• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.374-378
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• 2011

To find alternative genetic resources for D-serine dehydratase (E.C. 4.3.1.18, dsdA) mediating the deamination of D-serine into pyruvate, metagenomic libraries were screened. The chromosomal dsdA gene of a wild-type Escherichia coli W3110 strain was disrupted by inserting the tetracycline resistance gene (tet), using double-crossover, for use as a screening host. The W3110 dsdA::tet strain was not able to grow in a medium containing D-serine as a sole carbon source, whereas wild-type W3110 and the complement W3110 dsdA::tet strain containing a dsdA-expression plasmid were able to grow. After introducing metagenome libraries into the screening host, a strain containing a 40-kb DNA fragment obtained from the metagenomic souce derived from a compost was selected based on its capability to grow on the agar plate containing D-serine as a sole carbon source. For identification of the genetic resource responsible for the D-serine degrading capability, transposon-${\mu}$ was randomly inserted into the 40-kb metagenome. Two strains that had lost their D-serine degrading ability were negatively selected, and the two 6-kb contigs responsible for the D-serine degrading capability were sequenced and deposited (GenBank code: HQ829474.1 and HQ829475.1). Therefore, new alternative genetic resources for D-serine dehydratase was found from the metagenomic resource, and the corresponding ORFs are discussed.

• Molecules and Cells
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• v.38 no.12
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• pp.1086-1095
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• 2015

The psychrophilic organism Colwellia psychrerythraea strain 34H produces extracellular polysaccharide substances to tolerate cold environments. Sedoheptulose 7-phosphate isomerase (GmhA) is essential for producing $\small{D}$-glycero-$\small{D}$-mannoheptose 7-phosphate, a key mediator in the lipopolysaccharide biosynthetic pathway. We determined the crystal structure of GmhA from C. psychrerythraea strain 34H (CpsGmhA, UniProtKB code: Q47VU0) at a resolution of $2.8{\AA}$. The tetrameric structure is similar to that of homologous GmhA structures. Interestingly, one of the catalytic residues, glutamate, which has been reported to be critical for the activity of other homologous GmhA enzymes, is replaced by a glutamine residue in the CpsGmhA protein. We also found differences in the conformations of several other catalytic residues. Extensive structural and sequence analyses reveal that CpsGmhA shows high similarity to Escherichia coli DnaA initiatorassociating protein A (DiaA). Therefore, the CpsGmhA structure reported here may provide insight into the structural and functional correlations between GmhA and DiaA among specific microorganisms.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.7
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• pp.3335-3340
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• 2016

Background: Oral submucous fibrosis (OSF) is a precancerous condition with a 4 to13% malignant transformation rate. Related to the habit of areca nut chewing it is mainly prevalent in South-east Asian countries where the habit of betel quid chewing is frequently practised. On chewing, alkaloids and polyphenols are released which undergo nitrosation and give rise to N-nitrosamines which are cytotoxic agents. CYP450 is a microsomal enzyme group which metabolizes various endogenous and exogenous chemicals including those released by areca nut chewing. CYP1A1 plays a central role in metabolic activation of these xenobiotics, whereas CYP2E1 metabolizes nitrosamines and tannins. Polymorphisms in genes that code for these enzymes may alter their expression or function and may therefore affect an individuals susceptibility regarding OSF and oral cancer. The present study was therefore undertaken to investigate the association of polymorphisms in CYP1A1 m2 and CYP2E1 (RsaI/PstI) sites with risk of OSF among areca nut chewers in the Northern India population. A total of 95 histopathologically confirmed cases of OSF with history of areca nut chewing not less than 1 year and 80, age and sex matched controls without any clinical signs and symptoms of OSF with areca nut chewing habit not less than 1 year were enrolled. DNA was extracted from peripheral blood samples and polymorphisms were analyzed by PCR-RFLP method. Gene polymorphism of CYP1A1 at NcoI site was observed to be significantly higher (p = 0.016) in cases of OSF when compared to controls. Association of CYP1A1 gene polymorphism at NcoI site and the risk of OSF (Odd's Ratio = 2.275) was also observed to be significant. However, no such association was observed for the CYP2E1 gene polymorphism (Odd's Ratio = 0.815). Our results suggest that the CYP1A1 gene polymorphism at the NcoI site confers an increased risk for OSF.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
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• v.22 no.4
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• pp.287-293
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• 2011

Objectives : The region of chromosome 5p14 is known to be associated with autism spectrum disorder (ASD). The cadherin9 (CDH9) and cadherin10 (CDH10) genes are located in the region of chromosome 5p14 and reported to be associated with ASD in the Caucasian population. We performed an association study to identify if single nucleotide polymorphisms (SNPs) located on the CDH9 and CDH10 genes are associated in the Korean population. Methods : Genomic DNA was extracted from the blood of 214 patients with ASD and 258 controls. SNPs selected from two genes were genotyped using an Illumina Golden-Gate Genotyping assay with VeraCode technology. Statistical analysis was performed using SAS and Plink software. Results : All controls and ASD patients were in Hardy-Weinberg equilibrium. In the results of logistic regression analyses for the genotype model and the chi-square test for the allele model, we found that SNPs on the CDH9 and CDH10 genes were not associated with ASD. Conclusion : Our data suggests that the CDH9 and CDH10 genes are not associated with ASD in the Korean population.

• Weed & Turfgrass Science
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• v.2 no.1
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• pp.38-46
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• 2013

With increasing environmental issues from synthetic chemical herbicides, microbe-originated herbicides could be a fascinating alternative in current agriculture. We isolated Streptomyces strains that produced herbicidal active metabolite(s) against a grass weed Digitaria sanguinalis. According to the result from 16S rDNA sequence comparison with the close strains, the best isolate (Code name MS-80673) was identified as Streptomyces scopuliridis KR-001. The closest type strain was Streptomyces scopuliridis RB72 which was previously reported as a bacteriocin producer. The optimal culture condition of S. scopuliridis KR-001 was $28^{\circ}C$, pH 7.0 and culture period 4 to7 days. Both of soil and foliar application of the crude culture broth concentrate was effective on several troublesome or noxious weed species such as a Sciyos angulatus in a greenhouse and field condition. Phytotoxic symptoms of the culture broth concentrate of S. scopuliridis KR-001 by foliar application were wilting and burndown of leaves, and stems followed by discoloration and finally plant death. In crops such as rice, wheat, barley, hot pepper and tomato, growth inhibition was observed. These results suggest that the new S. scopuliridis KR-001 strain producing herbicidal metabolites may be a new bio-herbicide candidate and/or may provide a new lead molecule for a more efficient herbicide.

• Journal of Life Science
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• v.18 no.2
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• pp.234-240
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• 2008

Anthocyanin synthesis in strawberry (Fragaria x ananassa cv Maehyang) begins approximately 26 days postflowering and continued throughout fruit ripening. A set of cDNA clones encoding the anthocyanin biosynthetic enzymes were isolated from strawberry. A pair of primers were designed for polymerase chain reaction (PCR) through the comparison of the nucleotide sequences of homologous genes from diverse plants. Reverse transcriptase-PCRs were performed using cDNA synthesized from ripe fruit total RNA and the primers corresponding to each gene. Eight genes of the anthocyanin pathway were cloned and confirmed by sequencing to code for phenylalanine ammonia lyase (PAL), 4-cummarate CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone-3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), anthocyanidine synthase (ANS), UDP-glucose:flavonoid-3-O-glucosyl-transferase (UFGT). Northern analyses showed that the corresponding genes were differentially expressed during the fruit development process. All genes except PAL were predominantly expressed in fruit. Expression of PAL, DFR and ANS was detected 10 days postflowering at the early stage of fruit development, declined for a while and sharply increased 22 days postflowering then showed a peak 34 days postflowering. The other genes, however, were not expressed up to 22 or 30 days postflowering when the initial fruit ripening events occur at the time of initiation of anthocyanin accumulation. The onset of anthocyanin synthesis in ripening strawberry coincides with a coordinated induction of the anthocyanin pathway genes, suggesting the involvement of regulatory genes. We propose that at least two different regulatory mechanisms playa role in the biosynthesis of anthocyanin during color development of strawberry.