• BMB Reports
• /
• 제53권6호
• /
• pp.299-310
• /
• 2020

Chronic liver disease progresses through several stages, fatty liver, steatohepatitis, cirrhosis, and eventually, it leads to hepatocellular carcinoma (HCC) over a long period of time. Since a large proportion of patients with HCC are accompanied by cirrhosis, it is considered to be an important factor in the diagnosis of liver cancer. This is because cirrhosis leads to an irreversible harmful effect, but the early stages of chronic liver disease could be reversed to a healthy state. Therefore, the discovery of biomarkers that could identify the early stages of chronic liver disease is important to prevent serious liver damage. Biomarker discovery at liver cancer and cirrhosis has enhanced the development of sequencing technology. Next generation sequencing (NGS) is one of the representative technical innovations in the biological field in the recent decades and it is the most important thing to design for research on what type of sequencing methods are suitable and how to handle the analysis steps for data integration. In this review, we comprehensively summarized NGS techniques for identifying genome, transcriptome, DNA methylome and 3D/4D chromatin structure, and introduced framework of processing data set and integrating multi-omics data for uncovering biomarkers.

• 한국어류학회지
• /
• 제21권2호
• /
• pp.129-133
• /
• 2009

본 연구는 RAPD PCR 분석을 통하여 한국의 서한아 수계(한강, 금강)와 남한아 수계(섬진강, 낙동강)에 서식하는 쉬리 집단들 간의 유전변이를 비교하였다. 4집단들 간의 유전적 변이를 분석한 결과, 사용한 12개의 random primer들 모두에서 서한아 수계 집단과 남한아 수계의 집단들을 구분하여 주는 특이적 PCR 단편들을 확인할 수 있었다. 유전적 유사도 분석에서 한강, 금강의 서한아 수계 집단들과 섬진강, 낙동강의 남한아 수계 집단들의 유전적 유사도는 0.49~0.53로 낮게 나타났고 유전적 거리는 0.63~0.71로 높게 나타났다. 유전적 거리에 기초한 UPGMA dendrogram 분석에서도 서한아 수계와 남한아 수계의 집단들이 명확하게 구분되었다. 따라서 서한아와 남한아 수계의 쉬리 집단은 유전적 구조에 있어 큰 차이가 있으며, 남한아 수계의 쉬리는 서한아 수계 쉬리와 진화적으로 뚜렷하게 구분되는 집단으로 판단된다.

• Molecules and Cells
• /
• 제22권3호
• /
• pp.328-335
• /
• 2006

Imperatoxin A ($IpTx_a$), a 3.7 kDa peptide from the African scorpion Pandinus imperator, is an agonist of the skeletal muscle ryanodine receptor (RyR1). In order to study the structure of the toxin and its effect on RyR1, $IpTx_a$ cDNA was PCR-amplified using 3 pairs of primers, and the toxin was expressed in E. coli. The toxin was further purified by chromatography, and various point mutants in which basic amino acids were substituted by alanine were prepared by site-directed mutagenesis. Studies of single channel properties by the planar lipid bilayer method showed that the recombinant $IpTx_a$ was identical to the synthetic $IpTx_a$ with respect to high-performance liquid chromatography mobility, amino acid composition and specific effects on RyR1. Mutations of certain basic amino acids ($Lys^{19}$, $Arg^{23}$, and $Arg^{33}$) dramatically reduced the capacity of the peptide to activate RyRs. A subconductance state predominated when $Lys^8$ was substituted with alanine. These results suggest that some basic amino acid residues in $IpTx_a$ are important for activation of RyR1, and that $Lys^8$ plays an important role in regulating the gating mode of RyR1.

• Journal of Microbiology and Biotechnology
• /
• 제22권12호
• /
• pp.1613-1620
• /
• 2012

Bacterial wilt caused by Ralstonia solanacearum is a devastating disease of many economically important crops. Since there is no promising control strategy for bacterial wilt, phage therapy could be adopted using virulent phages. We used phage PE204 as a model lytic bacteriophage to investigate its biocontrol potential for bacterial wilt on tomato plants. The phage PE204 has a short-tailed icosahedral structure and double-stranded DNA genome similar to that of the members of Podoviridae. PE204 is stable under a wide range of temperature and pH, and is also stable in the presence of the surfactant Silwet L-77. An artificial soil microcosm (ASM) to study phage stability in soil was adopted to investigate phage viability under a controlled system. Whereas phage showed less stability under elevated temperature in the ASM, the presence of host bacteria helped to maintain a stable phage population. Simultaneous treatment of phage PE204 at $10^8$ PFU/ml with R. solanacearum on tomato rhizosphere completely inhibited bacterial wilt occurrence, and amendment of Silwet L-77 at 0.1% to the phage suspension did not impair the disease control activity of PE204. The biocontrol activities of phage PE204 application onto tomato rhizosphere before or after R. solanacearum inoculation were also investigated. Whereas pretreatment with the phage was not effective in the control of bacterial wilt, post-treatment of PE204 delayed bacterial wilt development. Our results suggested that appropriate application of lytic phages to the plant root system with a surfactant such as Silwet L-77 could be used to control the bacterial wilt of crops.

• 정보처리학회논문지D
• /
• 제16D권5호
• /
• pp.643-650
• /
• 2009

생명정보 대량 획득기술의 하나인 마이크로어레이(microarray)는 DNA와 각종 유전자 연구에 사용되는 도구로 확립되면서, 생명정보학(Bioinformatics)분야의 발전에 크게 기여하였다. 그러나 마이크로어레이는 생명정보학분야의 핵심기술 중 하나로 발전하였음에도 불구하고 실험으로 생성되는 데이터는 형태가 다양하고 매우 복잡한 형태를 갖기 때문에 데이터의 공유나 저장에서 많은 어려움을 겪고 있다. 본 논문에서는 마이크로어레이 데이터의 관리를 원활하게 하기위한 XML 기반의 표준 포맷인 MAGE-ML스키마에서 구조적으로 유사한 엘리먼트가 반복적으로 나타나는 특징과 대다수의 엘리먼트들이 특정 엘리먼트의 자식으로만 온다는 구조적 특징을 이용하여, MAGE-ML의 스키마를 단순화 하고 저장구조를 효율적으로 설계하는 방법을 제안한다. 이 방법에서 인라인 기법(Inlining Technique)을 이용한 스키마의 단순화와 새롭게 제시하는 엘리먼트의 구조적 형태를 기준으로 분류하는 기법을 이용한다. 이를 통하여 데이터베이스 스키마는 간략화 되며 테이블조인의 횟수가 줄어들고 성능은 향상된다.

• 생약학회지
• /
• 제41권3호
• /
• pp.166-173
• /
• 2010

Oxidative stress to proteins, lipids, or DNA is higher in human autopsy tissue and in rodent models of a number of neurodegenerative conditions, including Alzheimer's and Parkinson's disease. On the basis of this information, we established a screening system using N18-RE-105 cells to identify therapeutic agents that can protect cells from glutamate toxicity. During the course of our screening program, we recently isolated the active compound 9-hydroxy-$\alpha$-tocopherone ($\alpha$-TP), which prevents glutamate-induced cell death, from Viola mandshurica. The chemical structure of $\alpha$-TP was identified using spectroscopic methods and by comparison with literature values. Antioxidant activity and protective effects of $\alpha$-TP were evaluated by DPPH radical-scavenging assay, morphological assay, MTT reduction assay, and lactate dehydrogenase (LDH) release assay. These results suggest that $\alpha$-TP could be a new potential chemotherapeutic agent against neuronal diseases.

• The Plant Pathology Journal
• /
• 제33권4호
• /
• pp.362-369
• /
• 2017

White root rot disease, caused by the pathogen Rosellinia necatrix, is one of the world's most devastating plant fungal diseases and affects several commercially important species of fruit trees and crops. Recent global outbreaks of R. necatrix and advances in molecular techniques have both increased interest in this pathogen. However, the lack of information regarding the genomic structure and transcriptome of R. necatrix has been a barrier to the progress of functional genomic research and the control of this harmful pathogen. Here, we identified 10,616 novel full-length transcripts from the filamentous hyphal tissue of R. necatrix (KACC 40445 strain) using PacBio single-molecule sequencing technology. After annotation of the unigene sets, we selected 14 cell cycle-related genes, which are likely either positively or negatively involved in hyphal growth by cell cycle control. The expression of the selected genes was further compared between two strains that displayed different growth rates on nutritional media. Furthermore, we predicted pathogen-related effector genes and cell wall-degrading enzymes from the annotated gene sets. These results provide the most comprehensive transcriptomal resources for R. necatrix, and could facilitate functional genomics and further analyses of this important phytopathogen.

• Parasites, Hosts and Diseases
• /
• 제49권3호
• /
• pp.221-228
• /
• 2011

Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms for human malaria research because of their analogies to the human malaria in terms of structure, physiology, and life cycle. Exploiting the available genetic sequence information, we constructed a cDNA library from the erythrocytic stages of P. berghei and analyzed the expressed sequence tag (EST). A total of 10,040 ESTs were generated and assembled into 2,462 clusters. These EST clusters were compared against public protein databases and 48 putative new transcripts, most of which were hypothetical proteins with unknown function, were identified. Genes encoding ribosomal or membrane proteins and purine nucleotide phosphorylases were highly abundant clusters in P. berghei. Protein domain analyses and the Gene Ontology functional categorization revealed translation/protein folding, metabolism, protein degradation, and multiple family of variant antigens to be mainly prevalent. The presently-collected ESTs and its bioinformatic analysis will be useful resources to identify for drug target and vaccine candidates and validate gene predictions of P. berghei.

• 한국패류학회지
• /
• 제25권3호
• /
• pp.197-201
• /
• 2009

본 연구에서는 높은 변이를 나타내는 6개의 Microsatellite DNA 유전표식을 이용하여 독도지역에 서식하고 있는 자연산 전복집단의 유전적 다양성 및 집단구조를 파악하여 동 서 남해의 6개 지역집단과 비교 분석하였다. 그 결과 독도지역의 유전적 다양성은 6개 지역집단보다 높게 나타났으며 유전적 거리에 의한 유연관계 분석 결과에 있어서도 이들 집단과는 독립된 집단으로 나타났다. 이러한 결과는 6개 지역집단에 있어 방류전복의 높은 혼획비율에 의한 자연산 집단의 유전적 다양성이 축소되어진 결과라고 생각되어진다. 따라서 독도집단의 높은 유전적 다양성을 유지하고 보존하기 위해서는 이 지역의 유전적 다양성을 고려한 체계화된 전복종묘의 방류가 이루어져야하며, 방류를 한 이후에도 지속적인 유전학적 모니터링이 필요하다고 생각되어진다.

• 한국잠사학회:학술대회논문집
• /
• 한국잠사학회 1997년도 Progress and Future Development of Sericultural Science and Technology 40th Anniversary Commemoration Symposium
• /
• pp.51-72
• /
• 1997

Diapause hormone (DH) is a neuropeptide hormone which is secreted from the suboesophageal ganglion (SG) and is responsible for induction of embryonic diapause of the silkworm, Bombyx mori. DH is isolated from SGs and determined to be a 24 amino acid peptide amide. The cDNA encodes the polyprotein precursor from which DH, pheromone biosynthesis activating neuropeptide (PBAN) and three other neuropeptides are released and become matured. The C-terminal FXPRL-NH2 sequence of DH is essential but not sufficient for expression of full activity. Recently, we have isolated a unique hydrohobic peptide (VAP peptide) with a slight diapause egg induceing activity from organic solvent extracts of the male adult heads of the silkworm. The VAP peptide itself has no diapause inducing activity, but enhances DH activity through reducing ED50 value and the threshold concentration of DH. The DH-PBAN gene is composed of 6 exons interrupted by 5 introns and is expressed in 12 neurosecretory cells of the SG. The incubation of eggs at 25$^{\circ}C$, which induces embryonic diapause in the progeny, caused DH-PBAN mRNA content to increase at 5 different stages in the life cycle. By contrast, a 15$^{\circ}C$ incubation only induced expression of the gene at the late phrase adult stage. The temperature-controlled expression of DH-PBAN gene is closely correlated to the incidence of diapause, indicating that DH-PBAN gene expression is the initial event leading to diapause induction. DH acts to stimulate trehalase activity in developing ovary to bring about hyprglycogenism in mature eggs, a prerequisite metabolism for diapause initiation. Using in vivo and in vitro systems, DH is clearly shown to induce trehalase gene expression in developing ovaries. New protein synthesis is not needed for this process, but a Ca2+-dependent proteinkinase seems to be involved. Quite recently, we have sucessfully applied a new and potent trehalase inhibitor (Trehazoline) to reudce glycogen content in developing ovaries. The eggs deficient in glycogen were also able to enter diapause as the natural eggs do, so that we could provide the new egg system to reconsider the diapause associated metabolism other than the glycogen-sorbitol metabolic system.