• Genomics & Informatics
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• 제9권4호
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• pp.197-199
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• 2011

The biological interpretation of two-dimensional (2D) gel electrophoresis experiments is a key step toward understanding the functions of biological systems. We here present a web-based integrated database, called 2DSpotDB, for the management of proteome data derived from several pathogens. The 2DSpotDB was established as a part of the management of a pathogen proteome project at the Korea National Institute of Health. The goals of the 2DSpotDB implementation are to store and define important pathogen genes, retrieve information obtained by 2D polyacrylamide gel electrophoresis and mass spectrometry, and create an integrated system to provide pathogen proteome information for biological scientists. This database currently contains 14 gels and information on 387 protein spots, among which 329 proteins were identified and annotated.

• Mycobiology
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• 제37권3호
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• pp.171-182
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• 2009

Many aspergilli that belongs to ascomycetes have sexuality. In a homothallic or self-fertile fungus, a number of fruiting bodies or cleistothecia are formed in a thallus grown from a single haploid conidia or ascospores. Genome-sequencing project revealed that two mating genes (MAT) encoding the regulatory proteins that are necessary for controlling partner recognition in heterothallic fungi were conserved in most aspergilli. The MAT gene products in some self-fertile species were not required for recognition of mating partner at pheromone-signaling stage but required at later stages of sexual development. Various environmental factors such as nutritional status, culture conditions and several stresses, influence the decision or progression of sexual reproduction. A large number of genes are expected to be involved in sexual development of Emericella nidulans (anamorph: Aspergillus nidulans), a genetic and biological model organism in aspergilli. The sexual development process can be grouped into several development stages, including the decision of sexual reproductive cycle, mating process, growth of fruiting body, karyogamy followed by meiosis, and sporulation process. Complicated regulatory networks, such as signal transduction pathways and gene expression controls, may work in each stage and stage-to-stage linkages. In this review, the components joining in the regulatory pathways of sexual development, although they constitute only a small part of the whole regulatory networks, are briefly mentioned. Some of them control sexual development positively and some do negatively. Regarding the difficulties for studying sexual differentiation compare to asexual one, recent progresses in molecular genetics of E. nidulans enlarge the boundaries of understanding sexual development in the non-fertile species as well as in fertile fungi.

• Clinical and Experimental Pediatrics
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• 제53권3호
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• pp.273-285
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• 2010

Completion of the human genome project has allowed a deeper understanding of molecular pathophysiology and has provided invaluable genomic information for the diagnosis of genetic disorders. Advent of new technologies has lead to an explosion in genetic testing. However, this overwhelming stream of genetic information often misleads physicians and patients into a misguided faith in the power of genetic testing. Moreover, genetic testing raises a number of ethical, legal, and social issues. Diagnostic genetic tests can be divided into three primary but overlapping categories: cytogenetic studies (including routine karyotyping, high-resolution karyotyping, and fluorescent in situ hybridization studies), biochemical tests, and DNA-based diagnostic tests. DNA-based testing has grown rapidly over the past decade and includes preandpostnatal testing for the diagnosis of genetic diseases, testing for carriers of genetic diseases, genetic testing for susceptibility to common non-genetic diseases, and screening for common genetic diseases in a particular population. Theoretically, once a gene's structure, function, and association with a disease are well established, the clinical application of genetic testing should be feasible. However, for routine applications in a clinical setting, such tests must satisfy a number of criteria. These criteria include an acceptable degree of clinical and analytical validity, support of a quality assurance program, possibility of modifying the course of the diagnosed disease with treatment, inclusion of pre-and postnatal genetic counseling, and determination of whether the proposed test satisfies cost-benefit criteria and should replace or complement traditional tests. In the near future, the application of genetic testing to common diseases is expected to expand and will likely be extended to include individual pharmacogenetic assessments.

• Bulletin of the Korean Chemical Society
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• 제24권7호
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• pp.943-947
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• 2003

We have studied the migration behavior of single-stranded DNA using capillary gel electrophoresis under various conditions. It was found that optimum electric fields should be less than 150 V/cm for the good tradeoff between the separation time and the resolution. It seems that the gel matrix with the combination of different polymer average molecular weights is important to extend the maximum readable DNA bases. The total gel concentration less than 3.1% in the mixed gel system showed good separation efficiency up to 600 bases. The best result was obtained with the poy(ethylene)oxide (PEO) gel concentration of 1.2% of Mr 8,000,000 and 1.8% of Mr 600,000. We observed that the capillary length between 50 cm to 100 cm (effective length) should be employed for the optimization between the total DNA migration time and the maximum readable length. A trizma base-boric acid-ethlyenediaminetetraacetic acid (EDTA) (TBE) buffer was commonly used for DNA sequencing, but we found that 3-[tris(hydroxymethyl)methyl amino]-1-propane sulfonic acid (TAPS) buffer worked as well for the single-stranded DNA separation. Especially, TAPS buffer showed a good resolution for very short DNA bases (1 to 30 bases).

• 한국산학기술학회:학술대회논문집
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• 한국산학기술학회 2003년도 Proceeding
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• pp.57-64
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• 2003

Achieving the beneficiary goal of recent discovery in human genome project still needs a way to retrieve and analyze the exponentially expanding bio-related information. Research on bio-related fields naturally applies knowledge discovered to the current problem and make inferences to extract new information where shared concepts and data containing information need to be defined and used in a coherent way. In such a professional domain, while the need to help users reduce their work and to improve search results has been emerged. methods for systematic retrieval and adequate exchange of relevant information are still in their infancy. The design of our system aims at improving the quality of information retrieval in a professional domain by utilizing both corpus-based and concept-based ontology. Meta-rules of helping users to make an adequate query are formed into an ontology in the domain. The integration of those knowledge permits the system to retrieve relevant information in a more semantic and systematic fashion. This work mainly describes the query models with details of GUI and a secondary query generation of the system.

• Genomics & Informatics
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• 제19권3호
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• pp.24.1-24.7
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• 2021

Tracking the most recent advances in Coronavirus disease 2019 (COVID-19)-related research is essential, given the disease's novelty and its impact on society. However, with the publication pace speeding up, researchers and clinicians require automatic approaches to keep up with the incoming information regarding this disease. A solution to this problem requires the development of text mining pipelines; the efficiency of which strongly depends on the availability of curated corpora. However, there is a lack of COVID-19-related corpora, even more, if considering other languages besides English. This project's main contribution was the annotation of a multilingual parallel corpus and the generation of a recommendation dataset (EN-PT and EN-ES) regarding relevant entities, their relations, and recommendation, providing this resource to the community to improve the text mining research on COVID-19-related literature. This work was developed during the 7th Biomedical Linked Annotation Hackathon (BLAH7).

• 한국약용작물학회:학술대회논문집
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• 한국약용작물학회 2006년도 Proceedings of The Convention of The Korean Society of Applied Pharmacology
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• pp.23-39
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• 2006

The application of the knowledge from the Human Genome Project to clinical medicine will be through both industrial drug development and the application of pharmacogenomics (PG) to patient care. The slow uptake of clinical innovations into clinical practice can be frustrating, but understanding the history of acceptance and sustaining medical innovation is critically important to position PG to succeed. This primarily means that PG tests must have legitimacy; they must be thoroughly validated, must be cost-effective, must be widely accepted by medical practitioners, must be supported by public policy, and must have a way of being easily incorporated into current medical practice. They must also lead to actionalble decisions by health care providers for their patients. Innovative PG assays should be tested in the best US laboratories, and reimbursement for testing must be accepted at the federal and state level. The companies providing these PG tests should be capable of supporting the interpretation and use of the test throughout medical practice. Advances such as the addition of PG information to drug labeling and the routine use of validated biomarkers to determine choice of cancer chemotherapy have been made. The PG research community must pay attention to the principles that have been previously described for acceptance and sustaining medical innovations in order for PG to be widely accepted in clinical medical practice.

• IMMUNE NETWORK
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• 제3권3호
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• pp.235-241
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• 2003

Background: The protective immunity against tuberculosis (TB) involves both CD4+ T cells and CD8+ T cells. In our previous study, we defined four Mycobacterium tuberculosis derived peptide epitopes specific for HLA-$A^*0201$ restricted CD8+ T cells ($ThyA_{30-38}$, $RpoB_{127-135}$, $85B_{15-23}$, $PstA1_{75-83}$). In this study, we investigated the immune responses induced by these peptide specific CD8+ T cells in latently and chronically infected people with TB. Methods: We characterized these peptide specific CD8+ T cell population present in PBMC of both TB patients and PPD+healthy people using IFN-${\gamma}$elispot assay, intracellular staining and HLA-A2 dimer staining. Results: The frequency of peptide specific CD8+ T cell was in the range of 1 to 25 in $1.7{\times}10^5$ PBMC based on ex vivo IFN-${\gamma}$ elispot assay, demonstrating that these peptide specific CD8+ T cell responses are induced in both TB patients and PPD+ people. Short term cell lines (STCL) specific for these peptides proliferated in vitro and secreted IFN-${\gamma}$ upon antigenic stimulation in PPD+ donors. Lastly, HLA-$A^*0201$ dimer assays indicated that $PstA1_{75-83}$ specific CD8+ T cell population in PPD+ healthy donors is heterogeneous since approximately 25~33% of $PstA1_{75-83}$ specific CD8+ T cell population in PPD+ healthy donors produced IFN-${\gamma}$ upon peptide stimulation. Conclusion: Our results suggest that MHC class I restricted CD8+ T cell mediated immune responses to M. tuberculosis infection are induced in both TB patients and PPD + people; however, the CD8+ T cell population is functionally heterogeneous.

• Tuberculosis and Respiratory Diseases
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• 제59권3호
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• pp.272-278
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• 2005

배 경 : 결핵의 보호면역 반응에서 CD8+T 세포에 의한 여러 기전이 중요한 역할을 한다는 사실이 최근에 보고되고 있다. $IFN-{\gamma}$ 분비 외에도 결핵균으로 감염된 세포에 독성을 나타내어 직접 결핵균으로 감염된 세포를 제거하는 독성능 또한 그 역할이 중요하다고 알려지고 있는데, BCG 예방접종을 받은 개체에서도 이러한 균체항원에 특정한 CD8+T 세포의 독성능이 유도되어 있어서 보호면역 반응에서의 역할을 하는지 연구하였다. 대상 및 방법 : HLA-A*0201 과 A*0206를 표현하며 BCG 예방접종을 한 개체들의 혈액에서 백혈구를 분리하고 균체항원의 항원결정기 ($ThyA_{30-38}$) 에 대한 독성능과 ex vivo $IFN-{\gamma}$ 분비능을 유도하였다. 결 과 : 이들 대상에게서 $IFN-{\gamma}$ 분비능과 독성능이 유도되는 것을 관찰할 수 있었고, 또한 HLA-A*0201에 결합하여 CD8+T 세포의 면역 반응을 일으키는 $ThyA_{30-38}$ 펩티드들은 HLA-A*0206인 개체에서도 면역반응을 일으키는 것을 관찰할 수 있었다. 결 론 : 균체 항원에 특정한 CD8+T 세포들의 $IFN-{\gamma}$ 분비 능과 독성능이 BCG 백신주사를 맞은 개체에서 유도되어 있는 것을 관찰할 수 있었다. 따라서 이러한 균체항원에 특정한 CD8+T 세포들이 보호면역 반응에 관여한다는 것을 제시하며, 또한 HLA-A*0201 개체들과 HLA-A*0206 개체들을 대상으로 하는 백신이나 치료제로써 $ThyA_{30-38}$ 펩티드의 사용 가능성을 제시한다.

• 과학기술학연구
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• 제15권1호
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• pp.145-180
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• 2015

인간게놈프로젝트(HGP)는 지난 세기말 미국 영국 프랑스 중국 독일 일본의 컨소시엄이 수행한 거대과학이다. 그러나 한국에서의 HGP는 부족한 재원과 정부의 지원 미비 등으로 인해 일부 전문가 및 소수 난치병 환우들의 주장에도 불구하고 수행되지 못하였다. 이처럼 '90년대-한국의-HGP'는 구성되지 못했지만 포스트게놈 시대에 들어오면서 유전체의학이 활성화될 수 있게 된 사회적 메커니즘을 본 연구는 삼중나선 모델에 기반하여 분석하고자 한다. 포스트게놈 시대의 국내 유전체의학 연구들은 대학-기업-정부의 전통적 삼중나선 분류로는 정확히 설명이 안 되는 하이브리드 조직들을 중심으로 비로소 수행될 수 있었다. 국내 대학의 선도적 유전체연구자들은 기금부족 문제를 해결하기 위해 필수적으로 기업을 설립해야 했고, 이는 상업적 이익을 위해 선택적으로 벤처기업을 설립하는 선진국의 기업가적 대학과는 매우 다른 모습이다. 두 개의 사례연구를 통해 본 논문은 이 조직들이 사실상 뚜렷이 구별되기 어려운 대학과 기업의 연구 중합체(research assemblage)임을 보인다. 비슷한 맥락에서, 기업을 창업하지 않은 대학의 다른 유전체 연구자들도 정부와의 접점에서 구성되는 다양한 조직들을 통하고서야 비로소 유전체 연구를 수행할 수 있었다. 본고에서 '90년대-한국의-HGP'가 수행되지 못한 과학임을 주장하는 것은 결코 아니지만, 수행되지 못한 과학의 개념과 맥락적 유사성을 가졌던 게놈 연구가 활성화되기 위해서는 삼중나선의 변형적 수용이 필요했다는 점을 최종적으로 보이고자 한다.