• Clinical and Experimental Reproductive Medicine
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• 제38권3호
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• pp.126-134
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• 2011

Preimplantation genetic diagnosis (PGD) is gradually widely used in prevention of gene diseases and chromosomal abnormalities. Much improvement has been achieved in biopsy technique and molecular diagnosis. Blastocyst biopsy can increase diagnostic accuracy and reduce allele dropout. It is cost-effective and currently plays an important role. Whole genome amplification permits subsequent individual detection of multiple gene loci and screening all 23 pairs of chromosomes. For PGD of chromosomal translocation, fluorescence $in-situ$ hybridization (FISH) is traditionally used, but with technical difficulty. Array comparative genomic hybridization (CGH) can detect translocation and 23 pairs of chromosomes that may replace FISH. Single nucleotide polymorphisms array with haplotyping can further distinguish between normal chromosomes and balanced translocation. PGD may shorten time to conceive and reduce miscarriage for patients with chromosomal translocation. PGD has a potential value for mitochondrial diseases. Preimplantation genetic haplotyping has been applied for unknown mutation sites of single gene disease. Preimplantation genetic screening (PGS) using limited FISH probes in the cleavage-stage embryo did not increase live birth rates for patients with advanced maternal age, unexplained recurrent abortions, and repeated implantation failure. Polar body and blastocyst biopsy may circumvent the problem of mosaicism. PGS using blastocyst biopsy and array CGH is encouraging and merit further studies. Cryopreservation of biopsied blastocysts instead of fresh transfer permits sufficient time for transportation and genetic analysis. Cryopreservation of embryos may avoid ovarian hyperstimulation syndrome and possible suboptimal endometrium.

• Journal of Gastric Cancer
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• 제12권2호
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• pp.73-80
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• 2012

Purpose: The specific aim of this study is to unravel a DNA copy number alterations, and to search for novel genes that are associated with the development of Korean gastric cancer. Materials and Methods: We investigated a DNA copy number changes in 23 gastric adenocarcinomas by array-comparative genomic hybridization and quantitative real-time polymerase chain reaction analyses. Besides, the expression of UQCRFS1, which shows amplification in array-CGH, was examined in 186 gastric cancer tissues by an immunohistochemistry, and in 9 gastric cancer cell lines, as well as 24 gastric cancer tissues by immunoblotting. Results: We found common gains at 48 different loci, and a common loss at 19 different loci. Amplification of UQCRFS1 gene at 19q12 was found in 5 (21.7%) of the 23 gastric cancers in an array-comparative genomic hybridization and DNA copy number were increased in 5 (20.0%) out of the 25 gastric cancer in quantitative real-time polymerase chain reaction. In immunohistochemistry, the overexpression of the protein was detected in 105 (56.5%) out of the 186 gastric cancer tissues. Statistically, there was no significant relationship between the overexpression of UQCRFS1 and clinicopathologic parameters (P>0.05). In parallel, the overexpression of UQCRFS1 protein was confirmed in 6 (66.7%) of the 9 gastric cancer cell lines, and 12 (50.0%) of the 24 gastric cancer tissues by immunoblotting. Conclusions: These results suggest that the overexpression of UQCRFS1 gene may contribute to the development and/or progression of gastric cancer, and further supported that mitochondrial change may serve as a potential cancer biomarker.

• Journal of Microbiology and Biotechnology
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• 제29권5호
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• pp.794-808
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• 2019

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.

• Journal of Microbiology and Biotechnology
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• 제32권11호
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• pp.1485-1495
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• 2022

The development of a yeast strain capable of fermenting mixed sugars efficiently is crucial for producing biofuels and value-added materials from cellulosic biomass. Previously, a mutant Pichia stipitis YN14 strain capable of co-fermenting xylose and cellobiose was developed through evolutionary engineering of the wild-type P. stipitis CBS6054 strain, which was incapable of co-fermenting xylose and cellobiose. In this study, through genomic and transcriptomic analyses, we sought to investigate the reasons for the improved sugar metabolic performance of the mutant YN14 strain in comparison with the parental CBS6054 strain. Unfortunately, comparative whole-genome sequencing (WGS) showed no mutation in any of the genes involved in the cellobiose metabolism between the two strains. However, comparative RNA sequencing (RNA-seq) revealed that the YN14 strain had 101.2 times and 5.9 times higher expression levels of HXT2.3 and BGL2 genes involved in cellobiose metabolism, and 6.9 times and 75.9 times lower expression levels of COX17 and SOD2.2 genes involved in respiration, respectively, compared with the CBS6054 strain. This may explain how the YN14 strain enhanced cellobiose metabolic performance and shifted the direction of cellobiose metabolic flux from respiration to fermentation in the presence of cellobiose compared with the CBS6054 strain.

• Current Research on Agriculture and Life Sciences
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• 제32권1호
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• pp.43-52
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• 2014

Reactive oxygen and nitrogen species (ROS and RNS, respectively) are messengers that carry signals to alter the redox state in order to activate plant responses and other physiological processes, such as differentiation, aging, senescence, and pathogen defense. Quite a large number of genes are involved in this signaling and lead to oxidative stress in plants. Although the role of ROS/RNS during stress conditions is well documented, a comprehensive list of genes and comparative study of these genes has not yet been completed. Accordingly, the in silico identification of oxidative stress-related genes was performed for soybeans and Arabidopsis. These genes were also studied in relation to multiple domain prediction. The presence of domains like dehydogenase and ATPase suggests that these genes are involved in various metabolic processes, as well as the transportation of ions under optimal environmental conditions. In addition to a sequence analysis, a phylogenetic analysis was also performed to identify orthologous pairs among the soybean and Arabidopsis oxidative stress-related genes based on neighbor joining. This study was also conducted with the objective of further understanding the complex molecular signaling mechanism in plants under various stress conditions.

• Journal of Microbiology and Biotechnology
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• 제16권11호
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• pp.1773-1777
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• 2006

We evaluated the usefulness of DNA microarray as a comparative genomics tool, and tested the validity of the cutoff values for defining absent genes in test genomes. Three genome-sequenced E. coli strains (K-12, EDL933, and CFT073) were subjected to comparative genomic hybridization with DNA microarrays covering almost all ORFs of the reference strain K-12, and the microarray results were compared with the results obtained from in silico analyses of genome sequences. For defining the K-12 ORFs absent in test genomes (reference strain-specific ORFs), we applied and evaluated the cutoff level of -1. The average sequence similarity between ORFs, to which corresponding spots showed a log-ratio of>-1, was $96.9{\pm}4.8$. The numbers of spots showing a log-ratio of <-1 (P<0.05, t-test) were 90 (2.5%) and 417 (10.6%) for the EDL933 genome and the CFT073 genome, respectively. Frequency of false negatives (FN) was ca. 0.2, and the cutoff level of -1.3 was required to achieve the FN of 0.1. The average sequence similarity of the false negative ORFs was $77.8{\pm}14.8$, indicating that the majority of the false negatives were caused by highly divergent genes. We concluded that the microarray is useful for identifying missing or divergent ORFs in closely related prokaryotic genomes.

• Molecules and Cells
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• 제43권8호
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• pp.728-738
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• 2020

Time and cost-effective production of next-generation sequencing data has enabled the performance of population-scale comparative and evolutionary studies for various species, which are essential for obtaining the comprehensive insight into molecular mechanisms underlying species- or breed-specific traits. In this study, the evolutionary and functional analysis of Korean native pig (KNP) was performed using single nucleotide polymorphism (SNP) data by comparative and population genomic approaches with six different mammalian species and five pig breeds. We examined the evolutionary history of KNP SNPs, and the specific genes of KNP based on the uniqueness of non-synonymous SNPs among the used species and pig breeds. We discovered the evolutionary trajectory of KNP SNPs within the used mammalian species as well as pig breeds. We also found olfaction-associated functions that have been characterized and diversified during evolution, and quantitative trait loci associated with the unique traits of KNP. Our study provides new insight into the evolution of KNP and serves as a good example for a better understanding of domestic animals in terms of evolution and domestication using the combined approaches of comparative and population genomics.

• 대한임상검사과학회지
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• 제47권4호
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• pp.209-215
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• 2015

대장암은 우리나라에서 많이 발병하는 4대 암의 하나로써, 경제적인 발전을 통한 생활양식의 서구화 등으로 인해 매년 증가 추세에 있다. 따라서 대장암의 다양한 진단방법이 요구되고 있으며, 새로운 진단방법으로 가능한 Comparative Genomic Hybridization 실험을 하였다. 실험결과 Deletion은 5q (10%), 10q (17%), 17p (40%), 18p (23%), 18q (47%), 22q (23%)이며, 가장 많은 빈도로 관찰된 것은 18q, 17p, 22q로서 18q에서 47% (14/30)가, 17p에서 40% (12/30)가, 22q에서 23% (7/30)가 관찰되었다. Amplification은 염색체 6pq (10%), 7p (17%), 7q (33%), 8q (13%), 9pq (10%), 12q (17%), 13q (37%), 20p (23%), 20q (57%)부분에서 증폭이 보여졌다. 가장 많은 빈도로 관찰된 것은 20q, 13q, 7q로서 20q에서 57% (17/30)가, 13q에서 37% (11/30)가, 7q에서 33% (10/30)가 관찰되었다. 대장암의 위치에 따른 유전자 변이 양상은 우측 대장암이 평균 3.1개(증폭 1.7개, 결실 1.4개)인데 반해, 직장암은 평균 6.3개(증폭 3.7개, 결실 2.6개)로서 높았다(p<0.001). 림프절 전이에 따른 유전자 변이 양상은 전이가 없는 군에서는 평균 3.5개(증폭 2.2개, 결실 1.3개)인데 반해, 림프절 전이가 있는 군은 평균 6.3개(증폭 3.5개, 결실 2.8개)로서 높았다(p<0.003). 병기별에 따른 유전자 변이 양상은 I~II병기에서는 평균 3.5개(증폭 2.1개, 결실 1.4개)인데 반해, III~IV병기에서는 평균 6.0개(증폭 3.4개, 결실 2.6개)로서 높았다(p<0.006). 조직학적 분류에 따른 비교와 혈청 CEA 증가군에 대한 비교는 큰 차이가 없었다.

• Journal of Plant Biotechnology
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• 제5권4호
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• pp.193-195
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• 2003

A major goal of agricultural biotechnology is the discovery of genes or genetic loci which are associated with characteristics beneficial to crop production. This knowledge of genetic loci may then be applied to improve crop breeding. Agriculturally important genes may also benefit crop production through transgenic technologies. Recent years have seen an application of high throughput technologies to agricultural biotechnology leading to the production of large amounts of genomic data. The challenge today is the effective structuring of this data to permit researchers to search, filter and importantly, make robust associations within a wide variety of datasets. At the Plant Biotechnology Centre, Primary Industries Research Victoria in Melbourne, Australia, we have developed a series of tools and computational pipelines to assist in the processing and structuring of genomic data to aid its application to agricultural biotechnology resear-ch. These tools include a sequence database, ASTRA, for the processing and annotation of expressed sequence tag data. Tools have also been developed for the discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular markers from large sequence datasets. Application of these tools to Brassica research has assisted in the production of genetic and comparative physical maps as well as candidate gene discovery for a range of agronomically important traits.