• BMB Reports
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• v.54 no.1
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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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• v.36 no.4
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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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• v.56 no.2
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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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• v.12 no.4
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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.

• Journal of Internet Computing and Services
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• v.19 no.4
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• pp.135-150
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• 2018

The biological resources research data around the world are not only very critical themselves but should be shared and utilized. Up to now, the biological resources have been compiled and managed individually depending on the purpose and characteristics of the study without any clear standard. So, in this study, the data reference model would be suggested which is applicable in the phase ranging from the start of the construction of the information system and which can be commonly used. For this purpose, the data model of the related information system would be expanded based on the domestic and foreign standards and data control policy so that the data reference model which can be commonly applicable to individual information system would be developed and its application procedure would be suggested. In addition, for the purpose of proving the excellence of the suggested data reference model, the quality level would be verified by applying the Korgstie's data model evaluation model and its level of data sharing with the domestic and foreign standards would be compared. The test results of this model showed that this model is better than the conventional data model in classifying the data into 4 levels of resources, target, activities and performances and that it has higher quality and sharing level of data in the data reference model which defines the derivation and relation of entity.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.35 no.2B
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• pp.232-243
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• 2010

In this paper, various physiological signals of humans were measured and analyzed to inference their psychological state and biological information, and Bio-Signal Context aware system (BSC), which recognizes the current context of its users as well as the information of exterior environment and offers the service appropriate for them, was designed and implemented. The BSC extracts and analyzes the features from bio-signals, such as the measured electroencephalogram (EEG), electrocardiogram (ECG), and galvanic skin response (GSR), with its different sensors, has the input of the analyzed results, and discriminates four psychological states of rest, concentration, tension and melancholy. In addition to the results of the discriminated psychological states, the information of biological condition analyzed from the user's bio-signals, for example, heart rate variability (HRV), Galvanic skin response (GSR) and body temperature, and the information of external environment related to the user's are collected to offer the service fit for the user's present biological condition by inferring and recognizing the user's present situation.

• Proceedings of the Korean Society of Life Science Conference
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• 2000.06a
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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

• Journal of the Korean Data and Information Science Society
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• v.23 no.1
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• pp.39-51
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• 2012

Cluster analysis has proven to be a useful tool for investigating the association structure among genes and samples in a microarray data set. We applied several cluster validation measures to evaluate the performance of clustering algorithms for analyzing microarray gene expression data, including hierarchical clustering, K-means, PAM, SOM and model-based clustering. The available validation measures fall into the three general categories of internal, stability and biological. The performance of clustering algorithms is evaluated using simulated and SRBCT microarray data. Our results from simulated data show that nearly every methods have good results with same result as the number of classes in the original data. For the SRBCT data the best choice for the number of clusters is less clear than the simulated data. It appeared that PAM, SOM, model-based method showed similar results to simulated data under Silhouette with of internal measure as well as PAM and model-based method under biological measure, while model-based clustering has the best value of stability measure.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.25 no.12
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• pp.1935-1941
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• 2021

In order to develop an algorithm using deep learning, which has been recently applied to various fields, it is necessary to have rich, high-quality learning data. In this paper, we propose an acquisition system for biological signals that simultaneously collects bio-signal data such as optical videos, thermal videos, and voices, which are mainly used in developing deep learning algorithms and useful in derivation of information, and transmit them to the server. To increase the portability of the collector, it was made based on Raspberry Pi, and the collected data is transmitted to the server through the wireless Internet. To enable simultaneous data collection from multiple collectors, an ID for login was assigned to each subject, and this was reflected in the database to facilitate data management. By presenting an example of biological data collection for fatigue measurement, we prove the application of the proposed acquisition system.

• ALGAE
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• v.31 no.4
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• pp.373-378
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• 2016

Cochlodinium polykrikoides is a red-tide forming dinoflagellate that causes significant worldwide impacts on aquaculture industries and the marine ecosystem. There have been extensive studies on managing and preventing C. polykrikoides blooms, but it has been difficult to identify an effective method to control the bloom development. There is also limited genome information on the molecular mechanisms involved in its various ecophysiology and metabolism processes. Thus, comprehensive genome information is required to better understand harmful algal blooms caused by C. polykrikoides. We estimated the C. polykrikoides genome size using flow cytometry, with detection of the fluorescence of DNA stained with propidium iodide (PI). The nuclear genome size of C. polykrikoides was 100.97 Gb, as calculated by comparing its mean fluorescence intensity (MFI) to the MFI of Mus musculus, which is 2.8 Gb. The exceptionally large genome size of C. polykrikoides might indicate its complex physiological and metabolic characteristics. Our optimized protocol for estimating the nuclear genome size of a dinoflagellate using flow cytometry with PI can be applied in studies of other marine organisms.