OpenPlant Fellow wins 2016 Wellcome Trust Image Award

Fernán Federici, OpenPlant Fellow at the University of Cambridge and Director of the Synthetic Biology Lab at Pontificia Universidad Católica in Chile has been awarded a Wellcome Trust Image Award for his micrograph of maize leaves, shot in the Department of Plant Sciences in collaboration with Professor Jim Haseloff.

Fernán has enjoyed considerable success with his artistic images of bacteria and plants using microscopy, winning Wellcome Trust awards in 2011 and 2012. His image has appeared in multiple media outlets, including Nature News, the BBC and The Guardian.

More on the image via the Wellcome Trust >>

Looking inside a cluster of leaves from a young maize (corn) plant reveals lots of details and organised structure. Each curled leaf is made up of lots of small cells (small green square and rectangle shapes), and inside each cell is a nucleus (orange circle), the part of the cell which stores genetic information. Maize is one of the most widely grown cereal crops in the world. It is used as a staple food, in livestock feed, and as a raw material – such as for processing into high-fructose corn syrup. Genetically modified maize crops are being grown to be resistant to pests and herbicides.

Although seeming boring when viewed with the naked eye, maize leaves have such a delicate and intricate structure under the microscope, captured so wonderfully by this picture. The level of detail as demonstrated by the image reminds us how complex even relatively simple organisms are when seen on this scale.

James Cutmore, Picture Editor of BBC Focus

The image has been made freely available to use under a Creative Commons CC-BY-NC-ND 4.0 license.

OpenPlant’s showstopper; synthetic biology! – Public reaction at the Cambridge Science Festival

In March a team from the John Innes Centre brought the premise of synthetic biology to the public. As an annual event growing every year Cambridge Science Festival attracts people from across the city to learn about new developments in science and technology.

Stall activities ranged from the extraction of DNA from Strawberries (University of Cambridge) to investigating evolution first hand with primate skulls (Wellcome Genome Campus). OpenPlant’s stall featured a glimpse into synthetic biology.

A disassembled phone explained the idea that by knowing how each of the individual simple components work (a dialling pad to input your desired number, a vibrating receiver coil to change the electrical signal into a sound wave) you can build more elaborate systems.

A disassembled (and retro) telephone, showing simple components forming a complex system

You can then use this concept in a biological setting. Firstly you understand how genes work, then you break these into smaller components each with their individual job, for example a sequence to tell you when to switch on a biological system. Finally this can be combined in a living organism to produce a desirable trait.

At the Science Festival, the public used this idea to make weird and wonderful new lifeforms! A cat whose nose turns purple when a disease is nearby. Useful for medical diagnosis? Or how about sprouts that taste of strawberries when it snows, which many would no doubt relish at Christmas time? Or a personal favourite provided by one dad – a plant whose leaves turn gold when you water it.

A biological dream; leaves which turn gold when you water it

Obviously most of our new inventions that day were unlikely, no matter how much scientists persevere with them; I think a money tree is still a few years off. But the solid basis for such work is undertaken in laboratories throughout the world, and the public were undoubtedly positive about synthetic biology. Although everybody (well apart from a young girl who wished to use squids to inflict harm on unsavoury characters) was clear that it should be only used for good and moral solutions to problems. The OpenPlant team was able to stress ethical procedures are in place for this which many found comforting as sometimes the public can find scientists secretive at best.

The Cambridge Science Festival is a vibrant, thriving and free event. Not only do people gain a glimpse of the developments in science but it’s also rewarding to the scientists giving up their time to share their knowledge and discussing their subject area. And synthetic biology is a hot topic which everyone should be talking about.

Written by Nicola Capstaff – outplantish.wordpress.com

Cartoon is credited to Erin Zess, a PhD student at the John Innes Centre

The 2017 Cambridge Science Festival will take place on 13-26th March 2017 – www.sciencefestival.cam.ac.uk

OpenPlant Science, Art and Writing Workshop a success

Year 6 pupils at Stapleford Community Primary School (South Cambs) enjoyed an OpenPlant ­ Science, Art and Writing Trust day workshop at the end of January. Scientists Dr. Carlos A Lugo (TSL) and Marielle Vigouroux (JIC), together with SAW Trust coordinator, Dr. Jenni Rant (JIC), artist Chris Hann and writer Mike O’Driscoll, presented their OpenPlant Fund plant electrophysiology project through a series of activities themed around excitable media and circuits of plants, linking them to biological systems like the brain, heart and muscle.

The pupils used the Plant SpikerShield system wired up to a Venus flytrap plant and observed the signal when the trap closed. They also had fun working out the optimum time lapse between trigger hair taps for the trap to shut, flexed their muscles to light a bulb, listened to their heartbeat and tested brain signalling with Chinese whispers. With the invaluable help from a professional writer and artist, children were inspired by the science to write some amazing poems and create fantastic pieces of art. The children were very receptive, everyone had lots of fun and the feedback was incredibly positive. A big thank you to Ms Emma Wright, the year 6 teacher, for her warm welcome and her enthusiasm towards the project!

Comments from the kids;

‘In Science, I really enjoyed the reflex activity where we did Chinese whispers and were shining lights into our eyes to see how they react. Also, the venus fly trap was incredible, the way it would close if something tickles the hair inside’.

‘I enjoyed doing the science where I had sensors stuck to my arm, then I would tense my muscles to make the lights go red’.

‘I enjoyed the images of neurons and recreating them with dye, the result was rather satisfying. It was also fun doing the poetry’.

A comment from the teacher, Emma Wright;

The SAW day was fantastic. Throughout the day the children were all engaged with the variety of activities. The children also learnt a lot from the subject specialists that showed their subjects in a new light. Equally the children and teachers alike picked up hints and tips that could be used in the classroom again. I would highly recommend this for anyone.

Poems written in the workshop;

SCIENCE

by Ben

Icy, sapphire neurons racing around colliding,

Whispering Venus fly traps with dagger-like hairs,

Spearing out jaggedly.

A stampede of colours like two universes amalgamating,

A heartbeat,

Boom…..boom boom…….boom boom,

A vortex of multicolour zooms around in an oyster shape,

A scene of Africa with a paisley pattern confuses the brain.

PUMPING X-RAY

by Elijah

Pumping message swirling

Across rainbow chaos,

Pumping high to low,

Bu-bom…Bu-bom…Bu-bom,

X-ray signal making waves,

Tubes linking, waving sea into my brain.

www.sawtrust.org

Using electronic circuits to represent synthetic biology at the Youth STEMM Award mid-year conference

OpenPlant exhibited on gene circuits and synthetic biology at their stand at the exciting mid-year conference for the Youth STEMM Award. Around 200 pupils, aged 14­16, from schools around Norfolk attended the event at the John Innes Centre which included exhibits showcasing the science on site as well as a keynote talk from celebrity ethnobiologist James Wong. Read more about the Youth STEMM Award here.

The OpenPlant exhibit, run by Nadia Radzman, Don Nguyen and Colette Matthewman, explained gene circuits by comparing them to representative electronic circuits. Example gene circuits were explained to visitors, who then interacted with the electronic circuits and paired them with the gene circuit they represented. This use of electronics represented the concept of synthetic biology as an engineering discipline and opened up conversations around standard parts, components and modularisation ­- key principles of engineering. Pupils could also learn how scientists at the John Innes Centre get these gene circuits into Tobacco plants and had a go at infiltrating tobacco leaves (with water containing colouring). Plenty of information about case studies for the use of gene circuits in plants were given to complete the picture of what synthetic biology can achieve.

We were very impressed by how well the pupils interacted with the activities. The circuits caught the attention of those with a physics or engineering interest as well as those who were more focused on biology.

Meeting report: GARNet/OpenPlant CRISPR-Cas workshop

In September 2015, GARNet and OpenPlant organized a two-day workshop at the John Innes Centre that provided both background information and hands-on training for CRISPR-Cas technology. The report from that meeting is now online, co-authored by Dr Nicola Patron and Dr Colette Matthewman from OpenPlant along with GARNet colleagues.

Parry, G., Patron, N., Bastow, R., & Matthewman, C. (2016). Meeting report: GARNet/OpenPlant CRISPR-Cas workshop. Plant methods, 12(1), 1. 
Full text
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The article is fully Open Access under a CC-BY 4.0 license so it’s reproduced below!

Meeting report: GARNet/OpenPlant CRISPR-Cas workshop

• Geraint Parry†Email author,
• Nicola Patron†,
• Ruth Bastow and
• Colette Matthewman

†Contributed equally

Plant Methods201612:6
DOI: 10.1186/s13007-016-0104-
©  Parry et al. 2016

Received: 17 November 201
Accepted: 5 January 2016
Published: 27 January 2016

Abstract

Targeted genome engineering has been described as a “game-changing technology” for fields as diverse as human genetics and plant biotechnology. One technique used for precise gene editing utilises the CRISPR-Cas system and is an effective method for genetic engineering in a wide variety of plants. However, many researchers remain unaware of both the technical challenges that emerge when using this technique or of its potential benefits. Therefore in September 2015, GARNet and OpenPlant organized a two-day workshop at the John Innes Centre that provided both background information and hands-on training for this important technology.

Keywords

CRISPR Cas9 Gene Editing Genetic Engineering

Geraint Parry and Nicola Patron contributed equally to this manuscript

Background

Over the past few years, genome engineering (GE), the process of making targeted modifications to the genome, its contexts or its outputs, has been described as a “game-changing technology” for fields as diverse as human genetics and plant biotechnology. The ability to introduce specific changes to genomic loci adds a level of precision not previously available to molecular biologists working in multicellular eukaryotes. Despite overwhelming scientific opinion that Genetically Modified (GM) plants are safe and provide environmental and socioeconomic benefits, they remain broadly unpopular outside of the scientific community [1–3]. This has been blamed both on inaccurate media reporting and public concerns over the ownership of technologies that underpin food production [4–6]. Given these political and public opinions, plant scientists are particularly hopeful about the future use of GE technologies, which are likely to enable precise genetic changes to be made without the ongoing requirement for foreign DNA to be integrated the genome.

However, despite some countries ruling that plants with targeted mutations may not be regulated as GM, there is still much uncertainty [7, 8]. Even as the technologies behind GE are being optimized, the scientific community is engaging with stakeholders to highlight potential positive uses, including how it might be used to develop better crops. This is exemplified by a policy statement from the UK’s Biotechnology and Biological Sciences Research Council (BBSRC) on “New Techniques for Genetic Crop Improvement” that outlines positive uses for GE technologies [9].

The experimental protocols needed to implement these powerful techniques are yet to be embraced by many plant science laboratories. To address this issue GARNet [10] and OpenPlant [11] collaborated to organise a workshop to explain the background of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas technologies for GE in plants and to equip plant scientists with the skills required to implement Cas9-induced targeted mutagenesis. Over 140 researchers registered for the meeting, held at the John Innes Centre (UK), from as far-afield as Ireland and Poland, clearly demonstrating the appetite to apply these technologies to plant systems. The first day was open to all attendees and consisted of conventional ‘seminar-style’ presentations, while day two was a hands-on introduction for 30 researchers. This meeting was made possible by the kind support of Plant Methods.

Day one presentations

The meeting was opened by Dr. Jim Haseloff from The University of Cambridge who introduced synthetic biology in plant systems and Dr. Nicola Patron of The Sainsbury Laboratory, Norwich (TSL), the primary organiser, who provided a historical perspective on GE technologies. The specifics of these technologies are discussed in detail as part of this Plant Methodsthematic series. Keynote presentations were given by Professor Holger Puchta (Karlsruhe Institute of Technology) and Professor Bing Yang (Iowa State University) who each provided overviews and success stories from their own laboratories. These were followed by shorter talks from scientists at JIC, TSL and the University of Cambridge who are already working with CRISPR/Cas technologies.

Professor Puchta gave an inspiring talk that provided attendees with the history of his seminal work. He presented earlier work showing that induction of double strand breaks (DSBs) using site-specific endonucleases can enhance the freqeuncy of homologous recombination in plant cells through to his recent work using RNA-guided Cas9 nuclease to induce DSBs [12, 13]. He mentioned that the two most important molecular discoveries of his lifetime had been the Polymerase Chain Reaction (PCR) and GE technologies, the latter he described as having “hit him like a tsunami”. It was exciting to hear about his lab’s recent use of paired nickase variants of Cas9, which cut just one DNA strand, to induce larger endogenous deletions [13, 14]. Professor Puchta was extremely positive about the potential for GE and in his final perspectives noted that “Synthetic nuclease based DSB-induced DNA repair should be applicable for directed mutagenesis in all transformable plants”, and “in the long run synthetic nuclease-based GE will change plant breeding dramatically”. He also thought it possible that plants with targeted mutations might not be regulated in the same way as transgenic GM plants.

Professor Yang echoed this, presenting a letter from the United States Department of Agriculture (USDA) that informed him that the GE rice produced in his laboratory did not fall within its regulatory authority [14, 15]. Professor Yang documented his work on GE in maize and rice, showing that in cultivars where poor transformation efficiency was a significant bottleneck, GE technologies has sped up the process. He also described the induction of a large deletion of 245 kb in rice using RNA-guided Cas9 [15].

Dr. Laurence Tomlinson and Dr. Vladimir Nekrasov, both from TSL, presented their successful applications of RNA-guided Cas9 nuclease to induce targeted mutagenesis in tomatoes. Tomlinson’s work involved GA signaling whilst Nekrasov described the induction of targeted mutations to engineer pathogen-resistance. He took the audience through initial experimental design, through screening of putatively mutated plants to the identification of individuals showing resistance to powdery mildew. It took just 9 months to identify transgene-free, resistant plants with heritable mutations. Nekrasov confirmed that he and his supervisor, Professor Sophien Kamoun, are now investigating options to make their plants available to growers in regions where the pathogen is a significant problem, whilst also undertaking full-genome sequence analysis to determine if the plants contain any additional mutations. University of Cambridge PhD student, Bernando Pollak, introduced the liverwort Marchantia polymorpha, highlighting the ease by which its genome can be manipulated, as well as its potential as an easily engineerable chassis for synthetic biology. Many of the signaling pathways in Marchantialack the redundancy seen in vascular land plants [16] and so it has huge potential as a tool for the study of plant signaling. Additionally, Marchantia is haploid for a large portion of its life cycle and thus the application of programmable nucleases such as RNA-guided Cas9 are even easier to apply. Dr.Oleg Raitskin (TSL) described experiments to further optimize RNA-guided Cas9 nuclease mediated mutagenesis in plants, including the assessment of orthologues and mutants of Cas9 that may expand the number of possible targets in the genome. He also introduced the concepts behind digital droplet PCR and its implementation in the rapid, quantitative assessment of mutations.

The final presentation was delivered by Edward Perello, Chief Business Officer of Desktop Genetics [17], a UK-based software company who develop tools to support the application of CRISPR-associated technologies. Mr. Perello announced that their guide RNA selection software, Guidebook, now supports six plant genomes (Arabidopsis, rice, maize, wheat, barley and Physcomitrella). Plant scientists were encouraged to use this software, which is free for academics, as well as to contact the Desktop Genetics team with feedback and requests for new features and genomes.

Day two workshop

For the workshop on the second day, participants were given a detailed introduction to the methods used to induce targeted mutagenesis and gene deletions with RNA-guided Cas9 nuclease. This was a hands-on session designed to give the participants a full understanding of how to undertake three key aspects of the technique: selecting target sequences, constructing plasmid vectors, and screening target loci for induced mutations. The content was tailored for researchers working on any transformable plant species.

As well as discussing targeted mutagenesis, Dr. Patron provided an introduction to Type IIS mediated assembly methods for the facile construction of plasmid vectors. Dr. Patron is an advocate for the adoption of standards in bioengineering. She was the lead author on a recent manuscript that described a broadly agreed common genetic syntax for the exchange of DNA parts for plants [18]. In addition, Dr. Patron has contributed to a toolkit of standard parts for plants and created a series of informative online tutorials that introduces users to the Golden Gate Modular Cloning (MoClo) assembly standard [19, 20]. Participants were instructed in the use of published standard parts (Table 1), compatible with the MoClo binary plasmid backbones to build vectors for multiplexed Cas9-induced mutagenesis. The workshop materials have been provided on the GARNet website [21] but the main points are summarized below.

Designing single guide RNAs (sgRNAs) for use with Streptococcus pyogenes Cas9

Fig. 1

Interaction of a single guide RNA (sgRNA) expressed from a U6 promoter with its cognate genomic target (adapted from Belhaj et al. [23])

1. The target sequence, which is integrated into the single guide RNA (sgRNA), consists of 20 nucleotides (nt). In the genome, target sequences must be located immediately 5′ of an ‘NGG’ sequence, known as the ProtospacerAdjacent Motif (PAM) (Fig. 1). The 6–8nt immediately 5′ of the PAM are called the ‘seed region’ and should be 100 % identical to the target sequence. DSBs may still be induced at targets with one or more mismatches in the 5′ end of the target sequence. The induction of DSBs in sequences that do not exactly match the guide is known as ‘off-target activity’ and may be exploited for simultaneously inducing mutations in closely related sequences although the delivery of multiple sgRNAs that exactly match each target may be more successful.

2. RNA polymerase III (RNAPol-III) dependent promoters are generally used to transcribe sgRNAs. This is because of their precise transcriptional start site. As the target sequence comprises the 5′ end of the sgRNA, the start of transcription must be preserved. For example, the transcriptional start site of the Arabidopsis U6-26 promoter is a ‘G’ and therefore the transcript will begin with a ‘G’. This nt does not necessarily need to pair with the genomic target. If the desired target sequence does not start with a ‘G’ an additional 5′ non-pairing ‘G’ can be included, extending the target to 21 nts (Fig. 1).

3. If specific sgRNA identification software is not available for the genome of interest, target sequences can be identified using many DNA analysis software packages by searching for the degenerate sequence ‘N(20)NGG’. Cas9 has been shown to preferentially bind sgRNAs containing purines in the last 4 nucleotides of the spacer sequence whereas pyrimidines are disfavoured [25]. Although unconfirmed in plant systems, users may wish to select targets rich in purines by searching for ‘N(12)R(8)NGG’.

4. For purposes of creating functional ‘knock-outs’, two or more sgRNAs can be designed to the same gene, thus creating a small deletion. Constructs with multiple sgRNAs, the Cas9 and selection genes as well as other transcriptional units can be easily assembled using the MoClo plasmid system and published standard parts (Table 1) [20, 22, 26].

Once the constructs have been assembled, they are delivered to plant cells using established protocols for the species of interest. Although transient transfection of plasmids and direct delivery of protein-RNA complexes to protoplasts have resulted in targeted mutagenesis [27, 28], regeneration from protoplasts has not yet been established for many plant species. The assembled genes may be integrated as a transgene raft. The resulting transformants can then be analysed for lesions at the target locus. The final part of the workshop was dedicated to simple, rapid techniques for the identification of induced mutations at target loci.

Screening putatively mutagenised plants

Fig. 2

Detection of induced mutations. a If two single guide RNAs were delivered with the aim of deleting a fragment of DNA, oligonucleoitide primers flanking the targets can be used to PCR amplify the locus. Evidence of an amplicon, smaller that that obtained in a wildtype (WT) control is indicative of a deletion. The absence of an amplicon of equivalent size to the WT may indicate a homozygous deletion. b If the quantity of the deletion amplicon is low or absent, the genomic DNA can be digested with any restriction endonuclease (REN) with one or more recognition sites in the deletion region prior to PCR amplification. This will remove any wild-type sequence enabling the detection of deletions even if at low quantity in the sample. c Double strand breaks (DSBs) are most likely to occur three base pairs before the PAM in the seed-region of the target. Small insertion-deletion events at the target can be detected by digesting a PCR amplicon of the target locus with a REN for which the cognate sequence would be disrupted by imperfect repair of the DSB

1. Genomic DNA is purified and, if two sgRNAs were used, oligonucleoitide primers flanking the targets sites are used to PCR amplify the locus. Evidence of a deletion can be seen in the form of amplicons smaller than those obtained from a wild type control (Fig. 2a). The absence of the wildtype amplicon may indicate that the deletion was homozygous (Fig. 2a). The sequence of this band may confirm if both sister chromatids were repaired in the same way or if the plant is bialleic. If an amplicon corresponding to the wild-type is also present, the deletion may be heterozygous or, alternatively, the transgenes may be expressed in somatic tissues with cells in the sample showing multiple genotypes. In all cases the seeds will be collected and null-segregent progeny, which have not inherited the transgene, and (unless the deletion was homozygous in the primary transformants) progeny that have inherited the transgene analysed in the same way. The mutation can be classified as heritable and stable when progeny with the same mutant genotype as the parent are recovered and the transgene has been segregated out.

2. Following PCR amplification, if there is no evidence of smaller band indicating a deletion then two experiments are possible: The first is to digest the purified genomic DNA with a restriction endonuclease with one or more recognition sites between the targets and to PCR amplify the locus with oligonucleotide primers designed to the flanking regions (Fig. 2b). This pre-digestion will remove any wild-type sequence enabling the detection of deletions from just a few cells in the sample. Such plants are highly likely to be chimeric and will need to be progressed to a second generation. The second method allows the detection of small insertion-deletion events at the target rather than a deletion. A DSB is most likely to occur three base pairs before the PAM in the seed-region of the target (Fig. 1). If there is a restriction endonuclease recognition site that would be disrupted by imperfect repair of the DSB, a PCR amplicon of the target locus can be digested with this enzyme. Any amplicon showing resistance to digestion with this enzyme can be sequenced (Fig. 2c). A researcher with sufficient foresight will try to design a target region that contains RE sites that could be used for subsequent screening. Again, the mutation can be classified as heritable and stable when progeny with the same mutant genotype as the parent are recovered and the transgene has been segregated out.

Mutations are detected in at least some cells of at least 5–20 % of primary transformants, with much higher frequencies reported for some species [29]. This rate is dependent on the effectiveness of the specific sgRNAs and species-specific factors including the level of expression of Cas9 and sgRNAs achieved in the tissue to which the transgene is delivered.

One of the main criticisms of programmable nucleases for the induction of targeted mutations is the potential for off-target activity. Although many plant species can be easily backcrossed to ‘clean up’ the genetic background as is done for chemical or radiation-induced mutagenesis, off-targets can only be identified by sequencing either related target sites or the whole genome. Nevertheless, there is little doubt that GE technologies offer immediate opportunities for increasing genetic diversity in crop plants and for understanding the function of plant genes. The take-away message from this workshop was that the technique has enormous potential, but that it can be technically challenging to implement. A post-workshop survey received many positive responses about the breadth of the talks and especially regarding the day two workshop. However, there are still knowledge gaps in the plant science community and therefore GARNet will be organising a further CRISPR-Cas workshop as part of its general meeting, to be held in September 2016 (http://ww.ARNet2016.eebly.om).

Notes

Geraint Parry and Nicola Patron contributed equally to this manuscript

Declarations

Authors’ contributions

The article was prepared with equal contributions by GP and NP. RB and CM were involved in organisation of the workshop. All authors read and approved the final manuscript.

Acknowledgements

The authors would like to thank the GARNet Advisory Committee for suggestions toward development of the workshop.

Competing interests

The authors declare that they have no competing interests.

Funding

Geraint Parry and Ruth Bastow are funded by BBSRC grant BB/M004376/1. Nicola Patron and Colette Matthewman are funded by BBSRC grant BB/L014130/1.

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://reativecommons.rg/icenses/y/./), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://reativecommons.rg/ublicdomain/ero/./) applies to the data made available in this article, unless otherwise stated.

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New POSTnote on plant IP including genetic resources

A new POSTnote from The Parliamentary Office of Science and Technology considers the different intellectual property rights approaches available to plant breeders. Download PDF (392kB) >>

Plant breeding is an essential practice in agriculture and horticulture. Plant breeders may seek intellectual property rights (IPR) over plant varieties and breeding techniques to protect their investment in research. This POSTnote considers the different IPR approaches available to plant breeders.

Cambridge University Synthetic Biology Society Launches

Guest post by Olivia Lala, Publicity Officer, Cambridge University Synthetic Biology Society

A team of undergraduates including previous iGEM team members have just started a new society, the Cambridge University Synthetic Biology Society (CUSBS). Synthetic Biology (SynBio) is an emerging inter-disciplinary research field at the interface between engineering and the life sciences. Having secured £5000 in funding for the first year the society will focus on two student-led projects. The projects will provide the opportunity to get hands experience doing bio-hardware. As well as this there will be termly talks on new advances in the field given by experts and opportunities to do outreach at local schools.

The first event organised by the society and the Biological Society (BioSoc) included a talk by Dr Tom Ellis on Synthetic Biology - from synthetic genes to synthetic genomes. They are now looking for new members who would be interested in joining, anyone is welcome! A first taster session is being organised for the 23 January - more details to follow.

Anyone interested should email cusbs-executive@srcf.net

Registration opens for EUSynBioS Symposium 2016: Engineering Biology for a Better Future

EUSynBioS Symposium 2016: Engineering Biology for a Better Future

9 April, Imperial College London, London, United Kingdom

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We are witnessing an exciting time in the history of synthetic biology. Wide recognition of the field's tranformative potential over the past decade has inspired the emergence of a remarkable number of young synthetic biology initiatives and communities around the globe. By what principles, standards, and interactions can they best realise their potential in making the world a better place?

It is to approach this question that we will bring together an enthusiastic international group of young synthetic biologists (embracing undergraduate and graduate students as well as postdocs) for 1.5 days packed with stimulating talks, group discussions, bioindustry interaction, speed networking, and biohacking. Our overall goal is nothing less than to develop a vision for the young synthetic biology community.

Please check the event website for a more detailed schedule (regularly updated as speakers are confirmed).

OpenPlant researchers publish review of multi-gene engineering in plants with RNA-guided Cas9 nuclease

OpenPlant PI Nicola Patron and Oleg Raitskin (Earlham Institute, Norwich) have published a review on genome editing with RNA-guided Cas9 nuclease in plants, and the opportunities for multi-gene engineering.

Raitskin, O. and Patron, N.J., 2016. Multi-gene engineering in plants with RNA-guided Cas9 nuclease. Current Opinion in Biotechnology 37, p 69-75.

Highlights

• RNA-guided Cas9 nucleases have been employed for genome editing in several plant species.
• Several strategies for simultaneous expression of multiple sgRNAs have been demonstrated.
• Parallel DNA assembly methods enable rapid construction of vectors for plant genome editing.

The use of RNA-guided Cas9 endonuclease for the concurrent engineering of multiple genes has been demonstrated in a number of plant species. Although Cas9 is a large monomeric protein, the single guide RNA (sgRNA) that directs it to a specific DNA target sequence is small and easy to reprogram. It is therefore relatively simple to produce numerous sgRNAs to target multiple endogenous sequences. Several approaches to express multiple sgRNAs and Cas9 in plants for the purpose of simultaneous editing or transcriptional regulation of many genes have recently been reported.

For more information see the full article.

Cambridge-JIC iGEM Team open for applications until 26 Jan 2016

To apply: Please send a CV with covering note and ask your tutor or research supervisor to email a short recommendation to: Jenny Molloy Email: jcm80@cam.ac.uk

The new field of Synthetic Biology is based upon the adoption of (i) engineering principles of abstraction and modularity, (ii) computational tools from Systems Biology and (iii) new genetic engineering techniques and components - for the rational design and assembly of new biological systems. It is a practical subject, concerned with the construction of new living artifacts. The new interdisciplinary field is being propelled by the need for improved plant and microbial feedstocks, bioenergy sources, and new catalysts for bioprocessing. Synthetic Biology is seeing a rising tide of new scientific activities, research funding and commercial investment.

iGEM is an international undergraduate synthetic biology competition where student teams are given access to DNA parts from the Registry of Standard Biological Parts at the Massachusetts Institute of Technology (MIT). The aim is to use these and other new parts to design and construct new biological systems and operate them in living cells. (see: http://igem.org). Cambridge provided the first team from the UK (see: http://www.synbio.cam.ac.uk). Since 2005, there has been wide interdisciplinary support for a University of Cambridge team in the iGEM competition. The competition provides a practical, laboratory based experience, with a focus on bottom-up design and assembly techniques, standardised biological components and cellular devices. This year sees the introduction of a new track for the engineering of plants in the competition. We are drawing together a team who can contribute in an interdisciplinary way to development of new DNA parts, quantitative methods and instrumentation for engineering of plant systems.

The team will be run jointly with the John Innes Centre, an independent, international centre of excellence in plant science and microbiology based in Norwich, with a mission to improve agriculture, the environment, human health and well-being, and engage with policy makers.

Participation in the iGEM competition offers:

1. Interdisciplinarity and teamwork. Students from Biology, Engineering, Computing and the Physical Sciences participate in the iGEM team.
2. Hands-on practical experience. The iGEM competition provides laboratory experience with the handling of synthetic biological systems to provide better grounding in practical skills for future project work.
3. Project and group based learning. Students share team work in laboratory work, biological design, project management and presentation.
4. Student exchange. In addition to promoting improved collaboration across Cambridge, participation provides opportunities for links with scientists at the John Innes Centre, collaboration and international exchange.
5. Lab resources. The iGEM team will have access to labs equipped for handling biological systems and construction of hardware, including 3D printing.
6. Open Instrumentation. Students will be able to work with Arduino and Raspberry Pi-based microcontrollers and interface these with optics, microelectronics and motors for DIY instrumentation.

Application details:

iGEM studentship funding will be available for up to 10 first and second year Cambridge undergraduates to allow participation in the competition. The competition will start on Monday, 27th June 2016, and will be based in the Department of Plant Sciences, University of Cambridge. The first two weeks of the competition will include a crashcourse in Plant Synthetic Biology, with brainstorming and practical exercises. The studentships will include a stipend of £180 per week for ten weeks, registration fees for the competition, exchange visits with the John Innes Centre, access to state-of-the-art laboratory facilities and workshops and attendance at the global iGEM Jamboree at Boston, USA in November 2016.

Faculty advisors are:

Jim Ajioka (Pathology), Alexandre Kabla (Engineering), Jim Haseloff (Plant Sciences) and George Lomonossoff (John Innes Centre).

For further information on the competition see http://www.igem.org.

Simple changes underpin the evolution of a complex trait

OpenPlant PI Professor Julian Hibberd’s Lab published a significant step towards understanding the efficient form of photosynthesis known as the C4 pathway in The Plant Cell on the 15th of January 2016. In most photosynthetic organisms, ranging from bacteria to land plants, the first step of photosynthesis is catalysed by the enzyme RuBisCO. However, under warm, dry conditions the efficiency of Rubisco is reduced, which can lead to lower crop yields.

Some plants have evolved adaptations to overcome this problem, one of which is known as the C4 photosynthetic pathway, adoption of which allowed fast-growing species such as switchgrass to dominate savannahs and prairies. As C4 photosynthesis requires the co-ordinated action of many genes, Williams and Burgess et al. sought to identify C4 genes that are expressed in mesophyll cells and regulated by the same regulatory elements. Starting with a gene encoding carbonic anhydrase from the C4 species Gynandropsis gynandra they established that its regulation was mediated by a short sequence in the untranslated part of the gene. Furthermore, this sequence was found in additional C4 genes as well as orthologous genes from C3 species, and in each case, regulation appears to act on the translation of RNA to protein.

The work provides evidence that the complex C4 trait is underpinned by the repeated use of simple sequence motifs.

Williams BP, Burgess SJ, Reyna-Llorens I, Knerova J, Aubry S, Stanley S, Hibberd JM. (2016) An untranslated cis-element regulates the accumulation of multiple C4 enzymes in Gynandropsis gynandra mesophyll cells. The Plant Cell. 

OpenPlant Supported TReND/icipe bioinformatics workshop

RICHARD SMITH-UNNA DELIVERING A PLANT SYNTHETIC BIOLOGY SESSION AT ICIPE

The OpenPlant Fund supported TReND in Africa to include plant synthetic biology in their recent bioinformatics course held at icipe in Kenya. The course was a great success with 35 students selected from a total of 430 applicants. They learnt R and Unix programming basics, as well as advanced genomics techniques from a number of different areas of biology.

The plant synthetic biology session was delivered by Richard Smith-Unna (@blahah404), a PhD Student in the OpenPlant-affiliated Hibberd Lab at the Department of Plant Sciences, University of Cambridge.

TReND’s Jelena Aleksic recorded interviews with participants who described their experience of the course, you can view the playlist below and find more about TReND in Africa’s activities on their website.

Plant synthetic biology lecture at @icipe! Thank you @_OpenPlant for supporting #trendngs15 @TReNDinAfrica pic.twitter.com/NKs8BWC1fV

— Jelena Aleksic (@firegenome) December 4, 2015

Scientists produce beneficial natural compounds in tomato – with potential for industrial scale up

From the John Innes Centre news feed and featuring OpenPlant scientists Professor Cathie Martin and Dr Yang Zhang.

Given the opportunity to drink fifty bottles of wine or eat one tomato, which would you choose?

Scientists at the John Innes Centre have found a way to produce industrial quantities of useful natural compounds efficiently, by growing them in tomatoes.

The compounds are phenylpropanoids like Resveratrol, the compound found in wine which has been reported to extend lifespan in animal studies, and Genistein, the compound found in soybean which has been suggested to play a role in prevention of steroid-hormone related cancers, particularly breast cancer. 

As a result of the research led by Dr Yang Zhang and Dr Eugenio Butelli working in Professor Cathie Martin’s lab at the John Innes Centre, one tomato can produce the same quantity of Resveratrol as exists in 50 bottles of red wine. One tomato has also produced the amount of Genistein found in 2.5kg of tofu.

Drs Zhang and Butelli have been studying the effect of a protein called AtMYB12 which is found in Arabidopsis thaliana, a plant found in most UK gardens and used as a model plant in scientific investigation. 

The protein AtMYB12 activates a broad set of genes involved in metabolic pathways responsible for producing natural compounds of use to the plant. The protein acts a bit like a tap to increase or reduce the production of natural compounds depending on how much of the protein is present. 

What was interesting about the effect of introducing this protein into a tomato plant was how it acted to both increase the capacity of the plant to produce natural compounds (by activating phenylpropanoid production) and to influence the amount of energy and carbon the plant dedicated to producing these natural compounds. In response to the influence of the AtMYB12 protein, tomato plants began to create more phenylpropanoids and flavanoids and to devote more energy to doing this in fruit.

Introducing both AtMYB12 and genes from plants encoding enzymes specific for making Resveratrol in grape and Genistein in legumes, resulted in tomatoes that could produce as much as 80mg of novel compound per gram of dry weight –demonstrating that industrial scale up is possible. 

Tomatoes are a high yielding crop – producing up to 500 tonnes per hectare in countries delivering the highest yields (FAOSTAT 2013) and require relatively few inputs. Production of valuable compounds like Resveratrol or Genistein in tomatoes could be a more economical way of producing them than relying on artificial synthesis in a lab or extracting them in tiny quantities from traditional plant sources (e.g., grapes, soybeans, etc.). The tomatoes can be harvested and juiced and the valuable compounds can be extracted from the juice. The tomatoes themselves could potentially become the source of increased nutritional or medicinal benefit. 

Professor Cathie Martin said:

“Our study provides a general tool for producing valuable phenylpropanoid compounds on an industrial scale in plants, and potentially production of other products derived from aromatic amino acids. Our work will be of interest to different research areas including fundamental research on plants, plant/microbe engineering, medicinal plant natural products, as well as diet and health research.”

Dr Yang Zhang, said:

“Medicinal plants with high value are often difficult to grow and manage, and need very long cultivation times to produce the desired compounds. Our research provides a fantastic platform to quickly produce these valuable medicinal compounds in tomatoes. Target compounds could be purified directly from tomato juice. We believe our design idea could also be applied to other compounds such as terpenoids and alkaloids, which are the major groups of medicinal compounds from plants.”

This research was strategically funded by the BBSRC, the EU ATHENA collaborative project, the Major State Basic Research Development Program (973 Program) of China, the John Innes Foundation, and the DBT-CREST Fellowship.

Source: Scientists produce beneficial natural compounds in tomato – with potential for industrial scale up

Scientists produce beneficial natural compounds in tomato – with potential for industrial scale up

From the John Innes Centre news feed and featuring OpenPlant scientists Professor Cathie Martin and Dr Yang Zhang.

Given the opportunity to drink fifty bottles of wine or eat one tomato, which would you choose?

Scientists at the John Innes Centre have found a way to produce industrial quantities of useful natural compounds efficiently, by growing them in tomatoes.

The compounds are phenylpropanoids like Resveratrol, the compound found in wine which has been reported to extend lifespan in animal studies, and Genistein, the compound found in soybean which has been suggested to play a role in prevention of steroid-hormone related cancers, particularly breast cancer. 

As a result of the research led by Dr Yang Zhang and Dr Eugenio Butelli working in Professor Cathie Martin’s lab at the John Innes Centre, one tomato can produce the same quantity of Resveratrol as exists in 50 bottles of red wine. One tomato has also produced the amount of Genistein found in 2.5kg of tofu.

Drs Zhang and Butelli have been studying the effect of a protein called AtMYB12 which is found in Arabidopsis thaliana, a plant found in most UK gardens and used as a model plant in scientific investigation. 

The protein AtMYB12 activates a broad set of genes involved in metabolic pathways responsible for producing natural compounds of use to the plant. The protein acts a bit like a tap to increase or reduce the production of natural compounds depending on how much of the protein is present. 

What was interesting about the effect of introducing this protein into a tomato plant was how it acted to both increase the capacity of the plant to produce natural compounds (by activating phenylpropanoid production) and to influence the amount of energy and carbon the plant dedicated to producing these natural compounds. In response to the influence of the AtMYB12 protein, tomato plants began to create more phenylpropanoids and flavanoids and to devote more energy to doing this in fruit.

Introducing both AtMYB12 and genes from plants encoding enzymes specific for making Resveratrol in grape and Genistein in legumes, resulted in tomatoes that could produce as much as 80mg of novel compound per gram of dry weight –demonstrating that industrial scale up is possible. 

Tomatoes are a high yielding crop - producing up to 500 tonnes per hectare in countries delivering the highest yields (FAOSTAT 2013) and require relatively few inputs. Production of valuable compounds like Resveratrol or Genistein in tomatoes could be a more economical way of producing them than relying on artificial synthesis in a lab or extracting them in tiny quantities from traditional plant sources (e.g., grapes, soybeans, etc.). The tomatoes can be harvested and juiced and the valuable compounds can be extracted from the juice. The tomatoes themselves could potentially become the source of increased nutritional or medicinal benefit. 

Professor Cathie Martin said:

"Our study provides a general tool for producing valuable phenylpropanoid compounds on an industrial scale in plants, and potentially production of other products derived from aromatic amino acids. Our work will be of interest to different research areas including fundamental research on plants, plant/microbe engineering, medicinal plant natural products, as well as diet and health research.”

Dr Yang Zhang, said:

"Medicinal plants with high value are often difficult to grow and manage, and need very long cultivation times to produce the desired compounds. Our research provides a fantastic platform to quickly produce these valuable medicinal compounds in tomatoes. Target compounds could be purified directly from tomato juice. We believe our design idea could also be applied to other compounds such as terpenoids and alkaloids, which are the major groups of medicinal compounds from plants.”

This research was strategically funded by the BBSRC, the EU ATHENA collaborative project, the Major State Basic Research Development Program (973 Program) of China, the John Innes Foundation, and the DBT-CREST Fellowship.

Source: Scientists produce beneficial natural compounds in tomato – with potential for industrial scale up

2015 Nobel prize recognises importance of research into medicinal compounds made by plants and microbes.

From the John Innes Centre

Earlier this month the Nobel Prize for physiology and medicine was awarded to three scientists who pioneered the development of new drugs from plants and microbes, and in doing so, went on to save millions of lives.

Chinese scientist, Professor Youyou Tu, received half the Nobel prize for developing artemisinin, a drug from the wormwood plant which gave the world a desperately needed new therapy for treatment of malaria.

Professors Satoshi Omura and William Campbell received a quarter of the prize each for the development of ivermectin, a drug made by a bacterium called Streptomyces avermitilis. Ivermectin was originally intended to tackle parasitic infections in animals, but it also proved to be extremely effective as a simple and life-changing treatment for the human parasitic infections which cause river blindness and elephantiasis.

The John Innes Centre is a world leader in this area of science. Scientists in the Plant and Microbial Metabolism programme aim to understand how plants and microbes make diverse natural compounds, and to apply this knowledge to develop new therapeutics that can improve human and animal health. Two relevant examples of current JIC research are the continuing discovery of potential new antibiotics made by species of the bacterium Streptomyces, and the discovery of how the anti-cancer drug vincristine is made by the Madagascar periwinkle plant.

Streptomycetes and antibiotics

Streptomycetes are soil-dwelling bacteria that give rise to half of the antibiotics used in human and veterinary medicine and agriculture. Ivermectin is one of the best known examples; another is streptomycin for which Professor Selman Waksman was awarded the Nobel Prize for Medicine in 1952. Streptomycetes also produce compounds that are used as anti-cancer agents, herbicides and other pharmacologically active chemicals such as immuno-suppressants, and several enzymes that are important to the food industry. 

Following the huge advances in understanding antibiotic production by Streptomyces species stemming from the research of Professor David Hopwood at JIC from the 1960s onwards, Professor Merv Bibb and Dr Barrie Wilkinson and Dr Andy Truman are working to discover new compounds made by Streptomyces and related bacteria. Their discoveries build on the pioneering work of Omura, Campbell, Waksman, Hopwood and others, and are needed more urgently than ever in the face of the dwindling effectiveness of current antibiotics for many major diseases.

Fortunately, advanced methods of sequencing bacterial genomes have now revealed that these bacteria have the genetic capacity to make many diverse compounds with unexplored structures and properties. There is thus huge untapped potential for the discovery of new antibiotics. The John Innes researchers are using combinations of genetics, bioinformatics, chemistry and molecular biology to pinpoint and characterise new compounds of potential value, and to engineer the production of large amounts of these compounds for tests of their antibiotic properties. The researchers collaborate with other organisations and pharmaceutical companies to ensure that new compounds can be rapidly developed into drugs if they show therapeutic potential. 

The Madagascar Periwinkle (Catharanthus Roseus) - The plant that makes vincristine

Madagascar periwinkle and anti-cancer drugs

The Madagascar periwinkle plant produces rare complex compounds that are used as anticancer therapies. Vincristine, for example, is important for the treatment of several cancers. The drug has to be purified from the plant, and as a result it is very expensive and in short supply. Professor Sarah O’Connor is working with collaborators in Europe and the USA to discover how this and related compounds are made in the plant. Her discoveries will lead to better production methods for the anticancer compounds, and the development of novel, related compounds which may have new or enhanced therapeutic properties. She recently engineered yeast cells to produce a precursor to vincristine, using genes from the periwinkle plant. This development opens up the possibility of cheap, large scale production of vincristine in the future.

Many species of plants in addition to the Madagascar periwinkle produce valuable drugs. The antimalarial drug artemisinin discovered by Professor YouYou Tu in the wormwood plant is an outstanding example. Quinine, the original antimalarial therapy, comes from a South American tree, and plants also produce morphine, atropine and a host of other drugs in common use. JIC makes major contributions to the discovery of new therapeutic compounds from plants. As for bacteria, new information about plant genomes shows us that plants have a huge capacity for the production of potentially valuable molecules that have not yet been characterised. Genomic information also helps us to discover the compounds responsible for the therapeutic properties of plants used in traditional medicines. The research of Professors Sarah O’Connor, Anne Osbourn, Cathie Martin, Rob Field and George Lomonossoff and Dr Paul O’Maille is leading to the discovery of new compounds and how they are made in plants, to the synthesis of altered versions of therapeutic compounds expected to have novel properties, and to methods for engineering large scale production of plant-derived therapeutic compounds.

EU Workshop on Access and Benefit Sharing under Nagoya Protocol

More info and registration here

Context

The EU is a Party to the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilisation. The EU ABS Regulation, which transposes into the EU legal order the compliance pillar of the Protocol, became applicable as of 12 October 2014. The principal obligations of the Regulation – i.e. Article 4 on due diligence, Article 7 on monitoring user compliance and Article 9 on checks on user compliance – will become applicable as of 12 October 2015. In this context it is important that those who utilise genetic resources (i.e. conduct research and development on the genetic and/or biological composition of genetic resources, including through the application of biotechnology) are aware of the obligations arising from the Regulation, and that they can take the necessary measures to ensure their activities are compliant.

Workshop presentation

The workshop aims at providing the participants with knowledge about their obligations under the EU ABS Regulation and what they practically imply for their everyday work. In the first part of the workshop, the new legal framework will be explained, providing insight into the main provisions of the EU ABS Regulation. In the second part of the workshop, participants will have a chance to put the knowledge gained into practice through interactive case studies, based on real-life examples and realistic scenarios. The workshop should allow participants to better understand their obligations under the EU law, and to establish which steps they need to follow and which practical measures they should take when dealing with genetic resources originating from Parties to the Nagoya Protocol.

Target group

The workshop is targeted at senior academics and experienced researchers conducting research and development on genetic resources who have an interest in gaining an essential understanding of the new legal framework in the EU, in view of the ABS Regulation becoming fully operational later this year.

Scientists with an expertise in the ABS regulation are not targeted by this basic training workshop

Event on writing for The Conversation (23 Nov 2015)

The Conversation is a website aimed at providing expert opinion and comment from academics across the UK:Articles on the site are regularly carried on other sites, including The Guardian, Independent, CNN and IFLscience.

The site is a great opportunity to share your science with a wider audience and contribute commentary on synthetic biology and related fields.

The Office of External Affairs and Communications at the University of Cambridge is hosting an event on 23 November with Jonathan Este, Associate Editor at The Conversation.

"The University of Cambridge is now a member of the Conversation, meaning that our researchers have greater opportunity to write stories for the site, and will also be able to benefit from training sessions in writing opinion pieces for a general audience. This can benefit early-career as well as more established researchers.

Jonathan Este will give a short talk covering the following: · What is The Conversation?

· How can researchers get involved in writing features?

· What are the benefits?

· What training and support is available?

Professor Simon Redfern from the Department of Earth Sciences who is a regular columnist on the Science & Technology page of The Conversation will also talk about his experiences.

After the presentations there will be an opportunity to network with colleagues over tea, coffee and biscuits."

There are a limited number of places, so please do book your place here.

OpenPlant ERASynBio Summer School in New Phytologist

New Phytologist have published a report on the OpenPlant ERASynBio Summer School in plant synthetic biology authored by Nicola Patron, Colette Matthewman and collaborators at BBSRC.

European science policy is reflecting the increasing importance of synthetic biology as a tool to drive cutting-edge scientific developments. Significant strategic investment has been made, coordinated by the European Research Area Network for synthetic biology (ERASynBio), to ensure European synthetic biology research is coherent and world-leading. Strategies to achieve this include providing high-quality training for the next generation of synthetic biologists, and fostering international collaborations across a range of disciplines (ERASynBio, 2014). To realize these aims, ERASynBio has funded annual summer schools to bring together early career researchers from across ERASynBio partner countries for world-class synthetic biology training and networking. The second of these summer schools, which ran on 14–20 September 2014 at the John Innes Centre, Norwich, UK, was designed to provide the participants with ‘An introduction to synthetic biology in plant systems’ in conjunction with OpenPlant, a collaborative plant-focussed Synthetic Biology Research Centre linking the University of Cambridge, John Innes Centre and The Sainsbury Laboratory.

‘… an invaluable and enjoyable opportunity for early career researchers to learn from and engage with world-leading experts in plant synthetic biology.’

Read more via New Phytologist
Carmichael, R. E., Boyce, A., Matthewman, C., & Patron, N. J. (2015). An introduction to synthetic biology in plant systems. New Phytologist, 208(1), 20-22. DOI: 10.1111/nph.13433

OpenPlant at the UK Synthetic Biology 2015 Conference

Three OpenPlant group leaders spoke at the recent UK Synthetic Biology Conference:

Nicola Patron (The Sainsbury Laboratory)
Development and Application of Standards for Plant Synthetic Biology

Anne Osbourn (John Innes Centre)
Making new molecules

Alison Smith (University of Cambridge)
Using synthetic biology approaches to allow predictable metabolic engineering in algae

The full conference schedule can be found here and there are plans for a 2016 conference in Edinburgh with more involvement from PhD students and postdocs. You can see some highlights from #SBUK2015 below!