• 제목/요약/키워드: information biology

검색결과 1,487건 처리시간 0.032초

Spot the difference: Solving the puzzle of hidden pictures in the lizard genome for identification of regeneration factors

  • Chung, Jin Woong
    • BMB Reports
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    • 제49권5호
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    • pp.249-254
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    • 2016
  • All living things share some common life processes, such as growth and reproduction, and have the ability to respond to their environment. However, each type of organism has its own specialized way of managing biological events. Genetic sequences determine phenotypic and physiological traits. Based on genetic information, comparative genomics has been used to delineate the differences and similarities between various genomes, and significant progress has been made in understanding regenerative biology by comparing the genomes of a variety of lower animal models of regeneration, such as planaria, zebra fish, and newts. However, the genome of lizards has been relatively ignored until recently, even though lizards have been studied as an excellent amniote model of tissue regeneration. Very recently, whole genome sequences of lizards have been uncovered, and several attempts have been made to find regeneration factors based on genetic information. In this article, recent advances in comparative analysis of the lizard genome are introduced, and their biological implications and putative applications for regenerative medicine and stem cell biology are discussed.

한반도 미기록속 Eocanthecona Bergroth (노린재목: 노린 재아목: 노린재과: 주둥이노린재아과)에 대한 보고 (A New record of Genus Eocanthecona Bergroth (Hemiptera: Heteroptera: Pentatomidae: Asopinae) from the Korean Peninsula)

  • 이호단;김정곤;정성훈
    • 한국응용곤충학회지
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    • 제54권3호
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    • pp.257-261
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    • 2015
  • 한반도 주둥이노린재과의 미기록속 Eocanthecona 속을 처음으로 확인하고 Eocanthecona japanicola (Esaki & Ishihara, 1950)의 한반도 분포를 보고한다. 성충표본과 생식기 사진 등의 형태학적 정보 및 생태학적 정보가 함께 제공된다.

Efficient Mining of Interesting Patterns in Large Biological Sequences

  • Rashid, Md. Mamunur;Karim, Md. Rezaul;Jeong, Byeong-Soo;Choi, Ho-Jin
    • Genomics & Informatics
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    • 제10권1호
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    • pp.44-50
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    • 2012
  • Pattern discovery in biological sequences (e.g., DNA sequences) is one of the most challenging tasks in computational biology and bioinformatics. So far, in most approaches, the number of occurrences is a major measure of determining whether a pattern is interesting or not. In computational biology, however, a pattern that is not frequent may still be considered very informative if its actual support frequency exceeds the prior expectation by a large margin. In this paper, we propose a new interesting measure that can provide meaningful biological information. We also propose an efficient index-based method for mining such interesting patterns. Experimental results show that our approach can find interesting patterns within an acceptable computation time.

An Information-based Model for an Interactive Web Service with Agricultural Biotechnology

  • Kim, Chang-Kug;Seo, Young-Joo;Park, Dong-Suk;Hahn, Jang-Ho
    • Genomics & Informatics
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    • 제9권2호
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    • pp.85-88
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    • 2011
  • The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a biological information-based database. The major functions of the NABIC are focused on biotechnological developments for agricultural bioinformatics and providing a web-based service to construct bioinformatics workflows easily, such as protein function prediction and genome systems biology programs. The NABIC has concentrated on the functional genomics of major crops, building an integrated biotechnology database for agro-biotech information that focuses on the proteomics of major agricultural resources, such as rice, Chinese cabbage, rice Ds-tagging lines, and microorganisms.

Analysis of Partial cDNA Sequence from Human Fetal Liver

  • Kim, Jae-Wha;Song, Jae-Chan;Lee, In-Ae;Lee, Young-Hee;Nam, Myoung-Soo;Hahn, Yoon-Soo;Chung, Jae-Hoon;Choe, In-Seong
    • BMB Reports
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    • 제28권5호
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    • pp.402-407
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    • 1995
  • Single-run Partial cDNA sequencing was conducted on 1,592 randomly selected human fetal liver cDNA clones of Korean origin to isolate novel genes related to liver functions. Each partial cDNA sequence determined was analyzed by comparing it with the databases. GenBank, Protein Information Resource (PIR) and SWISS-PROT Protein Sequence Data Bank. From a set of 1.592 cDNA clones reported here, 1,433 (90.0% of the total) were informative cDNA sequences. The other 159 clones were identified as DNA sequences which had originated from the cloning vector. Among 1,433 informative partial cDNA sequences, 851 (59.3%) clones were revealed to be identical to known human genes. These known genes have been classified into 225 different kinds of genes. In addition, 340 clones (23.7%) showed various degrees of homology to previously known human genes. Ninety four (6.6%) clones contained various repeated sequences. Twenty four (1.7%) partial cDNA sequences were found to have considerable homology to known genes from evolutionarily distant organism such as yeast, rice, Arabidopsis, mouse and rat, based on database matches, whereas 124 (8.7%) had no Significant matches. Human homologues to functionally characterized genes from different organisms could be classified as candidates for novel human genes of similar functions. Information from the partial cDNA sequences in this study may facilitate the analysis of genes expressed in human fetal liver.

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Molecular Phylogeny and Geography of Korean Medaka Fish (Oryzias latipes)

  • Kang, Tae-Wook;Lee, Eun-Hye;Kim, Moo-Sang;Paik, Sang-Gi;Kim, Sang-Soo;Kim, Chang-Bae
    • Molecules and Cells
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    • 제20권1호
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    • pp.151-156
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    • 2005
  • The phylogeny and geography of the medaka (Oryzias latipes) populations of Korea were investigated by analyzing sequence data for the mitochondrial control region. From the 41 haplotypes including 25 Korean haplotypes detected in 64 Korean specimens and data for the Japanese and Chinese populations, phylogenetic and nested clade analyses were executed to examine the phylogeny of haplogroups and the relation of the genetic architecture of the haplotypes to the historical geography of the Korean medaka fish. The analyses suggest that there are two very distinct lineages of Korean medaka, and that these result from reproductive isolation mechanisms due to geographic barriers. The southeastern lineage has experienced recent range expansion to the western region. The northwestern lineage, sister to Chinese populations, showed evidence of internal range expansion with shared haplotypes.

Lineage Tracing: Computational Reconstruction Goes Beyond the Limit of Imaging

  • Wu, Szu-Hsien (Sam);Lee, Ji-Hyun;Koo, Bon-Kyoung
    • Molecules and Cells
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    • 제42권2호
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    • pp.104-112
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    • 2019
  • Tracking the fate of individual cells and their progeny through lineage tracing has been widely used to investigate various biological processes including embryonic development, homeostatic tissue turnover, and stem cell function in regeneration and disease. Conventional lineage tracing involves the marking of cells either with dyes or nucleoside analogues or genetic marking with fluorescent and/or colorimetric protein reporters. Both are imaging-based approaches that have played a crucial role in the field of developmental biology as well as adult stem cell biology. However, imaging-based lineage tracing approaches are limited by their scalability and the lack of molecular information underlying fate transitions. Recently, computational biology approaches have been combined with diverse tracing methods to overcome these limitations and so provide high-order scalability and a wealth of molecular information. In this review, we will introduce such novel computational methods, starting from single-cell RNA sequencing-based lineage analysis to DNA barcoding or genetic scar analysis. These novel approaches are complementary to conventional imaging-based approaches and enable us to study the lineage relationships of numerous cell types during vertebrate, and in particular human, development and disease.

In situ analysis of the bacterial community associated with the Korean salty fermented seafood jeotgal

  • Hyunjun Kim;Yoomin Ahn;Chulhee Park;Eungbin Kim
    • 환경생물
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    • 제39권4호
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    • pp.515-522
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    • 2021
  • Jeotgal is a salty and fermented traditional Korean fish sauce. Unlike most other previous studies that investigated samples purchased from retail markets, this study focused on samples of jeotgal with traceable history to Yeonggwang, a timehonored fishing village in Korea. Three jeotgal samples, which were made from small yellow croakers, largehead hairtail, and miscellaneous fish, were selected based on information obtained from interviews with local craftsmen and literature reviews. Bacterial community profiles of the three jeotgal samples were investigated to identify indicator (and potentially core) bacteria for jeotgal ripening. The 16S rRNA gene-based metagenomic analysis revealed that the dominant phyla and classes, (Gammaproteobacteria, Betaproteobacteria, Bacilli, and Clostridia) of the three different jeotgal were identical, albeit with different composition ratios. Diversification was evident beginning at the order level. Interestingly, each dominant order was mainly comprised of single members even at the genus level. The dominant genera included Halomonas, Tetragenococcus, Halanaerobium, Pseudomonas, Massilia, and Lentibacillus. This observed genus-level heterogeneity suggests that there are diverse bacterial signatures in jeotgal and that these can be used as indicators for jeotgal ripening and/or as starters to increase its sensory quality and functionality.