• 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.

• Korean Journal of Environmental Agriculture
• /
• v.30 no.1
• /
• pp.82-88
• /
• 2011

BACKGROUND: Tetracyclines (TCs) are mainly regulated as parent compounds by bioactivity-based screening methods in food. Especially with respect to antimicrobial residues, their metabolites/epimers are also highly concerning chemicals and traditionally applied microbial detection methods are needed to improve with validation for regulatory control. METHODS AND RESULTS: Detection capability and biological activity of tetracycline (TC), chlortetracycline (CTC), oxytetracycline (OTC) and their epimers; anhydrotetracycline (ATC), epianhydrotetracycline (EATC), epitetracycline (ETC), 4-epi-chlortetracycline (ECTC), 4-epianydrochlotetra-cycline (EACTC), 4-epioxychlortetracycline (EOTC), were measured by microbial growth inhibition screening method of Korea Food Code. CONCLUSION(S): Limited detection capabilities were found, B. megarerium and B. subtilis showed for TC and CTC, and B. subtilis for OTC. Biological potency of each epimer was also presented against various microorganisms, at the level from 50% to 96%, comparing with parent TCs. It is recommended that more advanced microbial screening methods with validation are needed, and biologically active epimers are to be considered as marker residues for MRL setting of regulatory control purpose.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.2
• /
• pp.283-294
• /
• 2007

Conventional culture-based methods of enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi) are being rapidly replaced by nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation. The foundation of these techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The next step in functional analysis of the ecosystem is to measure how specific and, or, predominant members of the ecosystem are operating and interacting with other groups. It is also apparent that techniques which optimise the analysis of complex microbial communities rather than the detection of single organisms will need to address the issues of high throughput analysis using many primers/probes in a single sample. Nearly all the molecular ecological techniques are dependant upon the efficient extraction of high quality DNA/RNA representing the diversity of ruminal microbial communities. Recent reviews and technical manuals written on the subject of molecular microbial ecology of animals provide a broad perspective of the variety of techniques available and their potential application in the field of animal science which is beyond the scope of this treatise. This paper will focus on nucleic acid based molecular methods which have recently been developed for studying major functional groups (cellulolytic bacteria, protozoa, fungi and methanogens) of microorganisms that are important in nutritional studies, as well as, novel methods for studying microbial diversity and function from a genomics perspective.

• Journal of Microbiology
• /
• v.44 no.4
• /
• pp.403-408
• /
• 2006

The purpose of this study was to determine the efficacy of a nucleic acid sequence-based amplification (NASBA) method of detecting noroviruses in artificially and naturally contaminated shellfish. We used 58 fecal samples that tested positive for noroviruses with electron microscopy (EM) to develop an NASBA assay for these viruses. Oligonucleotide primers targeting the polymerase coding region were used to amplify the viral RNA in an isothermal process that resulted in the accumulation of RNA amplicons. These amplicons were detected by hybridization with digoxigenin-labeled oligonucleotide probes that were highly specific for genogroup I (GI) and genogroup II (GII) of noroviruses. The expected band of 327bp appeared in denaturing agarose gel without any nonspecific band. The specific signal for each amplicon was obtained through Northern blotting in many repeats. All fecal samples of which 46(79.3%) belonged to GII and 12(20.6%) belonged to GI were positive for noroviruses by EM and by NASBA. Target RNA concentrations as low as 5pg/ml were detected in fecal specimens using NASBA. When the assay was applied to artificially contaminated shellfish, the sensitivity to nucleic acid was 100pg/1.5g shellfish tissue. The potential use of this assay was also confirmed in naturally contaminated shellfish collected from different ponds in Guangzhou city of China, of which 24 (18.76%) out of 128 samples were positive for noroviruses; of these, 19 (79.6%) belonged to GII and 5 (20.4%) belonged to GI. The NASBA assay provided a more rapid and efficient way of detecting noroviruses in fecal samples and demonstrated its potential for detecting noroviruses in food and environmental samples with high specificity and sensitivity.

• Biomedical Science Letters
• /
• v.21 no.4
• /
• pp.165-171
• /
• 2015

Microbial pathogens are responsible for most of the rapidly-spreading deadly infectious diseases against humans. Thus, there is an urgent need for efficient and rapid detection methods for infectious microorganisms. The detection methods should not only be targeted and specific, but they have to be encompassing of potential changes of the pathogen as it evolves and mutates quickly during an epidemic or pandemic. The existing diagnostics such as the antibody-based ELISA immunoassay and PCR methods are too selective and narrowly focused; they are insufficient to capture newly evolved mutant strains of the pathogen. Here, we introduce a fresh perspective on some new technologies, including aptamers and next generation sequencing for pathogen detection. These technologies are not in their infancy; they are reasonably mature and ready, and they hold great promise for unparalleled applications in pathogen detection.

• Journal of Microbiology and Biotechnology
• /
• v.18 no.5
• /
• pp.815-820
• /
• 2008

Two culture-independent methods, namely ribosomal DNA libraries and denaturing gradient gel electrophoresis (DGGE), were adopted to examine the microbial community of a Malaysian light crude oil. In this study, both 16S and 18S rDNAs were PCR-amplified from bulk DNA of crude oil samples, cloned, and sequenced. Analyses of restriction fragment length polymorphism (RFLP) and phylogenetics clustered the 16S and 18S rDNA sequences into seven and six groups, respectively. The ribosomal DNA sequences obtained showed sequence similarity between 90 to 100% to those available in the GenBank database. The closest relatives documented for the 16S rDNAs include member species of Thermoincola and Rhodopseudomonas, whereas the closest fungal relatives include Acremonium, Ceriporiopsis, Xeromyces, Lecythophora, and Candida. Others were affiliated to uncultured bacteria and uncultured ascomycete. The 16S rDNA library demonstrated predomination by a single uncultured bacterial type by >80% relative abundance. The predomination was confirmed by DGGE analysis.

• 한국환경농학회:학술대회논문집
• /
• 2009.07a
• /
• pp.119-126
• /
• 2009

In recent years, research at the Environmental Microbial and Food Safety Laboratory (EMFSL), Agricultural Research Service (ARS) has focused on the development of novel image-based sensing technologies to address agro-food safety concerns, and transformation of these novel technologies into practical instrumentation for industrial implementations. The line-scan-based hyperspectral imaging techniques have often served as a research tool to develop rapid multispectral methods based on only a few spectral bands for rapid online applications. We developed a newer line-scan hyperspectral imaging platform for high-speed inspection on high-throughput processing lines, capable of simultaneous multiple inspection algorithms for different agro-food safety problems such as poultry carcass inspection for wholesomeness and apple inspection for fecal contamination and defect detection. In addition, portable imaging devices were developed for in situ identification of contamination sites and for use by agrofood producer and processor operations for cleaning and sanitation inspection of food processing surfaces. The aim of this presentation is to illustrate recent advances in the above agro.food safety sensing technologies.

• Restorative Dentistry and Endodontics
• /
• v.49 no.1
• /
• pp.4.1-4.9
• /
• 2024

Objectives: This study aims to correlate caries-causing microorganism load, lactic acid estimation, and blood groups to high caries risk in diabetic and non-diabetic individuals and low caries risk in healthy individuals. Materials and Methods: This study includes 30 participants divided into 3 groups: Group A, High-risk caries diabetic individuals; Group B, High-risk caries non-diabetic individuals; and Group C, Low-risk caries individuals. The medical condition, oral hygiene, and caries risk assessment (American Dental Association classification and International Caries Detection and Assessment System scoring) were documented. Each individual's 3 mL of saliva was analyzed for microbial load and lactic acid as follows: Part I: 2 mL for microbial quantity estimation using nutrient agar and blood agar medium, biochemical investigation, and carbohydrate fermentation tests; Part II: 0.5 mL for lactic acid estimation using spectrophotometric analysis. Among the selected individuals, blood group correlation was assessed. The χ² test, Kruskal-Wallis test, and post hoc analysis were done using Dunn's test (p < 0.05). Results: Group A had the highest microbial load and lactic acid concentration, followed by Groups B and C. The predominant bacteria were Lactobacilli (63.00 ± 15.49) and Streptococcus mutans (76.00 ± 13.90) in saliva. Blood Group B is prevalent in diabetic and non-diabetic high-risk caries patients but statistically insignificant. Conclusions: Diabetic individuals are more susceptible to dental caries due to high microbial loads and increased lactic acid production. These factors also lower the executing tendency of neutrophils, which accelerates microbial accumulation and increases the risk of caries in diabetic individuals.

• Journal of environmental and Sanitary engineering
• /
• v.15 no.4
• /
• pp.105-113
• /
• 2000

We have isolated 65 strains(2.0%) of Y. enterocolitica among 3,219 water samples from 380 spring water sites in Seoul from 1994 to 1999. The biochemical characteristics of isolated strains revealed that TSI was A/A, urea, M.R.($37^{\circ}C$), nitrate, motility($37^{\circ}C$), sorbitol, maltose, manitol, arabinose, mannose, trehalose, xylose were positive(100%) and H$_2$S, arginine, lysine, oxidase, citrate, V.P.($37^{\circ}C$), DNase, motility($37^{\circ}C$), dulcitol, adonitol, lactose and raffinose were negative(100%). In in vitro virulence test, positive rate of AAG and CRMOX were 9.2% and 4.6%, respectively. However in the virulence gene detectable gene detectable test by multiplex-PCR using ail, yst, virF genes, 65 strains were all negative, meaning that Y.enterocolitica strains from domestic spring water were not detected for the virulence. Otherwise, mutiplex-PCR which using ail, yst and subgenus-specific primer pair was the best for identifying the virulence of Y. enterocolitica.

• Preventive Nutrition and Food Science
• /
• v.17 no.2
• /
• pp.172-176
• /
• 2012

Doenjang is a traditional Korean fermented soybean product that provides a major source of protein. In this study, a total of 18 different home-made doenjang samples were examined for the presence of foodborne pathogens and the total aflatoxin levels. Using an enzyme-linked immunosorbent assay to assess microbial quality and potential public health risk, we showed that total coliform levels in the doenjang samples ranged from 0 to $4.43{\pm}2.32{\times}10^6\;CFU/g$, and the maximum limit of Bacillus cereus was $4.67{\pm}2.0{\times}10^5\;CFU/g$. However, other foodborne pathogens, such as Staphylococcus aureus, Escherichia coli O157:H7 and Salmonella spp., were not detected among the tested samples. One of the samples (S3) showed a maximum limit of $42.2{\pm}9.1\;{\mu}g/kg$ for aflatoxin levels, which was above the safety limit allowed by the Codex Alimentarius Commission (CAC) regulatory agency. Further research is necessary to determine whether and how doenjang safety can be improved via elimination/reduction of microbial contamination during fermentation and storage or using microbial starter cultures for its fermentation.