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IBISBA 2020 f2f

Files and projects to support the IBISBA 2020 f2f

Web page: Not specified

Funding details:
No funding details specified

Related items

IBISBA Admin adminproject_administratorprogramme_administrator

Projects: Uncurated Protocols Library, Development Project, TRANSCRIPTPROM - Integrative and comparative analyses of response of Pichia pastoris, FLOX: FLavin-containing OXidoreductases, PlanOvac, Muconic Acid Production, HIGHFLUX, Promoters 4 Pichia, An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data, Template library, Evocolour - The evolution and genetics of Flavobacteria forming structurally coloured colonies for sustainable biomaterials, Extreme - Genomic approach for extremozymes screening of thermophilic/anaerobic Caldicoprobacter algerensis strain, HMOzyme, PILOT-MP - Pilot scale process development for microbial proteins, UMB - Upscaling and optimisation of microalgae production for bivalves hatchery, Example data library, Public announcements and documents, IBISBA Library, Biocare, MEOX, Co-culture, Yarrofuel, Plastic putida, Lipro-algae

Institutions: Administration

Munazah Andrabi adminproject_administratorprogramme_administrator

Projects: Uncurated Protocols Library, Development Project, FLOX: FLavin-containing OXidoreductases, PlanOvac, HIGHFLUX, SporeDel, Yeast Glycerol, Galambr, SULFOCEL, An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data, spreadsheet test, Template library, Muconic Acid Production in Yeast, Muconic Acid Developemnt from Yeast

Institutions: UNIMAN - The University of Manchester, UAB - Universitat Autònoma de Barcelona, CNR - Consiglio Nazionale delle Ricerche, INSAT - Institut National des Science Appliquees de Toulouse, VTT - Teknologian tutkimuskeskus VTT Oy, VITO - Vlaamse Instelling voor Technologisch Onderzoek N.V.

Stefan Helfrich adminproject_administratorprogramme_administrator

Projects: Uncurated Protocols Library, Development Project, TestProjectForPopulation, PopulationTest2, Muconic Acid Population Sample

Institutions: KNIME GmbH

https://orcid.org/0000-0003-3549-8649
Jasper Koehorst project_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: Uncurated Protocols Library, Development Project, Muconic Acid Production, An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data, spreadsheet test, Example project, Template library

Institutions: WUR - Wageningen University & Research

https://orcid.org/0000-0001-8172-8981
Alan Williams project_administrator

Projects: Uncurated Protocols Library, Development Project, spreadsheet test, Example project, Muconic Acid Developemnt from Yeast

Institutions: UNIMAN - The University of Manchester

https://orcid.org/0000-0003-3156-2105
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually requires the presence of a N- terminal signal peptide (SP) and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted.
However, prediction of a SP does not guarantee that the protein is actually secreted and current
...

Programme: IBISBA 2020 f2f

Public web page: Not specified

Start date: 1st Jul 2019

End date: 31st Dec 2019

Muconic Acid Population Sample
No description specified

Programme: IBISBA 2020 f2f

Public web page: Not specified

PopulationTest2
No description specified

Programme: IBISBA 2020 f2f

Public web page: Not specified

Muconic Acid Developemnt from Yeast

Genetic manipulations and optimisation of experimental conditions to improve synthesis of Muconic acid from yeast.

Programme: IBISBA 2020 f2f

Public web page: Not specified

Administration

Country:  France

City: Not specified

Web page: Not specified

KNIME GmbH

Country:  Germany

City: Konstanz

Web page: https://www.knime.com/

UNIMAN - The University of Manchester

Country:  United Kingdom

City: Manchester

Web page: http://www.manchester.ac.uk/

WUR - Wageningen University & Research

Country:  Netherlands

City: Wageningen

Web page: https://www.wur.nl

Strain engineering
Muconic Acid Population Sample
No description specified

Snapshots: No snapshots

Computational strain design
Muconic Acid Population Sample
No description specified

Snapshots: No snapshots

Strain Engineering for Yeast
Muconic Acid Developemnt from Yeast
No description specified

Snapshots: No snapshots

Strain Management for Yeast
Muconic Acid Developemnt from Yeast
No description specified

Snapshots: No snapshots

Strain engineering
PopulationTest2
No description specified

Snapshots: No snapshots

Assemble parts
Muconic Acid Population Sample
No description specified

Person responsible: Not available

Snapshots: No snapshots

Transformation of production host
Muconic Acid Population Sample
No description specified

Person responsible: Not available

Snapshots: No snapshots

Metabolic strain design
Muconic Acid Population Sample
No description specified

Person responsible: Not available

Snapshots: No snapshots

Transformation of production host
Muconic Acid Developemnt from Yeast
No description specified

Person responsible: Munazah Andrabi

Snapshots: No snapshots

Assemble Parts
Muconic Acid Developemnt from Yeast
No description specified

Person responsible: Munazah Andrabi

Snapshots: No snapshots

Signal Peptide Predictions
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data
No description specified

Contributor: Munazah Andrabi

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Prepare transformation competent cells of the cloning host organism
Muconic Acid Population Sample
No description specified

Contributor: Stefan Helfrich

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Prepare liquid cultivation medium for transformation
Muconic Acid Population Sample
No description specified

Contributor: Stefan Helfrich

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Prepare solid cultivation medium for transformation
Muconic Acid Population Sample
No description specified

Contributor: Stefan Helfrich

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Prepare cultivation media for making glycerol stocks
Muconic Acid Population Sample
No description specified

Contributor: Stefan Helfrich

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

1 hidden item
Aspergillus niger CBS513.88 protein model verification of four selected proteins
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data
No description specified

Creator: Munazah Andrabi

Contributor: Munazah Andrabi

Download
Aspergillus niger centered protein clusters with a positive SignalP3 prediction
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data
No description specified

Creator: Munazah Andrabi

Contributor: Munazah Andrabi

Download
Population XLSX
Muconic Acid Population Sample
No description specified

Creator: Stefan Helfrich

Contributor: Stefan Helfrich

TasCu file
Muconic Acid Population Sample
No description specified

Creator: Stefan Helfrich

Contributor: Stefan Helfrich

Synthetic DNA Construct
Muconic Acid Developemnt from Yeast
No description specified

Creator: Munazah Andrabi

Contributor: Munazah Andrabi

1 hidden item
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

Abstract (Expand)

Background The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually …y requires the presence of a N-terminal signal peptide (SP) and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted. However, prediction of a SP does not guarantee that the protein is actually secreted and current in silico prediction methods suffer from gene-model errors introduced during genome annotation. Results A majority rule based classifier that also evaluates signal peptide predictions from the best homologs of three neighbouring Aspergillus species was developed to create an improved list of potential signal peptide containing proteins encoded by the Aspergillus niger genome. As a complement to these in silico predictions, the secretome associated with growth and upon carbon source depletion was determined using a shotgun proteomics approach. Overall, some 200 proteins with a predicted signal peptide were identified to be secreted proteins. Concordant changes in the secretome state were observed as a response to changes in growth/culture conditions. Additionally, two proteins secreted via a non-classical route operating in A. niger were identified. Conclusions We were able to improve the in silico inventory of A. niger secretory proteins by combining different gene-model predictions from neighbouring Aspergilli and thereby avoiding prediction conflicts associated with inaccurate gene-models. The expected accuracy of signal peptide prediction for proteins that lack homologous sequences in the proteomes of related species is 85%. An experimental validation of the predicted proteome confirmed in silico predictions.

Authors: Machtelt Braaksma, Elena S Martens-Uzunova, Peter J Punt, Peter J Schaap

Date Published: 1st Dec 2010

Publication Type: Journal

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