• Journal of Microbiology and Biotechnology
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• 제26권11호
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• pp.1863-1870
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• 2016

Antimicrobial peptides/proteins (AMPs) are present in all types of organisms, from microbes and plants to vertebrates and invertebrates such as insects. The grasshopper Oxya chinensis sinuosa is an insect species that is widely consumed around the world for its broad medicinal value. However, the lack of available genetic information for this species is an obstacle to understanding the full potential of its AMPs. Analysis of the O. chinensis sinuosa transcriptome and expression profile is essential for extending the available genetic information resources. In this study, we determined the whole-body transcriptome of O. chinensis sinuosa and analyzed the potential AMPs induced by bacterial immunization. A high-throughput RNA-Seq approach generated 94,348 contigs and 66,555 unigenes. Of these unigenes, 36,032 (54.14%) matched known proteins in the NCBI database in a BLAST search. Functional analysis demonstrated that 38,219 unigenes were clustered into 5,499 gene ontology terms. In addition, 26 cDNAs encoding novel AMPs were identified by an in silico approach using public databases. Our transcriptome dataset and AMP profile greatly improve our understanding of O. chinensis sinuosa genetics and provide a huge number of gene sequences for further study, including genes of known importance and genes of unknown function.

• Journal of Ginseng Research
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• 제34권1호
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• pp.17-22
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• 2010

Sesquiterpenes are found naturally in plants and insects as defensive agents or pheromones. They are produced in the cytosolic acetate/mevalonate pathway for isoprenoid biosynthesis. The inducible sesquiterpene synthases (STS), which are responsible for the transformation of the precursor farnesyl diphosphate, appear to generate very few olefinic products that are converted to biologically active metabolites. In this study, we isolated the STS gene from Panax ginseng C.A. Meyer, designated PgSTS, and investigated the correlation between its expression and various abiotic stresses using real-time PCR. PgSTS cDNA was observed to be 1,883 nucleotides long with an open reading frame of 1,707 bp, encoding a protein of 568 amino acids. The molecular mass of the mature protein was determined to be 65.5 kDa, with a predicted isoelectric point of 5.98. A GenBank BlastX search revealed the deduced amino acid sequence of PgSTS to be homologous to STS from other plants, with the highest similarity to an STS from Lycopersicon hirsutum (55% identity, 51% similarity). Real-time PCR analysis showed that different abiotic stresses triggered significant induction of PgSTS expression at different time points.

• 한국환경과학회지
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• 제15권10호
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• pp.983-988
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• 2006

The textile remains have been affected largely by environmental factors including microorganisms because they were composed of organic compounds to be easy to damage. So, we selected 8 strains of the 131 isolated strains from museum environments and textile remains by high pretense activity, and identified them for measuring the antibacterial activity of Gingko biloba extracts. They were identified Genus Arthrobacter spp. 3 strains (Arthrobacter nicotiannae A12, Arthrobacter sp B12, Arthrobacter oxidans B13), Cenus Bacillus spp. 2 strains (Bacillus licheniformis D9, Bacillus cereus D33), Genus Pseudomonas spp. 2 strains (Pseudomonas putida A24, Pseufomonas fluorescene C21) and a Genus Staphylococcus sp. 1 strain (Staphylococcus pasteuri D3) as closest strains through the blast search of NCBI. Though antibacterial activity of the extracts of Gingko biloba leaves as MIC was lower than that of other pharmaceutical antibiotics. However the extracts was crude extracts, the extracts might have good antibacterial against most of the isolates from museum. Especially, the antifungal activity of Gingko biloba is known previously, the extracts of Gingko biloba leaves has possibility of usage as a good natural material for conservation of remains.

• Genomics & Informatics
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• 제3권4호
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• pp.133-141
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• 2005

Most of the endogenous retroviral genes integrated into the primate genome after the split of New World monkeys in the Oligocene era, approximately 33 million years ago. Because they can change the structure of adjacent genes and move between and within chromosomes they may play important roles in evolutionas well as in many kinds of disease and the creation of genetic polymorphism. Comparative analysis of HERVs (human endogenous retroviruses) and their LTR (long terminal repeat) elements in the primate genomes will help us to understand the possible impact of HERV elements in the evolution and phylogeny of primates. For example, HERV-K LTR and SINE-R elements have been identified that have been subject to recent change in the course of primate evolution. They are specific elements to the human genome and could be related to biological function. The HERV-M element is related to the superfamily of HERV-K and is integrated into the periphilin gene as the truncated form, 5'LTR-gag-pol-3'LTR. PCR and RT-PCR approaches indicated that the insertion of various retrotransposable elements in a common ancestor genome may make different transcript variants in different primate species. Examination of the HERV-W elementrevealed that env fragments were detected on human chromosomes 1, 3-7, 12, 14, 17, 20, and X, whilst the pol fragments were detected on human chromosomes 2-8, 10-15, 20, 21, X, and Y. Bioinformatic blast search showed that almost full-length of the HERV-W family was identified on human chromosomes 1-8, 11-15, 17, 18, 21, and X. Expression analysis of HERV-W genes (gag, pol, and env) in human tissues by RT-PCR indicated that gag and pol were expressed in specific tissues, whilst env was constituitively expressed in all tissues examined. DNA sequence based phylogenetic analysis indicated that the gag, pol and env genes have evolved independently during primate evolution. It will thus be of considerable interest to expand the current HERV gene information of various primates and disease tissues.

• International Journal of Industrial Entomology and Biomaterials
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• 제27권2호
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• pp.219-227
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• 2013

The purpose of this study was to quickly and effectively identify the Nosema disease of bumblebees in Gangwon Province in Korea. Bumblebees are crucial pollinators of various crops, and microsporidia are the critical pathogens of these hosts. When bumblebees are infected with Nosema bombi, their abdomens can become distended. Paralyzed and infected workers often become sluggish and die early. We have identified the morphology of the microsporidium by light and electron microscopy, and found it to have fairly small oval spores, as has been described previously in many other articles. For the specific and sensitive diagnosis of the microsporidian parasite N. bombi in bumblebees, we have developed an improved method of the polymerase chain reaction (PCR) for expeditious diagnosis. Two pairs of primers were tested on N. bombi and the related microsporidia Nosema apis and Nosema sp., both of which infect Bombus ignitus and Bombus hypocrita sapporoensis. Furthermore, we have verified and analyzed the 16SrRNA sequence data of N. bombi in bumblebees by using the Basic Local Alignment Search Tool (BLAST) server at the National Center for Biotechnology Information.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2006년도 International Meeting of the Microbiological Society of Korea
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• pp.29-31
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• 2006

In a previous report, we showed that enzyme $IIA^{Glc}(EIIA^{Glc}$ of Escherichia coli phosphotransferase system (PTS) interacts with and regulates activity of FrsA (fermentation/respiration switch protein). A BLAST search revealed that orthologs of FrsA exist only in some Gram-negative bacteria such as E. coli, Salmonella typhimurium, Shigella flexneri, Yersinia pestis, Vibrio cholerae, Vibrio vulnificus, Vibrio parahemeolyticus, and Photorhabdus luminescens and all of these species are facultative anaerobes belonging to the ${\gamma}-proteobacterial$ group, and most of them are highly pathogenic. Ligand-fishing experiments using $EIIA^{Glc}$ of Vibrio vulnificus ($vEIIA^{Glc}$) as bait revealed that $vEIIA^{Glc}$ also interacts with vFrsA in a phosphorylation state-dependent manner. The frsA mutant of Vibrio vulnificus showed remarkably reduced cytotoxicity to HeLa cells and reduced lethality to mice compared to wild type. Comparison of extracellular proteomes between the mutant and wild type indicated that hemolysin was not produced in the frsA mutant. Characterization of another protein interacting with $vEIIA^{Glc}$ will be discussed.

• Genomics & Informatics
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• 제3권3호
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• pp.86-93
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• 2005

Human brain EST data provide important clues for our understanding of the molecular biology associated with the function of the normal brain and the molecular pathophysiology with brain disorders. To systematically and efficiently study the function and disorders of the human brain, 45,773 human brain ESTs were collected from 27 human brain cDNA libraries, which were constructed from normal brains and brain disorders such as brain tumors, Parkinson's disease (PO) and epilepsy. An analysis of 45,773 human brain ESTs using our EST analysis pipeline resulted in 38,396 high-quality ESTs and 35,906 ESTs, which were coalesced into 8,246 unique gene clusters, showing a significant similarity to known genes in the human RefSeq, human mRNAs and UniGene database. In addition, among 8,246 gene clusters, 4,287 genes ($52\%$) were found to contain full-length cONA clones. To facilitate the extraction of useful information in collected these human brain ESTs, we developed a user-friendly interface system, the Korea Brain Unigene Database (KBUD). The KBUD web interface allows access to our human brain data through three major search modes, the BioCarta pathway, keywords and BLAST searches. Each result when viewed in KBUD offers comprehensive information concerning the analyzed human brain ESTs provided by our data as well as data linked to various other publiC databases. The user-friendly developed KBUD, the first world-wide web interface for human brain EST data with ESTs of human brain disorders as well as normal brains, will be a helpful system for developing a better understanding of the underlying mechanisms of the normal brain well as brain disorders. The KBUD system is freely accessible at http://kugi.kribb.re.kr/KU/cgi -bin/brain. pI.

• Environmental Analysis Health and Toxicology
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• 제26권
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• pp.10.1-10.7
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• 2011

Objects: Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used as a model organism in aquatic ecotoxicological studies, and considering the potential of C. riparius larvae as a bio-monitoring species, little is known about its genome sequences. This study reports the results of an Expressed Sequence Tags (ESTs) sequencing project conducted on C. riparius larvae using 454 pyrosequencing. Method: To gain a better understanding of C. riparius transcriptome, we generated ESTs database of C.ripairus using pyrosequencing method. Results: Sequencing runs, using normalized cDNA collections from fourth instar larvae, yielded 20,020 expressed sequence tags, which were assembled into 8,565 contigs and 11,455 singletons. Sequence analysis was performed by BlastX search against the National Center for Biotechnology Information (NCBI) nucleotide (nr) and uniprot protein database. Based on the gene ontology classifications, 24% (E-value${\leq}1^{-5}$) of the sequences had known gene functions, 24% had unknown functions and 52% of sequences did not match any known sequences in the existing database. Sequence comparison revealed 81% of the genes have homologous genes among other insects belonging to the order Diptera providing tools for comparative genome analyses. Targeted searches using these annotations identified genes associated with essential metabolic pathways, signaling pathways, detoxification of toxic metabolites and stress response genes of ecotoxicological interest. Conclusions: The results obtained from this study would eventually make ecotoxicogenomics possible in a truly environmentally relevant species, such as, C. riparius.

• Journal of the Korean Wood Science and Technology
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• 제33권1호통권129호
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• pp.1-6
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• 2005

본 연구는 국내에 서식하는 일본흰개미(Reticulitermes speratus)의 생리적 특성에 관한 기초연구로서 흰개미의 커뮤니케이션 수단인 페로몬을 후각수용기로 이동시키는 odorant-binding proteins (OBPs)의 발현 양상을 조사하기 위해서 수행되었다. 경남 진주에서 채집된 일개미와 병정개미로부터 더듬이와 다리를 각각 떼어낸 후 OBP가 존재하는지 확인하기 위하여 RT-PCR을 수행하였다. 일개미의 경우 OBP-1의 발현은 더듬이와 다리에서 모두 관찰되었으며, OBP-2와 OBP-3의 발현은 오직 더듬이에서만 관찰할 수 있었다. 병정개미의 경우 OBP-1의 발현은 일개미에서와 마찬가지로 더듬이와 다리 모두에서 관찰할 수 있었으나, OBP-2가 관찰되지 않았으며, 일개미의 더듬이에서만 관찰되었던 OBP-3의 발현을 병정개미에서는 더듬이와 다리 모두에서 볼 수 있었다. 일개미와 병정개미에서 OBP 발현 양상의 차이는 그들의 역할에 따른 분화적 특이성에 기인한 것으로 생각된다.

• Molecules and Cells
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• 제23권3호
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• pp.287-303
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• 2007

Expressed sequence tags (ESTs) and differentially expressed cDNAs from the self-fertilizing fish, Kryptolebias marmoratus were mined to develop alternative biomarkers for endocrine-disrupting chemicals (EDCs). 1,577 K. marmoratus cDNA clones were randomly sequenced from the 5'-end. These clones corresponded to 1,518 and 1,519 genes in medaka dbEST and zebrafish dbEST, respectively. Of the matched genes, 197 and 115 genes obtained Unigene IDs in medaka dbEST and zebrafish dbEST, respectively. Many of the annotated genes are potential biomarkers for environmental stresses. In a differential display reverse transcriptase-polymerase chain reaction (DD RT-PCR) study, 56 differential expressed genes were obtained from fish liver exposed to bisphenol A. Of these, 16 genes were identified after BLAST search to GenBank, and the annotated genes were mainly involved in catalytic activity and binding. The expression patterns of these 16 genes were validated by real-time RT-PCR of liver tissue from fish exposed to bisphenol A. Our findings suggest that expression of these 16 genes is modulated by endocrine disrupting chemicals, and therefore that they are potential biomarkers for environmental stress including EDCs exposure.