Weeding the Gems

OpenPlant is one of the BBSRC Synthetic Biology hubs and is a collaboration between researchers at the Cambridge University and in the John Innes Centre and The Sainsbury lab in Norwich. Last week the inaugural public OpenPlant meeting took place in the Department of Plant Science in Cambridge and had the broad remit to introduce the ideals of the program whilst highlighting the excellent science that is ongoing in the labs affiliated with the project. GARNet were very pleased to be able to attend the event which involved being part of the judging panel for the OpenPlant Fund as well as being able to interact with many significant members of the world synthetic biology research.

Day One: OpenPlant Fund

One of the key aims of OpenPlant is to support innovative synthetic biology research in any and all possible areas. To that end, the OpenPlant grant has the facility to fund small (£4K+1K) grants to Cambridge and Norwich researchers who come up with novel collaborative ideas. Throughout the day each of the 17 applicants gave a five-minute pitch to explain and sell their ideas. This is the full list of pitches and as advertised, they covered all aspects of what could be considered synthetic biology, from projects that built on already established research to those that were the result of real blue-sky thinking.

More conventional lab-based projects included the development of codon-optimisation tools in Chlamydomonas or investigating LysM receptor-like kinases in legumes and cereals. The proposed in silico projects included development of an ‘Open-Pi image’, which is low-cost system for image analysis and a project proposed by TGAC PI Rob Davey to look into setting up a hackathon to develop software for synbio literature mining. The more ‘unconventional’ synbio projects included two that are linked to the development of synbio resources in Africa, in collaboration with the organisation TrendinAfrica. Undoubtedly the most enthusiastic presentation came from Paolo Bombelli, whose vision is to set up the ‘Big-Algal Open Experiment’ that aims to provide low-cost algal growth incubators to involve school groups across the UK in the study of algal growth.

It was encouraging that many PhD students and postdocs took the opportunity to come up with innovative ideas that had the support of their relevant PIs. Some of the presentations were a little ‘flabby’ which may have been a consequence of knowing there was funding for 20 projects, with ‘only’ 17 presentations. Ultimately OpenPlant was happy to fund each of the proposals although in a few cases the judges asked for clarifications and amendments prior to that final agreement. Overall it was a very strong start to the Open Plant Fund and with another 4 years of funding, hopefully these projects will encourage other researchers to apply in coming years. As a community-facing organisation, GARNet would hope to see researchers outside of the OpenPlant sites getting involved in the development of collaborative ideas that might be submitted to future funding rounds.

Days 2-3: OpenPlant Forum

The meat of the meeting took place over two days and involved formal presentations across a range of topics important to the ideas and emphasis of OpenPlant. The section headings were: ‘Frameworks for Open Innovation’, ‘Open DNA parts and assembly’, ‘Foundational Systems’, ‘Plant-based Bioproduction’ and ‘OpenPlant and Open technologies’ that followed opening presentations from Cambridge project lead Jim Haseloff, who outlined the aims of OpenPlant and the keynote lecture from Tom Knight, founder of the recently minted Ginkgo Bioworks. Tom has been involved since the beginnings of synthetic biology and gave an interesting talk about both the history of the field and its future opportunities.

The first session entitled ‘Frameworks for Open Innovation’ touched upon one of the key tenants of OpenPlant, which is to encourage the free and open exchange of technology. The ultimate aim of this is in the development of an OpenMTA that would allow free transfer of materials between labs, in the hope of aiding innovation and collaboration. Linda Kahl from the Biobricks foundation outlined the history of Material Transfer Agreements and the challenges of moving toward an oMTA. Perhaps the most alarming statistic presented was that with the current MTA system, ~50% of academics were discouraged from continuing with their experiments due to difficulties obtaining samples.

Throughout the meeting it was very encouraging that the plant science community appears to have a more enlightened opinion about the potential uptake of the oMTA. Although it is a great idea to establish this oMTA, researchers will require a mechanism to give future (non-financial) attribution for the work they have put in. We will watch this space with interest. This topic was the subject of the ‘Intellectual Property Working Group’ meeting that following the OpenPlant Forum and GARNet was honoured to be able to sit in on the early discussions where experts in this area discussed what might be possible with an oMTA system. Look out for updates on the OpenPlant website for updates as this challenging process moves forward.

Prior to the first session Randy Rettberg from the iGEM organization announced the exciting news that there will be a specific ‘plant –track’ in the iGEM 2016 competition. This will hopefully inspire more teams to use a plant chassis in their projects. GARNet will certainly look to encourage plant academics to support teams in 2016. In the 2015 competition there are 14 teams from the UK so hopefully these numbers will rise in coming years.

It was clear throughout this meeting both in formal presentations/ questiontime and during informal discussions that the ‘DNA of iGEM runs through the worldwide synthetic biology community’ as many of those who are involved with iGEM are advocates of the competition for their entire careers. If you don’t know much about the competition then take a look through their extensive catalogue of information on the iGEM website.

The second session was led off by Nicola Patron from The Sainsbury Lab who explained the foundation and rationale behind developing a common syntax for DNA parts, which has been discussed elsewhere on the GARNet blog. Later Christian Rogers explained how the Engineering Nitrogen Synbiosis for Africa (ENSA) project had embraced the need for a common set of DNA parts across their many projects. In addition he presented that there is the beginnings of a consensus across each of the large Gates Foundation funded projects (ENSA, C4 rice and RIPE) to be more efficient in the way they carry out tasks, which includes creation of DNA tools. It was reassuring to know that there are academic researchers who are attempting solve some of the coming ‘big problems for humanity’ in part using synthetic biology techniques.

Between Nicola and Christian’s talks, Fernan Federici introduced his project that looked at low cost gene assembly systems by showing a stunning set of images. In addition Markus Gershater, who used to work as a plant scientist but is now the co-founder of Syntace introduced their Antha software, which is their answer to dealing with biological complexity that aims to ease the automation of synthetic biological process. No doubt this will be software that is implemented in many synthetic biology labs in years to come.

Sessions 3 and 4 treaded more familiar ground for those of use with a background of plant molecular cell biology as the talks focused either on the potential for using ‘newer’ experimental organisms (cyanobacteria, algae, marchantia) and on successful bioproduction in plant systems. Arguably most striking was the work from Cathie Martin’s group by Yang Zhang that documented their successful production of many medicinal compounds in tomato fruit. In one particularly exciting instance, they used CRISPR technology to knockdown one enzyme in a biosynthetic pathway so that an intermediate was ‘shunted’ into the production of Genistein.

Eva Thuenemann from the lab of George Lomonossoff presented the latest developments from the HyperTrans project, which uses transient expression in tobacco leaves to produce valuable bioactive compounds (such a flu vaccine). She detailed the steps that are involved to ensure that your gene of interest is expressed in the right amounts and that the product correctly interacts with co-expressed proteins. It was clearly stated that it’s not just a case of transforming your clone and having guaranteed reliable expression! Excitingly Eva mentioned the opening of a new high-throughout facility for HyperTrans expression on the JIC campus in late 2016. In addition they are currently searching for researchers to suggest clones for ‘proof of concept’ experiments at the facility. More on this in the coming months….

The final session entitled ‘OpenPlant and Open Technologies’ took a wider view about what it means to be ‘open’. Chas Bountra gave an inspirational talk about the progress his organisation is making in reducing the time and money that is wasted within the pharmaceutical industry, while attempting to streamline the process of getting a novel drug to market. Rob Mullins (University of Cambridge) then told the story of how and why the incredibly successful Raspberry Pi computer was developed and how they were able to bring this technology into schools and to the community, all without becoming a big business and succumbing to the pressures of the profit margin.

Finally Jim Ajioka gave the cautionary tale of their attempts to obtain regulatory support for the Arsenic sensor that was developed following the work of a previous iGEM team. It was a sadly frustrating tale of having an important tool available to use that gets incredibly held up in European red tape before it is either able to get to the market or more importantly to the people who would benefit from it.

Overall the meeting was a great start to the OpenPlant era and it will be especially interesting to keep up with the developments of the ‘OpenPlant Fund’ed projects in the coming year. Next years meeting has already been advertised as happening in Norwich July 26-27^th 2016 so if you are intrigued as to the progress of the research that is being funded by OpenPlant, then put the dates in your diary!! After all the meetings are ‘Open’.