• International Journal of Industrial Entomology and Biomaterials
• /
• 제15권2호
• /
• pp.137-143
• /
• 2007

Lactate dehydrogenase (LDH) is a ubiquitous enzyme that plays a significant role in the clinical diagnosis of pathologic processes. Discovery of the LDH (BmLDH) gene in B. mori may shed light on its role in the biology of Lepidoptera species, and afford further understanding of the function of the enzyme. In this study, we used the bioinformatics tools to identify LDH gene in B. mori. Sequence analysis showed that BmLDH cDNA contains a 996 bp open reading frame, encoding 331 AA proteins, with seven introns. Compared with hHLDH (human heart LDH), BmLDH contained the same key active sites. Domain search and protein fold recognition analyses provide compelling evidences that the deduced protein is a LDH. Using the computer program MEGA3, we conducted a search for homologs of BmLDH among many eukaryotic species and confirmed that the BmLDH was conserved in all organisms investigated. This gene has been registered in GenBank under the accession number EU000385.

• 사상체질의학회지
• /
• 제13권1호
• /
• pp.17-23
• /
• 2001

Purpose This study was carried out ro apply the knowledge of bioinformatics to the quantification of constitutional information. Methods To objectify consitirutional knowledge, several uselful methods including Bayesian estimate, position specific score matrix, entropy, phylogenetic tree, simulated annealing were discussed. Results and Conclusion It is obvious that bioinformatic methods can be the most important tool for the objectification of constitutional medicine.

• Genomics & Informatics
• /
• 제14권4호
• /
• pp.230-233
• /
• 2016

Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost. The genotype data in our study comprised a total of 129 samples, varying from 4 to 39 samples. After quality control there were ~29,000 single nucleotide polymorphisms (SNPs) for which $r^2$ value was calculated. Average distance between SNP pairs was 1.14 Mb across all breeds. Average $r^2$ between adjacent SNP pairs ranged between was 0.1 for Yanbian to 0.3 for Qinchuan. Effective population size of the breeds based on $r^2$ varied from 16 in Hainan to 226 in Yanbian. Amongst the Korean native breeds effective population size of Brindle Hanwoo was the least with Ne = 59 and Brown Hanwoo was the highest with Ne = 83. The effective population size of the Korean cattle breeds has been decreasing alarmingly over the past generations. We suggest appropriate measures to be taken to prevent these local breeds in their native tracts.

• Journal of Animal Science and Technology
• /
• 제58권4호
• /
• pp.15.1-15.6
• /
• 2016

Background: Our previous study had identified the SNP (g.81966377T > C) and indel (g.81966364D > I) located in the promoter of APM1 to have a significant effect on marbling in Hanwoo. APM1 encodes an adipocytokine called adiponectin, which plays a significant role in lipogenesis. The aim of this study was to verify and validate the effect of the SNP and indel on marbling and other carcass traits in a large, representative, countrywide population of Hanwoo cattle. The carcass traits measured were marbling (MAR), backfat thickness (BFT), loin eye area (LEA), and carcass weight (CAW). Results: Primers were designed to amplify 346 bp of the genomic segment that contained the targeted SNP (g.81966377) and the indel (g.81966364). After data curation, the genotypes of 8,378 individuals identified using direct sequencing analysis estimated frequencies for C (0.686) and T (0.314) respectively showing genotype frequencies for CC (0.470), CT (0.430) and TT (0.098). The genotypes were significantly associated with MAR, BFT and LEA. The indel had significant effect on marbling (P < .0001) with strong additive genetic effects. The allele frequencies was estimated at (DEL, 0.864) and insertion (INS, 0.136) presenting genotypes of D/D (75.63 %), D/I (21.44 %), and I/I (2.92 %). Significant departure from Hardy-Weinberg equilibrium was not detected for both the SNP and the indel. Conclusion: The SNP genotypes showed significant association with MAR, BFT and LEA with strong additive genetic effects, while the indel was significantly associated with MAR. The results confirmed that the variants can be used as a genetic marker for improving marbling in Hanwoo.

• Journal of Applied Biological Chemistry
• /
• 제60권3호
• /
• pp.249-256
• /
• 2017

The Monascus azaphilone (MAz) pigment is a well-known food colorant that has yellow, orange and red components. The structures of the yellow and orange MAz differ by two hydride reductions, with yellow MAz being the reduced form. Orange MAz can be non-enzymatically converted to red MAz in the presence of amine derivatives. It was previously demonstrated that mppE and mppG are involved in the biosynthesis of yellow and orange MAz, respectively. However, ${\Delta}mppE$ and ${\Delta}mppG$ knockout mutants maintained residual production of yellow and orange MAz, respectively. In this study, we deleted the region encompassing mppD, mppE and mppG in M. purpureus and compared the phenotype of the resulting mutant (${\Delta}mppDEG$) with that of an mppD knockout mutant (${\Delta}mppD$). It was previously reported that the ${\Delta}mppD$ strain retained the ability to produce MAz but at approximately 10% of the level observed in the wildtype strain. A chemical analysis demonstrated that the ${\Delta}mppDEG$ strain was still capable of producing both yellow and orange MAz, suggesting the presence of minor MAz route(s) not involving mppE or mppG. Unexpectedly, the ${\Delta}mppDEG$ strain was observed to accumulate fast-eluting pigments in a reverse phase high-performance liquid chromatography analysis. A LC-MS analysis identified these pigments as ethanolamine derivatives of red MAz, which had been previously identified in an mppE knockout mutant that produces high amounts of orange MAz. Although the underlying mechanism is largely unknown, this study has yielded an M. purpureus strain that selectively accumulates red MAz.

• Asian-Australasian Journal of Animal Sciences
• /
• 제31권4호
• /
• pp.473-479
• /
• 2018

Objective: The study was designed to perform a genome-wide association (GWA) and partitioning of genome using Illumina's PorcineSNP60 Beadchip in order to identify variants and determine the explained heritability for the total number of teats in Yorkshire pig. Methods: After screening with the following criteria: minor allele frequency, $MAF{\leq}0.01$; Hardy-Weinberg equilibrium, $HWE{\leq}0.000001$, a pair-wise genomic relationship matrix was produced using 42,953 single nucleotide polymorphisms (SNPs). A genome-wide mixed linear model-based association analysis (MLMA) was conducted. And for estimating the explained heritability with genome- or chromosome-wide SNPs the genetic relatedness estimation through maximum likelihood approach was used in our study. Results: The MLMA analysis and false discovery rate p-values identified three significant SNPs on two different chromosomes (rs81476910 and rs81405825 on SSC8; rs81332615 on SSC13) for total number of teats. Besides, we estimated that 30% of variance could be explained by all of the common SNPs on the autosomal chromosomes for the trait. The maximum amount of heritability obtained by partitioning the genome were $0.22{\pm}0.05$, $0.16{\pm}0.05$, $0.10{\pm}0.03$ and $0.08{\pm}0.03$ on SSC7, SSC13, SSC1, and SSC8, respectively. Of them, SSC7 explained the amount of estimated heritability along with a SNP (rs80805264) identified by genome-wide association studies at the empirical p value significance level of 2.35E-05 in our study. Interestingly, rs80805264 was found in a nearby quantitative trait loci (QTL) on SSC7 for the teat number trait as identified in a recent study. Moreover, all other significant SNPs were found within and/or close to some QTLs related to ovary weight, total number of born alive and age at puberty in pigs. Conclusion: The SNPs we identified unquestionably represent some of the important QTL regions as well as genes of interest in the genome for various physiological functions responsible for reproduction in pigs.

• Asian-Australasian Journal of Animal Sciences
• /
• 제20권9호
• /
• pp.1334-1341
• /
• 2007

This study identified hepatic differentially expressed genes (DEGs) affecting the marbling of muscle. Most dietary nutrients bypass the liver and produce plasma lipoproteins. These plasma lipoproteins transport free fatty acids to the target tissue, adipose tissue and muscle. We examined hepatic genes differentially expressed in a differential-display reverse transcription-polymerase chain reaction (ddRT-PCR) analysis comparing high- and low-marbled Hanwoo steers. Using 60 arbitrary primers, we found 13 candidate genes that were upregulated and five candidate genes that were downregulated in the livers of high-marbled Hanwoo steers compared to low-marbled individuals. A BLAST search for the 18 DEGs revealed that 14 were well characterized, while four were not annotated. We examined four DEGs: ATP synthase F0, complement component CD, insulin-like growth factor binding protein-3 (IGFBP3) and phosphatidylethanolamine binding protein (PEBP). Of these, only two genes (complement component CD and IGFBP3) were differentially expressed at p<0.05 between the livers of high- and low-marbled individuals. The mean mRNA levels of the PEBP and ATP synthase F0 genes did not differ significantly between the livers of high- and low-marbled individuals. Moreover, these DEGs showed very high inter-individual variation in expression. These informative DEGs were assigned to the bovine chromosome in a BLAST search of MS marker subsets and the bovine genome sequence. Genes related to energy metabolism (ATP synthase F0, ketohexokinase, electron-transfer flavoprotein-ubiquinone oxidoreductase and NADH hydrogenase) were assigned to BTA 1, 11, 17, and 22, respectively. Syntaxin, IGFBP3, decorin, the bax inhibitor gene and the PEBP gene were assigned to BTA 3, 4, 5, 5, and 17, respectively. In this study, the in silico physical maps provided information on the specific location of candidate genes associated with economic traits in cattle.

• Journal of Animal Science and Technology
• /
• 제51권6호
• /
• pp.459-470
• /
• 2009

The aim of this study was to analyze the proteome of proliferating bovine satellite cells from longissimus dorsi, deep pectoral and semitendinosus muscle depots which had been subjected to hormonal deprivation or addition in culture. For hormone deprivation or addition studies, the cells were either grown in 10% charcoal-dextran stripped fetal bovine serum (CD-FBS) or in 10% FBS supplemented medium. Further to analyze the effect of insulin like growth factor (IGF-1) and testosterone (TS), the cells were grown in 10% CD-FBS containing IGF-1 (10 ng/ml) or TS (10 nM). Results have shown that hormone deprivation had a negative impact on proliferation of the cells from each of the muscle depots. In case of IGF-1 and TS addition, the proliferation levels were low compared with that of the cells grown in 10% FBS. Hence, to gain the insights of the proteins that are involved in such divergent levels of proliferation, the proteome of such satellite cells proliferating under the above mentioned conditions were analyzed using 2D-DIGE and MALDI-ToF/ToF. Thirteen proteins during hormone deprivation and nine proteins from hormone addition were found to be differentially expressed in all the cultures of the cells from the three depots. Moreover, the results highlighted in this study offer a role for each differentially expressed protein with respect to its effect on positive or negative regulation of cell proliferation.

• Asian Pacific Journal of Cancer Prevention
• /
• 제15권19호
• /
• pp.8155-8159
• /
• 2014

Background: Breast cancer is the serious health concern in India causing the highest mortality rate in females, which occurs due to uncontrolled cell division and can be metastasize to other parts of the human body. Interactions with estrogen receptor (ER) alpha are mainly responsible for the malignant tumors with regulation of the transcription of various genes as a transcription factor. Most of the drugs currently used for the breast cancer treatment produce various side effects and hence we focused on natural compounds which do not exhibit any toxic effect against normal human cells. Materials and Methods: Structure of human ER was retrieved from the Protein Data Bank and the structures of flavonoid compounds have been collected from PubChem database. Molecular docking and drug likeness studies were performed for those natural compounds to evaluate and analyze the anti-breast cancer activity. Results: Finally two compounds satisfying the Lipinski's rule of five were reported. The two compounds also exhibited highest binding affinity with human ER greater than 10.5 Kcal/mol. Conclusions: The results of this study can be implemented in the drug designing pipeline.

• BMB Reports
• /
• 제42권7호
• /
• pp.411-417
• /
• 2009

Transcriptional activation domain (TAD) in virion protein 16 (VP16) of herpes simplex virus does not have any globular structure, yet exhibits a potent transcriptional activity. In order to probe the structural basis for the transcriptional activity of VP16 TAD, we have used NMR spectroscopy to investigate its detailed structural features. Results show that an unbound VP16 TAD is not merely "unstructured" but contains four short motifs (residues 424-433, 442-446, 465-467 and 472-479) with transient structural order. Pre-structured motifs in other intrinsically unfolded proteins (IUPs) were shown to be critically involved in target protein binding. The 472-479 motif was previously shown to bind to $hTAF_{II}31$, whereas the $hTAF_{II}31$-binding ability of other motifs found in this study has not been addressed. The VP16 TAD represents another IUP whose pre-structured motifs mediate promiscuous binding to various target proteins.