Jasper Koehorst

About Jasper Koehorst:
No description specified

SEEK ID: https://hub.ibisba.eu/people/107

Location:  Netherlands

Expertise: Data Management, Software Engineering, Genetics, Microbiology, Molecular Biology, Bioinformatics

Tools: R, Python, Java, Computational and theoretical biology, Genetic analysis

ORCID: https://orcid.org/0000-0001-8172-8981

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IBISBA public documents

This programme is for making IBISBA documents available to the public.

Projects: IBISBA 1.0 deliverables, PREP-IBISBA deliverables

Web page: Not specified

IBISBA

IBISBA is designed to accelerate end-to-end bioprocess development, linking best-in-class R&D facilities to provide seamless multi-technology services.

Focusing on the different R&D phases in bioprocess development, IBISBA offers services related to computer-assisted design of biocomponents, construction of enzymes and microbial strains, the fermentation, downstream processing and project knowledge asset management.

Projects: Uncurated Protocols Library, SULFOCEL, Template library, Muconic Acid Production in Yeast, Public announcements and documents, IBISBA Library, Curated Protocols Library, Test, DBTL-P, test

Web page: http://www.ibisba.eu

IBISBA 2020 f2f

Files and projects to support the IBISBA 2020 f2f

Projects: An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data, Example testing project

Web page: Not specified

TransNational Access

IBISBA offers access to best-in-class facilities and know-how. Clients from academia, SMEs and big industry can find tailored solutions for their R&D needs.

Using a H2020 funding framework, IBISBA currently offers limited opportunities to researchers to obtain subsidised access to IBISBA specialised research structures and facilities, including contribution to user's travel and subsistence costs. Open Calls are launched regularly, inviting researchers from all sectors (academia and industry) ...

Projects: TRANSCRIPTPROM - Integrative and comparative analyses of response of Pichia pastoris, FLOX: FLavin-containing OXidoreductases, PlanOvac, HIGHFLUX, SporeDel, Yeast Glycerol, Galambr, Muconic Acid Production, Promoters 4 Pichia, 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, Biocare, MEOX, Coculture, YarroFuels, PlasticPutida, Lipro-alga, Cyanofcs, ENGINEER4ARGININE, Upscale of the biocatalytic transformation of Free Fatty Acids into high-value products (BIOFFA), B-PAC, BIOFFA, GLYCOMICS, KorallionBio, MAROX, PROTEIFROM, SUPI

Web page: https://www.ibisba.eu/Our-Offer/Subsidised-Access

IBISBA 1.0 deliverables

This project collects together the IBISBA 1.0 deliverables

Programme: IBISBA public documents

Public web page: Not specified

PREP-IBISBA deliverables

This project make available the deliverables of the PREP-IBISBA project

Programme: IBISBA public documents

Public web page: Not specified

Coculture

Co-Culture for improved lignocellulose fractionation and elicitation of enzymatic activies - Omics on co-culture of trichoderma reesei or Phanerochaete chrysosporium

Programme: TransNational Access

Public web page: Not specified

Uncurated Protocols Library

The collection of protocols that have not yet been curated by IBISBA WP6

Programme: IBISBA

Public web page: http://www.ibisba.eu

Muconic Acid Production

Construction of a P. putida KT2440 producing cis,cis-muconate from glucose, benzoate, or p-coumarate

Programme: TransNational Access

Public web page: Not specified

UNLOCK

Country:  Netherlands

City: Wageningen

Web page: http://m-unlock.nl/

WUR - Wageningen University & Research

Country:  Netherlands

City: Wageningen

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

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Unlock metadata template
Template library

The unlock metadata template using a modified version of the ISA structure.

This is superseded by https://hub.ibisba.eu/file_templates/1

Creator: Jasper Koehorst

Submitter: Jasper Koehorst

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IBISBA Populator template
Template library

This is the template that can be used to populate your project using the IBISBA Populator software that is part of the IBISBA Hub. More information can be found here https://ibisba.github.io/handbook/ibisba_hub/project/

Creator: Jasper Koehorst

Submitter: Jasper Koehorst

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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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