• Proceedings of the Korea Inteligent Information System Society Conference
• /
• 2002.05a
• /
• pp.417-422
• /
• 2002

인공면역시스템을 이용한 침입탐지시스템 개발을 위해 적용한 동적 클론 선택(Dynamic Clonal Selection) 알고리즘과 그의 문제점을 소개하고 보다 개선된 동적 클론 선택 알고리즘을 제안한다. 이전 연구에서 침입탐지시스템이 흔히 접하게 되는 상황, 즉 과거 안정적으로 관찰되었던 정상행위가 합법적인 요인들로 인하여 갑작스러운 변화를 보일 경우 과거 생성되었던 기억탐지자가 정상행위를 비정상행위로 오류 판단하는 것을 막기 위하여 인간면역시스템의 체세포 돌연변이 (somatic hypermutation)를 이용하여 유전자 라이브러리를 진화시키는 방법을 첨가한 동적 클론 선택 알고리즘을 소개한다.

• BMB Reports
• /
• v.51 no.11
• /
• pp.584-589
• /
• 2018

Secondary prevention via earlier detection would afford the greatest chance for a cure in premalignant lesions. We investigated the exomic profiles of non-malignant and malignant changes in head and neck squamous cell carcinoma (HNSCC) and the genomic blueprint of human papillomavirus (HPV)-driven carcinogenesis in oropharyngeal squamous cell carcinoma (OPSCC). Whole-exome (WES) and whole-genome (WGS) sequencing were performed on peripheral blood and adjacent non-tumor and tumor specimens obtained from eight Korean HNSCC patients from 2013 to 2015. Next-generation sequencing yielded an average coverage of $94.3{\times}$ for WES and $35.3{\times}$ for WGS. In comparative genomic analysis of non-tumor and tumor tissue pairs, we were unable to identify common cancer-associated early mutations and copy number alterations (CNA) except in one pair. Interestingly, in this case, we observed that non-tumor tonsillar crypts adjacent to HPV-positive OPSCC appeared normal under a microscope; however, this tissue also showed weak p16 expression. WGS revealed the infection and integration of high-risk type HPV16 in this tissue as well as in the matched tumor. Furthermore, WES identified shared and tumor-specific genomic alterations for this pair. Clonal analysis enabled us to infer the process by which this transitional crypt epithelium (TrCE) evolved into a tumor; this evolution was accompanied by the subsequent accumulation of genomic alterations, including an ERBB3 mutation and large-scale CNAs, such as 3q27-qter amplification and 9p deletion. We suggest that HPV16-driven OPSCC carcinogenesis is a stepwise evolutionary process that is consistent with a multistep carcinogenesis model. Our results highlight the carcinogenic changes driven by HPV16 infection and provide a basis for the secondary prevention of OPSCC.

• Current Research on Agriculture and Life Sciences
• /
• v.24
• /
• pp.1-8
• /
• 2006

When tea trees were introduced to Korea peninsular from China? Historically, Mr. Taeryum, an envoy of Shilla dynasty brought tea seeds from China during Tang dynasty and the seeds were planted at Jiri Mt. by the order of King Heungduk at AD828. During Koryo Dynasty(918 1392), Buddhism spread rapidly all over the country and the tea culture reached its highest stage of prosperity. At the Chosun Dynasty, however, the ceremonial drinking of tea vanished almost completely due to the flourishing Confucian tradition, a kind of substitution of Buddhism. But a few people have supported the traditional tea culture by themselves. Since the independence of Korea soon after the World War II at 1945, Korean War have been exploded at 1950. After economic evolution have been succeeded at 1980, the cultivation area of tea trees has been increased about 2,000ha and the cultural tradition of tea drinking has become popular again at a tea consume quantities amounted to 100g per capita at 2004. The northern limited area of tea plant is lined on the southern part of Korea peninsular. It is very small region compared to China about one million ha and to Japan over 60 thousand ha. It is problem not only the area of tea fields but also the methodology of tea cultivation, for examples without clonal cultivars and mechanical systems. WTO treatments was discussing with Korea, China and Japan government at 2005. Green tea custom is very high at 514% in Korea. If three countries will be agreed the imported tax will be cut off, the Korean tea farmers will be confused because of unstable situation of tea markets. All most of tea farmers should be made the tea fields by seeding not clonal propagation. Because of clonal cultivars have not developed in Korea, there have not been the research institutes for tea plants and manufactures before 1992. Now there are three research institute of tea in Korea; Tea Experiment Station at Bosung of Jeonnam Agricultural Research & Extension Services, Mokpo Experimental Station of National Institute of Crop Science, and Green Tea Cluster Institute of Hadong. Mokpo and Hadong Research Station were established at 2004 and at 2005 but Bosung Station was established at 1992. Seven clonal tea cultivers were selected at Bosung Station; Bohyang, Myngsun, Chanlok, Sunhyang, Mihyang, Jinhyang and Ohsun until 2004. Mokpo Experimental Institute was started the tea provenance testing about 4 provenances: Kangwon-do, Jeonlabuk-do, Jeonlanam-do, and Kyungsangnam-do. Korean new tea cultivers should be selected because Koran wild tea population have been high genetic variation. If tea breeding research will be successful to select new clonal cultivers, the tea farmers of Korea will be stable after WTO treatment with each country.

• Genomics & Informatics
• /
• v.16 no.4
• /
• pp.17.1-17.6
• /
• 2018

Tumor heterogeneity, the cellular mosaic of multiple lineages arising from the process of clonal evolution, has continued to thwart multi-omics analyses using traditional bulk sequencing methods. The application of single-cell sequencing, in concert with existing genomics methods, has enabled high-resolution interrogation of the genome, transcriptome, epigenome, and proteome. Applied to cancers, these single-cell multi-omics methods bypass previous limitations on data resolution and have enabled a more nuanced understanding of the evolutionary dynamics of tumor progression, immune evasion, metastasis, and treatment resistance. This review details the growing number of novel single-cell multi-omics methods applied to tumors and further discusses recent discoveries emerging from these approaches, especially in regard to immunotherapy.

• BMB Reports
• /
• v.36 no.1
• /
• pp.78-81
• /
• 2003

The prevention of cancer is one of the most important public health and medical practices of the $21^{st}$ century. We have made much progress in this new emerging field, but so much remains to be accomplished before widespread use and practice become common place. Cancer chemoprevention encompasses the concepts of inhibition, reversal, and retardation of the cancer process. This process, called carcinogenesis, requires 20-40 years to reach the endpoint called invasive cancer. It typically follows multiple, diverse and complex pathways in a stochastic process of clonal evolution. These pathways appear amenable to inhibition, reversal or retardation at various points. We must therefore identify key pathways in the evolution of the cancer cell that can be exploited to prevent this carcinogenesis process. Basic research is identifying many genetic lesions and epigenetic processes associated with the progression of precancer to invasive disease. Many of these early precancerous lesions favor cell division over quiescence and protect cells against apoptosis when signals are present. Many oncogenes are active during early development and are reactivated in adulthood by aberrant gene promoting errors. Normal regulatory genes are mutated, making them insensitive to normal regulatory signals. Tumor suppressor genes are deleted or mutated rendering them inactive. Thus there is a wide range of defects in cellular machinery which can lead to evolution of the cancer phenotype. Mistakes may not have to appear in a certain order for cells to progress along the cancer pathway. To conquer this diverse disease, we must attack multiple key pathways at once for a predetermined period of time. Thus, agent combination prevention strategies are essential to decrease cancer morbidity. Furthermore, each cancer type may require custom combination of prevention strategies to be successful.

• The Korean Journal of Ecology
• /
• v.17 no.3
• /
• pp.299-310
• /
• 1994

Intraspecific clonal interactions have important influences on a population structure of the cellular slime mold (CSM). This study was to investigate whether or not evolutionary change in a population could be induced by clonal competition, and to elucidate how various clones in a population evolve in a homogeneous environment of laboratory culture. The characteristic clones of Polysphondylium pallidum which had different resource consumption rates (RCR) and mating types I and II were selected for study. Investigation was conducted for 4 experimental time interval $(T_0-T_4)$; one experimental time interval took almost 10-14 days from inoculation to havest of fruiting bodies. Two sets of 50 clones were cultured from 50 clones at To, and RCR variations of the population were compared between $(T_0\;and\;T_4)$ for each set of clones. Each clone of the CSM had a diverse resource consumption rate, or growth rate, in a homogeneous and limited Cerophyl agar plate despite the passage of 48-56 generations from the beginning of the experiment. Diverse clones with different growth rate could coexist in one site of the homogeneous agar plate as well as heterogeneous soil microenvironment. When there was high clonal diversity of RCR, a clone in a population had high chances to encounter other clones with resultant increased clonal competition. In one set, 26 of 37 clones of mating type I were changed to mating type Il for the 4 experimental time intervals, which indicated that the rate of competitive exclusion among clones during total experiment from $(T_0\;to\;T_4)$ was 0.703. In another set, 31 of 37 clones of mating type I were changed to mating type II , having the rate of competitive exclusion 0.838. The frequency of each of mat~ng types changed by 0.93-1.29% in each successive generation. The competitive exclusion among clones occurred by 1.26-1.75% when approximately $2.6{\times}10^8$ bacterial cells were provided as food and thereafter one generation of myxamoebae of CSM elapsed at room temperature. This finding implicated that in the vegetative state of P, pallidurn there was 1.26-1.75% probabil~ty of evolutionary change per generation changing from one clone to another clone.

• Clinical and Experimental Pediatrics
• /
• v.50 no.6
• /
• pp.519-523
• /
• 2007

Aplastic anemia is a rare disease, which is characterized by pancytopenia and hypocellular bone marrow without infiltration of abnormal cells or fibrosis. The incidence in Asia is higher than in the West and new cases are diagnosed at a rate of 5.1 per million pediatric populations per year in Korea. The pathophysiology is understood roughly by defective hematopoiesis, impaired bone marrow micro-environment and immune mechanism. Treatments are performed on basis of pathogenesis and selected depending on the severity. Immunosuppressive therapy with antilymphocyte or antithymocyte globulin and cyclosporine is effective in the majority of patients but has some problems including relapse or clonal evolution. Recently, there have been clinical trials of immunosuppression with hematopoietic growth factors or other drugs. Allogeneic hematopoietic stem cell transplantation (HSCT) is curative in children with severe aplastic anemia. The overall survival in HSCT from HLA-identical sibling is higher than alternative donor, including HLA matched unrelated donor or cord blood. We have to consider quality of life after HSCT because of high survival rate. However, chronic graft versus host disease and graft failure are important factors that affect the quality of life and overall survival. We need further investigation to make new regimens aimed at overcoming these risk factors and perform clinical trials.

• Genomics & Informatics
• /
• v.18 no.1
• /
• pp.3.1-3.8
• /
• 2020

Patient-derived xenograft (PDX) mouse models are frequently used to test the drug efficacy in diverse types of cancer. They are known to recapitulate the patient characteristics faithfully, but a systematic survey with a large number of cases is yet missing in lung cancer. Here we report the comparison of genomic characters between mouse and patient tumor tissues in lung cancer based on exome sequencing data. We established PDX mouse models for 132 lung cancer patients and performed whole exome sequencing for trio samples of tumor-normal-xenograft tissues. Then we computed the somatic mutations and copy number variations, which were used to compare the PDX and patient tumor tissues. Genomic and histological conclusions for validity of PDX models agreed in most cases, but we observed eight (~7%) discordant cases. We further examined the changes in mutations and copy number alterations in PDX model production and passage processes, which highlighted the clonal evolution in PDX mouse models. Our study shows that the genomic characterization plays complementary roles to the histological examination in cancer studies utilizing PDX mouse models.

• 한국생물공학회:학술대회논문집
• /
• 2005.10a
• /
• pp.899-903
• /
• 2005

Two infectious species of Streptococcosis pathogens were detected by multiplex PCR assay. Detection rates of Streptococcus iniae and S. parauberis could reach 44.9% and 55.1% respectively for one year during 2004 to 2005 in Jeju island. These findings showed that S. parauberis strains were important pathogen with streptococcosis of olive flounder in Jeju island. These findings showed that S. parauberis strains were important pathogen with streptococcosis of olive flounder in Jeiu island. In the present study we have investigated the interspecific relationship of all Jeju area of S. parauberis by RAPD analysis. Represent strains divided to four groups by RAPD fingerprints. The important differences observed between the olive flounder isolates suggest that they could constitute a well-differentiated group or a separate clonal line within this bacterial species. Though, serological research of S. parauberis strains in Jeju island not exist yet. These strains doing the serological evolution.

• Journal of Microbiology
• /
• v.45 no.1
• /
• pp.69-74
• /
• 2007

Escherichia coli is a clonal species, and occurs as both commensal and pathogenic strains, which are normally classified on the basis of their O, H, and K antigens. The O-antigen (O-specific polysaccharide), which consists of a series of oligosaccharide (O-unit) repeats, contributes major antigenic variability to the cell surface. The O-antigen gene cluster of E. coli O66 was sequenced in this study. The genes putatively responsible for the biosynthesis of dTDP-6-deoxy-L-talose and GDP-mannose, as well as those responsible for the transfer of sugars and for O-unit processing were identified based on their homology. The function of the wzy gene was confirmed by the results of a mutation test. Genes specific for E. coli O66 were identified via PCR screening against representatives of 186 E. coli and Shigella O type strains. The comparison of intergenic sequences located between galF and the O-antigen gene cluster in a range of E. coli and Shigella showed that this region may perform an important function in the homologous recombination of the O-antigen gene clusters.