OpenPlant seeks a Laboratory Research Technician (Fixed Term)

More info and application >>>

A position is open for a Research Technician in the OpenPlant Laboratory in Cambridge, based in the Department of Plant Sciences at the University of Cambridge, under the direction of Prof. Jim Haseloff.

Work there will focus on the development of foundational technologies for engineering of the model plant Marchantia polymorpha. The newly renovated laboratory houses state of the art equipment for automated DNA assembly, genome editing, plant transformation, cytometry and high throughput microscopy.

The appointee will work closely to the OpenPlant Laboratory Manager and the successful candidate will be involved in: - Assisting in the maintenance of the lab and providing general laboratory support work. - Supporting plant transformation and tissue culture workflows in a high throughput environment. - Providing technical support for microbiological, molecular biology and microscopy experiments in a synthetic biology lab.

The successful candidate will have a background in molecular biology or synthetic biology, and demonstrate an ability to work independently. Experience with tissue culture procedures, plant work, synthetic biology techniques, microscopy, and laboratory management will be advantageous.

Fixed-term: The funds for this post are available until 2 September 2019 in the first instance.

OpenPlant lab mentioned in 'Microalgae as a microcosm of plant biotech'

Source: Microalgae as a microcosm of plant biotech

Orlando de Lange has a blog post up on 'Microalgae as a microcosm of plant biotech' mentioning the work of Alison Smith's Lab at the University of Cambridge, plus several others using Chlamydomonas for classical biotechnology and synthetic biology. Worth a quick read!

And of course I won’t leave out synthetic biology. Several labs seem to be exploring the potential for synthetic biology with microalgae.Alison Smith’s lab in Cambridge has long studied mircroalgal metabolism, with an eye to biofuel production and has more recently begun churning out tools for engineering Chlamydomonas.

Workshop: From Big Data to Discovery in Plant Science (21-22 April 2016)

Integrating Large Data into Plant Science21–22 April 2016 Dartington Hall, Totnes, Devon

Organisers: Sabina Leonelli, Ruth Bastow, Geraint Parry, David Salt Further information >>>

Aims of the workshop This workshop brings together prominent biologists, data scientists, database leads, publishers, representatives of learned societies and funders to discuss ways of harnessing and integrating large plant data to foster discovery. Over the last decade, data infrastructures such as cloud, grids and repositories have garnered attention and funding as crucial tools to facilitate the re-use of existing datasets. This is a complex task, and within plant science a variety of strategies have been developed to collect, combine and mine research data for new purposes. This workshop aims to review these strategies, identify examples of best practices and successful re-use both within and beyond plant science, and discuss both technical and institutional conditions for effective data mining.

In particular, workshop participants will

• assess how effective the mining of existing large datasets and their re-use by others has been in advancing plant biology,
• identify current bottlenecks and barriers in the data dissemination, mining and reuse pipelines,
• highlight areas of plant science that are falling behind in the big data era,
• explore how data infrastructures can effectively harness community knowledge,
• evaluate business models and incentives for data users to donate resources, acknowledge databases and provide feedback that can be widely shared and provide added value to the resource.

The workshop is jointly organized by the Exeter Centre for the Study of Life Sciences (Egenis) and GARNet, with funding from BBSRC and the European Research Council.

Participation to this workshop is free, but numbers are limited. Prospective participants are required to register as soon as possible by sending an email containing a brief statement of motivation for interest in the workshop to Geraint Perry.

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

Register >>>

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.

Apply to CUTEC Sustainable Futures Challenge with your sustainable synthetic biology ideas

sustainable_future_2016

In line with the theme of this year’s CUTEC’s Technology Ventures Conference (TVC), this new, interactive initiative will gather the best and brightest Cambridge students, academics, staff, and alumni to tackle problems relating to the question:

“How can we enable sustainable supply and production of food and water in a sustainable fashion?”

A resource is defined as a source or supply from which a benefit/need can be obtained in order to function effectively. The UN has estimated that in 15 years we will need 30% more water, 45% more energy, and 50% more food than today. The percent of arable land in the world is estimated to be 13.31% with only 4.71% sustaining permanent crops. However, by rethinking what counts as a “resource” people are finding clever ways to produce food in inhospitable environments, for example one experiment in the desert of Qatar takes advantage of abundant sunlight and seawater to turn out 75 kg of vegetables per square meter. How can we adapt to less than ideal environments to continue to live comfortably while supporting a planet of over 7 billion humans?

We will place scientists, engineers, business students, social scientists, and artists on teams to solve one of three challenges: (1) Compost, (2) Soil structure, and (3) Seed distribution. Solutions will need to take into account and will be judged on efficiency, sustainability, and economy.

Teams will workshop their ideas with industry experts at four workshops over the course of eight weeks and then present their solutions on stage at the TVC in front of investors, academics, students, and incubators.

CLICK TO FIND OUT ABOUT THE LAUNCH EVENT >>>

CLICK HERE TO REGISTER TO THE SFC >>>

The Challenges

Compost Challenge

Studies show that compost use in arable rotations can improve yields and resilience. Tons of organic, compostable material is thrown out in cities every day. How can we create an economical way to sort and get organic waste from cities to farms?

Soil Structure Challenge

The physical structure of soil affects crop development and yields.  Detailed soil structure tests can be performed in labs, but this is time consuming and costly. Can we make better in-the-field tool(s) to let allow farmers to check soil structure and resilience?

Seed Distribution Challenge

Cover-cropping is a great way to rehabilitate soil and can provide wide ranging benefits in farming systems. The most success often comes with mixing multiple species; however, these species have seeds of different sizes and shapes which makes it difficult to spread them evenly using current technology. Can we create a way to make it practical for farmers to sow seeds of different sizes?

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.

ContentMine Workshop & Hackathon at TGAC: mining for synthetic biology

poster

Find out more and register >>>

Supported by the OpenPlant Fund

Interested in using mining technologies for synthetic biology?

Content mining technologies hold much potential for maximising scientific discovery and the reuse of research through automated searching, indexing and analysing of scientific literature.

In this workshop, we aim to educate and engage technologists and biologists who are interested in using mining technologies for synthetic biology; to better enable access to research literature and data in plant synthetic biology.

The hackathon on Day Two aims to improve searching and indexing of plant synthetic biology texts through open source technology platforms developed by the Grassroots Genomics project at TGAC and the ContentMine platform from the University of Cambridge.

Target Audience

Best suited to biologists and bioinformaticians who have some experience of using command line tools or the enthusiasm to pick this up! As such, formal programming experience is not a requirement, but you may find it useful to attend the Software Carpentry Bootcamp held at TGAC prior to this event.

Course prerequisites: Basic prior knowledge of programming concepts.

Course details

The registration fee is £50.00 (plus booking fee of 2.13 per cent) – refundable on attendance (minus booking fee) which will be processed post event.

We are also able to reimburse up to two nights accommodation with a limit of £80.00 per night (receipts required).

Scientific Organisers:

Emily Angiolini, The Genome Analysis Centre (TGAC), UK Rob Davey, The Genome Analysis Centre (TGAC), UK Richard Smith-Unna, University of Cambridge, UK

Course Faculty:

Rob Davey, The Genome Analysis Centre (TGAC), UK Richard Smith-Unna, University of Cambridge, UK

Further Details:

Venue: The Genome Analysis Centre (TGAC), UK Application deadline: Friday 26 February 2016 Participation: First come, first served

OpenPlant Fund now open for applications! Deadline 4 March 2016

The OpenPlant Fund will support innovative, open and interdisciplinary projects relevant to plant Synthetic  Biology over 2015-19. Around 20 six-month projects per year will receive £4k each, with an  additional £1k awarded on completion for follow-on and outreach. The first round of applications for 2016 is now open and will close on 4 March!

The aim of the fund is to promote the development of plant Synthetic Biology as an interdisciplinary  field and to facilitate exchange between The University of Cambridge, the John Innes Centre and The Sainsbury Laboratory for the development of open technologies and responsible innovation in the context of Synthetic Biology.

Download: Poster | Flyer

Apply now >>>

(logged-in users only)

Applicants should be graduate students or postdoctoral workers at the University of Cambridge, the John Innes Centre or The Sainsbury Laboratory. The team must be interdisciplinary, must contain members from both Norwich and Cambridge and may contain external collaborators of any type. Applicants must have agreement from their research supervisor and cost-code sponsor that the  proposed project and management of the allocated funding will fit with their existing work. All proposals must lead to tangible, publicly documented and open outcomes, which could include (but are not limited to) the following:

• Design files and prototype for a hardware project
• Software development and documentation
• White paper arising from a workshop
• Educational resource
• Synthesis and sharing of useful DNA parts or vectors.

For more information and to apply see the OpenPlant Fund webpage.

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.