• BMB Reports
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• v.42 no.12
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• pp.823-828
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• 2009

Techniques for analyzing protein-DNA interactions on a genome-wide scale have recently established regulatory roles for distal enhancers. However, the large sizes of higher eukaryotic genomes have made identification of these elements difficult. Information regarding sequence conservation, exon annotation and repetitive regions can be used to reduce the size of the search region. However, previously developed resources are inadequate for consolidating such information. CONVIRT is a web resource for the identification of transcription factor binding sites and also features comparative genomics. Genomic information on ortholog-independent conserved regions, exons, repeats and sequences is integrated into the virtual chromosome, and statistically over-represented single or combinations of transcription factor binding sites are sought. CONVIRT provides regulatory network analysis for several organisms with long promoter regions and permits inter-species genome alignments. CONVIRT is freely available at http://biosoft.kaist.ac.kr/convirt.

• Genomics & Informatics
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• v.5 no.2
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• pp.88-91
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• 2007

Repetitive sequences such as SINE, LINE, and LTR elements form a major part of eukaryotic genomes. A literature search tool that summarizes the information contained within repeat elements would provide biologists in the field of genomics with a useful tool for analyzing genomic sequence features. We developed a java program designed to make literature access easier by using two search engines simultaneously. RepWeb is a web-based search system that provides a user friendly interface for searching the reference data and journals for information related to repeat elements by using the search engines, Google Scholar and PubMed, simultaneously. It provides an interface that displays the repeat element- related biological information, and includes useful functions such as the production of a repeat tree, clickable links to PubMed and Google Scholar, exporting, and sorting a field into date, author, journal and title.

• Proceedings of the KSMRM Conference
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• 2001.11a
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• pp.104-104
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• 2001

Purpose： In this study, we investigated the possible motor pathways of hemiplegic stroke patients usin combined TMS and BOLD fMRI approach and evaluated the correlation between TMS a fMRI methods. Method： Four subjects, who demonstrated left hemiplegia after stroke, are included. TMS was performed using a Dantec Mag2 stimulator (Dantec Company, USA) in single puls mode with figure eight-shaped coil. Following TMS localization, The BOLD T2＊-weight images were acquired with echo planar imaging sequence (TR = 1.2 sec, TE = 60 msec, and flip angle = 90). Motor activation was studied by means of a repetitive fing flexion-extension task. The stimulation protocol comprised 10 cycles of alternating activati and rest (10 images per cycle). Total 60 cycles were performed and each cycle take abou 1.5 sec. The resulting images were then analyzed with STIMULATE (CMRR, U, o Minnesota) to generate functional maps using a student t-test (p < 0.0005) and cluste analysis.

• Journal of Veterinary Clinics
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• v.39 no.5
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• pp.282-285
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• 2022

Compulsive behavior is a sequence of movements usually derived from normal maintenance behaviors that are performed out of context in a repetitive, exaggerated, ritualistic, and sustained manner. In general, the treatment plan includes environmental management, behavior modifications, and psychotropic medications, however, the prognosis is varied. In this case report, a 9-year-old neutered male miniature poodle presented with a lifelong history of tail chasing and mutilation. Based on the behavioral history, observations, and physical examination, compulsive disorder was diagnosed. The dog's compulsive tail chasing behavior improved only with a combination of psychotropic medications, including fluoxetine, trazodone, and gabapentin.

• Journal of Microbiology and Biotechnology
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• v.11 no.5
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• pp.788-797
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• 2001

The usefulness of three PCR methods were evaluated for the epidemiological typing of Staphylococcus aureus: an enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), repetitive extragenic palindromic element PCR (REP-PCR), and 16S-23S intergenic spacer PCR (ITS-PCR). The analysis was performed using a collection of S. aureus strains comprised of 6 reference and 79 isolates from patients with various diseases. Among the 85 S. aureus strains tested, 6 references and 6 isolates were found to be susceptible to methicillin, whereas the remaining 73 isolates were resistant to it. PCR methods are of special concern, as conventional phenotypic methods are unable to clearly distinguish among methicillin-resistant S. aureus (MRSA) strains. The ability of the techniques to detect different unrelated types was found to be as follows: ERIC-PCR, 19 types; REP-PCR, 36 types; and ITS-PCR, 14 types. On the basis of combining the ERIC, REP, and ITS fingerprints, the 85 S. aureus strains were grouped into 56 genetic types (designated G1 to G56). The diversities for the 85 S. aureus strains, calculated according to Simpson\`s index, were 0.88 for an ERIC-PCR, 0.93 for a REP-PCR, and 0.48 for an ITS-PCR, and the diversity increased up to 0.97 when an ERIC-PCR and REP-PCR were combined. The above discrimination indices imply that the genetic heterogeneity of S. aureus strains is high. Accordingly, this study demonstrates that DNA sequences from highly conserved repeats of a genome, particularly a combination of ERIC sequences and REP elements, are a convenient and accurate tool for the subspecies-specific discrimination and epidemiologic tracking of S. aureus.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.2
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• pp.119-122
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• 2013

Repetitive strings such as periods have been studied vigorously in so diverse fields as data compression, computer-assisted music analysis, bioinformatics, and etc. In bioinformatics, periods are highly related to repetitive patterns in DNA sequences so called tandem repeats. In some cases, quite similar but not the same patterns are repeated and thus we need approximate string matching algorithms to study tandem repeats in DNA sequences. In this paper, we propose a new definition of approximate periods of strings based on distance sum. Given two strings $p({\mid}p{\mid}=m)$ and $x({\mid}x{\mid}=n)$, we propose an algorithm that computes the minimum approximate period distance based on distance sum. Our algorithm runs in $O(mn^2)$ time for the weighted edit distance, and runs in O(mn) time for the edit distance, and runs in O(n) time for the Hamming distance.

• The Plant Pathology Journal
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• v.39 no.1
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• pp.88-107
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• 2023

In the present investigation, bacterial isolates from infected apple trees causing apple canker during winter were studied in the northern Gyeongbuk Province, Korea. The pathogen was identified as Pseudomonas syringae pv. syringae (Pss) through various physiological and biochemical characterization assays such as BIOLOG, gas chromatography of fatty acid methyl esters, and 16S rRNA. Bioassays for the production of phytotoxins were positive for syringopeptin and syringomycin against Bacillus megaterium and Geotrichum candidum, respectively. The polymerase chain reaction (PCR) method enabled the detection of toxin-producing genes, syrB1, and sypB in Pss. The differentiation of strains was performed using LOPAT and GATTa tests. Pss further exhibited ice nucleation activity (INA) at a temperature of -0.7℃, indicating an INA⁺ bacterium. The ice-nucleating temperature was -4.7℃ for a non-treated control (sterilized distilled water), whereas it was -9.6℃ for an INA^- bacterium Escherichia coli TOP10. These methods detected pathogenic strains from apple orchards. Pss might exist in an apple tree during ice injury, and it secretes a toxin that makes leaves yellow and cause canker symptoms. Until now, Korea has not developed antibiotics targeting Pss. Therefore, it is necessary to develop effective disease control to combat Pss in apple orchards. Pathogenicity test on apple leaves and stems showed canker symptoms. The pathogenic bacterium was re-isolated from symptomatic plant tissue and confirmed as original isolates by 16S rRNA. Repetitive element sequence-based PCR and enterobacterial repetitive intergenic consensus PCR primers revealed different genetic profiles within P. syringae pathovars. High antibiotic susceptibility results showed the misreading of mRNA caused by streptomycin and oxytetracycline.

• Journal of Applied Biological Chemistry
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• v.59 no.1
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• pp.63-68
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• 2016

This study was performed to assess the microbiological quality of Brassica campestris var. narinosa microgreen from harvesting and processing steps. The samples were analyzed for total viable cell counts (TVC), coliforms, Enterobacteriaceae, Escherichia coli, Salmonella spp., Listeria monocytogenes, Vibrio parahaemolyticus, Bacillus cereus, and Staphylococcus aureus. The total viable counts of microgreen (whole leaves) and environment samples from harvesting steps were higher than 6.8 log CFU/g and the contamination level of coliforms in the samples were 3.2 log CFU/g and 3.5 log CFU/g of microgreen and soil, respectively. In case of microgreen samples collected from processing steps, the contamination level of TVC and coliforms were higher in raw materials than samples obtained from later stages of processing, i.e. washing, drain, and final products. The contamination levels of B. cereus in raw materials and environments decreased approximately 1.4 log CFU/g in final products. S. aureus was detected in soil samples but Salmonella spp., Listeria monocytogenes, Vibrio parahaemolyticus and pathogenic E. coli was not detected. In order to identify the sources of contamination for microgreen, the genetic similarity of B. cereus isolates obtained from harvesting and processing steps were compared using the repetitive-sequence-based polymerase chain reaction method. B. cereus isolates obtained from harvesting environments and microgreen were clustered with a similarity greater than 95%. In case of B. cereus isolates obtained from microgreen and environmental samples at processing steps showed low genetic similarity.

• Korean Journal of Food Science and Technology
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• v.37 no.6
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• pp.1005-1011
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• 2005

Widespread distributions of repetitive DNA elements in bacteria genomes are useful for analysis of genomes and should be exploited to differentiate food-borne pathogenic bacteria among and within species. Enterobacterial repetitive intergenic consensus (ERIC) sequence has been used for ERIC-PCR genomic fingerprinting to identify and differentiate bacterial strains from various environmental sources. ERIC-PCH genomic fingerprinting was applied to detect and differentiate four major Gram-negative food-borne bacterial pathogens, Esherichia coli, Salmonella, Shigella, and Vibrio. Target DNA fragments of pathogens were amplified by ERIC-PCR reactions. Dendrograms of subsequent PCR fingerprinting patterns for each strain were constructed, through which relative similarity coefficients or genetic distances between different strains were obtained numerically. Numerical comparisons revealed ERIC-PCR genotyping is effective for differentiation of strains among and within species of food-borne bacterial pathogens, showing ERIC-PCR fingerprinting methods can be utilized to differentiate isolates from outbreak and to determine their clonal relationships among outbreaks.

• Journal of Life Science
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• v.14 no.3
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• pp.521-524
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• 2004

This experiment was carried out to analyze genetic characteristics and to develop the breed specific DNA marker for Cheju-native horse. If this marker contains high repetitive sequences, it is possible to convert a RAPD marker of interest into a single-locus PCR marker called a sequence characterized amplified region(SCAR). Twenty six Cheju-native horse and Fifty thoroughbred genomic DNA were pooled and PCR. were accomplished using 800 random primers. Comparing the pooled DNA from Cheju-native horse and thoroughbred, we found 9 primers which identified markers present in the pooled DNA from breed but absent in the other breed. Among 9 random primers, 6 primers were thoroughbred specific and 3 primers were Cheju-native horse specific. Testing individual horse revealed that 5 marker showed the similar band pattern between Cheju-native horse and Thoroughbred. However, 4 marker were wholly absent in breed while present in the other breed. UBC $126_{3500bp}$, UBC $162_{500bp}$, and UBC $244_{1200bp}$ was detected only Thoroughbred and UBC $562_{560bp}$was detected Cheju-native horse, respectively. After determining of the cloned breed-specific fragment sequence, we designed the SCAR-primers and carried out PCR. Compared to random primer, RAPD-SCAR primer didn't show significantly higher specific band. However, RAPD analysis is useful for genetic characterization of Cheju-native horse.