• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.153-160
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• 2010

The present study was carried out for the isolation of bacteriocin-producing enterococci from indigenous sources. Gram-positive enterococci are known for having the ability to produce enterocins with good antimicrobial potential. A total of 34 strains were isolated from processed dairy products of Pakistan and seven out of them were found to be member of genus Enterococcus on selective enumeration. Biochemical and molecular characterization revealed that four of these isolates (IJ-03, IJ-07, IJ-11, and IJ-12) were Enterococcus faecalis and three (IJ-06, IJ-21, and IJ-31) were Enterococcus faecium. Local processed cheese was the source of all enterococcal isolates, except E. faecium IJ-21 and IJ-31, which were isolated from indigenous yoghurt and butter samples, respectively. Bacterial isolates were sensitive to commonly used antibiotics except methicillin and kanamycin. They also lacked critical virulence determinants, mainly cytolysin (cyl), gelatinase (gel), enterococcal surface protein (esp), and vancomycin resistance (vanA and vanB). Polymerase chain reaction amplification identified that enterocin A and P genes were present in the genome of E. faecium IJ-06 and IJ-21, whereas the E. faecium IJ-31 genome showed only enterocin P genes. No amplification was observed for genes that corresponded with the enterocins 31, AS-48, L50A, and L50B, and ent 1071A and 1071B. There were no signals of amplification found for E. faecalis IJ-11, indicating that the antimicrobial activity was because of an enterocin different from those checked by PCR. Hence, the indigenous bacterial isolates have great potential for bacteriocin production and they had antibacterial activity against a variety of closely related species.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2010.10a
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• pp.11-11
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• 2010

The Korean ginseng, Panax ginseng C. A. Meyer is a popular medicinal herb in Araliaceae. Genetic map in crops provides valuable information for breeding, genetic and genomic researches. However, little information is available for construction of genetic map in ginseng. Up to now, we have produced large amounts of expressed sequence tags (ESTs) from four ginseng cultivars (37Mb, 49Mb, 39Mb, 47Mb from Gopoong, Gumpoong, Chunpoong and Yunpoong respectively using pyrosequencing technique and 5Mb from normalized full-length cDNA library of Chunpoong) to obtain comprehensive information of gene expression, and constructed EST database including ESTs from public database. Till now, we designed 261 SSR primer sets using EST sequences and identified 106 intergenic polymorphic markers. And 44 of the 106 showed polymorphisms among panax ginseng cultivars. Among 44 markers, 27 SSR polymorphic markers were inspected to 51 $F_2$ population from Yunpoong x Chunpoong, which showed good at the fitness of Mendellian segregation ratio 1:2:1. To enrich the number of markers, and thus construct high resolution genetic map which can be used as frame map for further genome sequencing. we are planning to develop large scale EST-derived SNP markers which are available in the F2 population. This study provides genetic information as well as foundation for ginseng researches such as genetics, genomics, breeding, and the final goal for whole genome sequencing. This study was supported by Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry and Fisheries, Republic of Korea (Grant No. 609001-051SB210).

• Korean Journal of Ichthyology
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• v.1 no.1_2
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• pp.35-41
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• 1989

An examination of the karyotypes, DNA values and nuclear sizes of three scups was undertaken as part of the study of cytogenetical evolution of order Perciformes. The chromosome number 2n=48 was the same in all three species but the numbers of chromosome arm were not identical. The distribution of genome size and nuclear volumes among species was continuous ranging from 1.287 pg and $20.78\;{\mu}m^3$ for Pagrus major down to 1.237 pg and $20.56\;{\mu}m^3$ for Acanthopagrus schlegeli. Above results indicate the possible role of pericentric inversions in the karyotypic evolution of these species.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.11
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• pp.5799-5804
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• 2012

Family with sequence similarity 189, member B (FAM189B), alias COTE1, a putative oncogene selected by microarray, for the first time was here found to be significantly up-regulated in hepatocellular carcinoma (HCC) specimens and HCC cell lines. mRNA expression of COTE1 in HCC samples and cell lines was detected by reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR, while protein expression of COTE1 in HCC tissues was assessed by immunohistochemistry. In addition, invasion of HCC cells was observed after overexpressing or silencing COTE1. In the total of 48 paired HCC specimens, compared with the adjacent non-cancer tissues, the expression of COTE1 was up-regulated in 31 (p<0.01). In HCC cell lines, COTE1 expression was significantly higher than in normal human adult liver (p<0.01). Overexpression of COTE1 enhanced HCC-derived LM6 and MHCC-L cellular invasion in vitro. In contrast, COTE1 knockdown via RNAi markedly suppressed these phenotypes, as documented in LM3 and MHCC-H HCC cells. Mechanistic analyses indicated that COTE1 could physically associate with WW domain oxidoreductase (WWOX), a tumor suppressor. COTE1 may be closely correlated with invasion of hepatocellular carcinoma (HCC) cells and thus may serve as an effective target for gene therapy.

• Journal of Crop Science and Biotechnology
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• v.11 no.4
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• pp.263-268
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• 2008

Bacterial leaf pustule (BLP) caused by Xanthomonas axonopodis pv. glycines is a serious disease to make pustule and chlorotic haloes in soybean [Glycine max (L). Merr.]. While inheritance mode and map positions of the BLP resistance gene, rxp are known, no sequence information of the gene was reported. In this study, we made five near isogenic lines (NILs) from separate backcrosses (BCs) of BLP-susceptible Hwangkeumkong $\times$ BLP-resistant SS2-2 (HS) and BLP-susceptible Taekwangkong$\times$ SS2-2 (TS) through foreground and background selection based on the four-stage selection strategy. First, 15 BC individuals were selected through foreground selection using the simple sequence repeat (SSR) markers Satt486 and Satt372 flanking the rxp gene. Among them, 11 BC plants showed the BLP-resistant response. The HS and TS lines chosen in foreground selection were again screened by background selection using 118 and 90 SSR markers across all chromosomes, respectively. Eventually, five individuals showing greater than 90% recurrent parent genome content were selected in both HS and TS lines. These NILs will be a unique biological material to characterize the rxp gene.

• Genomics & Informatics
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• v.14 no.2
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• pp.62-68
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• 2016

Osteoporosis is a medical condition of global concern, with increasing incidence in both sexes. Bone mineral density (BMD), a highly heritable trait, has been proven a useful diagnostic factor in predicting fracture. Because medical information is lacking about male osteoporotic genetics, we conducted a genome-wide association study of BMD in Korean men. With 1,176 participants, we analyzed 4,414,664 single nucleotide polymorphisms (SNPs) after genomic imputation, and identified five SNPs and three loci correlated with bone density and strength. Multivariate linear regression models were applied to adjust for age and body mass index interference. Rs17124500 ($p=6.42{\times}10^{-7}$), rs34594869 ($p=6.53{\times}10^{-7}$) and rs17124504 ($p=6.53{\times}10^{-7}$) in 14q31.3 and rs140155614 ($p=8.64{\times}10^{-7}$) in 15q25.1 were significantly associated with lumbar spine BMD (LS-BMD), while rs111822233 ($p=6.35{\times}10^{-7}$) was linked with the femur total BMD (FT-BMD). Additionally, we analyzed the relationship between BMD and five genes previously identified in Korean men. Rs61382873 (p = 0.0009) in LRP5, rs9567003 (p = 0.0033) in TNFSF11 and rs9935828 (p = 0.0248) in FOXL1 were observed for LS-BMD. Furthermore, rs33997547 (p = 0.0057) in ZBTB and rs1664496 (p = 0.0012) in MEF2C were found to influence FT-BMD and rs61769193 (p = 0.0114) in ZBTB to influence femur neck BMD. We identified five SNPs and three genomic regions, associated with BMD. The significance of our results lies in the discovery of new loci, while also affirming a previously significant locus, as potential osteoporotic factors in the Korean male population.

• Clinical and Experimental Reproductive Medicine
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• v.30 no.4
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• pp.325-331
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• 2003

Objective: To investigate the association of genetic background between MTHFR A1298C genotype and male infertility. Materials and Methods: We compared 377 infertile males with 396 healthy fertile males with one or more offspring. Infertile males were classified into four subtypes (281 azoospermia, 26 oligoasthenoteratozoospermia (OAT), 59 severe OAT and 11 remnants) by World Health Organization (WHO). Pyrosequencing analysis for MTHFR (methylenetetrahydrofolatereductase) A1298C variation was performed on polymerase chain reaction (PCR) product of study group. To validate pyrosequencing data of A1298C variation for randomly selected 50 samples, we compared the pyrosequencing result with the PCR-RFLP (Restriction Fragment Length Polymorphism) result of MTHFR A1298C genotype. Results: We studied MTHFR A1298C variation by pyrosequencing. A1298C variation data (1298 AC; p=0.2166 and 1298 CC; p=0.5056) of MTHFR gene was no significant difference in between fertile and infertile males. Conclusion: The genetic analysis in MTHFR gene didn't appear genetic difference in Korean fertile and infertile males. We require further study for MTHFR gene in infertile males.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.9
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• pp.1400-1410
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• 2020

Objective: Genome-wide association study and two meta-analysis based on GWAS performed to explore the genetic mechanism underlying variation in pig number born alive (NBA) and total number born (TNB). Methods: Single trait GWAS and two meta-analysis (single-trait meta analysis and multi-trait meta analysis) were used in our study for NBA and TNB on 3,121 Yorkshires from 4 populations, including three different American Yorkshire populations (n = 2,247) and one British Yorkshire populations (n = 874). Results: The result of single trait GWAS showed that no significant associated single nucleotide polymorphisms (SNPs) were identified. Using single-trait meta analysis and multi-trait meta analysis within populations, 11 significant loci were identified associated with target traits. Spindlin 1, vascular endothelial growth factor A, forkhead box Q1, msh homeobox 1, and LHFPL tetraspan submily member 3 are five functionally plausible candidate genes for NBA and TNB. Compared to the single population GWAS, single-trait Meta analysis can improve the detection power to identify SNPs by integrating information of multiple populations. The multiple-trait analysis reduced the power to detect trait-specific loci but enhanced the power to identify the common loci across traits. Conclusion: In total, our findings identified novel genes to be validated as candidates for NBA and TNB in pigs. Also, it enabled us to enlarge population size by including multiple populations with different genetic backgrounds and increase the power of GWAS by using meta analysis.

• Molecules and Cells
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• v.19 no.1
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• pp.104-113
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• 2005

Large inversions are well characterized in the chloroplast genomes of land plants. In contrast, reports of small inversions are rare and involve limited plant groups. In this study, we report the widespread occurrence of small inversions ranging from 5 to 50 bp in fully and partially sequenced chloroplast genomes of both monocots and dicots. We found that small inversions were much more common than large inversions. The small inversions were scattered over the chloroplast genome including the IR, SSC, and LSC regions. Several small inversions were uncovered in chloroplast genomes even though they shared the same overall gene order. The majority of these small inversions were located within 100 bp downstream of the 3' ends of genes. All had inverted repeat sequences, ranging from 11 to 24 bp, at their ends. Such small inversions form stem-loop hairpin structures that usually have the function of stabilizing the corresponding mRNA molecules. Intra-molecular recombination between the inverted sequences in the stem-forming regions are responsible for generating flip-flop orientations of the loops. The presence of two different orientations of the stem-loop in the trnL-F noncoding region of a single species of Jasminum elegans suggests that a short inversion can be generated within a short period of time. Small inversions of non-coding sequences may influence sequence alignment and character interpretation in phylogeny reconstructions, as shown in nine species of Jasminum. Many small inversions may have been generated by parallel or back mutation events during chloroplast genome evolution. Our data indicate that caution is needed when using chloroplast non-coding sequences for phylogenetic analysis.

• Genomics & Informatics
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• v.11 no.1
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• pp.55-57
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• 2013

Growing numbers of studies employ cell line-based systematic short interfering RNA (siRNA) screens to study gene functions and to identify drug targets. As multiple sources of variations that are unique to siRNA screens exist, there is a growing demand for a computational tool that generates normalized values and standardized scores. However, only a few tools have been available so far with limited usability. Here, we present siMacro, a fast and easy-to-use Microsoft Office Excel-based tool with a graphic user interface, designed to process single-condition or two-condition synthetic screen datasets. siMacro normalizes position and batch effects, censors outlier samples, and calculates Z-scores and robust Z-scores, with a spreadsheet output of >120,000 samples in under 1 minute.