• Genomics & Informatics
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• 제16권3호
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• pp.65-70
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• 2018

The non-coding DNA in eukaryotic genomes encodes a language which programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this short report was to determine the impact of primary DNA sequence on the epigenomic landscape across 200-base pair genomic units by integrating nine publicly available ChromHMM Browser Extensible Data files of the Encyclopedia of DNA Elements (ENCODE) project. The nucleotide frequency profiles of nine chromatin annotations with the units of 200 bp were analyzed and integrative Markov chains were built to detect the Markov properties of the DNA sequences in some of the active chromatin states of different ChromHMM regions. Our aim was to identify the possible relationship between DNA sequences and the newly built chromatin states based on the integrated ChromHMM datasets of different cells and tissue types.

• Animal cells and systems
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• 제6권4호
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• pp.323-326
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• 2002

One hundred and three random complementary DNA clones representing rainbow trout intestine were par1i811y sequenced as an approach to analyze the transcribed sequences of its genome. Of the sequences generated, 60.0% of the ESTs were represented by 40 known genes. Thirty-five clones of unknown gene products potentially represented 34 novel genes. The most Bbundantly represented messages were the 28S ribosomal protein (6.5%) and beta actin (5.8%). The genes involved in ribosome formation (18%) accounted for the major gene expression. Development of EST panels representing the genes expressed in a particular tissue will be useful in determining the role of these genes in normal function and in response to developmental, hormonal, environmental and physiological changes.

• Genomics & Informatics
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• 제19권1호
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• pp.3.1-3.12
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• 2021

Functional interpretation of noncoding genetic variants associated with complex human diseases and traits remains a challenge. In an effort to enhance our understanding of common germline variants associated with lung cancer, we categorize regulatory elements based on eight major cell types of human lung tissue. Our results show that 21.68% of lung cancer-associated risk variants are linked to noncoding regulatory elements, nearly half of which are cell type-specific. Integrative analysis of high-resolution long-range chromatin interactome maps and single-cell RNA-sequencing data of lung tumors uncovers number of putative target genes of these variants and functionally relevant cell types, which display a potential biological link to cancer susceptibility. The present study greatly expands the scope of functional annotation of lung cancer-associated genetic risk factors and dictates probable cell types involved in lung carcinogenesis.

• Genomics & Informatics
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• 제19권3호
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• pp.25.1-25.5
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• 2021

The coronavirus disease 2019 (COVID-19) pandemic has led to a flood of research papers and the information has been updated with considerable frequency. For society to derive benefits from this research, it is necessary to promote sharing up-to-date knowledge from these papers. However, because most research papers are written in English, it is difficult for people who are not familiar with English medical terms to obtain knowledge from them. To facilitate sharing knowledge from COVID-19 papers written in English for Japanese speakers, we tried to construct a dictionary with an open license by assigning Japanese terms to MeSH unique identifiers (UIDs) annotated to words in the texts of COVID-19 papers. Using this dictionary, 98.99% of all occurrences of MeSH terms in COVID-19 papers were covered. We also created a curated version of the dictionary and uploaded it to Pub-Dictionary for wider use in the PubAnnotation system.

• Molecules and Cells
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• 제44권7호
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• pp.433-443
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• 2021

Multi-omics approaches are novel frameworks that integrate multiple omics datasets generated from the same patients to better understand the molecular and clinical features of cancers. A wide range of emerging omics and multi-view clustering algorithms now provide unprecedented opportunities to further classify cancers into subtypes, improve the survival prediction and therapeutic outcome of these subtypes, and understand key pathophysiological processes through different molecular layers. In this review, we overview the concept and rationale of multi-omics approaches in cancer research. We also introduce recent advances in the development of multi-omics algorithms and integration methods for multiple-layered datasets from cancer patients. Finally, we summarize the latest findings from large-scale multi-omics studies of various cancers and their implications for patient subtyping and drug development.

• Journal of Microbiology and Biotechnology
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• 제24권5호
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• pp.639-647
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• 2014

Laccases have a broad range of industrial applications. In this study, we immobilized laccase on $SiO_2$ nanoparticles to overcome problems associated with stability and reusability of the free enzyme. Among different reagents used to functionally activate the nanoparticles, glutaraldehyde was found to be the most effective for immobilization. Optimization of the immobilization pH, temperature, enzyme loading, and incubation period led to a maximum immobilization yield of 75.8% and an immobilization efficiency of 92.9%. The optimum pH and temperature for immobilized laccase were 3.5 and $45^{\circ}C$, respectively, which differed from the values of pH 3.0 and $40^{\circ}C$ obtained for the free enzyme. Immobilized laccase retained high residual activities over a broad range of pH and temperature. The kinetic parameter $V_{max}$ was slightly reduced from 1,890 to 1,630 ${\mu}mol/min/mg$ protein, and $K_m$ was increased from 29.3 to 45.6. The thermal stability of immobilized laccase was significantly higher than that of the free enzyme, with a half-life 11- and 18-fold higher at temperatures of $50^{\circ}C$ and $60^{\circ}C$, respectively. In addition, residual activity was 82.6% after 10 cycles of use. Thus, laccase immobilized on $SiO_2$ nanoparticles functionally activated with glutaraldehyde has broad pH and temperature ranges, thermostability, and high reusability compared with the free enzyme. It constitutes a notably efficient system for biotechnological applications.

• Genomics & Informatics
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• 제21권2호
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• pp.16.1-16.14
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• 2023

Coronavirus disease 2019 (COVID-19) is a viral infection produced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus epidemic, which was declared a global pandemic in March 2020. The World Health Organization has recorded around 43.3 billion cases and 59.4 million casualties to date, posing a severe threat to global health. Severe COVID-19 indicates viral pneumonia caused by the SARS-CoV-2 infections, which can induce fatal consequences, including acute respiratory distress syndrome (ARDS). The purpose of this research is to better understand the COVID-19 and ARDS pathways, as well as to find targeted single nucleotide polymorphism. To accomplish this, we retrieved over 100 patients' samples from the Sequence Read Archive, National Center for Biotechnology Information. These sequences were processed through the Galaxy server next generation sequencing pipeline for variant analysis and then visualized in the Integrative Genomics Viewer, and performed statistical analysis using t-tests and Bonferroni correction, where six major genes were identified as DNAH7, CLUAP1, PPA2, PAPSS1, TLR4, and IFITM3. Furthermore, a complete understanding of the genomes of COVID-19-related ARDS will aid in the early identification and treatment of target proteins. Finally, the discovery of novel therapeutics based on discovered proteins can assist to slow the progression of ARDS and lower fatality rates.

• 농업생명과학연구
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• 제46권4호
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• pp.9-20
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• 2012

Eugenol은 많은 식물에서 eugenol synthase에 의해 생합성되는 phenylpropene 계통의 휘발성 화합물이다. 그러나, 토마토 과실에서의 특징은 밝혀져 있지 않다. 이에 따라 토마토 'Micro-Tom'으로부터 RACE 기법을 이용하여 완전장 cDNA를 클로닝 하여, SlEGS라 명명하였다. SlEGS의 open reading frame은 921bp로, 307개의 아미노산 서열을 갖는 단백질로 번역되었다. BLAST 결과에 따라 SlEGS는 PhEGS1 및 CbEGS2와 각 67.1, 69.4%의 높은 상동성을 갖는 것으로 나타났다. CLC genomics workbench 프로그램을 이용하여 SlEGS의 아미노산 구성을 분석하였고, Swiss-PDB viewer 프로그램에서 homology modeling 기법으로 SlEGS의 3차원 단백질 구조를 구축한 후 ProSA-web 툴로 3차원 구조의 안정성을 확인 하였다. 또한 ExPASy의 ProtParam 툴을 이용하여 SlEGS의 생리화학적 특성을 분석 하였다. SlEGS의 추정 분자량은 33.93kDA이고 등전점(pI)은 5.85로 산성인 것으로 나타났다. 이와 더불어 SlEGS의 흡광 계수(EC), 불안정성 지수(II), alipathic 지수(AI), GRAVY값 등의 생리화학적 특성에 대한 분석을 실시 하였다.

• Genomics & Informatics
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• 제18권1호
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• pp.8.1-8.10
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• 2020

The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www. bioexpress.re.kr/.

• Asian-Australasian Journal of Animal Sciences
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• 제29권7호
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• pp.1044-1051
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• 2016

The present study compared the differential functions of two groups of adjuvants, Montanide incomplete Seppic adjuvant (ISA) series and Quil A, cholesterol, dimethyl dioctadecyl ammonium bromide, and Carbopol (QCDC) formulations, in chicken by analyzing published microarray data associated with each type of vaccine adjuvants. In the biological function analysis for differentially expressed genes altered by two different adjuvant groups, ISA series and QCDC formulations showed differential effects when chickens were immunized with a recombinant immunogenic protein of Eimeria. Among the biological functions, six categories were modified in both adjuvant types. However, with respect to "Response to stimulus", no biological process was modified by the two adjuvant groups at the same time. The QCDC adjuvants showed effects on the biological processes (BPs) including the innate immune response and the immune response to the external stimulus such as toxin and bacterium, while the ISA adjuvants modified the BPs to regulate cell movement and the response to stress. In pathway analysis, ISA adjuvants altered the genes involved in the functions related with cell junctions and the elimination of exogenous and endogenous macromolecules. The analysis in the present study could contribute to the development of precise adjuvants based on molecular signatures related with their immunological functions.