• BMB Reports
• /
• v.37 no.6
• /
• pp.648-656
• /
• 2004

This paper deals with the development of a predictive probabilistic model, a composite dependency-reflecting model (CDRM), which was designed to detect core promoter regions and transcription start sites (TSS) in vertebrate genomic DNA sequences, an issue of some importance for genome annotation. The model actually represents a combination of first-, second-, third- and much higher order or long-range dependencies obtained using the expanded maximal dependency decomposition (EMDD) procedure, which iteratively decomposes data sets into subsets on the basis of dependency degree and patterns inherent in the target promoter region to be modeled. In addition, decomposed subsets are modeled by using a first-order Markov model, allowing the predictive model to reflect dependency between adjacent positions explicitly. In this way, the CDRM allows for potentially complex dependencies between positions in the core promoter region. Such complex dependencies may be closely related to the biological and structural contexts since promoter elements are present in various combinations separated by various distances in the sequence. Thus, CDRM may be appropriate for recognizing core promoter regions and TSSs in vertebrate genomic contig. To demonstrate the effectiveness of our algorithm, we tested it using standardized data and real core promoters, and compared it with some current representative promoter-finding algorithms. The developed algorithm showed better accuracy in terms of specificity and sensitivity than the promoter-finding ones used in performance comparison.

• Journal of Microbiology
• /
• v.40 no.3
• /
• pp.245-247
• /
• 2002

A genomic DNA library of the fungus Trametes versicolor was constructed in a yeast integration vector which contains the URA3 gene of the budding yeast Saccharomyces cerevisiae and the gene responsible for hygromycin B resistance, and fragments acting as autonomously replicating sequences (ARSes) in the budding yeast were identified from the genomic DNA library. Sixteen recombinant plasmids from the library transformed the budding yeast Saccharomyces cerevisiae to Ura+ at high frequencies. They were maintained stably under selective conditions, but were gradually lost from yeast cells at different rates under nonselective conditions, indicating that they contain eukaryotic origins of DNA replication and exist as extrachromosomal plasmids. Base sequences of four ARS DNAs among the 16 cloned fragments revealed that all or the four contain at least one 11 bp ［(A/T)TTTA(T/C)(A/G)TTT(A/T)］consensus sequence of the budding yeast ARS.

• Smart Media Journal
• /
• v.2 no.4
• /
• pp.34-40
• /
• 2013

Rapid sequencing of individual genomes with next generation sequencer opens new horizon to biology and personalized medicine. The analyzed sequences help to check several genomic abnormality, genomic expression, epigenomic phenotypes, gene annotation after assembly of their reads. Several trials integrating genomic information and clinical data will assist disease diagnostics and clinical treatments. To have a large step towards individualized medicine, development of smart interface linking specialized sequence data to the public is necessary.

• Journal of Dairy Science and Biotechnology
• /
• v.30 no.1
• /
• pp.31-36
• /
• 2012

Lactobacillus rhamnosus GG(ATCC 53103) is one of the best researched probiotic strains in the world. Studies in children have shown that Lactobacillus rhamnosus GG effectively prevents early atopic disease in patients with high risk. The active molecules associated with the immunostimulatory sequence and anti-allergy effects of L. rhamnosus GG have not yet been identified. Unmethylated CpG motifs in bacterial DNA have a mitogenic effect in mouse immune cells, CpG-containing ISS oligodeoxynucleotides are potent Th1 adjuvants, effective in both preventing and reversing Th2-biased immune deviation in allergy models. The genomic DNA of L. rhamnosus GG is a potent inducer of murine B cell and dendritic cell immunoactivation. In L. rhamnosus GG genomic DNA, ID35 shows high activity in ISS assays in both mice and humans. The effects of ID35 result from a unique TTTCGTT motif located at its 5'-end, and its effects are comparable with murine prototype CpG 1826. L. rhamnosus GG is known to secrete proteinaceous pili encoded by the spaCBA gene cluster. The presence of pili structures may be essential for its adhesion to human intestinal mucus, explaining the prolonged duration of intestinal residence of this bacterium, compared to that of non-piliated lactobacilli.

• Mycobiology
• /
• v.42 no.4
• /
• pp.311-316
• /
• 2014

Lichen studies, including biodiversity, phylogenetic relationships, and conservation concerns require definitive species identification, however many lichens can be challenging to identify at the species level. Molecular techniques have shown efficacy in discriminating among lichen taxa, however, obtaining genomic DNA from herbarium and fresh lichen thalli by conventional methods has been difficult, because lichens contain high proteins, polysaccharides, and other complex compounds in their cell walls. Here we report a rapid, easy, and inexpensive protocol for extracting PCR-quality DNA from various lichen species. This method involves the following two steps: first, cell breakage using a beadbeater; and second, extraction, isolation, and precipitation of genomic DNA. The procedure requires approximately 10 mg of lichen thalli and can be completed within 20 min. The obtained DNAs were of sufficient quality and quantity to amplify the internal transcribed spacer region from the fungal and algal lichen components, as well as to sequence the amplified products. In addition, 26 different lichen taxa were tested, resulting in successful PCR products. The results of this study validated the experimental protocols, and clearly demonstrated the efficacy and value of our KCl extraction method applied in the fungal and algal samples.

• Molecules and Cells
• /
• v.19 no.3
• /
• pp.303-309
• /
• 2005

The end of eukaryotic genomic DNA is capped by a specialized structure called as "telomere" which consists of the repetitive array of nucleotide sequence, TTAGGG, in humans and mice, and a variety of binding proteins. Telomerase is a ribonucleoprotein (RNP) complex responsible for the elongation of telomeres to maintain the genomic integrity, and is composed of telomerase reverse transcriptase (TERT), telomerase RNA component (TERC), and their associated factors regulating the catalytic activity of telomerase. Although it is now apparent that telomerase protects cells from apoptosis via the maintenance of genomic integrity by stabilizing telomeres, our understanding for the physiological role of telomerase is yet far from completion, and emerging evidence suggests that telomerase has additional extratelomeric roles in mediating cell survival and anti-apoptotic functions against various cytotoxic stresses. Here we summarize and discuss how telomerase and telomeres are involved in mediating cellular protection against apoptosis.

• Proceedings of the Korean Society of Plant Pathology Conference
• /
• 2003.10a
• /
• pp.14-14
• /
• 2003

Potato virus X (PVX), the type member of Potexvirus genus, is a flexuous rod-shaped virus containing a single-stranded (＋) RNA. Infection by PVX produces genomic plus- and minus-strand RNAs and two major subgenomic RNAs (sgRNAs). To understand the mechanism for PVX replication, we are studying the cis- and/or trans-acting elements required for RNA replication. Previous studies have shown that the conserved sequences located upstream of two major sgRNAs, as well as elements in the 5' non-translated region (NTR) affect accumulation of genomic and sg RNAs. Complementarity between sequences at the 5' NTR and those located upstream of two major sgRNAs and the binding of host protein(s) to the 5' NTR have shown to be important for PVX RNA replication. The 5 NTR of PVX contains single-stranded AC-rich sequence and stem-loop structure. The potential role(s) of these cis-elements on virus replication, assembly, and their interaction with viral and host protein(s) during virus infection will be discussed based on the data obtained by in vitro binding, in vitro assembly, gel shift mobility assay, host gene expression profiling using various mutants at these regions.

• BMB Reports
• /
• v.35 no.5
• /
• pp.513-517
• /
• 2002

We describe a new method for identifying the sequences that signal the start of translation, and the boundaries between exons and introns (donor and acceptor sites) in human mRNA. According to the mandatory keyword, ORGANISM, and feature key, CDS, a large set of standard data for each signal site was extracted from the ASCII flat file, gbpri.seq, in the GenBank release 108.0. This was used to generate the scoring matrices, which summarize the sequence information for each signal site. The scoring matrices take into account the independent nucleotide frequencies between adjacent bases in each position within the signal site regions, and the relative weight on each nucleotide in proportion to their probabilities in the known signal sites. Using a scoring scheme that is based on the nucleotide scoring matrices, the method has great sensitivity and specificity when used to locate signals in uncharacterized human genomic DNA. These matrices are especially effective at distinguishing true and false sites.

• BMB Reports
• /
• v.37 no.1
• /
• pp.53-58
• /
• 2004

With advances in determining the entire DNA sequence of the human genome, it is now critical to systematically identify the function of a number of genes in the human genome. These biological challenges, especially those in human diseases, should be addressed in human cells in which conventional (e.g. genetic) approaches have been extremely difficult to implement. To overcome this, several approaches have been initiated. This review will focus on the development of a novel 'chemical genetic/genomic approach' that uses small molecules to 'probe and identify' the function of genes in specific biological processes or pathways in human cells. Due to the close relationship of small molecules with drugs, these systematic and integrative studies will lead to the 'medicinal systems biology approach' which is critical to 'formulate and modulate' complex biological (disease) networks by small molecules (drugs) in human bio-systems.

• Journal of Embryo Transfer
• /
• v.10 no.1
• /
• pp.91-100
• /
• 1995

3.3kb 웅성특이 DNA(pEM39 plasmid DNA)가 성 특이 DNA 검색자로 활용되어질 수 있는가를 확인하기 위하여 구조적인 분석을 Southern blotting, DNA sequencing과 computer program 분석을 통하여 실시하였다. 전체 3.3kb에서 유래된 약 1kb 단위의 단편을 이용하여 표지된 짧은 DNA probe들은 Southern blot 분석에서 웅성특이성을 나타내었다. McGraw와 Jeon의 sequence에 대한 유사성 비교 자료로부터 여러 부분의 conserved region을 찾아내고 이것을 기초로 하여 5개의 primer set들을 선발하였다. Conserved region에 존재하면서 computer program에 의해서 선발되어진 PMS1과 2의 primer set가 최종적으로 PCR 분석을 위하여 선정되었다. 이 primer set를 사용한 PCR 분석에서, 1ng부터 10pg까지의 웅성 genomic DNA에서 PCR 산물을 얻을 수 있었으며, 자성의 경우는 어떠한 산물도 찾을 수 없었다. PCR에 이용할 수정란의 시료는 2 세포기의 수정란에서 얻었으며 순수 분리된 genomic DNA에서 확립된 조건에서 PCR을 수행하였다. 8개의 수정란을 분석한 결과 4개의 웅성과 4개의 자성 수정란을 확인하였다. 이러한 결과는 선정된 primer set가 돼지 수정란의 성을 조기 감별하는데 효율적인 DNA probe로 사용될 수 있다는 것을 암시한다.