Association between a single nucleotide polymorphism in the bovine chemerin gene and carcass traits in Qinchuan cattle

Qinchuan is a red or yellow draft and beef breed in China. In order to identify a predictor of carcass traits on the basis of associations between carcass traits and gene polymorphism, variation in the bovine chemerin gene was investigated using PCR-single-strand conformational polymorphism and DNA sequencing. An SNP of A868G located in exon 2 of the Bos taurus chemerin gene was detected in 716 samples of six breeds (Jiaxian red, Luxi, Nan yang, Qinchuan, Simmental and Luxi crossbred steers, and Xia'nan), all in China, and three genotypes (AA, AG and GG) were found. Based on the χ(2) test, the AA/AG/GG genotype frequencies of all six breeds were found to be in Hardy-Weinberg equilibrium. A possible association of A868G with some carcass traits was investigated in 106 Qinchuan cattle. Animals with the AG genotype were found to have significantly lower mean loin eye area and meat tenderness compared to those with the AA and GG genotypes. However, there was no significant association between any individual haplotype and backfat thickness, water holding capacity or marbling score. We suggest that A868G could be used as a molecular marker in marker-assisted selection for carcass traits.     

Characterization and nucleotide sequence of the gene for the common alpha subunit of the bovine pituitary glycoprotein hormones.

The gene coding for the common alpha subunit of the bovine pituitary glycoprotein hormones was isolated from a bovine genomic library. The gene spans roughly 16.5 kbp, contains three intervening sequences, and codes for a message of approximately 730 nucleotides. The complete coding region of the gene was sequenced as well as 315 nucleotides of 5' flanking sequence and the entire intron C. Only a single base difference was found when the sequence of the gene was compared with that of the cDNA. Genomic blotting experiments suggest the presence of a single alpha subunit gene. Comparison of the bovine and human alpha subunit genes indicated that the high level of homology observed in the coding regions has been maintained throughout the 5' and 3' untranslated regions, and at least 90 nucleotides of the 5'flanking regions. Additionally, there is an 18 base pair sequence present in both the 5' flanking and 5' untranslated regions of the gene that is homologous to a region of the chick ovalbumin gene. This ovalbumin sequence has been suggested as a binding site for the progesterone receptor-complex.     

Characterization of eight single nucleotide polymorphism markers in Aedes aegypti

Sequencing of part of seven genes from Aedes aegypti collected in 16 Brazilian cities revealed the existence of 53 single nucleotide polymorphisms (SNPs), representing one SNP every 52 base pairs. From these 53 SNPs, we selected eight that are independent and highly polymorphic. We describe the use of these markers for differentiation of Brazilian populations of A. aegypti. These are the first SNPs developed for delineating population structure in A. aegypti, and will be a useful complement to epidemiological studies.     

Characterization of a frequent polymorphism in the coding sequence of the Tp53 gene in colonic cancer patients and a control population

Summary We describe a simple method for characterizing a frequent polymorphism (that subsitutes an arginine for a proline) in the coding sequence of the Tp53 gene in patients with colonic cancer and in a control population. We could find no evidence that this polymorphism is associated with a marked predisposition to colorectal cancer.     

Characterization of genomic single nucleotide polymorphism via colorimetric detection using a single gold nanoprobe

Identification of specific nucleic acid sequences mediated by gold nanoparticles derivatized thiol-modified oligonucleotides (Au–nanoprobes) has been proven to be a useful tool in molecular diagnostics. Here, we demonstrate that, on optimization, detection may be simplified via the use of a single Au–nanoprobe to detect a single nucleotide polymorphism (SNP) in homo- or heterozygote condition. We validated this non-cross-linking approach through the analysis of 20 clinical samples using a single specific Au–nanoprobe for an SNP in the FTO (fat mass and obesity-associated) gene against direct DNA sequencing. Sensitivity, specificity, and limit of detection (LOD) were determined, and statistical differences were calculated by one-way analysis of variance (ANOVA) and a post hoc Tukey’s test to ascertain whether there were any differences between Au–nanoprobe genotyped groups. For the first time, we show that the use of a single Au–nanoprobe can detect SNP for each genetic status (wild type, heterozygous, or mutant) with high degrees of sensitivity (87.50%) and specificity (91.67%).     

Cloning and nucleotide sequence of the gene coding for citrate synthase from a thermotolerant Bacillus sp.

The structural gene coding for citrate synthase from the gram-positive soil isolate Bacillus sp. strain C4 (ATCC 55182) capable of secreting acetic acid at pH 5.0 to 7.0 in the presence of dolime has been cloned from a genomic library by complementation of an Escherichia coli auxotrophic mutant lacking citrate synthase. The nucleotide sequence of the entire 3.1-kb HindIII fragment has been determined, and one major open reading frame was found coding for citrate synthase (ctsA). Citrate synthase from Bacillus sp. strain C4 was found to be a dimer (Mr, 84,500) with a subunit with an Mr of 42,000. The N-terminal sequence was found to be identical with that predicted from the gene sequence. The kinetics were best fit to a bisubstrate enzyme with an ordered mechanism. Bacillus sp. strain C4 citrate synthase was not activated by potassium chloride and was not inhibited by NADH, ATP, ADP, or AMP at levels up to 1 mM. The predicted amino acid sequence was compared with that of the E. coli, Acinetobacter anitratum, Pseudomonas aeruginosa, Rickettsia prowazekii, porcine heart, and Saccharomyces cerevisiae cytoplasmic and mitochondrial enzymes.     

Cloning and nucleotide sequence of the gene coding for citrate synthase from a thermotolerant Bacillus sp.

The structural gene coding for citrate synthase from the gram-positive soil isolate Bacillus sp. strain C4 (ATCC 55182) capable of secreting acetic acid at pH 5.0 to 7.0 in the presence of dolime has been cloned from a genomic library by complementation of an Escherichia coli auxotrophic mutant lacking citrate synthase. The nucleotide sequence of the entire 3.1-kb HindIII fragment has been determined, and one major open reading frame was found coding for citrate synthase (ctsA). Citrate synthase from Bacillus sp. strain C4 was found to be a dimer (Mr, 84,500) with a subunit with an Mr of 42,000. The N-terminal sequence was found to be identical with that predicted from the gene sequence. The kinetics were best fit to a bisubstrate enzyme with an ordered mechanism. Bacillus sp. strain C4 citrate synthase was not activated by potassium chloride and was not inhibited by NADH, ATP, ADP, or AMP at levels up to 1 mM. The predicted amino acid sequence was compared with that of the E. coli, Acinetobacter anitratum, Pseudomonas aeruginosa, Rickettsia prowazekii, porcine heart, and Saccharomyces cerevisiae cytoplasmic and mitochondrial enzymes.     

Characterization of 13 single nucleotide polymorphism markers for chum salmon

We report the characterization of 13 single nucleotide polymorphism (SNP) genotyping assays for chum salmon (Oncorhynchus keta). These assays are based on the 5′‐nuclease reaction and thus facilitate high‐throughput genotyping with minimal optimization time. Because data generated using these markers may be transported and combined across laboratories, SNPs offer the potential to reduce the amount of redundant work being done in mixture and migratory studies of chum salmon.     

Characterization of 19 single nucleotide polymorphism markers for coho salmon

We report 39 single nucleotide polymorphisms (SNPs) observed in 23 nuclear DNA sequences in coho salmon Oncorhynchus kisutch. High‐throughput genotyping assays based on the 5′‐nuclease reaction were developed for 17 of these nuclear SNPs and for two previously published mitochondrial DNA SNPs. Minor allele frequency differences (Δq) among collections were between 5.2% and 51.2%, resulting in per locus F_ST estimates of 0.00–0.24 with an average of 0.09.     

Karyotype and single nucleotide polymorphism of the prolactin gene in milking bucks

There is no genetic disease known currently to be linked to prolactin or its receptor in goats. Given the essential role of this hormonal system in the physiology of the mammary gland, we reasoned that genetic anomalies of Prl/PrlR genes could be related to the occurrence of mammary diseases. Karyotyping was performed, and the single nucleotide polymorphisms (SNPs) of the prolactin gene were investigated in goats with gynecomastia and galactorrhea (“milking bucks”). The results showed that the karyotype was identical between milking bucks and normal males (2n = 60, XY). Two heterozygous SNPs, G8895A and A8898C, were detected in exon 5 of the prolactin gene, and they corresponded to two amino acid substitutions, lysine (Lys) → glutamate (Glu)₁₄₅ and threonine (Thr) → proline (Pro)₁₄₆. The first mutation was found in only one milking buck; the second was found in both milking bucks and in four normal males. The alignment analysis for homology of the complete coding sequence (CDS) of the prolactin gene among cattle, sheep, goat, dog, rabbit and human indicated that the 145th amino acid, Glu, was highly conserved in the prolactin gene of all species that exhibited gynecomastia in males. However, the 146th amino acid was Pro for goat, sheep, cattle and dog, and isoleucine (Ile) for rabbit and human. These mutations occurred in the loop region, between the third and the fourth helices of prolactin, which would affect backbone chemical shifts indirectly by changing the average chemical environment of the backbone amides. It was presumed that the second mutation (Thr → Pro₁₄₆) may be associated with gynecomastia in bucks. Further studies are needed to confirm the assumption.