Publications

Abstract (Expand)

Sulfolobus solfataricus P2 grows on different carbohydrates as well as alcohols, peptides and amino acids. Carbohydrates such as D-glucose or D-galactose are degraded via the modified, branched ...

Authors: Patrick Haferkamp, B. Tjaden, Lu Shen, C. Brasen, Theresa Kouril, Bettina Siebers

Date Published: 30th Apr 2019

Journal: Front Microbiol

Abstract (Expand)

Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells. METHODS: ...

Authors: D. Waltemath, J. Karr, F. Bergmann, V. Chelliah, M. Hucka, M. Krantz, W. Liebermeister, P. Mendes, C. Myers, P. Pir, B. Alaybeyoglu, N. Aranganathan, K. Baghalian, A. Bittig, P. Burke, M. Cantarelli, Y. Chew, R. Costa, J. Cursons, T. Czauderna, A. Goldberg, H. Gomez, J. Hahn, T. Hameri, D. Gardiol, D. Kazakiewicz, I. Kiselev, V. Knight-Schrijver, C. Knupfer, Matthias König, D. Lee, A. Lloret-Villas, N. Mandrik, J. Medley, B. Moreau, H. Naderi-Meshkin, S. Palaniappan, D. Priego-Espinosa, M. Scharm, M. Sharma, K. Smallbone, N. Stanford, J. H. Song, T. Theile, M. Tokic, N. Tomar, V. Toure, J. Uhlendorf, T. Varusai, L. Watanabe, F. Wendland, M. Wolfien, J. Yurkovich, Y. Zhu, A. Zardilis, A. Zhukova, F. Schreiber

Date Published: 16th Jun 2016

Journal: IEEE Trans Biomed Eng

Abstract:

Not specified

Authors: Antoine Buetti-Dinh, Olga Dethlefsen, Ran Friedman, Mark Dopson

Date Published: 26th May 2016

Journal: Not specified

Abstract (Expand)

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about ...

Authors: S. Lien, B. F. Koop, S. R. Sandve, J. R. Miller, M. P. Kent, T. Nome, Torgeir R. Hvidsten, J. S. Leong, D. R. Minkley, A. Zimin, Fabian Grammes, H. Grove, Arne Gjuvsland, B. Walenz, R. A. Hermansen, K. von Schalburg, E. B. Rondeau, A. Di Genova, J. K. Samy, J. Olav Vik, M. D. Vigeland, L. Caler, U. Grimholt, S. Jentoft, D. Inge Vage, P. de Jong, T. Moen, M. Baranski, Y. Palti, D. R. Smith, J. A. Yorke, A. J. Nederbragt, A. Tooming-Klunderud, K. S. Jakobsen, X. Jiang, D. Fan, Y. Hu, D. A. Liberles, R. Vidal, P. Iturra, S. J. Jones, I. Jonassen, A. Maass, S. W. Omholt, W. S. Davidson

Date Published: 18th Apr 2016

Journal: Nature

Abstract (Expand)

Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level ...

Authors: D. Nickerson, K. Atalag, B. de Bono, J. Geiger, Carole Goble, S. Hollmann, J. Lonien, Wolfgang Müller, B. Regierer, Natalie Stanford, Martin Golebiewski, P. Hunter

Date Published: 7th Apr 2016

Journal: Interface Focus

Abstract (Expand)

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have ...

Authors: M. D. Wilkinson, M. Dumontier, I. J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. W. Boiten, L. B. da Silva Santos, P. E. Bourne, J. Bouwman, A. J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C. T. Evelo, R. Finkers, A. Gonzalez-Beltran, A. J. Gray, P. Groth, Carole Goble, J. S. Grethe, J. Heringa, P. A. 't Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S. J. Lusher, M. E. Martone, A. Mons, A. L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. A. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M. A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, Katy Wolstencroft, J. Zhao, B. Mons

Date Published: 16th Mar 2016

Journal: Sci Data

Abstract:

Not specified

Authors: Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim Clark, Mercè Crosas, Ingrid Dillo, Olivier Dumon, Scott Edmunds, Chris T. Evelo, Richard Finkers, Alejandra Gonzalez-Beltran, Alasdair J.G. Gray, Paul Groth, Carole Goble, Jeffrey S. Grethe, Jaap Heringa, Peter A.C ’t Hoen, Rob Hooft, Tobias Kuhn, Ruben Kok, Joost Kok, Scott J. Lusher, Maryann E. Martone, Albert Mons, Abel L. Packer, Bengt Persson, Philippe Rocca-Serra, Marco Roos, Rene van Schaik, Susanna-Assunta Sansone, Erik Schultes, Thierry Sengstag, Ted Slater, George Strawn, Morris A. Swertz, Mark Thompson, Johan van der Lei, Erik van Mulligen, Jan Velterop, Andra Waagmeester, Peter Wittenburg, Katherine Wolstencroft, Jun Zhao, Barend Mons

Date Published: 15th Mar 2016

Journal: Sci. Data

Abstract (Expand)

Glycolysis is the main pathway for ATP production in the malaria parasite Plasmodium falciparum and essential for its survival. Following a sensitivity analysis of a detailed kinetic model for glycolysis ...

Authors: Dawie Van Niekerk, Gerald P. Penkler, Francois du Toit, Jacky Snoep

Date Published: 1st Feb 2016

Journal: FEBS J

Abstract (Expand)

African trypanosomes are an excellent system for quantitative modelling of post-transcriptional mRNA control. Transcription is constitutive and polycistronic; individual mRNAs are excised by trans ...

Authors: Abeer Fadda, M. Ryten, D. Droll, Federico Rojas, V. Farber, Jurgen Haanstra, C. Merce, Barbara Bakker, Keith Matthews, Christine Clayton

Date Published: 26th Aug 2014

Journal: Mol Microbiol

Abstract (Expand)

The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has ...

Authors: Fiona Achcar, Abeer Fadda, Jurgen Haanstra, Eduard Kerkhoven, Dong-Hyun Kim, Alejandro Leroux, T. Papamarkou, Federico Rojas, Barbara Bakker, Mike Barrett, Christine Clayton, Mark Girolami, Luise Krauth-Siegel, Keith Matthews, Rainer Breitling

Date Published: 7th May 2014

Journal: Adv Microb Physiol

Abstract (Expand)

Escherichia coli is a facultatively anaerobic bacterium. With glucose if no external electron acceptors are available, ATP is produced by substrate level phosphorylation. The intracellular redox balance ...

Authors: Katja Bettenbrock, Hao Bai, Michael Ederer, Jeff Green, Klaas Hellingwerf, Michael Holcombe, S. Kunz, Matthew Rolfe, Guido Sanguinetti, Oliver Sawodny, Poonam Sharma, Sonja Steinsiek, Robert Poole

Date Published: 7th May 2014

Journal: Adv Microb Physiol

Abstract (Expand)

DEAD-box RNA helicases play important roles in remodeling RNA molecules and in facilitating a variety of RNA-protein interactions that are key to many essential cellular processes. In spite of the ...

Authors: Martin Lehnik-Habrink, Leonie Rempeters, Akos T Kovács, Christoph Wrede, Claudia Baierlein, Heike Krebber, Oscar Kuipers, Joerg Stuelke

Date Published: 24th Nov 2012

Journal: J. Bacteriol.

Abstract (Expand)

BACKGROUND: Pseudomonas putida KT2442 is a natural producer of polyhydroxyalkanoates (PHAs), which can substitute petroleum-based non-renewable plastics and form the basis for the production of tailor-made ...

Authors: Ignacio Poblete Castro, I. F. Escapa, C. Jager, J. Puchalka, Carolyn Lam, Dietmar Schomburg, Auxi Prieto, Vitor Martins Dos Santos

Date Published: 20th Mar 2012

Journal: Microb Cell Fact

Abstract (Expand)

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' ...

Authors: Susanna-Assunta Sansone, Philippe Rocca-Serra, Dawn Field, Eamonn Maguire, Chris Taylor, Oliver Hofmann, Hong Fang, Steffen Neumann, Weida Tong, Linda Amaral-Zettler, Kimberly Begley, Tim Booth, Lydie Bougueleret, Gully Burns, Brad Chapman, Tim Clark, Lee-Ann Coleman, Jay Copeland, Sudeshna Das, Antoine de Daruvar, Paula de Matos, Ian Dix, Scott Edmunds, Chris T Evelo, Mark J Forster, Pascale Gaudet, Jack Gilbert, Carole Goble, Julian L Griffin, Daniel Jacob, Jos Kleinjans, Lee Harland, Kenneth Haug, Henning Hermjakob, Shannan J Ho Sui, Alain Laederach, Shaoguang Liang, Stephen Marshall, Annette McGrath, Emily Merrill, Dorothy Reilly, Magali Roux, Caroline E Shamu, Catherine A Shang, Christoph Steinbeck, Anne Trefethen, Bryn Williams-Jones, Katy Wolstencroft, Ioannis Xenarios, Winston Hide

Date Published: 28th Jan 2012

Journal: Nat. Genet.

Abstract (Expand)

GlnK is an important nitrogen sensor protein in Streptomyces coelicolor. Deletion of glnK results in a medium-dependent failure of aerial mycelium and spore formation and loss of antibiotic production. ...

Authors: E. Waldvogel, A. Herbig, F. Battke, R. Amin, M. Nentwich, K. Nieselt, T. E. Ellingsen, A. Wentzel, D. A. Hodgson, W. Wohlleben, Y. Mast

Date Published: 29th Oct 2011

Journal: Appl Microbiol Biotechnol

Abstract (Expand)

Systems biology research is typically performed by multidisciplinary groups of scientists, often in large consortia and in distributed locations. The data generated in these projects tend to be ...

Authors: None

Date Published: 29th Sep 2011

Journal: Meth. Enzymol.

Abstract (Expand)

The steady-state level of each mRNA in a cell is a balance between synthesis and degradation. Here, we use high-throughput RNA sequencing (RNASeq) to determine the relationship between mRNA degradation ...

Authors: Theresa Manful, Abeer Fadda, Christine Clayton

Date Published: 26th Sep 2011

Journal: RNA

Abstract (Expand)

The mechanism of action of antimicrobial peptides is, to our knowledge, still poorly understood. To probe the biophysical characteristics that confer activity, we present here a molecular-dynamics and ...

Authors: Anna D Cirac, Gemma Moiset, Jacek Mika, Armagan Koçer, Pedro Salvador, Bert Poolman, Siewert J Marrink, Durba Sengupta

Date Published: 18th May 2011

Journal: Biophys. J.

Abstract (Expand)

A constructed lactate dehydrogenase-negative mutant of Enterococcus faecalis V583 grows at the same rate as the wild type, but ferments glucose to ethanol, formate, and acetoin. Microrray analysis ...

Authors: Ibrahim Mehmeti, Maria Jonsson, Ellen M Fergestad, Geir Mathiesen, Ingolf Nes, Helge Holo

Date Published: 8th Feb 2011

Journal: Not specified

Abstract (Expand)

Oxygen availability is the major determinant of the metabolic modes adopted by Escherichia coli. Whilst much is known about E. coli gene expression and metabolism under fully aerobic and anaerobic ...

Authors: Matthew Rolfe, Alexander Ter Beek, Alison Graham, Eleanor W Trotter, H M Shahzad Asif, Guido Sanguinetti, Joost Teixeira De Mattos, Robert Poole, Jeff Green

Date Published: 22nd Jan 2011

Journal: Not specified

Abstract (Expand)

Bacillus subtilis possesses interlinked routes for the synthesis of proline. The ProJ-ProA-ProH route is responsible for the production of proline as an osmoprotectant, and the ProB-ProA-ProI route ...

Authors: Jeanette Brill, Tamara Hoffmann, Harald Putzer, Erhard Bremer

Date Published: 13th Jan 2011

Journal: Microbiology (Reading, Engl.)

Abstract (Expand)

SUMMARY: TFInfer is a novel open access, standalone tool for genome-wide inference of transcription factor activities from gene expression data. Based on an earlier MATLAB version, the software has now ...

Authors: H M Shahzad Asif, Matthew Rolfe, Jeff Green, Neil D Lawrence, Magnus Rattray, Guido Sanguinetti

Date Published: 24th Aug 2010

Journal: Bioinformatics

Abstract (Expand)

African trypanosomes have emerged as promising unicellular model organisms for the next generation of systems biology. They offer unique advantages, due to their relative simplicity, the availability ...

Authors: Barbara Bakker, Luise Krauth-Siegel, Christine Clayton, Keith Matthews, Mark Girolami, Hans Westerhoff, Paul A M Michels, Rainer Breitling, Mike Barrett

Date Published: 6th May 2010

Journal: Parasitology

Abstract (Expand)

Domesticated laboratory strains of Bacillus subtilis readily take up and integrate exogenous DNA. In contrast, "wild" ancestors or Bacillus strains recently isolated from the environment can ...

Authors: Reindert Nijland, J Grant Burgess, Jeff Errington, Jan-Willem Veening

Date Published: 11th Jan 2010

Journal: PLoS ONE

Abstract (Expand)

Bacillus subtilis strain 168 produces the extremely stable and broad-spectrum lantibiotic sublancin 168. Known sublancin 168-susceptible organisms include important pathogens, such as Staphylococcus ...

Authors: Thijs R H M Kouwen, Erik N Trip, Emma L Denham, Mark J J B Sibbald, Jean-Yves F Dubois, Jan Maarten Van Dijl

Date Published: 8th Sep 2009

Journal: Antimicrob. Agents Chemother.

Abstract (Expand)

We have developed a general scenario of prebiotic physicochemical evolution during the Earth's Hadean eon and reviewed the relevant literature. We suggest that prebiotic chemical evolution started ...

Authors: Jan Spitzer, Bert Poolman

Date Published: 3rd Jun 2009

Journal: Microbiol. Mol. Biol. Rev.

Abstract (Expand)

BACKGROUND: During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene ...

Authors: Kay Nieselt, Florian Battke, Alexander Herbig, Per Bruheim, Alexander Wentzel, Øyvind Jakobsen, Håvard Sletta, M. Tauqeer Alam, Maria Elena Merlo, Jay Moore, Walid Omara, Edward R Morrissey, Miguel A Juarez-Hermosillo, Antonio Rodríguez-García, Merle Nentwich, Louise Thomas, Mudassar Iqbal, Roxane Legaie, William Gaze, Gregory Challis, R Jansen, Lubbert Dijkhuizen, David Rand, David Wild, Michael Bonin, Jens Reuther, Wolfgang Wohlleben, Maggie Smith, Nigel Burroughs, Juan-Francisco Martin, David Hodgson, Eriko Takano, Rainer Breitling, Trond Ellingsen, Elizabeth Wellington

Date Published: 28th May 2009

Journal: BMC Genomics

Abstract (Expand)

Mycobacterium tuberculosis can utilize various nutrients including nitrate as a source of nitrogen. Assimilation of nitrate requires the reduction of nitrate via nitrite to ammonium, which is then ...

Authors: Sven Malm, Yvonne Tiffert, Julia Micklinghoff, Sonja Schultze, Insa Joost, Isabel Weber, Sarah Horst, Birgit Ackermann, Frank Schmidt, Wolfgang Wohlleben, Stefan Ehlers, Robert Geffers, Jens Reuther, Franz-Christoph Bange

Date Published: 1st Apr 2009

Journal: Microbiology (Reading, Engl.)

Abstract (Expand)

Fumarate and nitrate reduction regulatory (FNR) proteins are bacterial transcription factors that coordinate the switch between aerobic and anaerobic metabolism. In the absence of O(2), FNR binds a ...

Authors: Adrian J Jervis, Jason C Crack, Gaye White, Peter J Artymiuk, Myles R Cheesman, Andrew J Thomson, Nick E Le Brun, Jeff Green

Date Published: 4th Mar 2009

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

Abstract (Expand)

The plant circadian clock generates rhythms with a period close to 24 h, and it controls a wide range of physiological and developmental oscillations in habitats under natural light/dark cycles. Among ...

Authors: Y. Niwa, T. Yamashino, T. Mizuno

Date Published: 24th Feb 2009

Journal: Plant Cell Physiol

Abstract (Expand)

The twin arginine translocation (Tat) system transports folded proteins across the bacterial plasma membrane. In Gram-negative bacteria, membrane-bound TatABC subunits are all essential for activity, ...

Authors: James P Barnett, René van der Ploeg, Robyn T Eijlander, Anja Nenninger, Sharon Mendel, Rense Rozeboom, Oscar Kuipers, Jan Maarten Van Dijl, Colin Robinson

Date Published: 25th Nov 2008

Journal: FEBS J.

Abstract (Expand)

The alternative sigma factor sigma(B) of Bacillus subtilis is responsible for the induction of the large general stress regulon comprising approximately 150-200 genes. YqgZ, a member of the sigma(B) ...

Authors: Alexander Reder, Dirk Höper, Christin Weinberg, Ulf Gerth, Martin Fraunholz, Michael Hecker

Date Published: 14th Jul 2008

Journal: Mol. Microbiol.

Abstract (Expand)

Streptomyces coelicolor GlnR is a global regulator that controls genes involved in nitrogen metabolism. By genomic screening 10 new GlnR targets were identified, including enzymes for ammonium assimilation ...

Authors: Yvonne Tiffert, Petra Supra, Reinhild Wurm, Wolfgang Wohlleben, Rolf Wagner, Jens Reuther

Date Published: 7th Jan 2008

Journal: Mol. Microbiol.

Abstract (Expand)

All regulatory processes require components that sense the environmental or metabolic conditions of the cell, and sophisticated sensory proteins have been studied in great detail. During the last few ...

Authors: Fabian M Commichau, Joerg Stuelke

Date Published: 11th Dec 2007

Journal: Mol. Microbiol.

Abstract (Expand)

ABSTRACT: BACKGROUND: The Gram-positive bacterium Bacillus subtilis is an important producer of high quality industrial enzymes and a few eukaryotic proteins. Most of these proteins are secreted into ...

Authors: Jessica C Zweers, Imrich Barák, Dörte Becher, Arnold Jm Driessen, Michael Hecker, Vesa P Kontinen, Manfred J Saller, L'udmila Vavrová, Jan Maarten Van Dijl

Date Published: 2nd Dec 2007

Journal: Microb. Cell Fact.

Abstract (Expand)

Catechol and 2-methylhydroquinone (2-MHQ) cause the induction of the thiol-specific stress response and four dioxygenases/glyoxalases in Bacillus subtilis. Using transcription factor arrays, the MarR-type ...

Authors: Stefanie Töwe, Montira Leelakriangsak, Kazuo Kobayashi, Nguyen Van Duy, Michael Hecker, Peter Zuber, Haike Antelmann

Date Published: 27th Aug 2007

Journal: Mol. Microbiol.

Abstract (Expand)

Bistable systems play an important role in the functioning of living cells. Depending on the strength of the necessary positive feedback one can distinguish between (irreversible) "one-way ...

Authors: Thomas Millat, Sree N Sreenath, Radina P Soebiyanto, Jayant Avva, Kwang-Hyun Cho, Olaf Wolkenhauer

Date Published: 17th Jan 2007

Journal: BioSystems

Abstract (Expand)

Absolute measurements of protein abundance are important in the understanding of biological processes and the precise computational modeling of biological pathways. We developed targeted LC-MS/MS assays ...

Authors: J. C. Wolters, J. Ciapaite, K. van Eunen, K. E. Niezen-Koning, A. Matton, R. J. Porte, P. Horvatovich, Barbara Bakker, R. Bischoff, H. P. Permentier

Date Published: No date defined

Journal: J Proteome Res

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