• 제목/요약/키워드: SPECIFIC DIVERSITY

검색결과 691건 처리시간 0.029초

Comparative Genomics Profiling of Clinical Isolates of Helicobacter pylori in Chinese Populations Using DNA Microarray

  • Han, Yue-Hua;Liu, Wen-Zhong;Shi, Yao-Zhou;Lu, Li-Qiong;Xiao, Shudong;Zhang, Qing-Hua;Zhao, Guo-Ping
    • Journal of Microbiology
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    • 제45권1호
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    • pp.21-28
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    • 2007
  • In order to search for specific genotypes related to this unique phenotype, we used whole genomic DNA microarray to characterize the genomic diversity of Helicobacter pylori (H. pylori) strains isolated from clinical patients in China. The open reading frame (ORF) fragments on our microarray were generated by PCR using gene-specific primers. Genomic DNA of H. pylori 26695 and J99 were used as templates. Thirty-four H. pylori isolates were obtained from patients in Shanghai. Results were judged based on In(x) transformed and normalized Cy3/Cy5 ratios. Our microarray included 1882 DNA fragments corresponding to 1636 ORFs of both sequenced H. pylori strains. Cluster analysis, revealed two diverse regions in the H. pylori genome that were not present in other isolates. Among the 1636 genes, 1091 (66.7%) were common to all H. pylori strains, representing the functional core of the genome. Most of the genes found in the H. pylori functional core were responsible for metabolism, cellular processes, transcription and biosynthesis of amino acids, functions that are essential to H. pylori's growth and colonization in its host. In contrast, 522 (31.9%) genes were strain-specific genes that were missing from at least one strain of H. pylori. Strain-specific genes primarily included restriction modification system components, transposase genes, hypothetical proteins and outer membrane proteins. These strain-specific genes may aid the bacteria under specific circumstances during their long-term infection in genetically diverse hosts. Our results suggest 34 H. pylori clinical strains have extensive genomic diversity. Core genes and strain-specific genes both play essential roles in H. pylori propagation and pathogenesis. Our microarray experiment may help select relatively significant genes for further research on the pathogenicity of H. pylori and development of a vaccine for H. pylori.

EvoSNP-DB: A database of genetic diversity in East Asian populations

  • Kim, Young Uk;Kim, Young Jin;Lee, Jong-Young;Park, Kiejung
    • BMB Reports
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    • 제46권8호
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    • pp.416-421
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    • 2013
  • Genome-wide association studies (GWAS) have become popular as an approach for the identification of large numbers of phenotype-associated variants. However, differences in genetic architecture and environmental factors mean that the effect of variants can vary across populations. Understanding population genetic diversity is valuable for the investigation of possible population specific and independent effects of variants. EvoSNP-DB aims to provide information regarding genetic diversity among East Asian populations, including Chinese, Japanese, and Korean. Non-redundant SNPs (1.6 million) were genotyped in 54 Korean trios (162 samples) and were compared with 4 million SNPs from HapMap phase II populations. EvoSNP-DB provides two user interfaces for data query and visualization, and integrates scores of genetic diversity (Fst and VarLD) at the level of SNPs, genes, and chromosome regions. EvoSNP-DB is a web-based application that allows users to navigate and visualize measurements of population genetic differences in an interactive manner, and is available online at [http://biomi.cdc.go.kr/EvoSNP/].

Diversification and domain evolution of molluskan metallothioneins: a mini review

  • Nam, Yoon Kwon;Kim, Eun Jeong
    • Fisheries and Aquatic Sciences
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    • 제20권6호
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    • pp.8.1-8.18
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    • 2017
  • Background: Metallothionein (MT) is a multifunctional protein playing important roles in homeostatic regulation and detoxification of metals. Mollusk species have been considered as useful sentinel platforms for MT-based biomarker approaches, and they have been reported to display an extraordinary structural diversity of MT proteins. However, potential diversity of molluskan MTs has not been fully explored and recent updates have suggested the need of revision of evolutionary hypothesis for molluskan MTs. Results: Based on bioinformatic analysis and phylogenetic evidences, novel divergence mechanisms and paths were hypothesized in both gastropod and bivalve MT groups. Our analyses are suggestive of the taxon- or lineage-specific domain multiplication/duplication from the ancestral or prototypic MT. Diversification and selection of molluskan MTs might be driven by the needs for acquiring metal selectiveness, specialized novel function, and improved capacity of metal detoxification under environmentally stressed conditions. Conclusion: The structural diversity and variations of molluskan MTs are significantly larger than previously understood. Undoubtedly, molluskan MTs have undergone dynamic divergent processes in their evolutionary histories, giving rise to the great diversity of domain structures in extant MT isoforms. Novel evolutionary paths for molluskan MTs newly proposed in this review could shed additional light onto the revision of the hypothesis for evolutionary differentiation of MTs in the molluskan lineage.

Genetic Diversity Analysis of Maintaining Lines for Kenyan Sunflower (Helianthus annus L.) Using Allele Specific SSR Markers

  • Mwangi, Esther W.;Lee, Myung-Chul;Sung, Jung Suk;Marzougui, Salem;Bwalya, Ernest C.
    • 한국자원식물학회:학술대회논문집
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    • 한국자원식물학회 2019년도 춘계학술대회
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    • pp.61-61
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    • 2019
  • In any crop breeding program Selection and use of genetically diverse genotypes to develop cultivars with a broad genetic base is important. Molecular markers play a major role in selecting diverse genotypes. Molecular breeding programs of the crop can be made more efficient by use of molecular markers. The present study was done with an aim of analyzing genetic diversity and the population structure in 24 accessions of sunflower (Helianthus annus L.) from Kenya genetic diversity using 35 EST-SSR and gSSR primers.Out of the 35 markers 3 were not polymorphic as they indicated Polymorphic Information content( PIC) of value 0.00 and so the data analysis was done using 32 markers . The 32 set of markers used produced 29 alleles ranging from 2 to 7with a mean of 3.0 alleles per locus.The average value of polymorphic information contents(PIC) were 0.3 .Genetic diversity analysis using these markers revealed 3 major clusters. This result could be useful for designing strategies to make elite hybrid and inbreeding of crossing block for breeding and future molecular breeding programs to make elite variety.

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Effect of Non-indigenous Bacterial Introductions on Rhizosphere Microbial Community

  • Nogrado, Kathyleen;Ha, Gwang-Su;Yang, Hee-Jong;Lee, Ji-Hoon
    • 한국환경농학회지
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    • 제40권3호
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    • pp.194-202
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    • 2021
  • BACKGROUND: Towards achievement of sustainable agriculture, using microbial inoculants may present promising alternatives without adverse environmental effects; however, there are challenging issues that should be addressed in terms of effectiveness and ecology. Viability and stability of the bacterial inoculants would be one of the major issues in effectiveness of microbial pesticide uses, and the changes within the indigenous microbial communities by the inoculants would be an important factor influencing soil ecology. Here we investigated the stability of the introduced bacterial strains in the soils planted with barley and its effect on the diversity shifts of the rhizosphere soil bacteria. METHODS AND RESULTS: Two different types of bacterial strains of Bacillus thuringiensis and Shewanella oneidensis MR-1 were inoculated to the soils planted with barley. To monitor the stability of the inoculated bacterial strains, genes specific to the strains (XRE and mtrA) were quantified by qPCR. In addition, bacterial community analyses were performed using v3-v4 regions of 16S rRNA gene sequences from the barley rhizosphere soils, which were analyzed using Illumina MiSeq system and Mothur. Alpha- and beta-diversity analyses indicated that the inoculated rhizosphere soils were grouped apart from the uninoculated soil, and plant growth also may have affected the soil bacterial diversity. CONCLUSION: Regardless of the survival of the introduced non-native microbes, non-indigenous bacteria may influence the soil microbial community and diversity.

Simple Assessment of Taxonomic Status and Genetic Diversity of Korean Long-Tailed Goral (Naemorhedus caudatus) Based on Partial Mitochondrial Cytochrome b Gene Using Non-Invasive Fecal Samples

  • Kim, Baek-Jun
    • Proceedings of the National Institute of Ecology of the Republic of Korea
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    • 제2권1호
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    • pp.32-41
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    • 2021
  • South Korea presently harbors less than 800 long-tailed gorals (Naemorhedus caudatus), an endangered species. I report for the first time on the taxonomic status and genetic diversity of the Korean species using non-invasive fecal sampling based on mitochondrial cytochrome b gene sequence analyses. To determine the taxonomic status of this species, I reconstructed a consensus neighbor-joining tree and generated a minimum spanning network combining haplotype sequences obtained from feces with a new goral-specific primer set developed using known sequences of the Korean goral and related species (e.g., Russian goral, Chinese goral, Himalayan goral, Japanese serow, etc.). I also examined the genetic diversity of this species. The Korean goral showed only three different haplotypes. The phylogenetic tree and parsimony haplotype network revealed a single cluster of Korean and Russian gorals, separate from related species. Generally, the Korean goral has a relatively low genetic diversity compared with that of other ungulate species (e.g., moose and red deer). I preliminarily showcased the application of non-invasive fecal sampling to the study of genetic characteristics, including the taxonomic status and genetic diversity of gorals, based on mitochondrial DNA. More phylogenetic studies are necessary to ensure the conservation of goral populations throughout South Korea.

디지털 PCR을 응용한 특정 amoA유전자를 가진 질산화 Archaea 동정 (Identification of the Nitrifying Archaeal Phylotype Carrying Specific amoA Gene by Applying Digital PCR)

  • 박병준;박수제;이성근
    • 미생물학회지
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    • 제43권3호
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    • pp.232-235
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    • 2007
  • 해양 및 토양에서의 암모니아 산화는 세균에 비해 Crenarchaeota 그룹의 archaea에 의해 우세하게 일어나고 있음이 알려졌다. 서해 갯벌에서, 배양에 의존하지 알고, 특정 암모니아 산화유전자(amoA)를 가진 archaea을 동정하고자 디지털 PCR법을 응용한 nested PCR법을 개발하였다. amoA와 16S rRNA유전자가 동시에 증폭된 샘플의 분석결과, 16S rRNA유전자에 비해 amoA 유전자의 다양성 이 높았으며, I.1a 그룹의 crenarchaea가 I.1b 그룹의 crenarchaea보다 갯벌지역에서 암모니아 산화에 우점적으로 기여하고 있음을 알 수 있었다. 본 연구에서 시도된, 디지털 PCR과 multiplex-nested PCR을 접목한 접근법을 이용하면 특정 기능유전자를 가진 미생물을 환경에서 검증하는데 응용할 수 있을 것이다.

Development of PCR-Based Sequence Characterized DNA Markers for the Identification and Detection, Genetic Diversity of Didymella bryoniae with Random Amplified polymorphic DNA(RAPD)

  • Kyo, Seo-Il;Shim, Chang-Ki;Kim, Dong-Kil;Baep, Dong-Won;Lee, Seon-Chul;Kim, Hee-Kyu
    • 한국식물병리학회:학술대회논문집
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    • 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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    • pp.130-130
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    • 2003
  • Gummy stem blight pathogen is very difficult not only to monitor the inoculum levels prior to host infection, and also it is destructive and hard to control in field condition. We have applied RAPD technique to elucidate the genetic diversity of the genomic DNA of Didymella bryoniae and also to generate specific diagnostic DNA probe useful for identification and detection. The 40 primers produced clear bands consistently from the genomic DNA of twenty isolates of Didymella bryoniae, and two hundred seventy-three amplified fragments were produced with 40 primers. The combined data from 273 bands was analyzed by a cluster analysis using UPGMA method with an arithmetic average program of NTSYS-PC (Version 1.80) to generate a dendrogram. At the distance level of 0.7, two major RAPD groups were differentiated among 20 strains. RAPD group (RG) I included 8 isolates from watermelon except one isolate from melon. RAPD group (RG) IV included 12 isolates from squash, cucumber, watermelon and melon.. In amplification experiment with SCAR specific primer RG1F-RG1R resulted in a single band of 650bp fragment only for 8 isolates out of 20 isolates that should be designated as RAPD Group 1. However, same set of experiment done with RGIIF-RGIIR did not result in any amplified product.. Our attempts to detect intraspecific diversity of ITS region of rDNA by amplifying ITS region and 17s rDNA region for 20 isolates and restriction digestion of amplified fragment with 12 enzymes did not reveal polymorphic band. In order to develop RAPD markers for RGIV specific primer, a candidate PCR fragment( ≒1.4kb) was purified and Southern hybridized to the amplified fragment RGIV isolates. This promising candidate probe recognized only RGIV isolates

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아종특이적 STS 마커를 이용한 벼 품종의 유전다양성 분석 (Genetic Diversity of Rice Collections using Subspecies-specific STS Markers)

  • 김봉성;강문수;고희종
    • 한국육종학회지
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    • 제41권2호
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    • pp.101-105
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    • 2009
  • 전 세계에서 광범위하게 수집한 벼 유전자원 320개를 63개의 아종특이적마커로 분석하여 유전자원의 다양성, 유연관계 및 유전집단의 구조분석을 하여 아종특이적마커의 아종판별 효율을 검정하고 아종의 게놈 구성을 검토하고자 본 시험을 수행하였다. 1. 본 연구에서 사용한 63개의 아종특이적 마커는 벼 품종을 인디카와 자포니카 두 아종으로 구분하는데 효과적으로 이용할 수 있었다. 2. 실험에 사용한 320개의 벼 유전자원들은 자포니카군(128개)과 인디카군(178개)으로 나눌 수 있었고 Basmati370, Shennong27 등 14개 품종은 중간형 admixture형태의 품종으로 구분할 수 있었다.

시대적 맥락에 따른 문화다양성 개념의 해석과 실천: 전라북도 사례로 본 문화다양성의 지역화와 맥락적 정책 방향 (Understandings and Practices of the Concept of Cultural Diversity in the Historical Context : Localization of cultural diversity and Contextual future policies)

  • 장세길;신지원;육수현
    • 지역과문화
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    • 제8권1호
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    • pp.25-53
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    • 2021
  • 이 연구는 시대적 맥락에 따라 문화다양성의 해석과 실천이 달라졌다는 전제 아래, 문화다양성의 지역화에 필요한 정책 방향을 모색하는 데 목적이 있다. 첫째, 이 연구에서는 정치투쟁의 결과로 나타난 문화다양성 개념의 해석과 정책실천의 중층성을 분석하여 시대적 맥락에 따라 문화다양성을 해석하고 실천하는 자세가 필요함을 밝혔다. 둘째, 전라북도를 사례로 사회적 소수자가 지역에서 경험한 차별과 문화정책 관계자의 인식을 분석하여 지역에서도 문화다양성이 중층적으로 해석되고 실천됨을 확인하였다. 셋째, 정부 정책의 한계에 대응하여 지역에서 문화다양성 정책을 수립하는데 고려해야 할 방향을 제안하였다. 제안한 내용은 정책의 탈중앙화와 지역차원의 정책 발굴, '분배의 정치'에서 '인정의 정치'로 전환, 분리가 아닌 접촉면을 늘리는 상호문화주의적 접근이다.