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Biphasic response as a mechanism against mutant takeover in tissue homeostasis circuits

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 ...

Author: Karin Omer,Alon Uri

Date Published: 26th Jun 2017

Journal: Mol Syst Biol

DOI: 10.15252/msb.20177599

Citation: Mol Syst Biol 13(6) : 933

Created: 31st Jul 2018 at 11:34

Frequency doubling in the cyanobacterial circadian clock

Molecular Systems Biology

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 ...

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

Date Published: 22nd Dec 2016

Journal: Mol Syst Biol

DOI: 10.15252/msb.20167087

Citation: Mol Syst Biol 12(12) : 896

Created: 30th Jul 2018 at 15:36

Entrainment of heterogeneous glycolytic oscillations in single cells

Yeast glycolytic oscillations

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 ...

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

Date Published: 1st Aug 2015

Journal: Sci Rep

DOI: 10.1038/srep09404

Citation: Sci Rep 5(1) : 415

Created: 16th Jul 2018 at 15:58, Last updated: 17th Jul 2018 at 09:21

From steady-state to synchronized yeast glycolytic oscillations I: model construction.

Yeast glycolytic oscillations

Abstract (Expand)

UNLABELLED: 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 ...

Authors: Dawie Van Niekerk, Jacky Snoep, du Preez F. B.,Kooi B.,Rohwer J. M.

Date Published: No date defined

Journal: FEBS J

PubMed ID: 22712534

Citation: FEBS J. 2012 Aug;279(16):2810-22. doi: 10.1111/j.1742-4658.2012.08665.x. Epub 2012 Jul 9.

Created: 17th Jul 2018 at 09:19

From steady-state to synchronized yeast glycolytic oscillations II: model validation.

Yeast glycolytic oscillations

Abstract (Expand)

UNLABELLED: In an accompanying paper [du Preez et al., (2012) FEBS J279, 2810-2822], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. Here we ...

Authors: Dawie Van Niekerk, Jacky Snoep, du Preez F. B.

Date Published: No date defined

Journal: FEBS J

PubMed ID: 22686585

Citation: FEBS J. 2012 Aug;279(16):2823-36. doi: 10.1111/j.1742-4658.2012.08658.x. Epub 2012 Jul 5.

Created: 17th Jul 2018 at 09:18

Sustained glycolytic oscillations in individual isolated yeast cells

Yeast glycolytic oscillations

Abstract:

Not specified

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

Date Published: 1st Aug 2012

Journal: Not specified

DOI: 10.1111/j.1742-4658.2012.08639.x

Citation: Sustained glycolytic oscillations in individual isolated yeast cells 279(16) : 2837

Created: 16th Jul 2018 at 16:33, Last updated: 16th Jul 2018 at 16:37

Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells

Yeast glycolytic oscillations

Abstract:

Not specified

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

Date Published: 3rd Jan 2014

Journal: Not specified

DOI: 10.1016/j.febslet.2013.11.028

Citation: Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells 588(1) : 3

Created: 16th Jul 2018 at 16:28, Last updated: 16th Jul 2018 at 16:29

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum T

SysMetEx

(Show All)

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

DOI: 10.1128/AEM.02091-17

Citation: Appl Environ Microbiol 84(3) : e02091-17

Created: 16th Jul 2018 at 16:25, Last updated: 16th Jul 2018 at 16:25

Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells

Yeast glycolytic oscillations

Abstract:

Not specified

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

Date Published: 1st Jun 2014

Journal: FEBS J

DOI: 10.1111/febs.12820

Citation: FEBS J 281(12) : 2784

Created: 16th Jul 2018 at 16:09, Last updated: 16th Jul 2018 at 16:10

Cell size and morphological properties of yeast Saccharomyces cerevisiae in relation to growth temperature

MOSES

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

DOI: 10.1093/femsyr/foy052

Citation: Cell size and morphological properties of yeast Saccharomyces cerevisiae in relation to growth temperature 18(6) : 603

Created: 12th Jul 2018 at 21:12, Last updated: 12th Jul 2018 at 21:15

Photosynthate partitioning to starch in Arabidopsis thaliana is insensitive to light intensity but sensitive to photoperiod due to a restriction on growth in the light in short photoperiods.

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Abstract (Expand)

Photoperiod duration can be predicted from previous days, but irradiance fluctuates in an unpredictable manner. To investigate how allocation to starch responds to changes in these two environmental ...

Authors: Virginie Mengin, Pyl E. T.,Alexandre Moraes T.,Sulpice R.,Krohn N.,Encke B.,Stitt M.

Date Published: No date defined

Journal: Plant Cell Environ

PubMed ID: 28628949

Citation: Plant Cell Environ. 2017 Nov;40(11):2608-2627. doi: 10.1111/pce.13000. Epub 2017 Aug 17.

Created: 28th Jun 2018 at 12:46

Phytochrome, Carbon Sensing, Metabolism, and Plant Growth Plasticity.

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

(Show All)

Abstract:

Not specified

Authors: Johanna Krahmer, Ashwin Ganpudi, Ammad Abbas, Andrew Romanowski, Karen Halliday

Date Published: No date defined

Journal: Plant Physiol

PubMed ID: 29254984

Citation: Plant Physiol. 2018 Feb;176(2):1039-1048. doi: 10.1104/pp.17.01437. Epub 2017 Dec 18.

Created: 28th Jun 2018 at 09:52

Phytochrome B regulates resource allocation in Brassica rapa.

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Abstract (Expand)

Crop biomass and yield are tightly linked to how the light signaling network translates information about the environment into allocation of resources, including photosynthates. Once activated, the ...

Authors: Andrej Arsovski, Jennifer Nemhauser, Zemke J. E.,Haagen B. D.,Kim S. H.

Date Published: No date defined

Journal: J Exp Bot

PubMed ID: 29514292

Citation: J Exp Bot. 2018 May 19;69(11):2837-2846. doi: 10.1093/jxb/ery080.

Created: 28th Jun 2018 at 09:50

Characterization of the Weimberg Pathway in Caulobacter crescentus

XyloCut

(Show All)

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, Celina Tufvegren, Lisa Wasserstrom, Gunnar Liden, Jonsdottir Glaser Sara

Date Published: 1st Jun 2018

Journal: Fermentation

DOI: 10.3390/fermentation4020044

Citation: Fermentation 4(2) : 44

Created: 13th Jun 2018 at 10:49, Last updated: 13th Jun 2018 at 10:51

pSSAlib: The partial-propensity stochastic chemical network simulator

Early Metabolic Injury (LiSyM-EMI - Pillar I)

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

Date Published: 4th Dec 2017

Journal: PLoS Comput Biol

DOI: 10.1371/journal.pcbi.1005865

Citation: PLoS Comput Biol 13(12) : e1005865

Created: 8th Jun 2018 at 17:48, Last updated: 8th Jun 2018 at 17:49

A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule.

Early Metabolic Injury (LiSyM-EMI - Pillar I)

Abstract (Expand)

Bile, the central metabolic product of the liver, is transported by the bile canaliculi network. The impairment of bile flow in cholestatic liver diseases has urged a demand for insights into its ...

Authors: Lutz Brusch, Meyer K.,Ostrenko O.,Bourantas G.,Morales-Navarrete H.,Porat-Shliom N.,Segovia-Miranda F.,Nonaka H.,Ghaemi A.,Verbavatz J. M.,Sbalzarini I.,Kalaidzidis Y.,Weigert R.,Zerial M.

Date Published: No date defined

Journal: Cell Syst

PubMed ID: 28330614

Citation: Cell Syst. 2017 Mar 22;4(3):277-290.e9. doi: 10.1016/j.cels.2017.02.008. Epub 2017 Mar 18.

Created: 8th Jun 2018 at 17:45

Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology.

Early Metabolic Injury (LiSyM-EMI - Pillar I)

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

Date Published: No date defined

Journal: Bioinformatics

PubMed ID: 24443380

Citation: Bioinformatics. 2014 May 1;30(9):1331-2. doi: 10.1093/bioinformatics/btt772. Epub 2014 Jan 17.

Created: 8th Jun 2018 at 17:26

Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis.

Example use cases

Abstract (Expand)

We used parameter scanning to emulate changes to the limiting rate for steps in a fitted model of glucose-derepressed yeast glycolysis. Three flux-control regimes were observed, two of which were under ...

Author: Pritchard L.,Kell D. B.

Date Published: No date defined

Journal: Eur J Biochem

PubMed ID: 12180966

Citation: Eur J Biochem. 2002 Aug;269(16):3894-904.

Created: 11th Apr 2018 at 13:50

Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data.

MESI-STRAT

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

Date Published: No date defined

Journal: J Biol Chem

PubMed ID: 24129579

Citation: J Biol Chem. 2013 Nov 29;288(48):34555-66. doi: 10.1074/jbc.M113.474908. Epub 2013 Oct 15.

Created: 28th Mar 2018 at 23:22

Suppression of indoleamine-2,3-dioxygenase 1 expression by promoter hypermethylation in ER-positive breast cancer.

MESI-STRAT

(Show All)

Abstract (Expand)

Kynurenine formation by tryptophan-catabolic indoleamine-2,3-dioxygenase 1 (IDO1) plays a key role in tumor immune evasion and inhibition of IDO1 is efficacious in preclinical models of breast cancer. ...

Authors: Ines Heiland, Karl-Heinz Kellner, Sarah Schott, Christiane Opitz, Dewi D. L.,Mohapatra S. R.,Blanco Cabanes S.,Adam I.,Somarribas Patterson L. F.,Berdel B.,Kahloon M.,Thurmann L.,Loth S.,Heilmann K.,Weichenhan D.,Mucke O.,Wimberger P.,Kuhlmann J. D.,Plass C.,Platten M.,Gerhauser C.,Trump S.

Date Published: No date defined

Journal: Oncoimmunology

PubMed ID: 28344890

Citation: Oncoimmunology. 2017 Jan 3;6(2):e1274477. doi: 10.1080/2162402X.2016.1274477. eCollection 2017.

Created: 21st Mar 2018 at 14:18

Gene expression profiling of primary male breast cancers reveals two unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel prognostic biomarker.

MESI-STRAT

Abstract (Expand)

INTRODUCTION: Male breast cancer (MBC) is a rare and inadequately characterized disease. The aim of the present study was to characterize MBC tumors transcriptionally, to classify them into comprehensive ...

Author: Johansson I.,Nilsson C.,Berglund P.,Lauss M.,Ringner M.,Olsson H.,Luts L.,Sim E.,Thorstensson S.,Fjallskog M. L.,Hedenfalk I.

Date Published: No date defined

Journal: Breast Cancer Res

PubMed ID: 22333393

Citation: Breast Cancer Res. 2012 Feb 14;14(1):R31. doi: 10.1186/bcr3116.

Created: 19th Mar 2018 at 11:35

Copy number profiling by array comparative genomic hybridization identifies frequently occurring BRCA2-like male breast cancer.

MESI-STRAT

Abstract (Expand)

Genomic aberrations can be used to subtype breast cancer. In this study, we investigated DNA copy number (CN) profiles of 69 cases of male breast cancer (MBC) by array comparative genomic hybridization ...

Author: Biesma H. D.,Schouten P. C.,Lacle M. M.,Sanders J.,Brugman W.,Kerkhoven R.,Mandjes I.,van der Groep P.,van Diest P. J.,Linn S. C.

Date Published: No date defined

Journal: Genes Chromosomes Cancer

PubMed ID: 26355282

Citation: Genes Chromosomes Cancer. 2015 Dec;54(12):734-44. doi: 10.1002/gcc.22284. Epub 2015 Sep 10.

Created: 14th Mar 2018 at 11:09

Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon.

GenoSysFat, DigiSal

(Show All)

Abstract (Expand)

Atlantic salmon migrates from rivers to sea to feed, grow and develop gonads before returning to spawn in freshwater. The transition to marine habitats is associated with dramatic changes in the ...

Authors: Gareth Gillard, Thomas Harvey, Arne Gjuvsland, Yang Jin, Magny Sidsel Thomassen, Jacob Seilø Torgersen, Torgeir R. Hvidsten, Jon Olav Vik, Sandve Simen, Lien S.,Leaver M.

Date Published: No date defined

Journal: Mol Ecol

PubMed ID: 29431879

Citation: Mol Ecol. 2018 Feb 12. doi: 10.1111/mec.14533.

Created: 19th Feb 2018 at 13:18

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics.

de.NBI-SysBio

(Show All)

Abstract (Expand)

SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature ...

Authors: Ulrike Wittig, Maja Rey, Renate Kania, Wolfgang Müller, Weidemann A.

Date Published: No date defined

Journal: Nucleic Acids Res

PubMed ID: 29092055

Citation: Nucleic Acids Res. 2018 Jan 4;46(D1):D656-D660. doi: 10.1093/nar/gkx1065.

Created: 29th Jan 2018 at 09:32

Proteome turnover in the green alga Ostreococcus tauri by time course 15N metabolic labeling mass spectrometry.

Millar group

Abstract (Expand)

Protein synthesis and degradation determine the cellular levels of proteins, and their control hence enables organisms to respond to environmental change. Experimentally, these are little known proteome ...

Author: Martin S. F.,Munagapati V. S.,Salvo-Chirnside E.,Kerr L. E.,Le Bihan T.

Date Published: No date defined

Journal: J Proteome Res

PubMed ID: 22077659

Citation: J Proteome Res. 2012 Jan 1;11(1):476-86. doi: 10.1021/pr2009302. Epub 2011 Dec 1.

Created: 14th Jan 2018 at 23:40

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles.

Millar group

Abstract (Expand)

BACKGROUND: Unicellular cyanobacteria of the genus Cyanothece are recognized for their ability to execute nitrogen (N2)-fixation in the dark and photosynthesis in the light. An understanding of these ...

Author: Aryal U. K.,Stockel J.,Krovvidi R. K.,Gritsenko M. A.,Monroe M. E.,Moore R. J.,Koppenaal D. W.,Smith R. D.,Pakrasi H. B.,Jacobs J. M.

Date Published: No date defined

Journal: BMC Syst Biol

PubMed ID: 22133144

Citation: BMC Syst Biol. 2011 Dec 1;5:194. doi: 10.1186/1752-0509-5-194.

Created: 14th Jan 2018 at 23:38

Stable Core Gut Microbiota across the Freshwater-to-Saltwater Transition for Farmed Atlantic Salmon

GenoSysFat

(Show All)

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

DOI: 10.1128/AEM.01974-17

Citation: Appl Environ Microbiol 84(2) : e01974-17

Created: 9th Jan 2018 at 14:26, Last updated: 9th Jan 2018 at 14:30

Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis.

Millar group

Abstract (Expand)

The diurnal cycle strongly influences many plant metabolic and physiological processes. Arabidopsis thaliana rosettes were harvested six times during 12-h-light/12-h-dark treatments to investigate ...

Author: Blasing O. E.,Gibon Y.,Gunther M.,Hohne M.,Morcuende R.,Osuna D.,Thimm O.,Usadel B.,Scheible W. R.,Stitt M.

Date Published: No date defined

Journal: Plant Cell

PubMed ID: 16299223

Citation: Plant Cell. 2005 Dec;17(12):3257-81. doi: 10.1105/tpc.105.035261. Epub 2005 Nov 18.

Created: 4th Dec 2017 at 22:36

Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes.

Millar group

Abstract (Expand)

The balance between the supply and utilization of carbon (C) changes continually. It has been proposed that plants respond in an acclimatory manner, modifying C utilization to minimize harmful periods ...

Author: Usadel B.,Blasing O. E.,Gibon Y.,Retzlaff K.,Hohne M.,Gunther M.,Stitt M.

Date Published: No date defined

Journal: Plant Physiol

PubMed ID: 18305208

Citation: Plant Physiol. 2008 Apr;146(4):1834-61. doi: 10.1104/pp.107.115592. Epub 2008 Feb 27.

Created: 4th Dec 2017 at 22:35

Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis.

Millar group, TiMet

Abstract (Expand)

Plants use the circadian clock to sense photoperiod length. Seasonal responses like flowering are triggered at a critical photoperiod when a light-sensitive clock output coincides with light or darkness. ...

Author: Flis A.,Sulpice R.,Seaton D. D.,Ivakov A. A.,Liput M.,Abel C.,Millar A. J.,Stitt M.

Date Published: No date defined

Journal: Plant Cell Environ

PubMed ID: 27075884

Citation: Plant Cell Environ. 2016 Sep;39(9):1955-81. doi: 10.1111/pce.12754. Epub 2016 Jul 15.

Created: 4th Dec 2017 at 14:22

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