• Mycobiology
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• 제46권4호
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• pp.361-369
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• 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.

• International journal of advanced smart convergence
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• 제8권1호
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• pp.1-8
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• 2019

Coronaviruses are known respiratory pathogens. In the past, most human coronaviruses were thought to cause mild symptoms such as cold. However recently, as seen in the Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS), infectious diseases with severe pulmonary disease and respiratory symptoms are caused by coronaviruses, making research on coronaviruses become important. Considering previous studies, we constructed 'HCoV-IMDB (Human Corona Virus Immune Database)' to systematically provide genetic information on human coronavirus and host immune information, which can be used to analyze the interaction between human coronavirus and host immune proteins. The 'HCoV-IMDB' constructed in the study can be used to search for genetic information on human coronavirus and host immune protein and to download data. A BLAST search specific to the human coronavirus, one of the database functions, can be used to infer genetic information and evolutionary relationship about the query sequence.

• 한국정보관리학회:학술대회논문집
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• 한국정보관리학회 2000년도 제7회 학술대회 논문집
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• pp.129-132
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• 2000

GIS(Geographic Information System) tool has been applied to determine a spatial difference of weed population density in paddy field and it has introduced to rice yield difference among counties as well as to rice blast in Korea. There was highly difference between sampling sites in terms of spatial analysis which may imply to be able to apply this tool for the precesion agriculture in the 21 century.

• BMB Reports
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• 제39권4호
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• pp.441-447
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• 2006

Abuse of drugs can elicit compulsive drug seeking behaviors upon repeated administration, and ultimately leads to the phenomenon of addiction. We developed a procedure for the standardization of microarray gene expression data of rat brain in drug addiction and stored them in a single integrated database system, focusing on more effective data processing and interpretation. Another characteristic of the present database is that it has a systematic flexibility for statistical analysis and linking with other databases. Basically, we adopt an intelligent SQL querying system, as the foundation of our DB, in order to set up an interactive module which can automatically read the raw gene expression data in the standardized format. We maximize the usability of this DB, helping users study significant gene expression and identify biological function of the genes through integrated up-to-date gene information such as GO annotation and metabolic pathway. For collecting the latest information of selected gene from the database, we also set up the local BLAST search engine and non-redundant sequence database updated by NCBI server on a daily basis. We find that the present database is a useful query interface and data-mining tool, specifically for finding out the genes related to drug addiction. We apply this system to the identification and characterization of methamphetamine-induced genes' behavior in rat brain.

• Asian-Australasian Journal of Animal Sciences
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• 제26권8호
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• pp.1144-1151
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• 2013

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

• 한국균학회지
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• 제40권3호
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• pp.141-144
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• 2012

자연환경에서 분포하고 있는 효모의 mycoflora를 확인하고 궁극적으로 이들을 고부가가치의 산업에 응용하기 위한 연구의 일환으로 대전과 인근 충남지역 일부의 야생화들을 채집하여 효모들을 분리, 동정하였다. 대전지역 야생화 42점에서 32종의 효모들을 54균주 분리하였고 이들 중 Cryptococcus 속균과 Phodotonula 속균 등이 우점균이었으며 Metschnikowia 속균과 같이 희귀 효모들을 20여종 분리하였다. 대전 인근의 충남 금산군과 논산군 일부지역의 야생화 28점에서 모두 18종의 효모들을 26균주 분리하였다. 이들 균 중에서 Candida 속균과 Pseudozyma 속균 등이 우점균으로 분리되었다.

• Journal of Life Science
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• 제11권1호
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• pp.39-41
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• 2001

Cytohesin family has been thought to participate in inside-outside signaling linking growth factor receptor stimulation of PI 3-kinase to cell adhesion and stimulate nucleotide exchange of ARF through its Sec7 domain. The genomic structure of the cytohesin family was analyzed by BLAST search using cDNA and genomic DNA sequences from the GeneBank database. The cytohesin-2 was encoded by 12 exons. while the cytohesin-4 was encoded by 13 exons. The Sec7 and PH domains were not encoded by separate exons. In an analysis of retroviral integration, those two families did not contain any retroviral elements in introns or exons. The phylogenetic tree calculated by the neighbor-joining method suggests that the cytohesin-1 family was closely related to cytohesin-3 (ARNO3) family. These date could be of great use in further studies for resolving the exact function and evolution of the cytohesin family.

• Parasites, Hosts and Diseases
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• 제43권4호
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• pp.149-156
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• 2005

Four hundred and sixty five randomly selected clones from a cDNA library of Blattella germanica were partially sequenced and searched using BLAST as a means of analyzing the transcribed sequences of its genome. A total of 363 expressed sequence tags (ESTs) were generated from 465 clones after editing and trimming the vector and ambiguous sequences. About $42\%$ (154/363) of these clones showed significant homology with other data base registered genes. These new B. germanica genes constituted a broad range of transcripts distributed among ribosomal proteins, energy metabolism, allergens, proteases, protease inhibitors, enzymes, translation, cell signaling path-ways, and proteins of unknown function. Eighty clones were not well-matched by database searches, and these rep-resent new B. germanica-specific ESTs. Some genes which drew our attention are discussed. The information obtained increases our understanding of the B. germanica genome.

• 화약ㆍ발파
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• 제25권1호
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• pp.67-77
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• 2007

본 연구에서는 NATM 터널 시공사이클에서 필수적으로 수행되는 천공작업 시 획득할 수 있는 정보를 통해 굴착 대상 암반의 특성을 평가하는 방안에 대해 고찰하였다. 활용 가능한 천공데이터는 천공속도, 피트압, 토크 등이 있으며, 이러한 인자들과 암반 특성들과의 상관관계를 규명하고자 하며 이러한 결과를 토대로 향후 정량적 발파설계를 위한 가이드라인을 제안하고자 하였다.

• 한국버섯학회지
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• 제2권3호
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• pp.145-148
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• 2004

이 연구는 약용버섯 번데기 동충하초로부터 특이적 자실체 형성 유전자를 선별하기 위하여 수행하였다. cDNA는 버섯의 분화 4단계 균사체, 원기, 미성숙 자실체, 성숙한 자실체로부터 분리한 각각의 total RNA를 이용하여 합성하였다. 특이적으로 발현된 유전자의 선별은 cDNA와 랜덤한 primer set을 이용한 DD-PCR에 의해 수행되었고, pGEM 클로닝 벡터를 이용하여 6개의 partial 유전자 서열을 확인하였다. 6개의 DD-PCR product는 보고된 유전자와 유사도를 확인하기 위해 NCBI BLAST search를 사용하여 GenBank에서 비교하였고, 6개의 유전자는 보고되지 않은 유전자임을 확인하였다.