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Objectives
 

WP 1 Coordination and management (MGT)

Lead beneficiary: CSIC

Other participants: UNI VALENCIA / BIOFACTION KG

[a] Co-ordination of all project activities and contact with Commission representatives.

[b] Achieving timely submission of the project’s financial and scientific reports

[c] Organize consortium meetings, Summer Schools and an International Workshop

[d] Assessment of project progress, results, impact and dissemination.

[e] Maintain Project webpage and organize Webinars

[f]  Ensure compliance with the Consortium Agreement.

WP 2 Molecular tools, computational tools and standards for physical assembly (RTD)

Lead beneficiary: IMPERIAL

Other participants: CSIC / ETH ZURICH / ISTHMUS SARL

[a] Development of a DNA assembly standard based on an automated wet protocol.

[b] Setting a broad host range plasmid and transposon vector platform for device deployment

[c] Automation of part characterization to a professional standard in single cells and populations

[d] Low-level dynamic models that connect sequences with functional parameters.

[e] Implement experimental and computational benchmarks throughout the Project lifetime.

WP 3 Transfer functions through the gene expression flow (RTD)

Lead beneficiary: UNI BIRMINGHAM

Other participants: CSIC / IMPERIAL / ETH ZURICH / ITQB UNLISBOA / CNRS

[a] Quantification of the transfer function RNAP recruitment transcript formation (PoPs)

[b] Identification of genomic /cellular sites that sustain a high transcriptional capacity.

[c] Composition rules and implementation of transcripts with a predetermined stability.

[d] Construction novel regulons regulated by pairs of new sigmas with matching, specific TFs.

WP 4 Functional composition and context-insensitivity (RTD)

Lead beneficiary: CNRS

Other participants: ETH ZURICH / UNI BIRMINGHAM / ITQB UNLISBOA

[a] Definition of the minimal DNA-sequence elements that are responsible for the largest part of context

sensitivity at the start and the end of any given gene: formatting of transcriptional / translational insulators.

[b] Parameterization of translation initiation signals and protein stability tags along with compositional rules for

their incorporation to expression devices.

[c] Standardization of genome-scale regulatory systems applicable to the design of concurrent co-expression (in time and space) of engineered / synthetic DNA sequences encoding heterologous activities


WP 5 Information systems, interfaces and descriptive languages (RTD)

Lead beneficiary: IMPERIAL

Other participants: ETH ZURICH / ISTHMUS SARL

a] Organization and validation of the SynBIS template for ontological categorisation of biological parts, including both data and metadata, conformance statements for the different part types and development of conformance testing software.

[b] Setup of an Information Infrastructure to handle data and documentation in different formats and enabling

a standards converter to handle comparison of experimental results and models to import/export info of the

SynBIS system.

[c] Development of a platform for system testing and device development, including circuit plug-in and interplay

with chassis e.g. intertwining model and experimentation to assess how circuit interact with the host networks.

WP 6 System assembly, characterization, and parameterization (RTD)

Lead beneficiary: ETH ZURICH

Other participants: IMPERIAL

[a] Assembly of a set of 10 reporter proteins fulfilling a list of functional requirements to allow comprehensive

analysis in a limited number of highly simplified protocols on standard analysis platforms (promoter strength,

mRNA stability, activity output).

[b] Implementation (building upon the results of WP2, WP4 and WP5 in DNA assembly) of combinatorial

recombinations of standardized reporter systems and parameterization of the corresponding protein expression models for determining their suitability for systems design.

[c] Generation of conversion tables for current reporter systems to the reporter genes/products that are used in

this WP and to PoPs (connection to WP3).

[d] Engineering novel reporters with conditional lifespans.

WP 7 Formatted construction and validation of biosensors and biocatalysts (RTD)

Lead beneficiary: UNIL

Other participants: CSIC / BIRD / UNI SUTTGART

[a] Categorization of parts comprising existing sensing elements responsive to signals outside the cell and responsive to signals inside the cell and expanding their target specificity and connectivity.

[b] Construction and testing of a variety of designs of gene reporter circuitry for signal amplification,

signal-to-noise ratios, background reduction and context-dependency of response, using bioreporter cells

[c] Definition of the regulatory nodes and boundaries of the stringent response network and deep refactoring of

the key elements for uncoupling engineered devices amino acid catabolism/anabolism (connection to WP3 and

WP4).

[d] Validation and characterization of metabolically-uncoupled catalysts


WP 8 Training and outreach (OTHER)

Lead beneficiary: UNI VALENCIA

Other participants: CSIC

[a] Planning and implementation of a training program and dissemination developed throughout the project,

aiming at assisting to fuel the SB community with novel researchers by contributing to a meaningful education in this cross-disciplinary area.

[b] Organization and management of Synthetic Biology Workhops, Summer Schools and one stakeholder’s

meeting.

WP 9 Societal and economic dimensions and ramifications of biological standards (RTD)

Lead beneficiary: BIOFACTION KG

Other participants: CSIC / TUM / EUDIN

[a] Examination and reporting on new aspects of risk, ethics, intellectual property and public perception which

are connected to biological standardisation and are not covered by identical issues re. traditional genetic

engineering.

[b] Exploration and implementation of novel channels of interactions with extended audiences, e.g. the media

and industry in order to show the multifaceted implications and importance of the standardisation propositions

developed in our project.

Work packages:

Coordinator: Consejo Superior de Investigaciones Científicas (CSIC) - Centro Nacional de Biotecnología (CNB)

C/ Darwin, 3  - 28049 Madrid (Spain)                              

Tel. +34 91 585 45 73    -   E-mail: stflow-project@cnb.csic.es  - www.cnb.csic.es