Publications

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

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

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

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, Sulman Shafeeq, Oscar Kuipers, Nikolay Zenkin, Jan-Willem Veening, Herber M.,Attaiech L.,Klumpp S.

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, Kreutz Clemens

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

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

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

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

Date Published: 28th Nov 2011

Journal: FEMS Microbiol. Lett.

Abstract:

Not specified

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

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: Yulia Yuzenkova, Nikolay Zenkin, Roghanian Mohammad

Date Published: 27th Jan 2011

Journal: Not specified

Abstract:

Not specified

Authors: Erhard Bremer, Pittelkow Marco

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, Nicolas Pierre,Richard Hugues,Bessières Philippe,Aymerich Stéphane

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, Joerg Stuelke, Lammers Christoph R,Michna Raphael

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: Nikolay Zenkin, Yuzenkova Yulia

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

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

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

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

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

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, Ingolf Nes, Helge Holo, Saleihan Zhian

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: Eriko Takano, Hsiao Nai-Hua,Gottelt Marco

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

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

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: Joerg Stuelke, Görke Boris

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

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, Maiwald T.,Bohl S.,Kollmann M.,Kreutz C.,Timmer J.,Klingmuller U.

Date Published: 13th Dec 2005

Journal: FEBS J

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