Publications

Abstract (Expand)

Atlantic salmon can synthesize polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic acid (20:5n-3), arachidonic acid (20:4n-6) and docosahexaenoic acid (22:6n-3) via activities of very long ...

Authors: Alex K. Datsomor, Nikola Zic, Keshuai Li, Rolf E. Olsen, Yang Jin, Jon Olav Vik, Rolf B. Edvardsen, Fabian Grammes, Anna Wargelius, Per Winge

Date Published: 1st Dec 2019

Journal: Sci Rep

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)

Factors affecting the establishment of the gut microbiota in animals living in marine environments remain largely unknown. In terrestrial animals, however, it is well established that the juvenile ...

Authors: Yang Jin, Inga Leena Angell, Sandve Simen, Lars Snipen, Y Olsen, Knut Rudi

Date Published: 24th Jan 2019

Journal: Aquacult. Environ. Interact.

Abstract:

Not specified

Authors: Tjasa Kumelj, Snorre Sulheim, Alexander Wentzel, Eivind Almaas

Date Published: 7th Dec 2018

Journal: Biotechnol. J.

Abstract:

Not specified

Authors: Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba, Samuel H Friedman, Alan Garny, John H Gennari, Padraig Gleeson, Martin Golebiewski, Mike Hucka, Nick Juty, Chris Myers, Brett G Olivier, Herbert M Sauro, Martin Scharm, Jacky Snoep, Vasundra Toure, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath

Date Published: 21st Nov 2018

Journal: Not specified

Abstract:

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Author: Timon Oefelein

Date Published: 20th Nov 2018

Journal: SCS

Abstract (Expand)

Plants sense light and temperature changes to regulate flowering time. Here, we show that expression of the Arabidopsis florigen gene, FLOWERING LOCUS T (FT), peaks in the morning during spring, a ...

Authors: Y. H. Song, A. Kubota, M. S. Kwon, M. F. Covington, N. Lee, E. R. Taagen, D. Laboy Cintron, D. Y. Hwang, R. Akiyama, S. K. Hodge, H. Huang, N. H. Nguyen, D. A. Nusinow, A. J. Millar, K. K. Shimizu, T. Imaizumi

Date Published: 27th Sep 2018

Journal: Nat Plants

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:

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Authors: Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Mike Hucka, Sarah M. Keating, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath

Date Published: 25th Apr 2018

Journal: Not specified

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Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well ...

Authors: Stephan Christel, Malte Herold, Soeren Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson

Date Published: 1st Feb 2018

Journal: Appl Environ Microbiol

Abstract (Expand)

Gut microbiota associations through habitat transitions are fundamentally important yet poorly understood. One such habitat transition is the migration from freshwater to saltwater for anadromous fish, ...

Authors: Knut Rudi, Inga Leena Angell, Phillip B. Pope, Jon Olav Vik, Simen Rød Sandve, Lars Snipen

Date Published: 15th Jan 2018

Journal: Appl Environ Microbiol

Abstract (Expand)

Chemical reaction networks are ubiquitous in biology, and their dynamics is fundamentally stochastic. Here, we present the software library pSSAlib, which provides a complete and concise implementation ...

Authors: Oleksandr Ostrenko, Pietro Incardona, Rajesh Ramaswamy, Lutz Brusch, Ivo F. Sbalzarini

Date Published: 4th Dec 2017

Journal: PLoS Comput Biol

Abstract (Expand)

Nucleic acids, which constitute the genetic material of all organisms, are continuously exposed to endogenous and exogenous damaging agents, representing a significant challenge to genome stability and ...

Authors: Nima Borhan Fakouri, Jon Ambæk Durhuus, Christine Elisabeth Regnell, Maria Angleys, Claus Desler, Md Mahdi Hasan-Olive, Ana Martín-Pardillos, Anastasia Tsaalbi-Shtylik, Kirsten Thomsen, Martin Lauritzen, Vilhelm A. Bohr, Niels de Wind, Linda Hildegard Bergersen, Tim Rasmussen

Date Published: 1st Dec 2017

Journal: Sci Rep

Abstract:

Not specified

Authors: None

Date Published: 24th Oct 2017

Journal: Not specified

Abstract (Expand)

In (hyper)thermophilic organisms metabolic processes have to be adapted to function optimally at high temperature. We compared the gluconeogenic conversion of 3-phosphoglycerate via 1,3-bisphosphoglycerate ...

Authors: Theresa Kouril, J. J. Eicher, Bettina Siebers, Jacky Snoep

Date Published: 7th Oct 2017

Journal: Microbiology

Abstract (Expand)

Sulfolobus solfataricus is a thermoacidophilic Archaeon that thrives in terrestrial hot springs (solfatares) with optimal growth at 80 degrees C and pH 2-4. It catabolizes specific carbon sources, such ...

Authors: Sofia Figueiredo, Theresa Kouril, D. Esser, Patrick Haferkamp, Patricia Wieloch, Dietmar Schomburg, Peter Ruoff, Bettina Siebers, Jörg Schaber

Date Published: 12th Jul 2017

Journal: PLoS One

Abstract (Expand)

Tissues use feedback circuits in which cells send signals to each other to control their growth and survival. We show that such feed- back circuits are inherently unstable to mutants that misread the ...

Authors: Omer Karin, Uri Alon

Date Published: 26th Jun 2017

Journal: Mol Syst Biol

Abstract (Expand)

Constraint based methods, such as the Flux Balance Analysis, are widely used to model cellular growth processes without relying on extensive information on the regulatory features. The regulation is ...

Authors: Henning Lindhorst, Sergio Lucia, Rolf Findeisen, Steffen Waldherr

Date Published: 13th Jun 2017

Journal: Not specified

Abstract (Expand)

Adaptive Laboratory Evolution (ALE) is increasingly being used as a technique for untargeted strain optimization. This work aimed at developing an automated and miniaturized ALE approach based on ...

Authors: A. Radek, Niklas Tenhaef, M. F. Muller, Christian Brüsseler, W. Wiechert, Jan Marienhagen, T. Polen, Stephan Noack

Date Published: 30th May 2017

Journal: Bioresour Technol

Abstract (Expand)

The thermoacidophilic Crenarchaeon Sulfolobus solfataricus is a model organism for archaeal adaptation to extreme environments and renowned for its ability to degrade a broad variety of substrates. It ...

Authors: Helge Stark, Jacqueline Wolf, Andreas Albersmeier, Trong Khoa Pham, Julia D. Hofmann, Bettina Siebers, Jörn Kalinowski, Phil Wright, Meina Neumann-Schaal, Dietmar Schomburg

Date Published: 29th May 2017

Journal: FEBS J

Abstract (Expand)

PCB 153 is one of the most abundant PCB congeners detected in biological samples. It is a persistent compound that is still present in the environment despite the ban on production and use of PCBs in ...

Author: Fekadu Yadetie, Eystein Oveland, Anne Døskeland, Frode Berven Anders Goksøyr, Odd André Karlsen

Date Published: 1st Apr 2017

Journal: Aquatic Toxicology

Abstract:

Not specified

Authors: Wolfgang Müller, Meik Bittkowski, Martin Golebiewski, Renate Kania, Maja Rey, Andreas Weidemann, Ulrike Wittig

Date Published: 1st Mar 2017

Journal: Datenbank Spektrum

Abstract (Expand)

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special ...

Authors: F. Schreiber, G. D. Bader, P. Gleeson, Martin Golebiewski, M. Hucka, N. Le Novere, C. Myers, D. Nickerson, B. Sommer, Dagmar Waltemath

Date Published: 12th Feb 2017

Journal: J Integr Bioinform

Abstract (Expand)

Signaling through the AKT and ERK pathways controls cell proliferation. However, the integrated regulation of this multistep process, involving signal processing, cell growth and cell cycle progression, ...

Authors: Lorenz Adlung, S. Kar, Marie-Christine Wagner, B. She, Sajib Chakraborty, J. Bao, S. Lattermann, M. Boerries, Hauke Busch, P. Wuchter, A. D. Ho, J. Timmer, Marcel Schilling, T. Hofer, U. Klingmuller

Date Published: 27th Jan 2017

Journal: Mol Syst Biol

Abstract (Expand)

Gram-positive Streptomyces bacteria produce thousands of bioactive secondary metabolites, including antibiotics. To systematically investigate genes affecting secondary metabolism, we developed a ...

Authors: Z. Xu, Y. Wang, K. F. Chater, H. Y. Ou, H. H. Xu, Z. Deng, M. Tao

Date Published: 8th Jan 2017

Journal: Appl Environ Microbiol

Abstract (Expand)

Organisms use circadian clocks to generate 24-h rhythms in gene expression. However, the clock can interact with other pathways to generate shorter period oscillations. It remains unclear how these ...

Authors: Bruno MC Martins, Arijit K Das, Liliana Antunes, James CW Locke

Date Published: 22nd Dec 2016

Journal: Mol Syst Biol

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)

BACKGROUND: Defects in genes involved in mitochondrial fatty-acid oxidation (mFAO) reduce the ability of patients to cope with metabolic challenges. mFAO enzymes accept multiple substrates of different ...

Authors: Karen Van Eunen, C. M. Volker-Touw, A. Gerding, A. Bleeker, J. C. Wolters, W. J. van Rijt, A. M. Martines, K. E. Niezen-Koning, R. M. Heiner, H. Permentier, A. K. Groen, D. J. Reijngoud, Terry G.J. Derks, Barbara Bakker

Date Published: 7th Dec 2016

Journal: BMC Biol

Abstract (Expand)

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. ...

Authors: Katy Wolstencroft, Olga Krebs, Jacky Snoep, Natalie Stanford, Finn Bacall, Martin Golebiewski, Rostyslav Kuzyakiv, Quyen Nguyen, Stuart Owen, S. Soiland-Reyes, Jakub Straszewski, D. D. van Niekerk, Alan Williams, L. Malmstrom, Bernd Rinn, Wolfgang Müller, Carole Goble

Date Published: 3rd Dec 2016

Journal: Nucleic Acids Res

Abstract (Expand)

Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of these metabolic and underlying regulatory processes allow a detailed ...

Authors: Maksim Zakhartsev, Irina Medvedeva, Yuriy Orlov, Ilya Akberdin, Olga Krebs, Waltraud Schulze

Date Published: 1st Dec 2016

Journal: BMC Plant Biol

Abstract (Expand)

Ataxia telangiectasia (A-T) is a rare autosomal recessive disease characterized by progressive neurodegeneration and cerebellar ataxia. A-T is causally linked to defects in ATM, a master regulator of ...

Authors: Evandro Fei Fang, Henok Kassahun, Deborah L. Croteau, Morten Scheibye-Knudsen, Krisztina Marosi, Huiming Lu, Raghavendra A. Shamanna, Sumana Kalyanasundaram, Ravi Chand Bollineni, Mark A. Wilson, Wendy B. Iser, Bradley N. Wollman, Marya Morevati, Jun Li, Jesse S. Kerr, Qiping Lu, Tyler B. Waltz, Jane Tian, David A. Sinclair, Mark P. Mattson, Marianne B. Nilsen, Vilhelm A. Bohr

Date Published: 1st Oct 2016

Journal: Cell Metabolism

Abstract (Expand)

Archaea are characterised by a complex metabolism with many unique enzymes that differ from their bacterial and eukaryotic counterparts. The thermoacidophilic archaeon Sulfolobus solfataricus is known ...

Authors: Jacqueline Wolf, Helge Stark, K. Fafenrot, Andreas Albersmeier, Trong Khoa Pham, K. B. Muller, B. Meyer, L. Hoffmann, L. Shen, Stefan Albaum, Theresa Kouril, K. Schmidt-Hohagen, M. Neumann-Schaal, C. Brasen, J. Kalinowski, Phil Wright, Sonja-Verena Albers, Dietmar Schomburg, Bettina Siebers

Date Published: 10th Sep 2016

Journal: Mol Microbiol

Abstract (Expand)

MOTIVATION: A major goal of drug development is to selectively target certain cell types. Cellular decisions influenced by drugs are often dependent on the dynamic processing of information. Selective ...

Authors: Bernhard Steiert, Jens Timmer, C. Kreutz

Date Published: 3rd Sep 2016

Journal: Bioinformatics

Abstract (Expand)

In systems biology, one of the major tasks is to tailor model complexity to information content of the data. A useful model should describe the data and produce well-determined parameter estimates and ...

Authors: T. Maiwald, H. Hass, Bernhard Steiert, Joep Vanlier, R. Engesser, A. Raue, F. Kipkeew, H. H. Bock, D. Kaschek, C. Kreutz, Jens Timmer

Date Published: 3rd Sep 2016

Journal: PLoS One

Abstract (Expand)

BACKGROUND: Methylmecury (MeHg) is a widely distributed environmental pollutant with considerable risk to both human health and wildlife. To gain better insight into the underlying mechanisms of ...

Authors: Fekadu Yadetie, S. Bjorneklett, H. K. Garberg, E. Oveland, F. Berven, A. Goksoyr, O. A. Karlsen

Date Published: 9th Aug 2016

Journal: BMC Genomics

Abstract (Expand)

Lung cancer, with its most prevalent form non-small-cell lung carcinoma (NSCLC), is one of the leading causes of cancer-related deaths worldwide, and is commonly treated with chemotherapeutic drugs ...

Authors: R. Merkle, Bernhard Steiert, F. Salopiata, S. Depner, A. Raue, N. Iwamoto, M. Schelker, H. Hass, M. Wasch, M. E. Bohm, O. Mucke, D. B. Lipka, C. Plass, W. D. Lehmann, C. Kreutz, J. Timmer, Marcel Schilling, U. Klingmuller

Date Published: 6th Aug 2016

Journal: PLoS Comput Biol

Abstract (Expand)

Plants sense the light environment through an ensemble of photoreceptors. Members of the phytochrome class of light receptors are known to play a critical role in seedling establishment, and are among ...

Authors: Deyue Yang, Daniel D. Seaton, Johanna Krahmer, Karen J. Halliday

Date Published: 5th Jul 2016

Journal: Proc Natl Acad Sci USA

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 (Expand)

Wild-type Corynebacterium glutamicum has no endogenous metabolic activity for utilizing the lignocellulosic pentose d-xylose for cell growth. Therefore, two different engineering approaches have been ...

Authors: A. Radek, M. F. Muller, J. Gatgens, L. Eggeling, K. Krumbach, J. Marienhagen, Stephan Noack

Date Published: 15th Jun 2016

Journal: J Biotechnol

Abstract:

Not specified

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

Date Published: 26th May 2016

Journal: Not specified

Abstract (Expand)

OBJECTIVE: The aim of this study was to assess the relationship between fluorine-18 fluorodeoxyglucose (F-FDG) uptake and molecular biological markers in esophageal squamous cell carcinoma (ESCC) ...

Authors: Y. Hirose, H. Kaida, A. Kawahara, S. Matono, T. Tanaka, S. Kurata, M. Kage, M. Ishibashi, T. Abe

Date Published: 25th May 2016

Journal: Nucl Med Commun

Abstract (Expand)

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease in industrialized countries and is increasing in prevalence. The pathomechanisms, however, are poorly understood. This study ...

Authors: Madlen Matz-Soja, Christiane Rennert, Kristin Schönefeld, Susanne Aleithe, Jan Boettger, Wolfgang Schmidt-Heck, Thomas S Weiss, Amalya Hovhannisyan, Sebastian Zellmer, Nora Klöting, Angela Schulz, Jürgen Kratzsch, Reinhardt Guthke, Rolf Gebhardt

Date Published: 17th 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)

Mesenchymal stromal cells (MSCs) from human bone marrow serve as a resource for cell-based therapies in regenerative medicine. Clinical applications require standardized protocols according to good ...

Authors: P. Wuchter, M. Vetter, Rainer Saffrich, A. Diehlmann, K. Bieback, A. D. Ho, P. Horn

Date Published: 19th Feb 2016

Journal: Exp Hematol

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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

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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)

In previous studies human mesenchymal stromal cells (MSCs) maintained the "stemness" of human hematopoietic progenitor cells (HPCs) through direct cell-cell contact in two-dimensional co-culture ...

Authors: P. Wuchter, Rainer Saffrich, S. Giselbrecht, C. Nies, H. Lorig, S. Kolb, A. D. Ho, E. Gottwald

Date Published: 30th Jan 2016

Journal: Cell Tissue Res

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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)

Selecting an efficient small set of adjustable parameters to improve metabolic features of an organism is important for a reduction of implementation costs and risks of unpredicted side effects. In ...

Authors: Egils Stalidzans, Ivars Mozga, Jurijs Sulins, Peteris Zikmanis

Date Published: 2016

Journal: IEEE/ACM Trans. Comput. Biol. and Bioinf.

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We propose a hierarchical modelling approach to construct models for disease states at the whole-body level. Such models can simulate effects of drug-induced inhibition of reaction steps on the whole-body ...

Authors: Jacky Snoep, Kathleen Green, J. Eicher, D. C. Palm, G. Penkler, F. du Toit, N. Walters, R. Burger, H. V. Westerhoff, Dawie Van Niekerk

Date Published: 27th Nov 2015

Journal: Biochemical Society Transactions

Abstract (Expand)

The mitochondrial NAD pool is particularly important for the maintenance of vital cellular functions. Although at least in some fungi and plants, mitochondrial NAD is imported from the cytosol by carrier ...

Authors: M. R. VanLinden, C. Dolle, I. K. Pettersen, V. A. Kulikova, Marc Niere, G. Agrimi, S. E. Dyrstad, F. Palmieri, A. A. Nikiforov, K. J. Tronstad, Mathias Ziegler

Date Published: 13th Nov 2015

Journal: J Biol Chem

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Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA ...

Authors: A. Flis, A. P. Fernandez, T. Zielinski, V. Mengin, R. Sulpice, K. Stratford, A. Hume, A. Pokhilko, M. M. Southern, D. D. Seaton, H. G. McWatters, M. Stitt, K. J. Halliday, Andrew Millar

Date Published: 16th Oct 2015

Journal: Open Biol

Abstract (Expand)

Canonized view on temperature effects on growth rate of microorganisms is based on assumption of protein denaturation, which is not confirmed experimentally so far. We develop an alternative concept, ...

Authors: Maksim Zakhartsev, Xuelian Yang, Matthias Reuss, Hans Otto Pörtner

Date Published: 1st Aug 2015

Journal: Journal of Thermal Biology

Abstract (Expand)

Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression ...

Authors: Anna-Karin Gustavsson, Caroline B. Adiels, Bernhard Mehlig, Mattias Goksör

Date Published: 1st Aug 2015

Journal: Sci Rep

Abstract (Expand)

Modeling of dynamical systems using ordinary differential equations is a popular approach in the field of systems biology. Two of the most critical steps in this approach are to construct dynamical ...

Authors: A. Raue, Bernhard Steiert, M. Schelker, C. Kreutz, T. Maiwald, H. Hass, J. Vanlier, Christian Tönsing, Lorenz Adlung, R. Engesser, W. Mader, T. Heinemann, J. Hasenauer, Marcel Schilling, T. Hofer, E. Klipp, F. Theis, U. Klingmuller, B. Schoberl, J. Timmer

Date Published: 3rd Jul 2015

Journal: Bioinformatics

Abstract (Expand)

Signaling pathways are characterized by crosstalk, feedback and feedforward mechanisms giving rise to highly complex and cell-context specific signaling networks. Dissecting the underlying relations ...

Authors: L. A. D'Alessandro, R. Samaga, T. Maiwald, S. H. Rho, S. Bonefas, A. Raue, N. Iwamoto, A. Kienast, K. Waldow, R. Meyer, Marcel Schilling, J. Timmer, S. Klamt, U. Klingmuller

Date Published: 23rd Apr 2015

Journal: PLoS Comput Biol

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)

The intra- and extracellular concentrations of 16 metabolites were measured in chemostat (D = 0.1 h−1) anaerobic cultures of the yeast Saccharomyces cerevisiae CEN.PK-113-7D growing on minimal medium. ...

Authors: Maksim Zakhartsev, Oliver Vielhauer, Thomas Horn, Xuelian Yang, Matthias Reuss

Date Published: 1st Apr 2015

Journal: Metabolomics

Abstract (Expand)

Sustainable production of target compounds such as biofuels and high-value chemicals for pharmaceutical, agrochemical, and chemical industries is becoming an increasing priority given their current ...

Authors: Natalie Stanford, P. Millard, N. Swainston

Date Published: 24th Mar 2015

Journal: Front Cell Dev Biol

Abstract (Expand)

Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, ...

Authors: Daniel Seaton, R. W. Smith, Y. H. Song, D. R. MacGregor, K. Stewart, G. Steel, J. Foreman, S. Penfield, T. Imaizumi, Andrew Millar, K. J. Halliday

Date Published: 21st Jan 2015

Journal: Mol Syst Biol

Abstract (Expand)

Hepatitis C virus (HCV) is a major cause of chronic liver disease affecting around 130 million people worldwide. While great progress has been made to define the principle steps of the viral life cycle, ...

Authors: M. Poenisch, P. Metz, H. Blankenburg, A. Ruggieri, J. Y. Lee, D. Rupp, I. Rebhan, K. Diederich, Lars Kaderali, F. S. Domingues, M. Albrecht, V. Lohmann, H. Erfle, Ralf Bartenschlager

Date Published: 8th Jan 2015

Journal: PLoS Pathog

Abstract (Expand)

Increasing antibiotic resistance in pathogenic bacteria necessitates the development of new medication strategies. Interfering with the metabolic network of the pathogen can provide novel drug targets ...

Authors: Nadine Veith, Margrete Solheim, Koen Van Grinsven, B. G. Olivier, Jennifer Levering, R. Grosseholz, Jeroen Hugenholtz, Helge Holo, Ingolf Nes, Bas Teusink, Ursula Kummer

Date Published: 19th Dec 2014

Journal: Appl Environ Microbiol

Abstract (Expand)

Kinetoplastea such as trypanosomatid parasites contain specialized peroxisomes that uniquely contain enzymes of the glycolytic pathway and other parts of intermediary metabolism and hence are called ...

Authors: Balázs Szöör, Jurgen Haanstra, Melisa Gualdrón-López, Paul AM Michels

Date Published: 1st Dec 2014

Journal: Current Opinion in Microbiology

Abstract (Expand)

STAT5A and STAT5B are important transcription factors that dimerize and transduce activation signals of cytokine receptors directly to the nucleus. A typical cytokine that mediates STAT5 activation is ...

Authors: M. E. Boehm, Lorenz Adlung, Marcel Schilling, S. Roth, U. Klingmuller, W. D. Lehmann

Date Published: 7th Nov 2014

Journal: J Proteome Res

Abstract (Expand)

Biomass-derived d-xylose represents an economically interesting substrate for the sustainable microbial production of value-added compounds. The industrially important platform organism Corynebacterium ...

Authors: A. Radek, K. Krumbach, J. Gatgens, Volker Wendisch, W. Wiechert, M. Bott, Stephan Noack, J. Marienhagen

Date Published: 12th Oct 2014

Journal: J Biotechnol

Abstract (Expand)

For adaptation between anaerobic, micro-aerobic and aerobic conditions Escherichia coli's metabolism and in particular its electron transport chain (ETC) is highly regulated. Although it is known ...

Authors: None

Date Published: 30th Sep 2014

Journal: PLoS One

Abstract (Expand)

Multistable gene regulatory systems sustain different levels of gene expression under identical external conditions. Such multistability is used to encode phenotypic states in processes including ...

Authors: None

Date Published: 24th Sep 2014

Journal: Nucleic Acids Res

Abstract (Expand)

Mesenchymal stromal cells (MSCs) possess broad immunomodulatory capacities that are currently investigated for potential clinical application in treating autoimmune disorders. Third-party MSCs suppress ...

Authors: G. Malcherek, N. Jin, A. G. Huckelhoven, J. Mani, L. Wang, U. Gern, A. Diehlmann, P. Wuchter, A. Schmitt, B. Chen, A. D. Ho, M. Schmitt

Date Published: 17th Sep 2014

Journal: Leukemia

Abstract (Expand)

Understanding how dynamic molecular networks affect whole-organism physiology, analogous to mapping genotype to phenotype, remains a key challenge in biology. Quantitative models that represent processes ...

Authors: Yin Hoon Chew, B. Wenden, A. Flis, Virginie Mengin, J. Taylor, C. L. Davey, C. Tindal, H. Thomas, H. J. Ougham, P. de Reffye, M. Stitt, M. Williams, Robert Muetzelfeldt, Karen Halliday, Andrew Millar

Date Published: 10th Sep 2014

Journal: Proc Natl Acad Sci U S A

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)

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)

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)

BACKGROUND: Polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs) with harmful effects in animals and humans. Although PCB 153 is one of the most abundant among PCBs detected in ...

Authors: F. Yadetie, O. A. Karlsen, M. Eide, C. Hogstrand, A. Goksoyr

Date Published: 19th Jun 2014

Journal: BMC Genomics

Abstract:

Not specified

Authors: Anna-Karin Gustavsson, Dawie Van Niekerk, Caroline B. Adiels, Bob Kooi, Mattias Goksör, Jacky Snoep

Date Published: 1st Jun 2014

Journal: FEBS J

Abstract (Expand)

BACKGROUND AIMS: Human mesenchymal stem or stromal cells (MSCs) represent a potential resource not only for regenerative medicine but also for immunomodulatory cell therapies. The application of different ...

Authors: P. Wuchter, K. Bieback, H. Schrezenmeier, M. Bornhauser, L. P. Muller, H. Bonig, W. Wagner, R. Meisel, P. Pavel, T. Tonn, P. Lang, I. Muller, M. Renner, G. Malcherek, Rainer Saffrich, E. C. Buss, P. Horn, M. Rojewski, A. Schmitt, A. D. Ho, R. Sanzenbacher, M. Schmitt

Date Published: 20th May 2014

Journal: Cytotherapy

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)

In the presence of oxygen (O2) the model bacterium Escherichia coli is able to conserve energy by aerobic respiration. Two major terminal oxidases are involved in this process - Cyo has a relatively ...

Authors: Hao Bai, Matthew Rolfe, Wenjing Jia, S. Coakley, Robert Poole, Jeff Green, Michael Holcombe

Date Published: 24th Apr 2014

Journal: PLoS Comput Biol

Abstract (Expand)

The efficient redesign of bacteria for biotechnological purposes, such as biofuel production, waste disposal or specific biocatalytic functions, requires a quantitative systems-level understanding of ...

Authors: None

Date Published: 27th Mar 2014

Journal: Front Microbiol

Abstract (Expand)

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report ...

Authors: Dagmar Waltemath, Frank T. Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet

Date Published: 15th Mar 2014

Journal: Stand. Genomic Sci.

Abstract (Expand)

The respiratory chain of E. coli is branched to allow the cells' flexibility to deal with changing environmental conditions. It consists of the NADH:ubiquinone oxidoreductases NADH dehydrogenase I ...

Authors: None

Date Published: 27th Jan 2014

Journal: PLoS One

Abstract:

Not specified

Authors: Anna-Karin Gustavsson, Dawie Van Niekerk, Caroline B. Adiels, Mattias Goksör, Jacky Snoep

Date Published: 3rd Jan 2014

Journal: Not specified

Abstract (Expand)

Maintenance of monovalent cation homeostasis (mainly K(+) and Na(+)) is vital for cell survival, and cation toxicity is at the basis of a myriad of relevant phenomena, such as salt stress in crops and ...

Authors: Joaquin Ariño, Ebru Aydar, Samuel Drulhe, Daniel Ganser, Jesus Jorrin, Matthias Kahm, Falko Krause, Silvia Petrezselyova, Lynne Yenush, Olga Zimmermannová, G. Paul H. van Heusden, Maik Kschischo, Jost Ludwig, Chris Palmer, Jose Ramos, Hana Sychrova

Date Published: 2014

Journal: Advances in Microbial Systems Biology

Abstract (Expand)

In many plants, starch is synthesized during the day and degraded during the night to avoid carbohydrate starvation in darkness. The circadian clock participates in a dynamic adjustment of starch ...

Authors: Daniel Seaton, O. Ebenhoh, Andrew Millar, A. Pokhilko

Date Published: 18th Dec 2013

Journal: J R Soc Interface

Abstract (Expand)

The interaction between the stromal cell-derived factor-1 alpha (SDF-1alpha, CXCL12) and its chemokine receptor CXCR4 has been reported to regulate stem cell migration, mobilization and homing. The ...

Authors: P. Wuchter, C. Leinweber, Rainer Saffrich, M. Hanke, V. Eckstein, A. D. Ho, M. Grunze, A. Rosenhahn

Date Published: 14th Dec 2013

Journal: Cell Tissue Res

Abstract (Expand)

Dynamic models of metabolism can be useful in identifying potential drug targets, especially in unicellular organisms. A model of glycolysis in the causative agent of human African trypanosomiasis, ...

Authors: Eduard Kerkhoven, Fiona Achcar, V. P. Alibu, R. J. Burchmore, I. H. Gilbert, M. Trybilo, N. N. Driessen, D. Gilbert, Rainer Breitling, Barbara Bakker, Mike Barrett

Date Published: 5th Dec 2013

Journal: PLoS Comput Biol

Abstract (Expand)

We previously demonstrated that leukemia cell lines expressing CD44 and hematopoietic progenitor cells (HPC) from umbilical cord blood (CB) showed rolling on hyaluronic acid (HA)-coated surfaces under ...

Authors: M. Hanke, I. Hoffmann, C. Christophis, M. Schubert, V. T. Hoang, A. Zepeda-Moreno, N. Baran, V. Eckstein, P. Wuchter, A. Rosenhahn, A. D. Ho

Date Published: 22nd Nov 2013

Journal: Biomaterials

Abstract (Expand)

BACKGROUND AIMS: Mesenchymal stromal cells (MSCs) resemble an essential component of the bone marrow niche for maintenance of stemness of hematopoietic progenitor cells (HPCs). Perturbation of the C-X-C ...

Authors: A. Ludwig, Rainer Saffrich, V. Eckstein, T. Bruckner, W. Wagner, A. D. Ho, P. Wuchter

Date Published: 10th Oct 2013

Journal: Cytotherapy

Abstract (Expand)

Expression of the catabolic network in Escherichia coli is predominantly regulated, via oxygen availability, by the two-component system ArcBA. It has been shown that the kinase activity of ArcB is ...

Authors: P. Sharma, S. Stagge, M. Bekker, K. Bettenbrock, K. J. Hellingwerf

Date Published: 7th Oct 2013

Journal: PLoS One

Abstract:

Not specified

Authors: M. Schmitt, L. P. Muller, G. Keysser, H. M. Lorenz, A. D. Ho, P. Wuchter

Date Published: 4th Sep 2013

Journal: Dtsch Med Wochenschr

Abstract (Expand)

Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational ...

Author: R. C. Edgar

Date Published: 18th Aug 2013

Journal: Nat Methods

Abstract (Expand)

Green fluorescent protein (GFP) offers efficient ways of visualizing promoter activity and protein localization in vivo, and many different variants are currently available to study bacterial cell ...

Authors: W. Overkamp, K. Beilharz, R. Detert Oude Weme, A. Solopova, H. Karsens, A. Kovacs, J. Kok, Oscar Kuipers, Jan-Willem Veening

Date Published: 16th Aug 2013

Journal: Appl Environ Microbiol

Abstract:

Not specified

Authors: None

Date Published: 25th Jul 2013

Journal: PLoS Comput Biol

Abstract (Expand)

Four enzymes of the gluconeogenic pathway in Sulfolobus solfataricus were purified and kinetically characterized. The enzymes were reconstituted in vitro to quantify the contribution of temperature ...

Authors: Theresa Kouril, Dominik Esser, Julia Kort, Hans Westerhoff, Bettina Siebers, Jacky Snoep

Date Published: 20th Jul 2013

Journal: FEBS J.

Abstract (Expand)

We present an experimental and computational pipeline for the generation of kinetic models of metabolism, and demonstrate its application to glycolysis in Saccharomyces cerevisiae. Starting from an ...

Authors: K. Smallbone, H. L. Messiha, K. M. Carroll, C. L. Winder, N. Malys, W. B. Dunn, E. Murabito, N. Swainston, J. O. Dada, F. Khan, P. Pir, E. Simeonidis, I. Spasic, J. Wishart, D. Weichart, N. W. Hayes, D. Jameson, D. S. Broomhead, S. G. Oliver, S. J. Gaskell, J. E. McCarthy, N. W. Paton, H. V. Westerhoff, D. B. Kell, P. Mendes

Date Published: 9th Jul 2013

Journal: FEBS Lett

Abstract (Expand)

In pathogenic trypanosomes, trypanothione synthetase (TryS) catalyzes the synthesis of both glutathionylspermidine (Gsp) and trypanothione [bis(glutathionyl)spermidine, T(SH)2]. Here we present a ...

Authors: None

Date Published: 3rd Jul 2013

Journal: J. Biol. Chem.

Abstract (Expand)

Streptococcus pyogenes (group A Streptococcus, GAS) is an important human pathogen causing mild superficial infections of skin and mucous membranes, but also life-threatening systemic diseases. S. ...

Authors: None

Date Published: 1st Jul 2013

Journal: Protein Expression and Purification

Abstract:

Not specified

Authors: Anna Feldman-Salit, Silvio Hering, H. Messiha, Nadine Veith, Vlad Cojocaru, Antje Sieg, Hans Westerhoff, Bernd Kreikemeyer, Rebecca Wade, Tomas Fiedler

Date Published: 17th May 2013

Journal: Journal of Biological Chemistry

Abstract (Expand)

In response to changing extracellular pH levels, phosphate-limited continuous cultures of Clostridium acetobutylicum reversibly switches its metabolism from the dominant formation of acids to the ...

Authors: None

Date Published: 3rd May 2013

Journal: Appl. Microbiol. Biotechnol.

Abstract (Expand)

Systems metabolomics, the identification and quantification of cellular metabolites and their integration with genomics and proteomics data, promises valuable functional insights into cellular biology. ...

Authors: T. Maier, J. Marcos, J. A. Wodke, B. Paetzold, M. Liebeke, R. Gutierrez-Gallego, Luis Serrano

Date Published: 20th Apr 2013

Journal: Mol Biosyst

Abstract (Expand)

In systems biology, quantitative experimental data is the basis of building mathematical models. In most of the cases, they are stored in Excel files and hosted locally. To have a public database for ...

Authors: L. Shi, L. Jong, Ulrike Wittig, P. Lucarelli, Markus Stepath, S. Mueller, L. A. D'Alessandro, Ursula Klingmüller, Wolfgang Müller

Date Published: 4th Apr 2013

Journal: J Integr Bioinform

Abstract (Expand)

Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of ...

Authors: Judith Wodke, J. Puchalka, M. Lluch-Senar, J. Marcos, Eva Yus, M. Godinho, R. Gutierrez-Gallego, V. A. dos Santos, Luis Serrano, Edda Klipp, T. Maier

Date Published: 4th Apr 2013

Journal: Mol Syst Biol

Abstract (Expand)

In a continuous culture under phosphate limitation the metabolism of Clostridium acetobutylicum depends on the external pH level. By comparing seven steady-state conditions between pH 5.7 and pH 4.5 ...

Authors: None

Date Published: 1st Feb 2013

Journal: Microbial Biotechnology

Abstract (Expand)

BACKGROUND AND METHODOLOGY: Recently, we reported on a new class of naphthoquinone derivatives showing a promising anti-trypanosomatid profile in cell-based experiments. The lead of this series (B6, ...

Authors: S. Pieretti, Jurgen Haanstra, M. Mazet, R. Perozzo, C. Bergamini, F. Prati, R. Fato, G. Lenaz, G. Capranico, R. Brun, Barbara Bakker, P. A. Michels, L. Scapozza, M. L. Bolognesi, A. Cavalli

Date Published: 17th Jan 2013

Journal: PLoS Negl Trop Dis

Abstract (Expand)

Background The stressosome is a bacterial signalling complex that responds to environmental changes by initiating a protein partner switching cascade, which leads to the release of the alternative sigma ...

Authors: Ulf Liebal, Thomas Millat, Jon Marles-Wright, Rick Lewis, Olaf Wolkenhauer

Date Published: 2013

Journal: BMC Syst Biol

Abstract (Expand)

Research in Systems Biology involves integrating data and knowledge about the dynamic processes in biological systems in order to understand and model them. Semantic web technologies should be ideal ...

Authors: None

Date Published: 2013

Journal: The Semantic Web – ISWC 2013

Abstract:

Not specified

Authors: Pablo I. Nikel, Victor De Lorenzo

Date Published: 2013

Journal: Metabolic Engineering

Abstract:

Not specified

Authors: Adrienne Zaprasis, J. Brill, M. Thuring, G. Wunsche, M. Heun, H. Barzantny, Tamara Hoffmann, Erhard Bremer

Date Published: 28th Dec 2012

Journal: Applied and Environmental Microbiology

Abstract (Expand)

The Twin-arginine Translocation (Tat) pathway is known to translocate fully folded proteins across bacterial, archaeal and organellar membranes. To date, the mechanisms involved in processing, proofreading ...

Authors: Vivianne J Goosens, Andreas Otto, Corinna Glasner, Carmine G Monteferrante, René van der Ploeg, Michael Hecker, Dörte Becher, Jan Maarten Van Dijl

Date Published: 22nd Dec 2012

Journal: J. Proteome Res.

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)

Glycine betaine is an effective osmoprotectant for Bacillus subtilis. Its import into osmotically stressed cells led to the build-up of large pools, whose size was sensitively determined by the degree ...

Authors: Tamara Hoffmann, Annette Wensing, Margot Brosius, Leif Steil, Uwe Voelker, Erhard Bremer

Date Published: 24th Nov 2012

Journal: J. Bacteriol.

Abstract (Expand)

ABSTRACT: BACKGROUND: With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies ...

Authors: Michal Kolar, Jörn Meier, Ville Mustonen, Michael Lässig, Johannes Berg

Date Published: 21st Nov 2012

Journal: BMC Syst Biol

Abstract (Expand)

The high osmolarity glycerol (HOG) pathway in yeast serves as a prototype signalling system for eukaryotes. We used an unprecedented amount of data to parameterise 192 models capturing different ...

Authors: J. Schaber, R. Baltanas, A. Bush, E. Klipp, A. Colman-Lerner

Date Published: 15th Nov 2012

Journal: Mol Syst Biol

Abstract (Expand)

Plant and microbial metabolic engineering is commonly used in the production of functional foods and quality trait improvement. Computational model-based approaches have been used in this important ...

Author: M. Bekaert

Date Published: 14th Nov 2012

Journal: PLoS One

Abstract (Expand)

The Gram-positive soil bacterium Bacillus subtilis uses glucose and malate as the preferred carbon sources. In the presence of either glucose or malate, the expression of genes and operons for the ...

Authors: Frederik M Meyer, Joerg Stuelke

Date Published: 10th Nov 2012

Journal: FEMS Microbiol. Lett.

Abstract (Expand)

Methylmercury (MeHg) is a widely distributed contaminant polluting many aquatic environments, with health risks to humans exposed mainly through consumption of seafood. The mechanisms of toxicity of ...

Authors: Fekadu Yadetie, O. A. Karlsen, A. Lanzen, K. Berg, P. Olsvik, C. Hogstrand, A. Goksoyr

Date Published: 30th Oct 2012

Journal: Aquat Toxicol

Abstract (Expand)

In Escherichia coli several systems are known to transport glucose into the cytoplasm. The main glucose uptake system under batch conditions is the glucose phosphoenolpyruvate:carbohydrate phosphotransferase ...

Authors: None

Date Published: 8th Oct 2012

Journal: Journal of Bacteriology

Abstract (Expand)

How cells dynamically respond to fluctuating environmental conditions depends on the architecture and noise of the underlying genetic circuits. Most work characterizing stress pathways in the model ...

Authors: None

Date Published: 4th Oct 2012

Journal: Environ. Microbiol.

Abstract (Expand)

The increase in volume and complexity of biological data has led to increased requirements to reuse that data. Consistent and accurate metadata is essential for this task, creating new challenges in ...

Authors: Katy Wolstencroft, Stuart Owen, Matthew Horridge, Simon Jupp, Olga Krebs, Jacky Snoep, Franco Du Preez, Wolfgang Müller, Robert Stevens, Carole Goble

Date Published: 1st Oct 2012

Journal: Concurrency Computat.: Pract. Exper.

Abstract (Expand)

We develop a strategic ‘domino’ approach that starts with one key feature of cell function and the main process providing for it, and then adds additional processes and components only as necessary to ...

Authors: None

Date Published: 1st Sep 2012

Journal: Biochimica et Biophysica Acta (BBA) - Bioenergetics

Abstract (Expand)

The respiratory chain of Escherichia coli contains three quinones. Menaquinone and demethylmenaquinone have low midpoint potentials and are involved in anaerobic respiration, while ubiquinone, which ...

Authors: Poonam Sharma, Joost Teixeira De Mattos, Klaas J. Hellingwerf, Martijn Bekker

Date Published: 1st Sep 2012

Journal: Not specified

Abstract (Expand)

In Bacillus subtilis and its relatives carbon catabolite control, a mechanism enabling to reach maximal efficiency of carbon and energy sources metabolism, is achieved by the global regulator CcpA ...

Authors: Bogumila Marciniak, Monika Pabijaniak, Anne de Jong, Robert Dűhring, Gerald Seidel, Wolfgang Hillen, Oscar Kuipers

Date Published: 17th Aug 2012

Journal: BMC Genomics

Abstract (Expand)

Understanding gene regulation requires knowledge of changes in transcription factor (TF) activities. Simultaneous direct measurement of numerous TF activities is currently impossible. Nevertheless, ...

Authors: Matthew Rolfe, Andrea Ocone, Melanie R Stapleton, Simon Hall, Eleanor W Trotter, Robert Poole, Guido Sanguinetti, Jeff Green

Date Published: 8th Aug 2012

Journal: Open Biol

Abstract:

Not specified

Authors: Anna-Karin Gustavsson, Dawie Van Niekerk, Caroline B. Adiels, Franco B. du Preez, Mattias Goksör, Jacky Snoep

Date Published: 1st Aug 2012

Journal: Not specified

Abstract (Expand)

The respiratory chain of Escherichia coli contains three different cytochrome oxidases. Whereas the cytochrome bo oxidase and the cytochrome bd-I oxidase are well characterized and have been shown to ...

Authors: Poonam Sharma, Klaas J Hellingwerf, Maarten J Teixeira de Mattos, Martijn Bekker

Date Published: 27th Jul 2012

Journal: Appl. Environ. Microbiol.

Abstract (Expand)

The active center of multi-subunit RNA polymerase consists of two modules, the Mg(2+) module, holding the catalytic Mg(2+) ion, and a module made of a flexible domain, the Trigger Loop. Uniquely, the ...

Authors: Yulia Yuzenkova, Mohammad Roghanian, Nikolay Zenkin

Date Published: 10th Jul 2012

Journal: Transcription

Abstract (Expand)

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. Using a small subset of experimental data, the original ...

Authors: Franco Du Preez, David D van Niekerk, Bob Kooi, Johann M Rohwer, Jacky Snoep

Date Published: 21st Jun 2012

Journal: The FEBS journal

Abstract (Expand)

In an accompanying paper [du Preez et al., (2012) FEBS J doi: 10.1111/j.1742-4658.2012.08665.x], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. ...

Authors: Franco Du Preez, David D van Niekerk, Jacky Snoep

Date Published: 13th Jun 2012

Journal: The FEBS journal

Abstract (Expand)

BACKGROUND: Systems biology approaches to study metabolic switching in Streptomyces coelicolor A3(2) depend on cultivation conditions ensuring high reproducibility and distinct phases of culture growth ...

Authors: A. Wentzel, P. Bruheim, A. Overby, O. M. Jakobsen, H. Sletta, W. A. Omara, D. A. Hodgson, T. E. Ellingsen

Date Published: 9th Jun 2012

Journal: BMC Syst Biol

Abstract (Expand)

Bacillus subtilis synthesizes large amounts of the compatible solute proline as a cellular defense against high osmolarity to ensure a physiologically appropriate level of hydration of the cytoplasm ...

Authors: Tamara Hoffmann, Carsten von Blohn, Agnieszka Stanek, Susanne Moses, Helena Barzantny, Erhard Bremer

Date Published: 8th Jun 2012

Journal: Appl. Environ. Microbiol.

Abstract (Expand)

Encouraging more broad and inclusive data sharing in today's world will involve concerted community efforts to overcome technical barriers and human foibles. Vivien Marx investigates. (includes ...

Author: Vivien Marx

Date Published: 7th Jun 2012

Journal: Nat Biotechnol

Abstract (Expand)

Yeast glycolytic oscillations have been studied since the 1950s in cell-free extracts and intact cells. For intact cells, sustained oscillations have so far only been observed at the population level, ...

Authors: Anna-Karin Gustavsson, David D van Niekerk, Caroline B Adiels, Franco Du Preez, Mattias Goksör, Jacky Snoep

Date Published: 23rd May 2012

Journal: The FEBS journal

Abstract (Expand)

RNA processing and degradation are key processes in the control of transcript accumulation and thus in the control of gene expression. In Escherichia coli, the underlying mechanisms and components of ...

Authors: Martin Lehnik-Habrink, Rick Lewis, Ulrike Mäder, Joerg Stuelke

Date Published: 8th May 2012

Journal: Mol. Microbiol.

Abstract (Expand)

Our quantitative knowledge of carbon fluxes in the long slender bloodstream form (BSF) Trypanosoma brucei is mainly based on non-proliferating parasites, isolated from laboratory animals and kept in ...

Authors: Jurgen Haanstra, A. van Tuijl, J. van Dam, W. van Winden, A. G. Tielens, J. J. van Hellemond, Barbara Bakker

Date Published: 8th May 2012

Journal: Int J Parasitol

Abstract (Expand)

The origin of translation and the genetic code is one of the major mysteries of evolution. The advantage of templated protein synthesis could have been achieved only when the translation apparatus had ...

Authors: None

Date Published: 28th Apr 2012

Journal: J. Mol. Evol.

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)

The circadian clocks that drive daily rhythms in animals are tightly coupled among the cells of some tissues. The coupling profoundly affects cellular rhythmicity and is central to contemporary ...

Authors: B. Wenden, D. L. Toner, S. K. Hodge, R. Grima, Andrew Millar

Date Published: 13th Apr 2012

Journal: Proc Natl Acad Sci U S A

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)

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)

Determining transcriptional regulator activities is a major focus of systems biology, providing key insight into regulatory mechanisms and co-regulators. For organisms such as Escherichia coli, ...

Authors: M. Iqbal, Y. Mast, R. Amin, D. A. Hodgson, W. Wohlleben, N. J. Burroughs

Date Published: 13th Mar 2012

Journal: Nucleic Acids Res

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)

To gain more insight into the butanol stress response of Clostridium acetobutylicum the transcriptional response of a steady state acidogenic culture to different levels of n-butanol (0.25-1%) was ...

Authors: Katrin Schwarz, Wouter Kuit, Christina Grimmler, Armin Ehrenreich, Servé Kengen

Date Published: 1st Mar 2012

Journal: Journal of Biotechnology

Abstract (Expand)

Lactic acid-producing bacteria survive in distinct environments, but show common metabolic characteristics. Here we studied the dynamic interactions of the central metabolism in Lactococcus lactis, ...

Authors: None

Date Published: 14th Feb 2012

Journal: The FEBS journal

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)

BACKGROUND: Ontologies are being developed for the life sciences to standardise the way we describe and interpret the wealth of data currently being generated. As more ontology based applications begin ...

Authors: Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens

Date Published: 25th Jan 2012

Journal: BMC bioinformatics

Abstract (Expand)

Kinetic models of metabolism require detailed knowledge of kinetic parameters. However, due to measurement errors or lack of data this knowledge is often uncertain. The model of glycolysis in the ...

Authors: None

Date Published: 19th Jan 2012

Journal: PLoS Comput Biol

Abstract (Expand)

Transcription and translation are coupled in bacteria, meaning that translation takes place co-transcriptionally. During transcription-translation, both machineries mutually affect each others' ...

Authors: Daniel Castro-Roa, Nikolay Zenkin

Date Published: 3rd Jan 2012

Journal: Nucleic acids research

Abstract (Expand)

In Bacillus subtilis the σB mediated general stress response provides protection against various environmental and energy related stress conditions. To better understand the general stress response, ...

Authors: Ulf Liebal, Praveen Kumar Sappa, Thomas Millat, Leif Steil, Georg Homuth, Uwe Voelker, Olaf Wolkenhauer

Date Published: 2012

Journal: Mol. BioSyst.

Abstract (Expand)

Many of the complex systems found in biology are comprised of numerous components, where interactions between individual agents result in the emergence of structures and function, typically in a highly ...

Authors: Michael Holcombe, Salem Adra, Mesude Bicak, Shawn Chin, Simon Coakley, Alison Graham, Jeff Green, Chris Greenough, Duncan Jackson, Mariam Kiran, Sheila MacNeil, Afsaneh Maleki-Dizaji, Phil McMinn, Mark Pogson, Robert Poole, Eva Qwarnstrom, Francis Ratnieks, Matthew Rolfe, Rod Smallwood, Tao Sun, David Worth

Date Published: 2012

Journal: Integr Biol (Camb)

Abstract (Expand)

A metabolite profiling study of the antibiotic producing bacterium Streptomyces coelicolor A3(2) has been performed. The aim of this study was to monitor intracellular metabolite pool changes occurring ...

Authors: A. Wentzel, H. Sletta, T. E. Ellingsen, P. Bruheim

Date Published: 2012

Journal: Metabolites

Abstract (Expand)

RightField is a Java application that provides a mechanism for embedding ontology annotation support for scientific data in Microsoft Excel or Open Office spreadsheets. The result is semantic annotation ...

Authors: Katy Wolstencroft, Stuart Owen, Matthew Horridge, Wolfgang Müller, Finn Bacall, Jacky Snoep, Franco du Preez, Quyen Nguyen, Olga Krebs, Carole Goble

Date Published: 2012

Journal: Knowledge Engineering and Knowledge Management

Abstract (Expand)

The RNA degradosome is a multiprotein macromolecular complex that is involved in the degradation of messenger RNA in bacteria. The composition of this complex has been found to display a high degree ...

Authors: Joseph Newman, Lorraine Hewitt, Cecilia Rodrigues, Alexandra S Solovyova, Colin Harwood, Rick Lewis

Date Published: 16th Dec 2011

Journal: J. Mol. Biol.

Abstract (Expand)

Common laboratory strains of Bacillus subtilis encode two glutamate dehydrogenases: the enzymatically active protein RocG and the cryptic enzyme GudB that is inactive due to a duplication of three amino ...

Authors: Katrin Gunka, Stefan Tholen, Jan Gerwig, Christina Herzberg, Joerg Stuelke, Fabian M Commichau

Date Published: 16th Dec 2011

Journal: J. Bacteriol.

Abstract (Expand)

The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published ...

Authors: Dagmar Waltemath, Richard Adams, Frank T Bergmann, Michael Hucka, Fedor Kolpakov, Andrew K Miller, Ion I Moraru, David Nickerson, Sven Sahle, Jacky Snoep, Nicolas Le Novère

Date Published: 15th Dec 2011

Journal: BMC Syst Biol

Abstract (Expand)

Bacteria in the genus Streptomyces are soil-dwelling oligotrophs and important producers of secondary metabolites. Previously, we showed that global messenger RNA expression was subject to a series of ...

Authors: L. Thomas, D. A. Hodgson, A. Wentzel, K. Nieselt, T. E. Ellingsen, J. Moore, E. R. Morrissey, R. Legaie, W. Wohlleben, A. Rodriguez-Garcia, J. F. Martin, N. J. Burroughs, E. M. Wellington, M. C. Smith

Date Published: 8th Dec 2011

Journal: Mol Cell Proteomics

Abstract (Expand)

In the field of metabolomics, GC–MS has rather established itself as a tool for semi-quantitative strategies like metabolic fingerprinting or metabolic profiling. Absolute quantification of intra- or ...

Authors: Oliver Vielhauer, Maksim Zakhartsev, Thomas Horn, Ralf Takors, Matthias Reuss

Date Published: 1st Dec 2011

Journal: Journal of Chromatography B

Abstract:

Not specified

Authors: Oliver Vielhauer, Maksim Zakhartsev, Thomas Horn, Ralf Takors, Matthias Reuss

Date Published: 1st Dec 2011

Journal: Journal of Chromatography B

Abstract (Expand)

Pausing of transcription is an important step of regulation of gene expression in bacteria and eukaryotes. Here we uncover a factor-independent mechanism of transcription pausing, which is determined ...

Authors: Aleksandra Bochkareva, Yulia Yuzenkova, Vasisht R Tadigotla, Nikolay Zenkin

Date Published: 29th Nov 2011

Journal: EMBO J.