• Environmental Engineering Research
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• v.11 no.4
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• pp.173-180
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• 2006

Autotrophic nitrogen removal and its microbial community from a laboratory scale upflow anaerobic sludge bed reactor were characterized with dynamic behavior of nitrogen removal and sequencing result of molecular technique (DNA extraction, PCR and amplification of 16S rDNA), respectively. In the experiment treating inorganic wastewater, the anaerobic granular sludge from a full-scale UASB reactor treating industrial wastewater was inoculated as seed biomass. The operating results revealed that an addition of hydroxylamine would result in lithoautotrophic ammonium oxidation to nitrite/nitrate, and also hydrazine would play an important role for the success of sustainable nitrogen removal process. Total N and ammonium removal of 48% and 92% was observed, corresponding to nitrogen conversion of 0.023 g N/L-d. The reddish brown-colored granular sludge with a diameter of $1{\sim}2\;mm$ was observed at the lower part of sludge bed. The microbial characterization suggests that an anoxic ammonium oxidizer and an anoxic denitrifying autotrophic nitrifier contribute mainly to the nitrogen removal in the reactor. The results revealed the feasibility on development of high performance lithoautotrophic nitrogen removal process with its microbial granulation.

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

• Ocean policy research
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• v.33 no.2
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• pp.183-204
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• 2018

Whaling has been banned in Republic of Korea after the declaration of the moratorium on the commercial whaling by the International Whaling Commission (IWC) since 1986. Korean government followed the moratorium immediately. However whale meat market has been kept by the bycaught whales and dolphins. So Korean government established a rule to control and trace whale meat in the market in 2011. The rule has some loopholes to allow illegally taken whale meat smuggle into the market. This study investigates the flaws in the current rule and recommend the way to overcome that defects. The first step is to prevent the entry of the illegal whale meat into the market. Minor change of the current law would be a solution. The next measure is to increase the sampling rate of the whale DNA that allowed to distribute in the market. The DNA database would be a powerful tools to identify illegal whale meat which is existing in the market. Korean government is operating three kind of food traceability systems. However, because of the legal limitations and the opposition of the non-governmental animal rights organizations, it is difficult to include whale meat to the existing systems. So the last step is to establish a new Traceability System with a state-of-the-art IT technology like as blockchain. The three measures mentioned above would increase the transparency in the whale meat market and prevent the entry of the illegal products.

• The Korean Journal of Malacology
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• v.20 no.2
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• pp.165-169
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• 2004

The BLAST server for the mollusk was constructed on the basis of the Intel Server Platform SC-5250 dual Xeon 2.8 GHz cpu and Linux operating system. After establishing the operating system, we installed NCBI (National Center for Biotechnology Information) WebBLAST package after web server configuration for cgi (common gate interface) (http://chimp.kribb.re.kr/mollusks). To build up the stand alone blast, we conducted as follows: First, we downloaded the genome information (mitochondria genome information), DNA sequences, amino acid sequences related with mollusk available at NCBI. Second, it was translated into the multifasta format that was stored as database by using the formatdb program provided by NCBI. Finally, the cgi was used for the Stand Alone Blast server. In addition, we have added the vector, Escherichia coli, and repeat sequences into the server to confirm a potential contamination. Finally, primer3 program is also installed for the users to design the primer. The stand alone BLAST gave us several advantages: (1) we can get only the data that agree with the nucleotide sequence directly related with the mollusks when we are searching BLAST; (2) it will be very convenient to confirm contamination when we made the cDNA or genomic library from mollusks; (3) Compared to the current NSBI, we can quickly get the BLAST results on the mollusks sequence information.

• 한국사회정책
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• v.25 no.4
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• pp.39-67
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• 2018

The Korean welfare state has achieved remarkable development during the last two decades, but simultaneously we have witnessed growing prevalent social conflicts and exclusion in the society. This research argues that the source of current problems lies in the nature of the Korean welfare regime, so called, 'paternalistic liberalism'. The paternalistic liberalism has been formulated by the combination of legacies of the developmental state and neo-liberalism. Paternalism with the growth-oriented and employment-centered approach has been a significant factor to restrict individuals' freedom and happiness in the Korean welfare state. It has also been embedded in the Korean welfare state such as social insurance, workfare programs, and centralized social services. In this context, this research proposes social liberalism, pursuing real freedom for all, as a new paradigm for the Korean welfare state. Breaking from the old path, Freecurity, combining freedom and security, which is argued to be the upgraded version of flexicurity, is also newly proposed as the operating model of social liberalism.

• Clinical and Experimental Reproductive Medicine
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• v.48 no.1
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• pp.61-68
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• 2021

Objective: This study was conducted to investigate the relationship of semen parameters in samples used for intracytoplasmic sperm injection (ICSI) with fertilization and pregnancy rates in infertile couples. Methods: In this prospective study of Infertile couples with male factor infertility that had undergone ICSI, fractions of the same semen samples obtained for microinjection (to ensure the best predictability) were evaluated to determine the semen parameters and sperm DNA fragmentation index (DFI) on the day of oocyte recovery. Results: In total, 120 couples completed the study and were subdivided into fertilized (n=87) and non-fertilized couples (n=33). The fertilized couples were further classified into pregnant (n=48) and non-pregnant (n=39) couples. Compared to non-fertilized and non-pregnant couples, fertilized and pregnant couples showed statistically significantly higher sperm viability and percentage of normal sperm morphology, as well as significantly lower sperm DFI values. A receiver operating characteristic curve analysis of data from the 120 ICSI cycles showed that sperm viability, normal sperm morphology percentages, and sperm DFI were significant prognostic indicators of fertilization at cutoff values of 40%, 7%, and 46%, respectively. A sperm DFI of 46% showed sensitivity and specificity of 95% and 90%, respectively, for predicting fertilization, and no clinical pregnancies occurred in couples with a sperm DFI above 46%. Conclusion: Semen parameters from the ICSI day sample, especially sperm viability, normal morphology, and DFI, had an impact on fertilization and pregnancy outcomes in ICSI cycles.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.11
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• pp.4467-4474
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• 2014

Background: We aimed to comprehensively review the evidence for using sputum DNA to detect non-small cell lung cancer (NSCLC). Materials and Methods: We searched PubMed, Science Direct, Web of Science, Chinese Biological Medicine (CBM), Chinese National Knowledge Infrastructure (CNKI), Wanfang, Vip Databases and Google Scholar from 2003 to 2013. The meta-analysis was carried out using a random-effect model with sensitivity, specificity, diagnostic odd ratios (DOR), summary receiver operating characteristic curves (ROC curves), area under the curve (AUC), and 95% confidence intervals (CI) as effect measurements. Results: There were twenty-two studies meeting the inclusion criteria for the meta-analysis. Combined sensitivity and specificity were 0.62 (95%CI: 0.59-0.65) and 0.73 (95%CI: 0.70-0.75), respectively. The DOR was 10.3 (95%CI: 5.88-18.1) and the AUC was 0.78. Conclusions: The overall accuracy of the test was currently not strong enough for the detection of NSCLC for clinical application. Dscovery and evaluation of additional biomarkers with improved sensitivity and specificity from studies rated high quality deserve further attention.

• Genomics & Informatics
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• v.11 no.1
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• pp.46-51
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• 2013

Normal-karyotype acute myeloid leukemia (NK-AML) is a highly malignant and cytogenetically heterogeneous hematologic cancer. We searched for somatic mutations from 10 pairs of tumor and normal cells by using a highly efficient and reliable analysis workflow for whole-exome sequencing data and performed association tests between the NK-AML and somatic mutations. We identified 21 nonsynonymous single nucleotide variants (SNVs) located in a coding region of 18 genes. Among them, the SNVs of three leukemia-related genes (MUC4, CNTNAP2, and GNAS) reported in previous studies were replicated in this study. We conducted stepwise genetic risk score (GRS) models composed of the NK-AML susceptible variants and evaluated the prediction accuracy of each GRS model by computing the area under the receiver operating characteristic curve (AUC). The GRS model that was composed of five SNVs (rs75156964, rs56213454, rs6604516, rs10888338, and rs2443878) showed 100% prediction accuracy, and the combined effect of the three reported genes was validated in the current study (AUC, 0.98; 95% confidence interval, 0.92 to 1.00). Further study with large sample sizes is warranted to validate the combined effect of these somatic point mutations, and the discovery of novel markers may provide an opportunity to develop novel diagnostic and therapeutic targets for NK-AML.

• Genomics & Informatics
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• v.15 no.1
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• pp.11-18
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• 2017

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, 'ChIPseeker' performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.

• Journal of the Korea Society of Computer and Information
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• v.18 no.6
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• pp.1-8
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• 2013

In this paper, we design and implement a firmware for low-cost small PCR devices. To minimize machine code size, the proposed firmware controls real-time tasks simultaneously only with support of the hardware interrupt, but without support of the operating system program. The proposed firmware has the host-local structure in which the firmware receives operation commands from PC and sends operation results to PC through usb communication. We implement a low-cost small PCR device with the proposed firmware loaded on microchip PIC18F4550 chip, and verify that the implemented PCR device significantly reduces cost and volume size of existing commercial PCR devices with a similar performance.