• Title/Summary/Keyword: gene discovery

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First Discovery of Stereostratum corticioides Causing Rust on the Culm of the Bamboo Pseudosasa japonica

  • Su-Hyun Kim;Tae-Jin Choi
    • 식물병연구
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    • 제30권1호
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    • pp.20-25
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    • 2024
  • A fungus strain Stereostratum corticioides PKVL1, belonging to the family Pucciniaceae that causes rust in plants, was discovered on the sheath of the bamboo Pseudosasa japonica leading to the death of the infected bamboo in the following year. Microscopic observation of the yellow fungal mass revealed teliospores with an oval, one-septate (two-celled) structure. The average length and width of teliospores were 31.83±3.57 ㎛ and 20.74±1.72 ㎛, respectively. The large-subunit ribosomal RNA gene was amplified using the LR0R and LR7 primers, showing that the strain PKVL1 had a similarity of 99.34% to previously reported S. corticioides. In particular, the two Stereostratum strains form a separate cluster among the fungi in the family Pucciniaceae. This is the first report in the Republic of Korea of fungal rust occurring on the culm of bamboo rather than on the leaves.

Cryptic variation, molecular data, and the challenge of conserving plant diversity in oceanic archipelagos: the critical role of plant systematics

  • Crawford, Daniel J.;Stuessy, Tod F.
    • 식물분류학회지
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    • 제46권2호
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    • pp.129-148
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    • 2016
  • Plant species on oceanic islands comprise nearly 25% of described vascular plants on only 5% of the Earth's land surface yet are among the most rare and endangered plants. Conservation of plant biodiversity on islands poses particular challenges because many species occur in a few and/or small populations, and their habitats on islands are often disturbed by the activity of humans or by natural processes such as landslides and volcanoes. In addition to described species, evidence is accumulating that there are likely significant numbers of "cryptic" species in oceanic archipelagos. Plant systematists, in collaboration with others in the botanical disciplines, are critical to the discovery of the subtle diversity in oceanic island floras. Molecular data will play an ever increasing role in revealing variation in island lineages. However, the input from plant systematists and other organismal biologists will continue to be important in calling attention to morphological and ecological variation in natural populations and in the discovery of "new" populations that can inform sampling for molecular analyses. Conversely, organismal biologists can provide basic information necessary for understanding the biology of the molecular variants, including diagnostic morphological characters, reproductive biology, habitat, etc. Such basic information is important when describing new species and arguing for their protection. Hybridization presents one of the most challenging problems in the conservation of insular plant diversity, with the process having the potential to decrease diversity in several ways including the merging of species into hybrid swarms or conversely hybridization may generate stable novel recombinants that merit recognition as new species. These processes are often operative in recent radiations in which intrinsic barriers to gene flow have not evolved. The knowledge and continued monitoring of plant populations in the dynamic landscapes on oceanic islands are critical to the preservation of their plant diversity.

PubMine: An Ontology-Based Text Mining System for Deducing Relationships among Biological Entities

  • Kim, Tae-Kyung;Oh, Jeong-Su;Ko, Gun-Hwan;Cho, Wan-Sup;Hou, Bo-Kyeng;Lee, Sang-Hyuk
    • Interdisciplinary Bio Central
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    • 제3권2호
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    • pp.7.1-7.6
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    • 2011
  • Background: Published manuscripts are the main source of biological knowledge. Since the manual examination is almost impossible due to the huge volume of literature data (approximately 19 million abstracts in PubMed), intelligent text mining systems are of great utility for knowledge discovery. However, most of current text mining tools have limited applicability because of i) providing abstract-based search rather than sentence-based search, ii) improper use or lack of ontology terms, iii) the design to be used for specific subjects, or iv) slow response time that hampers web services and real time applications. Results: We introduce an advanced text mining system called PubMine that supports intelligent knowledge discovery based on diverse bio-ontologies. PubMine improves query accuracy and flexibility with advanced search capabilities of fuzzy search, wildcard search, proximity search, range search, and the Boolean combinations. Furthermore, PubMine allows users to extract multi-dimensional relationships between genes, diseases, and chemical compounds by using OLAP (On-Line Analytical Processing) techniques. The HUGO gene symbols and the MeSH ontology for diseases, chemical compounds, and anatomy have been included in the current version of PubMine, which is freely available at http://pubmine.kobic.re.kr. Conclusions: PubMine is a unique bio-text mining system that provides flexible searches and analysis of biological entity relationships. We believe that PubMine would serve as a key bioinformatics utility due to its rapid response to enable web services for community and to the flexibility to accommodate general ontology.

Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants

  • Kim, Kyung;Seong, Moon-Woo;Chung, Won-Hyong;Park, Sung Sup;Leem, Sangseob;Park, Won;Kim, Jihyun;Lee, KiYoung;Park, Rae Woong;Kim, Namshin
    • Genomics & Informatics
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    • 제13권2호
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    • pp.31-39
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    • 2015
  • Sequencing depth, which is directly related to the cost and time required for the generation, processing, and maintenance of next-generation sequencing data, is an important factor in the practical utilization of such data in clinical fields. Unfortunately, identifying an exome sequencing depth adequate for clinical use is a challenge that has not been addressed extensively. Here, we investigate the effect of exome sequencing depth on the discovery of sequence variants for clinical use. Toward this, we sequenced ten germ-line blood samples from breast cancer patients on the Illumina platform GAII(x) at a high depth of ${\sim}200{\times}$. We observed that most function-related diverse variants in the human exonic regions could be detected at a sequencing depth of $120{\times}$. Furthermore, investigation using a diagnostic gene set showed that the number of clinical variants identified using exome sequencing reached a plateau at an average sequencing depth of about $120{\times}$. Moreover, the phenomena were consistent across the breast cancer samples.

Unrecorded species of Korean invertebrates discovered through the project of 'Discovery of Korean Indigenous Species' III

  • Su-Jung Ji;Jongwoo Jung;Sa Heung Kim;Dong-Ha Ahn;Min-Seop Kim;Jeounghee Lee;Hee-Min Yang;Geon Hyuk Lee;Eunjung Nam;Taeseo Park;Anna B. Jost;Huyen T. M. Pham;Jina Park;Joohee Park;Seoyoung Keum;Ivana Karanovic;Tomislav Karanovic;Joong-Ki Park;Chuleui Jung;Gi-Sik Min
    • Journal of Species Research
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    • 제12권4호
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    • pp.341-354
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    • 2023
  • This is the third series of catalogs reporting on Korean species discovered through the 'Discovery of Korean Indigenous Species'. This catalog includes 22 species of invertebrates, excluding insects. The catalog includes the scientific name, an abridged list of synonyms, collection sites, distribution, diagnosis, and figures for each species. Additionally, we provide the newly assigned Korean name, specimen voucher, and, if available, mitochondrial CO1 or 16S gene sequences of the species listed. All species identified and documented here will be officially listed on the 'National Species List of Korea', a database maintained by the National Institute of Biological Resources(NIBR).

An International Collaborative Program To Discover New Drugs from Tropical Biodiversity of Vietnam and Laos

  • Soejarto, Djaja D.;Pezzuto, John M.;Fong, Harry H.S.;Tan, Ghee Teng;Zhang, Hong Jie;Tamez, Pamela;Aydogmus, Zeynep;Chien, Nguyen Quyet;Franzblau, Scott G.;Gyllenhaal, Charlotte;Regalado, Jacinto C.;Hung, Nguyen Van;Hoang, Vu Dinh;Hiep, Nguyen Tien;Xuan, Le Thi;Hai, Nong Van;Cuong, Nguyen Manh;Bich, Truong Quang;Loc, Phan Ke;Vu, Bui Minh;Southavong, Boun Hoong
    • Natural Product Sciences
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    • 제8권1호
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    • pp.1-15
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    • 2002
  • An International Cooperative Biodiversity Group (ICBG) program based at the University of Illinois at Chicago initiated its activities in 1998, with the following specific objectives: (a) inventory and conservation of of plants of Cuc Phuong National Park in Vietnam and of medicinal plants of Laos; (b) drug discovery (and development) based on plants of Vietnam and Laos; and (c) economic development of communities participating in the ICBG project both in Vietnam and Laos. Member-institutions and an industrial partner of this ICBG are bound by a Memorandum of Agreement that recognizes property and intellectual property rights, prior informed consent for access to genetic resources and to indigenous knowledge, the sharing of benefits that may arise from the drug discovery effort, and the provision of short-term and long-term benefits to host country institutions and communities. The drug discovery effort is targeted to the search for agents for therapies against malaria (antimalarial assay of plant extracts, using Plasmodium falciparum clones), AIDS (anti-HIV-l activity using HOG.R5 reporter cell line (through transactivation of the green fluorescent protein/GFP gene), cancer (screening of plant extracts in 6 human tumor cell lines - KB, Col-2, LU-l, LNCaP, HUVEC, hTert-RPEl), tuberculosis (screening of extracts in the microplate Alamar Blue assay against Mycobacterium tuberculosis $H_{37}Ra\;and\;H_{37}Rv),$ all performed at UIC, and CNS-related diseases (with special focus on Alzheimer's disease, pain and rheumatoid arthritis, and asthma), peformed at Glaxo Smith Kline (UK). Source plants were selected based on two approaches: biodiversity-based (plants of Cuc Phuong National Park) and ethnobotany-based (medicinal plants of Cuc Phuong National Park in Vietnam and medicinal plants of Laos). At mc, as of July, 2001, active leads had been identified in the anti-HIV, anticancer, antimalarial, and anti- TB assay, after the screening of more than 800 extracts. At least 25 biologically active compounds have been isolated, 13 of which are new with anti-HIV activity, and 3 also new with antimalarial activity. At GSK of 21 plant samples with a history of use to treat CNS-related diseases tested to date, a number showed activity against one or more of the CNS assay targets used, but no new compounds have been isolated. The results of the drug discovery effort to date indicate that tropical plant diversity of Vietnam and Laos unquestionably harbors biologically active chemical entities, which, through further research, may eventually yield candidates for drug development. Although the substantial monetary benefit of the drug discovery process (royalties) is a long way off, the UIC ICBG program provides direct and real-term benefits to host country institutions and communities.

인체세포주에서 저선량 $^{99m}Tc$에 의해 발현되는 방사선 적응반응에 관련된 유전자에 관한 연구 (Genes Associated with Radiation Adaptive Response Induced by Low Level Radiation from $^{99m}Tc$ in Human Cell Lines)

  • 권안성;범희승;최찬;김지열;임욱빈
    • 대한핵의학회지
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    • 제35권5호
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    • pp.313-323
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    • 2001
  • 목적: 저선량 방사선에 의해 그 이후의 고선량 방사선에 저항이 생기는 유익한 반응을 보인다는 방사선적응반응이라는 현상이 알려져 있지만, 저선량 방사선이 어떤 기작에 의해 이런 반응을 일으키는지에 대해서는 아직 알려지지 않고 있다. 본 연구에서는 정상 인체세포주에서 저선량 $^{99m}Tc$에 의해 방사선적응반응이 유도되는지를 확인하고, 이 때 활성화되는 유전자를 찾아보고자 하였다. 대상 및 방법: 인체 정상 림프구 세포주인 NC-37 세포주 $2{\times}10^6mL$개의 세포에 $^{99m}Tc$을 148 MBq/mL로부터 148 Bq/mL의 농도가 되도록 10배씩 희석하여 첨가하고 44시간동안 배양하였다. 결과: 각각의 군에 대해 이상 염색체를 계수하여 148 KBq/mL의 $^{99m}Tc$을 첨가한 군에서 방사선적응반응이 가장 현저하게 유도되었음을 확인하였다. 이 세포군에서 mRNA를 추출하고 여기에서 cDNA를 만든 후 gene discovery array (GDA) 여과기를 이용하여 대조군에 비해 발현이 증가된 casein kinase II beta chain, immunoglobulin, HLA-B 그리고 아직 알려지지 않은 2개의 유전자 등 6개의 유전자를 찾아내었다. Representational difference analysis (RDA)법을 통해서는 대조군에 비해 발현이 증가된 유전자 클론을 20개 찾아내었다. 결론: 인체세포주 NC-37에서 저선량의 $^{99m}Tc$에 의해 방사선적응반응이 유도된다는 사실을 밝혔으며, 이때 다수의 유전자가 발현된다는 사실을 알 수 있었다.

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SNP Discovery in the Leptin Promoter Gene and Association with Meat Quality and Carcass Traits in Korean Cattle

  • Chung, E.R.;Shin, S.C.;Shin, K.H.;Chung, K.Y.
    • Asian-Australasian Journal of Animal Sciences
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    • 제21권12호
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    • pp.1689-1695
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    • 2008
  • Leptin, the hormone product of the obese gene, is secreted predominately from white adipose tissue and regulates feed intake, energy metabolism and body composition. It has been considered a candidate gene for performance, carcass and meat quality traits in beef cattle. The objective of this study was to identify SNPs in the promoter region of the leptin gene and to evaluate the possible association of the SNP genotypes with carcass and meat quality traits in Korean cattle. We identified a total of 25 SNPs in the promoter region (1,208-3,049 bp upstream from the transcription start site) of the leptin gene, eleven (g.1508C>G, g.1540G>A, g.1545G>A, g.1551C>T, g.1746T>G, g.1798ins(G), g.1932del(T), g.1933del(T), g.1934del(T), g.1993C>T and g.2033C>T) of which have not been reported previously. Their sequences were deposited in GenBank database with accession number DQ202319. Genotyping of the SNPs located at positions g.2418C>G and g.2423G>A within the promoter region was performed by direct sequencing and PCR-SSCP method to investigate the effects of SNP genotypes on carcass and meat quality traits in Korean cattle. The SNP and SSCP genotypes from the two mutations of the leptin promoter were shown to be associated with the BF trait. The average BF value of animals with heterozygous SNP genotype was significantly greater than that of animals with the homozygous SNP genotypes for the g.2418C>G and g.2423G>A SNPs (p<0.05). Analysis of the combined genotype effect in both SNPs showed that animals with the AC SSCP genotype had higher BF value than animals with BB or AA SSCP genotypes (p<0.05). These results suggest that SNP of the leptin promoter region may be useful markers for selection of economic traits in Korean cattle.

Laser Capture Microdissection을 이용한 유전자 발현 연구 (III) -생쥐 착상 부위 자궁 내강상피 조직에서 배아 병치 기간 동안 일어나는 유전자 발현에 관한 Microarray 분석- (Analysis of the Gene Expression by Laser Capture Microdissection (III) -Microarray Analysis of the Gene Expression at the Mouse Uterine Luminal Epithelium of the Implantation Sites during Apposition Period-)

  • 윤세진;전은현;박창은;고정재;최동희;차광열;김세년;이경아
    • Clinical and Experimental Reproductive Medicine
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    • 제29권4호
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    • pp.323-335
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    • 2002
  • Object: The present study was accomplished to obtain a gene expression profile of the luminal epithelium during embryo apposition in comparison of implantation (1M) and interimplantation (INTER) sites. Material and Method: The mouse uterine luminal epithelium from IM and INTER sites were sampled on day 4.5 (Day of vaginal plug = day 0.5) by Laser Captured Microdissection (LCM). RNA was extracted from LCM captured epithelium, amplified, labeled and hybridized to microarrays. Results from microarray hybridization were analyzed by Significance Analysis of Microarrays (SAM) method. Differential expression of some genes was confirmed by LCM followed by RT-PCR. Results: Comparison of IM and INTER sites by SAM identified 73 genes most highly ranked at IM, while 13 genes at the INTER sites, within the estimated false discovery rate (FDR) of 0.163. Among 73 genes at IM, 20 were EST/unknown function, and the remain 53 were categorized to the structural, cell cycle, gene/protein expression, immune reaction, invasion, metabolism, oxidative stress, and signal transduction. Of the 24 structural genes, 14 were related especially to extracellular matrix and tissue remodeling. Meanwhile, among 13 genes up-regulated at INTER, 8 genes were EST/unknown function, and the rest 5 were related to metabolism, signal transduction, and gene/protein expression. Among these 58 (53+5) genes with known functions, 13 genes (22.4%) were related with $Ca^{2+}$ for their function. Conclusions: Results of the present study suggest that 1) active tissue remodeling is occurring at the IM sites during embryo apposition, 2) the INTER sites are relatively quiescent than IM sites, and 3) the $Ca^{2+}$ may be a crucial for apposition. Search for human homologue of those genes expressed in the mouse luminal epithelium during apposition will help to understand the implantation process and/or implantation failure in humans.

MNNG 처리에 의해 조절되는 암발생 유발 유전자의 조사 (MNNG-Regulated Differentially Expressed Genes that Contribute to Cancer Development in Stomach Cells)

  • 김태진;김명관;정동주
    • 대한임상검사과학회지
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    • 제53권4호
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    • pp.353-362
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    • 2021
  • 암은 전 세계적인 건강문제이다. 암의 종류는 다양하나 암의 발생과정에서의 유사성은 상당히 높다. 모든 암은 유전자의 발현 변화가 있다는 점에서 공통점을 갖는다. 암 발생과정에서 변화되는 유전자의 발현을 이해하는 것은 암치료제나 암백신 개발에 큰 도움을 줄 것이다. 이번 연구에서는 잘 알려진 암발생 물질인 MNNG를 이용하여 정상 위세포에서 암발생 시 변화되는 유전자 발현을 분석하였다. MNNG 처리에 의해 정상 세포와는 다르게 발현되는 유전자인 DEG들을 찾고 이들을 암세포에서 발현되는 DEG들과 비교하였다. 여기에 더해 DEG의 단백질 결과물들의 기능과 단백질들 간의 결합을 분석하여 단순히 유전자의 발현뿐만 아니라 이들 단백질의 신호전달 과정에서의 연관성도 함께 분석하였다. 이 결과 위암 발생과정에서 관여하는 유전자들과 이들 유전자의 단백질 결과물들의 상호 작용을 밝히게 되었다.