• Asian Pacific Journal of Cancer Prevention
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• v.15 no.14
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• pp.5861-5865
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• 2014

High risk forms of the human papilloma virus (HPV) are generally accepted as necessary causative agents for cervical cancer. Recently, a possible relation between HPV and oral squamous cell carcinoma (OSCC) has also been noticed. The present study was conducted to investigate the prevalence of HPV infection in OSCCs in Wuhan city. DNA samples were collected from fresh tissues in 200 patients with OSCC and 68 normal controls. The polymerase chain reaction and direct sequencing were used to identify the HPV types in the samples. The prevalence of HPV of all types in the OSCC group was higher than in the control group (55/200 vs 2/68, OR=11.5, 95% CI=2.6-50.2). HPV16 and HPV18 were the main types detected, with HPV6 was the only low-risk type identified. High-risk HPV types HPV16 and HPV18 are prevalent in OSCC patients and may participate in the development of OSCC with traditional risk factors, tobacco and alcohol, possibly exerting synergistic effects. The results of multinomial logistic regression showed that those who smoked, consumed alcohol and with HPV infection have the highest risk of developing oral cancer (OR=13.3, 95% CI=3.1-56.8). Adjusted for age, smoking and alcohol use, HPV infection was independently associated with oral squamous cell carcinoma.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.9
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• pp.5067-5072
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• 2013

Background: The phosphatidylinositol 3-kinase (PI3K) pathway plays a significant role in apoptosis, cellular proliferation and motility. The aim of the present study was to analyze mutations and gene expression profiles of the PI3KCA gene to determine any role in breast carcinomas. Materials and Methods: We analyzed 38 breast cancers for mutations in the two PIK3CA hotspots in exons 9 and 20 by direct sequencing of DNA obtained from biopsy samples. We have also analyzed expression of the PI3KCA gene in 38 breast carcinoma tumor and corresponding control tissue samples at the mRNA level by RT-PCR. The Fisher's exact test ($2{\times}2$ only) was performed using MedCalc software for to examine associations with mRNA levels. Results: In the present study a total of 13 cases demonstrated somatic mutations. In 9/13 cases 1633 G>A (E545K) were found in exon 9, whereas in exon 20, 4/13 cases had 3140A>G mutation. Our combined analysis showed PI3KCA mutations present in 34% of human breast cancer patients. In our study, we have also clearly found significantly higher expression in breast cancer tissues in comparison with control tissues (p=0.001). Conclusions: PIK3CA mutation is an emerging tumor marker that, in the future, might be used in the process of choosing a treatment. The detection of PI3KCA mutation might have important clinical implications for diagnosis, progression and therapy.

• Korean Journal of Organic Agriculture
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• v.20 no.3
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• pp.327-343
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• 2012

In order to develop a high cellulolytic direct-fed microorganism (DFM) for ruminant productivity improvement, this study isolated cellulolytic bacteria from the rumen of Holstein dairy cows, and compared their cellulolytic abilities via DM degradability, gas production and cellulolytic enzyme activities. Twenty six bacteria were isolated from colonies grown in Dehority's artificial (DA) medium with 2% agar and cultured in DA medium containing filter paper at $39^{\circ}C$ for 24h. 16s rDNA gene sequencing of four strains from isolated bacteria showed that H8, H20 and H25 strains identified as Ruminococcus flavefaciens, and H23 strain identified as Fibrobacter succinogenes. H20 strain had higher degradability of filter paper compared with others during the incubation. H8 (R. flavefaciens), H20 (R. flavefaciens), H23 (F. succinogenes), H25 (R. flavefaciens) and RF (R. flavefaciens sijpesteijn, ATCC 19208) were cultured in DA medium with filter paper as a single carbon source for 0, 1, 2, 3, 4 and 6 days without shaking at $39^{\circ}C$, respectively. Dry matter degradability rates of H20, H23 and H25 were relatively higher than those of H8 and RF since 2 d incubation. The cumulative gas production of isolated cellulolytic bacteria increased with incubation time. At every incubation time, the gas production was highest in H20 strain. The activities of carboxymethylcellulase (CMCase) and Avicelase in the culture supernatant were significantly higher in H20 strain compared with others at every incubation time (p<0.05). Therefore, although further researches are required, the present results suggest that H20 strain could be a candidate of DFM in animal feed due to high cellulolytic ability.

• BMB Reports
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• v.42 no.8
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• pp.529-534
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• 2009

Marbling score (MS) is the major trait that affects carcass quality in beef cattle. In this study, we investigated the association between genetic polymorphisms of the adipose differentiation-related protein gene (ADFP) and carcass traits in Korean cattle (also known as Hanwoo). Using direct DNA sequencing in 24 unrelated Korean cattle, 25 novel polymorphisms were identified within all exons and their flanking regions of ADFP, including the promoter region (1.5 kb). Among them, 21 polymorphic sites were selected for genotyping in the beef cattle (n = 425). Statistical analyses revealed that one promoter polymorphism (c.-56-18A > G) was associated with MS (P = 0.009). The 'A' allele of c.-56-18A > G exerted a lowering effect on MS, e.g., the lowest MS was found in 'A/A' (MS = 2.09 ${\pm}$ 1.23), intermediate in 'A/G' (MS = 2.11 ${\pm}$ 1.31), and the highest in 'G/G' (MS = 2.47 ${\pm}$ 1.47). Our findings suggest that these polymorphisms in ADFP might be important genetic factors involved in carcass quality in beef cattle.

• Genomics & Informatics
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• v.7 no.4
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• pp.195-202
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• 2009

BIRC5 (Survivin) belongs to the inhibitor of apoptosis gene family. The BIRC5 protein inhibits caspases and consequently blocks apoptosis. Thus, BIRC5 contributes to the progression of cancer allowing for continued cell proliferation and survival. In this study, we identified eight sequence variants of BIRC5 through direct DNA sequencing. Among the eight single nucleotide polymorphisms (SNPs), six common variants with frequencies higher than 0.05 were selected for larger-scale genotyping (n=1,066). Results of the study did not show any association between the promoter region polymorphisms and the clearance of hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) occurrence. This is in line with a previous study in which polymorphisms in the promoter region does not influence the function of BIRC5. Initially, we were able to detect a signal with the ＋9194A>G, which disappeared after multiple corrections but led to a change in amino acid. Similarly, we were also able to detect an association signal between two haplotypes (haplotype-2 and haplotype-5) on the onset age of HCC and/or HCC occurrence, but the signals also disappeared after multiple corrections. As a result, we concluded that there was no association between BIRC5 polymorphisms and the clearance HBV infection and/or HCC occurrence. However, our results might useful to future studies.

• Korean Journal of Veterinary Research
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• v.60 no.1
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• pp.1-7
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• 2020

We investigated the genotypes of Leptospira spp. detected in symptomatic dogs in Thailand. During April to December 2012, 6 out of 41 client-owned dogs were diagnosed with leptospirosis based on polymerase chain reaction tests. All of the infected dogs showed clinical symptoms related to leptospirosis. Direct genotyping of the causative agent of the canine leptospirosis was conducted from the archival DNA samples extracted from urine or blood of those 6 infected dogs. Sequencing of the partial 16S rRNA and lipL32 genes from all samples identified Leptospira (L.) interrogans as the infecting species. Multilocus sequence typing tests were successful for 2 out of 6 samples. The sequence type (ST) was identified as ST50 for both samples where the profile corresponded to L. interrogans species and Bataviae serogroup. The presence of this genotype of Leptospira has never been reported in Thailand. Thus, our findings showed the existence of ST50 L. interrogans serogroup Bataviae and the ability to cause leptospirosis in dogs in Thailand.

• Journal of Microbiology
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• v.43 no.4
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• pp.325-330
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• 2005

Rhodococcus sp. strain YU6 was isolated from soil for the ability to grow on o-xylene as the sole carbon and energy source. Unlike most other o-xylene-degrading bacteria, YU6 is able to grow on p-xylene. Numerous growth substrate range experiments, in addition to the ring-cleavage enzyme assay data, suggest that YU6 initially metabolizes 0- and p-xylene by direct aromatic ring oxidation. This leads to the formation of dimethylcatechols, which was further degraded largely through meta-cleavage path-way. The gene encoding meta-cleavage dioxygenase enzyme was PCR cloned from genomic YU6 DNA using previously known gene sequence data from the o-xylene-degrading Rhodococcus sp. strain DK17. Subsequent sequencing of the 918-bp PCR product revealed a $98\%$ identity to the gene, encoding meth-ylcatechol 2,3-dioxygenase from DK17. PFGE analysis followed by Southern hybridization with the catechol 2,3-dioxygenase gene demonstrated that the gene is located on an approximately 560-kb megaplasmid, designated pJY J1

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.12
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• pp.5147-5152
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• 2016

Background: Investigations of methods for detection of mutations have uncovered major weaknesses of direct sequencing and pyrosequencing, with their high costs and low sensitivity in screening for both known and unknown mutations. High resolution melting (HRM) analysis is an alternative tool for the rapid detection of mutations. Here we describe the accuracy of HRM in screening for KRAS and BRAF mutations in metastatic colorectal cancer (mCRCs) samples. Materials and Methods: A total of 1000 mCRC patients in Mehr Hospital, Tehran, Iran, from Feb 2008 to May 2012 were examined for KRAS mutations and 242 of them were selected for further assessment of BRAF mutations by HRM analysis. In order to calculate the sensitivity and specificity, HRM results were checked by pyrosequencing as the golden standard and Dxs Therascreen as a further method. Results: In the total of 1,000 participants, there were 664 (66.4%) with wild type and 336 (33.6%) with mutant codons 12 and/or 13 of the KRAS gene. Among 242 samples randomly checked for the BRAF gene, all were wild type by HRM. Pyrosequencing and Dxs Therascreen results were in line with those of the HRM. In this regard, the sensitivity and specificity of HRM were evaluated as 100%. Conclusion: The findings suggest that the HRM, in comparison with DNA sequencing, is a more appropriate method for precise scanning of KRAS and BRAF mutations. It is also possible to state that HRM may be an attractive technique for the detection of known or unknown somatic mutations in other genes.

• Journal of Microbiology
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• v.44 no.4
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• pp.423-431
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• 2006

Among 53 Acinetobacter baumannii isolates collected in 2004, nine imipenem-resistant isolates were obtained from clinical specimens taken from patients hospitalized in Busan, Korea. Nine carbapenemase-producing isolates were further investigated in order to determine the mechanisms underlying resistance. These isolates were then analyzed via antibiotic susceptibility testing, microbiological tests of carbapenemase activity, pI determination, transconjugation test, enterobacterial repetitive consensus (ERIC)-PCR, and DNA sequencing. One outbreak involved seven cases of infection by A. baumannii producing OXA-23 ${\beta}-lactamase$, and was found to have been caused by a single ERIC-PCR clone. During the study period, the other outbreak involved two cases of infection by A. baumannii producing IMP-1 ${\beta}-lactamase$. The two clones, one from each of the outbreaks, were characterized via a modified cloverleaf synergy test and an EDTA-disk synergy test. The isoelectric focusing of the crude bacterial extracts detected nitrocefin-positive bands with pI values of 6.65 (OXA-23) and 9.0 (IMP-1). The PCR amplification and characterization of the amplicons via direct sequencing showed that the clonal isolates harbored $bla_{IMP-1}$ or $bla_{oxA-23}$ determinants. The two clones were characterized by a multidrug resistance phenotype that remained unaltered throughout the outbreak. This resistance encompassed penicillins, extended-spectrum cephalosporins, carbapenems, monobactams, and aminoglycosides. These results appear to show that the imipenem resistance observed among nine Korean A. baumannii isolates could be attributed to the spread of an IMP-lor OXA-23-producing clone. Our microbiological test of carbapenemase activity is a simple method for the screening of clinical isolates producing class D carbapenemase and/or class B $metallo-{\beta}-lactamase$, in order both to determine their clinical impact and to prevent further spread.

• Journal of Microbiology and Biotechnology
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• v.16 no.9
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• pp.1377-1383
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• 2006

Among 46 Acinetobacter baumannii isolates collected in 2004, two imipenem-resistant isolates were obtained from clinical specimens taken from patients hospitalized in Busan, Republic of Korea. Two carbapenemase-producing isolates were further investigated to determine the mechanism of resistance. These isolates were analyzed by antibiotic susceptibility testing, microbiological tests of carbapenemase activity, determination of pI, transconjugation test, enterobacterial repetitive consensus (ERIC)-PCR, and DNA sequencing. Two cases of infection by A. baumannii producing the IMP-1 ${\beta}$-lactamase were detected. The isolates were characterized by a modified cloverleaf synergy test and EDTA-disk synergy test. Isoelectric focusing of crude bacterial extracts revealed nitrocefin-positive bands with a pI value of 9.0. PCR amplification and characterization of the amplicons by direct sequencing indicated that the isolates carried a $bla_{IMP-l}$ determinant. The isolates were characterized by a multidrug resistance phenotype, including penicillins, extended-spectrum cephalosporins, carbapenems, and aminoglycosides. These results indicate that the observed imipenem resistance of two Korean A. baumannii isolates was due to the spread of an IMP-1-producing clone. Our microbiological test of carbapenemase activity is simple to screen class B metallo-${\beta}$-lactamase-producing clinical isolates to determine their clinical impact and to prevent further spread. This study shows that the $bla_{IMP-l}$ resistance determinant, which is emerging in Korea, may become an emerging therapeutic problem, since clinicians are advised not to use extended-spectrum cephalosporins, imipenem, and aminoglycosides. This observation emphasizes the importance of having effective control measures in Asian hospitals, such as early detection of colonized patients, isolation procedures, and a judicious use of antibiotics.