Assays

What is an Assay?

73 Assays visible to you, out of a total of 75

Progress curve XLA

Computational pathway design for biotechnological applications

Conversion of XLAC to XA by Caulobacter crescentus XLA, measured in NMR.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis XLA

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.979.2

Created: 30th Mar 2019 at 18:41, Last updated: 6th Jan 2020 at 15:17

Progress curve XAD

Computational pathway design for biotechnological applications

Conversion of XA to KDX by Caulobacter crescentus XAD, measured in NMR.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis XAD

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.980.2

Created: 30th Mar 2019 at 18:42, Last updated: 6th Jan 2020 at 15:17

Progress curve KDXD

Computational pathway design for biotechnological applications

Conversion of KDX to KGSA by Caulobacter crescentus KDXD, measured in NMR.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis KDXD

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.981.2

Created: 30th Mar 2019 at 18:43, Last updated: 6th Jan 2020 at 15:17

Progress curve KGSADH

Computational pathway design for biotechnological applications

Conversion of KGSA to KG by Caulobacter crescentus KGSADH, measured in NMR.

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis KGSADH

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.982.2

Created: 30th Mar 2019 at 18:44, Last updated: 6th Jan 2020 at 15:17

Biphasic control can provide mutant resistance to stem-cell homeostatic circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 4D: Biphasic control can provide mutant ...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:32

Biphasic control can provide mutant resistance to stem-cell homeostatic circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 4C: Biphasic control can provide mutant ...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:32, Last updated: 31st Jul 2018 at 10:32

Frequency-dependent selection of mutant pancreatic beta cells.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 2: Frequency-dependent selection of muta...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:31

Biphasic control can resist mutant invasion of feedback circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 1G: Biphasic control can resist mutant i...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:30

Biphasic control can resist mutant invasion of feedback circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 1H: Biphasic control can resist mutant i...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:29

Biphasic control can resist mutant invasion of feedback circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 1D: Biphasic control can resist mutant i...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:29

Biphasic control can resist mutant invasion of feedback circuits.

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Karin et al (2017) Molecular Systems Biology

Study: Figure 1C: Biphasic control can resist mutant i...

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 31st Jul 2018 at 10:28

Frequency doubling in the cyanobacterial circadian clock

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Martins et al (2016) Molecular Systems Biology

Study: Figure 4B: A minimal mathematical model, contai...

Organisms: No organisms

Models: Frequency doubling in the cyanobacterial circad...

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 30th Jul 2018 at 19:17

Frequency doubling in the cyanobacterial circadian clock

Molecular Systems Biology

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Martins et al (2016) Molecular Systems Biology

Study: Figure 6C and D: The clock-sigC circuit represe...

Organisms: No organisms

Models: Frequency doubling in the cyanobacterial circad...

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 30th Jul 2018 at 14:58

gustavsson1-4 models

Yeast glycolytic oscillations

No description specified

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glycolytic oscillations in individual isolated ...

Study: Sustained glycolytic oscillations in individual...

Organisms: No organisms

Models: gustavsson1-4 models

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Jul 2018 at 14:38

gustavsson5 model

Yeast glycolytic oscillations

Model of glycolytic oscillations in individual yeast cells in microfluidic flow chamber

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glycolytic oscillations in individual isolated ...

Study: Allosteric regulation of phosphofructokinase co...

Organisms: No organisms

Models: gustavsson5 model

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Jul 2018 at 14:18

PGK 30C data

SulfoSys, SulfoSys - Biotec

Experimental data for the yeast PGK incubations at 30C, with and without recycling of ATP.

Submitter: Jacky Snoep

Assay type: Metabolite Concentration

Technology type: Technology Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-30C

Organisms: No organisms

SOPs: No SOPs

Data files: PGK yeast with recycling of ATP, PGK yeast without recycling of ATP

Snapshots: No snapshots

Created: 28th Sep 2017 at 10:08, Last updated: 8th Nov 2017 at 14:21

PGK 70 data

SulfoSys, SulfoSys - Biotec

Changes in metabolite concentrations were either quantified via 31P NMR or enzymatically

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: NMR

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-70C

Organisms: No organisms

SOPs: No SOPs

Data files: Sso PGK (14 ug/ml) in presence of recycling sys..., Sso PGK (28 ug/ml) in presence of recycling sys..., Sso PGK in absence of recycling system, 31P NMR..., Sso PGK in presence of ATP recycling system at ...

Snapshots: No snapshots

Created: 28th Sep 2017 at 11:16, Last updated: 8th Nov 2017 at 14:21

BPG degradation

SulfoSys, SulfoSys - Biotec

BPG degradation at 70C

Submitter: Jacky Snoep

Assay type: Metabolite Concentration

Technology type: Technology Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: BPG stability

Organisms: No organisms

SOPs: No SOPs

Data files: BPG degradation at 70

Snapshots: No snapshots

Created: 28th Sep 2017 at 11:17, Last updated: 8th Nov 2017 at 14:21

PGK-GAPDH 30

SulfoSys, SulfoSys - Biotec

No description specified

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-GAPDH 30C & 70C

Organisms: No organisms

SOPs: No SOPs

Data files: PGK-GAPDH 30, 3PG, GAP & BPG, PGK-GAPDH 30, PYR

Snapshots: No snapshots

Created: 28th Sep 2017 at 11:58, Last updated: 8th Nov 2017 at 14:21

PGK-GAPDH 70

SulfoSys, SulfoSys - Biotec

No description specified

Submitter: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-GAPDH 30C & 70C

Organisms: No organisms

SOPs: No SOPs

Data files: PGK-GAPDH 70

Snapshots: No snapshots

Created: 28th Sep 2017 at 12:01, Last updated: 8th Nov 2017 at 14:21

Source data for Figure 2: Experimental time-resolved quantitative immunoblot data

Molecular Systems Biology

No description specified

Submitter: Dawie van Niekerk

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Adlung et al (2017) Molecular Systems Biology

Study: Figure 2: Model calibration with time-resolved ...

Organisms: No organisms

SOPs: No SOPs

Data files: Source data for Figure 2B, Source data for Figure 2C, Source data for Figure 2D, Source data for Figure 2E, Source data for Figure 2F BaF3, Source data for Figure 2F mCFU-E, Source data for Figure 2G BaF3, Source data for Figure 2G mCFU-E

Snapshots: No snapshots

Created: 11th Jan 2017 at 10:38, Last updated: 8th Nov 2017 at 14:21

GAPDH

SulfoSys

Kinetic characterisation of glyceraldehyde 3-phosphate dehydrogenase

Submitter: Jacky Snoep

Assay type: Enzymatic Assay

Technology type: Initial Rate Experiment

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Organisms: Sulfolobus solfataricus

SOPs: Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts

Data files: GAPDH Kinetic Data

Snapshots: No snapshots

Created: 1st Aug 2013 at 11:37, Last updated: 8th Nov 2017 at 14:21

TPI

SulfoSys

Kinetic characterisation of triose phosphate isomerase

Submitter: Jacky Snoep

Assay type: Enzymatic Assay

Technology type: Initial Rate Experiment

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Organisms: Sulfolobus solfataricus

SOPs: Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts

Data files: TPI Kinetic Data

Snapshots: No snapshots

Created: 1st Aug 2013 at 14:02, Last updated: 8th Nov 2017 at 14:21

FBPAase

SulfoSys

Kinetic characterisation of fructose 1,6-bisphosphate aldolase phosphatase

Submitter: Jacky Snoep

Assay type: Enzymatic Assay

Technology type: Initial Rate Experiment

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Organisms: Sulfolobus solfataricus

SOPs: Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts

Data files: FBPAase Kinetic data

Snapshots: No snapshots

Created: 1st Aug 2013 at 14:05, Last updated: 8th Nov 2017 at 14:21

Temperature Degradation of Gluconeogenic Intermediates

SulfoSys

Temperature degradation of BPG, GAP and DHAP

Submitter: Jacky Snoep

Assay type: Metabolite Concentration

Technology type: Technology Type

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Organisms: Sulfolobus solfataricus

SOPs: No SOPs

Data files: Temperature Degradation of Gluconeogenic Interm...

Snapshots: No snapshots

Created: 1st Aug 2013 at 14:15, Last updated: 8th Nov 2017 at 14:21

Experimental Validation Gluconeogenesis in S. solfataricus

SulfoSys

Experimental data for the conversion of 3PG to F6P and the gluconeogenic pathway intermediates

Submitter: Jacky Snoep

Assay type: Metabolite Concentration

Technology type: Technology Type

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Carbon Loss at High Temperature

Organisms: Sulfolobus solfataricus

SOPs: No SOPs

Data files: Experimental Data for Reconstituted Gluconeogen..., Simulation for Reconstituted Gluconeogenic System

Snapshots: No snapshots

Created: 1st Aug 2013 at 14:22, Last updated: 8th Nov 2017 at 14:21

Source data for Figure 3A: Experimental quantitative immunoblotting data.

Molecular Systems Biology

No description specified

Submitter: Dawie van Niekerk

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Bachmann et al (2011) Molecular Systems Biology...

Study: Figure 3A: Model calibration with experimental ...

Organisms: No organisms

SOPs: No SOPs

Data files: Source data for Figure 3A: Experimental quantit...

Snapshots: No snapshots

Created: 3rd Mar 2016 at 10:01, Last updated: 8th Nov 2017 at 14:21

PGK

SulfoSys

Kinetic characterisation of phosphoglycerate kinase

Submitter: Jacky Snoep

Assay type: Enzymatic Assay

Technology type: Initial Rate Experiment

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Organisms: Sulfolobus solfataricus

SOPs: Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts

Data files: PGK Kinetic Data

Snapshots: No snapshots

Created: 1st Aug 2013 at 09:14, Last updated: 8th Nov 2017 at 14:21

Kinetic model of antibiotic-mediated inhibition of ribosomes

Molecular Systems Biology

No description specified

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Srimani et al (2017) Molecular Systems Biology

Study: Figure 2C Panel ii: After the removal of the ex...

Organisms: No organisms

Models: Kinetic model of antibiotic-mediated inhibition...

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 26th Sep 2017 at 09:59, Last updated: 8th Nov 2017 at 14:21

PGK 30C model

SulfoSys, SulfoSys - Biotec

A model for the PGK reaction of yeast in presence or absence of the ATP recycling reactions

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Investigation: Phosphoglycerate kinase acts as a futile cycle ...

Study: PGK-30C

Organisms: No organisms

Models: PGK yeast Fig1a, PGK yeast with/without recycling

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 28th Sep 2017 at 10:28, Last updated: 8th Nov 2017 at 14:21

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