박사

산업균주로서 Bacillus licheniformis의 유전체 및 transcript 분석에 대한 연구 = Study on the analysis of genome and transcript of Bacillus licheniformis as an industrial strain

오현화 2016년
논문상세정보
' 산업균주로서 Bacillus licheniformis의 유전체 및 transcript 분석에 대한 연구 = Study on the analysis of genome and transcript of Bacillus licheniformis as an industrial strain' 의 주제별 논문영향력
논문영향력 선정 방법
논문영향력 요약
주제
  • bacillus licheniformis
  • transcript
  • 유전체
동일주제 총논문수 논문피인용 총횟수 주제별 논문영향력의 평균
84 0

0.0%

' 산업균주로서 Bacillus licheniformis의 유전체 및 transcript 분석에 대한 연구 = Study on the analysis of genome and transcript of Bacillus licheniformis as an industrial strain' 의 참고문헌

  • 식품의약품안전처
    식품원료 길라잡이-식품원료 관리제도 해설서-. 7, 1-51 [2011]
  • Zankari, E., Hasman, H, Cosentino, S., Vestergaard, M., Rasmussen, S., Lund, O., Aarestrup, F. M., and Larsen, M. V. 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chenmother, 67(11), 2640-2644.
  • Yun, S. H., Kim, Y. S., So, S. K., Jeong, D. Y., Hahn, K. S. and Uhm, T. B. 2009. Detection of plcR-papR Genes by PCR in Identifying Enterotoxin Genes-Harboring Bacillus cereus Strains. Kor. J. Microbiol., 45 (4), 425-429.
  • Wang, Z., Gerstein M., and Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet., 10, 57-63.
  • Wang, H. K., Nq, Y. K., Koh, E., Yao, L., Chien, A. S., Lin, H. X., and Lee, Y. K. 2015. RNA-Seq reveals transcriptomic interactions of Bacillus subtilis natto and Bifidobacterium animalis subsp. lactis in whole soybean solid-state co-fermentation. Food Microbiology, 51, 25-32.
  • Veith, B., Herzberg, C., Stechel, S., Feesche, J., Maurer, K. H., Ehrenreich, P., B umer, S., Henne, A., Liesegang, H., Merkl, R., Ehrenreich, A., and Gottschalk, G. 2004. The complete genome sequence of Bacillus licheniformis DSM13, an Organism with Great Industrial Potential, J Mol Microbiol Biotechnolol, 7, 204-211.
  • Thompson, J. D., Higgins, D. G., and Gibson, T. J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignmentthrough sequence weighting,position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673-4680.
  • The pharmaceutical society of japan., 2005. Methods of Analysis in health science. Kanehara and co. Ltd., Tokyo, 180-182.
  • Tatusov, R. L., Galperin, M. Y., Natale, D. A., and Koonin, E. V. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acid Research, 28, 33-36.
  • Tamura, K., and Nei, M. 1993. Estimation of the number of nucleotide substitutionsin the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10(3), 512-526.
  • Suzuki, H., amada, C., and Kato, K. 2006. γ-Glutamyl compounds and their enzymatic production using bacterial γ-glutamyltranspeptidase. Amino Acids, 32, 333-340.
  • Sohn, B. H., Kwon, S. C., and Oh, K. H. 2008. Fibrinolytic activity and proteomic analysis of Bacillus licheniformis HK-12 isolated from Chungkuk-Jang. Journal of the Korea Academia-Industrial cooperation Society, 9, 800-806.
  • Směl , D., Pechov , P., Komprd , T., Klejdus, B., and Kub ň, V. 2003. Liquid chromatographic determination of biogenic amines in a meat product during fermentation and long-term storage. Czech J. FoodSci. 21, 167-175.
  • Shin, D. H., Kwon, D. Y., Kim, Y. S., and Jeong, D. Y. 2011. Science and technology of Korean Gochujang. Public health edu.
  • Schulz, M. E., Guinebretiere, M. H., Monthan, A., Berge, O., Fricker, M., and Svensson, B. 2006. Toxin gene profling of enterotoxic and emetic Bacillus cereus. FEMS Microbiol Lett., 260(2), 232-240.
  • Schallmey, M., Singh, A., and Ward, O. P. 2004. Developments in the use of Bacillus species for industrial production. Can J Microbiol., 50, 1-17.
  • Salkinoja-Salonen, M. S., Vuorio, R., Andersson, M. A., K mpfer, P., Andersson, M. C., Honkanen-Buzalski, T., and Scoging, A. C. 1999. Toxigenic strains of Bacillus licheniformis related to food poisoning. Appl Environ Microbiol., 65, 4637-4645.
  • Robinson, M. D., and Oshlack, A. 2010. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol., 11, R25.
  • Rey, M. W., Ramaiya, P., Nelson B. A., Brody-Karpin, S. D., Zaretsky, E. J., Tang, M., ... and Berka, R. M. 2004. Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biology, vol 5(10), R77.
  • Rawlings, N. D., Barrett, A. J., and Finn, R. 2016. Twenty years of the MEROPS database of proteolytic enzymes, their substrate and inhibitors. Nucleic Acids Research, 44, 343-350.
  • Rasko, D. A., Rosovitz, M. J., kstad, O. A., Fouts, D. E., Jiang, L., Cer, R. Z., Kolst , A. B., Gill, S. R., and Ravel, J. 2007. Complete Sequence Analysis of Novel Plasmids from Emetic and Periodontal Bacillus cereus Isolates Reveals a Common Evolutionary History among the B. cereus-Group Plasmids, Including Bacillus anthracis pXO1. Journal Of Bacteriology, 189(1), 52-64.
  • Periwal, V., Patowary, A., Vellarikkal, S. K., Gupta, A., Singh, M., Mittal A., ... and Scaria, V. 2015. Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome. PLoS One, 10(4), e0122979.
  • Pedersen, P. B., Bj rnvad, M. E., Rasmussen, M. D., and Petersen, J. N. 2002. Cytotoxic potential of industrial strains of Bacillus sp. Regul Toxicol Pharmacol, 36, 155-161.
  • Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., ... and Stevens, R. 2013. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Research, 42, 206-214.
  • Nishito, Y., Osana, Y., Hachiya, T., Popendorf, K., Toyoda, A., Fujiyama, A., Itaya, M., and Sakakibara, Y. 2010. Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics, 11, 243.
  • Nam, Y. D., Park, S. L. , and Lim, S. I. 2012. Microbial composition of the Korean traditional food “kochujang” analyzed by a massive sequencing technique. Journal of Food Science, 77, 250-256.
  • Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods, 5(7), 621-628.
  • Medini, D., Donati, C., Tettelin, H., Masignani, V., and Rappuoli, R. 2005. The microbial pan-genome. Current Opinion in Genetics and Development, 15, 589–594.
  • Medema, M. H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M. A., Weber, T., Takano, E., and Breitling, R. 2011. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Research, 39, 339-346.
  • Maclean, D., D.G. Jones, J., and Studholme, D. J. 2009. Application of ‘next-generation’ sequencing technologies to microbial genetics. Nature Review| Microbiology, 7, 287-296.
  • Linchao, S., and Bremer, H. 1986. Effect of the bacterial-growth rate on replication control of plasmid pBR322 in Escherichia coli. Mol. Gen. Genet., 203, 143-149.
  • Li, Y., Triccas, J.A., and Ferenci, T. 1997. A novel levansucrase-levanase gene cluster in Bacillus stearothermophilus ATCC12980. Biochimica et Biophysica Acta., 1353, 203-208.
  • Lee, J. M., Jang, J. H., Oh, N. S., and Han, M. S. 1996. Bacterial distribution of Kochujang, KOREAN J. FOOD SCI. TECHNOL., 28(2), 260-266.
  • Lee, J. H., and Kim, K. H. 2015. Comparative analysis of core and pan-genomes of order Nitrosomonadales. 52(4), 329-337.
  • Lee, I., Kim, Y. O., Park, S. C., and Chun, J. 2016. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. International Journal of Systematic and Evolutionary Microbiology, 66, 1100-1103.
  • Lee, B. K. 1999. Immunomodulation materials of fermented soybean products.
  • Lecture 3 presented at 2nd Symposium for Soybean Fermentation Foods, The Research Institute of Soybean Fermentation Food. Yeungnam Univ. Korea.
  • Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., Alloni, G., Azevedo, V., ... and Danchin, A. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature, 390, 249-256.
  • Kumar, S., Stecher, G., and Tamura K. 2015. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Dataset., Molecular Biology and Evolution.
  • Knapen, M. H. J., Schurgers, L. J., and Vermeer, C. 2007. Vitamin K2 supplementation improves hip bone geometry and bone strength indices in postmenopausal woman. Osteoporos Int., 18, 963-972.
  • Kim, Y. S., Kim, M. C., Kwon, S. W., Kim, S. J., Park, I. C., and Ka, J. O. 2011. Analyses of bacterial communities in meju, a Korean traditional fermented soybean bricks, by cultivation-based and pyrosequencing methods. The Journal of Microbiology, 49(3), 340-348.
  • Kim, Y. S., Jeong, J. O., Cho, S. H., Jeong, D. Y., and Uhm, T. B. 2012. Antimicrobial and Biogenic Amine-Degrading Activity of Bacillus licheniformis SCK B11 Isolated from Traditionally Fermented Red Pepper Paste. Korean Journal of Microbiology, 48, 163-170.
  • Kim, W., Choi, K., Kim, Y., Park, H., Choi, J., Lee, Y., Oh, H., Kwon, I., and Lee, S. 1996. Purification and characterization of a Fibrinolytic enzyme produced from Bacillus sp. strain CK 11-4 Screened from Chungkook-Jang. Applied and Environmental Microbiology, 62(7), 2482-2488.
  • Jeon, S. B. 2015. Isolation and characterization of Bacillus species suitable for soybean fermentation. Published master’s theses, Chonbuk National University, JeonJu.
  • Jeon S. B., Ryu, M. S., Kim, Y. S., Jo, S. W., Jeong, D. Y., and Uhm, T. B. 2013. Isolation and Identification of Bacillus Strains with Antagonistic Properties against Film-forming Yeasts Overgrown in Low Salted Soybean Pastes. Korean Journal of Microbiology, 49, 286-291.
  • Jahn, C. E., Charkowski, A. O., and Willis, D. K. 2008. Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation. Journal of Microbiological Methods, 75, 318-324.
  • Ivanova, N., Sorokin, A., Anderson, I., Galleron, N., Candelon, B., Kapatral, V., ... and Kyrpides, N. 2003. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature, 423(6935), 87-91.
  • Haubold, B., and Wiehe, T. 2004. Comparative genomics: methods and applications, Naturwissenschaften, 91, 405-421.
  • Graunm, P. E. and Lund, T. 1997. Bacillus cereus and its food poisoning toxins. FEMS Microbiology Letters, 157, 223-228.
  • Durham, D. R., Stewart, D. B., and Stellwag, E. J. 1987. Novel Alkalineand Heat-Stable Serine Proteases from Alkalophilic Bacillus sp. Strain GX6638. Journal of Bacteriology, 169(6), 2762-2768.
  • Dischinger, J., Josten, M., Szekat, C., Sahl, H. G., and Bierbaum, G. 2009. Production of the Novel Two-Peptide Lantibiotic Lichenicidin by Bacillus licheniformis DSM 13. PLoS ONE , 4(8), e6788.
  • Dillies, M. A., Rau, A., Aubert J., Hennequet-Antier, C., Jeanmouqin, M., Servant, N., ... and Jaffr zic, F. 2012. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Briefings In Bioinformatics, 14(6), 671-683.
  • Cheigh, H. S., Lee, J. S., and Lee, C. Y. 1993. Antioxidative characteristics of melanoidin related products fractionated from fermented soybean sauce. J Korea Sco Food Nutr., 22, 570-575.
  • Candela, T., and Fouet, A. 2006. Poly-gamma-glutamate in bacteria. Molecular Microbiology, 60(5), 1091-1098.
  • Aziz, R. K., Bartels, D., Best, A. A., Dejongh, M., Disz, T., Edwards, R. A., and Formsma, K. 2008. The RAST Server: Rapid Annotations using Subsystems Technology, BMC genomics, 9, 75.
  • Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome biol, 11, R106.
  • Agata, N., and Ohta, M. 2002. Identification and molecular characterization of the genetic locus for biosynthesis of the emetic toxin, cereulide, of Bacillus cereus. Abstr Ann Meeting Am Soc Microbiol., 102, 374.