• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
• /
• 2015.05a
• /
• pp.294-297
• /
• 2015

Recently, big data analysis which is based on machine learning has been gained a lot of attentions in various fields. Especially, agriculture is considered as one promising field that machine learning algorithm can be efficiently utilized and accordingly, lots of works have been done so far. However, most of the researches are focusing on the forecast of weather or analysis of genome, and machine learning algorithm for livestock management, especially which uses individual data of livestocks, e.g., temperature and movement, are not properly investigated yet. In this work, we propose fast abnormal livestock detection algorithm based on machine learning, more specifically expectation maximization, such that livestock which has problem can be efficiently and promptly found. In our proposed scheme, livestocks are divided into two clusters using expectation maximization based on their bionic data and the abnormal livestock can be detected by comparing the size of two clusters. Especially, we divide the case in which single livestock has problem and the case in which livestocks have epidemic such that fast response is enabled when epidemic case. Moreover, our algorithm does not need statistical information.

• Genomics & Informatics
• /
• v.16 no.2
• /
• pp.22-29
• /
• 2018

Incorporation of unique barcodes into fission yeast gene deletion collections has enabled the identification of gene functions by growth fitness analysis. For fine tuning, it is important to examine barcode sequences, because mutations arise during strain construction. Out of 8,708 barcodes (4,354 strains) covering 88.5% of all 4,919 open reading frames, 7,734 barcodes (88.8%) were validated as high-fidelity to be inserted at the correct positions by Sanger sequencing. Sequence examination of the 7,734 high-fidelity barcodes revealed that 1,039 barcodes (13.4%) deviated from the original design. In total, 1,284 mutations (mutation rate of 16.6%) exist within the 1,039 mutated barcodes, which is comparable to budding yeast (18%). When the type of mutation was considered, substitutions accounted for 845 mutations (10.9%), deletions accounted for 319 mutations (4.1%), and insertions accounted for 121 mutations (1.6%). Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (~28%) and well above the predicted error of Sanger sequencing (~2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. When the mutation rate was analyzed by position within 20-mer barcodes using the 1,284 mutations from the 7,734 sequenced barcodes, there was no significant difference between up-tags and down-tags at a given position. The mutation frequency at a given position was similar at most positions, ranging from 0.4% (32/7,734) to 1.1% (82/7,734), except at position 1, which was highest (3.1%), as in budding yeast. Together, well-defined barcode sequences, combined with the next-generation sequencing platform, promise to make the fission yeast gene deletion library a powerful tool for understanding gene function.

• Journal of Plant Biotechnology
• /
• v.36 no.1
• /
• pp.75-80
• /
• 2009

In order to develop transgenic sweetpotato plants [Ipomoea batatas (L.) Lam. cv. Yulmi] with enhanced tolerance to oxidative stress, we constructed transformation vectors expressing 2-Cys peroxiredoxin (Prx) gene under the control of the stress-inducible SWPA2 or enhanced 35S promoter (named as SP or EP). Transgenic sweetpotato plants were attempted to generate from embryogenic calli using an Agrobacterium-mediated transformation system. Embryogenic calli gave rise to somatic embryos and then converted into plantlets on MS medium containing 100 mg/L kanamycin. Transgenic plants were regenerated in the same medium. Southern blot analysis confirmed that the Prx gene was inserted into the genome of the plants. To further study we selected the transgenic plant lines with enhanced tolerance against methyl viologen (MV). When sweetpotato leaf discs were subjected to methyl MV at $20{\mu}M$, transgenic plants showed about 40% higher tolerance than non-transgenic or empty vector-transformed plants.

• Journal of Life Science
• /
• v.27 no.6
• /
• pp.694-701
• /
• 2017

Mycoplasma genitalium represents the smallest genome among mono-cultivable prokaryotes. To discover and compare the orthologs (conservative genes) among M. genitalium and 14 prokaryotes that are uncultivable and have less orthologs than M. genitalium, COG (clusters of orthologous groups of protein) analyses were applied. The analyzed prokaryotes were M. genitalium, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans, four intracellular plant pathogenic eubacteria of Candidatus Phytoplasma genus, and nine endosymbiotic eubacteria of phloem- and xylem-feeding insects. Among 367 orthologs of M. genitalium, 284 orthologs were conservative between M. genitalium and at least one other prokaryote. All 15 prokaryotes commonly have 29 orthologs, representing the significance of proteins in life. They belong to 25 translation-related, including 22 ribosomal proteins, 3 subunits of RNA polymerase, and 1 protein-folding-related. Among the 15 prokaryotes, 40 orthologs were only found in all four Candidatus Phytoplasma. The other nine Candidatus, all endosymbionts with insects, showed only a single common COG0539 (ribosomal protein S1), representing the diversity of orthologs among them. These results might provide clues to understand conservative genes in uncultivable prokaryotes, and may be helpful in industrial areas, such as handling prokaryotes producing amino acids and antibiotics, and as precursors of organic synthesis.

• Journal of Animal Science and Technology
• /
• v.47 no.2
• /
• pp.177-186
• /
• 2005

Xenotransplantation may help to overcome the critical shortage of human tissues and organs for human transplantation, Swine represents an ideal source of such organs owing to their anatomical and physiological similarities to human besides their plentiful supply, However, the use of organs across the species barrier may be associated with the risk of transmission of pathogens, specially porcine endogenous retroviruses (PERVs).• Although most of these potential pathogens could be eliminated by pathogen-free breeding, PERVs are not eliminated by this treatment. PERVs are integrated into the genome of all pigs and produced by normal pig cells and infect human cells. They belong to gamma retroviruses and are of three classes viruses: A, B and C. In the present study, PCR based cloning was performed with chromosomal DNA extracted from pigs from domestic pigs in Korea. Amplified PCR fragments of about 1.5 Kb, covering the partial env gene, were cloned into pCR2.l-TOPO vectors and sequenced. A total of 91 env clones were obtained from domestic pigs, Berkshire, Duroc, Landrace and Yorkshire in Korea. Phylogenetic analysis of these genes revealed the presence of only PERV class A and B in the proportion of 58 % and 42 %, respectively. Among these, 28 clones had the correct open reading frame: 18 clones in class A and 10 clones in class B. Since both these PERV classes are polytropic and have the capacity to infect human cells, our data suggest that proviral PERVs have the potential to generate infectious viruses during or after xenotransplantation in human.

• Korean Journal of Microbiology
• /
• v.51 no.1
• /
• pp.1-6
• /
• 2015

The term "P2 sir-associated helper inefficiency" has been used to define the inefficient helper capability of P2 sir mutants for their satellite bacteriophage P4. The aim of this study was to investigate the factors overcoming P2 sir-associated helper inefficiency. At first, we verified whether the P2 cos region containing P4 sid71 cosP2 could overcome P2 sir-associated helper inefficiency with P2 sir3. The result was that P4 sid71 cosP2 could not overcome P2 sir-associated helper inefficiency with P2 sir3. Instead of cos region of P2, the size of the DNA packaged into a $P2_{sir}$-sized head seems to be important for overcoming P2 sir-associated helper inefficiency. In the present work, three kinds of P4 derivatives with packaged DNA sizes between those of P4 ost1 and P4 ost2, were constructed through DNA manipulation. In one P4 derivative, P4 sid71 delRI::apr, the size of the packaged DNA was identified with a CsCl buoyant equilibrium density gradient experiment. According to the burst sizes of the P4 derivatives, they could overcome P2 sir3-associated helper inefficiency. The size of the P4 derivative DNA suitable for packaging into a $P2_{sir3}$-sized head was 28-29 kb.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2010.10a
• /
• pp.14-14
• /
• 2010

Vitamin C (ascorbic acid) is an essential component for collagen biosynthesis and also for the proper functioning of the cardiovascular system in humans. Unlike most of the animals, humans lack the ability to synthesize ascorbic acid on their own due to a mutation in the gene encoding the last enzyme of ascorbate biosynthesis. As a result, vitamin C must be obtained from dietary sources like plants. In this study, we have developed two different kinds of transgenic potato plants (Solanumtuberosum L. cv. Taedong Valley) overexpressing strawberry GalUR and mouse GLoase gene under the control of CaMV 35S promoter with increased ascorbic acid levels. Integration of the these genes in the plant genome was confirmed by PCR and Southern blotting. Ascorbic acid(AsA) levels in transgenic tubers were determined by high-performance liquid chromatography(HPLC). The over-expression of these genes resulted in 2-4 folds increase in AsA intransgenic potato and the levels of AsA were positively correlated with increased geneactivity. The transgenic lines with enhanced vitamin C content showed enhanced tolerance to abiotic stresses induced by methyl viologen(MV), NaCl or mannitol as compared to untransformed control plants. The leaf disc senescence assay showed better tolerance in transgenic lines by retaining higher chlorophyll as compared to the untransformed control plants. Present study demonstrated that the over-expression of these gene enhanced the level of AsA in potato tubers and these transgenics performed better under different abiotic stresses as compared to untransformed control. We have also investigated the mechanism of the abiotic stress tolerance upon enhancing the level of the ascorbate in transgenic potato. The transgenic potato plants overexpressing GalUR gene with enhanced accumulation of ascorbate were investigated to analyze the antioxidants activity of enzymes involved in the ascorbate-glutathione cycle and their tolerance mechanism against different abiotic stresses under invitro conditions. Transformed potato tubers subjected to various abiotic stresses induced by methyl viologen, sodium chloride and zinc chloride showed significant increase in the activities of superoxide dismutase(SOD, EC 1.15.1.1), catalase, enzymes of ascorbate-glutathione cycle enzymes such as ascorbate peroxidase(APX, EC 1.11.1.11), dehydroascorbate reductase(DHAR, EC 1.8.5.1), and glutathione reductase(GR, EC 1.8.1.7) as well as the levels of ascorbate, GSH and proline when compared to the untransformed tubers. The increased enzyme activities correlated with their mRNA transcript accumulation in the stressed transgenic tubers. Pronounced differences in redox status were also observed in stressed transgenic potato tubers that showed more tolerance to abiotic stresses when compared to untransformed tubers. From the present study, it is evident that improved to lerance against abiotic stresses in transgenic tubers is due to the increased activity of enzymes involved in the antioxidant system together with enhanced ascorbate accumulated in transformed tubers when compared to untransformed tubers. At moment we also investigating the role of enhanced reduced glutathione level for the maintenance of the methylglyoxal level as it is evident that methylglyoxal is a potent cytotoxic compound produced under the abiotic stress and the maintenance of the methylglyoxal level is important to survive the plant under stress conditions.

• Korean Journal of Microbiology
• /
• v.52 no.1
• /
• pp.120-124
• /
• 2016

A certain size of DNA (28-29 kb long) to be packaged into P2-size head and the mutation in sid gene of bacteriophage P4 are the major factors to overcome "P2 sir-associated helper inefficiency". To clarify whether the presence of sid mutation is essential to overcome "P2 sir-associated helper inefficiency" or not, we tested the P4 derivative, P4 delRI::kmr, which is $sid^+$ and whose genome size supposed to be 28.5 kb long in the case of being packaged into $P2_{sir3}$-sized large head. As P4 delRI::kmr showed the low EOP with P2 sir3 lysogen, P4 delRI::kmr phage stock was prepared in P2 sir3 lysogen host to increase the EOP with P2 sir3 lysogen. Through this process, P4 delRI::kmr had been adapted for P2 sir3 lysogen. With a CsCl buoyant equilibrium density gradient experiment and gel electrophoresis of the isolated DNA, it was evident that the adaptation of P4 delRI::kmr for P2 sir3 lysogen was caused by the conformational change of DNA to be packaged into large head. The burst size determination experiments with P4 delRI::kmr phage stock adapted for P2 sir3 lysogen and normal P4 delRI::kmr phage stock showed that not the sid mutation but the size of DNA to be packaged (28-29 kb long) was essential to overcome "P2 sir-associated helper inefficiency".

• Journal of Intelligence and Information Systems
• /
• v.13 no.2
• /
• pp.55-68
• /
• 2007

DNA sequence alignment algorithms in computational molecular biology have been improved by diverse methods. In this paper, we proposed a DNA sequence alignment algorithm utilizing quality information and a fuzzy inference method utilizing characteristics of DNA sequence fragments and a fuzzy logic system in order to improve conventional DNA sequence alignment methods using DNA sequence quality information. In conventional algorithms, DNA sequence alignment scores were calculated by the global sequence alignment algorithm proposed by Needleman-Wunsch applying quality information of each DNA fragment. However, there may be errors in the process for calculating DNA sequence alignment scores in case of low quality of DNA fragment tips, because overall DNA sequence quality information are used. In the proposed method, exact DNA sequence alignment can be achieved in spite of low quality of DNA fragment tips by improvement of conventional algorithms using quality information. And also, mapping score parameters used to calculate DNA sequence alignment scores, are dynamically adjusted by the fuzzy logic system utilizing lengths of DNA fragments and frequencies of low quality DNA bases in the fragments. From the experiments by applying real genome data of NCBI (National Center for Biotechnology Information), we could see that the proposed method was more efficient than conventional algorithms using quality information in DNA sequence alignment.

• Laboraroty Animal Research
• /
• v.34 no.4
• /
• pp.166-175
• /
• 2018

Recombination activating gene-2 (RAG-2) plays a crucial role in the development of lymphocytes by mediating recombination of T cell receptors and immunoglobulins, and loss of RAG-2 causes severe combined immunodeficiency (SCID) in humans. Rag-2 knockout mice created using homologous recombination in ES cells have served as a valuable immunodeficient platform, but concerns have persisted on the specificity of Rag-2-related phenotypes in these animals due to the limitations associated with the genome engineering method used. To precisely investigate the function of Rag-2, we recently established a new Rag-2 knockout FVB mouse line ($Rag-2^{-/-}$) manifesting lymphopenia by employing a CRISPR/Cas9 system at Center for Mouse Models of Human Disease. In this study, we further characterized their phenotypes focusing on histopathological analysis of lymphoid organs. $Rag-2^{-/-}$ mice showed no abnormality in development compared to their WT littermates for 26 weeks. At necropsy, gross examination revealed significantly smaller spleens and thymuses in $Rag-2^{-/-}$ mice, while histopathological investigation revealed hypoplastic white pulps with intact red pulps in the spleen, severe atrophy of the thymic cortex and disappearance of follicles in lymph nodes. However, no perceivable change was observed in the bone marrow. Moreover, our analyses showed a specific reduction of lymphocytes with a complete loss of mature T cells and B cells in the lymphoid organs, while natural killer cells and splenic megakaryocytes were increased in $Rag-2^{-/-}$ mice. These findings indicate that our $Rag-2^{-/-}$ mice show systemic lymphopenia with the relevant histopathological changes in the lymphoid organs, suggesting them as an improved Rag-2-related immunodeficient model.