• Journal of Microbiology and Biotechnology
• /
• 제22권5호
• /
• pp.649-653
• /
• 2012

A temperate phage was isolated from emetic Bacillus cereus NCTC 11143 by mitomycin C and characterized by transmission electron microscopy and DNA and protein analyses. Whole genome sequencing of Bacillus phage 11143 was performed by GS-FLX. The phage has a dsDNA genome of 39,077 bp and a 35% G+C content. Bioinformatic analysis of the phage genome revealed 49 putative ORFs involved in replication, morphogenesis, DNA packaging, lysogeny, and host lysis. Bacillus phage 11143 could be classified as a member of the Siphoviridae family by morphology and genome structure. Genomic comparisons at the DNA and protein levels revealed homologous genetic modules with patterns and morphogenesis proteins similar to those of other Bacillus phages. Thus, Bacillus phages might have a mosaic genetic relationship.

• Plant Biotechnology Reports
• /
• 제5권4호
• /
• pp.317-322
• /
• 2011

We determined the nuclear DNA content (genome size) of over 35 accessions each of bamboo and rattan species from Southeast Asia. The 2C DNA per nucleus was quantified by flow cytometry. The fluorescence of nuclei isolated from the leaves and stained with propidium iodide was measured. The genome size of the bamboo species examined was between 2.5 and 5.9 pg DNA per 2C nucleus. The genome size of the rattan species examined ranged from 1.8 to 10.5 pg DNA per 2C nucleus. This information will be useful for scientists working in diverse areas of plant biology such as biotechnology, biodiversity, genome analysis, plant breeding, physiology and molecular biology. Such data may be utilized to attempt to correlate the genome size with the ploidy status of bamboo species in cases where ploidy status has been reported.

• Journal of Plant Biology
• /
• 제35권3호
• /
• pp.253-257
• /
• 1992

Potyvirus group에 속하는 것으로 알려진 마늘 모자이크 바이러스 (GMV)가 식물에서 병을 유도하는 메카니즘을 이해하기 위하여, 마늘에 존재하는 GMV에 대한 cDNA clone인 clone 29-6을 분리하였다. Northern blot 분석에 의해 이 바이러스의 genome size는 약 9 kb이고, 또한 clone 29-6은 GLV genome과 유사성이 없었으며, 마늘잎으로부터 분리된 $poly(A)^{+}$ RNA와 강하게 hybridization되었다. 이러한 사실은 이 cDNA clone이 마늘에 감염하여 모자이크 병반을 유도하는 GMV에 대한 cDNA clone 중의 하나인 것으로 생각되었다. Clone 29-6을 probe으로 사용하여 마늘 바이러스의 cDNA 은행을 탐색하여 이와 중첩되는 clone을 선별하여 염기서열을 결정한 결과 이들의 염기서열이 중첩부위에서 서로 일치하지 않았는데 이는 마늘은 여러 형태의 GMV에 의해 감염되어 있음을 암시한다.

• Genomics & Informatics
• /
• 제14권3호
• /
• pp.90-95
• /
• 2016

Nuclear mitochondrial DNA segment (Numt) insertion describes a well-known phenomenon of mitochondrial DNA transfer into a eukaryotic nuclear genome. However, it has not been well understood, especially in plants. Numt insertion patterns vary from species to species in different kingdoms. In this study, the patterns were surveyed in nine plant species, and we found some tip-offs. First, when the mitochondrial genome size is relatively large, the portion of the longer Numt is also larger than the short one. Second, the whole genome duplication event increases the ratio of the shorter Numt portion in the size distribution. Third, Numt insertions are enriched in exon regions. This analysis may be helpful for understanding plant evolution.

• Biotechnology and Bioprocess Engineering:BBE
• /
• 제5권3호
• /
• pp.159-163
• /
• 2000

The genome sequencing project has generated and will contitute to generate enormous amounts of sequence data. Since the first complete genome sequence of bacterium Haemophilus in fluenzae was published in 1995, the complete genome sequences of 2 eukaryotic and about 22 prokaryotic organisms have detemined. Given this everincreasing amounts of sequence information, new strategies are necessary to efficiently pursue the phase of the geome project- the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip technology was developed to efficienfly identify the differential expression pattern of indepondent biogical samples. DNA chip provides a new tool for genome expreesion analysis that may revolutionize revolutionize many aspects of human kife including mew surg discovery and human disease diagnostics.

• 한국생명과학회:학술대회논문집
• /
• 한국생명과학회 2003년도 제40회 국제학술심포지움
• /
• pp.14-27
• /
• 2003

The genomes of Arabidopsis and rice have been fully sequenced. Genomic sequencing provides global information about genome structure and organization. A comprehensive research account of our recent studies conducted on genome painting, comparative genomics and genome fusion is provided in order to project the prospects of plant cytogenetic research in post-genomics era. Genome analysis by GISH using genome painting is demonstrated as an excellent means suitable for visualization of a whole genome, since total genomic DNA representing the overall molecular composition of the genome is used as a probe. FISH on extended DNA fibers has been developed for high-resolution FISH and has contributed to determining the copy number and order of genes. We have also mapped a number of genes involving starch synthesis on wheat chromosomes by FISH and compared the position of these genes on linkage map of rice. Macro synteny between wheat and rice can be observed by comparing the location of these genes in spite of the fact that the size of DNA per chromosome differs by 20 fold in two. Moreover, to approach our goal towards making bread and udon noodles from rice flour in future by incorporating bread making and the noodle qualifies in rice, we have been successful in introducing large genomic DNA fragments containing agronomically important genes of wheat into a rice by successive introduction of large insert BAC clones, there by expanding genetic variability in rice. We call this method genome fusion.

• Asian-Australasian Journal of Animal Sciences
• /
• 제27권11호
• /
• pp.1532-1539
• /
• 2014

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.

• Genomics & Informatics
• /
• 제2권1호
• /
• pp.30-35
• /
• 2004

To investigate the XIST gene expression and its effect in a Klinefelter's patient, we used Klinefelter's syndrome (XXY) patient with azoospermia and also used a normal male (XY) and a normal female (XX) as the control, We were performed cytogenetic analysis, Y chromosomal microdeletion assay (Yq), semi-quantitative RT-PCR, and the Northern blot for Klinefelter's syndrome (KS) patient, a female and a male control, We extracted total RNA from the KS patient, and from the normal cells of the female and male control subjects using the RNA prep kit (Qiagen), cDNA microarray contained 218 human X chromosome-specific genes was fabricated. Each total RNA was reverse transcribed to the first strand cDNA and was labeled with Cy-3 and Cy-5 fluorescein, The microarray was scanned by ScanArray 4000XL system. XIST transcripts were detected from the Klinefelters patient and the female by RT-PCR and Northern blot analysis, but not from the normal male, In the cDNA microarray experiment, we found 24 genes and 14 genes are highly expressed in KS more than the normal male and females, respectively. We concluded that highly expressed genes in KS may be a resulted of the abnormal X inactivation mechanism.

• Journal of Microbiology and Biotechnology
• /
• 제17권6호
• /
• pp.945-951
• /
• 2007

DNA-DNA hybridization has been established as an important technology in bacterial species taxonomy and phylogenetic analysis. In this study, we analyzed how the efficiency with which the genomic DNA from one species hybridizes to the genomic DNA of another species (DNA-DNA hybridization) in microarray analysis relates to the similarity between two genomes. We found that the predicted DNA-DNA hybridization based on genome sequence similarity correlated well with the experimentally determined microarray hybridization. Between closely related strains, significant numbers of highly divergent genes (>55% identity) and/or the accumulation of mismatches between conserved genes lowered the DNA-DNA hybridization signal, and this reduced the hybridization signals to below 70% for even bacterial strains with over 97% 16S rRNA gene identity. In addition, our results also suggest that a DNA-DNA hybridization signal intensity of over 40% indicates that two genomes at least shared 30% conserved genes (>60% gene identity). This study may expand our knowledge of DNA-DNA hybridization based on genomic sequence similarity comparison and further provide insights for bacterial phylogeny analyses.

• 한국유전체학회:학술대회논문집
• /
• 한국유전체학회 2005년도 The 14th Korea Genome Conference
• /
• pp.74-74
• /
• 2005