Author Archive for synbiochem

International Research Alliance for Antiboiotic Discovery and Development Network

SYNBIOCHEM Co-director Eriko Takano is a founding participant in this new network which is one of eight networks awarded funding within the JPIAMR 2018 call for transnational networks “Building the Foundation of the JPIAMR Virtual Research Institute”. Each funded network will receive €50,000 to establish expertise clusters to identify research community needs and develop ideas to form the foundation for the JPIAMR Virtual Research Institute (JPIAMR-VRI). The IRAADD network includes internationally renowned groups with excellence in AMR research focussing on early stages of antibiotic discovery and development. This expert team will include natural products researchers, medical microbiologists, bioinformaticians, medicinal chemists and target-based drug designers, as well advisory partners from global alliances focussing on antibiotic development such as DNDi/GARDP and IMI-ENABLE. The network partners ill set up a cooperative platform to allow the sharing of scientific research data, translational knowledge and expert advice for the strategic development of new and advanced projects with the aim to take collaborative scientific research in the early stages of antibiotics discovery and development to a new level.

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New partnership with SynbiCITE

SynbiCITE launches new five-year strategy. Dedicated to promoting the adoption and use of synthetic biology by industry, SynbiCITE has announded the launch of a new 5-year strategy underpinned by a new £5M grant from UK Research and Innovation and other sources. SynbiCITE 2.0 aims to expand and develop SynbiCITE’s reach within the UK’s synthetic biology innovation and academic ecosystem, and create a single highly interconnected UK innovation cluster.

This will be driven through:

  • New partnerships with Manchester (SYNBIOCHEM), Bristol and Edinburgh.
  • Relocation to the new Imperial West Campus
  • Further interactions with the other UK SBRCs and academic synthetic biology community
  • Establishment of a UK-wide consortium and industry club.

Launch of an IB infra-structure strategy: European recognition for the IBISBA project

IBISBA: Industrial Biotechnology and Synthetic Biology Accelerator

SYNBIOCHEM is part of IBISBA 1.0, a H2020 funded infrastructure project that aims to create a pan-European network of research infrastructures that will support research in industrial biotechnology.

This project brings together R&D facilities from 9 EU member states (including the University of Manchester, SYNBIOCHEM and FAIRDOM data management) and access to first class infrastructure.

On 11th September the European Science Forum for Research Infra-structure will launch the 2018 European Infra-structure Roadmap which will include IBISBA. This ESFRI recognition of IBISBA opens up development that will allow IBISBA to create services that aim to accelerate the preindustrial R&D phases of bioprocess development, thus supporting industrial biotechnology and promoting its role as a key enabling technology of the bio-economy. Read more here:pr_IBISBA SYNBIOCHEM 2

A transnational access programme (Launching 17th September 2018) will provide a mechanism to access IBISBA training and equipment by the wider scientific community. Please see website for information.

https://www.ibisba.eu/

Responsible Research and Innovation – A Manchester Perspective.

What is Responsible Research and Innovation? Barbara Ribeiro and Philip Shapira have written a short briefing paper that provides an overview of responsible research and innovation (RRI), with concise highlights about principles of responsibility, the emergence of RRI in the UK and Europe, the EPSRC AREA framework, and RRI in Manchester. To read, go to: http://synbiochem.co.uk/rri-manchester-perspective/

An automated Design-Build-Test-Learn pipeline

The SYNBIOCHEM automated pipeline for the discovery and optimisation of biosynthetic pathways for microbial production of fine chemicals has been published in Nature: Communications Biology.

The microbial production of fine and speciality chemicals promises to deliver bio-sustainable manufacturing solutions of the future. In this article we present an integrated Design-Build-Test-Learn pipeline which is designed to be agnostic to target compound and applicable to any chemical compound of interest. The paper demonstrates the application of the pipeline for 2 of our core chemical classes with improved production titres.

Article can be found: https://www.nature.com/articles/s42003-018-0076-9

Faster genome evolution methods to transform yeast

Scientists have created a new way of speeding up the genome evolution of baker’s yeast Saccharomyces cerevisiae, the same yeast we use for bread and beer production.

This is to develop a synthetic yeast strain that can be transformed on demand, making it particularly attractive for industrial biotechnology applications, such as the mass production of advanced medicines to treat illnesses such as Malaria and Tuberculosis (TB). It could also have massive implications for the future study of DNA.

Led by Professor Patrick Cai at the Manchester Institute of Biotechnology, in collaboration with Prof. Junbiao Dai from the Shenzhen Institute of Advanced Technology at the Chinese Academy of Sciences, two back-to-back papers are being published in Nature Communications on May 22nd, 2018.

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eForFuel: Fuels from CO2 and Electricity

C3 Biotechnologies Ltd is taking part in eForFuel, an exciting EU-funded research and innovation initiative that seeks to provide a sustainable replacement of fossil fuels by using electricity and microorganisms to convert CO2 into renewable fuels.

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Updates can be found at www.eforfuel.eu and on Twitter @eforfuel

New – The University of Manchester Presidential Fellowships

The University is inviting the brightest academic talent to apply for The University of Manchester Presidential Fellowships. We’re interested in early-career academics who can deliver world-leading research and teaching, and become the inspiring leaders of the future. Applicants should have a high academic standing, a growing reputation in research, and the specialist knowledge needSYNBIOCHEM - About - Manchester Institute of Biotechnologyed to develop exemplary research programmes and methodologies. Applicants with an interest in SynBio/IB particularly welcome! See more: https://www.brightest-minds.manchester.ac.uk 

 

Selenzyme: Enzyme selection tool for pathway design

SYNBIOCHEM - Research

Enzymes are proteins found in every living organism, catalysing biochemical reactions and involved in multiple biological processes. Industrial biotechnology utilises enzymes in a large variety of applications such as in sectors including food, cosmetics, pharmaceuticals and advanced materials. However, finding the right combination of enzymes for a desired process is often extremely challenging. Selenzyme, developed by researchers at the Manchester Synthetic Biology Research Centre (SYNBIOCHEM), Manchester Institute of Biotechnology, is a freely available online tool that assists the scientist in the selection of the enzymes for his/her experiment. The user is guided through several decision steps in order to shortlist the best candidates, graphically presenting key information about the enzymes. Selenzyme is a key component of the automated pipeline at the SYNBIOCHEM where we are aiming to provide greener, more sustainable routes for microbial production of fine chemicals.

Carbonell, P., Wong, J., Swainston, N., Takano, E., Turner, N. J., Scrutton, N. S., Kell, D.B., Breitling, R. Faulon, J.L. (2018). Selenzyme: Enzyme selection tool for pathway design. Bioinformatics, bty065. http://doi.org/10.1093/bioinformatics/bty065

RetroPath2.0 workflow for Retrosynthesis

Retrosynthesis is a long-standing problem first introduced by Chemistry Nobel Laureate J.E. Corey in the late 1960s.  Taking advantage of recent progresses made in machine learning the problem has been revisited. In two papers SYNBIOCHEM teamed up with MICALIS Institute at INRA (France) to explore the use of retrosynthesis in biology. Both articles are making use of RetroPath2.0 a versatile, open source, easy to use and modifiable scientific workflow. In the first paper [1] the tool is used to perform retrosynthesis in the context of metabolic and biosensor engineering and is validated using actual examples of successful experimental implementations. In the second paper [2] the tool is used to perform inverse molecular design and search bioactive molecules in the chemical space as well as to create extended metabolic maps that can be used to annotate mass spectrometry data coming from a metabolomics pipeline. Because RetroPath2.0 is freely available on the workflow repository platform myExperiment.org [3] and is solely based on open source tools it is anticipated that community contributions will likely expand further its features.

[1] Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering 2017, https://doi.org/10.1016/j.ymben.2017.12.002

[2] Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. J. Cheminformatics 2017, in press https://doi.org/10.1101/158147

[3] RetroPath2.0 download page: https://www.myexperiment.org/workflows/4987.html