The 16 bp deletion in 1830 nt added a SP1 site and a 6 bp deletion in 3219 nt removed two MZF1 sites. Seven deletion polymorphisms were covered in introns of linkage genes of UCP2 and UCP3, showing that UCPs have conservation and genetic reliability.
Keywords: pig; UCP2 ; UCP3 ; deletion
Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences by Shihua Duan; Baorong Lu; Zhong Li; Jiping Tong; Jin Kong; Wen Yao; Shaoqing Li; Yingguo Zhu (pp. 113-129).
Species in the genus Oryza (Poaceae) contain 10 genomic types and are distributed in pan-tropics of the world. To explore phylogenetic relationships of Oryza species having the AA-genome, DNA sequences of the chloroplast trnL intron and trnL-trnF spacer, mitochondrial nad1 intron 2, and nuclear internal transcribed spacer were analyzed, based on materials from 6 cultivated (O. sativa and O. glaberrima) and 13 wild accessions, in addition to a CC-genome species (O. officinalis) that was used as an outgroup. Analyses of the combined sequence data set from different sources provide a much better resolution of the AA-genome species than the individual data set, indicating the limitation of a single gene in phylogenetic reconstruction. The phylogeny based on the combined data set demonstrated an apparent grouping of the AA-genome Oryza species that was well associated with their geographic origin, although the Australian O. meridionalis showed its affinity with the African species. The geographic pattern of the phylogenetic relationship was probably attributed to the frequent genetic exchange and introgression among the AA-genome species from the same continents. In addition, Asian cultivated rice O. sativa showed its close relation to O. rufipogon and O. nivara, whereas African cultivated rice O. glaberrima was closely linked to O. barthii and O. longistaminata, indicating the independent domestication of the two cultivated species in different geographic locations.
Keywords: Oryza ; rice; phylogenetic relationship; AA genome; DNA sequences
Relationship Between mRNA Stability and Length: An Old Question with a New Twist by Liang Feng; Deng-Ke Niu (pp. 131-137).
The half-life of individual mRNA plays a central role in controlling the level of gene expression. However, the determinants of mRNA stability have not yet been well defined. Most previous studies suggest that mRNA length does not affect its stability. Here, we show significant negative correlations between mRNA length and stability in human and Escherichia coli, but not in Saccharomyces cerevisiae or Bacillus subtilis. This finding suggests the possibility that endonucleolytic attacks by RNA endonuclease and/or mechanical damage may strongly influence mRNA stability in both prokaryotes and eukaryotes.
Keywords: mRNA half-life; mRNA-decay rate; mRNA length; mRNA degradation
An InDel Polymorphism in Exon 6 of IGF2 Associated with the Breeding Value of Polish Holstein-Friesian Bulls
by K. Flisikowski; T. Adamowicz; T. Strabel; T. Jankowski; M. Switonski; L. Zwierzchowski (pp. 139-143).
MspI Allelic Pattern of Bovine Growth Hormone Gene in Indian Zebu Cattle (Bos indicus) Breeds by M. Sodhi; M. Mukesh; B. Prakash; B. P. Mishra; R. C. Sobti; Karn P. Singh; Satbir Singh; S. P. S. Ahlawat (pp. 145-153).
The MspI allelic variation in intron III of the bovine growth hormone (bGH) gene was explored using PCR-RFLP in 750 animals belonging to 17 well-recognized breeds of Indian zebu cattle (Bos indicus) reared in different geographic locations of the country. Restriction digestion analysis of a 329-bp PCR fragment of the bGH intron III region with MspI restriction enzyme revealed two alleles (MspI− and MspI+) and two genotypes (−/− and +/−) across the 17 cattle breeds studied. The allelic frequency varied from 0.67 to 0.94 for MspI (−) and from 0.06 to 0.33 for MspI (+) across the 17 breeds, with a combined average frequency of 0.87 and 0.13, respectively. No animal with +/+ genotype was detected across the samples analyzed. The chi-square test showed that the difference in MspI allelic frequency was not significant (p > 0.05), regardless of the geographic origin, coat color, or utility of the cattle breed. The high MspI (−) allele frequencies obtained for Indian zebu cattle in this study are in sharp contrast to those reported for taurine breeds from northern Europe, Mediterranean countries, and America. Findings of this study further substantiate the hypothesis that the MspI (−) allele has an Indian origin.
Keywords: Indian zebu cattle; bovine growth hormone gene; genetic variation; MspI allele