• 대한의생명과학회지
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• 제13권4호
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• pp.251-261
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• 2007

A myofiber of skeletal muscle is composed of myofibrils, sarcolemma (plasma membrane), and constameres, which anchor the myofibrils to the sarcolemma. Achvillin is a recently identified F-actin binding muscle protein, co-isolates with dystrophin and caveolin-3 in low-density sarcolemma of striated muscle, and colocalizes with dystrophin at costameres, the specialized adhesion sites in muscle. Archvillin also binds to nebulin and localizes at myofibrillar Z-discs, the lateral boundaries of the sarcomere in muscle. However other roles of archvillin on the dynamics of myofibrillogenesis remain to be defined. The goal of this study is, by using siRNA-mediated gene silencing technique, to investigate the effect of archvillin on the dynamics of myofibrillogenesis in cell culture of a mouse skeletal myogenic cell line (C2C12), where presumptive myoblasts withdraw from the cell cycle, fuse, undergo de novo myofibrillogenesis, and differentiate into mature myotubes. The roles of archvillin in the assembly and maintenance of myofibril and during the progression of myofibrillogenesis induced in skeletal myoblast following gene silencing in the cell culture were investigated. Fluorescence microscopy demonstrated that the distribution of archvillin was changed along the course of myofibril assembly with nebulin, vinculin and F-actin and then located at Z-lines with nebulin. Fluorescence microscopy demonstrated that knockdown of mouse archvillin expression led to an impaired assembly of new myofibrillar clusters and delayed fusion and myofibrillogenesis although the mouse archvillin siRNA did not affect those expressions of archvillin binding proteins, such as nebulin and F-actin. This result is corresponded with that of RT-PCR and western blots. When the perturbed archvillin was rescued by co-transfection with GFP or Red tagged human archvillin construct, the inhibited cell fusion and myotube formation was recovered. By using siRNA technique, archvillin was found to be involved in early stage of myofibrillogenesis. Therefore, the current data suggest the idea that archvillin plays critical roles on cell fusion and dynamic myofibril assembly.

• Journal of Applied Biological Chemistry
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• 제63권3호
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• pp.189-195
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• 2020

The soybean (Glycine max L.), also known as the soya bean, is an economically important legume species. Pathogens are always major threats for soybean cultivation. Several pathogens negatively affect soybean production. The soybean is also known as a susceptible host to many viruses. Recently, we carried out systematic analyses to identify viruses infecting soybeans using soybean transcriptome data. Our screening results showed that only few soybean transcriptomes contained virus-associated sequences. In this study, we further carried out bioinformatics analyses using a soybean flower bud transcriptome for virus identification, genome assembly, and single nucleotide variations (SNVs). We assembled the genome of Soybean yellow common mosaic virus (SYCMV) isolate China and revealed two SNVs. Phylogenetic analyses using three viral proteins suggested that SYCMV isolate China is closely related to SYCMV isolates from South Korea. Furthermore, we found that replication and mutation of SYCMV is relatively low, which might be associated with flower bud tissue. The most interesting finding was that SYCMV was not detected in the cytoplasmic male sterility (CMS) line derived from the non-CMS line that was severely infected by SYCMV. In summary, in silico analyses identified SYCMV from the soybean flower bud transcriptome, and a nearly complete genome of SYCMV was successfully assembled. Our results suggest that the low level of virus replication and mutation for SYCMV might be associated with plant tissues. Moreover, we provide the first evidence that male sterility might be used to eliminate viruses in crop plants.

• 생명과학회지
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• 제30권7호
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• pp.625-629
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• 2020

바다는 바이러스를 포함하는 다양한 생물체의 풍부한 자원을 제공한다. 본 연구에서는 계절에 따른 제주 바다의 해양 미생물 군집을 확인하기 위해 3월과 12월에 해수 샘플을 수집하여 total RNA를 추출, HiSeq2000 및 de novo 전사체 어셈블리를 사용한 NGS를 실시하였다. 그 결과, 3월 및 12월 시료에서 각각 652,984 및 163,759 개의 전사체를 확인하였다. 3월 샘플에서는 해양 박테리아가 우점하였으나 12월 샘플에서는 진핵생물이 우점하였다. 박테리아 군집은 두 샘플간에 상이하였으며, 이는 계절 변화 동안 박테리아 군집이 변화하였음을 보여주었다. 또한, 해양바이러스를 확인하기 위하여, Megablast를 사용하여 바이러스 참조 데이터베이스에 전사체를 검색하였다. 해양박테리아를 감염시키는 박테리오파지가 두 샘플에서 우점하는 것을 확인하였다. 그러나, 우리는 두 개의 전사체에서 다양한 헤르페스바이러스와 관련된 transcripts가 풍부함을 확인하였으며, 이는 제주도 인근 바다에서 물고기를 감염시키는 헤르페스바이러스의 위협 가능성을 나타낸다. 종합하면, 우리의 데이터는 해양 커뮤니티 연구 및 가능한 해양 바이러스 병원체를 식별하는 데 유용할 것이다.

• 생명과학회지
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• 제30권3호
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• pp.291-297
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• 2020

본 연구는 차세대 염기서열 분석법(NGS)을 이용하여 방어의 microsatellite 마커를 개발하고, 개발된 마커를 이용하여 방어 집단의 유전적 특성을 분석하기 위해 수행되었다. 차세대 염기서열 분석 장비인 Illumina Hiseq2500를 이용하여 총 28,873,374개의 read들을 얻어 assembly를 수행한 결과, 전체의 약 1.6%에 해당하는 466,359개의 read들이 assembly 되었으며, 이 read들의 총 길이는 7,247,216,874 bp로 확인되었다. 크기가 518 bp 이상이 되는 contig는 30.729개로 나타났으며, 이 중 microsatellite 영역을 포함하는 contig 132개(0.43%)를 1차로 선별하고, PCR 증폭 여부 및 유전자형 분석을 통해 microsatellite 후보 60개를 2차로 선별하였다. 그 중 방어집단의 마커로서 유용한 15개의 microsatellite 마커를 선택하였다. 방어집단을 대상으로 개발된 15개의 microsatellite 마커로 분석한 결과, 관찰된 유효 대립유전자수(N_A)는 평균 18.5(11~30)로 나타났다. 평균 관측치 이형접합도(H_O)와 평균기대치 이형접합도(H_E)는 각각 0.812(0.431~0.972)와 0.896(0.782~0.949)으로 나타났다. 다형성이 관찰된 모든 microsatellite 마커 간의 연관불평형은 나타나지 않았으며, 해산어의 평균 H_E 값인 0.79 이상의 수치를 나타내었다. 따라서 본 연구에서 개발된 15개의 microsatellite 마커는 방어 집단의 유전적 다양성 분석에 유용할 것으로 사료된다.

• 생명과학회지
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• 제33권8호
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• pp.623-631
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• 2023

본 연구는 차세대 염기서열 분석법(NGS)을 사용하여 벤자리의 microsatellite 마커를 개발하고, 개발한 마커를 사용하여 벤자리 집단의 유전학적 특성을 분석하기 위해 수행되었다. 차세대 염기서열 분석 장비인 Illumina Hiseq X ten을 사용하여 총 402,244,934개의 read들을 얻어 assembly를 실행한 결과, 전체의 약 0.33%에 해당하는 1,320,995개의 read들이 assembly 되었으며, 이 read들의 총 길이는 705,613,658 bp로 확인되었다. 크기가 640 bp 이상이 되는 contig는 952,326개로 나타났으며, 이 중 microsatellite 영역을 포함하는 contig를 151개(0.016%)로 1차 선별하고, PCR 증폭 여부를 통해 microsatellite 후보 34개를 2차로 선별하였다. 그 중 벤자리 집단의 마커로서 유용한 15개의 microsatellite 마커를 최종 선택하였다. 새로 개발한 15개의 microsatellite 마커를 사용하여 벤자리 집단을 대상으로 분석한 결과, 관찰된 유효 대립유전자 수(N_A)는 평균 12(6~25)로 나타났다. 평균 관측치 이형접합도(H_O)와 평균 기대치 이형접합도(H_E)는 각각 0.750(0.530-0.873)와 0.793 (0.647-0.895)으로 나타냈으며, 이는 해산어의 평균 값인 0.79와 유사한 수치를 나타내었다. 따라서 본 연구에서 개발한 15개의 microsatellite 마커는 벤자리 집단의 유전학적 특성 분석에 유용할 것으로 사료된다.

• Journal of Plant Biotechnology
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• 제43권4호
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• pp.417-421
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• 2016

The complete chloroplast genome sequence of Panax ginseng breeding line 'G07006', showing higher salt tolerance, was confirmed by de novo assembly using whole genome next-generation sequences. The complete chloroplast (CP) genome size is 156,356 bp, including two inverted repeats (IRs) of 52,060 bp, separated by the large single-copy (LSC 86,174 bp) and the small single-copy (SSC 18,122 bp) regions. One hundred fourteen genes were annotated, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among them, 18 sites were duplicated in the inverted repeat regions. By comparative analyses of the previously identified CP genome sequences of nine cultivars of P. ginseng and that of G07006, five useful SNPs were defined in this study. Since three of the five SNPs were cultivar-specific to Chunpoong and Sunhyang, they could be easily used for distinguishing from other ginseng accessions. However, on arranging SNPs according to their gene location, the G07006 genotype was 'GTGGA', which was distinct from other accessions. This complete chloroplast DNA sequence could be conducive to discrimination of the line G07006 (salt-tolerant) and further enhancement of the genetic improvement program for this important medicinal plant.

• Journal of Plant Biotechnology
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• 제43권4호
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• pp.411-416
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• 2016

NGS 기술은 전체 게놈 시퀀싱 및 reference 게놈에 alignment에 의해 돌연변이 표현형에 관련된 돌연변이 식별에 이용한다. 그러나 품종 및 계통들을 resequence 하였을 경우 기존의 reference 게놈에 구조적 변이가 보이며, reference와 맞지 않는 게놈지역에서 돌연변이들은 단순한 alignment로 찾을 수 없다. 본 리뷰에서는 NGS 기술을 이용하여 돌연변이체로부터 변이 관련 유전자를 식별하는 MutMap, MutMap-Gap 및 MutMap+ 방법을 기술하였고 지금까지의 연구현황에 대해 기술하였다. 아울러 이들 방법은 nucleotide-binding site-leucine rich repeat (NBS-LRR) 그룹들의 병 저항성 유전자와 같이 구조적 변이를 가진 유전자를 분리하는 등 유용성에 대해 고찰하였다.

• Journal of Microbiology and Biotechnology
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• 제27권3호
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• pp.591-597
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• 2017

Maribacter dokdonensis DSW-8 was isolated from the seawater off Dokdo in Korea. To investigate the genomic features of this marine bacterium, we sequenced its genome and analyzed the genomic features. After de novo assembly and gene prediction, 16 contigs totaling 4,434,543 bp (35.95% G+C content) in size were generated and 3,835 protein-coding sequences, 36 transfer RNAs, and 6 ribosomal RNAs were detected. In the genome of DSW-8, genes encoding the proteins associated with gliding motility, molybdenum cofactor biosynthesis, and utilization of several kinds of carbohydrates were identified. To analyze the genomic relationships among Maribacter species, we compared publically available Maribacter genomes, including that of M. dokdonensis DSW-8. A phylogenomic tree based on 1,772 genes conserved among the eight Maribacter strains showed that Maribacter speices isolated from seawater are distinguishable from species originating from algal blooms. Comparison of the gene contents using COG and subsystem databases demonstrated that the relative abundance of genes involved in carbohydrate metabolism are higher in seawater-originating strains than those of algal blooms. These results indicate that the genomic information of Maribacter species reflects the characteristics of their habitats and provides useful information for carbon utilization of marine flavobacteria.

• Journal of Microbiology and Biotechnology
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• 제27권8호
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• pp.1419-1427
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• 2017

As probiotics play an important role in maintaining a healthy gut flora environment through antitoxin activity and inhibition of pathogen colonization, they have been of interest to the medical research community for quite some time now. Probiotic bacteria such as Lactobacillus plantarum, which can be found in fermented food, are of particular interest given their easy accessibility. We performed whole-genome sequencing and genomic analysis on a GB-LP1 strain of L. plantarum isolated from Korean traditional fermented food; this strain is well known for its functions in immune response, suppression of pathogen growth, and antitoxin effects. The complete genome sequence of GB-LP1 is a single chromosome of 3,040,388 bp with 2,899 predicted open reading frames. Genomic analysis of GB-LP1 revealed two CRISPR regions and genes showing accelerated evolution, which may have antibiotic and antitoxin functions. The aim of the present study was to predict strain specific-genomic characteristics and assess the potential of this new strain as lactic acid bacteria at the genomic level using in silico analysis. These results provide insight into the L. plantarum species as well as confirm the possibility of its utility as a candidate probiotic.

• 한국동물위생학회지
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• 제39권1호
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• pp.41-49
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• 2016

In the present study, fast and robust methods for the next generation sequencing (NGS) were developed for analysis of PRRSV full genome sequences, which is a positive sensed RNA virus with a high degree of genetic variability among isolates. Two strains of PRRSVs (VR2332 and VR2332-R) which have been maintained in our laboratory were used to validate our methods and to compare with the sequence registered in GenBank (GenBank accession no. EF536003). The results suggested that both of strains had 100% coverage with the reference; the VR2332 had the coverage depth from minimum 3 to maximum 23,012, for the VR2332-R from minimum 3 to maximum 41,348, and 22,712 as an average depth. Genomic data produced from the massive sequencing capacities of the NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequence methods which require the knowledge of conserved regions, the NGS allows de novo assembly of the full viral genomes. Therefore, our results suggested that these methods using the NGS massively facilitate the generation of more full genome PRRSV sequences locally as well as nationally in regard of saving time and cost.