New LinkedIn group for synthetic biology centres: The Synbio Network

The Synbio Centres and the Foundries in the UK

In this Linked-In group present and former members of the UK Synthetic Biology Research Centres, the DNA foundries and the Synbio Innovation and Knowledge Centre can connect with each other. Through this group we aim to maintain and build the network of synbio scientists in and outside the UK. This provides us with a forum through which we can stay in touch, make new connections, stay up to date on developments in the sector, exchange ideas, and build new collaborations. Please join our group and spread the word among your colleagues!

https://www.linkedin.com/groups/13754621/

OpenPlant Forum 2019: Smart Design for the Future of Bio-economy

The last OpenPlant forum took place last month at Murray Edwards College, Cambridge. With this year’s focus being on “smart design for the future of bio-economy” the speakers provided insights into current, innovative and exciting research.

Bio-economy refers to all economic activity derived from biological research activity focussed on creating or improving industrial processes. The bio-economy injects a gross value of £153 billion into the British economy, generating over 4 million jobs (Office of National Statistics, 2012).

The bio-economy also presents excellent growth prospects as bioscience and biotechnology have the potential to develop new, more economically and environmentally sustainable solutions to current global challenges.

OpenPlant Biomaker showcases

Professor Jim Haselhoff (University of Cambridge) introducing the Biomaker challenge at the 2019 OpenPlant Forum.

The first day of the conference welcomed this round’s OpenPlant Biomaker teams to present their midway reports. Each interdisciplinary team has five months to design and produce either (i) low-cost instruments for biology or (ii) develop a biological resource or outreach project. Having already received an initial funding worth £1,000, teams were also given the opportunity to apply for follow-on funding of £2,000.

This year’s projects ranged from early-stage cancer detection and biophotovoltaic powered soil sensors to outreach in schools and capacity building in Africa. With each of the 25 teams presenting innovative projects, there truly was a wide range of exciting ideas to hear about.  You can read more about individual projects via the Biomaker hackster platform. Goodluck to all the teams who have applied for the follow-on funding!

OpenPlant Forum

The second day of the forum saw the official start to the conference, with Professor Jim Haselhoff introducing the OpenPlant joint initiative which promotes i) interdisciplinary exchange, ii) open technologies and iii) responsible innovation for improvement of sustainable agriculture and conservation.

Professor Susan Rosser (University of Edinburgh) and Professor George Lomonossoff (John Innes Centre) spoke in the first session of the day, presenting under the theme of mammalian and plant engineering, respectively. After a short break, Dr Leopold Parts (Wellcome Sanger Institute), Professor Jun Biao Dai (Shenzhen Institute of Advanced Technology, China) and Professor Jason Chin (MRC Laboratory of Molecular Biology) gave presentations on their work involving the use of synthetic gene systems.

The last presentations of the day came from Dr Sarah-Jane Dunn (Microsoft Research) on automated reasoning for biological networks, alongside Dr Daphne Ezer (Allan Turing Institute) and Professor Martin Howard (John Innes Centre) who also spoke under the topic of modelling and machine learning for biological systems.

Synbio start-ups panel - From left to right: Tim Brears (Evonetix), Jim Ajioka (Colorifix), Eyal Maori (Tropic Biosciences), Rob Field (Iceni Diagnostics), and Eugenio Butelli (Persephone Bio).

The day ended with a panel with representatives from the synbio start-ups Colorifix, Tropic Biosciences, Iceni Diagnostics, Persephone Bio and Evonetix, who had an interesting discussion with the audience about building and running a synthetic biology start-up in the present-day bioeconomy.

The final day of the forum focussed on the topics of novel approaches and technologies, and the reprogramming multicellular systems; we welcomed talks from the likes of Benedict Diederich and René Richter from the Bio-Nanoimaging group in the Leibniz Institute of Photonic Technology (Germany) on an open-source optical toolbox that can make cutting edge imaging techniques affordable and available, Dr Stephanie Mack (cancer research UK) and Professor Wendy Harwood (John Innes Centre) who spoke about genome editing techniques in mammalian and plant systems respectively, and Dr Somenath Bakshi (University of Cambridge) who informed us on his research on understanding and engineering biological networks.

With Marchantia as a model system being a hot topic for the second half of the day, Professor Mario Arteaga-Vazquez (University of Veracruz, Mexico) spoke of dicer-mediated reprogramming of cell fate specification in this system, followed by talks of  Dr Susana Sauret-Gueto and Dr Eftychis Frangedakis (University of Cambridge) who updated us on the advances in the Marchantia research in the Haseloff Lab.

The final evening of the OpenPlant Forum 2019

Throughout the day we were updated on the recent research activities in the OpenPlant centre by exciting talks by post-doc and PhD students from various different research groups. A wide range of topics were covered, including: vaccine development, insect pheromone production, plant metabolite biosynthesis, transient expression systems, cell wall engineering, plant immune responses, and transcriptional regulation in cyanobacteria.

With the final talk of the conference delivered by Roger Castells-Graells (John Innes Centre) on virus maturation, the last OpenPlant conference came to an end. We would like to thank all those who attended as well as those who made the conference possible and worked diligently behind the scenes to make such an exciting conference happen.

Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid

OpenPlant PI Chris Howe and colleagues published their work on control of plastid gene expression in the dinoflagellate Amphidinium carterae:

Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid

Richard G.Dorrell, R. Ellen R.Nisbet, Adrian C.Barbrook, Stephen J.L.Rowden, and Christopher J.Howe

Protist 170(4), August 2019, Pages 358-373

Abstract:

The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed “minicircles”. These minicircles may contain genes, or no recognisable coding information. Transcripts produced from minicircles may undergo unusual processing events, such as the addition of a 3' poly(U) tail. To date, little is known about the genetic or transcriptional diversity of non-coding sequences in peridinindinoflagellate plastids. These sequences include empty minicircles, and regions of non-coding DNA in coding minicircles. Here, we present an integrated plastid genome and transcriptome for the model peridinin dinoflagellate Amphidinium carterae, identifying a previously undescribed minicircle. We also profile transcripts covering non-coding regions of the psbA and petB/atpA minicircles. We present evidence that antisense transcripts are produced within the A. carterae plastid, but show that these transcripts undergo different end cleavage events from sense transcripts, and do not receive 3' poly(U) tails. The difference in processing events between sense and antisense transcripts may enable the removal of non-coding transcripts from peridinin dinoflagellate plastid transcript pools.

Build your own DNA Dave school workshop

Synthetic biology is an emerging field of research that has potential for huge impact through both societal and economic benefits. The processes and details that need to be understood to appreciate the potential for synthetic biology require a basic understanding of how genes are regulated and transcribed to make proteins and products.

DNA Dave - the DNA transcription and translation robot.

Science festivals provide an opportunity for scientists to engage with a mixed audience, that typically spend 5-10 minutes visiting individual stands. The SAW trust, together with OpenPlant, came up with the idea to build an interactive robot that could help people understand the processes involved with DNA transcription and translation; this resulted in the birth of “DNA Dave”. Dave’s head resembles the nucleus of a cell, where the double stranded DNA can be found. The DNA strands then split and one strand is transcribed into single stranded RNA that leaves the nucleus via pores, in this case represented by DNA Dave’s neck. The RNA enters the cell cytoplasm (DNA Dave’s body) and is translated by the ribosomes which produce a sequence of amino acids; this process is represented by the turning of a cog that causes a sequence of lights to flash.

Having taken the DNA Dave robot to many science festivals, it has proven to be an engaging, approachable robot, that not only helps to explain the key synthetic biology principles of DNA transcription and translation, but through doing so, enables new conversations linking key principles to scientific applications.

DNA Dave at the Cambridge Science Festival 2017

One common question that we were asked at science festivals by school teachers, was whether the DNA Dave robot was available for schools to hire. This got the ball rolling on the next DNA Dave project.

With the help of the Biomakers fund, we have set out to convert the original DNA Dave robot into a training robot and create a cross disciplinary workshop for schools, in which the schools learn to build their own DNA Dave. To achieve this, the current robot will be modified to become an effective training tool, where by all the internal workings of the robot will be accessible for hands on training. Moreover, the current micro-controller (an Arduino board) will be exchanged for a board more commonly used in schools, a micro:bit board.

DNA Dave’s current Arduino uno break out board which will be replaced by a Micro:bit board

For our launch workshop we plan on producing a workshop template, a “how to” coding and build guide, a DNA Dave CAD drawing, and materials suitable for a robot build. Students will then design and build their own DNA Dave robot using the how to guide and materials supplied, as well as receiving support and advise from us during the process.

The main principle of the workshop and robot design is to familiarise students with the process of DNA transcription and translation, but students will be given the opportunity to develop skills across coding, technical design, electronics and biology. In addition to this, all students who take part will be exposed to subjects and topics that they may not already have an interest in and therefore potentially develop an interest in a new field.

At the end of the robot builds, we hope to gather all the new DNA Dave’s to an event during the next Norwich Science Festival where schools can showcase their designs. This showcase event will also serve as an opportunity for schools to discuss their project experiences, ideas and introduce the project to new schools.

Check out our hackster profile to keep up to date with our project.

- Dr Jenni Rant, Ioannis Tamvakis and Sami Stebbings

Developer at a Bristol BioDesign Institute spin-out

Rosa Biotech is looking for a developer:

We are looking for a driven team player to support our journey of redefining biosensing and diagnostics.  Drawing upon input from our scientific research team, you will build and develop statistical/machine-learning (ML) prediction and classification algorithms for Rosa Biotech’s biosensing technology. In addition, we see broader programming and data opportunities for instance in programming its experimental robotics platforms. 

Full job description and person specification here

To apply for this role send your CV and a covering letter to hr@rosabio.tech 

Closing date is 17:00 on Friday 16th August

Transformation of the dinoflagellate chloroplasts to enable studies on coral bleaching

eLife 8:e45292 Figure 5: A chloroplast localization for chloramphenicol acetyl transferase.

Dinoflagellate algae are of enormous ecological importance as they form symbiosis with corals, providing fixed carbon to their hosts. Environmental stresses such as raised temperature lead to breakdown of the symbiosis, expulsion of the dinoflagellates, and coral bleaching. Little is known about why the symbiosis breaks down, although the generation of reactive oxygen species in the chloroplast is probably involved. Dinoflagellates have long been resistant to transformation, which has hampered research into bleaching.

With funding from the Gordon and Betty Moore Foundation, Chris Howe’s lab in the Cambridge Biochemistry Department has succeeded in transforming the chloroplast of a model dinoflagellate, Amphidinium carterae (Nimmo IC et al. (2019) Genetic transformation of the dinoflagellate chloroplast. eLife 8:e45292 DOI: https://doi.org/10.7554/eLife.45292). They exploited the highly unusual organisation of the chloroplast genome – fragmented into plasmid-like ‘minicircles’ – to make shuttle vectors for biolistic transformation. This should open the way for studies on how environmental stresses affect dinoflagellate chloroplast function and ultimately lead to coral bleaching.