• Asian Pacific Journal of Cancer Prevention
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• v.14 no.11
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• pp.7007-7010
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• 2013

Background: In the literature, data concerning the relationship between breast cancer and HLA class II gene polymorphisms are limited, so the aim of this study was to determine if HLA-DQB1 and HLA-DRB1 MHC class-II alleles may confer susceptibility or resistance to the disease among Jordanian females. Materials and Methods: This case control study enrolled 56 Royal Hospital breast cancer patients and 60 age matched healthy controls, all of whom provided blood samples (2011-2013). A questionnaire was filled after signing a consent form and DNA was extracted, nucleic acids being amplified for assessment of HLA-DQB1 and HLA-DRB1 alleles by muliplex INNO-LiPA and allele typing carried out by reverse hybridization. Comparison of HLA-DQB1 and HLA-DRB1 allele distributions was carried out with paired t-test and chi-square statistics. Risk factors were assessed by odd ratios with 95% confidence intervals. Results: A significant negative correlation was observed between $HLADQB1^*$ 02 alleles and breast cancers (p=0.013). No significant associations were observed among $HLADQB1^*$ 03, 04, 05 and 06 or among $HLA-DRB1^*$ 01, 03, 04, 07, 08, 10, 11, 13, 14 and 15. Conclusions: $HLADQB1^*$ 02 alleles may provide positive protection against breast tumor risk among Jordanians, but not $HLADQB1^*$ 03, 04, 05 and 06 or $HLA-DRB1^*$ 01, 03, 04, 07, 08, 10, 11, 13, 14 and 15 alleles.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.11
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• pp.6961-6964
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• 2013

Human papillomavirus (HPV) is a major cause of cervical cancer. More than 100 HPV genotypes have been identified; however the distribution varies geographically and according to ethnicity. The purpose of this study was to investigate the prevalence and distribution of HPV subtypes among Northeast Thai women. Subjects included 198 cases of SCCA and 198 age-matched, healthy controls. HPV-DNA was amplified by PCR using the consensus primers GP5+/6+ system followed by reverse line blot hybridization genotyping. The prevalence of high-risk HPV infection was 21 (10.1%) and 152 (76.8%) in the controls and in the cases, respectively. High-risk HPV significantly increased the risk for cervical cancer with an OR of 42.4 (95%CI: 22.4-81.4, p<0.001) and an adjusted OR of 40.7-fold (95%CI: 21.5-76.8, p <0.001). HPV-16 was the most prevalent HPV type in the SCCA (56.2%) followed by HPV-58 (17.8%) and HPV-18 (13.6%); whereas HPV-58 (46.4%) was a prominent genotype in the controls followed by HPV-16 (39.3%) and unidentified HPV types (25.0%). These findings indicate that HPV infection remains a critical risk factor for SCCA; particularly, HPV-16, HPV-58 and HPV-18. In order to eradicate cervical cancer, sustained health education, promoted use of prophylactics and a HPV-58 vaccine should be introduced in this region.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.106-111
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• 2005

For breeding of a new rootstock for eggplant production, somatic hybrids between two species, Solanum integrifolium and S. sanitwongsei were obtained through protoplast fusion. The former species has been commonly used for rootstock for eggplant production in Japan. Eggplants on these rootstocks are more productive than ungrafted plants, but are susceptible to bacterial wilt caused Ralstonia solanacearum. While the latter species is resistant, the growth of eggplants on this rootstock is rather slow and low yield. Protoplast of both species were isolated from cotyledons, and inactivated with iodoacetamide or UV-irradiation, then fused electrically. The fused products were then cultured. Regenerated plantlets were then transplanted on soil then maintained in a green house. The plants were classified into four groups. Those in the first group showed morphological characters intermediate of the parentalspecies. The plants bore fruit with viable seeds. The plants showed a chromosome number of 2n=48, the sum of those of the parental species, and are suggested to be symmetric fusion products. While plants in the other groupswas less vigorous and showed chromosome number 2n= 68 to 72 suggesting asymmetric fusion products by genomic in situ hybridization(GISH). Isozyme pattern of shikimate dehydrogenase (SKDH; EC 1.1.1.25), isocitrate dehydrogenase (IDH; EC 1.1.1.41) and phosphoglucomutase (PGM; EC 2.7.5.1) showed that 24 regenerated plants in three groups were somatic hybrids. Analysis of random amplified polymorphic DNA (RAPD) showed that 43 S. integrifolium-specific and 57 S. sanitwongsei-specific bands were all found in 24 plants. Both somatic hybrids and its S1 plants were found to be resistant to bacterial wilt, and eggplant grafted these plants using for rootstocks were more productive than grafted mother plants. Now, S1 progenies are used for commercial eggplant production in Osaka Prefecture.

• Molecular & Cellular Toxicology
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• v.5 no.3
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• pp.216-221
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• 2009

Bisphenol A (BPA) is commonly used in the production of pharmaceutical, industrial, and housing epoxy, as well as polycarbonate plastics. Owing to its extensive use, BPA can contaminate the environment either directly or through derivatives of these products. BPA has been classified as an endocrine disruptor chemicals (EDCs), and the primary toxicity of these EDCs in males involves the induction of reproductive system abnormality. First, in order to evaluate the direct effects on the Y chromosome associated with reproduction, we evaluated Y chromosome abnormalities using a Y chromosome microdeletion detection kit. However, we detected no Yq abnormality as the result of BPA exposure. Secondly, we performed high-density oligonucleotide array-based comparative genome hybridization (CGH) to assess genomic alteration as a component of our toxicity assessment. The results of our data analysis revealed some changes in copy number. Seven observed features were gains or losses in chromosomal DNA (P-value<1.0e-5, average log2 ratio>0.2). Interestingly, 21 probes of chr7:7312289-10272836 (qA1-qA2 in cytoband) were a commonly observed amplification (P-value 3.69e-10). Another region, chr14:4551029-10397399, was also commonly amplified (P-value 2.93e-12, average of log2 ratios in segment>0.3786). These regions include many genes associated with pheromone response, transcription, and signal transduction using ArrayToKegg software. These results help us to understand the molecular mechanisms underlying the reproductive effects induced by BPA.

• Korean Journal of Veterinary Research
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• v.55 no.2
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• pp.105-110
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• 2015

A real-time PCR assay using hybridization probe (HybProbe) has been developed to detect Brucella (B.) melitensis strains. The primer and HybProbe sets were designed based on the gap gene of chromosome I with a specific single nucleotide polymorphism of B. melitensis. Specificity of the assay was confirmed by comparison to reference Brucella species and other related strains. In the melting curve analysis, B. melitensis generated a peak at $67^{\circ}C$ unlike those for other Brucella species observed at $61^{\circ}C$. Sensitivity of the assay for B. melitensis ranged from 20 ng to 200 fg of genomic DNA. The ability to identify 94 Mongolian B. melitensis isolates using the real-time PCR assay was identical to that of classical biotyping methods and differential multiplex PCR. These data showed that this new molecular technique is a simple and quick method for detecting B. melitensis, which will be important for the control and prevention of brucellosis.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.5
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• pp.2903-2908
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• 2013

Background: Various oncogenes related to cancer have been extensively studied and several polymorphisms have been found to be associated with breast cancer. The current report outlines analysis of germ-line polymorphisms for C677T, A1298C (MTHFR), Leiden, R2 (FV) and 5G/4G (PAI-1) in Turkish breast cancer patients. We studied 51 cases diagnosed with invasive ductal and operable with lymph node-positive breast cancer and 106 women as a control group. Materials and Methods: Peripheric blood-DNA samples were used for genotyping by StripAssay technique which is based on the reverse-hybridization principle and real-time PCR methods and results were compared statistically. Results: The frequency of the MTHFR gene 677T and 1298A alleles were significantly higher in cancer patients than in the healthy subjects. The T allele frequency in codon 677 was 2.3-fold and C allele frequency was 3.1-fold increased in BC when compared to the control group for the MTHFR gene. Both differences were statistically significant (OR: 2.295, CI: 1.283-4.106), p<0.006 and (OR: 3.131, CI:1.826-5.369), p<0.0001 respectively. The R2 allele frequency of FV gene was 5.1-fold increased in the current BC when compared to the control group and that difference was also statistically significant (OR: 5.133, CI: 1.299-20.28), p<0.02. Conclusions: The present data suggest that germ-line polymorphisms of C677T, C1298A for MTHFR and R2 for FV are associated in breast cancer and may be additional prognostic markers related to breast cancer survival. The results now need to be confirmed in a larger group of patients.

• Journal of Korean Neurosurgical Society
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• v.46 no.4
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• pp.385-388
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• 2009

Objective : We analyzed the methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter in World Health Organization (WHO) grade III gliomas in association with other molecular markers to evaluate their prevalence. Methods : The samples of a total of 36 newly WHO grade III glioma patients including 19 anaplastic oligodendrogliomas (AO), 7 anaplastic oligoastrocytomas (AOA), and 10 anaplastic astrocytomas (AA) were analyzed. The methylation status of the MGMT gene promoter was confirmed by methylation-specific polymerase chain reaction. The 1p/19q chromosomal deletion status and EGFR amplification were assessed by Fluorescence In-Situ Hybridization. MGMT, EGFR, EGFRvlll, and p53 expression were analyzed by immunohistochemical staining. Results : The MGMT gene promoter was methylated in 32 (88.9%) and unmethylated in 4 (11.2%) Among them, all of the AO and AOA had methylated MGMT gene promoter without exception. Significant associations between MGMT gene promoter hypermethylation and 1p/19q deletion was observed (p=0.003). Other molecular markers failed to show significant associations between MGMT gene promoter statuses. Conclusion : There was extensive epigenetic silencing of MGMT gene in high grade gliomas with oligodendroglial component. Together with frequent 1p/19q co-deletion in oligodendroglial tumors, this may add plausible explanations supporting the relative favorable prognosis in oligodendroglial tumors compared with pure astrocytic tumors.

• Fisheries and Aquatic Sciences
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• v.18 no.2
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• pp.183-193
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• 2015

Several transgenic marine medaka Oryzias dancena strains harboring a green fluorescent protein (GFP) reporter construct regulated by an endogenous ${\beta}$-actin promoter were established and their expression characteristics in relation to transgene copy numbers were examined in 21 transgene genotypes. Most of the transgenic strains displayed transgene insertion patterns typical of microinjection-mediated introduction of foreign DNA into fish embryos, characterized by the random integration of multiple transgene copies (ranging from 1 - 282 copies per cell), often accompanied by the formation of concatemer(s), as assessed by genomic Southern blot hybridization analysis and qPCR. Transgenic strains showed ubiquitous and continued temporal and spatial expression patterns of the transgenic GFP during most of their life cycle, from the embryonic stage to adulthood, enabling assessment of the expression pattern of the endogenous ${\beta}$-actin gene. However, a comparative evaluation of transgene copy numbers and expression levels showed that copy number-dependent expression, the stability of the ubiquitous distribution and expression efficiency per transgene copy varied among the transgenic strains. Fluorescence expression levels were positively correlated with absolute transgene copy numbers, whereas the expression efficiency per transgene copy was inversely related to the number of transgene integrant copies. Data from this study will guide the selection of potentially desirable transgenic strains with ubiquitous expression of a fluorescent transgene, not only in this marine medaka species but also in other related model fish species.

• Journal of Microbiology and Biotechnology
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• v.22 no.4
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• pp.448-456
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• 2012

Thirty-seven carbofuran-degrading bacteria were isolated from agricultural soils, and their genetic and phenotypic characteristics were investigated. The isolates were able to utilize carbofuran as a sole source of carbon and energy. Analysis of the 16S rRNA gene sequence indicated that the isolates were related to members of the genera Rhodococcus, Sphingomonas, and Sphingobium, including new types of carbofuran-degrading bacteria, Bosea and Microbacterium. Among the 37 isolates, 15 different chromosomal DNA patterns were obtained by polymerase chain reaction (PCR) amplification of repetitive extragenic palindromic (REP) sequences. Five of the 15 representative isolates were able to degrade carbofuran phenol, fenoxycarb, and carbaryl, in addition to carbofuran. Ten of the 15 representative isolates had 1 to 8 plasmids. Among the 10 plasmid-containing isolates, plasmid-cured strains were obtained from 5 strains. The cured strains could not degrade carbofuran and other pesticides anymore, suggesting that the carbofuran degradative genes were on the plasmid DNAs in these strains. When analyzed with PCR amplification and dot-blot hybridization using the primers targeting for the previously reported carbofuran hydrolase gene (mcd), all of the isolates did not show any positive signals, suggesting that their carbofuran hydrolase genes had no significant sequence homology with the mcd gene.

• Journal of Crop Science and Biotechnology
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• v.10 no.3
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• pp.175-184
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• 2007

Two subspecies, japonica and indica, have been reported in rice, which differ in several ecotypic traits. However, reproductive barriers in hybrid progenies between subspecies have been major obstacles in breeding programs using inter-subspecific hybridization. As the first step to elucidate the reproductive barriers, we developed subspecies-specific(SS) STS markers in this study. A total of 765 STS primers were designed through comparing DNA sequences at every $2{\sim}3$cM interval between japonica and indica rices, which are available at Web DBs such as IRGSP, NCBI, TIGR, and GRAMENE, and tested for subspecies-specificity using 15 indica and 15 japonica varieties of diverse origin. Of them, 67 STS markers were identified as SS STS markers and their subspecies-specificity scores were estimated. The SS markers were dispersed throughout the genome along chromosomes. Of them, 64 SS markers were mapped on an RIL population derived from a Dasanbyeo(indica)/TR22183(japonica) cross. Genomic inclination of RILs was evaluated based on the genotyping with different types of markers. Association test between markers and segregation distortion revealed that segregation distortion might not be the cause of generating SS markers. The SS markers will be applicable to estimate the genomic inclination of varieties or lines and to study the differentiation of indica and japonica, and ultimately to breed true hybrid rice varieties in which desirable characters from both subspecies are recombined.