• Proceedings of the Microbiological Society of Korea Conference
• /
• 2002.10a
• /
• pp.22-26
• /
• 2002

There are a number of ways in which environmental microbiology and microbial ecology will benefit from DNA micro array technology. These include community genome arrays, SSU rDNA arrays, environmental functional gene arrays, population biology arrays, and there are clearly more different applications of microarray technology that can be applied to relevant problems in environmental microbiology. Two types of the applications, bacterial identification chip and functional gene detection chip, will be presented. For the bacterial identification chip, a new approach employing random genome fragments that eliminates the disadvantages of traditional DNA-DNA hybridization is proposed to identify and type bacteria based on genomic DNA-DNA similarity. Bacterial genomes are fragmented randomly, and representative fragments are spotted on a glass slide and then hybridized to test genomes. Resulting hybridization profiles are used in statistical procedures to identify test strains. Second, the direct binding version of microarray with a different array design and hybridization scheme is proposed to quantify target genes in environmental samples. Reference DNA was employed to normalize variations in spot size and hybridization. The approach for designing quantitative microarrays and the inferred equation from this study provide a simple and convenient way to estimate the target gene concentration from the hybridization signal ratio.

• Journal of Microbiology and Biotechnology
• /
• v.31 no.7
• /
• pp.903-911
• /
• 2021

Previous studies have modified microbial genomes by introducing gene cassettes containing selectable markers and homologous DNA fragments. However, this requires several steps including homologous recombination and excision of unnecessary DNA regions, such as selectable markers from the modified genome. Further, genomic manipulation often leaves scars and traces that interfere with downstream iterative genome engineering. A decade ago, the CRISPR/Cas system (also known as the bacterial adaptive immune system) revolutionized genome editing technology. Among the various CRISPR nucleases of numerous bacteria and archaea, the Cas9 and Cas12a (Cpf1) systems have been largely adopted for genome editing in all living organisms due to their simplicity, as they consist of a single polypeptide nuclease with a target-recognizing RNA. However, accurate and fine-tuned genome editing remains challenging due to mismatch tolerance and protospacer adjacent motif (PAM)-dependent target recognition. Therefore, this review describes how to overcome the aforementioned hurdles, which especially affect genome editing in higher organisms. Additionally, the biological significance of CRISPR-mediated microbial genome editing is discussed, and future research and development directions are also proposed.

• The KIPS Transactions:PartA
• /
• v.16A no.3
• /
• pp.143-152
• /
• 2009

One of the main issues in comparative genomics is to study chromosomal gene order in one or more related species. For this purpose, the whole genome alignment is usually applied to find the horizontal gene transfer, gene duplication, and gene loss between two related genomes. Also it is well known that the novel visualization tool with whole genome alignment is greatly useful for us to understand genome organization and evolution process. There are a lot of algorithms and visualization tools already proposed to find the "gene clusters" on genome alignments. But due to the huge size of whole genome, the previous visualization tools are not convenient to discover the relationship between two genomes. In this paper, we propose AlignScope, a novel visualization system for whole genome alignment, especially useful to find gene clusters between two aligned genomes. This AlignScope not only provides the simplified structure of genome alignment at any simplified level, but also helps us to find gene clusters. In experiment, we show the performance of AlignScope with several microbial genomes such as B. subtilis, B.halodurans, E. coli K12, and M. tuberculosis H37Rv, which have more than 5000 alignment pairs (matched DNA subsequence).

• Proceedings of the Korean Society for Applied Microbiology Conference
• /
• 2005.06a
• /
• pp.264-265
• /
• 2005

• Genomics & Informatics
• /
• v.7 no.3
• /
• pp.178-180
• /
• 2009

A few bioinformatics tools have been used to find out conserved regions as probes. We have developed a system based on a heuristic method with web interfaces to find out conserved regions against microbial genomes. The system runs in real time by using relative entropy in limited narrow regions and detecting similar regions between pair regions with local alignment. The system could be useful to find out conserved regions as genome-wide scale.

• Korean Journal of Microbiology
• /
• v.38 no.4
• /
• pp.267-275
• /
• 2002

We have developed GComp as an analysis tool for microbial genome comparison. This tool exploits BLAST or FASTA as a preprocessing program for local alignments to detect homologous regions, parses the homology search results, and generates tables and files to show homology relationship between two genomes at a glance. The interface for graphical representation of the comparative genomic analysis has been also implemented. Our test cases shows that the program can be useful in practice for intuitive and quantitative comparison of microbial genome sequence pairs as well as self-genome analysis. A few additional features have been devised and designed, which will be added in the further development.

• Asian-Australasian Journal of Animal Sciences
• /
• v.17 no.6
• /
• pp.877-884
• /
• 2004

Although gut microbial functions have been analyzed through cultivation of isolated microbes, molecular analysis without cultivation is becoming a popular approach in recent years. Gene cloning studies have partially revealed the mechanisms involved in fiber digestion of individual microbe. The molecular approach finally made it possible to analyze full genomes of the representative rumen cellulolytic bacteria Fibrobacter and Ruminococcus. The coming database may contain useful information such as regulation of gene expression relating to fiber digestion. Meanwhile, unculturable bacteria are still poorly characterized, even though they are main constituents of gut microbial ecosystem. The molecular analysis is essential to initiating the studies on these unculturable bacteria. The studies dealing with rumen and large intestine are revealing considerable complexity of the microbial ecosystems with many undescribed bacteria. These bacteria are being highlighted as possibly functional members contributing to feed digestion. Manipulation of gut bacteria and gut ecology for improving animal production is still at challenging stage. Bacteria newly introduced in the rumen, whether they are genetically modified or not, suffer from poor survival. In one of these attempts, Butyrivibrio fibrisolvens expressing a foreign dehalogenase was successfully established in sheep rumen to prevent fluoroacetate poisoning. This expands choice of forages in tropics, since many tropic plants are known to contain the toxic fluoroacetate. This example may promise the possible application of molecular breeding of gut bacteria to the host animals with significance in their health and nutrition. When inoculation strategies for such foreign bacteria are considered, it is obvious that we should have more detailed information of the gut microbial ecology.

• Proceedings of the Microbiological Society of Korea Conference
• /
• 2002.10a
• /
• pp.90-93
• /
• 2002

The revolution in molecular biology has given us greatly increased ability to obtain and to modify biological resources and to use them for the benefit of all humankind. The sequencing and the associated analysis of gene functions for a growing number of genomes will have an unprecedented effect on the uses of biological resources and the need for access to them. To investigate the diversity of microbial community in swamp, molecular systematic methods were applied. By amplified rDNA restriction analysis (ARDRA) and rDNA partial sequence analysis, $75\%$ of the isolates were known species. In case of uncultured analysis, almost all the selected clones were new species candidate. Especially archea and uncultured bacterial analyses, all clones were new taxon candidates. As for the eukaryotic diversity, several yeast form cultures were isolated from various samples of swamp. Among them, about $60\%$ of the isolates were easily identified. In case of a new species candidate, most strain were included in hymenomycetal yeasts.

• Journal of Microbiology
• /
• v.43 no.5
• /
• pp.411-416
• /
• 2005

The high-throughput sequencing of microbial genomes has resulted in the relatively rapid accumulation of an enormous amount of genomic sequence data. In this context, the problem posed by the detection of promoters in genomic DNA sequences via computational methods has attracted considerable research attention in recent years. This paper addresses the development of a predictive model, known as the dependence decomposition weight matrix model (DDWMM), which was designed to detect the core promoter region, including the -10 region and the transcription start sites (TSSs), in prokaryotic genomic DNA sequences. This is an issue of some importance with regard to genome annotation efforts. Our predictive model captures the most significant dependencies between positions (allowing for non­adjacent as well as adjacent dependencies) via the maximal dependence decomposition (MDD) procedure, which iteratively decomposes data sets into subsets, based on the significant dependence between positions in the promoter region to be modeled. Such dependencies may be intimately related to biological and structural concerns, since promoter elements are present in a variety of combinations, which are separated by various distances. In this respect, the DDWMM may prove to be appropriate with regard to the detection of core promoter regions and TSSs in long microbial genomic contigs. In order to demonstrate the effectiveness of our predictive model, we applied 10-fold cross-validation experiments on the 607 experimentally-verified promoter sequences, which evidenced good performance in terms of sensitivity.

• Proceedings of the Microbiological Society of Korea Conference
• /
• 2009.05a
• /
• pp.46-47
• /
• 2009