• Biomolecules & Therapeutics
• /
• 제30권1호
• /
• pp.98-116
• /
• 2022

The small GTPase RhoA has been studied extensively for its role in actin dynamics. In this study, multiple bioinformatics tools were applied cooperatively to the microarray dataset GSE64714 to explore previously unidentified functions of RhoA. Comparative gene expression analysis revealed 545 differentially expressed genes in RhoA-null cells versus controls. Gene set enrichment analysis (GSEA) was conducted with three gene set collections: (1) the hallmark, (2) the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and (3) the Gene Ontology Biological Process. GSEA results showed that RhoA is related strongly to diverse pathways: cell cycle/growth, DNA repair, metabolism, keratinization, response to fungus, and vesicular transport. These functions were verified by heatmap analysis, KEGG pathway diagramming, and direct acyclic graphing. The use of multiple gene set collections restricted the leakage of information extracted. However, gene sets from individual collections are heterogenous in gene element composition, number, and the contextual meaning embraced in names. Indeed, there was a limit to deriving functions with high accuracy and reliability simply from gene set names. The comparison of multiple gene set collections showed that although the gene sets had similar names, the gene elements were extremely heterogeneous. Thus, the type of collection chosen and the analytical context influence the interpretation of GSEA results. Nonetheless, the analyses of multiple collections made it possible to derive robust and consistent function identifications. This study confirmed several well-described roles of RhoA and revealed less explored functions, suggesting future research directions.

• 한국생물정보학회:학술대회논문집
• /
• 한국생물정보시스템생물학회 2001년도 제2회 생물정보 워크샵 (DNA Chip Bioinformatics)
• /
• pp.61-86
• /
• 2001

All cancers are caused by abnormalities in DNA sequence. Throughout life, the DNA in human cells is exposed to mutagens and suffers mistakes in replication, resulting in progressive, subtle changes in the DNA sequence in each cell. Since the development of conventional and molecular cytogenetic methods to the analysis of chromosomal aberrations in cancers, more than 1,800 recurring chromosomal breakpoints have been identified. These breakpoints and regions of nonrandom copy number changes typically point to the location of genes involved in cancer initiation and progression. With the introduction of molecular cytogenetic methodologies based on fluorescence in situ hybridization (FISH), namely, comparative genomic hybridization (CGH) and multicolor FISH (m-FISH) in carcinomas become susceptible to analysis. Conventional CGH has been widely applied for the detection of genomic imbalances in tumor cells, and used normal metaphase chromosomes as targets for the mapping of copy number changes. However, this limits the mapping of such imbalances to the resolution limit of metaphase chromosomes (usually 10 to 20 Mb). Efforts to increase this resolution have led to the "new"concept of genomic DNA chip (1 to 2 Mb), whereby the chromosomal target is replaced with cloned DNA immobilized on such as glass slides. The resulting resolution then depends on the size of the immobilized DNA fragments. We have completed the first draft of its Korean Genome Project. The project proceeded by end sequencing inserts from a library of 96,768 bacterial artificial chromosomes (BACs) containing genomic DNA fragments from Korean ethnicity. The sequenced BAC ends were then compared to the Human Genome Project′s publicly available sequence database and aligned according to known cancer gene sequences. These BAC clones were biotinylated by nick translation, hybridized to cytogenetic preparations of metaphase cells, and detected with fluorescein-conjugated avidin. Only locations of unique or low-copy Portions of the clone are identified, because high-copy interspersed repetitive sequences in the probe were suppressed by the addition of unlabelled Cotl DNA. Banding patterns were produced using DAPI. By this means, every BAC fragment has been matched to its appropriate chromosomal location. We have placed 86 (156 BAC clones) cytogenetically defined landmarks to help with the characterization of known cancer genes. Microarray techniques would be applied in CGH by replacement of metaphase chromosome to arrayed BAC confirming in oncogene and tumor suppressor gene: and an array BAC clones from the collection is used to perform a genome-wide scan for segmental aneuploidy by array-CGH. Therefore, the genomic DNA chip (arrayed BAC) will be undoubtedly provide accurate diagnosis of deletions, duplication, insertions and rearrangements of genomic material related to various human phenotypes, including neoplasias. And our tumor markers based on genetic abnormalities of cancer would be identified and contribute to the screening of the stage of cancers and/or hereditary diseases

• 한국생물정보학회:학술대회논문집
• /
• 한국생물정보시스템생물학회 2006년도 Principles and Practice of Microarray for Biomedical Researchers
• /
• pp.109-114
• /
• 2006

최근 Human 지놈 프로젝트를 포함한 다양한 종의 지놈 프로젝트가 수행되고 수많은 지놈정보가 생산되고 있으며 이를 해석하고 서로 연관성를 찾기 위한 다양한 연구가 진행되고 있다. 즉 최신 생명공학과 관련된 연구방향이 DNA의 구조적 해석에서 기능 해석과 유전자들의 상호연관성을 규명하는 방향으로 변화하고 있으며 이를 위한 강력한 도구로서 DNA microarray (DNA chip)는 방대한 양의 지놈 정보를 이용하여 단시간에 대량으로 고속처리하여 효율적으로 유전자 기능을 분석할 수 있는 주목받고 있는 방법이다. DNA microarray 실험과 분석에 있어 데이터분석, 재현성, 종간의 비교, 확인실험 및 비용 등의 문제가 있지만 유전자발현양상 데이터로부터 정확한 환자의 예후를 예측할 수 있는 비교적 적은 유전자 그룹의 진단마커를 찾거나, 하나의 유전자가 아니라 mouse 전체 지놈의 유전자발현 패턴을 인간의 암을 위시한 각종 질병 연구를 위한 발현 신호나 변화 등을 발견하여 신약개발 등에 활용하고자 하는 시도가 활발히 진행되고 있다. 서로 다른 종간에 비슷한 phenotype의 유전자발현도 진화적으로 보존되었다는 전제 하에서 지놈 sequence의 비교연구가 가능하고 DNA microarray 발현 데이터에 근거하여 독립적으로 각 종간의 유전자발현패턴을 비교함으로써 난치병 등을 새롭게 분류할 수 있다. 즉, 암세포 등에서 유전자발현 양상은 유전학적, 환경적 alteration들이 잘 반영되어 있다고 간주하고, 이러한 양상을 바탕으로 인간의 암을 위시한 다양한 질병 연구를 위한 최적의 mouse 모델을 찾을 수 있고, 이는 결국 새로운 치료 방법 개발이나 맞춤의학 실현에 중요한 역할을 할 것으로 기대된다. 특히 pathway 타겟으로 하는 치료를 위해서는 Human-mouse 비교를 통한 발현 신호를 찾는 것이 진단에서는 매우 유용한 방법이다. 이를 위한 고성능의 분석방법이나 시스템의 개발이 중요하게 된다.. 관류의 정도와 조영증강정도를 중심으로 관류 MR 영상소견과 조직학적 소견을 관련지어 분석하였다. 결과: 조영증강 T1강조MR영상에서 환상조영증강을 보이는 다형성 교보세포종 2예에서는 변연부 외륜이 고관류를, 중심부의 괴사부위는 저관류로 나타났다. 저등급 교종은 경계가 불분명한 저관류부위로 보였다. 뇌농양 2예는 변연부 외륜이 경도의 고관류를, 중심부는 저관류로 나타났다. 뇌수막종은 미만성의 균일한 중등도 혹은 고도의 고관류로 보였으며, 임파종과 배아종은 경계가 명확한 저관류부위로 나타났다. 신경세포종은 종괴\ulcorner 일부에 중등도 혹은 고도의 고관류부위가 관찰되었고, 전이암은 다수병변중 일부에서 중등도의 고관류를 보였다. 방사선괴사는 저관류부위내에 국소적 고관류부위를 보였다. 결론: 관류 MR영상은 뇌종양의 관류상태를 비교적 잘 반영하며, 조직학적 특성을 예측하는데에 도움을 주 수 있을 것으로 기대된다. 뇌종야에서의 관류MR영상의 분명한 역할을 규명하기 위해서는 앞으로 더 많은 임상적 연구가 필요할 것으로 생각된다.조증 환자의 자극성 전타액내 lactobacilli양은 peroxidase system을 함유한 세치제를 사용한 군에서 대조군에 비해 상대적으로 낮게 나타났으나(p = 0.067) 통계학적 유의성은 없었다.같은 예에서 찾아 볼 수 있다. 첫째, 발음상으로 동사의 변화형에서 "porte[$p{\jmath}rte$](들다: 현재형), porte[$p{\jmath}rte$](과거분사형), porta[$p{\jmath}rte$](단순과거형)"등이 대립되며, 이휘 "Porto[$p{\jmath}rte$](포르토)"와도 대립된다. 둘째, 어휘적 대립 "le haut[$l{\partial}o$](위)/l'eau[lo](물)"와 형태론적 대립 "le[$l{\partial}$](정관사, 남성단수)/l

• Molecules and Cells
• /
• 제38권8호
• /
• pp.685-696
• /
• 2015

Rice is a model plant widely used for basic and applied research programs. Plant cell wall proteins play key roles in a broad range of biological processes. However, presently, knowledge on the rice cell wall proteome is rudimentary in nature. In the present study, the tightly-bound cell wall proteome of rice callus cultured cells using sequential extraction protocols was developed using mass spectrometry and bioinformatics methods, leading to the identification of 1568 candidate proteins. Based on bioinformatics analyses, 389 classical rice cell wall proteins, possessing a signal peptide, and 334 putative non-classical cell wall proteins, lacking a signal peptide, were identified. By combining previously established rice cell wall protein databases with current data for the classical rice cell wall proteins, a comprehensive rice cell wall proteome, comprised of 496 proteins, was constructed. A comparative analysis of the rice and Arabidopsis cell wall proteomes revealed a high level of homology, suggesting a predominant conservation between monocot and eudicot cell wall proteins. This study importantly increased information on cell wall proteins, which serves for future functional analyses of these identified rice cell wall proteins.

• Journal of Veterinary Science
• /
• 제25권3호
• /
• pp.47.1-47.12
• /
• 2024

Importance: Staphylococcus aureus and Escherichia coli contribute to global health challenges by forming biofilms, a key virulence element implicated in the pathogenesis of several infections. Objective: The study examined the efficacy of various generations of cephalosporins against biofilms developed by pathogenic S. aureus and E. coli. Methods: The development of biofilms by both bacteria was assessed using petri-plate and microplate methods. Biofilm hydrolysis and inhibition were tested using first to fourth generations of cephalosporins, and the effects were analyzed by crystal violet staining and phase contrast microscopy. Results: Both bacterial strains exhibited well-developed biofilms in petri-plate and microplate assays. Cefradine (first generation) showed 76.78% hydrolysis of S. aureus biofilm, while significant hydrolysis (59.86%) of E. coli biofilm was observed by cefipime (fourth generation). Similarly, cefuroxime, cefadroxil, cefepime, and cefradine caused 78.8%, 71.63%, 70.63%, and 70.51% inhibition of the S. aureus biofilms, respectively. In the case of E. coli, maximum biofilm inhibition (66.47%) was again shown by cefepime. All generations of cephalosporins were more effective against S. aureus than E. coli, which was confirmed by phase contrast microscopy. Conclusions and Relevance: Cephalosporins exhibit dual capabilities of hydrolyzing and inhibiting S. aureus and E. coli biofilms. First-generation cephalosporins exhibited the highest inhibitory activity against S. aureus, while the third and fourth generations significantly inhibited E. coli biofilms. This study highlights the importance of tailored antibiotic strategies based on the biofilm characteristics of specific bacterial strains.

• Biomolecules & Therapeutics
• /
• 제18권2호
• /
• pp.184-190
• /
• 2010

Clinical cases of pure red cell aplasia (PRCA) have been reported during the recombinant human erythropoietin (EPO) therapy for the anemia patients. PRCA is a rare hematological disorder leading to a severe anemia due to an almost complete stop of red blood cell production. Antibody (Ab)-associated PRCA is caused by the EPO-neutralizing Abs that eliminate the biological activity of EPO. In order to detect anti-EPO Abs in human sera, we performed conventional ELISA, directly coated bridging ELISA, and streptavidin coated bridging ELISA, and compared their sensitivity and specificity. Some false positive results were obtained in the conventional ELISA. One positive sample was detected successfully by streptavidin coated bridging ELISA, which was not appeared in the directly coated bridging ELISA. In conclusion, streptavidin coated bridging ELISA was substantially sensitive and specific format and one out of sixty-eight serum samples was proved to be anti-EPO positive.

• Journal of Plant Biotechnology
• /
• 제42권4호
• /
• pp.298-311
• /
• 2015

포도는 전 세계적으로 가장 많이 재배되는 과수 작물 중의 하나로서 재배과정에서 많은 병해충이나 기상재해와 같은 스트레스에 직면한다. 과실의 고품질과 더불어 병충해 저항성인 품종 또는 내재해성 품종을 육성하는 것은 포도 생산에서 매우 중요한 과정이다. 고전적인 교배 육종을 이용한 신품종의 개발은 포장을 관리하는 데에 많은 노동력과 비용이 요구되며 오랜 시간이 소요되는 단점이 있다. 유용형질을 지닌 새로운 품종의 개발에 이용할 분자육종기술은 포도 육종프로램에서 전통적인 교배육종효율을 증진시킬 수 있는 매우 유용한 기술로 여겨진다. 포도의 유전체 해독을 완성함으로써 신품종육성에 활용될 유용유전자를 대량으로 발굴할 수 있고, 기능을 분석하는데 큰 도움을 주고 있다. 포도의 비교유전체, 전사체, 후성유전체, 유전체에 근거한 유전자 발굴, 분자마커 개발 등의 연구는 과실의 품질, 병해와 스트레스에 대한 저항성 기작을 구명하는데 중요한 단서를 제공하고 포도 육종에 유용하게 활용될 것이다.

• 한국콘텐츠학회논문지
• /
• 제10권8호
• /
• pp.104-110
• /
• 2010

생명과학 분야에서 컴퓨터를 활용할 수 있는 대표적인 예로는 서열화, 서열화 분석, 비교, 진화, 돌연변이 추적, 약 설계를 위한 유사성 비교, 단백질 기능 예측, 그리고 세포 메커니즘과 질병 발생에서의 유전자 역할 예측 등 다양한 분야를 들 수 있다. 생명공학 연구자들에게는 이와 같은 작업을 위한 도구들이 요구되고 있다. 본 논문에서는 바이오 데이터 분석을 위한 기존 시스템의 문제점을 파악하고, 이를 개선할 수 있는 시스템 설계에 초점을 맞추었다. 또한 각각의 분석 작업을 개선할 수 있고 서로 독립적으로 진행되는 기존의 시스템을 통합할 수 있는 통합 분석 시스템을 설계하고자 한다.

• Asian-Australasian Journal of Animal Sciences
• /
• 제20권7호
• /
• pp.1115-1119
• /
• 2007

This study was conducted to determine the difference between satellite cells (porcine) and myoblasts (C2C12) in their differentiation under the influence of 2, 4-thiazolidindion. C2C12 myoblast cells and porcine satellite cells (isolated from 10 d old $Landrace{\times}Duroc$ piglets) were grown to absolute confluency. Post confluent cells (day 0) were further exposed to adipogenic induction medium along with 2, 4-thiazolidindion ($8{\mu}M$) for 2 d. Thereafter, cells were exposed to 2, 4-thiazolidindion alone every 2 d till day 10 and analysed. The control was cultured in differentiation medium without any treatment. Increased (p<0.05) expression of transcriptional factors i.e. C/EBP-${\alpha}$ and PPAR-${\gamma}$ and transition of cells to adipocyte morphology was noticed from 2 d and 4 d onwards in satellite cells (Porcine) and myoblasts (C2C12) respectively. Myogenesis was observed to be suppressed completely in case of satellite cells compared to myoblasts in response to 2, 4-thiazolidindion. Pax-7 (transcriptional factor) appeared as a sole entity to satellite cells only, as it was not identified in case of myoblasts. Although both the cells were converting to adipoblasts, the degree of their conversion was different in response to 2, 4-thiazolidindion. Therefore, the hypothesis that satellite cells contribute various domains to the growing myoblasts appeared obscured and found to be dependent on the proliferative energy/or degree of fusion. However, it revealed satellite cells as currency to myoblasts/muscle.

• 한국미생물·생명공학회지
• /
• 제46권3호
• /
• pp.194-200
• /
• 2018

Glycogen plays important roles in bacteria. Its structure and storage capability have received more attention recently because of the potential correlations with environmental durability and pathogenicity. However, the low level of intracellular glycogen makes extraction and structure characterization difficult, inhibiting functional studies. Bacteria grown in regular media such as lysogeny broth and tryptic soy broth do no accumulate large amounts of glycogen. Comparative analyses of bacterial media reported in literature for glycogen-related studies revealed that there was no consistency in the recipes reported. Escherichia coli $DH5{\alpha}$ is a convenient model organism for gene manipulation studies with respect to glycogen. Additionally, M9 minimal salts medium is widely used to improve glycogen accumulation, although its composition varies. In this study, we optimized the M9 medium by adjusting the concentrations of itrogen source, tryptone, carbon source, and glucose, in order to achieve a balance between the growth rate and glycogen accumulation. Our result showed that $1{\times}M9$ minimal salts medium containing 0.4% tryptone and 0.8% glucose was a well-balanced nutrient source for enhancing the growth and glycogen storage in bacteria. This result will help future investigations related to bacterial physiology in terms of glycogen function.