Call for participation in 4th International Synthetic & Systems Biology Summer School - to be held in Cambridge!

The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school at the Robinson College - University of Cambridge - UK on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts.

Biology meets Computer Science & Engineering

Recent advances in DNA synthesis have increased our ability to build biological systems. Synthetic Biology aims at streamlining the design and synthesis of robust and predictable biological systems using engineering design principles. Designing biological systems requires a deep understanding of how genes and proteins are organized and interact in living cells: Systems Biology aims at elucidating the cellular organization at gene, protein and network level using computational and biochemical methods.

The school provides a stimulating environment for students (from Master students to PhD students), Post-Docs, early career researches, academics and industry leaders. Participants will also have the chance to present their results (with Oral Talks and Posters), and to interact with their peers, in a friendly and constructive environment.

July 17-21, 2017 - University of Cambridge, Robinson College, UK

Website | Email | Facebook

DEADLINES

Application: March 31, 2017 Notification Acceptance: April 10, 2017 Oral Presentation/Poster Submission: March 31, 2017 Notification of Decision for Oral/Poster Presentation: April 10, 2017

SPEAKERS:

* Antonino Cattaneo, Scuola Normale Superiore Pisa, Italy * Jasmin Fisher, Microsoft Research & Cambridge Systems Biology Centre, UK * Carole Goble, University of Manchester, UK * Jim Haseloff, University of Cambridge, UK * Jay Keasling, University of California, Berkeley, USA Lawrence Berkeley National Laboratory, USA Joint BioEnergy Institute, USA * Edda Klipp, Humboldt University, Germany * Natalio Krasnogor, Centre for Synthetic Biology and Bioexploitation, Newcastle University, UK * Markus Ralser, Cambridge Systems Biology Centre, University of Cambridge, UK & The Francis Crick Institute London, UK * Uwe Sauer, Institute of Molecular Systems Biology, ETH Zurich, Switzerland * Sarah Teichmann, Wellcome Trust Sanger Institute & EMBL, European Bioinformatics Institute, UK

SCHOOL DIRECTORS:

* Massimo Gulisano, University of Catania, Italy * Giuseppe Nicosia, University of Catania, Italy * Steve G. Oliver, University of Cambridge, UK

[Closes 10 Jan 2017] BBSRC 16ALERT: Mid-Range Equipment Initiative

BBSRC are inviting applications from eligible researchers to purchase items of mid-range research equipment.

View full details and apply via BBSRC >>

Background

Advanced research equipment and the development of capability in its creative use is a key component in maintaining the competitiveness of the UK research base. The RCUK Strategic Framework for Capital Investment ‘Investing for growth: Capital Infrastructure for the 21st Century’ explains the important roles of acquiring state-of-the-art equipment into the science base, and the rapid development of people skilled in its use.

The capital equipment budget for this call is approximately £10M.

Applications for mid-range equipment costing over the current OJEU threshold (currently £115k net of VAT and import duty, £138k inc VAT) must enhance the capability of the UK research base in areas of science in our remit (see 'Our portfolio' in related links). Applications will typically be from groups of researchers in one or more eligible institutions, for instrumentation to be deployed on a multi-project/multi-use basis.

Scope

This is a capital funding call; awards will only fund the purchase of equipment and limited installation costs. No resource or other associated costs may be requested, and funding for the costs of research using the equipment should be found through other project funding. Consequently, in order to ensure sustainable equipment usage, applicants need to demonstrate their potential for obtaining continued support, for example via a track record of successful competitive grant funding, or through host institution commitments.

We encourage:

• applications for equipment that is widely used and underpins capability in the priority areas in our refreshed strategic plan (although the call is open to all scientific areas within our remit)
• applications that seek to pioneer the use of emerging advanced research technology
• applications that seek to utilise equipment in novel applications

Our strategic plan recognises that 'biological discovery is increasingly being driven by ground-breaking technologies, such as high-throughput genomic and proteomic analysis and next generation biological imaging, that generate massive and complex datasets'. To support these technologies, requests for pipelines of associated technologies (e.g. automated high-throughput platforms or workflows) will be supported where they come together to form a connected whole, and where the total cost is over the OJEU threshold (the value of each individual component must also be over £10k).

Computing infrastructure proposals should address a need for resources (such as cloud or high-performance computing installations) for large-scale data analysis, e.g. genome assembly, metagenomics and real-time image analysis that build on existing BBSRC investment and funded research activity. Computing equipment may also be requested in support of advanced research technologies where the scale of the data generated will necessitate significant new computing/data management resources (the total cost of the equipment must be over the OJEU threshold and the value of each individual component must also be over £10k).

Applications may seek the costs of initial service maintenance contracts, where these can be purchased upfront as part of a package with the relevant equipment. If these are required, they should be itemised as part of the requested equipment costs and must be fully justified. Costs of service maintenance contracts will not be paid beyond the end date of any successful awards.

Effective and efficient use of research equipment and instrumentation is dependent on trained staff, particularly where equipment will be available to multiple users. The application must set out the arrangements for the technical support of the equipment and the professional development of the individuals involved, including access to training and sustainability of the technical staff in question. Commitments to staff posts for the running and maintenance of the equipment, as well as for the training of users (where applicable), should be provided in the form of host institution contribution(s). Provision of staff, support and training will form part of the assessment criteria. BBSRC may establish a network of such staff for the consideration of professional development issues and relevant individuals would be expected to participate.

Value for money will be an important factor in assessment. Consequently, whilst contributions from the host institution(s) and/or other external sources are not mandatory, they are strongly encouraged.

In accordance with the Wakeham recommendations to maximize the use of equipment and to encourage sharing, the arrangements for managing access to the equipment and the prioritisation of its use should be fully described. Award holders will be expected to put arrangements in place for providing advice and support to others wishing to assess the potential of the technology for their own research.

Collaboration and the extension of access to the instrumentation to industry and public sector users that would enhance the potential impact of research is encouraged, and any arrangements for this should be explained in the application.

Where more than one instrument of a similar type or application is funded through the 16ALERT call, or where a range of capabilities is established that are applicable to the same research field, we may expect grant holders to operate within a network to share expertise and coordinate access.

Applicants are asked to provide details of the institutional environment into which the equipment will be integrated (e.g. existing facilities and related equipment, housing, technical and scientific support staff, plans for on-going management and maintenance of equipment). Multidisciplinary applications, spanning the remits of more than one Research Council, may be considered if the majority of the research in which the equipment will be utilised falls within our remit. Applications where the majority of the research falls outside our remit will be rejected (see 'Our portfolio' in related links).

Applicants uncertain whether the science in their proposal is within our remit must contact us before submission. If an application contains components of proposed research that fall outside our remit, we may seek the advice of other Councils as part of the assessment process.

Eligibility

16ALERT is open to institutions and researchers normally eligible to apply to BBSRC managed-mode calls; this includes BBSRC approved HEIs, strategically funded institutes and Independent Research Organisations (IROs)

• Categories of eligible organisations can be found in section 3 of our grants guide (see downloads)
• A list of IROs can be found in the RCUK eligibility guidance (see external links)

Applications that include principal or co-investigators who are not eligible to apply for funding, and/or from ineligible organisations will be rejected.

A research organisation may submit more than one application; however there is a limit on the number of applications from an investigator or consortium. Details of limitations are in the call guidance.

How to apply

Applicants should refer to the call guidance (see application downloads below).

Applications must be submitted using the Joint Electronic Submission (Je-S) system (see external links) by 10 January 2017, 4pm.

Plants at iGEM2016: guest post by Geraint Parry

This article is authored by Gerant Parry and originally appeared on the GARNet blog, it is republished with permission. 

Photo credit: the iGEM Foundation and Justin Knight

Take a look over there! As even the name suggests, the iGEM Giant Jamboree is a conference like no other.

Consider that there are 2500 mostly undergraduate students from all around the world, the vast majority of them at their first conference and each giving presentations that are being critically assessed. This provides a clue as to the kind of frenetic and excited energy that characterises this event.

For those a little confused, the International Genetically Engineered Machine Foundation oversees and organizes iGEM, which is synthetic biology competition for groups of participants who are usually hosted by academic institutions. The basic idea is that a group of students works through the summer on a completely novel project that conforms to the principles of synthetic biology, before presenting it in the aforementioned Giant Jamboree.

As this is a competition, each project is judged on metrics that assess many aspects of the teams work. These include the contribution of biobricks to the iGEM registry (an impressive selection of molecular parts that are held within a standardised plasmid), the development of their novel project, initiating collaborations with other teams and their attempts to integrate human practices and public engagement into their project. By meeting certain criteria each team is eligible for Gold, Silver or Bronze medals alongside special prizes for different project categories.

Given registrations, student stipends, research expenses, travel and accommodation, putting forward even a small team can stretch to at least £20K. Therefore this is not a something to be taken lightly. To this financial requirement must be added the time donated by a team of instructors and advisors that support the students. However regardless of the cost, one thing is certain; for those students who participate, attend, present and are inspired by the Jamboree, it can be a career-defining moment.

Plant Synthetic Biology can make for a challenging summer!

Plant experimental chassis have not been widely used during the ten years of the iGEM competition where bacteria, yeast, mammalian cell lines or cell-free systems offer time efficient alternatives for the usual 10-week research period. However the iGEM foundation, alongside a group of committed advocates have recently developed the Phytobricks cloning standard, which is based on a recently published standard syntax within the Golden Gate cloning system. The aim is to lower the barrier of accessibility for teams to start plant projects and the evidence from this years competition seems to suggest that this is slowly happening. The 2016 iGEM team from Valencia-UPV is advised by plant synthetic biologist Diego Orzaez and their project submitted phytobricks for the expression of a split Cas9 system. They showed that the two halves of the Cas9 protein could reconstitute and was active in a tobacco expression system. They have documented this work on their Parts pages and this is hopefully a resource that will be used by future iGEM teams. Their team was very successful at the jamboree, winning a gold medal alongside specific awards for the best hardware  and software.

Another successful team with a plant project was from SCAU-China who had, over the course of at least two years, added an additional two genes to conventional Golden rice. This produces a ‘brown rice’ that produces the natural keto-carotenoid Astaxanthin, which is thought to have beneficial anti-oxidant properties. This is clearly a significant research project that has been badged with the iGEM logo and as such was very positively received by the judges. Although they did not submit parts in the Phytobricks standard it was exciting to see such a potentially high profile plant-project feature at the jamboree.   These projects are well deserving of their awards and their work builds upon years of expertise contained within the supporting labs. This highlights one of the challenges for the competitive element of iGEM; namely how teams can be equally judged when they have hugely varying levels of support. Fortunately it appears that this is not a significant issue as each team is able to take positives from their own performances and are happy to celebrate the excellent projects that they each had individually put together.

Remarkably the iGEM competition includes at least 30 high school teams and one of these, GDSYZX in China, worked with plant light responsive promoters that they added to the Parts Registry.

Algae on the rise.

A number of teams including Cambridge-JIC, Linkoping University in Sweden and USP_UNIFESP in Brazil used the algae Chlamydomonas_reinhardtii in their projects. Cambridge team had most success in their project that generated a set of parts in the Phytobrick standard that can be used in future algal projects. In addition they created a remarkable blueprint for the production of a prototype Genegun for plant transformation, costing just £300, making it accessible for less well funded labs. The other two teams mentioned above were hoping to use Chlamydomonas to produce either biofuels or spider silk protein and although the ambition of both projects outstripped their achievements this year, iGEM is all about thinking big: sometimes it works, sometimes not!

The team from Pretoria in South Africa took on an extremely ambitious plan called WattsApatmer to create ‘plant batteries’ by using short aptamers to attach either photosystem II or a laccase enzyme to either pole of an electrical circuit held within a novel graphene scaffold. The students made some progress with this and the project serves to highlight the blue-sky thinking that undergraduate students undertake as part of this competition. It is clearly difficult to make enormous progress over a summer project but there were so many amazing project ideas on display at this iGEM I hope that the host institutions can find finances to develop some of these ideas so that some can come to fruition to add value to the time already committed to these projects.

Europe on Top

From a UK and European perspective the iGEM jamboree was a huge success with Imperial College and LMU TU Munich taking the overall undergrad and overgrad awards respectively, with remarkable projects that highlighted the talent of their students and the level of support their receive from their host institutions.

The UK was represented by over 20 teams, the third most numerous behind the USA and China. Aside from Imperial College, the teams from Exeter, Dundee, Dundee Schools, Cambridge-JIC, Oxford, Sheffield, UCL, Glasgow and Manchester gained Gold medals. There is little doubt that the UK is developing a cohort of talented synthetic biologists who will be the research leaders of the future.

Overall we look forward to seeing the number of plant projects increase over the years to come. The development of the Phytobrick standard will undoubtedly help in this goal for students to come up with ideas to test the possibility of using plants in their projects.

There are exciting times ahead for plant synthetic biology!

Cambridge iGEM team win Gold Medal and Best Plant Synthetic Biology Prize at prestigious international competition

Summary: A team of Cambridge students have been awarded a Gold Medal and Best Plant Synthetic Biology Prize for their entry into the International Genetically Engineered Machine (iGEM) Competition 2016.

iGEM is a prestigious international Synthetic Biology competition designed to challenge university students from around the world. This year more than 300 teams entered iGEM and came together on 27-31 October at the annual Giant Jamboree in Boston. The Jamboree represents a culmination of a summer’s worth of work, with the teams competing for prizes while learning from experts across the world. iGEM teams are tasked with designing a genetically modified system using ‘BioBricks’, a set of standardised biological parts, with the aim of having ‘a positive impact on their communities and the world’. The competition aims to bring synthetic bology, the melding of biology and engineering - to the forefront of research, in an effort to design innovative biological systems.

This year, the Cambridge team consisted of four Engineering and six Natural Sciences undergraduates, with support from faculty member advisors in Plant Sciences, Pathology, Engineering, Chemical Engineering & Biotechnology, and Physics - as well as engineering experts Cambridge Consultants, who sponsored the team.

Together they aimed to create a toolkit for algal chloroplast engineering, a process that holds great potential for producing everything from biofuels to edible vaccines both efficiently and in large quantities. In just ten weeks the team managed to generate a library of tested parts optimised for Chlamydomonas algae, build a gene gun for less than 1/100th of the current commercial price and design a genetic tool which helps achieve transformation of all DNA contained within a chloroplast (homoplasmy) in a much shorter timeframe than previously possible. This work won them a Gold Medal and the 2016 Best Plant Synthetic Biology Prize (overgrad category).

iGEM team member Ciara McCarthy said of the project: “We met a huge variety of people working in different disciplines, and spread our ideas about our project and synthetic biology as a whole through articles and outreach events. The opportunities that iGEM has given us will continue to have an influence well beyond this summer.”

The University of Cambridge is at the forefront of the plant synthetic biology field as co-host of the OpenPlant research centre. This is the first year that iGEM has featured a Plant Prize and Co-Director of OpenPlant Professor Jim Haseloff, who organised the first UK iGEM team in 2005, delivered a popular workshop on standards and tools for engineering plants to the global gathering of young synthetic biologists. Explaining the importance of plants as ‘chassis’ for synthetic biology, and the significance of the Cambridge iGEM project, Haseloff emphasised their sustainability. “We think that biological technologies are the underpinning of the 21st century’s industrial processes,” he said. “Plants are cheap and inherently sustainable, and have a major role to play in our future.”

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