iGEM

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

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.”

Cambridge-JIC iGEM Update: Using low-cost, well-documented, open-source hardware for synthetic biology

The OpenPlant-supported Cambridge-JIC iGEM Team are exploring open source synthetic biology tools for chloroplast engineering in algae. The following was authored by Cambridge JIC- iGEM team member Claire Restarick and is reposted with permission from the Cambridge Consultants blog. Since our initial blog post, we’ve spent many hours finalising designs for our genetic assemblies, which are now in the process of being synthesised. Once these are complete, we will begin the challenging task of completing four rounds of experiments before our deadline in September.

While our biologists are making significant headway in the lab, there have also been advancements on the hardware and engineering side. Our designs for low-cost, open-source lab equipment to support our Chlamydomonas transformation protocol have started to take shape – with the first stages of assembly taking place. This equipment will include a growth facility with light control, temperature regulation and imaging capabilities (linked to a dedicated Twitter account, @RPi_camigem2016), as well as a gene gun which, if successful, will transform cells by firing DNA-coated tungsten microparticles directly into them at high pressure.

iGEM Presentation

The decision to make our hardware low cost and open source developed from recent trips to publicise our project at synthetic biology conferences in Paris and Norwich. At the Bio NightScience event hosted by the Centre de Recherches Interdisciplinaires (CRI) at the Cité des Sciences et de l’Industry, we presented our project to the conference and heard from many projects originating from Makespaces – collaborative community labs with little-to-no budget. We found its use of plant synthetic biology was hindered by the high cost of commercial equipment to culture and transform plant and algal cells. This inspired us to design low-cost equipment, which could make the area of plant synthetic biology more accessible to these creative workspaces, and other small research institutions.

The issue of documentation for open-source hardware for synthetic biology was raised repeatedly during the Open Plant Forum, hosted by the John Innes Centre in Norwich. A lack of clear, detailed protocols online makes it near impossible for the average novice builder to construct these devices. Having struggled ourselves to find appropriate parts and clear designs online, we have placed a focus on thoroughly documenting our designs, to make our open-source designs truly accessible for everyone.

To support both the hardware and biology aspects of the project, we have also continued our work on mathematical modelling, developing an open-source, integrated, kinetic model of Cas9-mediated gene insertion. We also held our first meeting with the director of the Cambridge-based Centre for Global Equality, to begin developing the human practices element of our project – understanding its impact and integrating this within the design and aims of the different parts.

Now past the halfway point of our project’s timeline, we feel well on track to meeting our project’s ambitious goals. Thanks to the continued support of our advisors at the Plant Sciences Department, and specialist advice from Cambridge Consultants, all aspects of our project are developing the potential to have an impact on both the scientific and non-scientific communities.

Note from Cambridge ConsultantsSynthetic biology has huge potential to solve many of today’s critical challenges in healthcare, agriculture, energy and the environment. That’s why Cambridge Consultants has decided to sponsor the Cambridge University team at iGEM 2016 – the international genetically engineered machine competition run by MIT. As part of our sponsorship, we are acting as mentors – giving the team access to more than 700 Cambridge Consultants engineers and scientists worldwide to help solve problems during this year’s project.

The iGEM team is also grateful for support from:

  • OpenPlant
  • University of Cambridge, School of Biological Sciences
  • BBSRC, the Wellcome Trust, and the Society for Experimental Biology

Syngenta offers iGEM Sponsorship for manufacturing Resilient RNA-based biocontrols

2016Syngenta are offering iGEM teams sponsorship funding to explore areas of innovation surrounding RNA-based Biocontrols. After the introduction of a Special Plant Prize into iGEM and adoption of the 'PhytoBricks' plant common syntax, championed by OpenPlant labs, several plant-focused iGEM teams are participating in this year's competition and may be interested in the opportunity. From Syngenta: "The challenge with RNA-based biocontrols is finding the balance between scaling up the use of this highly effective agricultural tool while also being able to clearly demonstrate the value to multiple stakeholders. Syngenta and other developers of this tool must show clear demonstration of value creation through both the technological development (what this tool is developed to support) and communication development (how the tool is effectively explained and rolled out).

We are looking for iGEMers to explore technical practices that take into account the implementation of such a tool, which also involves thinking through human practices."

For more information and instructions on how to apply, see the iGEM website.