Publications

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

Date Published: 15th Jan 2018

Journal: Appl Environ Microbiol

Abstract:

Not specified

Authors: None

Date Published: 24th Oct 2017

Journal: Not specified

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, Patrick Haferkamp, Patricia Wieloch, Dietmar Schomburg, Peter Ruoff, Bettina Siebers, Jörg Schaber, Esser D.

Date Published: 12th Jul 2017

Journal: PLoS One

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, Steffen Waldherr, Lucia Sergio,Findeisen Rolf

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

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, Bettina Siebers, Phil Wright, Dietmar Schomburg, Hofmann Julia D.,Kalinowski Jörn,Neumann-Schaal Meina

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

Date Published: 1st Apr 2017

Journal: Aquatic Toxicology

Abstract:

Not specified

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

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

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

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 ...

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

Date Published: 8th Jan 2017

Journal: Appl Environ Microbiol

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 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, Jakub Straszewski, Alan Williams, Bernd Rinn, Wolfgang Müller, Carole Goble, Soiland-Reyes S.,van Niekerk D. D.,Malmstrom L.

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)

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

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, Kreutz C.

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

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, Bjorneklett S.,Garberg H. K.,Oveland E.,Berven F.,Goksoyr A.,Karlsen O. A.

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

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 ...

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

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

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

Date Published: 15th Jun 2016

Journal: J Biotechnol

Abstract:

Not specified

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

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) ...

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

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

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

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

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

Date Published: 16th 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: Rainer Saffrich, Wuchter P.,Vetter M.,Diehlmann A.,Bieback K.,Ho A. D.,Horn P.

Date Published: 19th Feb 2016

Journal: Exp Hematol

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)

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, Jacky Snoep, Penkler Gerald P.,du Toit Francois

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

Date Published: 30th Jan 2016

Journal: Cell Tissue Res

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)

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, Mozga Ivars,Sulins Jurijs,Zikmanis Peteris

Date Published: 2016

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

Abstract (Expand)

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, Dawie Van Niekerk, Eicher J.,Palm D. C.,Penkler G.,du Toit F.,Walters N.,Burger R.,Westerhoff H. V.

Date Published: 27th Nov 2015

Journal: Biochemical Society Transactions

Abstract (Expand)

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

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, Matthias Reuss, Yang Xuelian,Pörtner Hans Otto

Date Published: 1st Aug 2015

Journal: Journal of Thermal Biology

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

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

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: 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)

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, Matthias Reuss, Vielhauer Oliver,Horn Thomas,Yang Xuelian

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, Millard P.,Swainston N.

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

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

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, Jennifer Levering, Jeroen Hugenholtz, Helge Holo, Ingolf Nes, Bas Teusink, Ursula Kummer, Olivier B. G.,Grosseholz R.

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

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

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

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 ...

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

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, Robert Muetzelfeldt, Andrew Millar, Wenden B.,Flis A.,Mengin V.,Taylor J.,Davey C. L.,Tindal C.,Thomas H.,Ougham H. J.,de Reffye P.,Stitt M.,Williams M.,Halliday K. J.

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, 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)

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

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, Kreutz Clemens

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 ...

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

Date Published: 19th Jun 2014

Journal: BMC Genomics

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

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, Federico Rojas, Barbara Bakker, Mike Barrett, Christine Clayton, Mark Girolami, Luise Krauth-Siegel, Keith Matthews, Rainer Breitling, Papamarkou T.

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, Matthew Rolfe, Guido Sanguinetti, Oliver Sawodny, Poonam Sharma, Sonja Steinsiek, Robert Poole, Kunz S.

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, Robert Poole, Jeff Green, Michael Holcombe, Coakley S.

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

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

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, Andrew Millar, Ebenhoh O.,Pokhilko A.

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

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, Rainer Breitling, Barbara Bakker, Mike Barrett, Alibu V. P.,Burchmore R. J.,Gilbert I. H.,Trybilo M.,Driessen N. N.,Gilbert D.

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 ...

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

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

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 ...

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

Date Published: 7th Oct 2013

Journal: PLoS One

Abstract:

Not specified

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

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: Edgar R. C.

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

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, Hans Westerhoff, Bettina Siebers, Jacky Snoep, Esser Dominik,Kort Julia

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 ...

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

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, Nadine Veith, Vlad Cojocaru, Antje Sieg, Hans Westerhoff, Bernd Kreikemeyer, Rebecca Wade, Tomas Fiedler, Messiha H.

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

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

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

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

Date Published: 17th Jan 2013

Journal: PLoS Negl Trop Dis

Abstract:

Not specified

Authors: Victor De Lorenzo, Nikel Pablo I.

Date Published: 2013

Journal: Metabolic Engineering

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, Rick Lewis, Olaf Wolkenhauer, Marles-Wright Jon

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

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

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

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, Leif Steil, Uwe Voelker, Erhard Bremer, Wensing Annette,Brosius Margot

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

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 ...

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

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: Bekaert M.

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: Joerg Stuelke, Meyer Frederik M

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, Karlsen O. A.,Lanzen A.,Berg K.,Olsvik P.,Hogstrand C.,Goksoyr A.

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, Olga Krebs, Jacky Snoep, Franco Du Preez, Wolfgang Müller, Carole Goble, Horridge Matthew,Jupp Simon,Stevens Robert

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, Martijn Bekker, Hellingwerf Klaas J.

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, Gerald Seidel, Wolfgang Hillen, Oscar Kuipers, Pabijaniak Monika,de Jong Anne,Dűhring Robert

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

Date Published: 8th Aug 2012

Journal: Open Biol

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, Martijn Bekker, Hellingwerf Klaas J,de Mattos Maarten J Teixeira

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, Nikolay Zenkin, Roghanian Mohammad

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, Jacky Snoep, van Niekerk David D,Kooi Bob,Rohwer Johann M

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, Jacky Snoep, van Niekerk David D

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 ...

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

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, Erhard Bremer, von Blohn Carsten,Stanek Agnieszka,Moses Susanne,Barzantny Helena

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: Marx Vivien

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

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

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, Barbara Bakker, van Tuijl A.,van Dam J.,van Winden W.,Tielens A. G.,van Hellemond J. J.

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: 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)

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

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: 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)

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, Carolyn Lam, Dietmar Schomburg, Auxi Prieto, Vitor Martins Dos Santos, Escapa I. F.,Jager C.,Puchalka J.

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, ...

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

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: 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)

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, Armin Ehrenreich, Servé Kengen, Grimmler Christina

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

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

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: Nikolay Zenkin, Castro-Roa Daniel

Date Published: 3rd Jan 2012

Journal: Nucleic acids research

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 ...

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

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, Wolfgang Müller, Finn Bacall, Jacky Snoep, Quyen Nguyen, Olga Krebs, Carole Goble, Horridge Matthew,du Preez Franco

Date Published: 2012

Journal: Knowledge Engineering and Knowledge Management

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, Uwe Voelker, Olaf Wolkenhauer, Homuth Georg

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

Date Published: 2012

Journal: Integr Biol (Camb)

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, Colin Harwood, Rick Lewis, Hewitt Lorraine,Rodrigues Cecilia,Solovyova Alexandra S

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

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

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 ...

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

Date Published: 8th Dec 2011

Journal: Mol Cell Proteomics

Abstract:

Not specified

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

Date Published: 1st Dec 2011

Journal: Journal of Chromatography B

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

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

Date Published: 29th Nov 2011

Journal: EMBO J.

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 (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible database storing comprehensive information about biochemical reactions and their kinetic properties. SABIO-RK offers standardized data manually ...

Authors: Renate Kania, Maja Rey, Olga Krebs, Isabel Rojas, Wolfgang Müller, Wittig Ulrike,Golebiewski Martin,Shi Lei,Jong Lenneke,Algaa Enkhjargal,Weidemann Andreas,Sauer-Danzwith Heidrun,Mir Saqib,Bittkowski Meik,Wetsch Elina

Date Published: 18th Nov 2011

Journal: Nucleic Acids Res.

Abstract (Expand)

In the post-genomic era, most components of a cell are known and they can be quantified by large-scale functional genomics approaches. However, genome annotation is the bottleneck that hampers our ...

Authors: Ulrike Mäder, Lope A. Florez, Joerg Stuelke, Schmeisky Arne G

Date Published: 16th Nov 2011

Journal: Nucleic Acids Res.

Abstract (Expand)

Enterococcus faecalis V583 was grown in a glucose-limited chemostat at three different (0.05 h(-1), 0.15 h(-1) and 0.4 h(-1)) growth rates. The fermentation pattern changed with growth rate, from a ...

Authors: Ibrahim Mehmeti, Martijn Bekker, Ingolf Nes, Helge Holo, Faergestad Ellen M,Snipen Lars

Date Published: 1st Nov 2011

Journal: Applied and environmental microbiology

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. ...

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

Date Published: 29th Oct 2011

Journal: Appl Microbiol Biotechnol

Abstract (Expand)

Most organisms can choose their preferred carbon source from a mixture of nutrients. This process is called carbon catabolite repression. The Gram-positive bacterium Bacillus subtilis uses glucose as ...

Authors: Joerg Stuelke, Meyer Frederik M,Jules Matthieu,Mehne Felix M P,Le Coq Dominique,Landmann Jens J,Görke Boris,Aymerich Stéphane

Date Published: 14th Oct 2011

Journal: J. Bacteriol.

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)

Many bacteria undergo transitions between environments with differing O₂ availabilities as part of their natural lifestyles and during biotechnological processes. However, the dynamics of adaptation ...

Authors: Matthew Rolfe, Guido Sanguinetti, Robert Poole, Jeff Green, Trotter Eleanor W,Hounslow Andrea M,Craven C Jeremy,Williamson Michael P

Date Published: 27th Sep 2011

Journal: PLoS ONE

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: Abeer Fadda, Christine Clayton, Manful Theresa

Date Published: 26th Sep 2011

Journal: RNA

Abstract (Expand)

Sortases of Gram-positive bacteria catalyze the covalent C-terminal anchoring of proteins to the cell wall. Bacillus subtilis, a well-known host organism for protein production, contains two putative ...

Authors: Michael Hecker, Jan Maarten Van Dijl, Fasehee Hamidreza,Westers Helga,Bolhuis Albert,Antelmann Haike,Quax Wim J,Mirlohi Agha F,Ahmadian Gholamreza

Date Published: 31st Aug 2011

Journal: Proteomics

Abstract (Expand)

One of the main pathways for the detoxification of reactive metabolites in the liver involves glutathione conjugation. Metabolic profiling studies have shown paradoxical responses in glutathione-related ...

Authors: Franco Du Preez, Hans Westerhoff, Jacky Snoep, Geenen Suzanne,Reed Michael,Nijhout H Frederik,Kenna J Gerry,Wilson Ian D

Date Published: 24th Aug 2011

Journal: Eur J Pharm Sci

Abstract (Expand)

During the last few years scientists became increasingly aware that average data obtained from microbial population based experiments are not representative of the behavior, status or phenotype of ...

Authors: Imke De Jong, Oscar Kuipers, Jan-Willem Veening, Beilharz Katrin

Date Published: 16th Aug 2011

Journal: J Vis Exp

Abstract (Expand)

RNA processing and degradation is initiated by endonucleolytic cleavage of the target RNAs. In many bacteria, this activity is performed by RNase E which is not present in Bacillus subtilis and other ...

Authors: Ulrike Mäder, Joerg Stuelke, Lehnik-Habrink Martin,Schaffer Marc,Diethmaier Christine,Herzberg Christina

Date Published: 4th Aug 2011

Journal: Mol. Microbiol.

Abstract (Expand)

The control of mRNA stability is an important component of regulation in bacteria. Processing and degradation of mRNAs are initiated by an endonucleolytic attack, and the cleavage products are processively ...

Authors: Joseph Newman, Rick Lewis, Joerg Stuelke, Lehnik-Habrink Martin,Rothe Fabian M,Solovyova Alexandra S,Rodrigues Cecilia,Herzberg Christina,Commichau Fabian M

Date Published: 29th Jul 2011

Journal: J. Bacteriol.

Abstract (Expand)

Bacterial promoters are recognized by RNA polymerase (RNAP) σ subunit, which specifically interacts with the -10 and -35 promoter elements. Here, we provide evidence that the β' zipper, an ...

Authors: Yulia Yuzenkova, Nikolay Zenkin, Tadigotla Vasisht R,Severinov Konstantin

Date Published: 26th Jul 2011

Journal: EMBO J.

Abstract (Expand)

Bacillus subtilis is known to accumulate large amounts of the compatible solute proline via de novo synthesis as a stress protectant when it faces high-salinity environments. We elucidated the genetic ...

Authors: Tamara Hoffmann, Erhard Bremer, Brill Jeanette,Bleisteiner Monika

Date Published: 22nd Jul 2011

Journal: J. Bacteriol.

Abstract (Expand)

Genes are regulated because their expression involves a fitness cost to the organism. The production of proteins by transcription and translation is a well-known cost factor, but the enzymatic activity ...

Authors: Johannes Berg, Perfeito Lilia,Ghozzi Stéphane,Schnetz Karin,Lässig Michael

Date Published: 21st Jul 2011

Journal: PLoS Genet.

Abstract (Expand)

Segregation of replicated chromosomes is an essential process in all organisms. How bacteria, such as the oval-shaped human pathogen Streptococcus pneumoniae, efficiently segregate their chromosomes ...

Authors: Jan-Willem Veening, Minnen Anita,Attaiech Laetitia,Thon Maria,Gruber Stephan

Date Published: 22nd Jun 2011

Journal: Mol. Microbiol.

Abstract (Expand)

The development of disease may be characterized as a pathological shift of homeostasis; the main goal of contemporary drug treatment is, therefore, to return the pathological homeostasis back to the ...

Authors: Jacky Snoep, Hans Westerhoff, Kolodkin Alexey,Boogerd Fred C,Plant Nick,Bruggeman Frank J,Goncharuk Valeri,Lunshof Jeantine,Moreno-Sanchez Rafael,Yilmaz Nilgun,Bakker Barbara M,Balling Rudi

Date Published: 16th Jun 2011

Journal: Eur J Pharm Sci

Abstract:

Not specified

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

Date Published: 1st Jun 2011

Journal: Journal of Biotechnology