• Korean Journal of Veterinary Research
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• v.55 no.1
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• pp.31-39
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• 2015

The present study was conducted to determine the full rpoB and eight house-keeping gene sequences of 78 and 35, respectively, avian pathogenic E. coli (APEC) strains. Phylogenetic comparison with 66 E. coli and Shigella strains from GenBank and EMBL was also conducted. Based on the full rpoB sequence, 50 different rpoB sequence types (RSTs) were identified. RST 1 was assigned to a major RST that included 34.7% (50/144) of the analyzed strains. RST 2 to RST 50 were then assigned to other strains with higher nucleotide sequence similarity to RST 1 in order. RST 1, 11, and 23 were mixed with APEC along with human commensal and pathogenic strains while RST 2, 6, 9, 13-15, 22, 24, 25, 33, 34, 36, and 41 were unique to APEC strains. Only five APEC strains grouped into RST 32 and 47, which contained human pathogenic E. coli (HPEC). Thus, most of the APEC strains had genetic backgrounds different from HPEC strains. However, the minor APEC strains similar to HPEC should be considered potential zoonotic risks. The resolution power of multi-locus sequence typing (MLST) was better than RST testing. Nevertheless, phylogenetic analysis of rpoB was simpler and more economic than MLST.

• Asian-Australasian Journal of Animal Sciences
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• v.16 no.8
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• pp.1087-1092
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• 2003

As an experimental reference population, crosses between Korean native pig and Landraces were established and information on growth traits was recorded. Animals were genotyped for 24 microsatellite markers covering chromosomes 2, 6, and 7 for partial-genome scan to identify chromosomal regions that have effects on growth traits. quantitative trait loci (QTL) effects were estimated using interval mapping by the regression method under the line cross models with a test for imprinting effects. For test of presence of QTL, chromosome-wide and single position significance thresholds were estimated by permutation test and normal significance threshold for the imprinting test were derived. For tests against the Mendelian model, additive and dominance coefficients were permuted within individuals. Thresholds (5% chromosome-wide) against the no-QTL model for the analyzed traits ranged from 4.57 to 4.99 for the Mendelian model and from 4.14 to 4.67 for the imprinting model, respectively. Partial-genome scan revealed significant evidence for 4 QTL affecting growth traits, and 2 out of the 4 QTLs were imprinted. This study demonstrated that testing for imprinting should become a standard procedure to unravel the genetic control of multi-factorial traits. The models and tests developed in this study allowed the detection and evaluation of imprinted QTL.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.13
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• pp.5219-5223
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• 2015

Helicobacter pylori (H. pylori) infection as a serious problem in both adults and children can induce chronic gastritis, peptic ulcer disease (PUD), and possibly gastric cancer. The aim of the current study was to survey antibiotic resistance and also to determine influence of PPAR$\gamma$ polymorphism in patients with H. pylori infection. During an 11-month-period, 98 H. pylori isolates were collected from 104 biopsy specimens. In vitro susceptibility of H. pylori isolates to 4 antimicrobial agents metronidazole, clarithromycin, amoxicillin and tetracycline were assessed by quantitative method according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guideline. PPAR$\gamma$ polymorphism was determined using polymerase chain reaction-restriction fragment length polymorphism assay. The frequency of H. pylori infection in our study was 94.2%. In vitro susceptibility data showed that highest level of resistance was related to metronidazole (66.3%), and the majority of H. pylori isolates were highly susceptible to amoxicillin and tetracycline (94.9% and 96.9%, respectively). Genotypic frequencies were 25.5% for CC (Pro12Pro), 40.8% for GC (Pro12Ala) and 33.7% for GG (Ala12Ala). In our study, CG genotype had highest distributions among infected patients with H. pylori. The study suggests that the PPAR-$\gamma$ Pro12Ala polymorphism could be evaluated as a potential genetic marker for susceptibility to gastric cancer in the presence of H. pylori infection.

• Journal of Yeungnam Medical Science
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• v.34 no.2
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• pp.270-274
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• 2017

A nodular density was detected on a chest radiograph taken from a 57-year-old Korean woman who was visiting a hospital for a routine check. Chest computed tomography revealed a 4.8 cm lobulated mass in the right lung and another focal nodular lesion in the left lung; biopsies of both lungs revealed adenocarcinoma. We conducted DNA sequencing and peptide nucleic acid clamping to investigate the potential double primary lung cancer. The results verified that the mass in the right lung had a mutation in the epidermal growth factor receptor, whereas the nodule in the left lung had a wild-type sequence, showing that these two were genetically different cancers from one another. Thus, we demonstrate that genetic testing is useful in determining double primary lung cancer, and we herein report on this case.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.6
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• pp.793-798
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• 2006

The quality characteristics of semen are important indicators of the fertility of a boar. Development of genetic markers for the semen quality in boars will be beneficial to the improvement of porcine fertility. We investigated the relationship between the polymorphisms of epidermal growth factor (EGF), prostaglandin-endoperoxide synthase 2 (PTGS2) and prolactin receptor (PRLR) genes, and semen quality traits in boars. The genomic DNA of 233 boars (157 Duroc and 86 Landrace) from a central testing station was subjected to genotyping for surveying gene frequency. The EGF, PTGS2 and PRLR genotypes were determined using the restriction fragment length polymorphism method. Thirty-seven normal, mature Duroc boars from an AI center were also genotyped and their semen quality traits were collected. The effect of genotype on semen quality traits was analyzed by the least-squares means method using data corrected for season. The frequencies of the AA genotype of EGF, PTGS2 and PRLR in Duroc boars were 0.14, 0.01 and 0.66, respectively. In Landrace, the frequencies of the AA genotype were 0.03, 0.09 and 0.62, respectively. Boars with the BB genotype in EGF, with the AB genotype in PTGS2 and with the AA genotype in PRLR had significantly better semen quality with a higher percentage of normal sperm and a lower percentage of immature sperm than those with other genotypes. These findings imply that polymorphisms of EGF, PTGS2 and PRLR genes might be used as markers for improving the semen quality of boars.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.10
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• pp.1542-1549
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• 2018

Objective: Because lactation periods in dairy cows lengthen with increasing total milk production, it is important to predict individual productivities after 305 days in milk (DIM) to determine the optimal lactation period. We therefore examined whether the random regression (RR) coefficient from 306 to 450 DIM (M2) can be predicted from those during the first 305 DIM (M1) by using a RR model. Methods: We analyzed test-day milk records from 85,690 Holstein cows in their first lactations and 131,727 cows in their later (second to fifth) lactations. Data in M1 and M2 were analyzed separately by using different single-trait RR animal models. We then performed a multiple regression analysis of the RR coefficients of M2 on those of M1 during the first and later lactations. Results: The first-order Legendre polynomials were practical covariates of RR for the milk yields of M2. All RR coefficients for the additive genetic (AG) effect and the intercept for the permanent environmental (PE) effect of M2 had moderate to strong correlations with the intercept for the AG effect of M1. The coefficients of determination for multiple regression of the combined intercepts for the AG and PE effects of M2 on the coefficients for the AG effect of M1 were moderate to high. The daily milk yields of M2 predicted by using the RR coefficients for the AG effect of M1 were highly correlated with those obtained by using the coefficients of M2. Conclusion: Milk production after 305 DIM can be predicted by using the RR coefficient estimates of the AG effect during the first 305 DIM.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.3
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• pp.1219-1224
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• 2015

Background: To date several common mutations in BRCA1 and BRCA2 associated with breast cancer have been reported in different populations. However, the common BRCA1 and BRCA2 mutations among breast cancer patients in Iran have not been described in detail. Materials and Methods: To comprehensively assess the frequency and distribution of the most common BRCA1 and BRCA2 mutations in Iranian breast cancer patients, we conducted this meta-analysis on 13 relevant published studies indentified in a literature search on PubMed and SID. Results: A total of 11 BRCA1 and BRCA2 distinct common mutations were identified, reported twice or more in the articles, of which 10 (c.2311T>C, c.3113A>G, c.4308T>C, c.4837A>G, c.2612C>T, c.3119G>A, c.3548A>G, c.5213G>A c.IVS16-92A/G, and c.IVS16-68A/G) mutations were in BRCA1, and 1 (c.4770A>G) was in BRCA2. The mutations were in exon 11, exon 13, intron 16, and exon 20 of BRCA1 and exon 11 of BRCA2. All have been previously reported in different populations. Conclusions: These meta analysis results should be helpful in understanding the possibility of any first true founder mutation of BRCA1/BRCA2 in the Iranian population. In addition, they will be of significance for diagnostic testing, genetic counseling and for epidemiological studies.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.18 no.10
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• pp.551-558
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• 2017

To study and validate tissue-specific promoters and vectors, it is important to develop cell culture systems that retain the tissue and species specificity. Such systems are attractive alternatives to transgenic animal models. This study established a line of porcine mammary gland epithelial cells (PMECs) from a primary culture based on the cellular morphology and mRNA levels of porcine beta-casein (CSN2). The selected PMECs were stained with the cytokeratin antibody, and were shown to express milk protein genes (CSN2, lactoferrin, and whey acidic protein). In addition, to confirm the acini structure of PMEC932-7 in 3D culture, live cells were stained with SYTO-13 dye, which binds to nucleic acid. The acini of these PMECs on matrigel were formed by the aggregation of peripheral cells and featured a hollow lumens. The system was demonstrated by testing the effects of the culture conditions to cell culture including cell density and matrigel methods of the PMECs. These results suggest that PMECs possess the genetic and structural features of mammary epithelial cells.

• Journal of mucopolysaccharidosis and rare diseases
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• v.2 no.1
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• pp.19-22
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• 2016

Purpose: Mucolipidosis type II (ML II), also known as I-cell disease is an autosomal recessive inherited disorder of lysosomal enzyme transport caused by a deficiency of the uridine diphosphate (UDP)-N-acetylglucosamine:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc-phosphotransferase). Clinical manifestations are skeletal abnormalities, mental retardation, cardiac disease, and respiratory complications. A severely and rapidity progressive clinical course leads to death before 10 years of age. Methods/Results: In this study we diagnosed three cases of prenatal ML II in two different at-risk families. We compared two procedures -biochemical analysis and molecular analysis - for the prenatal diagnosis of ML II. Both methods require an invasive procedure to obtain specimens for the diagnosis. Biochemical analysis requires obtaining cell cultures from amniotic fluid for more than two weeks, and would result in a late diagnosis at 19 to 22 weeks of gestation. Molecular genetic testing by direct sequence analysis is usually possible when mutations are confirmed in the proband. Molecular analysis has an advantage in that it can be performed during the first-trimester. Conclusion: Molecular diagnosis is a preferable method when a prompt decision is necessary.

• Journal of Microbiology
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• v.43 no.2
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• pp.172-178
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• 2005

To determine the prevalence and genotypes of $\beta$-lactamases among clones of a metagenomic library from the cold-seep sediments of Edison seamount (10,000 years old), we performed pulse-field gel electrophoresis, antibiotic susceptibility testing, pI determination, and DNA sequencing analysis. Among the 8,823 clones of the library, thirty clones produced $\beta$-lactamases and had high levels of genetic diversity. Consistent with minimum inhibitory concentration patterns, we found that five ($167\%$) of thirty clones produced an extended-spectrum $\beta$-lactamase. 837- and 259-bp fragments specific to bla$_{TEM}$ genes were amplified, as determined by banding patterns of PCR amplification with designed primers. TEM­1 was the most prevalent $\beta$-lactamase and conferred resistance to ampicillin, piperacillin, and cephalothin. TEM-116 had a spectrum that was extended to ceftazidime, cefotaxime, and aztreonam. The resistance levels conferred by the pre-antibiotic era alleles of TEM-type $\beta$-lactamases were essentially the same as the resistance levels conferred by the TEM-type alleles which had been isolated from clinically resistant strains of bacteria of the antibiotic era. Our first report on TEM-type $\beta$-lactamases of the pre-antibiotic era indicates that TEM-type $\beta$-lactamases paint a picture in which most of the diversity of the enzymes may not be the result of recent evolution, but that of ancient evolution.