[Closes 1 Mar 2019] CSIRO Synthetic Biology Future Science Fellowships scheme

The third round of the CSIRO Synthetic Biology Future Science Platform Future Science Fellowships scheme is open – please see details below. These Fellowships provide an opportunity for early-to-mid career researchers (academic rank A-C in the Australian system) to develop their careers in synthetic biology research through collaboration with their Australasian host university (or other eligible host organisation) and CSIRO, Australia’s peak scientific research organisation. Applications close 5pm Australian Eastern Standard Time, Friday 1st March 2019.

Further information and application instructions for the Fellowships are available at: https://research.csiro.au/synthetic-biology-fsp/work-with-us/synbio-fellowships

The 2019 priority Application Domains are Health & Medicine, and Maximising Impact (social sciences). Applications in other Application Domains will also be accepted. We also have a technical priority area: BioFoundry use (high throughput robotic engineering; Foundry facilities are available). Further details can be found in the Priority Areas (see section under ‘Projects’ in the Instructions to Applicants).

Fellowship Enquiries: SynBioFSP@csiro.au

Foundry Enquiries: SynBioFoundry@csiro.au

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2019 CSIRO Synthetic Biology Future Science Fellowships

CSIRO’s Synthetic Biology Future Science Platform (SynBio FSP) is pleased to announce the opening of the third round of CSIRO Synthetic Biology Future Science Fellowships.

The scheme aims to attract outstanding national and international early- to mid-career postdoctoral researchers (equivalent to Australian Academic Levels A and B, or in exceptional circumstances, Level C) to expand Australian research capacity in synthetic biology. A key element of the SynBio FSP is establishment of a collaborative community of practice extending across CSIRO and Australia more broadly, and linking into international efforts in the field. Research projects must demonstrate an ability to build Australian capacity in synthetic biology.

Fellowships will be hosted at a Host Organisation (usually an Australian University, but other Australian research organisations may also be eligible) and will be a partnership between the Fellow, CSIRO, and the Host Organisation. Fellows will be employed by the Host Organisation but will maintain a strong linkage to CSIRO through a partnering CSIRO Mentor(s) and various joint activities designed to support development of a synthetic biology community of practice across Australia. Fellows will have a Visiting Scientist appointment at CSIRO and may spend a portion of time physically located within a CSIRO research group if appropriate for the Fellowship project.

How to apply?

Further information and application instructions for the Fellowships are available at: https://research.csiro.au/synthetic-biology-fsp/work-with-us/synbio-fellowships

Applications must be submitted by 5pm Australian Eastern Standard Time, Friday 1st March 2019.

The SynBio FSP strongly supports women and other minorities in STEM disciplines. We welcome applications from such individuals and greatly value the diversity they bring to the SynBioFSP. We recognise that women are less likely to apply for engineering-related Fellowships and Fellowships in general, and would therefore like to encourage applications from women. Processes are in place to recognise and properly assess output relative to opportunity, and opportunities for flexible working arrangements and career interruptions are embedded in the Fellowship rules.

Further enquiries can be directed to: SynBioFSP@csiro.au

[Closes 24 Jan 2019] OpenPlant Programme Manager job

Apply here >>> https://www.jic.ac.uk/vacancies/openplant-programme-manager-osbourn-group/

Main Purpose of the Job

Applications are invited for the position of an OpenPlant Programme Manager to be based at the John Innes Centre in Norwich. This position is part of the £13 M OpenPlant Synthetic Biology Research Centre, a large collaborative project led jointly by the John Innes Centre and the University of Cambridge (http://www.openplant.org). The successful applicant will work closely with Professor Anne Osbourn (Director, OpenPlant, Norwich) and other scientists at the John Innes Centre and the Earlham Institute to co-ordinate, integrate, trouble-shoot, evaluate and report on the progress of the overall programme. A key part of the responsibilities of the post holder will be (with Professor Osbourn) to liaise with Professor Jim Haseloff (Director, OpenPlant, Cambridge) and his team to enable the successful delivery of the scientific and strategic goals of this large and complex project. The post holder will also be expected to take an active role in OpenPlant engagement activities.

Further details can be found at https://www.jic.ac.uk/scientists/anne-osbourn/.

Key Relationships

The successful applicant will be line-managed by Professor Anne Osbourn and will work closely with scientists within OpenPlant at the John Innes Centre and the Norwich-based Earlham Institute to co-ordinate and enable the successful delivery of the Norwich-based parts of the OpenPlant programme. A key part of the responsibilities of the post holder will be (with Professor Osbourn) to liaise closely with Professor Jim Haseloff and his team to co-ordinate, integrate, trouble-shoot, evaluate and report on the progress of the overall programme. The post holder will also be expected to take an active role in OpenPlant engagement activities.

Main Activities & Responsibilities

• Oversee the day-to-day running of the OpenPlant Lab (Norwich) - co-ordinate, integrate, trouble-shoot, evaluate and assist with reporting on the progress of the overall programme

• Liaise closely with Professor Jim Haseloff, the Cambridge-based OpenPlant Project Manager, and scientists in the OpenPlant Lab (Cambridge) to ensure effective integration of the two-site Programme and to maximise opportunities for synergy

• Organise meetings, workshops, training courses, engagement activities and other events on behalf of OpenPlant

• Undertake other science engagement/social science activities relevant to OpenPlant

• As agreed with line manager, any other duties commensurate with the nature of the role

[Closes 22 Jan 2019] Tenure-track assistant professor position in Plant Genome Engineering

The department of Genetics Development and Cell Biology at Iowa State University (ISU) is inviting applications for a tenure-track assistant professor position in Plant Genome Engineering. They’re looking for a plant biologist who uses and/or develops genome editing technologies in their research.

Apply here >>> https://www.iastatejobs.com/postings/37758

GDCB seeks to hire a plant biologist who addresses fundamental or applied questions in the mechanisms of plant function and/or development at the cellular and molecular level using genome engineering such as CRISPR/Cas gene editing. Scientists developing resources that potentially reshape specific plant characteristics for the benefit of the environment and the human condition are strongly encouraged to apply.

Areas of interest will address or integrate Signature Themes at ISU in Biological Systems, Datarich Environments, and Environmental Sustainability, including but not limited to: molecular and cellular processes integral to plant health or disease, genome dynamics, phenomics, plant development, epigenetics, genetic and metabolic regulatory networks, and plant responses to environmental signals and stresses. Interdisciplinary or collaborative research is encouraged.

Responsibilities include building a nationally recognized research program that competes successfully for extramural funding, advancing the discipline through high-quality publications, mentoring students, and effective teaching of undergraduate and graduate courses. The successful candidate will demonstrate excellent communication and leadership skills and will share the university’s commitment to an inclusive environment that supports diversity.

GDCB and ISU provide an interactive, collegial environment of world-class scientists studying biological questions of fundamental importance, with particular strengths in plant sciences. Our faculty use experimental and computational approaches in an array of organisms, and participate in interdisciplinary graduate training programs in Plant Biology, Genetics and Genomics, Molecular, Cellular and Developmental Biology, Bioinformatics and Computational Biology, and an NSF Research Traineeship in Predictive Plant Phenomics.

Required Qualifications:

• Ph.D. in life sciences or related

• Published record of high-quality research

Preferred Qualifications:

• Demonstrated ability or clear potential to secure extramural funding

• Evidence of ability to develop a research program with potential for national distinction

• Research plan that enhances existing strengths at ISU

• Engagement in interdisciplinary or collaborative research

• Postdoctoral research experience

• Demonstrated ability or potential to excel in scholarly teaching

• Evidence of commitment to an inclusive climate that supports diversity and enableshonest and respectful exchange of ideas

Please visit https://www.iastatejobs.com/postings/37758 to view the entire vacancy and apply electronically. For full consideration, submit the application by January 22, 2018.

Improving homebrewing with the help of arduinos and XOD: Our Biomaker Challenge

We are a small, merry band of newbie Biomakers and amateur homebrewers and have started a project to monitor the progression of our fine brews in real time. By day we are two research scientists and a Biology teacher.

 We are looking to develop a piece of kit which allows us to see how quickly our homebrew is turned from a mixture of sugars in the initial malty extract into alcohol in beer. As sugars are converted to alcohol by the yeast, the density, or Specific Gravity (SG), of the liquid decreases and this is traditionally monitored by the means of a hydrometer. The SG decreases over time until it reaches a final plateau, at which point all of the sugars have been turned into alcohol. We are interested in monitoring how quickly this happens and how we can monitor it in real time.

Sam’s Biomaker Starter Kit arrives “what an exciting package to find on my desk first day back in the lab in 2019!”

An alcohol meter, testing beer immediately after brewing but before fermentation.

Image by Jeena on Wikipedia, shared under CC BY-SA 3.0

Getting started…

Initial challenges

As two of us have absolutely no prior knowledge of using Arduinos the first challenge has been to work out which end of the lead plugs into the laptop and which end into the Arduino. One of us has much more experience of programming, but not huge experience with Arduinos. It’s pretty much a ragtag skillset, held together with a Whatsapp group, copious mugs of tea, soup, swearing and an overarching dedication to the cause of better homebrew.

Initial thoughts

The learning curve of getting the Arduinos, laptops and components to talk to each other was incredibly steep. A few pointers from the ever-helpful Colette Matthewman helped immensely. Gratifyingly learning the XOD aspect of the project has been pretty straightforward. The online tutorials have stepped us through what we need to do in a logical manner.

 Our initial design has been modified, from just monitoring the height via the height sensor supplied, to attaching a Hall Sensor to the Arduino and attaching magnets to the hydrometer. We have developed ideas which can spring from this once we’ve got the basics in place and are quite excited (an overused word), about the potential scope of what we’re playing with.

 We are still very much in the early stages of the project, but are learning and have welcomed the opportunities to work towards a common goal (better beer), whilst acquiring new skills. This project has some way to run and will, no doubt, be adapted, modified and changed over time.

Follow our progress (intermittently) via twitter @dewhurst_ben, @popupcamptrout, @LP_Alwyn, @AutoBrewControl

More information about the Biomaker Challenge can be found at www.biomaker.org

[EoI deadline 15 Jan 2019] BBSRC/EPSRC Interdisciplinary Grants: Building Collaboration at the Physics of Life Interface

Expression of interest deadline: 15 January 2019, 16:00

Application deadline: 12 February 2019, 16:00

Full details at: https://bbsrc.ukri.org/funding/filter/2018-physics-of-life/

Summary

This is the first of two calls for proposals from the UK Research and Innovation (UKRI) Physics of Life Strategic Priority Fund to support internationally leading research that requires collaborative, interdisciplinary working to address key challenges at the interface of physics and the life sciences. This call will fund high-quality proposals that demonstrate deep integration of cutting edge experimental, theoretical and/or computational physics with life sciences research to advance our understanding of living systems in biological or biomedical contexts.

This UK Research and Innovation (UKRI) call, led by EPSRC with support from BBSRC and MRC, is making available up to £15 million, to include £13.2 million of resource funding and £1.8 million of capital funding. This call is open to staff of UK institutions who are eligible to receive funding from UK Research and Innovation (UKRI) as well as Public Sector Research Establishments (PSREs). Multi-institution applications are permitted.

Applicants interested in applying to this call must complete the intention to submit form on the call website by 16:00 on 15 January 2019. This information will primarily be used to manage potential conflicts when selecting the panel. Applicants will receive an email from UK Research and Innovation (UKRI) by 16:00 on Friday 18 January 2019 confirming our expectation that they will submit a full proposal. Full proposals must be submitted by 16:00 on 12 February 2019 and will be assessed directly by an interdisciplinary expert peer review panel from across the physics and life sciences communities.

We envisage high demand for funding, therefore we strongly discourage the premature submission of proposals which may benefit from further development in anticipation of the second Physics of Life call, which will be of a similar scale.

[Closes 6 Jan 2019] Post-doctoral researcher position in the Osbourn Group at John Innes Centre

Closing Date: 6 Jan 2019

>>> Apply here <<<

Grade SC6 Starting Salary: £31,250 - £35,400

Expected/Ideal Start Date: 01 Feb 2019

Duration: 17 Months

Main Purpose of the Job

Applications are invited for a Postdoctoral Scientist with expertise in natural product chemistry. The post involves extraction, analysis, purification and structural determination of medicinally important complex triterpene glycosides . The successful candidate will work with other researchers within the Osbourn lab as part of a multi-disciplinary team.

Further details of this project and the laboratory can be found at https://www.jic.ac.uk/scientists/anne-osbourn/.

Key Relationships

The successful applicant will be line-managed by Professor Anne Osbourn. The position is one of four postdoctoral positions funded by a Biotechnology and Biological Sciences Research Council (BBSRC) Super Follow-on Fund award for translational research. The successful applicant will work closely with this team and with John Innes Centre Metabolite Services.

Main Activities & Responsibilities

• Extraction, analysis, purification and strutcural determination of complex triterpenes (saponins)

• Prepare results, reports and manuscripts for publication in leading scientific journals and other relevant media

• Disseminate research findings though presentations to various audiences at internal, national and international meetings

• Collaborate with colleagues within the Institute in the development of original and world-class research, including contributing to research proposals and grant applications

• Liaise with industry and other external stakeholders

• Ensure research and record keeping is carried out in accordance with good practice, Scientific Integrity and in compliance with local policies and any legal requirements

• Contribute to the smooth running of the group, including the effective use of resources, supervision of visitors to the laboratory and assisting with training others, encouraging scientific excellence

• Continually strive for excellence, seeking out and acting on feedback and relevant learning and development opportunities

As agreed with line manager, any other duties commensurate with the nature of the role

[Closes 15 Jan 2019] Postdoctoral researcher post in bioinformatics and computational protein design

Job number: ACAD103712

Division/School: School of Chemistry

Contract type: Open Ended

Working pattern: Full time

Salary: £33,199 - £42,036 per annum

Closing date for applications: 15-Jan-2019

>>> Apply here <<<

A 2-year, BBSRC/EPSRC-funded, postdoctoral position is available to develop bioinformatics and computational tools for protein analysis and design. The post is in the protein design laboratory of Prof Dek Woolfson (Chemistry and Biochemistry, Bristol; https://woolfsonlab.wordpress.com/).

The post has two aspects: The first project involves the development of computational tools (bioinformatics and virtual reality (VR)) to facilitate in silico protein design. This is in collaboration with Dr Dave Glowacki (Chemistry and Computer Science, Bristol). Protein designs will be tested experimentally in the Woolfson lab. The second project involves the construction of a database for collating and interrogating atomic structures of protein-protein interactions (PPIs). This is in collaboration with Prof Andy Wilson (Chemistry, Leeds). This work will underpin experimental studies across the POPPI consortium of academic and industrial researchers (https://poppi.website/).

The protein-design work builds on the Woolfson group’s expertise in computational and experimental protein design. See: Thomson et al. (2014) Science 346, 485-488, DOI:10.1126/science.1257452; and Wood et al. (2017) Bioinformatics 33, 3043–3050, DOI:10.1093/bioinformatics/btx352. The aim is to combine this with expertise in VR and machine learning in the Glowacki group to create accessible, user-friendly tools for protein design. See: O’Connor et al. (2018) Science Advances 4, DOI: 10.1126/sciadv.aat2731.

The work on protein-protein interactions will contribute to an on-going computational and experimental effort to understand PPIs better. This understanding will be exploited in the design of peptide and small-molecule inhibitors of PPIs important to fundamental cellular processes and implicated in disease. See: Fletcher et al. (2018) Chem Sci 9, 7656-7665, DOI:10.1039/C8SC02643B. The aim is to generate a searchable database of PPIs of use to informaticians and experimentalists to interrogate and exploit PPIs.

The position is best suited to a talented and ambitious researcher with an interest in applying bioinformatics and computational biochemistry to protein science. Essential skills for this post include: an ability to program fluently in one or more computer languages, and ideally in Python; and experience with applications of bioinformatics, databases, or computer science in biochemistry or chemistry, and ideally in protein science. Desirable skills include: experience with computational protein design, databases for protein-structure analysis, molecular modelling in virtual reality environments, and in machine learning methods applied to protein science.

For informal enquiries, please contact: d.n.woolfson@bristol.ac.uk

The closing date for applications is Tuesday 15th January 2019.

We appreciate and value difference, seeking to attract, develop and retain a diverse mix of talented people that will contribute to the overall success of Bristol and help maintain our position as one of the world’s leading universities.

[Closes 14 Feb 2019] Four senior/lectureship posts available in Biological Sciences at Bristol University

Job number: ACAD103726

Division/School: School of Biological Sciences

Contract type: Open Ended

Working pattern: Full time

Salary: £43,267 - £51,630 per annum

Closing date for applications: 14-Feb-2019

>>> Apply here <<<

The School of Biological Sciences seeks four new academics at lecturer or senior lecturer level. Successful applicants will be research leaders with proven international track records commensurate with experience. They will drive influential research programmes that span the long-standing research strengths of the School: behavioural ecology and sensory biology, ecology and environmental change, evolutionary biology and plant and agricultural science.

Successful applicants will have strong interdisciplinary research portfolios and evidence of academic leadership along with strong commitment and aptitude for teaching at undergraduate and postgraduate level and roles across the spectrum of academic life.

A good fit to existing University Research Institutes and the Faculty of Life Sciences would also be an advantage.

For informal enquiries please contact Prof Claire Grierson (headofschool-biology@bristol.ac.uk).

The closing date for applications is 11:59pm on Thursday 14th February 2019. It is anticipated that interviews will be held during week commencing 1st April 2019.

[Close 18 Jan 2019] Two postdoc positions on AI and SynBio in Edinburgh Genome Foundry

The Edinburgh Genome foundry are looking for two post-doctoral researchers to work with the School of Engineering at the University of Edinburgh.

Research Associate in Mammalian Synthetic Biology

Closing Date: 18-Jan-2019

>>> Apply here <<<

Vacancy Ref: #046305

Contact Person: Dr Filippo Menolascina (Filippo.Menolascina@ed.ac.uk)

A 3 year, fixed term postdoctoral appointment is available within the School of Engineering at the University of Edinburgh to work on the automatic (re)design of synthetic promoters, primarily for mammalian cells, focusing on the control Chimeric Antigen Receptors expression.

As part of this project, the successful candidate will develop a microfluidics-based platform to perform high-throughput cell screening and will liaise with the Edinburgh Genome Foundry to build, and automatically model, large libraries of synthetic inducible promoters.

They will combine machine learning and computational optimisation to predict promoter strength, leakiness and automatically optimise promoter design to meet set specifications (e.g. maximise fold induction, minimise response time). They will also build a promoter to maximise sensitivity/specificity of transgene expression.

The ideal candidate should have a PhD with a background in Engineering or Computer Science and previous experience with techniques/protocols in Cell Biology and Microscopy. Experience with microfluidic device fabrication is desirable.

Research Associate in Microbial Synthetic Biology

Closing Date: 18-Jan-2019

>>> Apply here <<<

Vacancy Ref: #046306

Contact Person: Dr Filippo Menolascina (Filippo.Menolascina@ed.ac.uk)

A 2 year, fixed term postdoctoral appointment is available within the School of Engineering at the University of Edinburgh to work on the automatic engineering of synthetic microbial promoters.

As part of this project, the successful candidate will develop a microfluidics-based platform to perform high-throughput cell screening and will liaise with the Edinburgh Genome Foundry to build, and automatically model, large libraries of synthetic inducible promoters.

They will combine machine learning and computational optimisation to predict promoter strength, leakiness and automatically optimise promoter design to meet set specifications (e.g. maximise fold induction, minimise response time). They will also build a promoter to maximise sensitivity/specificity of transgene expression.

The ideal candidate should have a PhD with a background in Engineering or Computer Science and previous experience with techniques/protocols in Cell Biology and Microscopy. Experience with microfluidic device fabrication is desirable.

The Biomaker Challenge Winners and ways to get involved

The 2018 Summer Biomaker Challenge was wrapped up in October with a showcase event, but it not all over. Biomaker activities are still going strong! Below is a summary of activities as well as a write up of the Biomaker Fayre and the winning teams….

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Biomaker Activities

Winter Software Challenge (apply by 16 December 2018): Interested in programming? Low-cost hardware for science? Learning new skills with a team? We provide the hardware, you develop software nodes for integrating hardware with new graphical programming interface, XOD. More information at www.biomaker.org/apply-now - a quick, rolling application process so you can receive your kit and start playing ASAP!

Norwich Biomakers - An interdisciplinary network exploring the cross-over of biology with design, technology, engineering, electronics, software, art and much more. A place to learn about the latest technologies, share ideas and skills and shape projects. We meet up on a monthly basis.

Cambridge Synthetic Biology meetups - A clearing house for a wide variety of regular open meetings like Cafe Synthetique, Science Makers and the SRI Forums - with a particular focus on building tools and interdisciplinary research.

Cambridge Biomakespace - Scientists, engineers, students and entrepreneurs are developing the new Cambridge Biomakespace - an innovation space for building with biology in the historic MRC Laboratory of Molecular Biology building.

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The Biomaker Fayre

On Saturday 29 October, over 100 attendees came together in the University of Cambridge Department of Engineering to showcase and celebrate open-source technologies in research and education. The day consisted of a morning of talks followed by the Biomaker Fayre, where this year's ten Biomaker Challenge teams exhibited their projects alongside industry leaders and independent makers.

We started the day with some inspiring talks: Paolo Bombelli & Alasdair Davies on open tools for animal conservation and the "Powered by Plants" project, Grey Christoforo on hacking 3D printers to create better solar cells, Helene Steiner on OpenCell and teaching the next generation of designers to work with scientists, Richard Hayler on citizen science and education with Raspberry Pi and Julian Stirling on open instrumentation for Africa.

After a coffee break and lunch, we headed upstairs for the Biomaker Fayre. There was a festive feel to the space- gold balloons marked each exhibit, 3D-printed trophies were on display to be given out at the end of day, and attendees filled the space, excited to get involved and try out some hands-on demos.

Exhibits covered everything from a cartesian coordinate robot for dispensing fruit fly food to a wearable biosensor for monitoring vaginal discharge and a temperature-controlled container for sample transportation. Among the exhibitors were the ten Biomaker Challenge teams. In June, each team were given a £1000 grant and four months to turn their ideas for open source and DIY research tools into a reality.

The Biomaker Challenge judges were very impressed by each one of the projects and ended up deliberating for over an hour. In the end, the 3D-printed trophies (low-cost and DIY of course) were presented to the following teams:

Best Technology

Dual-View Imaging in a Custom-Built Light Sheet Microscope

Stephanie Hohn, Hannah Sleath, Rashid Khashiev, Francesco Boselli, Karen Lee

"The large variety of Biomaker projects was very inspiring. We had a lot of fun during the challenge and the feedback from people in different fields was really helpful. It was great to get in touch with programmers, engineers and designers. We received a great confidence boost for future more technical projects."

Stephanie Hohn (University of Cambridge)

Best Biology

Spectre, Low-cost whole-cell biosensors for environmental and medical surveillance.

Feng Geng, Boon Lim, Xiaoyu Chen, Jimmy Chen

"The Biomaker Challenge has provided us a great opportunity to extend our research into real-world application. As most of us come from a biological background, we faced a lot of difficulties on assembling the electronics and programming our Arduino kit. With three months of perseverance and constant guidance from our advisor Tony, we managed to come up with a customised, miniaturised spectrophotometer which can be used in conjunction with our whole-cell biosensor. We received an Arduino kit and sufficient funding to get us through the proof-of-concept stage of our project and from here, we are planning to further develop and optimise our device into a start-up company. It is amazing to think that it all starts with a small Biomaker Challenge Summer Project!"

Boon Lim, University of Oxford

Maker Spirit

Wearable biosensor for monitoring vaginal discharge

Tommaso Busolo, Giulia Tomasello, Michael Calabrese, James Che

"We all really enjoyed the multidisciplinary nature of the challenge, working with people from all sorts of backgrounds. We feel we now have a much clearer, hands-on insight into how the more diverse a collaboration is, the more relevant, impactful and exciting the results of ideas brainstorming can be!"

Michael Calabrese, University of Cambridge

Biomaker Challenge and Open Technology Workshop aimed to show the value of open, low-cost and DIY technologies as convening points for interactions between biologists and engineers. They are also important educational tools for those who are interested in developing technical skills and have great potential for improving the quality of science and increasing productivity in the lab for lower costs. With the proliferation of digital designs for 3D-printing and easily available consumer electronics like Arduino which has a huge community of users and lots of online help, designing your instrumentation around your experiment rather than vice versa has never been more possible.

Check out more photos from the day!

The descriptions of all prototypes are available at www.hackster.io/biomaker. To find out more about the most recent and upcoming competitions go to www.biomaker.org/biomaker-challenge to be kept up to date​​​​​​ with developments.

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Biomaker Challenge 2018 was funded by OpenPlant, a BBSRC/EPSRC Synthetic Biology Research Centre Grant BB/L014130/1. The Biomaker Challenge and Open Technology Workshop were coordinated by University of Cambridge's Synthetic Biology Strategic Research Initiative

Late night (biological) engineering in London

By Sami Stebbings

Once a month something amazing happens at the London Science Museum, and last month our collaborative team from OpenPlant, the SAW Trust, the University of East Anglia (UEA) and graphic recorder Rebecca Osborne, got to be part of it.

On the last Wednesday of every month, the London Science Museum opens its doors late into the evening to welcome adults to an engaging and free evening out, as part of the Science Museum Lates.

Each evening is themed around a different science topic, attracts around 4,000 guests per night and offers a relaxed atmosphere where you can walk around with a drink in hand whilst talking science.

This month’s theme was ‘The year of the engineer’ and we brought the synthetic biology edge to the night with our ‘Engineering Natural Products’ stand. With the help of Dr Richard Bowater (University of East Anglia), Hannah Griffiths (John Innes Centre) and of course DNA Dave, visitors were taken on a journey from the discovery of DNA through to how scientists engineer biological systems.

Our enthusiastic public engagement volunteers, Jenni Rant and Sami Stebbings (SAW Trust) and John Innes Centre PhD students' Hannah Griffiths and Shannon Woodhouse.

Our stand told the story of avenacin, a triterpene that is found in the roots of oat plants and helps make the plant resistant to fungal diseases. By understanding how these plants produce avenacin from the instruction in their DNA, we explored how scientists can engineer other biological systems to mimic their production. For example, can we transfer these genes from oat plants, into other crops, such as wheat which have no natural antifungal protection?

Guests had a plethora of activities to take part in, from our ‘Fishing for DNA’ activity, Avenacin Pathway puzzle, to getting up close and personal with an avenacin molecule using VR. They also had a chance to get hands on and infiltrate tobacco plants and see fluorescing oat seedlings!

With a steady stream of people throughout the night, the evening was a great success (not only because there was gin bar)! A massive thank you to all our collaborators who helped pull our stand and activities together, as well as the fantastically organised, London Science Museum team.

In was a great event to be part of and we hope to return to another Lates event sometime in the future!

OpenPlant Forum 2018: Engineering Plants for Bioproduction

Blog post by Dr Colette Matthewman

Over the past decade, synthetic biology has focussed much of its effort on microbial chassis as platform for bioproduction. The single cell simplicity and rapid life-cycles of these organisms, the prevalence of biological tools and the existing industry infrastructure for fermentation have made microbes a tempting playground for synthetic biologists wishing to make a range of chemicals and biomolecules, from flavours and fragrances to distributed manufacturing of highly complex metabolites for medicine, and an increasing number of companies are finding success in this arena (e.g. Ginkgo Bioworks, Amyris, Evolva, Antheia).

More recently, plants have been showing serious promise as viable production platforms for complex chemicals and biomolecules which in many cases simply can’t be made in single celled microbes. This year, the OpenPlant Forum explored some of the latest advances in plant bioproduction with inspiring talks from invited speakers and OpenPlant researchers highlighting a promising and exciting future for plant synthetic biology.

OpenPlant post-doc Ingo Appelhagen presents his work on anthocyanin pigment production in plant cell cultures.

The first morning of the Forum focused on tools for refactoring regulation and simple test platforms for plant synthetic biology. Prof. Ian Small (University of Western Australia) opened the meeting with a keynote on the potential for using engineered RNA bonding proteins to control organelle gene expression. OpenPlant PI, Prof. Paul Dupree described research in his on engineering of polysaccharide structures in plants. We also had the first examples of plant production platforms: Dr Ingo Appelhagen presented his recently published work on the production of colourful anthocyanin molecules in plant cell cultures, while Dr Eva Thuenemann introduced the HyperTrans system developed in the Lomonossoff lab at the John Innes Centre for the transient expression of proteins in Nicotiana benthamiana, a wild relative of tobacco. Eva is working on plant-based production of a protein that could be used in a vaccine against East Coast Fever, a devastating disease in cattle in Africa. The HyperTrans platform is used by the Lomonossoff lab and recently established company Leaf Expression Systems to produce therapeutic proteins and virus-like particles for vaccines, including recent work on a new vaccine for the eradication of Polio.

The afternoon session explored the cutting edge in production of complex plant-derived natural products in yeast, with a keynote from Prof. Christina Smolke (Stanford University), followed with an insight into the engineering of triterpene production in N. benthamiana by Dr James Reed in the Osbourn lab (John Innes Centre), recently reviewed in Plant Cell Reports. These projects rely heavily on chemical and enzymatic biodiversity in nature. Dr Sam Brockington (University of Cambridge) talked about harnessing the global network of botanic gardens for access to plant diversity for metabolic engineering and synthetic biology, introducing a global database of living plant, seed and tissue collections called “Plant Search” – a perfect sedgeway into a panel discussion on Harnessing Global Biodiversity where Sam was joined by Dr Nicola Patron (Earlham Institute), Mr David Rejeski (Environmental Law Institute), and Dr Jenni Rant (SAW Trust). The discussions ranged from public opinion on synthetic biology (explored through the Global Garden workshop) and benefit sharing and dematerialisation, through to how blockchain (like the bitcoin) is being used in environmental contexts and whether blockchain technology trends can be applied to create/assign value for biodiversity.

Prof. Ralf Reski with his moss bioreactors

Day two of the Forum continued on a theme of “Tools for Metabolic Engineering” with Prof. Claudia Vickers (University of Queensland) opening by introducing the Future Science Platform in Synthetic Biology that she leads at CSIRO, as well as numerous tools developed in her research lab. Claudia was followed by a trio of OpenPlant postdocs describing analysis to unravel the genetics of divergent metabolic pathways in Brassicaceae (Dr Zhenhua Liu), a search for new synthetic biology tools based on diversity of natural triterpene oxidation (Dr Michael Stephenson) and tools for engineering Marchantia’s chloroplasts (Dr Eftychis Frangedakis).

Moving on from the tools, we explored further plant-based bioproduction platforms, starting with an inspirational keynote from Prof. Ralf Reski (University of Freiburg) on the moss Physcomitrella patens that Ralf’s lab has established as a production platform for biopharmaceuticals, leading to foundation of the company Greenovation, which produces moss-aGal (agalsidase) for the treatment of Fabry disease, a rare but painful and potentially deadly disease. Subsequently, we heard from Prof. Alison Smith (University of Cambrige) about “Designer algae” and work towards predictable metabolic engineering in microalgae, and from Dr Eugenio Butelli (John Innes Centre) about the Tomato as a biofactory for making health promoting flavonoids.

The Forum was wrapped up for this year with a session on Sharing and Techno-Social Platforms, with an introduction from OpenPlant’s Prof Jim Haseloff, followed by Dr Linda Kahl (BioBricks Foundation) on the latest with the Open Material Transfer Agreement (Open MTA) which has been developed in collaboration with OpenPlant to enable sharing of DNA parts (publication coming soon!). Next up, Dr Joanne Kamens from not-for-profit plasmid distribution company, Addgene, revealed the freshly launched plant resource page and spoke about the upcoming adoption of the Open MTA as an option under which plasmids can be shared. Finally, Dr Richard Sever from bioRxiv spoke about preprint opportunities for synthetic biology.

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Join us in Cambridge for the OpenPlant Forum 2019 | 29 – 31 July

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