IBISBA 2020 f2f
Files and projects to support the IBISBA 2020 f2f
Web page: Not specified
Funding details: Related items
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, Curated Protocols Library
Institutions: Administration
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 Development from Yeast, Demo Project by Munazah, demo project 2
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.
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
I work in the eScience Lab at the University of Manchester
Programme: IBISBA 2020 f2f
Public web page: Not specified
Programme: IBISBA 2020 f2f
Public web page: Not specified
Genetic manipulations and optimisation of experimental conditions to improve synthesis of Muconic acid from yeast.
Programme: IBISBA 2020 f2f
Public web page: Not specified
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
Programme: IBISBA 2020 f2f
Public web page: Not specified
Submitter: Munazah Andrabi
Studies: Creation of DNA constructs, Receive #Input from #Test-HighThroughput #Test-Bioreactor #Upscale, Receive input from Design: strain and vector designs
Assays: Order/synthesize genetic material, Prepare genetic material for transformation, Prepare liquid cultivation medium for transformation, Prepare solid cultivation medium for transformation, Prepare transformation competent cells of the cloning host organism, Receive genetic material, Receive high-level step-by-step instructions for construction of DNA con..., Receive high-level step-by-step instructions for strain construction, Receive list of oligos in FASTA format to be ordered for DNA fragment co..., Receive list of primers in FASTA format for verification and the SOP of ..., Receive plasmid maps in SBOL format, Transformation of the genetic material into the cloning host organism
Submitter: Munazah Andrabi
Studies: Chassis embedment, Computational product pathway design, Criteria for successful outcome of #Design (Criteria to be available as ..., Design DNA constructs for expression host, Design growth medium and cultivation conditions, Evaluate and choose pathways, Genetic design for chassis, Information search, Output to Build, Receive input from #Upscale #Test-HighThroughput #Test-Bioreactor and #b..., Receive input from "select host and products" step, Select and/or design enzyme, Select genome editing strategy, Sending and receiving designs, Store information of design
Assays: Add production pathway to chassis SBML in silico, Additional trait design, Appropriate MTAs and other agreements in place, Bioprospecting for traits, Build designs made #Output, CRISPR/Cas9, Calculate expected yields, Calculation of theoretical yields/productivities carried out, Check for native enzymes with activity for heterologous metabolites, Choose enzyme sequences, Combinatorial assembly strategy, Consideration to the specificity of the process (for the product) (selec..., Convert reaction rules to complete reactions, Describe genetic constructs in SBOL format, Describe genetic constructs in SBOL format, Design expected to be stable in vivo, Design experiments to test phenotype, Design suits the chassis (and its genotype), Enumerate pathway options (Retropath,…), Estimate productivities, Evaluate and choose strains, Fill metabolic gaps, Freedom to operate (IPR considerations), Freedom to operate with regards to the tools #IPRConsiderations, Function-based in silico screening of candidate sequences, Generate candidate sequences (Enzyme search), Genome reannotation, Growth-product coupling. (e.g. OptKnock, RobustKnock, Minimal Cut Sets), Known pathways in literature, Known pathways in reaction databases, List DNA fragments to order, MAGE: genome engineering, Map metabolites between pathway and chassis, Membrane toxicity of intermediates, Obtain SBML models for production hosts, Obtain annotated genomes of production hosts, Optimize gene sequences, Optimized Bottleneck Energetics, Patent search, Pathway improvement by mutations, supporting/auxiliary pathways, enzymes..., Perform evaluation, Physiological constraints, Predicted effect of modifications on flux ratios expected to be measurab..., Process constraints., Propose desirable traits, Receive input from product pathway design, Receive list of genotypes, Receive name of product, Receive name of production host, Remove mobile regulatory elements, Retrieve the list of enzyme functions, Retrieve the list of gene additions, Retrieve the list of gene deletions, Retrieve the list of promoter types, SEVA/METABRICK, Moclo, Gibson pathway engineering @Wageningen, Score pathways without chassis, Screen growth conditions, Screen pathway options based on quality criteria, Screen potential substrates in silico, Search for native homologues of enzymes acting on the heterologous metab..., Select integration sites/loci, Select primers for vector assembly, Select promoter types, Select promoters, Select vector assembly strategy, Select vectors/plasmids/DNA constructs, Send list of gene additions, Send list of growth media and cultivation conditions to Test, Send output to build, Send predicted clone behavior to Test, Send strain designs to Build, Store the list of enzyme functions, Store the list of gene additions, Store the list of gene deletions, Store the list of genotypes, Store the list of promoter types, Test conditions considered and predicted strain behavior expected to be ..., Test conditions designed, Thermodynamic feasibility verification, Upscale conditions considered #UpscaleConsideration, Vector, promoter selection, plasmids, locus of integration, restriction ...
Submitter: Munazah Andrabi
Studies: Obtain relevant data for host, Obtain relevant data for product, Physiological constraints, Technoeconomic constraints
Assays: Collect relevant available (bibliographic, experimental) data (candidate..., DSP considerations, Estimate market value of product, Estimate product toxicity for chassis, Estimate product toxicity for chassis, Genome sequence, Genome-scale metabolic model (GEM), Intellectual Property (IP) constraints, Obtain physicochemical data (Toxicity, Solubility, InChI,…) for product, Oxygen requirements, Raw material requirements
Submitter: Munazah Andrabi
Studies: Creation of DNA constructs, Receive #Input from #Test-HighThroughput #Test-Bioreactor #Upscale, Receive input from Design: strain and vector designs
Assays: Order/synthesize genetic material, Prepare genetic material for transformation, Prepare liquid cultivation medium for transformation, Prepare solid cultivation medium for transformation, Prepare transformation competent cells of the cloning host organism, Receive genetic material, Receive high-level step-by-step instructions for construction of DNA con..., Receive high-level step-by-step instructions for strain construction, Receive list of oligos in FASTA format to be ordered for DNA fragment co..., Receive list of primers in FASTA format for verification and the SOP of ..., Receive plasmid maps in SBOL format, Transformation of the genetic material into the cloning host organism
Submitter: Munazah Andrabi
Studies: Chassis embedment, Computational product pathway design, Criteria for successful outcome of #Design (Criteria to be available as ..., Design DNA constructs for expression host, Design growth medium and cultivation conditions, Evaluate and choose pathways, Genetic design for chassis, Information search, Output to Build, Receive input from #Upscale #Test-HighThroughput #Test-Bioreactor and #b..., Receive input from "select host and products" step, Select and/or design enzyme, Select genome editing strategy, Sending and receiving designs, Store information of design
Assays: Add production pathway to chassis SBML in silico, Additional trait design, Appropriate MTAs and other agreements in place, Bioprospecting for traits, Build designs made #Output, CRISPR/Cas9, Calculate expected yields, Calculation of theoretical yields/productivities carried out, Check for native enzymes with activity for heterologous metabolites, Choose enzyme sequences, Combinatorial assembly strategy, Consideration to the specificity of the process (for the product) (selec..., Convert reaction rules to complete reactions, Describe genetic constructs in SBOL format, Describe genetic constructs in SBOL format, Design expected to be stable in vivo, Design experiments to test phenotype, Design suits the chassis (and its genotype), Enumerate pathway options (Retropath,…), Estimate productivities, Evaluate and choose strains, Fill metabolic gaps, Freedom to operate (IPR considerations), Freedom to operate with regards to the tools #IPRConsiderations, Function-based in silico screening of candidate sequences, Generate candidate sequences (Enzyme search), Genome reannotation, Growth-product coupling. (e.g. OptKnock, RobustKnock, Minimal Cut Sets), Known pathways in literature, Known pathways in reaction databases, List DNA fragments to order, MAGE: genome engineering, Map metabolites between pathway and chassis, Membrane toxicity of intermediates, Obtain SBML models for production hosts, Obtain annotated genomes of production hosts, Optimize gene sequences, Optimized Bottleneck Energetics, Patent search, Pathway improvement by mutations, supporting/auxiliary pathways, enzymes..., Perform evaluation, Physiological constraints, Predicted effect of modifications on flux ratios expected to be measurab..., Process constraints., Propose desirable traits, Receive input from product pathway design, Receive list of genotypes, Receive name of product, Receive name of production host, Remove mobile regulatory elements, Retrieve the list of enzyme functions, Retrieve the list of gene additions, Retrieve the list of gene deletions, Retrieve the list of promoter types, SEVA/METABRICK, Moclo, Gibson pathway engineering @Wageningen, Score pathways without chassis, Screen growth conditions, Screen pathway options based on quality criteria, Screen potential substrates in silico, Search for native homologues of enzymes acting on the heterologous metab..., Select integration sites/loci, Select primers for vector assembly, Select promoter types, Select promoters, Select vector assembly strategy, Select vectors/plasmids/DNA constructs, Send list of gene additions, Send list of growth media and cultivation conditions to Test, Send output to build, Send predicted clone behavior to Test, Send strain designs to Build, Store the list of enzyme functions, Store the list of gene additions, Store the list of gene deletions, Store the list of genotypes, Store the list of promoter types, Test conditions considered and predicted strain behavior expected to be ..., Test conditions designed, Thermodynamic feasibility verification, Upscale conditions considered #UpscaleConsideration, Vector, promoter selection, plasmids, locus of integration, restriction ...
Submitter: Munazah Andrabi
Investigation: Build
Assays: Receive high-level step-by-step instructions for construction of DNA con..., Receive high-level step-by-step instructions for strain construction, Receive list of oligos in FASTA format to be ordered for DNA fragment co..., Receive list of primers in FASTA format for verification and the SOP of ..., Receive plasmid maps in SBOL format
Submitter: Munazah Andrabi
Investigation: Build
Assays: Order/synthesize genetic material, Prepare genetic material for transformation, Prepare liquid cultivation medium for transformation, Prepare solid cultivation medium for transformation, Prepare transformation competent cells of the cloning host organism, Receive genetic material, Transformation of the genetic material into the cloning host organism
Submitter: Munazah Andrabi
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Build
Study: Creation of DNA constructs
Submitter: Munazah Andrabi
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Build
Study: Creation of DNA constructs
Submitter: Munazah Andrabi
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Design
Submitter: Munazah Andrabi
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Design
Submitter: Munazah Andrabi
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Design
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Abstract (Expand)
Authors: Machtelt Braaksma, Elena S Martens-Uzunova, Peter J Punt, Peter J Schaap
Date Published: 1st Dec 2010
Publication Type: Journal
