Jay Moore

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About Jay Moore:

Systems Biologist specialising in data integration, high-throughput sequence analysis, and evolutionary and comparative analyses.

SEEK ID: https://fairdomhub.org/people/175

Location: United Kingdom

ORCID: Not specified

Joined: 7th Apr 2009

Expertise: Bioinformatics, Software Engineering, Systems Biology, Comparative Genomics, Database and data warehouse design, High-throughput sequence analysis, Phylogenetics, Data Integration

Tools: SBML, Databases, Perl, R, EnsEMBL, BioMart, HTML, XML

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SysMO

SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".

The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.

Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...

Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep

Web page: http://sysmo.net/

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STREAM

Global metabolic switching in Streptomyces coelicolor

Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.

Programme: SysMO

Public web page: Not specified

Organisms: Streptomyces coelicolor

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University of Warwick

Country: United Kingdom

City: Not specified

Web page: Not specified

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Metabolism of Streptomyces coelicolor (SysMO STREAM)

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One of these activities is antibiotic production and is widespread in streptomycetes ...

Submitter: Jay Moore

Studies: ScoCyc metabolic pathway curation, Timeseries 1

Assays: Metabolic pathway curation, Online/offline measurements, metabolomics, proteomics, transcriptomics

Snapshots: No snapshots

Created: 26th May 2010 at 13:44, Last updated: 3rd Dec 2016 at 21:28

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ScoCyc metabolic pathway curation

STREAM, SYSTERACT

No description specified

Submitter: Jay Moore

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Assays: Metabolic pathway curation

Snapshots: No snapshots

Created: 4th Nov 2010 at 14:30, Last updated: 2nd Nov 2016 at 08:38

Timeseries 1

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Genotype: Wildtype (M145E) Medium: Phosphate-limited (F134)

Submitter: Jay Moore

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Assays: Online/offline measurements, metabolomics, proteomics, transcriptomics

Snapshots: No snapshots

Created: 26th May 2010 at 13:47, Last updated: 2nd Nov 2016 at 08:38

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Online/offline measurements

STREAM, SYSTERACT

No description specified

Submitter: Jay Moore

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Study: Timeseries 1

Organisms: Streptomyces coelicolor : M145 (wild-type / wild-type)

SOPs: Cell dry weight (CDW) determination of Streptom..., Contamination test of Streptomyces coelicolor c..., Generation of cell material from Streptomyces c..., Generation of cell material from Streptomyces c..., Generation of cell material from Streptomyces c..., Preparation of inoculum for Streptomyces coelic..., Sampling from Streptomyces coelicolor culture f... and 1 hidden item

Data files: Fermentor 199 cultivation data

Snapshots: No snapshots

Created: 26th May 2010 at 13:59, Last updated: 8th Nov 2017 at 14:21

transcriptomics

STREAM, SYSTERACT

No description specified

Submitter: Jay Moore

Assay type: Transcriptomics

Technology type: Custom Array

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Study: Timeseries 1

Organisms: Streptomyces coelicolor : M145 (wild-type / wild-type)

SOPs: No SOPs

Data files: Fermentor 199 transcriptomics

Snapshots: No snapshots

Created: 26th May 2010 at 14:23, Last updated: 8th Nov 2017 at 14:21

metabolomics

STREAM, SYSTERACT

No description specified

Submitter: Jay Moore

Assay type: Metabolite Profiling

Technology type: Gas Chromatography Mass Spectrometry

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Study: Timeseries 1

Organisms: Streptomyces coelicolor : M145 (wild-type / wild-type)

SOPs: MCF derivatization, Metabolome extraction, Spore batch generation

Data files: 1 hidden item

Snapshots: No snapshots

Created: 4th Nov 2010 at 13:50, Last updated: 8th Nov 2017 at 14:21

proteomics

STREAM, SYSTERACT

No description specified

Submitter: Jay Moore

Assay type: Proteomics

Technology type: Gas Chromatography Mass Spectrometry

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Study: Timeseries 1

Organisms: Streptomyces coelicolor : M145 (wild-type / wild-type)

SOPs: No SOPs

Data files: 2 hidden items

Snapshots: No snapshots

Created: 4th Nov 2010 at 13:53, Last updated: 8th Nov 2017 at 14:21

Metabolic pathway curation

STREAM, SYSTERACT

No description specified

Submitter: Jay Moore

Biological problem addressed: Metabolic Network

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Study: ScoCyc metabolic pathway curation

Organisms: Streptomyces coelicolor : M145 (wild-type / wild-type)

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 4th Nov 2010 at 14:34, Last updated: 8th Nov 2017 at 14:21

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A3(2)

Submitter: Jay Moore

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Streptomyces coelicolor

Genotypes: wild-type

Phenotypes: wild-type

Comment: Not specified

Created: 28th Apr 2010 at 16:21, Last updated: 19th Oct 2012 at 15:57

M145

Submitter: Jay Moore

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Streptomyces coelicolor

Genotypes: wild-type

Phenotypes: wild-type

Comment: Not specified

Created: 28th Apr 2010 at 16:21, Last updated: 19th Oct 2012 at 15:57

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Fermentor 199 cultivation data

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Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel

Submitter: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST...

Studies: Timeseries 1

Assays: Online/offline measurements

Created: 4th Nov 2010 at 13:41, Last updated: 5th Dec 2016 at 12:21

Fermentor 199 transcriptomics

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No description specified

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST...

Studies: Timeseries 1

Assays: transcriptomics

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Created: 4th Nov 2010 at 13:35, Last updated: 3rd Dec 2016 at 19:37

ScoCyc 14.5 release bundle

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Creators: Jay Moore, David Hodgson

Submitter: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 15th Nov 2010 at 14:41, Last updated: 15th Nov 2010 at 14:42

ScoCyc 14.6 release bundle

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Creators: Jay Moore, David Hodgson

Submitter: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 15th Nov 2010 at 14:40, Last updated: 15th Nov 2010 at 14:40

4 hidden items

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ScoCyc 14.5 release bundle

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Creators: Jay Moore, David Hodgson, Veronica Armendarez, Emma Laing , Govind Chandra, Mervyn Bibb

Submitter: Jay Moore

Model type: Metabolic network

Model format: BioPAX

Environment: Not specified

Organism: Streptomyces coelicolor

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 15th Nov 2010 at 14:43, Last updated: 15th Nov 2010 at 14:49

1 hidden item

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Spore batch generation

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Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel

Submitter: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST... and 1 hidden item

Studies: Timeseries 1 and 2 hidden items

Assays: metabolomics and 2 hidden items

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Created: 4th Nov 2010 at 14:10, Last updated: 4th Nov 2010 at 14:11

Metabolome extraction

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Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel

Submitter: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST...

Studies: Timeseries 1

Assays: metabolomics

Download

Created: 4th Nov 2010 at 14:10

MCF derivatization

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Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel

Submitter: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST...

Studies: Timeseries 1

Assays: metabolomics

Created: 4th Nov 2010 at 14:08

Proteomic Analysis of the Streptomyces coelicolor Proteome

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Creators: Louise Thomas, Maggie Smith

Submitter: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 26th May 2010 at 15:30

Total DNA Quantification

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Creators: Louise Thomas, Maggie Smith

Submitter: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 26th May 2010 at 15:29

Total RNA Quantification

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Creators: Louise Thomas, Maggie Smith

Submitter: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 26th May 2010 at 15:29

Total Protein Quantification

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Creators: Louise Thomas, Maggie Smith

Submitter: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 26th May 2010 at 15:28

Processing Streptomyces coelicolor cell pellets

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Creators: Louise Thomas, Maggie Smith

Submitter: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 26th May 2010 at 15:27

Contamination test of Streptomyces coelicolor culture

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Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A

Submitter: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST... and 1 hidden item

Studies: Timeseries 1 and 8 hidden items

Assays: Online/offline measurements and 8 hidden items

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Created: 26th May 2010 at 15:24, Last updated: 26th May 2010 at 15:24

Generation of cell material from Streptomyces coelicolor culture for metabolome analysis

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Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A

Submitter: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST... and 1 hidden item

Studies: Timeseries 1 and 8 hidden items

Assays: Online/offline measurements and 8 hidden items

Download

Created: 26th May 2010 at 15:23

Generation of cell material from Streptomyces coelicolor culture for transcriptome analysis

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Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A

Submitter: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST... and 1 hidden item

Studies: Timeseries 1 and 8 hidden items

Assays: Online/offline measurements and 8 hidden items

Download

Created: 26th May 2010 at 15:22

Generation of cell material from Streptomyces coelicolor culture for proteome analysis

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No description specified

Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A

Submitter: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST... and 1 hidden item

Studies: Timeseries 1 and 8 hidden items

Assays: Online/offline measurements and 8 hidden items

Download

Created: 26th May 2010 at 15:20

Cell dry weight (CDW) determination of Streptomyces coelicolor culture

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No description specified

Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A

Submitter: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST... and 1 hidden item

Studies: Timeseries 1 and 8 hidden items

Assays: Online/offline measurements and 8 hidden items

Download

Created: 26th May 2010 at 15:19, Last updated: 26th May 2010 at 15:19

Sampling from Streptomyces coelicolor culture for subsequent offline analyses

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No description specified

Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A

Submitter: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST... and 1 hidden item

Studies: Timeseries 1 and 8 hidden items

Assays: Online/offline measurements and 8 hidden items

Download

Created: 26th May 2010 at 15:17

Preparation of inoculum for Streptomyces coelicolor cultivation

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No description specified

Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A

Submitter: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST... and 1 hidden item

Studies: Timeseries 1 and 8 hidden items

Assays: Online/offline measurements and 8 hidden items

Download

Created: 26th May 2010 at 15:15

1 hidden item

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Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

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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: , , The STREAM Consortium (stream), , , ,

Date Published: 2010

Publication Type: Not specified

DOI: 10.1186/1471-2164-11-202

Citation:

Created: 26th May 2010 at 13:17, Last updated: 8th Dec 2022 at 17:25

The dynamic architecture of the metabolic switch in Streptomyces coelicolor

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BACKGROUND: During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene …

Authors: , Florian Battke, Alexander Herbig, , , , , , , , , Edward R Morrissey, Miguel A Juarez-Hermosillo, , Merle Nentwich, , Mudassar Iqbal, , , , , , , , Michael Bonin, , , , , , , , , ,

Date Published: 28th May 2009

Publication Type: Not specified

PubMed ID: 20053288

Citation:

Created: 26th May 2010 at 13:21, Last updated: 8th Dec 2022 at 17:25

Chapter 6. Regulation of antibiotic production by bacterial hormones

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Abstract (Expand)

Antibiotic production is regulated by numerous signals, including the so-called bacterial hormones found in antibiotic producing organisms such as Streptomyces. These signals, the gamma-butyrolactones, …

Authors: Nai-Hua Hsiao, Marco Gottelt,

Date Published: 21st Apr 2009

Publication Type: Not specified

PubMed ID: 19374982

Citation:

Created: 26th May 2010 at 14:42, Last updated: 8th Dec 2022 at 17:25

Probabilistic assignment of formulas to mass peaks in metabolomics experiments

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Abstract (Expand)

MOTIVATION: High-accuracy mass spectrometry is a popular technology for high-throughput measurements of cellular metabolites (metabolomics). One of the major challenges is the correct identification …

Authors: Simon Rogers, Richard A Scheltema, Mark Girolami,

Date Published: 18th Dec 2008

Publication Type: Not specified

PubMed ID: 19095699

Citation:

Created: 26th May 2010 at 15:08, Last updated: 8th Dec 2022 at 17:25

An approach to pathway reconstruction using whole genome metabolic models and sensitive sequence searching

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Abstract (Expand)

Metabolic models have the potential to impact on genome annotation and on the interpretation of gene expression and other high throughput genome data. The genome of Streptomyces coelicolor genome has …

Authors: Mansoor Saqi, Richard J B Dobson, Preben Kraben, ,

Date Published: 13th Nov 2008

Publication Type: Not specified

PubMed ID: 20134075

Citation:

Created: 27th May 2010 at 16:59, Last updated: 8th Dec 2022 at 17:25

Increasing the mass accuracy of high-resolution LC-MS data using background ions: a case study on the LTQ-Orbitrap

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Abstract (Expand)

With the advent of a new generation of high-resolution mass spectrometers, the fields of proteomics and metabolomics have gained powerful new tools. In this paper, we demonstrate a novel computational …

Authors: Richard A Scheltema, Anas Kamleh, David Wildridge, Charles Ebikeme, David G Watson, Michael P Barrett, ,

Date Published: 22nd Oct 2008

Publication Type: Not specified

PubMed ID: 18937253

Citation:

Created: 26th May 2010 at 15:08, Last updated: 8th Dec 2022 at 17:25

A bistable gene switch for antibiotic biosynthesis: the butyrolactone regulon in Streptomyces coelicolor

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Abstract (Expand)

Many microorganisms, including bacteria of the class Streptomycetes, produce various secondary metabolites including antibiotics to gain a competitive advantage in their natural habitat. The production … of these compounds is highly coordinated in a population to expedite accumulation to an effective concentration. Furthermore, as antibiotics are often toxic even to their producers, a coordinated production allows microbes to first arm themselves with a defense mechanism to resist their own antibiotics before production commences. One possible mechanism of coordination among individuals is through the production of signaling molecules. The gamma-butyrolactone system in Streptomyces coelicolor is a model of such a signaling system for secondary metabolite production. The accumulation of these signaling molecules triggers antibiotic production in the population. A pair of repressor-amplifier proteins encoded by scbA and scbR mediates the production and action of one particular gamma-butyrolactone, SCB1. Based on the proposed interactions of scbA and scbR, a mathematical model was constructed and used to explore the ability of this system to act as a robust genetic switch. Stability analysis shows that the butyrolactone system exhibits bistability and, in response to a threshold SCB1 concentration, can switch from an OFF state to an ON state corresponding to the activation of genes in the cryptic type I polyketide synthase gene cluster, which are responsible for production of the hypothetical polyketide. The switching time is inversely related to the inducer concentration above the threshold, such that short pulses of low inducer concentration cannot switch on the system, suggesting its possible role in noise filtering. In contrast, secondary metabolite production can be triggered rapidly in a population of cells producing the butyrolactone signal due to the presence of an amplification loop in the system. S. coelicolor was perturbed experimentally by varying concentrations of SCB1, and the model simulations match the experimental data well. Deciphering the complexity of this butyrolactone switch will provide valuable insights into how robust and efficient systems can be designed using "simple" two-protein networks.

Authors: Sarika Mehra, Salim Charaniya, , Wei-Shou Hu

Date Published: 2nd May 2008

Publication Type: Not specified

PubMed ID: 18628968

Citation:

Created: 26th May 2010 at 13:26, Last updated: 8th Dec 2022 at 17:25

New surveyor tools for charting microbial metabolic maps

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Abstract (Expand)

The computational reconstruction and analysis of cellular models of microbial metabolism is one of the great success stories of systems biology. The extent and quality of metabolic network reconstructions …

Authors: , Dennis Vitkup, Michael P Barrett

Date Published: 21st Nov 2007

Publication Type: Not specified

PubMed ID: 18026122

Citation:

Created: 26th May 2010 at 14:43, Last updated: 8th Dec 2022 at 17:25

MetaNetter: inference and visualization of high-resolution metabolomic networks

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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: Fabien Jourdan, , Michael P Barrett, David Gilbert

Date Published: 14th Nov 2007

Publication Type: Not specified

PubMed ID: 18003642

Citation:

Created: 26th May 2010 at 14:44, Last updated: 8th Dec 2022 at 17:25