• Asian-Australasian Journal of Animal Sciences
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• v.20 no.11
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• pp.1636-1650
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• 2007

As an initial step toward a better understanding of the genome structure of Korean cattle (Hanwoo breed) and initiation of the framework for genomic research in this bovine, the bacterial artificial chromosome (BAC) end sequencing of 21,024 clones was recently completed. Among these clones, BAC End Sequences (BESs) of 20,158 clones with high quality sequences (Phred score ${\geq}20$, average BES equaled 620 bp and totaled 23,585,814 bp), after editing sequencing results by eliminating vector sequences, were used initially to compare sequence homology with the known bovine chromosomal DNA sequence by using BLASTN analysis. Blast analysis of the BESs against the NCBI Genome database for Bos taurus (Build 2.1) indicated that the BESs from 13,201 clones matched bovine contig sequences with significant blast hits (E<$e^{-40}$), including 7,075 single-end hits and 6,126 paired-end hits. Finally, a total of 5,105 clones of the Korean cattle BAC clones with paired-end hits, including 4,053 clones from the primary analysis and 1,052 clones from the secondary analysis, were mapped to the bovine chromosome with very high accuracy.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.14-14
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• 2017

The discipline of plant breeding is experiencing a renaissance impacting crop improvement as a result of new technologies, however fundamental questions remain for predicting the phenotype and how the environment and genetics shape it. Inexpensive DNA sequencing, genotyping, new statistical methods, high throughput phenotyping and gene-editing are revolutionizing breeding methods and strategies for improving both quantitative and qualitative traits. Genomic selection (GS) models use genome-wide markers to predict performance for both phenotyped and non-phenotyped individuals. Aerial and ground imaging systems generate data on correlated traits such as canopy temperature and normalized difference vegetative index that can be combined with genotypes in multivariate models to further increase prediction accuracy and reduce the cost of advanced trials with limited replication in time and space. Design of a GS training population is crucial to the accuracy of prediction models and can be affected by many factors including population structure and composition. Prediction models can incorporate performance over multiple environments and assess GxE effects to identify a highly predictive subset of environments. We have developed a methodology for analyzing unbalanced datasets using genome-wide marker effects to group environments and identify outlier environments. Environmental covariates can be identified using a crop model and used in a GS model to predict GxE in unobserved environments and to predict performance in climate change scenarios. These new tools and knowledge challenge the plant breeder to ask the right questions and choose the tools that are appropriate for their crop and target traits. Contemporary plant breeding requires teams of people with expertise in genetics, phenotyping and statistics to improve efficiency and increase prediction accuracy in terms of genotypes, experimental design and environment sampling.

• Genomics & Informatics
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• v.17 no.3
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• pp.32.1-32.6
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• 2019

Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGISEQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGISEQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.

• Journal of KIISE:Databases
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• v.32 no.1
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• pp.24-42
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• 2005

Characteristics of biological data including genome sequences are heterogeneous and various. Although the need of management systems for genome sequencing which should reflect biological characteristics has been raised, most current biological databases provide restricted function as repositories for biological data. Therefore, this paper describes a management system of nucleotide sequences at the level of biological laboratories. It includes format transformation, editing, storing and retrieval for collected nucleotide sequences from public databases, and handles sequence produced by experiments. It uses BSML based on XML as a common format in order to extract data fields and transfer heterogeneous sequence formats. To manage sequences and their changes, version management system for originated DNA is required so as to detect transformed new sequencing appearance and trigger database update. Our experimental results show that applying active trigger rules to manage changes of sequences can automatically store changes of sequences into databases.

• Animal Bioscience
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• v.36 no.6
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• pp.973-979
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• 2023

Objective: The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system, which is the most efficient and reliable tool for precisely targeted modification of the genome of living cells, has generated considerable excitement for industrial applications as well as scientific research. In this study, we developed a gene-editing and detection system for chick embryo sexing during the embryonic stage. Methods: By combining the CRISPR/Cas9 technical platform and germ cell-mediated germline transmission, we not only generated Z chromosome-targeted knockin chickens but also developed a detection system for fluorescence-positive male chicks in the embryonic stage. Results: We targeted a green fluorescent protein (GFP) transgene into a specific locus on the Z chromosome of chicken primordial germ cells (PGCs), resulting in the production of Z^GFP-knockin chickens. By mating Z^GFP-knockin females (Z^GFP/W) with wild males (Z/Z) and using a GFP detection system, we could identify chick sex, as the GFP transgene was expressed on the Z chromosome only in male offspring (Z^GFP/Z) even before hatching. Conclusion: Our results demonstrate that the CRISPR/Cas9 technical platform with chicken PGCs facilitates the production of specific genome-edited chickens for basic research as well as practical applications.

• Journal of Microbiology and Biotechnology
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• v.33 no.11
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• pp.1506-1512
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• 2023

Quantitative analysis of adenosine triphosphate (ATP) has been widely used as a diagnostic tool in the food and medical industries. Particularly, the pathogenesis of a few diseases including inflammatory bowel disease (IBD) is closely related to high ATP concentrations. A bioluminescent D-luciferin/luciferase system, which includes a luciferase (FLuc) from the firefly Photinus pyralis as a key component, is the most commonly used method for the detection and quantification of ATP. Here, instead of isolating FLuc produced in recombinant Escherichia coli, we aimed to develop a whole-cell biocatalyst system that does not require extraction and purification of FLuc. To this end, the gene coding for FLuc was introduced into the genome of probiotic Saccharomyces boulardii using the CRISPR/Cas9-based genome editing system. The linear relationship (r² = 0.9561) between ATP levels and bioluminescence generated from the engineered S. boulardii expressing FLuc was observed in vitro. To explore the feasibility of using the engineered S. boulardii expressing FLuc as a whole-cell biosensor to detect inflammation biomarker (i.e., ATP) in the gut, a colitis mouse model was established using dextran sodium sulfate as a colitogenic compound. Our findings demonstrated that the whole-cell biosensor can detect elevated ATP levels during gut inflammation in mice. Therefore, the simple and powerful method developed herein could be applied for non-invasive IBD diagnosis.

• Genomics & Informatics
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• v.5 no.2
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• pp.68-76
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• 2007

Due to the increasing interest in SNPs and mutational hot spots for disease traits, it is becoming more important to define and understand the relationship between SNPs and their flanking sequences. To study the effects of flanking sequences on SNPs, statistical approaches are necessary to assess bias in SNP data. In this study we mainly applied Markov chains for SNP sequences, particularly those located in intronic regions, and for analysis of in-del data. All of the pertaining sequences showed a significant tendency to generate particular SNP types. Most sequences flanking SNPs had lower complexities than average sequences, and some of them were associated with microsatellites. Moreover, many Alu repeats were found in the flanking sequences. We observed an elevated frequency of single-base-pair repeat-like sequences, mirror repeats, and palindromes in the SNP flanking sequence data. Alu repeats are hypothesized to be associated with C-to-T transition mutations or A-to-I RNA editing. In particular, the in-del data revealed an association between particular changes such as palindromes or mirror repeats. Results indicate that the mechanism of induction of in-del transitions is probably very different from that which is responsible for other SNPs. From a statistical perspective, frequent DNA lesions in some regions probably have effects on the occurrence of SNPs.

• Journal of Microbiology and Biotechnology
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• v.27 no.2
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• pp.207-218
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• 2017

Clustered regulatory interspaced short palindromic repeats (CRISPR) in association with CRISPR-associated protein (Cas) is an adaptive immune system, playing a pivotal role in the defense of bacteria and archaea. Ease of handling and cost effectiveness make the CRISPR-Cas system an ideal programmable nuclease tool. Recent advances in understanding the CRISPR-Cas system have tremendously improved its efficiency. For instance, it is possible to recapitulate the chronicle CRISPR-Cas from its infancy and inaugurate a developed version by generating novel variants of Cas proteins, subduing off-target effects, and optimizing of innovative strategies. In summary, the CRISPR-Cas system could be employed in a number of applications, including providing model systems, rectification of detrimental mutations, and antiviral therapies.

• Genomics & Informatics
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• v.4 no.3
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• pp.125-128
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• 2006

We present an openfree hypertext (also known as wiki) web cluster called BioCC. BioCC is a novel wiki farm that lets researchers create hundreds of biological web sites. The web sites form an organic information network. The contents of all the sites on the BioCC wiki farm are modifiable by anonymous as well as registered users. This enables biologists with diverse backgrounds to form their own Internet bio-communities. Each community can have custom-made layouts for information, discussion, and knowledge exchange. BioCC aims to form an ever-expanding network of openfree biological knowledge databases used and maintained by biological experts, students, and general users. The philosophy behind BioCC is that the formation of biological knowledge is best achieved by open-minded individuals freely exchanging information. In the near future, the amount of genomic information will have flooded society. BioGG can be an effective and quickly updated knowledge database system. BioCC uses an opensource wiki system called Mediawiki. However, for easier editing, a modified version of Mediawiki, called Biowiki, has been applied. Unlike Mediawiki, Biowiki uses a WYSIWYG (What You See Is What You Get) text editor. BioCC is under a share-alike license called BioLicense (http://biolicense.org). The BioCC top level site is found at http://bio.cc/

• Molecules and Cells
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• v.42 no.11
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• pp.739-746
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• 2019

Significant knowledge about the pathophysiology of Alzheimer's disease (AD) has been gained in the last century; however, the understanding of its causes of onset remains limited. Late-onset AD is observed in about 95% of patients, and APOE4-encoding apolipoprotein E4 (ApoE4) is strongly associated with these cases. As an apolipoprotein, the function of ApoE in brain cholesterol transport has been extensively studied and widely appreciated. Development of new technologies such as human-induced pluripotent stem cells (hiPSCs) and CRISPR-Cas9 genome editing tools have enabled us to develop human brain model systems in vitro and readily manipulate genomic information. In the context of these advances, recent studies provide strong evidence that abnormal cholesterol metabolism by ApoE4 could be linked to AD-associated pathology. In this review, we discuss novel discoveries in brain cholesterol dysregulation by ApoE4. We further elaborate cell type-specific roles in cholesterol regulation of four major brain cell types, neurons, astrocytes, microglia, and oligodendrocytes, and how its dysregulation can be linked to AD pathology.