Publications

Abstract (Expand)

Caulobacter crescentus is a gram-negative bacterium that can utilize xylose as a substrate using the Weimberg pathway, which converts xylose to α-ketoglutarate in five steps without carbon loss. This ...

Authors: Henrik Almqvist, Sara Jonsdottir Glaser, Celina Tufvegren, Lisa Wasserstrom, Gunnar Liden

Date Published: 1st Jun 2018

Journal: Fermentation

Abstract (Expand)

Cell volume is an important parameter for modelling cellular processes. Temperature-induced variability of cellular size, volume, intracellular granularity, a fraction of budding cells of yeast ...

Authors: Maksim Zakhartsev, Matthias Reuss

Date Published: 26th Apr 2018

Journal: Not specified

Abstract (Expand)

Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas ...

Authors: J. J. Koehorst, J. C. van Dam, Ruben Van Heck, E. Saccenti, V. A. Dos Santos, M. Suarez-Diez, P. J. Schaap

Date Published: 7th Dec 2016

Journal: Sci Rep

Abstract (Expand)

The same pathway, such as the mitogen-activated protein kinase (MAPK) pathway, can produce different cellular responses, depending on stimulus or cell type. We examined the phosphorylation dynamics of ...

Authors: N. Iwamoto, L. A. D'Alessandro, S. Depner, B. Hahn, B. A. Kramer, P. Lucarelli, A. Vlasov, M. Stepath, M. E. Bohm, D. Deharde, G. Damm, D. Seehofer, W. D. Lehmann, U. Klingmuller, Marcel Schilling

Date Published: 4th Feb 2016

Journal: Sci Signal

Abstract (Expand)

Kinetic data of biochemical reactions are essential for the creation of kinetic models of biochemical networks. One of the main resources of such information is SABIO-RK, a curated database for kinetic ...

Author: Matthias König

Date Published: 2016

Journal: F1000Res

Abstract (Expand)

The enzymes in the Embden–Meyerhof–Parnas pathway of Plasmodium falciparum trophozoites were kinetically characterized and their integrated activities analyzed in a mathematical model. For validation ...

Authors: Gerald Penkler, Francois du Toit, Waldo Adams, Marina Rautenbach, Daniel C. Palm, Dawie Van Niekerk, Jacky Snoep

Date Published: 1st Apr 2015

Journal: FEBS J

Abstract (Expand)

Transcription by RNA polymerase may be interrupted by pauses caused by backtracking or misincorporation that can be resolved by the conserved bacterial Gre-factors. However, the consequences of such ...

Authors: Yulia Yuzenkova, Pamela Gamba, M. Herber, L. Attaiech, Sulman Shafeeq, Oscar Kuipers, S. Klumpp, Nikolay Zenkin, Jan-Willem Veening

Date Published: 6th Sep 2014

Journal: Nucleic Acids Res

Abstract (Expand)

Data-based mathematical modeling of biochemical reaction networks, e.g., by nonlinear ordinary differential equation (ODE) models, has been successfully applied. In this context, parameter estimation ...

Authors: Christian Tönsing, Jens Timmer, Clemens Kreutz

Date Published: 1st Aug 2014

Journal: Phys. Rev. E

Abstract (Expand)

The Bacillus subtilis catabolite control protein A (CcpA) is a global transcriptional regulator which is controlled by interactions with the phosphoproteins HPrSer46P and CrhP and with low molecular ...

Authors: Andrea Wünsche, Elke Hammer, Maike Bartholomae, Uwe Voelker, Andreas Burkovski, Gerald Seidel, Wolfgang Hillen

Date Published: 20th Apr 2012

Journal: The FEBS journal

Abstract (Expand)

How the human pathogen Streptococcus pneumoniae coordinates cell-wall synthesis during growth and division to achieve its characteristic oval shape is poorly understood. The conserved eukaryotic-type ...

Authors: Katrin Beilharz, Linda Nováková, Daniela Fadda, Pavel Branny, Orietta Massidda, Jan-Willem Veening

Date Published: 21st Mar 2012

Journal: Proceedings of the National Academy of Sciences of the United States of America

Abstract (Expand)

Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report ...

Authors: Pierre Nicolas, Ulrike Mäder, Etienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Bisicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L Denham, Mark J Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, Colin Harwood, Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, Rick Lewis, Wolfram Liebermeister, Anika March, Ruben Mars, Priyanka Nannapaneni, David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, Praveen Kumar Sappa, Franck Samson, Marc Schaffer, Benno Schwikowski, Leif Steil, Joerg Stuelke, Thomas Wiegert, Kevin M Devine, Anthony J Wilkinson, Jan Maarten Van Dijl, Michael Hecker, Uwe Voelker, Philippe Bessières, Philippe Noirot

Date Published: 3rd Mar 2012

Journal: Science

Abstract (Expand)

Bacillus subtilis possesses carbon-flux regulating histidine protein (Crh), a paralog of the histidine protein (HPr) of the phosphotransferase system (PTS). Like HPr, Crh becomes (de)phosphorylated in ...

Authors: Jens J Landmann, Susanne Werner, Wolfgang Hillen, Joerg Stuelke, Boris Görke

Date Published: 28th Nov 2011

Journal: FEMS Microbiol. Lett.

Abstract:

Not specified

Authors: Sonja Steinsiek, S. Frixel, Stefan Stagge, Katja Bettenbrock

Date Published: 1st Jun 2011

Journal: Journal of Biotechnology

Abstract (Expand)

The highly processive transcription by multi-subunit RNA polymerases (RNAP) can be interrupted by misincorporation or backtracking events that may stall transcription or lead to erroneous transcripts. ...

Authors: Mohammad Roghanian, Yulia Yuzenkova, Nikolay Zenkin

Date Published: 27th Jan 2011

Journal: Not specified

Abstract:

Not specified

Authors: Marco Pittelkow, Erhard Bremer

Date Published: 2011

Journal: Halophiles and Hypersaline Environments

Abstract (Expand)

Genomic tiling array transcriptomics and RNA-seq are two powerful and rapidly developing approaches for unbiased transcriptome analysis. Providing comprehensive identification and quantification of ...

Authors: Ulrike Mäder, Pierre Nicolas, Hugues Richard, Philippe Bessières, Stéphane Aymerich

Date Published: 10th Nov 2010

Journal: Curr. Opin. Biotechnol.

Abstract (Expand)

Systems biology relies increasingly on collaborations between several groups with different expertise. Therefore, the systems biology community is adopting standards that allow effective communication ...

Authors: Lope A. Florez, Christoph R Lammers, Raphael Michna, Joerg Stuelke

Date Published: 14th Oct 2010

Journal: Bioinformatics

Abstract (Expand)

The active center of RNA polymerase can hydrolyze phosphodiester bonds in nascent RNA, a reaction thought to be important for proofreading of transcription. The reaction proceeds via a general two ...

Authors: Yulia Yuzenkova, Nikolay Zenkin

Date Published: 1st Jun 2010

Journal: Proc. Natl. Acad. Sci. U.S.A.

Abstract (Expand)

Cell surface receptors convert extracellular cues into receptor activation, thereby triggering intracellular signaling networks and controlling cellular decisions. A major unresolved issue is the ...

Authors: V. Becker, Marcel Schilling, J. Bachmann, U. Baumann, A. Raue, T. Maiwald, J. Timmer, U. Klingmuller

Date Published: 20th May 2010

Journal: Science

Abstract (Expand)

Stability and biological activity of proteins is highly dependent on their physicochemical environment. The development of realistic models of biological systems necessitates quantitative information ...

Authors: Felix Bonowski, Ana Kitanovic, Peter Ruoff, Jinda Holzwarth, Igor Kitanovic, Van Ngoc Bui, Elke Lederer, Stefan Wölfl

Date Published: 23rd Dec 2009

Journal: PLoS ONE

Abstract (Expand)

Bacillus subtilis is the model organism for a large group of Gram-positive bacteria, the Firmicutes. Several online databases have been established over time to manage its genetic and metabolic ...

Authors: Christoph R Lammers, Lope A. Florez, Arne G Schmeisky, Sebastian F Roppel, Ulrike Mäder, Leendert Hamoen, Joerg Stuelke

Date Published: 3rd Dec 2009

Journal: Microbiology (Reading, Engl.)

Abstract (Expand)

Bacillus subtilis is a well-established cell factory for efficient secretion of many biotechnologically relevant enzymes that are naturally produced by it or related organisms. However, the use of B. ...

Authors: Thijs R H M Kouwen, Allan K Nielsen, Emma L Denham, Jean-Yves F Dubois, Ronald Dorenbos, Michael D Rasmussen, Wim J Quax, Roland Freudl, Jan Maarten Van Dijl

Date Published: 30th Nov 2009

Journal: Appl. Environ. Microbiol.

Abstract (Expand)

The molecular mechanisms underlying cell growth, cell division and pathogenesis in Streptococcus pneumoniae are still not fully understood. Single-cell methodologies are potentially of great value to ...

Authors: Alice Eberhardt, Ling J Wu, Jeff Errington, Waldemar Vollmer, Jan-Willem Veening

Date Published: 8th Sep 2009

Journal: Mol. Microbiol.

Abstract (Expand)

The roles of the two ldh genes of Enterococcus faecalis were studied using knockout mutants. Deletion of ldh-1 causes a metabolic shift from homolactic fermentation to ethanol, formate, and acetoin ...

Authors: Maria Jonsson, Zhian Saleihan, Ingolf Nes, Helge Holo

Date Published: 22nd May 2009

Journal: Appl. Environ. Microbiol.

Abstract (Expand)

Antibiotic production is regulated by numerous signals, including the so-called bacterial hormones found in antibiotic producing organisms such as Streptomyces. These signals, the gamma-butyrolactones, ...

Authors: Nai-Hua Hsiao, Marco Gottelt, Eriko Takano

Date Published: 21st Apr 2009

Journal: Meth. Enzymol.

Abstract (Expand)

The regulatory proteins AfsR and PhoP control expression of the biosynthesis of actinorhodin and undecylprodigiosin in Streptomyces coelicolor. Electrophoretic mobility shift assays showed that PhoP(DBD) ...

Authors: Fernando Santos-Beneit, Antonio Rodríguez-García, Alberto Sola-Landa, Juan-Francisco Martin

Date Published: 11th Feb 2009

Journal: Mol. Microbiol.

Abstract (Expand)

In many bacteria glucose is the preferred carbon source and represses the utilization of secondary substrates. In Bacillus subtilis, this carbon catabolite repression (CCR) is achieved by the global ...

Authors: Kalpana D Singh, Matthias H Schmalisch, Joerg Stuelke, Boris Görke

Date Published: 29th Aug 2008

Journal: J. Bacteriol.

Abstract (Expand)

Most bacteria can selectively use substrates from a mixture of different carbon sources. The presence of preferred carbon sources prevents the expression, and often also the activity, of catabolic ...

Authors: Boris Görke, Joerg Stuelke

Date Published: 17th Jul 2008

Journal: Nat. Rev. Microbiol.

Abstract (Expand)

The general stress regulon of Bacillus subtilis is controlled by the activity state of sigmaB, a transcription factor that is switched on following exposure to either physical or nutritional stress. ...

Authors: Adam Reeves, Ulf Gerth, Uwe Voelker, W G Haldenwang

Date Published: 22nd Jun 2007

Journal: J. Bacteriol.

Abstract (Expand)

High-quality quantitative data generated under standardized conditions is critical for understanding dynamic cellular processes. We report strategies for error reduction, and algorithms for automated ...

Authors: Marcel Schilling, T. Maiwald, S. Bohl, M. Kollmann, C. Kreutz, J. Timmer, U. Klingmuller

Date Published: 13th Dec 2005

Journal: FEBS J

Abstract (Expand)

Genomic aberrations can be used to subtype breast cancer. In this study, we investigated DNA copy number (CN) profiles of 69 cases of male breast cancer (MBC) by array comparative genomic hybridization ...

Authors: H. D. Biesma, P. C. Schouten, M. M. Lacle, J. Sanders, W. Brugman, R. Kerkhoven, I. Mandjes, P. van der Groep, P. J. van Diest, S. C. Linn

Date Published: No date defined

Journal: Genes Chromosomes Cancer

Abstract (Expand)

BioRxiv preprint, 4 April 2018. Abstract: Daily light-dark cycles (LD) drive dynamic regulation of plant and algal transcriptomes via photoreceptor pathways and 24-hour, circadian rhythms. Diel regulation ...

Authors: Zeenat B. Noordally, Matthew M. Hindle, Sarah F. Martin, Daniel Seaton, Ian Simpson, Thierry Le Bihan, Andrew Millar

Date Published: No date defined

Journal: Not specified

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