• Asian Pacific Journal of Cancer Prevention
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• 제16권11호
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• pp.4477-4487
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• 2015

In this review we summarize the results of studies employing high-throughput methods of profiling of HPV-associated cervical intraepithelial neoplasia (CIN) and squamous cell cervical cancers at key intracellular regulatory levels to demonstrate the unique identity of the landscape of molecular changes underlying this oncopathology, and to show how these changes are related to the 'natural history' of cervical cancer progression and the formation of clinically significant properties of tumors. A step-wise character of cervical cancer progression is a morphologically well-described fact and, as evidenced by genome-wide screenings, it is indeed the consistent change of the molecular profiles of HPV-infected epithelial cells through which they progressively acquire the phenotypic hallmarks of cancerous cells. In this sense, CIN/cervical cancer is a unique model for studying the driving forces and mechanisms of carcinogenesis. Recent research has allowed definition of the whole-genome spectrum of both random and regular molecular alterations, as well as changes either common to processes of carcinogenesis or specific for cervical cancer. Despite the existence of questions that are still to be investigated, these findings are of great value for the future development of approaches for the diagnostics and treatment of cervical neoplasms.

• Communications for Statistical Applications and Methods
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• 제16권6호
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• pp.915-923
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• 2009

광범위 유전자 연관(genome-wide association) 연구에서는 무수히 많은 유전자들 중에 인간의 질병에 관련된 유전자를 찾아왔다. 기존의 인간 질병에 관련된 유전자를 찾는 방법에서 이렇게 많은 유전자들 중에서 우수한 유전자를 찾는데 직접 이용할 시에는 계산이 복잡해지고 비용이 많이 들어가며 시간이 오래 걸린다는 단점이 생긴다. 따라서 이번 수많은 유전자들 중 주요 유전자 그룹을 찾는 방법으로 SNPHarvester가 개발되였다. 본 연구에서는 인간의 질병이 아닌 한우의 여러 경제형질에 관련된 우수 유전자를 SNPHarvester를 이용하여 17 개의 SNP들 중에서 우수한 유전자 그룹을 찾았고 의사결정나무(decision tree)를 이용하여 한우의 여러 경제형질을 높일 수 있는 SNP 그룹 내의 우수 유전자형도 함께 규명할 수 있었다.

• The Plant Pathology Journal
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• 제28권4호
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• pp.428-432
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• 2012

We determined the complete genome sequence of a Vietnamese isolate of Southern rice black-streaked dwarf virus (SRBSDV). Whole genome comparisons and phylogenetic analysis showed that the genome of the Vietnamese isolate shared high nucleotide sequence identities of over 97.5% with those of the reported Chinese isolates, confirming a common origin of them. Moreover, the greatest divergence between different SRBSDV isolates was found in the segments S1, S3, S4 and S6, which differs from the sequence alignment results between SRBSDV and Rice black streaked dwarf virus (RBSDV), implying that SRBSDV evolved in a unique way independent of RBSDV. This is the first report of a complete nucleotide sequence of SRBSDV from Vietnam and our data provides new clues for further understanding of molecular variation and epidemiology of SRBSDV in Southeast Asia.

• Mycobiology
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• 제42권4호
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• pp.322-330
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• 2014

The aim of this study was to identify and characterize new Flammulina velutipes laccases from its whole-genome sequence. Of the 15 putative laccase genes detected in the F. velutipes genome, four new laccase genes (fvLac-1, fvLac-2, fvLac3, and fvLac-4) were found to contain four complete copper-binding regions (ten histidine residues and one cysteine residue) and four cysteine residues involved in forming disulfide bridges, fvLac-1, fvLac-2, fvLac3, and fvLac-4, encoding proteins consisting of 516, 518, 515, and 533 amino acid residues, respectively. Potential N-glycosylation sites (Asn-Xaa-Ser/Thr) were identified in the cDNA sequence of fvLac-1 (Asn-454), fvLac-2 (Asn-437 and Asn-455), fvLac-3 (Asn-111 and Asn-237), and fvLac4 (Asn-402 and Asn-457). In addition, the first 19~20 amino acid residues of these proteins were predicted to comprise signal peptides. Laccase activity assays and reverse transcription polymerase chain reaction analyses clearly reveal that $CuSO_4$ affects the induction and the transcription level of these laccase genes.

• Genomics & Informatics
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• 제12권4호
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• pp.165-170
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• 2014

Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available.

• 미생물학회지
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• 제54권3호
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• pp.305-307
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• 2018

이 연구에서는 PacBio RS II 플랫폼을 사용하여 동해에서 분리된 해양 미생물 Pseudoalteromonas donghaensis $HJ51^T$의 전체 유전체 서열화를 수행하였다. 그 결과, 크기 3,646,857 bp, G + C 함량 41.8%인 염색체와 함께 크기 842,855 bp, G + C 함량 41.3% 및 크기 244,204 bp, G + C 함량 40.4%인 두 개의 플라스미드로 구성된 3개의 유전체 서열을 획득하였다. 이 유전체는 4,083개의 단백질 암호화 유전자와 127개의 RNA 유전자를 포함하고 있다. 다양한 생체 고분자 분해효소의 유전자원과 대장균과 유사한 세포외 단백질 분비 숙주로서의 개발에 이용될 수 있을 것으로 생각된다.

• Mycobiology
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• 제49권3호
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• pp.294-296
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• 2021

An endolichenic fungus, Xylaria grammica strain EL000614, showed strong nematicidal effects against plant pathogenic nematode, Meloidogyne incognita by producing grammicin. We report genome assembly of X. grammica EL000614 comprised of 25 scaffolds with a total length of 54.73 Mb, N50 of 4.60 Mb, and 99.8% of BUSCO completeness. GC contents of this genome were 44.02%. Gene families associated with biosynthesis of secondary metabolites or regulatory proteins were identified out of 13,730 gene models predicted.

• 미생물학회지
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• 제55권1호
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• pp.55-57
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• 2019

페놀과 같은 단환성 화합물을 분해하는 미생물인 Runella sp. ABRDSP2 균주는 담수로부터 분리되었다. 원형으로 완성된 하나의 chromosome과 3개의 plasmid로 구성된 유전체는 GC 함량이 44.4%인 총 7,613,819 bp의 크기를 나타내며 6,006개의 유전자를 인코딩하고 있다. ABRDSP2 균주는 monooxygenase, ring-cleaving dioxygenase 및 catechol 1,2-dioxygenase 등의 다수의 방향성 탄화수소를 분해하는 유전자를 함유하고 있다. 이런 전장 유전체는 Runella sp. ABRDSP2 균주가 다양한 생분해능력이 있음을 나타낸다.

• Journal of Animal Science and Technology
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• 제63권1호
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• pp.194-197
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• 2021

Salmonella enterica is a representative foodborne pathogen in the world. The S. enterica strain K_SA184 was isolated from the lamb (Ovis aries), which was collected from a local traditional market in South Korea. In this study, the S. enterica strain K_SA184 was sequenced using PacBio RS II and Illumina NextSeq 500 platforms. The final complete genome of the S. enterica strain K_SA184 consist of one circular chromosome (4,725,087 bp) with 52.3% of guanine + cytosine (G + C) content, 4,363 of coding sequence (CDS), 85 of tRNA, and 22 of rRNA genes. The S. enterica strain K_SA184 genome includes encoding virulence genes, such as Type III secretion systems and multidrug resistance related genes.

• Journal of Animal Science and Technology
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• 제63권2호
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• pp.461-464
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• 2021

Escherichia coli normally colonizes the lower intestine of animals and humans, but some serotypes are foodborne pathogens. The Escherichia coli K_EC180 was isolated from swine feces that were collected from a weaner pig. In this genome announcement, E. coli K_EC180 was sequenced using PacBio RS II and Illumina NextSeq 500 platforms. The complete chromosome of E. coli K_EC180 is composed of one circular chromosome (5,017,281 bp) with 50.4% of guanine + cytosine (G + C) content, 4,935 of coding sequence (CDS), 88 of tRNA, and 22 of rRNA genes. The complete genome of E. coli K_EC180 contains the toxin genes such as shiga-like toxins (stxA and stxB).