Publications

Abstract (Expand)

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)

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)

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)

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)

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

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)

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)

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:

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)

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)

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)

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)

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)

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)

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)

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

Date Published: 14th Oct 2011

Journal: J. Bacteriol.

Abstract (Expand)

Systems biology is a comprehensive quantitative analysis how the components of a biological system interact over time which requires an interdisciplinary team of investigators. System-theoretic methods ...

Authors: None

Date Published: 11th Nov 2010

Journal: Methods Mol. Biol.

Abstract (Expand)

We review recent observations on the mobility of macromolecules and their spatial organization in live bacterial cells. We outline the major fluorescence microscopy-based methods to determine the ...

Authors: None

Date Published: 16th Oct 2010

Journal: Curr. Opin. Biotechnol.

Abstract (Expand)

The recent years have seen tremendous progress towards the understanding of microbial metabolism on a higher level of the entire functional system. Hereby, huge achievements including the sequencing ...

Authors: Michael Kohlstedt, Judith Becker, Christoph Wittmann

Date Published: 7th Sep 2010

Journal: Appl. Microbiol. Biotechnol.

Abstract (Expand)

We determined the diffusion coefficients (D) of (macro)molecules of different sizes (from ∼0.5 to 600 kDa) in the cytoplasm of live Escherichia coli cells under normal osmotic conditions and osmotic ...

Authors: Jacek Mika, Geert Van Den Bogaart, Liesbeth Veenhoff, Victor Krasnikov, Bert Poolman

Date Published: 1st Jul 2010

Journal: Not specified

Abstract (Expand)

Metabolomics analysis, which aims at the systematic identification and quantification of all metabolites in biological systems, is emerging as a powerful new tool to identify biomarkers of disease, ...

Authors: None

Date Published: 17th Feb 2010

Journal: Parasitology

Abstract (Expand)

In vivo nuclear magnetic resonance (NMR) monitoring requires a high-density cell suspension, where cell precipitation should be avoided. We have designed a miniaturized cell agitator that fits entirely ...

Authors: Maksim Zakhartsev, Christian Bock

Date Published: 1st Feb 2010

Journal: Analytical Biochemistry

Abstract (Expand)

Background The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we ...

Authors: M. Tauqeer Alam, Maria Elena Merlo, The STREAM Consortium (stream), David Hodgson, Elizabeth Wellington, Eriko Takano, Rainer Breitling

Date Published: 2010

Journal: BMC Genomics

Abstract (Expand)

A major part of organismal complexity and versatility of prokaryotes resides in their ability to fine-tune gene expression to adequately respond to internal and external stimuli. Evolution has been ...

Authors: Sacha A F T van Hijum, Marnix H Medema, Oscar Kuipers

Date Published: 2nd Sep 2009

Journal: Microbiol. Mol. Biol. Rev.

Abstract (Expand)

Bacillus subtilis cells may opt to forgo normal cell division and instead form spores if subjected to certain environmental stimuli, for example nutrient deficiency or extreme temperature. The resulting ...

Authors: None

Date Published: 21st Jul 2009

Journal: Not specified

Abstract (Expand)

Staphylococcus aureus is a pathogenic bacterium that utilises quorum sensing (QS), a cell-to-cell signalling mechanism, to enhance its ability to cause disease. QS allows the bacteria to monitor their ...

Authors: Sara Jabbari, John King, Adrian J Koerber, Paul Williams

Date Published: 19th Feb 2009

Journal: J Math Biol

Abstract (Expand)

Bacillus subtilis serves as an excellent model to study protein secretion at a proteomic scale. Most of the extracellular proteins are exported from the cytoplasm via the secretory (Sec) pathway. Despite ...

Authors: Thijs R H M Kouwen, Haike Antelmann, René van der Ploeg, Emma L Denham, Michael Hecker, Jan Maarten Van Dijl

Date Published: 23rd Jan 2009

Journal: Proteomics

Abstract (Expand)

We have developed MINOMICS, a tool that allows facile and in-depth visualization of prokaryotic transcriptomic and proteomic data in conjunction with genomics data. MINOMICS generates interactive linear ...

Authors: Rutger W W Brouwer, Sacha A F T van Hijum, Oscar Kuipers

Date Published: 12th Nov 2008

Journal: Bioinformatics

Abstract (Expand)

Disulfide bonds are important for the correct folding, structural integrity, and activity of many biotechnologically relevant proteins. For synthesis and subsequent secretion of these proteins in ...

Authors: Thijs R H M Kouwen, Jean-Yves F Dubois, Roland Freudl, Wim J Quax, Jan Maarten Van Dijl

Date Published: 24th Oct 2008

Journal: Appl. Environ. Microbiol.

Abstract (Expand)

Bacillus subtilis has been developed as a model system for physiological proteomics. However, thus far these studies have mainly been limited to cytoplasmic, extracellular, and cell-wall attached ...

Authors: Annette Dreisbach, Andreas Otto, Dörte Becher, Elke Hammer, Alexander Teumer, Joost W Gouw, Michael Hecker, Uwe Voelker

Date Published: 21st May 2008

Journal: Proteomics

Abstract (Expand)

SUMMARY: We present a Cytoscape plugin for the inference and visualization of networks from high-resolution mass spectrometry metabolomic data. The software also provides access to basic topological ...

Authors: Fabien Jourdan, Rainer Breitling, Michael P Barrett, David Gilbert

Date Published: 14th Nov 2007

Journal: Bioinformatics

Abstract (Expand)

Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation ...

Authors: A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C. A. Ball, H. C. Causton, T. Gaasterland, P. Glenisson, F. C. Holstege, I. F. Kim, V. Markowitz, J. C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze-Kremer, J. Stewart, R. Taylor, J. Vilo, M. Vingron

Date Published: 1st Dec 2001

Journal: Nat Genet

Abstract (Expand)

The proteins cdc2 and cyclin form a heterodimer (maturation promoting factor) that controls the major events of the cell cycle. A mathematical model for the interactions of cdc2 and cyclin is constructed. ...

Author: J. J. Tyson

Date Published: 15th Aug 1991

Journal: Proc Natl Acad Sci U S A

Abstract (Expand)

Tryptophan is utilized in various metabolic routes including protein synthesis, serotonin, and melatonin synthesis and the kynurenine pathway. Perturbations in these pathways have been associated with ...

Authors: A. K. Stavrum, Ines Heiland, S. Schuster, P. Puntervoll, Mathias Ziegler

Date Published: No date defined

Journal: J Biol Chem

Abstract (Expand)

Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale ...

Authors: J. Starruss, W. de Back, Lutz Brusch, A. Deutsch

Date Published: No date defined

Journal: Bioinformatics

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