OpenPlant Fund opens to applications for £5000 grants on plant or cell-free synthetic biology

OpenPlant Fund offers £5000 to support open, interdisciplinary and innovative projects to engineer plant biology. Applications are now open until 1 Dec 2016 for projects led from University of Cambridge or Norwich Research Park with external collaborators welcome. For this round applications focused on cell-free synthetic biology are also encouraged.

The aim of the OpenPlant fund is to promote the development of plant Synthetic Biology as an interdisciplinary field and to develop open technologies and responsible innovation in the context of plant Synthetic Biology.

This call is also encouraging applications related to use of cell-free extracts from bacteria, plants, yeast or other organisms to transcribe and translate engineered DNA. Cell-free synthetic biology is gaining popularity for prototyping genetic circuits and metabolic pathways and has many applications from production of biologics to paper-based diagnostic tests and biosensors.

OpenPlant Fund teams facilitate exchange between The University of Cambridge, the John Innes Centre, The Earlham Institute and The Sainsbury Laboratory and therefore are led by researchers from these institutions, but are open to all external collaborators.

Download: Poster | Flyer | 2015/16 Report

Apply now >>>

Want to learn more and find collaborators?

Join us at a mixer event at the Panton Arms on 21 November 2016, 18:00-20:00. Great talks from a previous funded project on microfluidics and from the Cambridge spin-off Sphere Fluidics plus an opportunity to pitch your idea or find a team to join!

Eligibility

Applicants should be graduate students or postdoctoral workers at the University of Cambridge, the John Innes Centre or The Sainsbury Laboratory. The team must be interdisciplinary, must contain members from both Norwich and Cambridge and may contain external collaborators of any type. Applicants must have agreement from their research supervisor and cost-code sponsor that the proposed project and management of the allocated funding will fit with their existing work. All proposals must lead to tangible, publicly documented and open outcomes, which could include (but are not limited to) the following:

• Design files and prototype for a hardware project
• Software development and documentation
• White paper arising from a workshop
• Educational resource
• Synthesis and sharing of useful DNA parts or vectors.

For more information and to apply see the OpenPlant Fund webpage.

[Closes 13 Jan 2017] APEX award (Academies Partnership in Supporting Excellence in Cross-disciplinary research award)

apex-awards

The APEX award (Academies Partnership in Supporting Excellence in Cross-disciplinary research award) scheme offers established independent researchers an exciting opportunity to pursue genuine interdisciplinary and curiosity-driven research to benefit wider society.

In partnership with the British Academy, the Royal Academy of Engineering and the Royal Society (‘the Academies’) and with generous support from the Leverhulme Trust, the APEX award (Academies Partnership in Supporting Excellence in Cross-disciplinary research award) scheme offers established independent researchers, with a strong track record in their respective area, an exciting opportunity to pursue genuine interdisciplinary and curiosity-driven research to benefit wider society.

The objectives of this scheme are to:

• support outstanding interdisciplinary research which is unlikely to be supported through conventional funding programmes
• promote collaboration across disciplines, with a particular emphasis on the boundary between science and engineering and the social sciences and humanities
• support researchers with an outstanding track record, in developing their research in a new direction through collaboration with partners from other disciplines
• enable outstanding researchers to focus on advancing their innovative research through seed funding

You can apply for this scheme if you are:

• an exceptional researcher with a strong track record as an established independent researcher (this can include engineering researchers, humanities and social sciences scholars and scientists)
• based at a UK University or not-for-profit research institution for at least the duration of the project
• applicants will be expected to collaborate with a research partner from a different discipline from their own or a different university in the UK

More information >>

Café Synthetique - OpenPlant Fund Mixer and Microfluidics

Nov 24, 2016 from 06:00 PM to 08:45 PM

Panton Arms 43 Panton Street CB2 1HL, Cambridge.

Café Synthetique is the monthly meetup for the Cambridge synthetic biology community with informal talks, discussion and pub snacks.

This month we’ll hear from 2016 OpenPlant Fund grantees and discuss your ideas for open, innovative and interdisciplinary projects in cell-free or plant synthetic biology.

OpenPlant Fund Mixer

The OpenPlant Fund will support innovative, open and interdisciplinary projects relevant to plant Synthetic Biology over 2015-19. Around 20 six-month projects per year will receive £4k each, with an additional £1k awarded on completion for follow-on and outreach. We are now accepting applications with a submission deadline of 1 December 2016.

If you are interested in finding out more, come along to our mixer event on November 21st.

This event will be casual, and informative so that you can find out more about the fund, share ideas and meet potential collaborators – you do not need to have a proposal ready formulated beforehand.

The aim of the fund is to promote the development of plant Synthetic Biology as an interdisciplinary field and to facilitate exchange between The University of Cambridge, the John Innes Centre, the Ealham Institute and The Sainsbury Laboratory for the development of open technologies and responsible innovation in the context of Synthetic Biology.

In 2015 the OpenPlant Fund supported 16 projects with very diverse aims, from lab-based projects to generate and characterise DNA parts, through hardware and software projects to workshops in intellectual property, hackathons and outreach.

For more information on the fund, click here.

Microfluidics

This month, Café Synthetique will also include a series of talks on the emerging topic of microfluidics. This month’s speakers will include Ivan Reyna-Llorens, Steve Burgess, Florian Hollfelder, and Clive Smith from Sphere Fluidics.

”Plant ProChip: A microfluidic device for high-throughput analysis of genetic circuits in plant protoplasts.”

Ivan Reyna-Llorens is post-doctoral research associate in the Department of Plant Sciences.

”High Throughput Screening of Synthetic Biology Libraries by ESI Mass Spectrometry”

Clive Smith is principal chemist at Cambridge based company Sphere Fluidics.

”Plant ProChip: Exploring the Use of Microfluidics for High-throughput Screening in Plants”

Steve Burgess is a research staff member in the Department of Plant Sciences.

”Topic title TBC ”

Dr Florian Hollfelder is a principal investigator in the Department of Biochemistry.

Please join us in the Panton Arms pub at 6pm.

Guest Post: If you can protoplast, you can encapsulate

The following is a guest post from the SynBio Fund project ‘Development of a microfluidic device for high-throughput analysis of genetic circuits in plant protoplasts’ from by Steven Burgess, Ivan Reyna-Llorens, Christian R. Boehm, Sara Abalde-Cela and Paul Bennett. A continuation project, entitled ‘Establishing 3D Printed Microfluidics for Molecular Biology Workflows’, was funded through the OpenPlant Fund in 2016 and recently a second OpenPlant Fund grant was awarded for the project ‘Plant-ProChip 2.0: High throughput transformation of plant protoplast’.

You can read the original post on their project blog here >>

We started this project with the aim of testing whether it is possible to use microfluidics to analyse plant protoplasts, and I think we now have the answer. After numerous rounds of testing we have improved our working method and are now able to routinely isolate and encapsulate protoplasts. This has been done for two model plant species including A. thaliana, and everyone’s favorite Bryophyte –Marchantia polymorphia, the workhorse of the OpenPlant Project for plant synthetic biology (Figure 1).

Figure 1: Encapsulation of protoplasts from model plant species

So the take home message from this project is – if you can protoplast you can encapsulate! But the story does not end here. To be of real use, this process needs to be coupled to transformation of protoplasts. As a result, we teamed up with Oleg Raitskinfrom Nicola Patron’s group at the Earlham Institute. Oleg has been optimizing protoplast isolation and transformation using Nicotiana benthamiana and had a couple of tips for improving isolation, including the use of a cork borer instead of scalpel blade for cutting up tissues to minimize mechanical damage, cutting tissue when submerged in the enzyme mix and using a high ratio of DNA to protoplasts during PEG transformation.

This was a fruitful collaboration, Oleg managed to transform protoplasts with a nuclear targeted Venus reporter and these were encapsulated by Ziyi in the Chemistry department (Figure 2).

Figure 2: Encapsulation of N. benthamiana protoplats expressing a nuclear targeted Venus reporter

So putting all this work together, we have in hand a simple, but very powerful system that opens up a whole range of possibilities for rapid phenotyping in plants (Figure 3).

Figure 3: Schematic of microfluidic analysis of plant protoplasts and some of the potential applications.

One of the stipulations of the project was to pursue science in an open manner, so we have been putting up information on the website protocols.io. I highly recommend checking out the site if you haven’t done so already, it has a great set up for disseminating protocols. Further we believe microfluidics is a great technique, so would encourage others to have a go as well!

Looking to the future there are still a few things we would like to work on, The project was briefly presented at Cambridge’s Cafe Synthetique meet-up and we had some great feedback, such as trying Calcium alginate encapsulation as a means of improving protoplast viability. Sorting of protoplasts is the next major goal, and requires redesign of a new chip, and finally improving the efficiency of protoplast transformation by developing an on-chip procedure would be a big advantage. This round of our project has come to an end, but stay tuned for future developments.

Finally I want to finish this piece with a big thanks to Cambridge Synthetic Biology SRI for funding the work, it has been a great experience, and to encourage anyone who is interested in protoplasts or microfluidics to get in contact, we are always happy to chat!

OpenPlant stand at the first Norwich Science Festival

Roger Castells-Graells showing off the 80-sided virus structure built with the creative help of lots of kids at Norwich Science Festival.

In October 2016, Norwich hosted its first ever two-week long science festival. The event was a huge success and attracted an estimated 100,000 visitors. One weekend was dedicated to showcasing research from the Norwich Research Park, entitled ‘solving problems with science’ and the local OpenPlant team took the ‘Power of Plants’ stand that was originally designed and run at the Latitude Festival earlier in the year. We were joined for a day by Dr Katrin Geisler from the University of Cambridge to highlight the 'Power of Algae'.

In addition to this, we were joined by John Innes Centre scientist Roger Castells-Graells who brought his new project ‘VRICKS’ that was created at a recent OpenPlant Co-Lab interdisciplinary science design workshop. This extra activity fitted well alongside the hypertrans plant expression system game which used the example of making flu vaccines in plants. The concept of VRICKS is a resource for building 3D virus structures to explore the biology and the geometry of viral organisms. However, for the festival we wanted to draw on the strengths of people power to build a giant virus structure where everyone who visited the stand was able to make one piece!

Working together to plan and deliver at public events is a great team exercise for scientists to think about how best to translate their research using practical tasks and accessible dialogue. Taking time to explore your work with the public builds understanding and trust in the value of research and is particularly rewarding to do in your local city.  We are very much looking forward to the 2017 Norwich Science Festival!

A moment of calm checking the exhibit before the public arrive.

[Closes 4 Jan 2017] Readership in Synthetic Biology, University of Cambridge - Department of Engineering

Location: CambridgeSalary: £59,400 (Grade 11) Hours: Full Time Contract Type: Permanent Placed on: 2nd November 2016 Closes: 4th January 2017 Job Ref: NM09701

Applications are invited for a Readership in Synthetic Biology at the University of Cambridge. This is a tenure-track position at a level equivalent to Associate Professor and will be based in the Department of Engineering and is supported by the School of Biological Sciences (SBS). We particularly encourage applicants who complement current research within Engineering and SBS, and who are motivated to explore interdisciplinary collaborations. The successful candidate will have an established experimental research program in a topic including, but not limited to:

• Design and engineering of synthetic genetic circuits (both cellular and cell-free)
• Genome engineering
• Biosensing and biological signal processing
• Spatio-temporal gene regulation
• Engineering of multicellular interactions and tissue structure/function.

In addition, research may combine theoretical and numerical approaches with experiments. The successful candidate will have, or be expected to develop, a record of world-class research commensurate with the international reputation and top-rank research rating of the Department.

The candidate will be expected to contribute exciting and innovative teaching material to our rapidly growing bioengineering courses in the Engineering curriculum, with teaching and administration accounting for approximately 40% of the role. Teaching responsibilities will include contributing to undergraduate courses, supervising undergraduate projects, examining and supervising post-graduate students.

The position is based in the Engineering Department in Cambridge.

To apply online for this vacancy and to view further information about the role, please visit:

www.jobs.cam.ac.uk/job/10986. This will take you to the role on the University’s Job Opportunities pages. There you will need to click on the 'Apply online' button and register an account with the University's Web Recruitment System (if you have not already) and log in before completing the online application form.

In addition to this, please ensure that you upload the application documentation as follows:

• Curriculum Vitae (CV)
• A publications list
• Statement of professional, teaching and research experience and describe your future research plans (no more than two A4 pages)

If you upload any additional documents which have not been requested, we will not be able to consider these as part of your application.

The closing date for applications is Wednesday 4 January 2017. If you have any questions about the application process, please contact the HR Office (hr-office@eng.cam.ac.uk, +44 (0) 1223 332615).

Informal enquiries may be made to Dr Michael Sutcliffe (mpfs@eng.cam.ac.uk), +44 (0) 1223 332996.

Please quote reference NM09701 on your application and in any correspondence about this vacancy.

The University values diversity and is committed to equality of opportunity.

The University has a responsibility to ensure that all employees are eligible to live and work in the UK.

Integrative bacterial artificial chromosomes for DNA integration into the Bacillus subtilis chromosome

The research presented in the following publication was funded in part through the OpenPlant Fund.

Juhas, Mario, and James W. Ajioka. “Integrative bacterial artificial chromosomes for DNA integration into the Bacillus subtilis chromosome.”Journal of microbiological methods 125 (2016): 1-7.

Cambridge Repository Full-Text | Publisher Full-Text

Open Access publication under CC-BY 4.0

Abstract

Bacillus subtilis is a well-characterized model bacterium frequently used for a number of biotechnology and synthetic biology applications. Novel strategies combining the advantages of B. subtilis with the DNA assembly and editing tools of Escherichia coli are crucial for B. subtilis engineering efforts. We combined Gibson Assembly and λ red recombineering in E. coli with RecA-mediated homologous recombination in B. subtilisfor bacterial artificial chromosome-mediated DNA integration into the well-characterized amyE target locus of the B. subtilis chromosome. The engineered integrative bacterial artificial chromosome iBAC(cav) can accept any DNA fragment for integration into B. subtilis chromosome and allows rapid selection of transformants by B. subtilis-specific antibiotic resistance and the yellow fluorescent protein (mVenus) expression. We used the developed iBAC(cav)-mediated system to integrate 10 kb DNA fragment from E. coliK12 MG1655 into B. subtilis chromosome. iBAC(cav)-mediated chromosomal integration approach will facilitate rational design of synthetic biology applications in B. subtilis.

Keywords

• Bacterial artificial chromosome;
• Chromosomal integration;
• λ red recombineering;
• mVenus;
• RecA homologous recombination

OpenCon 2016 Cambridge

November 24th, 2016, 09:30-17:00

Betty and Gordon Moore Library Wilberforce Road Cambridge CB3 oWD

OpenCon 2016 is the student and early career academic professional conference on Open Access, Open Education, and Open Data being held in Washington, DC.

The OpenCon 2016 Cambridge satellite event will bring together students, early career academic professionals and open advocates from around Cambridge (although anyone from the surrounding areas are welcome to join us!)

This year’s theme is Building Impact Through Openness.

Our goal is to support and build the open community in Cambridge. We want to empower attendees to make a difference in their respective fields through open research, data, education and access.

This year’s committee have brought together a sensational program of world leading speakers but there is also time scheduled for focus group discussion around actions that we can take to make a change in the world.

Furthermore there’s ample time set aside in the day to ensure all the attendees will be able to share their ongoing activities (in the “silent” unconference) and hopefully build new collaborations for the future.

You can follow the main OpenCon event in held in Washington DC #OpenCon, and you can join the discussion around the Cambridge satellite event at #OpenConCam2016.

We look forward to seeing you there! Please reach out if you have any questions.

For more information and booking, click here.

The event is organised by Kirstie Whitaker, on behalf of the OpenCon Cambridge organising committee

More information about this event…

[Closes 17 Nov 2016] OpenPlant PDRA to engineer circadian rhythms

As part of the OpenPlant Project (www.openplant.org) the Webb Lab in Department of Plant Science, University of Cambridge are looking to hire a postdoctoral researcher to engineer circadian rhythms in the model plant Marchantia.

OpenPlant is a joint initiative between the University of Cambridge, John Innes Centre, TSL and the Earlham Institute, funded by BBSRC and EPSRC. OpenPlant is a synthetic biology programme that promotes interdisciplinary exchange, open technologies and responsible innovation for sustainable agriculture and conservation.

We are seeking to hire a trained plant molecular biologist to contribute to the foundational tools and trait engineering programmes of OpenPlant. Synthetic parts will be developed for the measurement and manipulation of circadian rhythms in the model plant Marchantia. The PDRA will use and contribute new tools to the OpenPlant parts library to permit the measurement, perturbation and visualisation of circadian rhythms using luminescent and fluorescent probes with advanced image analysis algorithms. The developed parts will be used to understand and engineer entrainment, which is the pathway by which circadian clocks synchronise with the environment.

You should have a PhD is a relevant subject. Experience of molecular genetics, including RNA analysis, making transgenic lines and handling transgenic organisms is essential. Knowledge of circadian rhythms in Arabidopsis is desirable.

Contact Professor Alex Webb for further details aarw2@cam.ac.uk

Fixed-term: The funds for this post are available for 2 years in the first instance.

More information and to apply >>

Cafe Synthetique - 'Chloroplast engineering' and 'Biomimetic materials'

Monday 17 October 2016, 18:00Panton Arms 43 Panton Street CB2 1HL, Cambridge.

Café Synthetique is the monthly meetup for the Cambridge synthetic biology community with informal talks, discussion and pub snacks.

iGEM Cambridge team 2016 are taking part in the prestigious iGEM synthetic biology competition. Focusing on chloroplast engineering, the team are interested in using chloroplasts to produce metabolic products, such as biofuels and edible vaccines.

Michelle L. Oyen is a Reader in the Bioengineering in the Mechanics and Materials Division and the Bioengineering research group in the Cambridge University Engineering Department. Her work involves research on mechanical behavior in biological materials with many of her projects having a distinct biomedical focus.

"InstaCHLAM, a toolbox for chloroplast engineering"

iGEM team 2016, Cambridge, Department of Plant Sciences, University of Cambridge

"Biomimetic materials for structural applications"

Michelle L. Oyen, Reader, Cambridge University Engineering Dept., The Nanoscience Centre

Please join us in the Panton Arms pub at 6pm.

More information about this event…

Image credit: Photo from BASF on Flicker, licensed under cc by-nc-nd/2.0/-Image source

18 Oct: Sculpting evolution: engineering biology to address global disease challenges

18 October 2016, 7:30pm - 9pm followed by drinks reception

Dr Kevin Esvelt (MIT Media Lab) and Professor Luke Alphey (Pirbright Institute, founder of Oxitec Ltd) examine the science, ethics and regulation of genetic engineering to control mosquito-borne disease. What promise does this emerging technology hold and how do we ensure it is used responsibly?

FREE Registration >>

Biologists can now design genetic systems that engineer evolution in powerful ways with social, legal, ethical and environmental implications for our future. Mosquito populations can already be engineered using cutting edge techniques to drastically reduce their numbers or make them resistant to transmitting diseases like malaria, dengue or the emerging Zika virus.

Synthetic biologist Dr Kevin Esvelt (MIT Media Lab) will introduce his work on gene drive systems which rapidly spread malaria resistance within populations while Professor Luke Alphey (Pirbright Institute) will discuss his work founding Oxitec, a UK company that was the first to release genetically modified male mosquitoes whose offspring fail to reproduce, leading to dramatic reductions in numbers.

What safeguards and regulations are required to ensure responsible use of such technologies? What does it mean for humans to use nature's tools in this way? How do we balance the direct benefits for global health with any risks to our shared environment?

Talks and dialogue on the idea of sculpting evolution will be followed by a drinks reception.

More information about this event…

19 Oct: Programmable biology in the test tube

Wednesday 19 October 2016, 10:00-16:00, Department Of Plant Sciences Downing Street, University of Cambridge, Cambridge.

  During the event, the OpenPlant Fund will launch a linked call for mini-grants to support interdisciplinary collaborations on the theme of in vitro synthetic biology.Synthetic gene circuits can be used to generate rapid and low-cost paper-based diagnostics for diseases including Zika and Ebola. Dr Vincent Noireaux (University of Minnesota), Dr Nick Rollins (Cambridge Consultants) and Dr Fernan Federici (Pontificia Universidad Católica de Chile and University of Cambridge) present the technology and its disruptive implications during this seminar and hands-on prototyping workshop.

Programme

10:00 Practical Session 1 - Introduction to cell-free system and assay set-up

12:00 Open lunchtime seminars, Large Lecture Theatre

Keynote: 'Cell-free Synthetic Biology', Dr Vincent Noireaux (University of Minnesota)

XylemDx and paper-based diagnostics', Dr Nick Rollins (Cambridge Consultants)Further talks TBCQ&A panel session on challenges and opportunities for in vitro synthetic biologyLaunch of an OpenPlant Fund call for innovative, interdisciplinary and open technology projectsIntroduction to forthcoming opportunities from Global Challenge Research Funds 14:00 Practical Session 2 - analysis of assay results

Joining for the lunchtime seminars only

Please register through eventbrite for your free ticket! Lunch is not included but you are welcome to bring your own.

Register for lunchtime seminars only >>

Applying for the practical workshop

Places are limited to a maximum of 30 for the practical session so we ask that you apply giving a brief statement about your interests and background by midnight on Mon 10 Oct. Places will be confirmed on Wed 12 Oct.

These spaces include attendance at the lunchtime talks and a free lunch. Please sign up only if you intend to join for the whole day.

Apply now for the practical workshop >>

Deadline Mon 10 Oct 2016, confirmation of places on Wed 12 Oct 2016.

Synthetic biology for regenerative medicine

Tuesday, November 8, 2016, 6:30 PMto8:00 PM

Old Divinity School, St John's College, St Johns St, Cambridge CB2 1TP, Cambridge

Professor Ron Weiss (MIT) introduces the design and implementation of synthetic gene circuits in mammalian systems, exploring the potential of this approach in regenerative medicine and stem cell engineering. The talk and dialogue will be followed by a wine reception and delicious finger buffet.

Professor Ron Weiss (MIT) is a pioneer of synthetic biology and is currently Professor of Biological Engineering at MIT in the Department of Biological Engineering and the Department of Electrical Engineering and Computer Science.

The Weiss lab uses computer engineering principles of abstraction, composition, and interface specifications to program cells with sensors and actuators precisely controlled by analog and digital logic circuitry encoded in synthetic gene networks. These circuits can be used to control the behaviour of individual and aggregated cells and from early work in bacteria, the lab has more recently explored transcriptional regulation in mammalian cells. Professor Weiss’s research has traced a journey from genetic parts to modules and is now devising therapeutic systems that more reliably direct stem cells to create new tissues. This work aims to move towards replacing the cells lost to disease or injury, pushing the frontiers of the nascent field of synthetic morphogenesis. In this talk, we will explore the potential of synthetic biology as an approach in regenerative medicine and stem cell engineering.

The talk and dialogue will be followed by a wine reception and delicious finger buffet.

Registration: £10/£5

This event is organised by the Synthetic Biology Strategic Research Initiative as part of our Michaelmas Term 2016 SynBio Forum. For more events please visit:

http://www.synbio.cam.ac.uk/events/forum

Please use this link to book attendance

Science Makers: drones for science

Science Makers is a monthly event to discuss and build low-cost, DIY and open hardware for science and education.

This month we're looking at the hot topic of drones, which are dropping in price and allowing more and more researchers to consider aerial studies which would previously have been prohibitively expensive. Drones are revolutionary in offering a fast and efficient way of collecting geological, atmospheric and wildlife data from above. Able to be equipped with on-board GPS navigation, sensory equipment, and even autopilots, many scientific groups are starting to catch on to the growing trend, with drones fast becoming the latest indispensable technology in many areas of science!

Hear from researchers building and using drones for science and get hands-on in the afternoon working on a project.

12:30 - Presentations and demos

Tom Swinfield - Conservation Scientist at RSPB

Working within the heavily degraded Harapan rainforest in Sumatra, Tom works on finding cost-effective, research-driven solutions to direct management of the forest. Part of his work involves optimising survey techniques to collect the best data possible, for which he has regularly utilises drones.

Nigel Butcher - Technical Development Officer at RSPB

Nigel organises the design and development of electronic devices for use in avian research undertaken by the RSPB. He has a particular focus on remote monitoring equipment and has experience working on drones for use in the field.

David Coomes - Professor in the Department of Plant Sciences, University of Cambridge

David leads a research group engaged in conserving biodiversity, with a focus on forest conservation and ecology. His group regularly utilises drone technology to measure carbon storage in forests.

13:30 - Pizza (£4 suggested donation)

14:30 - Making!

Hands-on drone project TBC

You are also welcome to work on your own projects.

RSVP here:

http://tiny.cc/54skfy 

SynBio SRI events in Cambridge, October

Sculpting evolution: engineering biology to address global disease challenges Venue: Howard Building, Downing College, Cambridge

Date: 18 October 2016, 7:30pm - 9pm followed by drinks reception

Register: http://tiny.cc/synbioforum-18Oct2016 Dr Kevin Esvelt (MIT Media Lab) and Professor Luke Alphey (Pirbright Insitute, founder of Oxitec Ltd) examine the science, ethics and regulation of  genetic engineering to control mosquito-borne disease. What promise does this emerging technology hold and how do we ensure it is used responsibly?

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Programmable biology in the test tube

Venue: Department of Plant Sciences, Downing Site

Date: 19 October 2016, 09:00-17:00, including talks and practical

Register: http://tiny.cc/synbioforum-19Oct2016 Synthetic gene circuits can be used to generate rapid and low-cost paper-based diagnostics for diseases including Zika and Ebola. Dr Vincent Noireaux (University of Minnesota), Dr Nick Rollins (Cambridge Consultants) and Dr Fernan Federici (Pontificia Universidad Católica de Chile and University of Cambridge) present the technology and its disruptive implications during these lunchtime seminars and a hands-on prototyping workshop (application required). The OpenPlant Fund will launch a linked call for mini-grants to support interdisciplinary collaborations on the theme of in vitro synthetic biology.

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Synthetic biology for regenerative medicine

Venue: Old Divinity School, St John’s College, St Johns St, Cambridge CB2 1TP

Date: 8 Nov 2016, 18:30 - 20:00 followed by networking reception with buffet

Registration (£10/£5): Link to be posted to http://www.synbio.cam.ac.uk when live Professor Ron Weiss (MIT) introduces the design  and implementation of synthetic gene circuits in mammalian systems, exploring the potential of this approach in regenerative medicine and stem cell engineering. The talk and dialogue will be followed by a wine reception and delicious finger buffet.

Interested in exploring cell-free synthetic biology for global health challenges? - APPLY for Development i-Teams by Friday October 7th

Have you ever wondered how new ideas can help people in the developing world? Are you interested in what Cambridge can do to help? If so, the Centre for Global Equality Development i-Teams programme is for you!The University of Cambridge SynBio SRI has put forward a synthetic biology-based project for the Development i-Teams Michaelmas 2016 'Exploring potential global health applications of cell-free extracts for rapid, low-cost, paper-based diagnostics', mentored by OpenPlant Fellow Dr. Fernan Federici. Find more information and how to apply below!

Global health applications of cell-free extracts for rapid, low-cost, paper-based diagnostics

Researcher : Dr. Fernan Federici, Plant Sciences, University of Cambridge and Pontificia Universidad Catolica de Chile

In vitro synthetic biology uses cell-free extracts from bacteria or other organisms to which DNA sequences encoding genetic circuits with useful functions are added and expressed. For example, a molecular sensor for Zika viral RNA or a pollutant heavy metal could be designed to produce a signal that regulates output of a measurable response, like high levels of a coloured chromoprotein. Beyond this simple example, DNA-encoded ‘logic gates’ could be constructed that respond in different ways to particular combinations of inputs or provide quantitative results.

Recent work combining this emerging technology with paper-based microfluidics has delivered rapid, low-cost paper tests for Ebola and Zika Virus and small molecule sensors such as glucose assays, which are stable in dried form for at least one year. As no genetic modification is involved, and a fully equipped lab is not required once the cell-free extract is produced and stably dried down, this technology is far more accessible to researchers in low-resource settings than in vivo synthetic biology. The initial cost of engineering biosensors is lowered very significantly.

The potential applications of this technology are directly relevant to diagnosing health and environmental problems faced by people developing countries. Many such problems pose significant challenges to their welfare and economic development e.g. pollution, tropical infectious diseases, animal disease, soil health. By promoting the development of a low-cost, low-resource technology platform the intention is to build capacity in-country for prototyping solutions to challenges identified as priorities locally.

The inventor of the technology, Dr. Fernan Federici, is working on open technologies including hardware and DNA parts that would further increase the ease and suitability of these cell-free systems for research, development and applied use in the global South. With reduced IP encumbrance, it is hoped that knowledge transfer can be accelerated and barriers to access reduced.

The Development i-Team will need to investigate two separate questions relevant to this technology.

First they will investigate the likely applications of paper-based synthetic gene networks in the developing world, and in particular will need to identify areas where local problems are not addressed by existing solutions and there is scope for developing local capacity for research in this area.

Secondly they will explore the commercial implications of building diagnostics based on open technologies that are freely shared and not protected by patent. How does this make a difference in the global South? How does it alter the typical value chain for such technologies? Could open approaches confer benefits in terms of access for the bottom three billion and in what contexts? In particular, are there any mechanisms of sharing IP with the local community which is directly affected by the problem?

More information on Development i-Teams and how to apply

The Centre for Global Equality and i-Teams are running the "Development i-Teams" programme for the fourth time this Michaelmas term. Teams will investigate ways in which real Cambridge innovations could be used in the developing world to improve people’s lives in a sustainable way.

This term’s projects are:

• Establishing sustainable community cloud infrastructures in the developing world;
• Exploring potential global health applications of cell-free extracts for rapid, low-cost, paper-based diagnostics;
• Farming and processing microalgae to address Vitamin B12 deficiency.

Development i-Teams is open to all students (undergraduates and post-graduates), post-docs and staff, as well as all members of the Centre for Global Equality - anyone with an interest in how technology can make the world a better place for the world's poorest.

The course runs on Tuesday evenings from the 18th of October to the  22nd of November, and there will be approximately 4 hours of individual work needed each week, mostly involving gathering real-world feedback from experts in international development.

For more details and to apply for a place on a team, see http://iteamsonline.org

For more information about the work of the Centre for Global Equality see http://centreforglobalequality.org

Nuffield Council on Bioethics publishes Genome editing: an ethical review

The Nuffield Council on Bioethics has today published the first findings of its programme of work looking at the recent and potential impact of recent advances in genome editing such as the CRISPR-Cas9 system across many areas of biological research.

The Council found evidence that, given its technical advantages and rates of uptake, genome editing is already having an almost unprecedented impact in research. The Council considered factors such as the extent to which the ethical questions raised by applications of the technology are novel, the likelihood of imminent advances in these areas and the possible effects of these advances in fields such as health care, food production, industry and public health.

Genome editing techniques are an essential tool for synthetic biology and while centred around more standard forms of single gene editing, the report acknowledges the field (sections 7.3-7.6) and the use of gene editing in food crops (5.1-5.17)

Synthetic Biology

"Synthetic biologists are self-consciously elaborating a novel field. They see the field as transforming biology as a practical discipline, not only in relation to the adoption of technical innovations, but also epistemically and institutionally (breaking down disciplinary barriers and reimagining biology as an engineering discipline), and socially and politically (e.g. the desire to build a community and to inculcate certain norms, including those of open source publication and responsible innovation practices). While, undoubtedly, genome editing has given a fillip to synthetic biology it does not, however, seem to have the same rhetorical significance here as in other areas of biology. This might be partly attributable to the fact that the natural reservoir of metaphor for synthetic biology is technical (engineering, construction) rather than textual (editing).

Synthetic biology does, however, offer an insight into possible ways of approaching genome editing as an innovation within research and industry that is essentially different to the translational approaches of biomedicine or, again, public health innovations. Owing, in part, to the different cultures that are integral to synthetic biology (e.g. that of computer science) and in part to lessons about innovation learned from the observation of other fields (e.g. nanotechnology), it has been common for synthetic biologists to adopt responsible innovation practices from the outset. These tend to see ethical reflection and social engagement as longitudinally integral to their practice (‘ethical by design’), as both guiding and governing research, rather than as challenges or decisions to be addressed at particular stages."

Plants

"Genome editing is currently used in research into plant breeding. Possible commercial uses include improvements in yield and pest resistance, increased drought tolerance, and increased nutritional benefit.

The impact of genome editing techniques is perhaps less revolutionary in plants than in humans, given the already long history of breeding strategies that have changed the genetic characteristics of virtually all crops – including selective breeding and first generation ‘genetically modified’ plants (mainly involving the insertion of genes that do not naturally occur in those plants).

However, genome editing could significantly speed up the progress of breeding programmes. It is thought that genome editing could reduce the time needed to generate the desired genetic characteristics in a plant population from 7-25 years to as few as 2-3 years since its target specificity effectively bypasses the need to go through a number of plant generations to achieve a particular genetic combination.

Depending on the regulatory and economic conditions, it could open up the field to smaller companies and, potentially, drive the development of characteristics other than the main commercially important traits like herbicide resistance."

Read the full report >>

7th October - SynBio for Schools: A multidisciplinary approach

Information and Ideas Meeting, Cambridge

Friday 7^th October, 16:30 – 18:30 Cambridge Makespace, 16 Mill Lane, Cambridge, CB2 1RX

Register here: https://goo.gl/forms/yCI9Y9D0IAspB5yj1

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Synthetic biology applies design and engineering approaches to biology, and promises to contribute solutions to pressing global challenges. The success of this highly interdisciplinary field depends not only on skills as diverse as molecular biology, computer modelling, engineering, social sciences and design, but also an ability of individuals to build bridges across disciplines. The Synthetic Biology for Schools project aims to bring together a set of activities and resources to enable school groups and science clubs to explore the synthetic biology space. Read more about the project below.

I invite you to join the meeting at 4.30pm on 7th October at Cambridge Makespace. Maybe you already have educational activities and resources that can be shared and fit into this context (including, but not limited to molecular biology, engineering, standards and modularisation, circuitry, computer modelling, responsible research and innovation). Maybe you are interested in developing new synthetic biology learning resources, or maybe you are interested in new activities that you can use to engage school pupils or the public.

This meeting coincides with the Co-Lab Big Making Weekend run by the Open Science School so that people from this event can also attend. Please check out their event pages if you would like to get involved in some of the ongoing projects.

There will be a second meeting and 1-day hackathon in Norwich in November (date TBC) for those who wish to join. It will not be essential to attend both meetings.

Project Overview Synthetic biologists in Norwich and Cambridge and collaborators from the Open Science School, The SAW Trust, and Universidad Catolica (Chile) are working on several ideas for developing educational materials, tools and practicals to bring multidisciplinary science and synthetic biology into schools. Some of these resources are already in development. In addition, open hardware is being created that could be used by schools to support practicals in this area. While each of these resources are valuable on their own, by bringing them together there is an opportunity for increasing their reach and effectiveness, and therefore their overall impact. In this project we propose to i) identify relevant activities, resources and amterials and bring them together into a comprehensive set to explain the principles, tools and applications of synthetic biology; ii) develop video and infographic materials that provide a context for these resources; iii) bring together key stakeholders and facilitate discussions with potential end users, and; iv) identify routes for dissemination and create an action plan to maximise their use. The outcome will be a complete package of activities, supporting information and hardware that can be successfully used in schools to introduce synthetic biology with a focus on plants, and to provide learning opportunities across a wide range of disciplines. Our intention within the scope of this project is to target the resources for schools in the local area, but we are also looking at national and international opportunities for dissemination. Initially we are looking at targetting school groups and science clubs from GCSE level on, but we will keep an open mind about target groups as there may be opportunities to pitch the resources towards different groups such as undergraduates, DIY bio communities and the general public.

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This project is funded by an OpenPlant Fund mini-grant.

[Closes 7 October 2016] Postdoctoral position in synthetic biology at University of Lausanne, Switzerland

Applications are invited for a postdoctoral position in the group of Professor Yolanda Schaerli, Department of Fundamental Microbiology, University of Lausanne, Switzerland to build synthetic gene regulatory networks in E. coli.

Postdoctoral position in synthetic biology

• Department of Fundamental Microbiology, University of Lausanne
• Starting date: March 1st 2017 or by arrangement

Qualification:

Candidates should hold a PhD in life sciences and have a strong background in synthetic and/or molecular biology. Experience with RNA circuits or computational modelling would be a plus.

Postdoctoral applicants should have one or more first-author publications in major peer-reviewed international journals. A good command of the English language, a high personal motivation to excel in science and a curious mind are required. 

Work description:

The Schaerli lab (www.yschaerli.com) carries out interdisciplinary research at the interface between synthetic, systems and evolutionary biology. We will move to the Department of Fundamental Microbiology, University of Lausanne in January 2017. We are looking for a motivated post-doc to join our team in Lausanne. 

The selected candidate will work on building synthetic gene regulatory networks in the chassis E. coli, using a combination of experimental and computational approaches. In the second phase of the project these networks will be subjected to laboratory evolution experiments to test evolutionary hypotheses. The postdoc will have the opportunity to lead research projects and work with motivated PhD and Master students. The qualified candidate will benefit from working in a very stimulating and international research environment in a young team with access to state of the art facilities.

How to apply:

Please send your full application including motivation letter, CV, list of publications and the names and addresses of three referees to: yolanda.schaerli at unil.ch.

Bio-start UK offers £200k of funding & support for your biotech startup - deadline 14th October 2016

SynbiCITE in partnership with Rainbow Seed Fund is running Bio-start, a competition to help promote the commercialisation the engineering of biology in the UK.

Bio-start is an annual competition designed to commercialise the engineering of biology and is currently seeking people and companies looking to solve significant global problems through synthetic biology.

The winner of Bio-start will receive up to £200K of equity free funding, labspace and access the London DNA Foundry. The competition provides entry into an accelerator programme with expert mentors and partners to support teams commercialise their ideas.

For further information on Bio-start please click here.

Scope of the competition

• Bio-start seeks applications that will enable the UK bioeconomy to grow and thrive
• Application areas can be in healthcare, agritech, clean tech, industrial biotech or any sector where engineering DNA is an essential component and makes use of synthetic biology
• Applications must not be service provision based
• Applicants do not need to be a company to enter, although to receive the prize the company must become solely incorporated in the UK
• A key screening criteria to enter the competition is IP status; you will need to show you can license the relevant IP and have support from your TTO or employer
• All first stage entrants should note the need to secure or demonstrate access to IP when applying