• Microbiology and Biotechnology Letters
• /
• v.46 no.2
• /
• pp.135-144
• /
• 2018

The rapid increase in number and diversity of Extended Spectrum ${\beta}$-Lactamases (ESBLs) producing Enterobacteriaceae in natural aquatic environment is a major health concern worldwide. This study investigates abundance and distribution of ESBL producing multidrug resistant Enterobacteriaceae and molecular characterization of ESBL genes among isolates from highly polluted stretch of river Yamuna, India. Water samples were collected from ten different sites distributed across Delhi stretch of river Yamuna, during 2014-15. A total of 506 non duplicate Enterobacteriaceae isolates were obtained. Phenotypic detection of ESBL production and antibiotic sensitivity for 15 different antibiotics were performed according to CLSI guidelines (Clinical and Laboratory Standard Institute, 2015). A subset of ESBL positive Enterobacteriaceae isolates were identified by 16S rRNA gene and screened for ESBL genes, such as $bla_{CTX-M}$, $bla_{TEM}$ and $bla_{OXA}$. Out of 506 non-duplicate bacterial isolates obtained, 175 (34.58%) were positive for ESBL production. Susceptibility pattern for fifteen antibiotics used in this study revealed higher resistance to cefazolin, rifampicin and ampicillin. A high proportion (76.57%) of ESBL positive isolates showed multidrug resistance phenotype, with MAR index of 0.39 at Buddha Vihar and Old Delhi Railway bridge sampling site. Identification and PCR based characterization of ESBL genes revealed the prevalence of $bla_{CTX-M}$ and $bla_{TEM}$ genes to be 88.33% and 61.66%, respectively. Co-occurrence of $bla_{CTX-M}$ and $bla_{TEM}$ genes was detected in 58.33% of the resistant bacteria. The $bla_{OXA}$ gene was not detected in any isolates. This study highlights deteriorating condition of urban aquatic environment due to rising level of ESBL producing Enterobacteriaceae with multidrug resistance phenotype.

• Toxicological Research
• /
• v.22 no.2
• /
• pp.95-102
• /
• 2006

Exposure to soluble nickel compound produces toxic effects on immune system, but the mechanism of action remains to be elucidated. Differential gene expression was studied to understand the potential molecular mechanism responsible for acute toxicity induced by nickel acetate in spleen cells. We exposed mouse spleen cells to nickel acetate with a nontoxic dose ($40{\mu}M$) and then extracted total RNA at 6 h and 12 h after exposure. The RNA was hybridized onto 10K mouse oligonucleotide microarrays, and data were analyzed using GeneSpring 7.1. Nickel had a modest effects on expression of many genes, in the range of 1.3-3 fold. The expression profile showed time-dependent changes in expression levels of differentially expressed genes, including some important genes related to cell cycle, apoptosis and DNA repair. In hierarchical cluster analysis of duplicate experiments, 111 genes were screened out. Out of these, 44 genes showing time- dependent up-regulation (>1.5 fold) and 38 genes showing down-regulation (>1.5 fold) at all time points were chosen for further analysis. The change in the expression of three genes (GPX1, GADD45B and FAIM) after nickel treatment was validated using RT-PCR. As a rule, a number of genes appear to be coordinately regulated between cell survival and cell death from nickel toxicity. In conclusion, changes in the gene profile in the spleen after nickel treatment are complex and genes with diverse functions are modulated. These findings will be contributed to the understanding of the complicated biological effects of nickel.

• Korean Journal of Plant Resources
• /
• v.15 no.3
• /
• pp.298-304
• /
• 2002

The inheritance of resistance to gall mite(Eriophys macrodonis) in boxthorn cultivars was studied with plants infected in open field. Segregation of the F$_1$ generation from crosses between resistant cultivars(Japan 1 and China 1) and susceptible line(CL42-56) hits a 3 resistant : 1 susceptible ratio, and the segregation ratio was 15 : 1 in cross between Japan 1 and China 1. It is concluded that gall mite resistance seemed to be controlled by two duplicate genes(El and E2), such that E1e1E2e2 symbolize the genotypes of China 1 and Japan 1. However, F, generation from Chungyanggugiza and CL42-56 cross did not showed clear segregation pattern but continuous variation was observed against gall mite resistance when resistance was determined on the basis of the percentage of galled leaves. Results indicated that the inheritance of resistance in Chungyanggugiza may be polygenic and complex. Also, Japan 1 and China 1 has a strong potential as a source of gall mite resistance, and Chungyanggugiza showing less resistance still has a valuable source.

• Korean Journal of Clinical Laboratory Science
• /
• v.43 no.2
• /
• pp.68-74
• /
• 2011

Pseudomonas aeruginosa is an aerobic, Gram-negative, glucose-nonfermenting bacterium, which has emerged as a serious opportunistic pathogen. Recently, outbreaks of carbapenem resistant P. aeruginosa give rise to significant therapeutic challenges for treating nosocomial infections. The genes of metallo-${\beta}$-lactamase (MBL), a powerful carbapenemase, are carried as a part of the mobile gene cassettes inserted into integrons playing an important role in rapid dissemination of antibiotic resistance genes among bacterial isolates. In this study, we investigated the prevalence of integron in imipenem resistant P. aeruginosa isolates. A total of 61 consecutive, non-duplicate, and imipenem resistant P. aeruginosa strains were isolated from a university hospital in the Chungcheong province of Korea. We employed repetitive extragenic palindromic sequence-based PCR (rep-PCR) method for the selection of clonally different P. aerusinosa strains. PCR and DNA sequencing were conducted for the detection of integrons. Twenty-one clonally different P. aeruginosa strains were isolated. Only one (P28) of the strains harbored $bla_{VIM-2}$ that was found as gene cassettes in class 1 integrons. Four of 21 carbapenem resistant P. aeruginosa strains harbored class 1 integron containing aminoglycoside resistance determinant. All of the integrons detected in the study contained more than one resistance gene cassette, which can mediate resistance to multiple antibiotics. To prevent further spreading of the multi-drug resistant P. aeruginosa, conseguent monitoring and clinical polices are required.

• The Plant Pathology Journal
• /
• v.32 no.2
• /
• pp.95-101
• /
• 2016

Inheritance of resistance to Fusarium wilt (FW) disease caused by Fusarium udum was investigated in pigeonpea using four different long duration FW resistant genotypes viz., BDN-2004-1, BDN-2001-9, BWR-133 and IPA-234. Based on the $F_2$ segregation pattern, FW resistance has been reported to be governed by one dominant gene in BDN-2004-1 and BDN-2001-9, two duplicate dominant genes in BWR-133 and two dominant complimentary genes in resistance source IPA-234. Further, the efficacy of six simple sequence repeat (SSR) markers namely, ASSR-1, ASSR-23, ASSR-148, ASSR-229, ASSR-363 and ASSR-366 reported to be associated with FW resistance were also tested and concluded that markers ASSR-1, ASSR-23, ASSR-148 will be used for screening of parental genotypes in pigeonpea FW resistance breeding programs. The information on genetics of FW resistance generated from this study would be used, to introgress FW resistance into susceptible but highly adopted cultivars through marker-assisted backcross breeding and in conventional breeding programs.

• Plant Resources
• /
• v.7 no.2
• /
• pp.116-122
• /
• 2004

We tried to isolating a noble gene from cucumber library with heterogeneouse RNA probe labeled DIG of Arabidopsis PIN3 gene. Two kinds of RNA probes which had no significant homology each others, were designed from the 5'- and 3'- prime nucleotides of the AtPIN3 gene. In the first and second screenings of the cDNA library of cucumber with the probes, two positive clones were identified with specific duplicate signals. However, we isolated cDNA fragments homologous with putative nucleases from Nicotiana, Arabidopsis, Cordialis, and Oryza sativa, there was no significant homology with any other PIN family genes.

• Proceedings of the Korean Statistical Society Conference
• /
• 2002.05a
• /
• pp.79-83
• /
• 2002

Since its introduction in 1995 by Schena et al. cDNA microarrays have been established as a potential tool for high-throughput analysis which allows the global monitoring of expression levels for thousands of genes simultaneously. One of the characteristics of the cDNA microarray data is that there is inherent noise even after the removal of systematic effects in the experiment. Therefore, replication is crucial to the microarray experiment. The assessment of reproducibility among replicates, however, has drawn little attention. Reproducibility may be assessed with several different endpoints along the process of data reduction of the microarray data. We define the reproducibility to be the degree with which replicate arrays duplicate each other. The aim of this note is to develop a novel measure of reproducibility among replicates in the cDNA microarray experiment based on the unprocessed data. Suppose we have p genes and n replicates in a microarray experiment. We first develop a measure of reproducibility between two replicates and generalize this concept for a measure of reproducibility of one replicate against the remaining n-1 replicates. We used the rank of the outcome variable and employed the concept of a measure of tracking in the blood pressure literature. We applied the reproducibility measure to two sets of microarray experiments in which one experiment was performed in a more homogeneous environment, resulting in validation of this novel method. The operational interpretation of this measure is clearer than Pearson's correlation coefficient which might be used as a crude measure of reproducibility of two replicates.

• Journal of Microbiology
• /
• v.45 no.4
• /
• pp.286-290
• /
• 2007

The purpose of this study was to investigate the prevalence and genetic mechanisms of erythromycin resistance in staphylococci. A total of 102 erythromycin resistant non-duplicate clinical isolates of staphylococci [78. coagulase negative stapylococci (CNS), 24 Staphylococcus aureus] were collected between October 2003 and August 2004 in Istanbul Faculty of Medicine in Turkey. The majority of the isolates were from blood and urine specimens. Antimicrobial susceptibilities were determined by the agar dilution procedure and the resistance phenotypes by the double disk induction test. A multiplex PCR was performed, using primers specific for erm(A), erm(B), erm(C), and msrA genes.. Among the 78 CNS isolates, 57.8% expressed the $MLS_{B}-constitutive$, 20.6% the $MLS_{B}-inducible$, and 21.6% the $MS_B$ phenotypes. By PCR, 78.2% of these isolates harbored the erm(C) gene, 8.9% erm(A), 6.4% erm(B), and 11.5% msrA genes. In S. aureus, the constitutive $MLS_B$ (58.3 %) was more common than the inducible phenotype (20.8%). erm(A) was detected in 50% and erm(C) in 62.5% of the isolates, while 37.5% contained both erm(A) and erm(C). erm(C)-associated macrolide resistance was the most prevalent in CNS, while ermC) and erm(A, C) was the most prevalent in S. aureus.

• Journal of Crop Science and Biotechnology
• /
• v.10 no.4
• /
• pp.237-242
• /
• 2007

Genome duplication(i.e. polyploidy) is a common phenomenon in the evolution of plants. The objective of this study was to achieve a comprehensive understanding of genome duplication for SNP discovery by Thymine/Adenine(TA) cloning for confirmation. Primer pairs were designed from 793 EST contigs expressed in the roots of a supernodulating soybean mutant and screened between 'Pureunkong' and 'Jinpumkong 2' by direct sequencing. Almost 27% of the primer sets were failed to obtain sequence data due to multiple bands on agarose gel or poor quality sequence data from a single band. TA cloning was able to identify duplicate genes and the paralogous sequences were coincident with the nonspecific peaks in direct sequencing. Our study confirmed that heterogeneous products by the co-amplification of a gene family member were the main cause of obtaining multiple bands or poor quality sequence data in direct sequencing. Counts of amplified bands on agarose gel and peaks of sequencing trace suggested that almost 27% of nonrepetitive soybean sequences were present in as many as four copies with an average of 2.33 duplications per segment. Copy numbers would be underestimated because of the presence of long intron between primer binding sites or mutation on priming site. Also, the copy numbers were not accurately estimated due to deletion or tandem duplication in the entire soybean genome.

• Tuberculosis and Respiratory Diseases
• /
• v.62 no.5
• /
• pp.406-416
• /
• 2007

Background: Single nucleotide polymorphisms (SNPs), which consist of a substitution of a single nucleotide pair, are the most abundant form of genetic variations occurring with a frequency of approximately 1 per 1000 base pairs. SNPs by themselves do not cause disease but can predispose humans to disease, modify the extent or severity of the disease or influence the drug response and treatment efficacy. Single nucleotide polymorphisms (SNPs), particularly those within the regulatory regions of the genes often influence the expression levels and can modify the disease. Studies examining the associations between SNP and the disease outcome have provided valuable insight into the disease etiology and potential therapeutic intervention. Traditionally, the genotyping of SNPs has been carried out using polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP), which is a low throughput technique not amenable for use in large-scale SNP studies. Recently, TaqMan real-time PCR chemistry was adapted for use in allelic discrimination assays. This study validated the accuracy and utility of real-time PCR technology for SNPs genotyping Methods: The SNPs in promoter sequence (-37 and -524) of lung cancer suppressor gene, RRM1 (ribonucleotide reductase M1 subunit) with the genomic DNA samples of 89 subjects were genotyped using both real-time PCR and PCR-RFLP. Results: The discordance rates were 2.2% (2 mismatches) in -37 and 16.3% (15 mismatches) in -524. Auto-direct sequencing of all the mismatched samples(17 cases) were in accord with the genotypes read by real-time PCR. In addition, 138 genomic DNAs were genotyped using real-time PCR in a duplicate manner (two separated assays). Ninety-eight percent of the samples showed concordance between the two assays. Conclusion: Real-time PCR allelic discrimination assays are amenable to high-throughput genotyping and overcome many of the problematic features associated with PCR-RFLP.