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Meng Sun*, Jolie M. Phan*, Nathan S. Kieswetter, Krystle K.Q. Yu, Malisa T. Smith, Huang Huang, Sanjana Gupta, Gerlinde Obermoser, Holden Terry Maecker, Akshaya Krishnan, Neha Gupta, Mary Rieck, Peter Acs, Mustafa Ghanizada, Shin-Heng Chiou, Purvesh Khatri, W. Henry Boom, Thomas R. Hawn, Catherine M. Stein, Harriet Mayanja-Kizza, Mark M. Davis*, Chetan Seshadri*
Abstract: A subset of individuals with a high probability of exposure to M. tuberculosis (M.tb) ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Patient Visit - Metadata, Tissue Collection - Metadata
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where the light accumulator (acc) has been eliminated by replacing it with immediate light input. This model was used to generate Figure 2F in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to environmental signals. New Phytologist. Originally ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, acc immediate - PLM_83, version 1
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where the light accumulator (acc) has been eliminated by setting its value to 1. This model was used to generate Figure 2F in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to environmental signals. New Phytologist. Originally submitted to ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, acc on - PLM_84, version 1
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of CCA1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2B in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, CCA1 degr D - PLM_86, version 1
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of CCA1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2B in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, CCA1 degr L - PLM_85, version 1
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the transcription rate of CCA1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2C in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, CCA1 prod D - PLM_88, version 1
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the transcription rate of CCA1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2C in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, CCA1 prod L - PLM_87, version 1
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the activation rate of TOC1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2E in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, TOC1 act D - PLM_92, version 1
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the activation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2E in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, TOC1 act L - PLM_91, version 1
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, TOC1 degr D - PLM_90, version 1
This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related Publications Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 1, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 2
Key enzymes of critical points in the pathways will be targeted for disruption by the generation of RNAi cell lines and lines which drive tetracycline-regulatable ectopic over expression of either wild type enzyme or, if appropriate, dominant-negative or mis-targeted mutants of these. In all cases perturbed lines will be analysed with respect to the mRNA, protein or enzymatic activities of other components of the subsystem, this being directed iteratively by the predictions from systems modelling. ...
We have already demonstrated that the key metabolites of polyamine biosynthesis (arginine, ornithine, putrescine and spermidine) can be identified using HILIC chromatography coupled to the Orbitrap mass spectrometer, as can glycine, glutamate and cysteine used in glutathione biosynthesis, glutathionyl spermidine and trypanothione itself. Furthermore the key metabolites of the methionine cycle (methionine, S-adenosyl methionine, decarboxylated S-adenosyl methionine, methylthioadenosine) can all ...
Submitter: Dong-Hyun Kim
Investigation: Metabolite profiling, quantification and flux q...
Assays: Intracellular metabolite concentrations in T. brucei under pH stress
This study aims to establish the optimum conditions and assay methods for measuring ATP levels
Submitter: Martin Valachovic
Investigation: Effect of Benzoic Acid on ATP Levels
Assays: Compare ATP extraction methods
Standard growth conditions and standard 'wild-type' Arabidopsis accession, with biomass data for whole rosettes, and in some cases, individual leaf area and leaf biomass data
Submitter: Andrew Millar
Investigation: Arabidopsis Framework Model v1, predicting rose...
Assays: Growth of Col-0 in 12hL:12hD
Altering the light:dark cycle of standard growth conditions and standard 'wild-type' Arabidopsis accession, with sucrose, starch and biomass data for whole rosettes
Submitter: Andrew Millar
Investigation: Arabidopsis Framework Model v1, predicting rose...
Standard growth conditions and 'wild-type' Arabidopsis accessions other than Col-0 and the 35S:miR156 transgenics, with biomass data for whole rosettes, and in some cases, individual leaf area and leaf biomass data
Follow-up to the validation experiments on FMv2, testing candidate mechanisms for high malate and fumarate accumulation in the Arabidopsis double mutant prr7prr9 and its parent accession Col. New collaborations with the groups of Teresa Fitzpatrick and TiMet partner Samuel Zeeman.
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Assimilation and partitioning of 14CO2 at night, Thiamine vitamers
Model simulations compared to experimental data from the literature (publications from Mizuno lab are linked), testing the FMv2.
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Mizuno lab, Flowering time in clock mutants, Mizuno lab, Hypocotyl length in clock mutants
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Biomass, leaf number and metabolites, FMv2 simulation
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Biomass and metabolites, FMv2 simulation
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Biomass and metabolites, FMv2 simulation
Assorted files prepared during the publication process of the FMv2, its validation and testing, mostly focussed on the Arabidopsis double mutant prr7prr9 and its parent accession Col. Data from other studies that are described separately, and linked by Atribution to the File records under this Study.
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Interspecies differences in sensitivity to chemical exposures pose a great challenge in toxicological risk assessments. How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical ...
Submitter: Sofie Söderström
Investigation: 1 hidden item
Assays: Chemical defensome genes for five fish species, Exposure response of defensome genes, Expression of defensome genes in early development of fish
Submitter: Matthew Rolfe
Investigation: Dynamical studies for different oxygen availabi...
Assays: Transcriptional profiling of E. coli during anaerobic to aerobic and aer...
Submitter: Michael Ederer
Investigation: Steady state studies for different oxygen avail...
Assays: ArcA phosphorylation at different aerobiosis levels (steady states), Determination of intracellular redox state by means of NAD/NADH ratio, Determination of intracellular redox state by means of ubiquinones (oxd/..., FNR activity at different aerobiosis levels (steady state), Literature Data from Alexeeva et al., J. Bacteriol., 2000, 2002, 2003, Measurement of cytochrome numbers, Physiological measurements from Sheffield chemostat, Steady State Oxygen Response of E. coli WT and two Electron Transport Ch..., Transcriptional profiling of steady states at different aerobiosis levels
Submitter: Yi Chen
Investigation: Exploring the Evolution of the Gene Ontology an...
For cells to accurately read out the genomic content, high fidelity during transcription is required. This is mainly established by the accuracy of the active centre of RNA polymerase (RNAP). Based on in vitro experiments with Escherichia coli RNAP it was also suggested that proofreading of transcription via RNA hydrolysis by RNAP may contribute to overall fidelity and processivity. RNAP’s intrinsic cleavage activity is stimulated by the highly conserved Gre factors suggesting that Gre factors ...
Submitter: Jan-Willem Veening
Investigation: Wetlab approach to transcription fidelity
Assays: RNA-Seq
Genotype: Wildtype (M145E) Medium: Phosphate-limited (F134)
Submitter: Jay Moore
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Assays: Online/offline measurements, metabolomics, proteomics, transcriptomics
TiMet flower specific protein detection network
Originally submitted to PLaSMo on 2012-03-02 12:39:54
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 flower specific protein detection network - PLM_57, version 1
Trial upload of the pollen netwrok from TiMet
Originally submitted to PLaSMo on 2012-02-27 12:17:46
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 Pollen network - PLM_54, version 1, TiMet 2011 Pollen network - PLM_54, version 2
PP interaction network exported from Cytoscape in XGMML
Originally submitted to PLaSMo on 2012-03-02 12:32:33
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 PP interaction network - PLM_56, version 1
Test for root network
Originally submitted to PLaSMo on 2012-02-27 14:24:59
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
The seed network, uploaded as a test from Cytoscape
Originally submitted to PLaSMo on 2012-02-24 11:41:50
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 seed network - PLM_53, version 1, TiMet 2011 seed network - PLM_53, version 2
Cytoscape shoot specific diurnal transcript oscillation.
Originally submitted to PLaSMo on 2012-03-02 12:42:30
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_5...
Cytoscape silqueue specific protein detection
Originally submitted to PLaSMo on 2012-03-02 12:44:13
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 silqueue specific protein detection network - PLM_59, version 1
To allow detailed visual analysis of the overall system and its parts, we used a customised version of our Vanted add-on LMME (Large Metabolic Model Explorer) to construct an overview graph showing one node per pathway and the respective interconnecting species. We performed a comprehensive analysis of node centralities on two levels: on the level of the individual pathways as well as on the level of an aggregated network which is composed of the individual pathways. This allows detailed ...
Submitter: Felicia Burtscher
Investigation: Graphical exploration and topological analysis
Assays: No Assays
Multi experimental approach to define the gene expression remodelling under potassium starvation conditions.
Submitter: Falko Krause
Investigation: K+ Starvation in Saccharomyces cerevisiae
Assays: LacZ Reporters, RT-PCR, Time Course Micro Array Experiment
Submitter: Falko Krause
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Assays: No Assays
Annotation retrieval
Submitter: Praveen kumar Sappa
Investigation: Redefining the Complete Transcriptome of Bacill...
Assays: Tiling Array analysis of glucose strarved B. subtilis cells
Growth of B.subtilis in shakeflask at 57°C; 16°C, 37°C(Control) and 1,2M NaCl in SMM.
Submitter: Praveen kumar Sappa
Investigation: Redefining the Complete Transcriptome of Bacill...
Assays: Tiling array analysis of continuous growth stress conditions in SMM
BMM EtOH, 16, 57 SMM NaCl
Submitter: Praveen kumar Sappa
Investigation: Redefining the Complete Transcriptome of Bacill...
Studies on the effect of deletion of genes encoding 14-3-3 proteins on the transcriptional response of yeast cells to potassium starvation.
Submitter: Falko Krause
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Assays: No Assays
Contains copy number per locus tag at different times of Growth between 0.25h and 96 hours. M. pneumoniae was grown in Batch, cells attached to the bottom of the flask (single cell layer), non stirred, non aerated.
Submitter: Niels Zondervan
Investigation: Modelling of M. pneumoniae metabolism
Assays: Transcriptomics assay of M. pneumoniae at diferent times of growth
Experiments using shake flask cultures to measure dynamics associated with sigB response.
Submitter: Ulf Liebal
Investigation: The transition from growing to non-growing Baci...
Assays: No Assays
"TRIFFID (Top-down Representation of Interactive Foliage and Flora Including Dynamics)" is a dynamic global vegetation model, which updates the plant distribution and soil carbon based on climate-sensitive CO2 fluxes at the land-atmosphere interface. The surface CO2 fluxes associated with photosynthesis and plant respiration are calculated in the MOSES 2 tiled land-surface scheme (Essery et al (In preparation)), on each atmospheric model timestep (normally 30 minutes), for each of 5 plant functional ...
This is a model of the circadian clock of Ostreococcus tauri, with a single negative feedback loop between TOC1 and CCA1 (a.k.a. LHY), and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011). The model has been tested in Copasi, where it reproduces the behaviour of the original (which consisted of equations loaded from a text file by a more or less custom C++ program).
Originally submitted to PLaSMo on 2010-05-04 11:27:33
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: Troein Ostreococcus clock 1-loop - PLM_7, version 1, Troein Ostreococcus clock 1-loop - PLM_7, version 2
Chemical structures, physicochemical properties and biological results for the compounds of the Ty-Box library