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Jay Moore

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

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

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

ORCID: Not specified

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Project positions

STREAM (University of Warwick)

Related items

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

University of Warwick

Country:  United Kingdom

City: Not specified

Web page: Not specified

Metabolism of Streptomyces coelicolor (SysMO STREAM)
STREAM, SYSTERACT

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.

One of these activities is antibiotic production and is widespread in streptomycetes
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ScoCyc metabolic pathway curation
STREAM, SYSTERACT
No description specified

Person responsible: Jay Moore

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Timeseries 1
STREAM, SYSTERACT

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

Person responsible: Jay Moore

Snapshots: No snapshots

proteomics
STREAM, SYSTERACT
No description specified

Contributor: Jay Moore

Assay type: Proteomics

Technology type: Gas Chromatography Mass Spectrometry

Snapshots: No snapshots

metabolomics
STREAM, SYSTERACT
No description specified

Contributor: Jay Moore

Assay type: Metabolite Profiling

Technology type: Gas Chromatography Mass Spectrometry

Snapshots: No snapshots

transcriptomics
STREAM, SYSTERACT
No description specified

Contributor: Jay Moore

Assay type: Transcriptomics

Technology type: Custom Array

Snapshots: No snapshots

Online/offline measurements
STREAM, SYSTERACT
No description specified

Contributor: Jay Moore

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Metabolic pathway curation
STREAM, SYSTERACT
No description specified

Contributor: Jay Moore

Biological problem addressed: Metabolic Network

Snapshots: No snapshots

M145

Contributor: Jay Moore

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Streptomyces coelicolor

Genotypes: wild-type

Phenotypes: wild-type

Comment: Not specified

A3(2)

Contributor: Jay Moore

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Streptomyces coelicolor

Genotypes: wild-type

Phenotypes: wild-type

Comment: Not specified

Fermentor 199 cultivation data
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No description specified

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

Contributor: Jay Moore

Fermentor 199 transcriptomics
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No description specified

Creators: Jay Moore, Juan-Francisco Martin, Antonio Rodríguez-García, Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel, Maggie Smith, Louise Thomas, Eriko Takano, Lubbert Dijkhuizen, Rainer Breitling, M. Tauqeer Alam, Anthony Palathingal, R Jansen, Maria Elena Merlo, Morris Swertz, Preben Krabben, Kay Nieselt, Wolfgang Wohlleben, Jens Reuther, David Hodgson, David Rand, David Wild, Elizabeth Wellington, Gregory Challis, Nigel Burroughs, Walid Omara, William Gaze, Brent Kiernan, Roxane Legaie

Contributor: Jay Moore

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ScoCyc 14.5 release bundle
STREAM
No description specified

Creators: Jay Moore, David Hodgson

Contributor: Jay Moore

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ScoCyc 14.6 release bundle
STREAM
No description specified

Creators: Jay Moore, David Hodgson

Contributor: Jay Moore

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4 hidden items
ScoCyc 14.5 release bundle
STREAM
No description specified

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

Contributor: Jay Moore

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Spore batch generation
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No description specified

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

Contributor: Jay Moore

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Metabolome extraction
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No description specified

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

Contributor: Jay Moore

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MCF derivatization
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No description specified

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

Contributor: Jay Moore

Proteomic Analysis of the Streptomyces coelicolor Proteome
STREAM
No description specified

Creators: Louise Thomas, Maggie Smith

Contributor: Jay Moore

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Total DNA Quantification
STREAM
No description specified

Creators: Louise Thomas, Maggie Smith

Contributor: Jay Moore

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Total RNA Quantification
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No description specified

Creators: Louise Thomas, Maggie Smith

Contributor: Jay Moore

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Total Protein Quantification
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No description specified

Creators: Louise Thomas, Maggie Smith

Contributor: Jay Moore

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Processing Streptomyces coelicolor cell pellets
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No description specified

Creators: Louise Thomas, Maggie Smith

Contributor: Jay Moore

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Contamination test 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

Contributor: Jay Moore

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Generation of cell material from Streptomyces coelicolor culture for metabolome 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

Contributor: Jay Moore

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Generation of cell material from Streptomyces coelicolor culture for transcriptome analysis
STREAM
No description specified

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

Contributor: Jay Moore

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Generation of cell material from Streptomyces coelicolor culture for proteome analysis
STREAM
No description specified

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

Contributor: Jay Moore

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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

Contributor: Jay Moore

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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

Contributor: Jay Moore

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Preparation of inoculum for Streptomyces coelicolor cultivation
STREAM
No description specified

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

Contributor: Jay Moore

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1 hidden item
Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor
STREAM

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 … have explored the underlying reorganization of the metabolome by combining computational predictions based on constraint-based modeling and detailed transcriptomics time course observations. Results We reconstructed the stoichiometric matrix of S. coelicolor, including the major antibiotic biosynthesis pathways, and performed flux balance analysis to predict flux changes that occur when the cell switches from biomass to antibiotic production. We defined the model input based on observed fermenter culture data and used a dynamically varying objective function to represent the metabolic switch. The predicted fluxes of many genes show highly significant correlation to the time series of the corresponding gene expression data. Individual mispredictions identify novel links between antibiotic production and primary metabolism. Conclusion Our results show the usefulness of constraint-based modeling for providing a detailed interpretation of time course gene expression data. Other Sections▼

Authors: M. Tauqeer Alam, Maria Elena Merlo, The STREAM Consortium (stream), David Hodgson, Elizabeth Wellington, Eriko Takano, Rainer Breitling

Date Published: 2010

Journal: BMC Genomics

The dynamic architecture of the metabolic switch in Streptomyces coelicolor
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Abstract (Expand)

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 … expression patterns during this switch, using a specifically designed Affymetrix genechip and a high-resolution time-series of fermenter-grown samples. RESULTS: Surprisingly, we find that the metabolic switch actually consists of multiple finely orchestrated switching events. Strongly coherent clusters of genes show drastic changes in gene expression already many hours before the classically defined transition phase where the switch from primary to secondary metabolism was expected. The main switch in gene expression takes only 2 hours, and changes in antibiotic biosynthesis genes are delayed relative to the metabolic rearrangements. Furthermore, global variation in morphogenesis genes indicates an involvement of cell differentiation pathways in the decision phase leading up to the commitment to antibiotic biosynthesis. CONCLUSIONS: Our study provides the first detailed insights into the complex sequence of early regulatory events during and preceding the major metabolic switch in S. coelicolor, which will form the starting point for future attempts at engineering antibiotic production in a biotechnological setting.

Authors: Kay Nieselt, Florian Battke, Alexander Herbig, Per Bruheim, Alexander Wentzel, Øyvind Jakobsen, Håvard Sletta, M. Tauqeer Alam, Maria Elena Merlo, Jay Moore, Walid Omara, Edward R Morrissey, Miguel A Juarez-Hermosillo, Antonio Rodríguez-García, Merle Nentwich, Louise Thomas, Mudassar Iqbal, Roxane Legaie, William Gaze, Gregory Challis, R Jansen, Lubbert Dijkhuizen, David Rand, David Wild, Michael Bonin, Jens Reuther, Wolfgang Wohlleben, Maggie Smith, Nigel Burroughs, Juan-Francisco Martin, David Hodgson, Eriko Takano, Rainer Breitling, Trond Ellingsen, Elizabeth Wellington

Date Published: 28th May 2009

Journal: BMC Genomics

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, … are produced in very small quantities, which has hindered their structural elucidation and made it difficult to assess whether they are being produced. In this chapter, we describe a rapid small-scale extraction method from either solid or liquid cultures in scales of one plate or 50 ml of medium. Also described is a bioassay to detect the gamma-butyrolactones by determining either the production of pigmented antibiotic of Streptomyces coelicolor or kanamycin resistant growth on addition of the gamma-butyrolactones. We also describe some insights into the identification of the gamma-butyrolactone receptor and its targets and also the gel retardation conditions with three differently labeled probes.

Authors: Nai-Hua Hsiao, Marco Gottelt, Eriko Takano

Date Published: 21st Apr 2009

Journal: Meth. Enzymol.

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 … of the observed mass peaks, including the assignment of their empirical formula, based on the measured mass. RESULTS: We propose a novel probabilistic method for the assignment of empirical formulas to mass peaks in high-throughput metabolomics mass spectrometry measurements. The method incorporates information about possible biochemical transformations between the empirical formulas to assign higher probability to formulas that could be created from other metabolites in the sample. In a series of experiments, we show that the method performs well and provides greater insight than assignments based on mass alone. In addition, we extend the model to incorporate isotope information to achieve even more reliable formula identification. AVAILABILITY: A supplementary document, Matlab code, data and further information are available from http://www.dcs.gla.ac.uk/inference/metsamp.

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

Date Published: 18th Dec 2008

Journal: Bioinformatics

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 … been sequenced and some 30% of the open reading frames (ORFs) lack any functional annotation. A recently constructed metabolic network model for S. coelicolor highlights biochemical functions which should exist to make the metabolic model complete and consistent. These include 205 reactions for which no ORF is associated. Here we combine protein functional predictions for the unannotated open reading frames in the genome with \'missing but expected\' functions inferred from the metabolic model. The approach allows function predictions to be evaluated in the context of the biochemical pathway reconstruction, and feed back iteratively into the metabolic model. We describe the approach and discuss a few illustrative examples.

Authors: Mansoor Saqi, Richard J B Dobson, Preben Kraben, David Hodgson, David Wild

Date Published: 13th Nov 2008

Journal: J Integr Bioinform

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 … method that improves the mass accuracy of the LTQ-Orbitrap mass spectrometer from an initial +/- 1-2 ppm, obtained by the standard software, to an absolute median of 0.21 ppm (SD 0.21 ppm). With the increased mass accuracy it becomes much easier to match mass chromatograms in replicates and different sample types, even if compounds are detected at very low intensities. The proposed method exploits the ubiquitous presence of background ions in LC-MS profiles for accurate alignment and internal mass calibration, making it applicable for all types of MS equipment. The accuracy of this approach will facilitate many downstream systems biology applications, including mass-based molecule identification, ab initio metabolic network reconstruction, and untargeted metabolomics in general.

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

Date Published: 22nd Oct 2008

Journal: Proteomics

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

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, Eriko Takano, Wei-Shou Hu

Date Published: 2nd May 2008

Journal: PLoS ONE

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 … is, however, limited by the current state of biochemical knowledge. Can experimental high-throughput data be used to improve and expand network reconstructions to include unexplored areas of metabolism? Recent advances in experimental technology and analytical methods bring this aim an important step closer to realization. Data integration will play a particularly important part in exploiting the new experimental opportunities.

Authors: Rainer Breitling, Dennis Vitkup, Michael P Barrett

Date Published: 21st Nov 2007

Journal: Nat. Rev. Microbiol.

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 … analysis. This open source, multi-platform software has been successfully used to interpret metabolomic experiments and will enable others using filtered, high mass accuracy mass spectrometric data sets to build and analyse networks. AVAILABILITY: http://compbio.dcs.gla.ac.uk/fabien/abinitio/abinitio.html

Authors: Fabien Jourdan, Rainer Breitling, Michael P Barrett, David Gilbert

Date Published: 14th Nov 2007

Journal: Bioinformatics

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