• Journal of Aquaculture
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• v.18 no.2
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• pp.130-132
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• 2005

Genomics research has two ultimate applied goals: to Isolate and clone genes of economic importance for bio-technology and gene-assisted selection (GAS), and to locate and use markers for marker-assisted selection (MAS) in selective breeding programs. To this end, we have identified linked markers for feed conversion efficiency growth rate, and disease resistance to enteric septicemia of catfish (ESC). Three microsatellite markers Ip266, Ip384, and Ip607 were identified to be linked to feed conversion efficiency. Similarly one marker each was identified to be linked to growth rate (Ip607) and disease resistance to ESC (Ip477). Ip607 marker linked to both growth rate and feed conversion efficiency, indicating that the QTL for both growth rate and feed conversion efficiency may either be the same or located in the same chromosomal region in the catfish genome. On phenotypic evaluation, certain traits such as growth rate can be accurately evaluated by body weight evaluation while other traits such as disease resistance can be quite complex. The linked DNA markers will be highly useful for MAS programs and for directing further efforts of genomic mapping for important quantitative traits.

• Mycobiology
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• v.48 no.4
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• pp.245-251
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• 2020

During a survey of putative fungal pathogens infecting oak trees in the Gangwon Province of the Republic of Korea, a fungus resembling a Ceratocystis sp. was repeatedly isolated from natural wounds on Quercus variabilis. Morphological comparisons and DNA sequence comparisons based on partial β-tubulin and TEF-1α gene regions showed that the fungus resided in a distinct lineage. This novel Ceratocystis species is described here as C. quercicola sp. nov. This is the first novel species of Ceratocystis to be reported from Korea. A pathogenicity test showed that it can cause lesions on inoculated trees but that it had a very low level of aggressiveness. The discovery of this fungus suggests that additional taxa residing in Ceratocystis are likely to be discovered in Korea in the future.

• Molecules and Cells
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• v.41 no.6
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• pp.506-514
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• 2018

The transcriptional regulation of genes determines the fate of animal cell differentiation and subsequent organ development. With the recent progress in genome-wide technologies, the genomic landscapes of enhancers have been broadly explored in mammalian genomes, which led to the discovery of novel specific subsets of enhancers, termed super-enhancers. Super-enhancers are large clusters of enhancers covering the long region of regulatory DNA and are densely occupied by transcription factors, active histone marks, and co-activators. Accumulating evidence points to the critical role that super-enhancers play in cell type-specific development and differentiation, as well as in the development of various diseases. Here, I provide a comprehensive description of the optimal approach for identifying functional units of super-enhancers and their unique chromatin features in normal development and in diseases, including cancers. I also review the recent updated knowledge on novel approaches of targeting super-enhancers for the treatment of specific diseases, such as small-molecule inhibitors and potential gene therapy. This review will provide perspectives on using super-enhancers as biomarkers to develop novel disease diagnostic tools and establish new directions in clinical therapeutic strategies.

• Genomics & Informatics
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• v.11 no.4
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• pp.191-199
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• 2013

High-throughput next-generation sequencing (NGS) technology produces a tremendous amount of raw sequence data. The challenges for researchers are to process the raw data, to map the sequences to genome, to discover variants that are different from the reference genome, and to prioritize/rank the variants for the question of interest. The recent development of many computational algorithms and programs has vastly improved the ability to translate sequence data into valuable information for disease gene identification. However, the NGS data analysis is complex and could be overwhelming for researchers who are not familiar with the process. Here, we outline the analysis pipeline and describe some of the most commonly used principles and tools for analyzing NGS data for disease gene identification.

• Biomolecules & Therapeutics
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• v.28 no.5
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• pp.381-388
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• 2020

Methamphetamine (METH) is a highly addictive psychostimulant and one of the most widely abused drugs worldwide. The continuous use of METH eventually leads to drug addiction and causes serious health complications, including attention deficit, memory loss and cognitive decline. These neurological complications are strongly associated with METH-induced neurotoxicity and neuroinflammation, which leads to neuronal cell death. The current review investigates the molecular mechanisms underlying METH-mediated neuronal damages. Our analysis demonstrates that the process of neuronal impairment by METH is closely related to oxidative stress, transcription factor activation, DNA damage, excitatory toxicity and various apoptosis pathways. Thus, we reach the conclusion here that METH-induced neuronal damages are attributed to the neurotoxic and neuroinflammatory effect of the drug. This review provides an insight into the mechanisms of METH addiction and contributes to the discovery of therapeutic targets on neurological impairment by METH abuse.

• Journal of Microbiology and Biotechnology
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• v.29 no.7
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• pp.1014-1021
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• 2019

In the bacterial community, unicellular organisms act together as a multicellular being. Bacteria interact within the community and programmed cell death (PCD) in prokaryotes is a sort of altruistic action that enables the whole population to thrive. Genetically, encoded cell death pathways are triggered by DNA damage or nutrient starvation. Given the environmental and bacterial diversity, different PCD mechanisms are operated. Still, their biochemical and physiological aspects remain unrevealed. There are three main pathways; thymineless death, apoptosis-like death, and toxin-antitoxin systems. The discovery of PCD in bacteria has revealed the possibility of developing new antibiotics. In this review, the molecular and physiological characteristics of the three types of PCD and their development potential as antibacterial agents are addressed.

• BMB Reports
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• v.55 no.7
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• pp.305-315
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• 2022

Transposable elements (TEs) are DNA sequences capable of mobilization from one location to another in the genome. Since the discovery of 'Dissociation (Dc) locus' by Barbara McClintock in maize (1), mounting evidence in the era of genomics indicates that a significant fraction of most eukaryotic genomes is composed of TE sequences, involving in various aspects of biological processes such as development, physiology, diseases and evolution. Although technical advances in genomics have discovered numerous functional impacts of TE across species, our understanding of TEs is still ongoing process due to challenges resulted from complexity and abundance of TEs in the genome. In this mini-review, we briefly summarize biology of TEs and their impacts on the host genome, emphasizing importance of understanding TE landscape in the genome. Then, we introduce recent endeavors especially in vivo retrotransposition assays and long read sequencing technology for identifying de novo insertions/TE polymorphism, which will broaden our knowledge of extraordinary relationship between genomic cohabitants and their host.

• Journal of Genetic Medicine
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• v.19 no.1
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• pp.1-6
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• 2022

Radiation therapy (RT) is a very important treatment for cancer that irradiates a large amount of radiation to lead cancer cells and tissues to death. The progression of RT in the aspect of personalized medicine has greatly advanced over the past few decades in the field of technical precision responding anatomical characteristics of each patient. However, the consideration of biological heterogeneity that makes different effect in individual patients has not actually applied to clinical practice. There have been numerous discovery and validation of biomarkers that can be applied to improve the efficiency of radiotherapy, among which those related to genomic information are very promising developments. These genome-based biomarkers can be applied to identify patients who can benefit most from altering their therapeutic dose and to select the best chemotherapy improving sensitivity to radiotherapy. The genomics-based biomarkers in radiation oncology focus on mutational changes, particularly oncogenes and DNA damage response pathways. Although few have translated into clinically viable tools, there are many promising candidates in this field. In this review the prominent mutation-based biomarkers and their potential for clinical translation will be discussed.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.2
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• pp.170-178
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• 2005

An in silico approach was developed to survey the genes expressed in four internal organs of pig: liver, kidney, spleen and small intestine. The major procedures of the approach included: (1) BLAST searching against GenBank "est_others" database using human cDNA sequences as queries to screen the porcine orthologous expressed sequence tags (ESTs), (2) classifying the porcine ESTs records by resources according to certain criteria and (3) analyzing data for ESTs specifically expressed in each organ. In order to do so, four Java programs were developed. Based on the ESTs available in the GenBank database, it was found that there were at least 2,100 genes expressed in these four organs, including 128 in the liver, 81 in the kidney, 780 in the spleen, and 1,423 in the small intestine respectively (a few genes co-expressed in these tissues). Gene expression patterns, such as co-expressed genes, preferentially expressed genes and basic active genes were also compared and characterized among these organs. This study provides a comprehensive model on how to use the bioinformatics approach and Genbank databases to facilitate the discovery of new genes in livestock species.

• Genomics & Informatics
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• v.10 no.3
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• pp.194-199
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• 2012

In addition to single-nucleotide polymorphisms (SNP), copy number variation (CNV) is a major component of human genetic diversity. Among many whole-genome analysis platforms, SNP arrays have been commonly used for genomewide CNV discovery. Recently, a number of CNV defining algorithms from SNP genotyping data have been developed; however, due to the fundamental limitation of SNP genotyping data for the measurement of signal intensity, there are still concerns regarding the possibility of false discovery or low sensitivity for detecting CNVs. In this study, we aimed to verify the effect of combining multiple CNV calling algorithms and set up the most reliable pipeline for CNV calling with Affymetrix Genomewide SNP 5.0 data. For this purpose, we selected the 3 most commonly used algorithms for CNV segmentation from SNP genotyping data, PennCNV, QuantiSNP; and BirdSuite. After defining the CNV loci using the 3 different algorithms, we assessed how many of them overlapped with each other, and we also validated the CNVs by genomic quantitative PCR. Through this analysis, we proposed that for reliable CNV-based genomewide association study using SNP array data, CNV calls must be performed with at least 3 different algorithms and that the CNVs consistently called from more than 2 algorithms must be used for association analysis, because they are more reliable than the CNVs called from a single algorithm. Our result will be helpful to set up the CNV analysis protocols for Affymetrix Genomewide SNP 5.0 genotyping data.