• Animal cells and systems
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• 제1권4호
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• pp.629-635
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• 1997

Previously we reported the migration and rearrangement of a chloroplast gene cluster into mitochondria. The exact genomic locations of the clusters, modes of the gene rearrangement and mechanisms of the interorganellar migration of the clusters have yet to be understood. The detailed analysis needs to include a larger region of DNA surrounding each cluster. To study DNA rearrangement and migration in more detail a cosmid library was constructed using the total rice genomic DNA including nuclear, chloroplast and mitochondrial DNA. From this cosmid library, a sub-library was obtained by selecting the clones hybridized to various regions of chloroplast DNA. According to the hybridization pattern 136 clones from the sub-library were classified into 29 groups. Detailed analysis of these clones revealed that in addition to authentic chloroplast DNA, the clones contain its homologs resulted from rearrangement and mutation. We analyzed two clones in detail, which contain different rp12 homologs resulted from rearrangement and/or migration, respectively.

• Journal of Microbiology
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• 제35권3호
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• pp.172-176
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• 1997

The Mycobacterium tuberculosis clinical isolates in Korea, showing different drug resistances, were analyzed by comparing large restriction fragment (LRF) patterns produced y digestion of genomic DNA with infrequent-cutting endonucleases of SpeI, AsnI and pulsed-field gel electrophoresis (PFGE). SpeI and AsnI allowed with AsnI and SpeI, strains yielded an absolutely identical pattern for Korean type's mycobacteria even though they showed different drug resisstance. However, when three M. tuberculosis strains, showing drug resistance, were digested with XbaI, patterns were different from those of the other M. tuberculosis strians which are susceptible to drugs. This stuyd reveals that the comparison of chromosomal restriction patterns is very useful as an additional aid for the differentiation and identification of M. tuberculosis strains showing drug resistances.

• Mycobiology
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• 제42권1호
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• pp.46-51
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• 2014

A degenerated strain of Pleurotus eryngii KNR2312 was isolated from a commercial farm. Random amplified polymorphic DNA analysis performed on the genomic DNA of the normal and degenerated strains of this species revealed differences in the DNA banding pattern. A unique DNA fragment (1.7 kbp), which appeared only in the degenerated strain, was isolated and sequenced. Comparing this sequence with the KNR2312 genomic sequence showed that the sequence of the degenerated strain comprised three DNA regions that originated from nine distinct scaffolds of the genomic sequence, suggesting that chromosome-level changes had occurred in the degenerated strain. Using the unique sequence, three sets of PCR primers were designed that targeted the full length, the 5' half, and the 3' half of the DNA. The primer sets P2-1 and P2-2 yielded 1.76 and 0.97 kbp PCR products, respectively, only in the case of the degenerated strain, whereas P2-3 generated a 0.8 kbp product in both the normal and the degenerated strains because its target region was intact in the normal strain as well. In the case of the P2-1 and P2-2 sets, the priming regions of the forward and reverse primers were located at distinct genomic scaffolds in the normal strain. These two primer sets specifically detected the degenerate strain of KNR2312 isolated from various mushrooms including 10 different strains of P. eryngii, four strains of P. ostreatus, and 11 other wild mushrooms.

• Asian-Australasian Journal of Animal Sciences
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• 제17권7호
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• pp.897-902
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• 2004

PSMC5 subunit, which belongs to the 26S proteasomal subunit family, plays an important role in the antigen presentation mediated by MHC class I molecular. Full-length cDNA of porcine PSMC5 was isolated using the in silico cloning and rapid amplification of cDNA ends (RACE). Amino acid was deduced and the primary structure was analyzed. Results revealed that the porcine PSMC5 gene shares the high degree of sequence similarity with its mammalian counterparts at both the nucleotide level and the amino acid level. The RT-PCR was performed to detect the porcine PSMC5 expression pattern in seven tissues and the result showed that high express level was observed in spleen, lung, marrow and liver while the low express level was in muscle. The full-length genomic DNA sequence of porcine PSMC5 gene was amplified by PCR and the genomic structure revealed that this gene was comprised by 12 exons and 11 introns. Best alignment of the cDNA and genomic exon DNA sequence presents 4 mismatches and this information potentially bears further study in gene polymorphisms.

• International Journal of Stem Cells
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• 제7권2호
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• pp.108-117
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• 2014

Background and Objectives: Genomic imprinting is an inheritance phenomenon by which a subset of genes are expressed from one allele of two homologous chromosomes in a parent of origin-specific manner. Even though fine-tuned regulation of genomic imprinting process is essential for normal development, no other means are available to study genomic imprinting in human during embryonic development. In relation with this bottleneck, differentiation of human embryonic stem cells (hESCs) into specialized lineages may be considered as an alternative to mimic human development. Methods and Results: In this study, hESCs were differentiated into three lineage cell types to analyze temporal and spatial expression of imprinted genes. Of 19 imprinted genes examined, 15 imprinted genes showed similar transcriptional level among two hESC lines and two human induced pluripotent stem cell (hiPSC) lines. Expressional patterns of most imprinted genes were varied in progenitors and fully differentiated cells which were derived from hESCs. Also, no consistence was observed in the expression pattern of imprinted genes within an imprinting domain during in vitro differentiation of hESCs into three lineage cell types. Conclusions: Transcriptional expression of imprinted genes is regulated in a cell type- specific manner in hESCs during in vitro differentiation.

• 한국미생물·생명공학회지
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• 제47권1호
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• pp.25-33
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• 2019

Lactobacillus rhamnosus BFE5264, isolated from a Maasai fermented milk product ("kule naoto"), was previously shown to exhibit bile acid resistance, cholesterol assimilation, and adhesion to HT29-MTX cells in vitro. In this study, we re-annotated and analyzed the previously reported complete genome sequence of strain BFE5264. The genome consists of a circular chromosome of 3,086,152 bp and a putative plasmid, which is the largest one identified among L. rhamnosus strains. Among the 2,883 predicted protein-coding genes, those with carbohydrate-related functions were the most abundant. Genome analysis of strain BFE5264 revealed two consecutive CRISPR regions and no known virulence factors or antimicrobial resistance genes. In addition, previously known highly variable regions in the genomes of L. rhamnosus strains were also evident in strain BFE5264. Pairwise comparison with the most studied probiotic strain L. rhamnosus GG revealed strain BFE5264-specific deletions, probably due to insertion sequence-mediated recombination. The latter was associated with loss of the spaCBA pilin gene cluster and exopolysaccharide biosynthetic genes. Comparative genomic analysis of the sequences from all available L. rhamnosus strains revealed that they were clustered into two groups, being within the same species boundary based on the average nucleotide identities. Strain BFE5264 had a sister group relationship with the group that contained strain GG, but neither ANI-based hierarchical clustering nor core-gene-based phylogenetic tree construction showed a clear distinctive pattern associated with the isolation source, implying that the genotype alone cannot account for their ecological niches. These results provide insights into the probiotic mechanisms of strain BFE5264 at the genomic level.

• International Journal of Computer Science & Network Security
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• 제21권8호
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• pp.196-202
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• 2021

DNA sequencing provides fundamental data in genomics, bioinformatics, biology and many other research areas. With the emergent evolution in DNA sequencing technology, a massive amount of genomic data is produced every day, mainly DNA sequences, craving for more storage and bandwidth. Unfortunately, managing, analyzing and specifically storing these large amounts of data become a major scientific challenge for bioinformatics. Those large volumes of data also require a fast transmission, effective storage, superior functionality and provision of quick access to any record. Data storage costs have a considerable proportion of total cost in the formation and analysis of DNA sequences. In particular, there is a need of highly control of disk storage capacity of DNA sequences but the standard compression techniques unsuccessful to compress these sequences. Several specialized techniques were introduced for this purpose. Therefore, to overcome all these above challenges, lossless compression techniques have become necessary. In this paper, it is described a new DNA compression mechanism of pattern matching extended Compression algorithm that read the input sequence as segments and find the matching pattern and store it in a permanent or temporary table based on number of bases. The remaining unmatched sequence is been converted into the binary form and then it is been grouped into binary bits i.e. of seven bits and gain these bits are been converted into an ASCII form. Finally, the proposed algorithm dynamically calculates the compression ratio. Thus the results show that pattern matching extended Compression algorithm outperforms cutting-edge compressors and proves its efficiency in terms of compression ratio regardless of the file size of the data.

• 한국발생생물학회지:발생과생식
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• 제10권2호
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• pp.141-146
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• 2006

본 연구는 한우의 지역별 유전적 다양성 및 집단간의 유연관계를 평가하기 위하여 경기, 강원, 충남, 충북, 전남, 전북, 경남 그리고 경북 8개 지역에서 비교적 지역간의 이동이 적은 번식우를 대상으로 공시축을 선발하여 분석을 실시하였다. 각 microsatellite marker의 평균 대립유전자의 수는 7.5개로 검출되었다. 관측된 대립유전자의 이형접합율을 보면 전북(CEB)과 전남(CEN)에서 가장 높게 나타났지만 기대되는 이형접합율은 전체 평균보다 낮은 값을 나타내고 있다. 이는 전북과 전남 지역에서 보유하고 있는 평균 대립유전자의 수가 적기 때문에 기인한 결과라고 할 수 있다. ETH225은 특정 대립유전자가 특정지역의 집단에서 높은 발현빈도를 보임으로써 지역간의 유전적 특징을 나타내는 지표로 활용할 수 있다. 경남 지역과 충북 지역간의 유전적 거리는 0.031로 가장 가까운 것으로 나타났으며, 전북과 충남 지역 사이의 유전적 거리가 0.154로 가장 먼 것으로 나타났다. 전북 지역과 다른 지역들과의 유전적 거리의 평균은 0.136으로 나타났다. 강원 지역 역시 다른 지역들과의 유전적 거리의 평균이 0.082로 대체적으로 멀게 나타나고 있다. 반변 경기와 경남 지역은 다른 지역들과 유전적 거리의 평균이 각각 0.056과 0.055로 가까운 것으로 나타났다. 전체 한우의 기대되는 이형접합율은 0.709로 나타나 다른 품종들에 비해 상당히 높은 다양성을 보유하고 있다.

• 한국축산식품학회지
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• 제27권2호
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• pp.150-156
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• 2007

본 연구는 서로 다른 상염색체에 위치하고 있는 초위성체 유전 표지를 활용한 한국재래돼지 집단의 개체 식별시스템 설정을 위해 수행되었다. 공시재료는 4품종에서 총 446두가 사용되었으며 13종의 좌위에 대한 개체별 유전자형을 분석하였다. 이들 13종에서 출현된 이형접합도는 0.286-0.686였으며 marker 다형성 정보량은 0.399-0.796로 나타났다. 한국 재래돼지 집단에서 나타난 대립 유전자 발현 특성은 다른 대조 품종 집단과 매우 상이한 결과를 나타냈다. S0228좌위는 전체 8종의 대립유전자가 나타난 가운데 다른 3품종에서는 발현이 되지 않은 235 대립유전자가 한국 재래돼지 집단에서만 발현이 되었다. 5종의 초위성체 유전 표지를 활용할 경우 누적 개체 식별력은 99.999%를 나타냈으며 두 마리의 서로 다른 개체가 서로 같은 유전자형을 가질 짝확률은 $0.36{\times}10^{-9}$으로 추정되었다. 따라서 10종의 선정된 유전 표지는 한국재래돼지 집단에서 적정 신뢰도를 제공할 수 있는 개체 식별 시스템을 설정할 수 있을 것으로 생각된다.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2002년도 총회 및 추계학술발표회
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• pp.117.1-117
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• 2002