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The recent application of next generation sequencing to developmental biology
Woori Kwak 한국발생생물학회 2014 한국발생생물학회 학술발표대회 Vol.2014 No.9
The advent of Next Generation Sequencing (NGS) technology has changed the research paradigm and become an essential tool for recent biological and medical study. In today’s market, there are several sequencing platforms which have specific sequencing principle, and the result of each sequencing platform has different characteristics among them. Hence, each sequencing method became more specialized for specific research purpose, and researchers who consider NGS analysis have to understand the very basic characteristics of each NGS platform. NGS is used in various studies and they are usually classified into 5 categories (Re-sequencing, RNA-seq, de novo assembly, Metagenomics and Epigenomics) of analysis. In this session, we will introduce the characteristics of sequencing platforms and examples of recent research on each of the 5 analysis categories. In addition, we will talk about the benefit of NGS study compared to the traditional study and how these NGS technologies can be applied in developmental biology research.
Kwak, Woori,Kim, Jin-Nam,Kim, Daewon,Hong, Jin Su,Jeong, Jae Hark,Kim, Heebal,Cho, Seoae,Kim, Yoo Yong Asian Australasian Association of Animal Productio 2014 Animal Bioscience Vol.27 No.11
Although growth rate is one of the main economic traits of concern in pig production, there is limited knowledge on its epigenetic regulation, such as DNA methylation. In this study, we conducted methyl-CpG binding domain protein-enriched genome sequencing (MBD-seq) to compare genome-wide DNA methylation profile of small intestine and liver tissue between fast- and slow-growing weaning piglets. The genome-wide methylation pattern between the two different growing groups showed similar proportion of CpG (regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence) coverage, genomic regions, and gene regions. Differentially methylated regions and genes were also identified for downstream analysis. In canonical pathway analysis using differentially methylated genes, pathways (triacylglycerol pathway, some cell cycle related pathways, and insulin receptor signaling pathway) expected to be related to growth rate were enriched in the two organ tissues. Differentially methylated genes were also organized in gene networks related to the cellular development, growth, and carbohydrate metabolism. Even though further study is required, the result of this study may contribute to the understanding of epigenetic regulation in pig growth.
( Woori Kwak ),( Kwondo Kim ),( Chul Lee ),( Chanho Lee ),( Jungsun Kang ),( Kyungjin Cho ),( Sook Hee Yoon ),( Dae-kyung Kang ),( Heebal Kim ),( Jaeyoung Heo ),( Seoae Cho ) 한국미생물 · 생명공학회 2016 Journal of microbiology and biotechnology Vol.26 No.4
Acute respiratory virus infectious diseases are a growing health problem, particularly among children and the elderly. Much effort has been made to develop probiotics that prevent influenza virus infections by enhancing innate immunity in the respiratory tract until vaccines are available. Lactobacillus plantarum GB-LP2, isolated from a traditional Korean fermented vegetable, has exhibited preventive effects on influenza virus infection in mice. To identify the molecular basis of this strain, we conducted a whole-genome assembly study. The single circular DNA chromosome of 3,284,304 bp was completely assembled and 3,250 proteinencoding genes were predicted. Evolutionarily accelerated genes related to the phenotypic trait of anti-infective activities for influenza virus were identified. These genes encode three integral membrane proteins, a teichoic acid export ATP-binding protein and a glucosamine - fructose-6-phosphate aminotransferase involved in host innate immunity, the nonspecific DNA-binding protein Dps, which protects bacteria from oxidative damage, and the response regulator of the three-component quorum-sensing regulatory system, which is related to the capacity of adhesion to the surface of the respiratory tract and competition with pathogens. This is the first study to identify the genetic backgrounds of the antiviral activity in L. plantarum strains. These findings provide insight into the anti-infective activities of L. plantarum and the development of preventive probiotics.
( Jun Sang Ham ),( Woori Kwak ),( Oun Ki Chang ),( Gi Sung Han ),( Seok Geun Jeong ),( Kuk Hwan Seol ),( Hyoun Wook Kim ),( Geun Ho Kang ),( Beom Young Park ),( Hyun Jeong Lee ),( Jong Geun Kim ),( Ky 한국미생물 · 생명공학회 2013 Journal of microbiology and biotechnology Vol.23 No.7
Using a newly constructed de novo assembly pipeline, finished genome level assembly had been conducted for the probiotic candidate strain E. faecalis KACC 91532 isolated from a stool samples of Korean neonates. Our gene prediction identified 3,061 genes in the assembled genome of the strain. Among these, nine genes were specific only for the E. faecalis KACC 91532, compared with all of the four known reference genomes (EF62, D32, V583, OG1RF). We identified genes related to phenotypic characters and detected E. faecalis KACC 91532-specific evolutionarily accelerated genes using dN/dS analysis. From these results, we found the potential risk of KACC 91532 as a useful probiotic strain and identified some candidate genetic variations that could affect the function of enzymes.
Song, Minyu,Kim, Hyaekang,Kwak, Woori,Park, Won Seo,Yoo, Jayeon,Kang, Han Byul,Kim, Jin-Hyoung,Kang, Sun-Moon,Van Ba, Hoa,Kim, Bu-Min,Oh, Mi-Hwa,Kim, Heebal,Ham, Jun-Sang Korean Society for Food Science of Animal Resource 2019 한국축산식품학회지 Vol.39 No.4
Bifidobacterium longum KACC 91563 secretes family 5 extracellular solute-binding protein via extracellular vesicle. In our previous work, it was demonstrated that the protein effectively alleviated food allergy symptoms via mast cell specific apoptosis, and it has revealed a therapeutic potential of this protein in allergy treatment. In the present study, we cloned the gene encoding extracellular solute-binding protein of the strain into the histidine-tagged pET-28a(+) vector and transformed the resulting plasmid into the Escherichia coli strain BL21 (DE3). The histidine-tagged extracellular solute-binding protein expressed in the transformed cells was purified using Ni-NTA affinity column. To enhance the efficiency of the protein purification, three parameters were optimized; the host bacterial strain, the culturing and induction temperature, and the purification protocol. After the process, two liters of transformed culture produced 7.15 mg of the recombinant proteins. This is the first study describing the production of extracellular solute-binding protein of probiotic bacteria. Establishment of large-scale production strategy for the protein will further contribute to the development of functional foods and potential alternative treatments for allergies.
( Sooyeon Lim ),( Dong Hoon Lee ),( Woori Kwak ),( Hakdong Shin ),( Hye Jin Ku ),( Jong Eun Lee ),( Gun Eui Lee ),( Heebal Kim ),( Sang Ho Choi ),( Sangryeol Ryu ),( Ju Hoon Lee ) 한국미생물 · 생명공학회 2015 Journal of microbiology and biotechnology Vol.25 No.1
Staphylococcus aureus is an important foodborne pathogen that causes diverse diseases ranging from minor infections to life-threatening conditions in humans and animals. To further understand its pathogenesis, the genome of the strain S. aureus FORC_001 was isolated from a contaminated food. Its genome consists of 2,886,017 bp double-stranded DNA with a GC content of 32.8%. It is predicted to contain 2,728 open reading frames, 57 tRNAs, and 6 rRNA operons, including 1 additional 5S rRNA gene. Comparative phylogenetic tree analysis of 40 complete S. aureus genome sequences using average nucleotide identity (ANI) revealed that strain FORC_001 belonged to Group I. The closest phylogenetic match was S. aureus MRSA252, according to a whole-genome ANI (99.87%), suggesting that they might share a common ancestor. Comparative genome analysis of FORC_001 and MRSA252 revealed two non-homologous regions: Regions I and II. The presence of various antibiotic resistance genes, including the SCCmec cluster in Region I of MRSA252, suggests that this strain might have acquired the SCCmec cluster to adapt to specific environments containing methicillin. Region II of both genomes contains prophage regions but their DNA sequence identity is very low, suggesting that the prophages might differ. This is the first report of the complete genome sequence of S. aureus isolated from a real foodborne outbreak in South Korea. This report would be helpful to extend our understanding about the genome, general characteristics, and virulence factors of S. aureus for further studies of pathogenesis, rapid detection, and epidemiological investigation in foodborne outbreak.
( Gopalsamy Gnanasekaran ),( Eun Jung Na ),( Han Young Chung ),( Suyeon Kim ),( You-tae Kim ),( Woori Kwak ),( Heebal Kim ),( Sangryeol Ryu ),( Sang Ho Choi ),( Ju-hoon Lee ) 한국미생물 · 생명공학회 2017 Journal of microbiology and biotechnology Vol.27 No.2
Yersinia enterocolitica is a well-known foodborne pathogen causing gastrointestinal infections worldwide. The strain Y. enterocolitica FORC_002 was isolated from the gill of flatfish (plaice) and its genome was sequenced. The genomic DNA consists of 4,837,317 bp with a GC content of 47.1%, and is predicted to contain 4,221 open reading frames, 81 tRNA genes, and 26 rRNA genes. Interestingly, genomic analysis revealed pathogenesis and host immune evasionassociated genes encoding guanylate cyclase (Yst), invasin (Ail and Inv), outer membrane protein (Yops), autotransporter adhesin A (YadA), RTX-like toxins, and a type III secretion system. In particular, guanylate cyclase is a heat-stable enterotoxin causing Yersinia-associated diarrhea, and RTX-like toxins are responsible for attachment to integrin on the target cell for cytotoxic action. This genome can be used to identify virulence factors that can be applied for the development of novel biomarkers for the rapid detection of this pathogen in foods.
Complete genome sequence and SNPs of <i>Raja pulchra</i> (Rajiformes, Rajidae) mitochondria
Hwang, Jae Yeon,Jin, Gwi-Deuk,Park, Jongbin,Kim, Heebal,Lee, Chang-Kyu,Kwak, Woori,Nam, Bo-Hye,An, Cheul Min,Park, Jung Youn,Park, Kyu-Hyun,Huh, Chul-Sung,Kim, Eun Bae Informa UK (Informa Healthcare) 2016 Mitochondrial DNA. Part A Vol.27 No.4
<P>Mitochondrial genomes were sequenced from five Raja pulchra individuals, and single-nucleotide polymorphisms (SNPs) were identified by comparing previously announced sequences in this study. Total 117 SNPs were detected and they were present in 2 rRNA genes, 9 tRNA genes, 13 protein coding genes and non-coding region. One deleted polymorphic site, which was located in 16S rRNA gene, was observed in two individuals. Six polymorphic sites were non-synonymous SNPs, which were distributed in ND1, ND2, ATP6 and ND4 gene. Phylogenic analysis validated current taxa. The genome sequences of R. pulchra mitochondria could be comparable information for understanding species divergence and genomic variation among the populations.</P>