• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.9
• /
• pp.4133-4136
• /
• 2015

Background: To analyze multi-source data including publications and patents, and try to draw the whole landscape of the research and development community in the field of gene therapy for breast cancer. Materials and Methods: Publications and patents were collected from the Web of science and databases of the five major patent offices of the world, respectively. Bibliometric methodologies and technology are used to investigate publications/patents, their contents and relationships. Results: A total of 2,043 items published and 947 patents from 1994 to 2013 including "gene therapy for breast cancer" were retrieved. The top five countries in global publication share were USA, China, Germany, Japan and England. On the other hand, USA, Australia, England, South Korea and Japan were the main producers of patents. The universities and enterprises of USA had the highest amount of publication and patents. Adenovirus- and retrovirus-based gene therapies and small interfering RNA (siRNA) interference therapies were the main topics both in publications and patents. Conclusions: The above results show that global research in the field of gene therapy for breast cancer is increasing and the main participants in this field are USA and Canada in North America, China, Japan and South Korea in Asia, and England, Germany, and Italy in Europe. Also, this article demonstrates the usefulness of bibliometrics to address key evaluation questions and define future areas of research.

• Journal of Microbiology and Biotechnology
• /
• v.16 no.5
• /
• pp.748-756
• /
• 2006

We propose a genome-scale clustering approach to identify whole genome relationships using the functional groups given by the Kyoto Encyclopedia of Genes and Genomes Orthology (KO) database. The metabolic capabilities of each organism were defined by the number of genes in each functional category. The archaeal, bacterial, and eukaryotic genomes were compared by simultaneously applying a two-step clustering method, comprised of a self-organizing tree algorithm followed by unsupervised hierarchical clustering. The clustering results were consistent with various phenotypic characteristics of the organisms analyzed and, additionally, showed a different aspect of the relationship between genomes that have previously been established through rRNA-based comparisons. The proposed approach to collect and cluster the metabolic functional capabilities of organisms should make it a useful tool in predicting relationships among organisms.

• Asian-Australasian Journal of Animal Sciences
• /
• v.24 no.6
• /
• pp.744-751
• /
• 2011

Meat production and quality traits in beef cattle are largely affected by genetic factors. Acetyl-Coenzyme A carboxylase-${\alpha}$ (ACACA) plays a key role in the regulation and metabolism of fatty acid biosynthesis in mammalian animals. The gene encoding ACACA enzyme was chosen as a candidate gene for carcass and meat traits. In this study, we investigated effects of single nucleotide polymorphisms (SNPs) in the ACACA gene on beef carcass and meat traits in Hanwoo (Korean cattle) populations. We have sequenced a fragment of intron I region of the Hanwoo ACACA gene and identified two SNPs. Genotyping of the two SNP markers (g.2344T>C and g.2447C>A) was carried out using PCR-SSCP analysis in 309 Hanwoo steers to evaluate their association with carcass and meat production traits. The g.2344C SNP marker showed a significant increasing effect on LW (p = 0.009) and CW (p = 0.017). Animals with the CC genotype had higher CW and LW compared with TT and TC genotypes (p<0.05). The g.2447A SNP marker was associated with higher MC (p = 0.019). Animals with the AA genotype had higher MC than animals with CC and CA genotypes (p<0.05). Although the degree of linkage disequilibrium (LD) was not strong between g.2344T>C and g.2447C>A in the LD analysis, four major haplotype classes were formed with two SNP information within the ACACA gene. We constructed haplotypes using the HaploView software package program and analyzed association between haplotypes and carcass traits. The haplotype of ACACA gene significantly affected the LW (p = 0.027), CW (p = 0.041) and MC (p = 0.036). The effect of h1 haplotype on LW and CW was larger than that of h3 haplotype. Animals with the h1 haplotype also had greater MC than did animals with h2 haplotype. Consequently, the ACACA gene could be useful as a DNA marker for meat production traits such as carcass yield and meat contents in Hanwoo.

• Asian-Australasian Journal of Animal Sciences
• /
• v.25 no.6
• /
• pp.800-805
• /
• 2012

Rice straw is an important roughage resource for ruminants in many rice-producing countries. In this study, a rice brittle mutant (BM, mutation in OsCesA4, encoding cellulose synthase) and its wild type (WT) were employed to investigate the effects of a cellulose synthase gene mutation on rice straw morphological fractions, chemical composition, stem histological structure and in situ digestibility. The morphological fractions investigation showed that BM had a higher leaf sheath proportion (43.70% vs 38.21%, p<0.01) and a lower leaf blade proportion (25.21% vs 32.14%, p<0.01) than WT. Chemical composition analysis showed that BM rice straw was significantly (p<0.01) higher in CP (crude protein), hemicellulose and acid insoluble ash (AIA) contents, but lower in dry matter (DM), acid detergent fiber (ADFom) and cellulose contents when compared to WT. No significant difference (p>0.05) was detected in neutral detergent fiber (NDFom) and ADL contents for both strains. Histological structure observation indicated that BM stems had fewer sclerenchyma cells and a thinner sclerenchyma cell wall than WT. The results of in situ digestion showed that BM had higher DM, NDFom, cellulose and hemicellulose disappearance at 24 or 48 h of incubation (p<0.05). The effective digestibility of BM rice straw DM and NDFom was greater than that of WT (31.4% vs 26.7% for DM, 29.1% vs 24.3% for NDFom, p<0.05), but the rate of digestion of the slowly digested fraction of BM rice straw DM and NDF was decreased. These results indicated that the mutation in the cellulose synthase gene could improve the nutritive value of rice straw for ruminants.

• Animal Bioscience
• /
• v.36 no.9
• /
• pp.1357-1366
• /
• 2023

Objective: This study aimed to identify the single-nucleotide polymorphisms (SNPs) in the dual-specificity phosphatase 8 (DUSP8) and insulin-like growth factor 2 (IGF2) genes and to explore their effects on inosine-5'-monophosphate (IMP), inosine, and hypoxanthine contents in Korean native chicken -red-brown line (KNC-R Line). Methods: A total sample of 284 (males, n = 127; females n = 157) and 230 (males, n = 106; females, n = 124) aged of 10 weeks old KNC-R line was used for genotyping of DUSP8 and IGF2 genes, respectively. One SNP (rs313443014 C>T) in DUSP8 gene and two SNPs (rs315806609A/G and rs313810945T/C) in IGF2 gene were used for genotyping by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and KASP methods, respectively. The Two-way analysis of variance of the R program was used to associate DUSP8 and IGF2 genotypes with nucleotide contents in KNC-R chickens. Results: The DUSP8 (rs313443014 C>T) was polymorphic in KNC-R line and showed three genotypes: CC, CT, and TT. The IGF2 gene (rs315806609A/G and rs313810945T/C) was also polymorphic and had three genotypes per SNP, including GG, AG, and AA for the SNP rs315806609A/G and genotypes: CC, CT, and TT for the SNP rs313810945T/C. Association resulted into a strong significant association (p<0.01) with IMP, inosine, and hypoxanthine. Moreover, the significant effect of sex (p<0.05) on nucleotide content was also observed. Conclusion: The SNPs in the DUSP8 and IGF2 genes might be used as genetic markers in the selection and production of chickens with highly flavored meat.

• Mycobiology
• /
• v.46 no.4
• /
• pp.361-369
• /
• 2018

The rice blast fungus, Magnaporthe oryzae, is an important pathogen of rice plants. It is well known that genes encoded in the genome have different evolutionary histories that are related to their functions. Phylostratigraphy is a method that correlates the evolutionary origin of genes with evolutionary transitions. Here we applied phylostratigraphy to partition total gene content of M. oryzae into distinct classes (phylostrata), which we designated PS1 to PS7, based on estimation of their emergence time. Genes in individual phylostrata did not show significant biases in their global distribution among seven chromosomes, but at the local level, clustering of genes belonging to the same phylostratum was observed. Our phylostrata-wide analysis of genes revealed that genes in the same phylostratum tend to be similar in many physical and functional characteristics such as gene length and structure, GC contents, codon adaptation index, and level of transcription, which correlates with biological functions in evolutionary context. We also found that a significant proportion of genes in the genome are orphans, for which no orthologs can be detected in the database. Among them, we narrowed down to seven orphan genes having transcriptional and translational evidences, and showed that one of them is implicated in asexual reproduction and virulence, suggesting ongoing evolution in this fungus through lineage-specific genes. Our results provide genomic basis for linking functions of pathogenicity factors and gene emergence time.

• Korean Journal of Plant Tissue Culture
• /
• v.28 no.1
• /
• pp.41-45
• /
• 2001

Transgenic tobacco plants were produced by the transformation of ginseng CAB gene using Agrobacterium tumefaciens LBA4404. The presence of CAB gene in the second generation of transgenic tobacco plant was confirmed by genomic PCR. The photosynthetic ability of transgenic plants was higher than normal tobacco plants and the maximum photosynthetic point of transgenic and normal tobacco plants was 500 $\mu$mol m$^{-2}$ s$^{-1}$ . The photosynthesis of C7, C11, 1, C14 cell lines was higher than normal plants at all the light intensities investigated. The photosynthesis of C2, C11, C14 cell lines in 90% dark condition was higher than normal plants. The chlorophyll contents of transgenic tobacco plants were almost same as normal plants. The % of dry weight, nicotine content, total sugar and nitrogen contents of harvested transgenic tobacco plant leaves were almost same as normal plants.

• Journal of Digital Contents Society
• /
• v.19 no.9
• /
• pp.1795-1801
• /
• 2018

Genome-Wide Association Study (GWAS) have been used to identify susceptibility genes for complex human diseases and many recent studies succeed to report common genetic factors for various diseases. Unfortunately, it is hard to understand all biological functions and mechanisms around the complex disease with GWAS only although the number of known associated genes with diseases is increased drastically because GWAS is a single locus based approach while not a gene but numerous factors may affect a disease associated pathways. PRaDA generates a combined report with genes, pathways and Gene Ontology (GO) using single nucleotide polymorphism (SNP) analysis output. The PRaDA reports not only directly associated pathways but also functionally related ones for identifying accumulated effects of low p-value SNPs. Through integrated information including indirect functional effects, user could have insights of overall disease mechanisms and markers.

• Proceedings of the Korea Contents Association Conference
• /
• 2018.05a
• /
• pp.319-320
• /
• 2018

여러 단계를 걸쳐 이루어지는 RNA-seq 분석 과정을 한 번에 처리할 수 있는 shell script 파이프라인을 구축하였다. 연구자들로 하여금 trimming, quality control, mapping, assembly, quantification 등 개별 과정을 거치지 않고, 한 줄의 커맨드 라인(command line) 만으로 유전자 발현량과 상대적 발현량 차이를 확인할 수 있는 fold change(FC) 값까지 얻을 수 있도록 하였다.

• Proceedings of the Korea Contents Association Conference
• /
• 2018.05a
• /
• pp.523-524
• /
• 2018

본 논문에서 구현한 시스템은 LMO를 생산하기 위하여 수행하는 실험과정 중 Protein coding을 변화시켜 인위적으로 변형된 생물체를 확보하기 위하여 수행하는 전처리 작업을 용이하게 수행 할 수 있도록 설계되고 구현되었다.