• Korean Journal of Environmental Agriculture
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• v.31 no.2
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• pp.170-174
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• 2012

BACKGROUND: Inappropriate discharge of wastewaters and industrial effluents are becoming detrimental to the aquatic environment. The presence of toxic substances on wastewaters can be detected by physicochemical and biological methods. However, physicochemical methods do not give any information about biological toxicity. Therefore, in this study we tried to detect the presence of toxic substance on waters using sulfur-oxidizing bacteria (SOB) as a bioassay. MATERIALS AND RESULTS: The SOB biosensor was first stabilized using synthetic stream water and operated in both continuous and semi-continuous mode. When the SOB biosensor was operated in continuous mode, the effluent electrical conductivity (EC) stabilized at~1.72 dS/m. While in the case of semi-continuous, the EC stabilized at~0.6 dS/m. The SOB system was also operated at different reaction times to ascertain the shortest reaction time for monitoring the toxicity. Finally, the SOB biosensor was fed with nitrite as toxic substance. When 5 mg/L of nitrite was added to the SOB system, the EC decreased immediately. However, the EC recovered after few cycle. CONCLUSION: This study shows that the SOB biosensor can be used as warning system to protect aquatic environment from hazardous materials. Although SOB biosensor can not give specific information about the toxic substances, it can assess whether the water is toxic or not.

• Journal of the Korean Data and Information Science Society
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• v.25 no.1
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• pp.119-130
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• 2014

This paper is based on water information system of NIE, National Institute of Environmental Research. We used monthly data of water quality from January, 2013 to August, 2013 starting from measuring point A (nbA) to measuring point N (nbN) located along the Nakdong river main stream. Statistical water quality analysis of BOD (biological oxygen demand) is specified by R programming depending on month, year, and points. Based on BOD measured from Nakdong river's measuring points, we used exploratory data analysis and locally weighted scatter plot smoother (Lowess) trend analysis, which is a method of non-parametic regression analysis, to analyze long-term water tendency and water quality distribution depending on points. Also, we analyzed the period and the measuring point of which the outliers are abundant. As a result, compared to BOD measured in nbM located in Busan along the downstream, BOD measured in nbG located in Daegu and nbI located in Changwon along the midstream showed higher rate of water pollution at a severe level.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.7
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• pp.3349-3355
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• 2012

Background and objectives: Chromosomal abnormalities play an important role in genesis of acute lymphoblastic leukemia (ALL) and have prognostic implications. Five major risk stratifying fusion genes in ALL are BCR-ABL, MLL-AF4, ETV6-RUNX11, E2A-PBX1 and SIL-TAL1. This work aimed to detect common chromosomal translocations and associated fusion oncogenes in adult ALL patients and study their relationship with clinical features and treatment outcome. Methods: We studied fusion oncogenes in 104 adult ALL patients using RT-PCR and interphase-FISH at diagnosis and their association with clinical characteristics and treatment outcome. Results: Five most common fusion genes i.e. BCR-ABL (t 9; 22), TCF3-PBX1 (t 1; 19), ETV6-RUNX1 (t 12; 21), MLL-AF4 (t 4; 11) and SIL-TAL1 (Del 1p32) were found in 82/104 (79%) patients. TCF3-PBX1 fusion gene was associated with lymphadenopathy, SIL-TAL1 positive patients had frequent organomegaly and usually presented with a platelets count of less than $50{\times}10^9/l$. Survival of patients with fusion gene ETV6-RUNX1 was better when compared to patients harboring other genes. MLL-AF4 and BCR-ABL positivity characterized a subset of adult ALL patients with aggressive clinical behaviour and a poor outcome. Conclusions: This is the first study from Pakistan which investigated the frequency of5 fusion oncogenes in adult ALL patients, and their association with clinical features, treatment response and outcome. Frequencies of some of the oncogenes were different from those reported elsewhere and they appear to be associated with distinct clinical characteristics and treatment outcome. This information will help in the prognostic stratification and risk adapted management of adult ALL patients.

• Genomics & Informatics
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• v.14 no.4
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• pp.222-229
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• 2016

Kimchi is a traditional Korean food prepared by fermenting vegetables, such as Chinese cabbage and radishes, which are seasoned with various ingredients, including red pepper powder, garlic, ginger, green onion, fermented seafood (Jeotgal), and salt. The various unique microorganisms and bioactive components in kimchi show antioxidant activity and have been associated with an enhanced immune response, as well as anti-cancer and anti-diabetic effects. Red pepper inhibits decay due to microorganisms and prevents food from spoiling. The vast amount of biological information generated by academic and industrial research groups is reflected in a rapidly growing body of scientific literature and expanding data resources. However, the genome, biological pathway, and related disease data are insufficient to explain the health benefits of kimchi because of the varied and heterogeneous data types. Therefore, we have constructed an appropriate semantic data model based on an integrated food knowledge database and analyzed the functional and biological processes associated with kimchi in silico. This complex semantic network of several entities and connections was generalized to answer complex questions, and we demonstrated how specific disease pathways are related to kimchi consumption.

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.5
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• pp.432-443
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• 2005

Microarray technology has contributed Significantly to the understanding of bacterial genetics and transcriptional regulation. One neglected aspect of this technology has been optimization of microarray-generated signals and quality of generated information. Full genome microarrays were developed for Clostridium acetobutylicum through spotting of PCR products that were designed with minimal homology with all other genes within the genome. Using statistical analyses it is demonstrated that Signal quality is significantly improved by increasing the hybridization volume. possibly increasing the effective number of transcripts available to bind to a given spot, while changes in labeled probe amounts were found to be less sensitive to improving signal quality. In addition to Q-RT-PCR, array validation was tested by examining the transcriptional program of a mutant (M5) strain lacking the pSOL1 178-gene megaplasmid relative to the wildtype (WT) strain. Under optimal conditions, it is demonstrated that the fraction of false positive genes is 1% when considering differentially expressed genes and 7% when considering all genes with signal above background. To enhance genomic-scale understanding of organismal physiology, using data from these microarrays we estimated that $40{\sim}55%$ of the C. acetobutylicum genome is expressed at any time during batch culture, similar to estimates made for Bacillus subtilis.

• Journal of the Korean Society of Fisheries and Ocean Technology
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• v.53 no.2
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• pp.160-168
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• 2017

In this study, we propose a method of optimal placement technique of artificial reef considering characteristics of sea areas and provide basic data for efficient budget execution. In addition, we will contribute to increasing the economic efficiency by improving the fisheries productivity by suggesting the scientific basis for the policy data and the increase of the catch through the resource creation based on the ecological information about the biology. Especially, in order to establish the effective disposition (optimum separation distance) of artificial reef considering characteristics of biological and engineering factors, it is necessary to review the artificial reef installation management regulations and investigate the biological effects of artificial reef facilities, is needed. Through this, it is expected that the ground data of the direction of the policy promotion will be derived by suggesting the placement condition of the artificial reef complex which can maximize the resource composition effect according to the target fish species.

• BMB Reports
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• v.41 no.3
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• pp.184-193
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• 2008

Living organisms are comprised of various systems at different levels, i.e., organs, tissues, and cells. Each system carries out its diverse functions in response to environmental and genetic perturbations, by utilizing biological networks, in which nodal components, such as, DNA, mRNAs, proteins, and metabolites, closely interact with each other. Systems biology investigates such systems by producing comprehensive global data that represent different levels of biological information, i.e., at the DNA, mRNA, protein, or metabolite levels, and by integrating this data into network models that generate coherent hypotheses for given biological situations. This review presents a systems biology framework, called the 'Integrative Proteomics Data Analysis Pipeline' (IPDAP), which generates mechanistic hypotheses from network models reconstructed by integrating diverse types of proteomic data generated by mass spectrometry-based proteomic analyses. The devised framework includes a serial set of computational and network analysis tools. Here, we demonstrate its functionalities by applying these tools to several conceptual examples.

• Journal of Ecology and Environment
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• v.35 no.4
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• pp.301-306
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• 2012

Determination of the minimum population size is an important component for the ex situ conservation of an endangered species. Here, we present the identification of collection strategies that most efficiently captured the genetic diversity of Brasenia schreberi J.F. Gmelin (water-shield) in natural populations from the mainland (MGC) and Jeju Island (JNS) of South Korea, using amplified fragment length polymorphism (AFLP) markers. A total of 313 and 383 polymorphic bands were detected in the MGC and JNS populations, respectively. All of the 140 sampled ramets were distinguishable by the presence of distinct AFLP phenotypes. According to the simulation of the individual sampling by maximization sampling, 25 and 28 individuals captured all of the genetic diversity in the MGC population (mainland of South Korea) and the JNS population (Jeju Island), respectively. The level of genetic diversity of the core collections was similar to the entire collection, indicating that the core collections very well represent the diversity of the entire collection. We therefore suggest a management unit of B. schreberi based on the genetic information for assessing the minimum population size for its ex situ conservation.

• Journal of Biosystems Engineering
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• v.43 no.1
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• pp.59-71
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• 2018

Purpose: Cellulose nanocrystals (CNCs) are natural polymers that have been promoted as a next generation of new, sustainable materials. CNCs are invaluable as reinforcing materials for composites because they can impart improved mechanical, chemical, and thermal properties and they are biodegradable. The purpose of this review is to provide researchers with information that can assist in the application of CNCs extracted from waste agricultural byproducts (e.g. rice husks, corncobs, pineapple leaves). Methods & Results: This paper presents the unique characteristics of CNCs based on agricultural byproducts, and lists processing methods for manufacturing CNCs from agricultural byproducts. Various mechanical treatments (microfluidization and homogenization) and chemical treatments (alkali treatment, bleaching and hydrolysis) can be performed in order to generate nanocellulose. CNC-based composite properties and various applications are also discussed. Conclusions: CNC-based composites from agricultural byproducts can be combined to meet end-use applications such as sensors, batteries, films, food packaging, and 3D printing by utilizing their properties. The review discusses applications in food engineering, biological engineering, and cellulose-based hydrogels.

• Journal of Microbiology and Biotechnology
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• v.24 no.10
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• pp.1445-1454
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• 2014

Severe acute respiratory syndrome (SARS), a disease that spread widely in the world during late 2002 to 2004, severely threatened public health. Although there have been no reported infections since 2004, the extremely pathogenic SARS coronavirus (SARS-CoV), as the causative agent of SARS, has recently been identified in animals, showing the potential for the re-emergence of this disease. Previous studies showed that 27 single nucleotide polymorphism (SNP) mutations among the spike (S) gene of this virus are correlated closely with the SARS pathogenicity and epidemicity. We have developed a SNP DNA microarray in order to detect and genotype these SNPs, and to obtain related information on the pathogenicity and epidemicity of a given strain. The microarray was hybridized with PCR products amplified from cDNAs obtained from different SARS-CoV strains. We were able to detect 24 SNPs and determine the type of a given strain. The hybridization profile showed that 19 samples were detected and genotyped correctly by using our microarray, with 100% accuracy. Our microarray provides a novel method for the detection and epidemiological surveillance of SARS-CoV.