• Asian Pacific Journal of Cancer Prevention
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• v.13 no.11
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• pp.5391-5397
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• 2012

Background: Neuroblastoma (NB), like most human cancers, is characterized by genomic instability, manifested at the chromosomal level as allelic gain, loss or rearrangement. Genetics methods, as well as conventional and molecular cytogenetics may provide valuable clues for the identification of target loci and successful search for major genes in neuroblastoma. We aimed to investigate AURKA and MYCN gene rearrangements and the chromosomal aberrations (CAs) to determine the prognosis of neuroblastoma. Methods: We performed cytogenetic analysis by G-banding in 25 cases [11 girls (44%) and 14 boys (66%)] and in 25 controls. Fluorescence in situ hybridization (FISH) with AURKA and MYCN gene probes was also used on interphase nuclei to screen for alterations. Results: Some 18.4% of patient cells exhibited CAs., with a significant difference between patient and control groups in the frequencies (P<0.0001). Some 72% of the cells had structural aberrations, and only 28% had numerical chnages in patients. Structural aberrations consisted of deletions, translocations, breaks and fragility in various chromosomes, 84% and 52% of the patients having deletions and translocations, respectively. Among these expressed CAs, there was a higher frequency at 1q21, 1q32, 2q21, 2q31, 2p24, 4q31, 9q11, 9q22, 13q14, 14q11.2, 14q24, and 15q22 in patients. 32% of the patients had chromosome breaks, most frequently in chromosomes 1, 2, 3, 4, 5, 8, 9, 11, 12, 19 and X. The number of cells with breaks and the genomic damage frequencies were higher in patients (p<0.001). Aneuploidies in chromosomes X, 22, 3, 17 and 18 were most frequently observed. Numerical chromosome abnormalities were distinctive in 10.7% of sex chromosomes. Fragile sites were observed in 16% of our patients. Conclusion: Our data confirmed that there is a close correlation between amplification of the two genes, amplification of MYCN possibly contributing significantly to the oncogenic properties of AURKA. The high frequencies of chromosomal aberrations and amplifications of AURKA and MYCN genes indicate prognostic value in children with neuroblastomas and may point to contributing factors in their development.

• Journal of Microbiology and Biotechnology
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• v.12 no.2
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• pp.318-326
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• 2002

The pathogenic marine bacterium Vibrio vulnificus is the causative agent of food-borne diseases such as life-threatening septicemia. To better understand this organism's strategies to survive osmotic stress, a mutant that was more sensitive to high osmolarity was screened from a library of mutants constructed by a random transposon mutagenesis. By a transposon-tagging method, putAP genes encoding a proline dehydrogenase and a proline permease were identified and cloned from V. vulnificus. The amino acid sequences deduced from nucleotide sequences of putAP from V. vulnificus were 38 to $59\%$ similar to those of PutA and PutP reported from other Enterobacteriaceae. Functions of putAP genes were assessed by the construction of mutants, whose putAP genes were inactivated by allelic exchanges. When proline as the sole carbon or nitrogen source was used, the putA mutant was not able to grow to the substantial level, revealing the proline dehydrogenase is the only enzyme for metabolic conversion of proline into other amino acids. Although the growth rate of the putP mutant on proline as the sole carbon or nitrogen source was significantly reduced, the mutant still grew. This indicated that at least one more proline permease is produced by V. vulnificus. The putP mutant decreased approximately $2-log_10$ CFU/ml after a hyperosmotic challenge, while the parent strain decreased approximately $l-log_10$ CFU/ml. This result suggests that the gene product of putP contributes to the osmotic tolerance of V. vulnificus.

• IMMUNE NETWORK
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• v.2 no.2
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• pp.86-90
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• 2002

Background: Host genetic polymorphisms in the HIV-1 co-receptor CCR5 and CCR2b and SDF-1, ligand for co-receptor CXCR4, have been known to be associated with the resistance of HIV infection and/or the delayed disease progression in HIV-infected patients. Methods: We examined the frequencies of SDF1-3'A and CCR2b-64I alleles of 354 Koreans including 100 HIV-uninfected persons, 13 discordant spouses of HIV-infected persons, and 241 HIV-infected persons. The genotyping assays of SDF1 and CCR2b genes were carried out by polymerase chain reaction-restriction fragment length polymorphism. Results: The frequencies of CCR2b-64I and SDF1-3'A alleles in Koreans were very high compared with Caucasians and blacks. Observed frequencies of CCR2b-64I and SDF1-3'A allelic variants were 25.1% and 28.7%, respectively. The frequency of the CCR2b-64I allele in Koreans was 2~4 times higher than those of other ethnic groups with the exception of Asian. The frequencies of CCR2b-64I and SDF1-3'A genotypes did not show the significant difference between HIV-infected and uninfected Koreans. However, the prevalence of CCR2b-64I genotype of the LTNP group was about two times higher than that of the remainder group (P< 0.05). Four (45%) out of 9 LTNPs (long-term nonprogressors) showed having the SDF1-3'A allele and 7 (78%) out of 9 LTNPs carried the CCR2b-64I allele. 3 (33%) out of 9 LTNPs had both SDF1-3'A and CCR2b-64I alleles. But none of 5 RPs (rapid progressors) appeared to have both SDF1-3'A and CCR2b-64I alleles. Conclusion: The different genetic backgrounds in study populations may affect the disease progression and the AIDS epidemic in each country. Further studies need to define whether high frequencies of CCR2b-64I and SDF1-3'A allelic variants may affect the HIV disease progression.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.8
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• pp.993-999
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• 2010

Serum lysozyme gene is one of the important genes influencing the immune system as its product can cause lysis of bacterial cell wall by cleaving the peptidoglycan layer. The present investigation on the serum lysozyme gene of Indian riverine buffalo was undertaken with the objectives to identify and characterize single nucleotide polymorphic patterns by PCR-SSCP method as well as to study the effect of different genotypes on serum lysozyme activity and somatic cell count. A total of 280 animals comprising four different famous bubaline breeds (Murrah, Mehsana, Surti and Bhadawari), spread over six different farms across the country were used for this study. A 276 bp (partial intron 2, complete exon 3 and partial intron 3) fragment of lysozyme gene was screened for polymorphism using the SSCP technique. Four genotypes namely AA, AB, BC and AC were observed, out of which BC genotype was found to be the most frequent. Among these three alleles, C allele (0.38) was most prevalent in these populations. Various SSCP allelic variants were cloned for sequencing and sequences were submitted to NCBI Genbank. From the alignment of the nucleotide sequences of various allelic variants, it was found that there were differences in 12 positions among the alleles, out of which maximum variation (at 8 places) was found in the intronic region. The allele A was closer to allele-C than allele-B. Allele B was phylogenetically equidistant from both of the other alleles. Mean lysozyme activity determined in serum samples of different animals of Murrah buffalo was $27.35{\pm}2.42\;{\mu}g$ per ml of serum, whereas the mean somatic cell count was $1.25{\pm}0.13{\times}10^5$ cells per ml of milk. The SSCP pattern-wise effects of various genotypes on lysozyme activity and SCC were analyzed. Although the mean values were apparently different in various genotypes, these differences were statistically non-significant. It can be concluded that the riverine buffaloes are sufficiently polymorphic with respect to serum lysozyme gene. The absence of AA genotype in Bhadawari breed of buffalo can be considered as a marker for breed characterization. The difference of four nucleotides in exon-3 indicates high selection pressure on the gene.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8227-8233
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• 2016

Background: To investigate polymorphisms in heat shock proteins A1B and A1L (HOM) and associated risk of oesophageal carcinoma in Northeast India. Materials and Methods: The study includes oesophageal cancer (ECA) patients attending general outpatient department (OPD) and endoscopic unit of Gauhati Medical College. Patients were diagnosed based on endoscopic and histopathological findings. Genomic DNA was typed for HSPA1B1267 and HSPA1L2437 SNPs using the polymerase chain reaction with restriction fragment length polymorphisms. Results: A total of 78 cases and 100 age-sex matched healthy controls were included in the study with a male: female ratio of 5:3 and a mean age of $61.4{\pm}8.5years$. Clinico-pathological evaluation showed 84% had squamous cell carcinoma and 16% were adenocarcinoma. Dysphagia grades 4 (43.5%) and 5 (37.1%) were observed by endoscopic and hispathological evaluation. The frequency of genomic variation of A1B from wild type A/A to heterozygous A/G and mutant G/G showed a positive association [chi sq=19.9, p=<0.05] and the allelic frequency also showed a significant correlation [chi sq=10.3, with cases vs. controls, OR=0.32, $p{\leq}0.05$]. The genomic variation of A1L from wild T/T to heterozygous T/C and mutant C/C were found positively associated [chi sq=7.02, p<0.05] with development of ECA. While analyzing the allelic frequency, there was no significant association [chi sq=3.19, OR=0.49, p=0.07]. Among all the risk factors, betel quid [OR=9.79, Chi square=35.0, p<0.05], tobacco [OR=2.95, chi square=10.6, p<0.05], smoking [OR=3.23, chi square=10.1, p<0.05] demonstrated significant differences between consumers vs. non consumers regarding EC development. Alcohol did not show any significant association [OR=1.34, chi square=0.69, p=0.4] independently. Conclusions: It can be concluded that the present study provides marked evidence that polymorphisms of HSP70 A1B and HSP70 A1L genes are associated with the development of ECA in a population in Northeast India, A1B having a stronger influence. Betel quid consumption was found to be a highly significant risk factor, followed by smoking and tobacco chewing. Although alcohol was not a potent risk factor independently, alcohol consumption along with tobacco, smoking and betel nut was found to contribute to development of ECA.

• Journal of Life Science
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• v.16 no.7 s.80
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• pp.1112-1118
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• 2006

Bordetella bronchiseptica, the agent of swine atrophic rhinitis and kennel cough in dogs, is a mucosal pathogen and produces the hydroxamate type alcaligin siderophore under iron-limited conditions. Genes involved in alcaligin siderophore biosynthesis are contained in an alcABCDE operon. In order to provide direct evidence for the role of AlcA in alcaligin biosynthesis, we needed a B. bronchiseptica mutant carrying alcA gene deletion. A 0.6 kb alcA 5'-flanking and 0.7kb 3'-flanking DNA fragments were PCR amplified with the use of pCP1.11 as a template DNA. The 5'-and 3'-flanking DNA fragments were joined in a suicide plasmid, resulting in a recombinant suicide plasmid pDM1. After introduction of pDM1 into B. bronchiseptica by conjugation, the allelic exchange technique was performed and a B. bronchiseptica alcA deletion mutant, named B. bronchiseptica H1, was obtained. The mutant strain produced reduced amount of siderophore as expected. When a plasmid containing complete alcA gene was transformed back into the mutant, the complemented mutant recovered ability of siderophore production. These results indicated that AlcA is one of essential components for the alcaligin siderophore biosynthesis. The mutant strains obtained in this study will be used in the further studies for the biochemical function of AlcA.

• Journal of Life Science
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• v.34 no.2
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• pp.79-85
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• 2024

SlyA is known as a transcriptional regulator that regulates the expression of hemolysin (HlyE) in E. coli, a member of the Enterobacteriaceae family such as Salmonella. However, Salmonella has the slyA gene but lacks the hlyE gene. Then, because we were curious about the role of SlyA in Salmonella, we constructed and explored a mutant strain with a deletion of the slyA gene. S. Typhimurium CK295 (ΔslyA) was constructed using an allelic exchange approach. In a comparative analysis between the wild-type and the CK295 strain, no significant differences were observed in growth characteristics, motility, total protein analyses, and secreted protein analyses. However, the CK295 strain exhibited slightly reduced biofilm formation compared to the wild-type. Interestingly, as a result of comparing the survival ability in macrophages, the mutant strain showed a 60% decrease in survival ability compared to the wild-type. To evaluate toxicity in mice, mortality was measured after oral administration to 6-week-old BALB/c mice. As a result, the LD₅₀ value of the CK295 (ΔslyA) was more than 100 times higher than that of wild-type S. Typhimurium 𝜒3339 in BALB/c. In conclusion, SlyA is presumed to regulate the expression of genes encoding virulence factors involved in the in vivo survival of Salmonella.

• The Journal of the Korean Society for Microbiology
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• v.34 no.6
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• pp.519-532
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• 1999

Helicobacter pylori is a causative agent of type B gastritis and plays a central role in the pathogenesis of gastroduodenal ulcer and gastric cancer. To elucidate the host-parasite relationship of the H. pylori infection on the basis of molecular biology, we tried to evaluate the genomic diversity of H. pylori. An ordered overlapping bacterial artificial chromosome (BAC) library of a Korean isolate, H. pylori 51 was constructed to set up a genomic map. A circular physical map was constructed by aligning ApaI, NotI and SfiI-digested chromosomal DNA. When the physical map of H. pylori 51 was compared to that of unrelated strain, H. pylori 26695, completely different restriction patterns were shown. Fifteen known genes were mapped on the chromosome of H. pylori 51 and the genetic map was compared with those of strain 26695 and J99, of which the entire genomic sequences were reported. There were some variability in the gene location as well as gene order among three strains. For further analysis on the genomic diversity of H. pylori, when comparing the genomic structure of 150 H. pylori Korean isolates with one another, genomic macrodiversity of H. pylori was characterized by several features: whether or not susceptible to restriction digestion of the chromsome, variation in chromosomal restriction fingerprint and/or high frequency of gene rearrangement. We also examined the extent of allelic variation in nucleotide or deduced amino acid sequences at the individual gene level. fucT, cagA and vacA were confirmed to carry regions of high variation in nucleotide sequence among strains. The plasticity zone and strain-specific genes of H. pylori 51 were analyzed and compared with the former two genomic sequences. It should be noted that the H. pylori 51-specific sequences were dispersed on the chromosome, not congregated in the plasticity zone unlike J99- or 26695-specific genes, suggesting the high frequency of gene rearrangement in H. pylori genome. The genome of H. pylori 51 shows differences in the overall genomic organization, gene order, and even in the nucleotide sequences among the H. pylori strains, which are far greater than the differences reported on the genomic diversity of H. pylori.

• Parasites, Hosts and Diseases
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• v.47 no.2
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• pp.145-151
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• 2009

This study examined the association of cytokine gene polymorph isms with intrahepatic bile duct wall fibrosis in human clonorchiasis. A total of 240 residents in Heilongjiang, China underwent ultrasonography, blood sampling, and stool examination. Single nucleotide polymorphism (SNP) sites for $IFN-{\gamma}$ (+874 T/A), IL-10 (-1,082 G/A, -819 C/T, -592 C/A), $TNF-{\alpha}$ (-308 G/A), and $TGF-{\beta}1$ (codon 10 T/C, codon 25 G/C) genes were observed with the TaqMan allelic discrimination assay. No significant correlation was observed between individual cytokine gene polymorphisms and intrahepatic duct dilatation (IHDD). Among individuals with clonorchiasis of moderate intensity, the incidence of IHDD was high in those with $IFN-{\gamma}$ intermediate-producing genotype, +874AT (80.0%, P=0.177), and in those with $TNF-{\alpha}$ low-producing genotype, -308GG (63.0%, P=0.148). According to the combination of $IFN-{\gamma}$ and $TNF-{\alpha}$ genotypes, the risks for IHDD could be stratified into high (intermediate-producing $IFN-{\gamma}$ and low producing $TNF-{\alpha}$), moderate, and low (low-producing $IFN-{\gamma}$ and high producing $TNF-{\alpha}$) risk groups. The incidence of IHDD was significantly different among these groups (P=0.022): 88.9% (odds ratio, OR=24.0) in high, 56.5% (OR=3.9) in moderate, and 25.0% (OR=1) in low risk groups. SNP of $IFN-{\gamma}$ and $TNF-{\alpha}$ genes may contribute to the modulation of fibrosis in the intrahepatic bile duct wall in clonorchiasis patients.

• Journal of Microbiology and Biotechnology
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• v.15 no.3
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• pp.616-625
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• 2005

It is likely that maltose could provide a good substrate for the bacteria in the intestine, when the pathogenic bacteria invade and colonize in human gut. For better understanding of this organism's maltose metabolism, a mutant that was not able to grow with maltose as a sole carbon source was screened from a library of mutants constructed by a random transposon mutagenesis. By a transposon-tagging method, malPQ genes encoding a maltodextrin phosphorylase and a 4-${\alpha}$-glucanotransferase, were identified and cloned from Vibrio vulnificus. The deduced amino acid sequences of malPQ from V. vulnificus were 48 to $91\%$ similar to those of MalP and MalQ reported from other Enterobacteriaceae. Functions of malPQ genes were assessed by the construction of mutants whose malPQ genes were inactivated by allelic exchanges. When maltose was used as the sole carbon source, neither malP nor malQ mutant was able to grow to a substantial level, revealing that the MalP and MalQ are the only enzymes for metabolic utilization of maltose. The malQ mutant exhibited decreased adherence toward intestinal epithelial cells in vitro, but there was no difference in the $LD_{50}s$ of the wild-type and the malQ mutant in mice. Therefore, it appears that MalQ is less important in the pathogenesis of V. vulnificus than would have been predicted by considering maltose as a most common sugar in the intestine, but not completely dispensable for virulence in mice.