Publications

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)

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) ...

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)

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)

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)

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)

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:

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)

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)

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)

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)

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)

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)

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 (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 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, Christoph Wittmann, Becker Judith

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, Bert Poolman, Van Den Bogaart Geert,Veenhoff Liesbeth,Krasnikov Victor

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, Bock Christian

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, David Hodgson, Elizabeth Wellington, Eriko Takano, Rainer Breitling, (stream) The STREAM Consortium

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

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, Koerber Adrian J,Williams Paul

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

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

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

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

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

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 ...

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

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: Tyson J. J.

Date Published: 15th Aug 1991

Journal: Proc Natl Acad Sci U S A

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: Tyson J. J.

Date Published: 15th Aug 1991

Journal: Proc Natl Acad Sci U S A

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