• 한국정보과학회논문지:소프트웨어및응용
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• 제35권6호
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• pp.347-356
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• 2008

마이크로어레이는 분자 생물학 실험에 있어 중요한 도구로 사용되고 있으며, 마이크로어레이 데이타 분석을 위한 다양한 계산학적 방법이 개발되어 왔다. 그러나, 기존 분석방법은 주어진 조건에 영향을 주는 개별 유전자를 추출하는 데 강한 방면, 유전자 간의 복합작용에 의한 영향을 분석하기 힘들다는 단점을 가지고 있다. 하이퍼망 모델은 생물학적인 네트워크 작용을 모방한 구조이며, 계산과정에서 요소간의 복합작용을 직접 고려하기 때문에 기존 방법에서 다루기 힘들었던 요소간 상호작용 분석이 가능하다는 장점을 가진다. 본 논문에서는 마이크로어레이 데이타를 기반으로 microRNA(miRNA) 프로파일 분석을 위한 하이퍼망 분류 기법을 소개한다. 하이퍼망 분류기는 miRNA 쌍을 기본 요소로 하여 진화 과정을 통해 miRNA 분류 데이타를 학습한다. 학습된 하이퍼망으로부터 유의하다.고 판단되는 miRNA 모듈을 쉽게 추출할 수 있으며, 사용자는 추출된 모듈의 유치미성을 직접 판단할 수 있다. 하이퍼망 분류기는 암 관련 miRNA 발현 데이타 분류 실험을 통해 91.46%의 정확도를 보임으로써 기존 기계학습 방법에 비해 뛰어난 성능을 보여주었으며, 하이퍼망 분석을 통해 생물학적으로 유의한 miRNA 모듈을 찾을 수 있음을 확인하였다.

• 한국발생생물학회지:발생과생식
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• 제7권1호
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• pp.1-7
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• 2003

사람을 비롯한 대부분의 동물들은 주변 환경의 영향을 받아 주기적인 생활을 영위하고 있다. 지구의 자전 및 공전으로 그리고 국소적으로 발생되는 주기적인 변화는 생명체의 행동으로 뚜렷하게 표출된다. 이러한 환경의 주기적인 변화는 오랜 기간의 진화과정을 통하여 생명체 내의 유전자로 각인되었으며, 이 유전자들은 발생 과정을 포함하는 성장 과정에서 리듬으로 발현된다. 환경의 변화는 결국 유전자로 정착하여 생체 시계로서 작용하며, 시상하부의 시신경교차상핵(suprachiasmatic nucleus, SCN)이 유력한 해부학적 위치이다. 따라서 생체 시계는 지구상에 살고 있는 생명체의 각종 리듬을 지배하여, 출생 및 사망, 수명, 행동, 생리, 세포 분열, 생화학적 반응 등등에 영향을 미친다. 리듬은 서서히 변화하는 환경의 변화에 맞도록 재조정된다. 생체 시계는 규칙적인 환경 변화를 예측하고 이에 미리 대비하게 하는 장점을 지니고 있다.

• BMB Reports
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• 제44권10호
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• pp.680-685
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• 2011

The AT-hook motif is a small DNA-binding protein motif that has been found in the high mobility group of non-histone chromosomal proteins. The Arabidopsis genome contains 29 genes encoding the AT-hook motif DNA-binding protein (AHL). Recent studies of Arabidopsis genes (AtAHLs) have revealed that they might play diverse functional roles during plant growth and development. In this report, we mined 20 AHL genes (OsAHLs) from the rice genome database using AtAHL genes as queries and characterized their molecular features. A phylogenetic tree revealed that OsAHL proteins can be classified into 2 evolutionary clades. Tissue expression pattern analysis revealed that all of the OsAHL genes might be functionally expressed genes with 3 distinct expression patterns. Nuclear localization analysis using transgenic Arabidopsis showed that several OsAHL proteins are exclusively localized in the nucleus, indicating that they may act as architectural transcription factors to regulate expression of their target genes during plant growth and development.

• BMB Reports
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• 제43권2호
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• pp.115-121
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• 2010

A large data set of Hanwoo (Korean cattle) ESTs was analyzed to obtain differential gene expression results for the following three libraries: intramuscular fat, longissimus dorsi muscle and liver. To better understand the gene expression profiles, we identified differentially expressed genes (DEGs) via digital gene expression analysis. Hierarchical clustering of genes was performed according to their relative abundance within the six separate groups (Hanwoo fat versus non-Hanwoo fat, Hanwoo muscle versus non-Hanwoo muscle and Hanwoo liver versus non-Hanwoo liver), producing detailed patterns of gene expression. We determined the quantitative traits associated with the highly expressed genes. We also provide the first list of putative regulatory elements associated with differential tissue expression in Hanwoo cattle. In addition, we conducted evolutionary analysis that suggests a subset of genes accelerated in the bovine lineage are strongly correlated with their expression in Hanwoo muscle.

• ALGAE
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• 제29권3호
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• pp.227-235
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• 2014

The red seaweed, Gracilaria tikvahiae McLachlan, was cultivated in open water farms in urbanized estuaries of Long Island Sound (26-30 psu of salinity) and New York City (20-25 psu), USA in 2011. Plants were harvested monthly from summer (August, $24^{\circ}C$) to fall (November, $13^{\circ}C$) and analyzed for total nitrogen, protein, and amino acid content. On a dry matter (DM) basis, nitrogen and protein significantly increased over the harvest period until October and then plateaued. Nitrogen increased from $22{\pm}1g\;kg^{-1}$ DM in August to $39{\pm}3g\;kg^{-1}$ DM in October (p < 0.001). Protein increased from $107{\pm}13g\;kg^{-1}$ DM in August to $196{\pm}5g\;kg^{-1}$ DM in November (p < 0.001). With two exceptions, amino acid concentrations expressed on a crude protein (CP) basis were similar over the harvest period. Essential amino acids accounted for $48{\pm}1%$ of all amino acids present with lysine and methionine averaging $56{\pm}2g\;kg^{-1}$ CP and $18{\pm}1g\;kg^{-1}$ CP, respectively. Histidine was underrepresented among essential amino acids and averaged $13{\pm}1g\;kg^{-1}$ CP. Taurine ranged from 2.1 to $3.2g\;kg^{-1}$ DM. With its moderate levels of lysine, methionine and taurine, ocean farmed G. tikvahiae has the potential of overcoming many nutrient deficiencies currently associated with terrestrial plant ingredients in alternative feeds for fish and shrimp.

• Journal of Plant Biotechnology
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• 제39권1호
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• pp.49-61
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• 2012

This review summarises the biology, discovery and applications of single nucleotide polymorphisms in complex polyploid crop genomes, with a focus on the important oilseed crop $Brassica$ $napus$. $Brassica$ $napus$ is an allotetraploid species, and along with soybean and oil palm is one of the top three most important oilseed crops globally. Current efforts are well underway to $de$ $novo$ assemble the $B.$ $napus$ genome, following the release of the related $B.$ $rapa$ 'A' genome last year. The next generation of genome sequencing, SNP discovery and analysis pipelines, and the associated challenges for this work in $B.$ $napus$, will be addressed. The biological applications of SNP technology for both evolutionary and molecular geneticists as well as plant breeders and industry are far-reaching, and will be invaluable to our understanding and advancement of the $Brassica$ crop species.

• Parasites, Hosts and Diseases
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• 제56권2호
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• pp.189-194
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• 2018

To determine that Paragonimus sp. is actively transmitted in a tropical area of the Pacific region of Ecuador where human cases of pulmonary paragonimiasis have recently been documented, a total of 75 freshwater crabs were collected from 2 different streams in the Pedernales area of $Manab\acute{i}$ Province, Ecuador. All collected crabs were identified as Hypolobocera guayaquilensis based on morphological characteristics of the male gonopods. The hepatopancreas of each crab was examined by compressing it between 2 glass plates followed by observation under a stereomicroscope. Excysted Paragonimus metacercariae were detected in 39 (52.0%) crabs and their densities varied from 1 to 32 per infected crab. There was a positive relationship between crab size and metacercarial density. Sequences of the second internal transcribed spacer region of the ribosomal RNA gene of the Paragonimus metacercariae obtained in this study were identical to those of Paragonimus mexicanus deposited in the DDBJ/EMBL/GenBank database. Thus, the present study is the first to confirm that the crab species H. guayaquilensis is the second intermediate host of P. mexicanus in $Manab\acute{i}$ Province, Ecuador. Because this crab might be the possible source of human infections in this area, residents should pay attention to improper crab-eating habits related with a neglected parasitic disease, i.e., paragonimiasis.

• Asian-Australasian Journal of Animal Sciences
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• 제20권7호
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• pp.1135-1155
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• 2007

Selenium is considered to be one of the most controversial trace elements. On the one hand, it is toxic at high doses and there is a great body of information related to environmental issues of Se contamination. On the other hand, Se deficiency is a global problem related to an increased susceptibility to various diseases of animals and humans and decreased productive and reproductive performance of farm animals. Optimisation of Se nutrition of poultry and farm animals will result in increased efficiency of egg, meat and milk production and even more important, will improve quality. From the data presented in the review it is clear that the main lesson which we have to learn from nature is how to use organic selenium in animal and human diets. Selenium-enriched yeast (Sel-Plex) is the result of such a lesson and it is just a matter of time before animal nutrition moves completely from using ineffective sodium selenite to organic selenium. Other lessons from nature will follow. Recent advances in genomics and proteomics, in association with descriptions of new selenoproteins, will be a driving force in reconsidering old approaches related to Se nutrition. Probably 90% of all Se research has been conducted with sodium selenite and we now understand that the natural form of selenium is different. The main advances in Se status assessment and Se requirements were established based on the activity of glutathione peroxidase (GSH-Px), an enzyme which for many years was considered to be the main selenoprotein. Recently it was discovered that it is only one of at least 25 various selenoproteins. Se research and practical applications are developing quickly and they are very exciting and promising.

• Journal of Microbiology and Biotechnology
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• 제19권3호
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• pp.250-256
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• 2009

Acinetobacter strain $KNF2022^T$ was isolated from tobacco plant roots during the screening of antiviral substances having inhibitory effects on Tobacco mosaic virus (TMV) and examined by phenotypic, chemotaxonomic, and genetic characterization. It was a nonmotile, Gram-negative bacterium. This strain contained Q-9 as the main respiratory quinone. The major cellular fatty acids of the isolate were 16:0, 18:1 w9c, and 16:1 w7c/15 iso 2OH. The DNA base composition was 44 mol%. Phylogenetic analysis based on the 16S rRNA sequence revealed that the isolate formed an evolutionary lineage distinct from other Acinetobacter species. Based on the evaluation of morphologic, physiologic, and chemotaxonomic characteristics, DNA-DNA hybridization values, and 16S rRNA sequence comparison, we propose the new species Acinetobacter antiviralis sp. nov., the type strain of which is $KNF2022^T$ (=KCTC $0699BP^T$).

• Journal of Microbiology and Biotechnology
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• 제27권3호
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• pp.439-449
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• 2017

Beauveria bassiana infects a number of pest species and is known to produce insecticidal substances, such as the nonribosomal peptides (NRPs) beauvericin and bassianolide. However, most NRPs and their biological roles in B. bassiana remain undiscovered. To identify NRPs that potentially contribute to pathogenesis, the 21 predicted NRP synthetases (NRPSs) or NRPS-like proteins of B. bassiana ARSEF 2860 were primarily ranked into three functional groups: basic metabolism (7 NRPSs), pathogenicity (12 NRPSs), and unknown function (2 NRPSs). Based on the transcript levels during in vivo growth on diamondback moth (Plutella xylostella (Linnaeus)), half of the Group II NRPSs were likely to be involved in infection. Given that the metabolites biosynthesized by these NRPSs remain to be determined, our result underlines the importance of the NRPSome in fungal pathogenesis, and will serve as a guide for future genomic mining projects to discover functionally essential and structurally diverse NRPs in fungal genomes.