Publications 2012 (Bielefeld)

Dissertations and publications in 2012 from the CLIB-GC at Bielefeld University.

Dissertations

Schwientek, Patrick February 2012, Genomics and Transcriptomics of the Industrial Acarbose Producer Actinoplanes sp. SE50/110

Trost, Eva June 2012, Das bakterielle Pangenom: Komparative Genomanalysen zur Identifizierung neuer Virulenzfaktoren des Corynebacterium diphtheriae-Clusters

Zakrzewski, Martha October 2012, Development of computational methods for the analysis of metagenome and metatranscriptome data

Schneider, Jessica October 2012, Sequenzanalyse, Annotation und Stoffwechselrekonstruktion der biotechnologisch relevanten Hefen Wickerhamomyces ciferii und Wickerhamomyces anomalus mit der RAPYD Platform

Publications

Zahoor A, Lindner SN, Wendisch VF (2012) Metabolic engineering of Corynebacterium glutamicum aimed at alternative carbon sources and new products. Computational and Structural Biotechnology Journal. 3 (4): e201210004.

Parreira, V.R., Costa, M., Eikmeyer, F.G., Blom, J., & Prescott, J.F. 2012. Sequence of Two Plasmids from Clostridium perfringens Chicken Necrotic Enteritis Isolates and Comparison with C. perfringens Conjugative Plasmids. PLoS ONE 7(11), e49753.

Maus, I., Wibberg, D., Stantscheff, R., Eikmeyer, F.G., Seffner, A., Boelter, J., Szczepanowski, R., Blom, J., Jaenicke, S., Konig, H., Pühler, A., & Schlüter, A. 2012. Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester. J Bact 194(19), 5487 - 5488.

Zakrzewski, M., Goesmann, A., Jaenicke, S., Jünemann, S., Eikmeyer, F.G., Szczepanowski, R., Al-Soud, W.A., Sørensen, S., Pühler, A., & Schlüter, A. 2012. Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. J Biotechnol 158(4), 248 - 258.

Eikmeyer F, Hadiati A, Szczepanowski R, Wibberg D, Schneiker-Bekel S, Rogers L M, Brown C J, Top E M, Pühler A, Schlüter A. The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution. Plasmid. Vol.68 pp 13-24.

Wibberg D, Heinl S, Eikmeyer F. G., Szczepanowski R, Blom J, Linke B, Goesmann A, Grabherr R, Schwab H, Pühler A, Schlüter A. Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage. (2012) J Biotechnol. Vol. 161 pp 153-66.

Stolze Y, Eikmeyer F. G., Wibberg D, Brandis G, Karsten C, Krahn I, Schneiker-Bekel S, Viehöver P, Barsch A, Keck M, Top EM, Niehaus K, Schlüter A. IncP; plasmids of Comamonas sp. and Delftia sp. strains isolated from a wastewater treatment plant mediate resistance to and decolorization of the triphenylmethane dye crystal violet. (2012) Microbiology. Vol. 158 :pp 2060-72.

Maus I, Wibberg D, Stantscheff R, Eikmeyer FG, Seffner A, Boelter J, Szczepanowski R, Blom J, Jaenicke S, König H, Pühler A, Schlüter A. (2012) Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester. J Bacteriol. Vol. 194:pp 5487-8.

Luque-Almagro V M, Acera F, Igeño I, Wibberg D, Roldán D, Sáez L P, Hennig M, Quesada A, Huertas J, Blom J, Merchán F, Escribano P, Jaenicke S, Estepa J, Guijo I, Martínez-Luque M, Macías D, Szczepanowski R, Becerra G, Ramirez S, Carmona I, Gutiérrez O, Manso I, Pühler A, Castillo F, Moreno-Vivián C, Schlüter A, Blasco R. Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344 Environ Microbiol. Vol.15(1): pp 253-70.

Wibberg D, Szczepanowski R, Eikmeyer FG, Pühler A, Schlüter A. The IncF plasmid pRSB225 isolated from a municipal wastewater treatment plant’s on-site preflooder combining antibiotic resistance and putative virulence functions is highly related to virulence plasmids identified in pathogenic E. coli isolates. Plasmid. Vol.69(2): pp 127-37.

Wibberg D, Jelonek L, Rupp O, Hennig M, Eikmeyer FG, Goesmann A, Hartmann A, Borriss R, Grosch R, Pühler A, Schlüter A. Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. J Biotechnol. 2012 Dec 29. doi:pii: S0168-1656(12)00758-4. 10.1016/j.jbiotec.2012.12.010. [Epub ahead of print]

Bonnin RA, Poirel L, Nordmann P, Eikmeyer FG, Wibberg D, Pühler A, Schlüter A. Complete sequence of broad-host-range plasmid pNOR-2000 harbouring the metallo-beta-lactamase gene blaVIM-2 from Pseudomonas aeruginosa. J Antimicrob Chemother. [Epub ahead of print]

Lauersen, K. J., Berger, H. Mussgnug, J. H. and O. Kruse. 2012. Efficient recombinant protein production and secretion from nuclear transgenes in Chlamydomonas reinhardtii. Journal of Biotechnology. Epub ahead of print:

Gorzolka K, Lissel M, Kessler N, Loch-Ahring S, Niehaus K (2012) Metabolite fingerprinting of barley whole seeds, endosperms, and embryos during industrial malting. J Biotechnol 159.3 / 177 - 187

Schwientek, P, Wendler, S, Neshat, A, Eirich, C, Rückert, C, Klein, A, Wehmeier, UF, Kalinowski, J, Stoye, J, Pühler, A. (2012). Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media. J Biotechnol. http://dx.doi.org/10.1016/j.jbiotec...

Wendler, S, Hürtgen, D, Kalinowski, J, Klein, A, Niehaus, K, Schulte, F, Schwientek, P, Wehlmann, H, Wehmeier, UF, Pühler, A. (2012). The cytosolic and extracellular proteomes of Actinoplanes sp. SE50/110 led to the identification of gene products involved in acarbose metabolism. J Biotechnol. 2012 Aug 31. doi:pii: S0168-1656(12)00613-X. 10.1016/j.jbiotec.2012.08.011. [Epub ahead of print]

Eikmeyer FG, Rademacher A, Hanreich A, Hennig M, Jaenicke J, Maus I, Wibberg D, Zakrzewski M, Pühler A, Klocke M and Schlüter A (2012). Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms. Biotechnology for Biofuels [Epub ahead of print].

Schröder J, Maus I, Meyer K, Wördemann S, Blom J, Jaenicke S, Schneider J, Trost E, Tauch A (2012). Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient. BMC Genomics 13:141.

La Russa, M., Bogen, C., Uhmeyer, A., Doebbe, A., Filippone, E., Kruse, O., Mussgnug, J.H., 2012. Functional analysis of three type-2 DGAT homologue genes for triacylglycerol production in the green microalga Chlamydomonas reinhardtii. J Biotechnol 2012 Nov 30;162(1):13-20

Bannert, A., Bogen, C., Esperschütz, J., Koubová, A., Buegger, F., Fischer, D., Radl, V., Fuß, R., Chrosáková, A., Elhottová, D., Simek, M., and M. Schloter. 2012. Anaerobic oxidation of methane in grassland soils used for cattle husbandry. Biogeosciences Discussions, Volume 9, pp.4919-4945.

Lenger, J., Schröder, M., Ennemann, E., Müller, B.. Wong, C.H., Noll, T.,Dierks, T., Hanson, S.R., Sewald, N. (2012) Evaluation of Sulfatase-Directed Quinone Methide Traps for Proteomics. Bioorganic & medicinal chemistry, 20(2): 622-627

Meleady, P.; Hoffrogge, R.; Henry, M.; Rupp, O.; Bort, J.H.; Clarke, C.; Brinkrolf, K.; Kelly, S.; Müller, B.; Doolan, P.; Hackl, M.; Beckmann, T.F.; Noll, T.; Grillari, J.; Barron, N.; Pühler, A.; Clynes, M.; Borth, N. (2012) Utilization and evaluation of CHO-specific sequence databases for mass spectrometry based proteomics. Biotechnology and bioengineering, 109(6): 1386-1394

Doerr D, Hu, K., Renly, S., Edlund, S., Davis, M., Lessler, J., Filter, M., Käsbohrer, A., Appel, B., Kaufman, J. Accelerating investigation of food-borne disease outbreaks using pro-active geospatial modeling of food supply chains. ACM SIGSPATIAL HealthGIS’12, November 6, 2012. Redondo Beach, CA, USA, Copyright 2012 ACM ISBN 978-1-4503-1703-0/12/11

Doerr, D., Thévenin, A. & Stoye, J. Gene family assignment-free comparative genomics. BMC Bioinformatics 13(Suppl 19), S3 (2012).

Barzantny H, Schröder J, Strotmeier J, Fredrich E, Brune I, Tauch A. The transcriptional regulatory network of Corynebacterium jeikeium K411 and its interaction with metabolic routes contributing to human body odor formation. J Biotechnol. 2012 Jun 15;159(3):235-48.

Barzantny H, Brune I, Tauch A. Molecular basis of human body odour formation: insights deduced from corynebacterial genome sequences. Int J Cosmet Sci. 2012 Feb;34(1):2-11.

Soares SC, Trost E, Ramos RT, Carneiro AR, Santos AR, Pinto AC, Barbosa E, Aburjaile F, Ali A, Diniz CA, Hassan SS, Fiaux K, Guimarães LC, Bakhtiar SM, Pereira U, Almeida SS, Abreu VA, Rocha FS, Dorella FA, Miyoshi A, Silva A, Azevedo V, Tauch A. Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production. J Biotechnol. 2012 Nov 29. doi:pii: S0168-1656(12)00708-0. 10.1016/j.jbiotec.2012.11.003. [Epub ahead of print]

Schröder J, Glaub A, Schneider J, Trost E, Tauch A. Draft genome sequence of Corynebacterium bovis DSM 20582, which causes clinical mastitis in dairy cows. J Bacteriol. 2012 Aug;194(16):4437. doi: 10.1128/JB.00839-12.

Trost E, Blom J, Soares Sde C, Huang IH, Al-Dilaimi A, Schröder J, Jaenicke S, Dorella FA, Rocha FS, Miyoshi A, Azevedo V, Schneider MP, Silva A, Camello TC, Sabbadini PS, Santos CS, Santos LS, Hirata R Jr, Mattos-Guaraldi AL, Efstratiou A, Schmitt MP, Ton-That H, Tauch A. Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia. J Bacteriol. 2012 Jun;194(12):3199-215. doi: 10.1128/JB.00183-12. Epub 2012 Apr 13.

Soares SC, Abreu VA, Ramos RT, Cerdeira L, Silva A, Baumbach J, Trost E, Tauch A, Hirata R Jr, Mattos-Guaraldi AL, Miyoshi A, Azevedo V. PIPS: pathogenicity island prediction software. PLoS One. 2012;7(2):e30848. doi: 10.1371/journal.pone.0030848. Epub 2012 Feb 15.

Schneider J, Rupp O, Trost E, Jaenicke S, Passoth V, Goesmann A, Tauch A, Brinkrolf K. Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities. FEMS Yeast Res. 2012 May;12(3):382-6

Sabbadini PS, Assis MC, Trost E, Gomes DL, Moreira LO, Dos Santos CS, Pereira GA, Nagao PE, Azevedo VA, Hirata Júnior R, Dos Santos AL, Tauch A, Mattos-Guaraldi AL. Corynebacterium diphtheriae 67-72p hemagglutinin, characterized as the protein DIP0733, contributes to invasion and induction of apoptosis in HEp-2 cells. Microb Pathog. 2012 Mar;52(3):165-76.

Cerdeira LT, Schneider MP, Pinto AC, de Almeida SS, dos Santos AR, Barbosa EG, Ali A, Aburjaile FF, de Abreu VA, Guimarães LC, Soares Sde C, Dorella FA, Rocha FS, Bol E, Gomes de Sá PH, Lopes TS, Barbosa MS, Carneiro AR, Jucá Ramos RT, Coimbra NA, Lima AR, Barh D, Jain N, Tiwari S, Raja R, Zambare V, Ghosh P, Trost E, Tauch A, Miyoshi A, Azevedo V, Silva A. Complete genome sequence of Corynebacterium pseudotuberculosis strain CIP 52.97, isolated from a horse in Kenya. J Bacteriol. 2011 Dec;193(24):7025-6.

Schneider J, Andrea H, Blom J, Jaenicke S, Rückert C, Schorsch C, Szczepanowski R, Farwick M, Goesmann A, Pühler A, Schaffer S, Tauch A, Köhler T, Brinkrolf K. Draft genome sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10. Eukaryot Cell. 2012 Dec;11(12):1582-3. doi: 10.1128/EC.00258-12.

Brinkrolf K, Schneider J, Knecht M, Rückert C, Tauch A. Draft genome sequence of Turicella otitidis ATCC 51513, isolated from middle ear fluid from a child with otitis media. J Bacteriol. 2012 Nov;194(21):5968-9. doi: 10.1128/JB.01412-12.

Brune I, Götker S, Schneider J, Rodionov DA, Tauch A. Negative transcriptional control of biotin metabolism genes by the TetR-type regulator BioQ in biotin-auxotrophic Corynebacterium glutamicum ATCC 13032. J Biotechnol. 2012 Jun 15;159(3):225-34. doi: 10.1016/j.jbiotec.2011.12.001. Epub 2011 Dec 11.

Schwientek P, Szczepanowski R, Rückert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Pühler A. The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics. 2012 Mar 23;13:112. doi: 10.1186/1471-2164-13-112.