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Katy Wolstencroft

About Katy Wolstencroft:

I am a Research Fellow at the University of Manchester, working in Bioinformatics and Computer Science. I am also a guest researcher at the Vrije Universiteit.My research interests include scientific workflows, semantic discovery, and applying ontology technologies to biological data

SEEK ID: https://demo.fairdomhub.org/people/132

Locations: United Kingdom, Netherlands

Expertise: Data Management, Bioinformatics, Biochemistry

Tools: Ontologies, Taverna, Web services, Workflows, Databases, Transcriptomics, Data Management

ORCID: Not specified

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Related items

SysMO DB

The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:

* facilitates and maximises the potential for data exchange between SysMO research groups;
* maximises the ‘shelf life’ and
...

Programme: SysMO

Public web page: http://www.sysmo-db.org/

SulfoSys

Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Programme: SysMO

Public web page: http://sulfosys.com/

Growth control of the eukaryote cell: a systems biology investigation into yeast
SysMO DB

Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking.

This investigation shows public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Organism: Saccharomyces Cerevisiae

Snapshots: Snapshot 1

Methods for interrelating 'omics data
SysMO DB

This Investigation was performed by SySMO DB team together with PALS in order to crete methods and best practices for capturing experimental data.

Snapshots: No snapshots

Glycolitic Flux in Lactococcus lactis
SysMO DB

An investigation into the control mechanisms of glycolytic flux in Lactococcus lactis.

This investigation represents the data and models published by Hoefnagel et al in JWS Online and in M.H.N. Hoefnagel, J. Hugenholtz and J.L. SnoepMol. Biol. Reports 29, 157-161 (2002)

Snapshots: No snapshots

Glycerol Synthesis in Saccharomyces cerevisiae
SysMO DB

Glycerol, a major by-product of ethanol fermentation by Saccharomyces cerevisiae, is of significant importance to the wine, beer, and ethanol production industries. This investigation aims to gain a clearer understanding of and to quantify the extent to which parameters of the pathway affect glycerol flux in S. cerevisiae.

This investigation represents the data and models submitted to JWS online by Cronwright et al
(http://jjj.biochem.sun.ac.za/cgi-bin/getMoreInfo.py?modeldir=cronwright) and
...

Snapshots: No snapshots

A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth
SysMO DB

Comprehensive high-throughput analyses at the levels of mRNAs, proteins, and metabolites, and studies on gene expression patterns are required for systems biology studies of cell growth [4,26-29]. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth
...

Person responsible: Katy Wolstencroft

Snapshots: No snapshots

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry
SysMO DB

This study examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes.

Person responsible: Jacky Snoep

Snapshots: No snapshots

The effects of Redox Charge on Glycolytic Flux
SysMO DB

A study which combines mathematical modelling and experimental measurements to determine the effects of redox charge on glycolytic flux

Person responsible: Jacky Snoep

Snapshots: No snapshots

Glycerol Synthesis Pathway
SysMO DB

This is a study of the glycerol synthesis pathway, using model predictions and experimental measurements

Person responsible: Katy Wolstencroft

Snapshots: No snapshots

2 hidden items
Changes in flux on the transcriptome
SysMO DB

Assay to measure gene expression of Saccharomyces cerevisiae (yeast) under different nutrient limitations

Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur

This data is public data taken from the BioInvestigation Index.

(http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)

Contributor: Katy Wolstencroft

Assay type: Transcriptional Profiling

Technology type: Microarray

Snapshots: No snapshots

Changes in flux on the metabolome
SysMO DB

Assay to measure metabolites of yeast saccharomyces cerevisiae under different nutrient limitations

Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur

This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)

Contributor: Katy Wolstencroft

Assay type: Metabolite Profiling

Technology type: Mass Spectrometry

Snapshots: No snapshots

Changes in flux on the proteome
SysMO DB

Assay to measure protein expression in yeast saccharomyces cerevisiae under different nutrient limitations

Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur

This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)

Contributor: Katy Wolstencroft

Assay type: Protein Expression Profiling

Technology type: Mass Spectrometry

Snapshots: No snapshots

Time course analysis of transcription
SysMO DB

Assay for transcriptional profiling time course in yeast treated with rapamycin

This is public data from the BioInvestigation Index (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-2)

Contributor: Katy Wolstencroft

Assay type: Transcriptional Profiling

Technology type: Microarray

Snapshots: No snapshots

NAD+ and NADH Kinetics, using 13C NMR
SysMO DB
No description specified

Contributor: Katy Wolstencroft

Assay type: Glucose Pulse

Technology type: NMR

Snapshots: No snapshots

1 hidden item
Neves_timeSeries
SysMO DB
No description specified

Creator: Jacky Snoep

Contributor: Katy Wolstencroft

Download
Cronwright Parameter Data
SysMO DB

Intracellular metabolite measurements used for validation of the gycerol synthesis pathway model

Creator: Jacky Snoep

Contributor: Katy Wolstencroft

a_microarray from BII-S-2
SysMO DB

Results of transcriptional profile in Saccharomyces cerevisiae after rapamycin treatment

Creator: Katy Wolstencroft

Contributor: Katy Wolstencroft

a_proteome from BII-S-1
SysMO DB

Results of proteomics profile in Saccharomyces cerevisiae under different experimental conditions

Creator: Katy Wolstencroft

Contributor: Katy Wolstencroft

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a_metabolome_BII-S-1
SysMO DB

results of metabolic profiling of Saccharomyces cerevisiae in different conditions

Creator: Katy Wolstencroft

Contributor: Katy Wolstencroft

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2 hidden items
Lactococcus lactis glycolysis
SysMO DB

Detailed kinetic model for glycolysis of L. lactis. The model is basically the same model as that published by Hoefnagel et al 2002 (Mol. Biol. Reports 29, 157-161). The change made to the model is to make external glucose a variable such that a glucose pulse can be simulated.

Creators: Jacky Snoep, Ana Rute Neves

Contributor: Katy Wolstencroft

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Metabolic Control Analysis of Glycerol Synthesis in Saccharomyces cerevisiae
SysMO DB

MCA of Glycerol Synthesis in Saccharomyces cerevisiae

Creators: Jacky Snoep, Garth R. Cronwright, Johann M. Rohwer, and Bernard A. Prior

Contributor: Katy Wolstencroft

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Nutrient_limited_stationary
SysMO DB

A stationary-phase culture (10ml) was used to inoculate the fermenter vessel.

Taken from ArrayExpress:
http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MEXP-115

Creator: Katy Wolstencroft

Contributor: Katy Wolstencroft

Download
2 hidden items
Metabolic control analysis of glycerol synthesis in Saccharomyces cerevisiae
SysMO DB

Abstract (Expand)

Glycerol, a major by-product of ethanol fermentation by Saccharomyces cerevisiae, is of significant importance to the wine, beer, and ethanol production industries. To gain a clearer understanding of … and to quantify the extent to which parameters of the pathway affect glycerol flux in S. cerevisiae, a kinetic model of the glycerol synthesis pathway has been constructed. Kinetic parameters were collected from published values. Maximal enzyme activities and intracellular effector concentrations were determined experimentally. The model was validated by comparing experimental results on the rate of glycerol production to the rate calculated by the model. Values calculated by the model agreed well with those measured in independent experiments. The model also mimics the changes in the rate of glycerol synthesis at different phases of growth. Metabolic control analysis values calculated by the model indicate that the NAD(+)-dependent glycerol 3-phosphate dehydrogenase-catalyzed reaction has a flux control coefficient (C(J)v1) of approximately 0.85 and exercises the majority of the control of flux through the pathway. Response coefficients of parameter metabolites indicate that flux through the pathway is most responsive to dihydroxyacetone phosphate concentration (R(J)DHAP= 0.48 to 0.69), followed by ATP concentration (R(J)ATP = -0.21 to -0.50). Interestingly, the pathway responds weakly to NADH concentration (R(J)NADH = 0.03 to 0.08). The model indicates that the best strategy to increase flux through the pathway is not to increase enzyme activity, substrate concentration, or coenzyme concentration alone but to increase all of these parameters in conjunction with each other.

Authors: Garth R Cronwright, Johann M Rohwer, Bernard A Prior

Date Published: 30th Aug 2002

Journal: Appl. Environ. Microbiol.

Is the glycolytic flux in Lactococcus lactis primarily controlled by the redox charge? Kinetics of NAD(+) and NADH pools determined in vivo by 13C NMR
SysMO DB

Abstract (Expand)

The involvement of nicotinamide adenine nucleotides (NAD(+), NADH) in the regulation of glycolysis in Lactococcus lactis was investigated by using (13)C and (31)P NMR to monitor in vivo the kinetics … of the pools of NAD(+), NADH, ATP, inorganic phosphate (P(i)), glycolytic intermediates, and end products derived from a pulse of glucose. Nicotinic acid specifically labeled on carbon 5 was synthesized and used in the growth medium as a precursor of pyridine nucleotides to allow for in vivo detection of (13)C-labeled NAD(+) and NADH. The capacity of L. lactis MG1363 to regenerate NAD(+) was manipulated either by turning on NADH oxidase activity or by knocking out the gene encoding lactate dehydrogenase (LDH). An LDH(-) deficient strain was constructed by double crossover. Upon supply of glucose, NAD(+) was constant and maximal (approximately 5 mm) in the parent strain (MG1363) but decreased abruptly in the LDH(-) strain both under aerobic and anaerobic conditions. NADH in MG1363 was always below the detection limit as long as glucose was available. The rate of glucose consumption under anaerobic conditions was 7-fold lower in the LDH(-) strain and NADH reached high levels (2.5 mm), reflecting severe limitation in regenerating NAD(+). However, under aerobic conditions the glycolytic flux was nearly as high as in MG1363 despite the accumulation of NADH up to 1.5 mm. Glyceraldehyde-3-phosphate dehydrogenase was able to support a high flux even in the presence of NADH concentrations much higher than those of the parent strain. We interpret the data as showing that the glycolytic flux in wild type L. lactis is not primarily controlled at the level of glyceraldehyde-3-phosphate dehydrogenase by NADH. The ATP/ADP/P(i) content could play an important role.

Authors: Ana Rute Neves, Rita Ventura, Nahla Mansour, Claire Shearman, Michael J Gasson, Christopher Maycock, Ana Ramos, Helena Santos

Date Published: 13th May 2002

Journal: J. Biol. Chem.

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry
SysMO DB

Abstract (Expand)

This paper examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes. In nongrowing, anaerobic, compressed … Saccharomyces cerevisiae the values of the kinetic parameters of most glycolytic enzymes were determined. For the other enzymes appropriate literature values were collected. By inserting these values into a kinetic model for glycolysis, fluxes and metabolites were calculated. Under the same conditions fluxes and metabolite levels were measured. In our first model, branch reactions were ignored. This model failed to reach the stable steady state that was observed in the experimental flux measurements. Introduction of branches towards trehalose, glycogen, glycerol and succinate did allow such a steady state. The predictions of this branched model were compared with the empirical behavior. Half of the enzymes matched their predicted flux in vivo within a factor of 2. For the other enzymes it was calculated what deviation between in vivo and in vitro kinetic characteristics could explain the discrepancy between in vitro rate and in vivo flux.

Authors: Firstname Lastname, J Passarge, C A Reijenga, E Esgalhado, C C van der Weijden, M Schepper, M C Walsh, B M Bakker, K van Dam, H V Westerhoff, Jacky Snoep

Date Published: 22nd Aug 2000

Journal: Eur. J. Biochem.

Taverna: a tool for building and running workflows of services
SysMO DB

Abstract (Expand)

Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians … to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from http://taverna.sourceforge.net/.

Authors: Duncan Hull, Katy Wolstencroft, Robert Stevens, Firstname Lastname, Mathew R Pocock, Peter Li, Tom Oinn

Date Published: 18th Jul 2006

Journal: Nucleic Acids Res.

Storing and annotating of kinetic data
SysMO DB

Abstract (Expand)

This paper briefly describes the SABIO-RK database model for the storage of reaction kinetics information and the guidelines followed within the SABIO-RK project to annotate the kinetic data. Such … annotations support the definition of cross links to other related databases and augment the semantics of the data stored in the database.

Authors: Firstname Lastname, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Ulrike Wittig

Date Published: 14th Sep 2007

Journal: In Silico Biol. (Gedrukt)

SysMO-db Presentation from ISMB
SysMO DB
No description specified

Creator: Katy Wolstencroft

Contributor: Katy Wolstencroft

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