• 한국균학회지
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• 제49권3호
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• pp.351-362
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• 2021

Penicillium is the most common fungal genus in various terrestrial and marine environments. The number of new and unrecorded Penicillium species from various substrates and habitats are continuously increasing. As part of a project to discover indigenous fungi in South Korea, three unrecorded Penicillium species were isolated from mudflats and seaweeds. Based on morphological characteristics and phylogenetic analyses of β-tubulin and calmodulin loci, they were identified as P. amaliae, P. infrabuccalum, and P. manginii. Here, we provide a detailed morphological description and sequence information of these previously unrecorded species.

• Molecules and Cells
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• 제42권7호
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• pp.512-522
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• 2019

Chromosomes located in the nucleus form discrete units of genetic material composed of DNA and protein complexes. The genetic information is encoded in linear DNA sequences, but its interpretation requires an understanding of three-dimensional (3D) structure of the chromosome, in which distant DNA sequences can be juxtaposed by highly condensed chromatin packing in the space of nucleus to precisely control gene expression. Recent technological innovations in exploring higher-order chromatin structure have uncovered organizational principles of the 3D genome and its various biological implications. Very recently, it has been reported that large-scale genomic variations may disrupt higher-order chromatin organization and as a consequence, greatly contribute to disease-specific gene regulation for a range of human diseases. Here, we review recent developments in studying the effect of structural variation in gene regulation, and the detection and the interpretation of structural variations in the context of 3D chromatin structure.

• BMB Reports
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• 제54권1호
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• pp.59-69
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• 2021

The ability to read, write, and edit genomic information in living organisms can have a profound impact on research, health, economic, and environmental issues. The CRISPR/Cas system, recently discovered as an adaptive immune system in prokaryotes, has revolutionized the ease and throughput of genome editing in mammalian cells and has proved itself indispensable to the engineering of immune cells and identification of novel immune mechanisms. In this review, we summarize the CRISPR/Cas9 system and the history of its discovery and optimization. We then focus on engineering T cells and other types of immune cells, with emphasis on therapeutic applications. Last, we describe the different modifications of Cas9 and their recent applications in the genome-wide screening of immune cells.

• ALGAE
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• 제36권4호
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• pp.333-340
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• 2021

Phylotranscriptomics is the study of phylogenetic relationships among taxa based on their DNA sequences derived from transcriptomes. Because of the relatively low cost of transcriptome sequencing compared with genome sequencing and the fact that phylotranscriptomics is almost as reliable as phylogenomics, the phylotranscriptomic analysis has recently emerged as the preferred method for studying evolutionary biology. However, it is challenging to perform transcriptomic and phylogenetic analyses together without programming expertise. This study presents a protocol for phylotranscriptomic analysis to aid marine biologists unfamiliar with UNIX command-line interface and bioinformatics tools. Here, we used transcriptomes to reconstruct a molecular phylogeny of dinoflagellate protists, a diverse and globally abundant group of marine plankton organisms whose large and complex genomic sequences have impeded conventional phylogenic analysis based on genomic data. We hope that our proposed protocol may serve as practical and helpful information for the training and education of novice phycologists.

• BMB Reports
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• 제56권2호
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• pp.49-55
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• 2023

Aging is characterized by a gradual decline in biological functions, leading to the increased probability of diseases and deaths in organisms. Previous studies have identified biological factors that modulate aging and lifespan, including non-coding RNAs (ncRNAs). Here, we review the relationship between aging and tRNA-derived small RNAs (tsRNAs), ncRNAs that are generated from the cleavage of tRNAs. We describe age-dependent changes in tsRNA levels and their functions in age-related diseases, such as cancer and neurodegenerative diseases. We also discuss the association of tsRNAs with aging-regulating processes, including mitochondrial respiration and reduced mRNA translation. We cover recent findings regarding the potential roles of tsRNAs in cellular senescence, a major cause of organismal aging. Overall, our review will provide useful information for understanding the roles of tsRNAs in aging and age-associated diseases.

• Journal of Species Research
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• 제12권4호
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• pp.355-361
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• 2023

In this paper, we present unrecorded protozoans of Korea that were discovered, through the 'Discovery of Korean Indigenous Species' project hosted by the 'National Institute of Biological Resources (NIBR)'. A taxonomic account is provided for each identified species, offering comprehensive information such as species name, Korean name, collection site, synonyms, specimen vouchers, diagnoses, and figures. This study introduces 13 previously unrecorded Korean protozoan species that are classified into three phyla: Amoebozoa, Cercozoa, and Ciliophora. Notably, the cercozoan family Chlamydophryidae was recorded in Korea for the first time, together with the discovery of three previously unreported genera: Diaphoropodon within Cercozoa, and Metauroleptus and Hemicycliostyla within Ciliophora.

• 한국미생물·생명공학회지
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• 제51권3호
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• pp.325-327
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• 2023

This paper presents the complete genome sequence of a novel marine actinomycete, Streptomyces sp. MMBL 11-1. The genome of Streptomyces sp. MMBL 11-1 was obtained through next-generation sequencing using the PacBio Sequel system and Illumina platform provided by Macrogen, Korea. The assembled genome consists of five contigs, with a total length of 8,496,900 bp and a G+C content of 71.6%. The genome harbors multiple biosynthetic gene clusters (BGCs) associated with producing microbial natural products (MNPs). The comprehensive genomic information of this type of strain will serve as a valuable resource for identifying other marine actinomycetes strains.

• 인터넷정보학회논문지
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• 제19권4호
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• pp.135-150
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• 2018

세계적으로 생물자원 연구데이터는 그 자체로 중요할 뿐만 아니라, 공유되고 활용되어야 한다. 본 논문에서는 명확한 기준 없이 각각의 연구목적과 특성에 따라 개별적으로 구축, 관리되고 있는 생물자원 연구데이터를 공동 활용 할 수 있도록 정보시스템의 구축 단계부터 적용 가능한 데이터 참조모델을 제시한다. 이를 위해 기존 관련 정보시스템의 데이터 모델을 국내외 표준 및 데이터 관리 정책을 기반으로 확장하여 개별 정보시스템에서 공동 활용 할 수 있는 데이터 참조모델을 개발하고 그 적용 절차를 제안한다. 또한, 제안하는 데이터 참조모델의 우수성을 입증하기 위하여 Krogstie의 데이터모델 평가모형을 적용하여 품질수준을 검증하고 국내외 표준들과의 데이터 공유수준을 비교한다. 실험 결과 기존 데이터 모델보다 데이터를 자원, 대상, 활동, 성과의 4단계로 분류하고 엔티티 도출 및 관계를 정의한 데이터 참조모델에서 데이터의 품질과 공유수준이 높게 나타나는 것을 확인 할 수 있었다.

• 한국통신학회논문지
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• 제35권2B호
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• pp.232-243
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• 2010

본 논문에서는 다양한 생체신호들을 이용하여 심리상태와 생체정보를 판별하고, 외부환경 정보와 함께 이용자의 현재 상황을 인식하여 그에 맞는 적절한 서비스를 제공하는 생체정보기반 상황인식시스템(Bio-Signal Context aware system :BSC)을 설계하고 구현한다. 본 논문에서 구현한 생체정보기반 상황인식시스템은 센서를 통하여 측정된 뇌파(EEG), 심전도(ECG), 피부전도도(GSR) 등의 생체신호들로부터 특징들을 추출하고 분석하였으며, 분석된 결과를 입력받아 평온, 집중, 긴장, 우울의 네 가지 심리상태를 판별하였다. 판별된 심리상태의 결과와 함께 심박변이도(HRV), 피부전도도, 체온 등의 생체신호로부터 분석된 생체 상황정보, 그리고 외부 환경의 상황정보로부터 이용자의 현재 상황을 추론하고 인식하여 현재 생체 상황에 맞는 적절한 서비스를 제공하였다.

• 한국생명과학회:학술대회논문집
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• 한국생명과학회 2000년도 제28회 학술심포지엄
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• pp.9-10
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• 2000

The aging process is multifactorial and results from the combined effects of inherited(genetic) and acquired factors including life style, food habits, physical activity, and diseases. That give rise to the various approaches in aging. We are trying to study biological changes with aging, In detail we are focused on gene and protein function accompanied by normal or abnormal aging process, especially our efforts are aimed at revealing the functional relationship of proteins in aging as a final product of gene. We expect that proteomic approach to the study of protein function involved in aging should give us variety of integrated data to understand biological changes of long lived lives, We have applied expression proteomics to rat liver bred in dietary restriction or in at libitum to elucidate the effects of food habit on aging. Expression proteomics shows us protein profile in a selected tissue or cells as a whole and gives us the information about protein expression level, posttranslational modification and degenerative modification of expressed proteins. Comparative analysis of young and old rat liver by two dimensional gels shows that gene expression of several proteins was down regulated in old rats and some protein expression level is increased with aging. Dietary restriction slows down these changes of gene expression and in some proteins there's no difference in protein expression level at same ages in comparison with rats bred in at libitum. About forty protein was identified by peptide mass fingerprint with MALDI-TOF and rest of the protein of interest is in the course of identification, Also we are trying to make mitochondrial and cytosolic proteom reference map. These suborganelle proteom map will gives us the information about low abundance proteins and cellular localization of proteins. Proteomics is a growing methodology to study biological system. High throughput qualitative and qualitative aspect of this approach will gives us large amount of integrated information and speed up our understanding about biological system