OpenPlant Forum 2019: Engineering Plants for Bioproduction

Blog post by Dr Colette Matthewman

Over the past decade, synthetic biology has focussed much of its effort on microbial chassis as platform for bioproduction. The single cell simplicity and rapid life-cycles of these organisms, the prevalence of biological tools and the existing industry infrastructure for fermentation have made microbes a tempting playground for synthetic biologists wishing to make a range of chemicals and biomolecules, from flavours and fragrances to distributed manufacturing of highly complex metabolites for medicine, and an increasing number of companies are finding success in this arena (e.g. Ginkgo Bioworks, Amyris, Evolva, Antheia).

More recently, plants have been showing serious promise as viable production platforms for complex chemicals and biomolecules which in many cases simply can’t be made in single celled microbes. This year, the OpenPlant Forum explored some of the latest advances in plant bioproduction with inspiring talks from invited speakers and OpenPlant researchers highlighting a promising and exciting future for plant synthetic biology.

 OpenPlant post-doc Ingo Appelhagen presents his work on anthocyanin pigment production in plant cell cultures.

OpenPlant post-doc Ingo Appelhagen presents his work on anthocyanin pigment production in plant cell cultures.

The first morning of the Forum focused on tools for refactoring regulation and simple test platforms for plant synthetic biology. Prof. Ian Small (University of Western Australia) opened the meeting with a keynote on the potential for using engineered RNA bonding proteins to control organelle gene expression. OpenPlant PI, Prof. Paul Dupree described research in his on engineering of polysaccharide structures in plants. We also had the first examples of plant production platforms: Dr Ingo Appelhagen presented his recently published work on the production of colourful anthocyanin molecules in plant cell cultures, while Dr Eva Thuenemann introduced the HyperTrans system developed in the Lomonossoff lab at the John Innes Centre for the transient expression of proteins in Nicotiana benthamiana, a wild relative of tobacco. Eva is working on plant-based production of a protein that could be used in a vaccine against East Coast Fever, a devastating disease in cattle in Africa. The HyperTrans platform is used by the Lomonossoff lab and recently established company Leaf Expression Systems to produce therapeutic proteins and virus-like particles for vaccines, including recent work on a new vaccine for the eradication of Polio.

The afternoon session explored the cutting edge in production of complex plant-derived natural products in yeast, with a keynote from Prof. Christina Smolke (Stanford University), followed with an insight into the engineering of triterpene production in N. benthamiana by Dr James Reed in the Osbourn lab (John Innes Centre), recently reviewed in Plant Cell Reports. These projects rely heavily on chemical and enzymatic biodiversity in nature. Dr Sam Brockington (University of Cambridge) talked about harnessing the global network of botanic gardens for access to plant diversity for metabolic engineering and synthetic biology, introducing a global database of living plant, seed and tissue collections called “Plant Search” – a perfect sedgeway into a panel discussion on Harnessing Global Biodiversity where Sam was joined by Dr Nicola Patron (Earlham Institute), Mr David Rejeski (Environmental Law Institute), and Dr Jenni Rant (SAW Trust). The discussions ranged from public opinion on synthetic biology (explored through the Global Garden workshop) and benefit sharing and dematerialisation, through to how blockchain (like the bitcoin) is being used in environmental contexts and whether blockchain technology trends can be applied to create/assign value for biodiversity.

 Prof. Ralf Reski with his moss bioreactors

Prof. Ralf Reski with his moss bioreactors

Day two of the Forum continued on a theme of “Tools for Metabolic Engineering” with Prof. Claudia Vickers (University of Queensland) opening by introducing the Future Science Platform in Synthetic Biology that she leads at CSIRO, as well as numerous tools developed in her research lab. Claudia was followed by a trio of OpenPlant postdocs describing analysis to unravel the genetics of divergent metabolic pathways in Brassicaceae (Dr Zhenhua Liu), a search for new synthetic biology tools based on diversity of natural triterpene oxidation (Dr Michael Stephenson) and tools for engineering Marchantia’s chloroplasts (Dr Eftychis Frangedakis).

Moving on from the tools, we explored further plant-based bioproduction platforms, starting with an inspirational keynote from Prof. Ralf Reski (University of Freiburg) on the moss Physcomitrella patens that Ralf’s lab has established as a production platform for biopharmaceuticals, leading to foundation of the company Greenovation, which produces moss-aGal (agalsidase) for the treatment of Fabry disease, a rare but painful and potentially deadly disease. Subsequently, we heard from Prof. Alison Smith (University of Cambrige) about “Designer algae” and work towards predictable metabolic engineering in microalgae, and from Dr Eugenio Butelli (John Innes Centre) about the Tomato as a biofactory for making health promoting flavonoids.

The Forum was wrapped up for this year with a session on Sharing and Techno-Social Platforms, with an introduction from OpenPlant’s Prof Jim Haseloff, followed by Dr Linda Kahl (BioBricks Foundation) on the latest with the Open Material Transfer Agreement (Open MTA) which has been developed in collaboration with OpenPlant to enable sharing of DNA parts (publication coming soon!). Next up, Dr Joanne Kamens from not-for-profit plasmid distribution company, Addgene, revealed the freshly launched plant resource page and spoke about the upcoming adoption of the Open MTA as an option under which plasmids can be shared. Finally, Dr Richard Sever from bioRxiv spoke about preprint opportunities for synthetic biology.


Join us in Cambridge for the OpenPlant Forum 2019 | 29 – 31 July

Save the date!

[Closes 14 September 2018] Technologist in DNA packaging and delivery in Edinburgh

This position is within Prof Alistair Elfick lab, School of Engineering and UK Centre for Mammalian Synthetic Biology (www.synbio.ed.ac.uk

The Role:

An important underpinning technology for synthetic biology is the synthesis of DNA. Technology has now advanced to the point where it is possible to affordably construct very large constructs up to chromosome scale. An emergent bottleneck is the delivery of this into the cell. The Technologist will be actively involved in contributing to the standard development programme of the UK Centre for Mammalian Synthetic Biology (UK-CMSB), in collaboration with the National Physical Laboratory. They will be primarily responsible for delivering technologies to achieve the packaging and non-viral delivery of large DNA constructs into mammalian cells, with their reduction to practise as standard protocols. Their secondary role is the support of collaboration with academic and research staff and students of the UK-CMSB. The post holder will ensure that the development of UK-CMSB technology standards supports and keeps pace with the research requirements, liaising with industry, collaborators and users, advising and training staff and students.

Fixed term for 2 years

Grade 7

Closing date Sept 14th 2018

Vacancy reference www.vacancies.ed.ac.uk  search for #044849

Contact Alistair.elfick@ed.ac.uk for further information

 

 

Colour bio-factories: anthocyanin production in plant cell cultures

 Bioreactors with engineered tobacco (left) and wild-type grape (right) cell cultures.

Bioreactors with engineered tobacco (left) and wild-type grape (right) cell cultures.

OpenPlant Postdoc, Ingo Appelhagen, in Prof Cathie Martin's lab in the John Innes Centre has recently published an article in the journal Metabolic Engineering about his research to develop a system for production of high-levels of anthocyanins in plant cell cultures.

Anthocyanins give many fruits and flowers their red, purple or blue colouration. The martin lab are interested in the beneficial effects of anthocyanins in our diets and their use as natural colourants in the food and cosmetic industries.

 

512px-Open_Access_PLoS.svg.png

Appelhagen I, Wulff-Vester AK, Wendell M, Hvoslef-Eide AK, Russell J, Oertel A, Martens S, Mock HP, Martin C, Matros A (2018). Colour bio-factories: Towards scale-up production of anthocyanins in plant cell cultures. Metabolic Engineering. Doi: https://doi.org/10.1016/j.ymben.2018.06.004

Abstract

Anthocyanins are widely distributed, glycosylated, water-soluble plant pigments, which give many fruits and flowers their red, purple or blue colouration. Their beneficial effects in a dietary context have encouraged increasing use of anthocyanins as natural colourants in the food and cosmetic industries. However, the limited availability and diversity of anthocyanins commercially have initiated searches for alternative sources of these natural colourants. In plants, high-level production of secondary metabolites, such as anthocyanins, can be achieved by engineering of regulatory genes as well as genes encoding biosynthetic enzymes. We have used tobacco lines which constitutively produce high levels of cyanidin 3-O-rutinoside, delphinidin 3-O-rutinoside or a novel anthocyanin, acylated cyanidin 3-O-(coumaroyl) rutinoside to generate cell suspension cultures. The cell lines are stable in their production rates and superior to conventional plant cell cultures. Scale-up of anthocyanin production in small scale fermenters has been demonstrated. The cell cultures have also proven to be a suitable system for production of 13C-labelled anthocyanins. Our method for anthocyanin production is transferable to other plant species, such as Arabidopsis thaliana, demonstrating the potential of this approach for making a wide range of highly-decorated anthocyanins. The tobacco cell cultures represent a customisable and sustainable alternative to conventional anthocyanin production platforms and have considerable potential for use in industrial and medical applications of anthocyanins.

The Mad Hatter's Tea-party at Boomtown

Following last year’s success at BoomTown Fair, we returned, alongside the SAW Trust, with an Alice In Wonderland themed delight for the senses, with science, art and writing activities to excite young minds.

 Table laid and ready for the first guests to arrive!

Table laid and ready for the first guests to arrive!

Now in its tenth year, BoomTown Fair attracts up to 60, 000 people and many of those came to visit us at Kidztown, with its impressive visual displays and interactive activities for families. 

Our stand entitled “The Mad Hatter’s Tea Party” revolved around workshops which had four stations for the children to rotate around. The tea parties began with the mad hatter revealing secret invisible ink messages to the children before the experiments could begin!

The children were tasked with many exciting science-based activities. Tasty treats the children could create included sweet, fizzy sherbet and rapid ice-cream made using an endothermic reaction and flavoured with plant flavourings (vanilla, coconut and strawberry). In addition to these, there were also many pigment-based activities inspired by all the bright colours in Wonderland, for the children to try. Including; natural plant pigment tissue tie-dyes and colour changing flowers and celery. The results of which decorated the tent throughout the weekend.

 

Carrying on with our use of plant products, the children also got to create their own fruit flavoured jelly balls, using alginate gelling agent, derived from algae, to go with a fizzy drink!

The final activity for the children was to write secret messages, which would be revealed by a new set of children, at the next tea party by the Mad Hatter.

 Some of our tea-party guests about to make sweet treats.

Some of our tea-party guests about to make sweet treats.

As well as the tea parties, there were also numerous activities and challenges for the children to engage with while the table was re-set. These activities included using microscopes to explore the microscopic world Alice enters when she shrinks, writing nonsense poems, like those the Mad Hatter recites at his tea party and pinning the grin on the Cheshire cat.

We had a range of craft activities available, providing the children with something to take home with them from their time at BoomTown. The children could make Wonderland inspired flower faces, clock necklaces, a Mad Hatter’s Hat and playing card bowties.

Across the three days the children were able to immerse themselves in a Wonderland of science, art and writing, feeding their curiosity with a range of thrilling experiments and allowing their creativity to run wild with exciting craft projects.

A big thank you to the entire team who helped with the preparations and running of “The Mad Hatters Tea Party” and to BoomTown for having us once again!

By Shannon Woodhouse

DSC_0031.JPG

An internship with the SynBio 4 Schools project

PhD student Camilla Stanton spent a three month internship, from May to August 2018, working with OpenPlant to build resources and materials for the Synthetic Biology for Schools (SynBio4Schools) project, funded through the OpenPlant Fund scheme. In this blog post she describes the project and the work that she completed during her placement.


Synthetic biology brings together researchers from a broad range of backgrounds to solve biological problems through rational design. While synthetic biology is increasingly being taught in universities, it remains under-represented in the national curriculum and teaching resources for GCSE and A-Level students. The SynBio 4 Schools project aims to solve this problem by creating a comprehensive educational resource package that teaches the principles of plant synthetic biology through practicals and case studies.

 SynBio4Schools activites and write-ups on display at the OpenPlant Forum, Norwich, 2018

SynBio4Schools activites and write-ups on display at the OpenPlant Forum, Norwich, 2018

I got involved with the SynBio 4 Schools project through a 3-month industrial placement as part of my PhD. My role was to assess and identify what resources could be included and to begin compiling them. An obvious starting place was to explore the activities and demonstrations that researchers in Norwich and Cambridge had already developed and tested. While these resources are valuable on their own, bringing them together creates a set of interlinked resources that support one another, greatly increasing their reach and impact. It is also an exciting opportunity to get contemporary research into schools, helping inspire the next generation of biological engineers!

During my placement, I worked in collaboration with researchers to discuss ideas for how their research could be used in a teaching-style activity, whether that be an experiment, worksheet or craft-based. We also had discussions about what sort of supporting material might be useful, such as articles, interviews or case studies. It was a really enjoyable process as it gave the scientists a unique opportunity to think more creatively about their work, and I got to hear some really innovative ideas for teaching some quite complex concepts.

 Some of the 3D printed virus structures from Roger Castells-Graells'  OpenPant Fund Project .

Some of the 3D printed virus structures from Roger Castells-Graells' OpenPant Fund Project.

I ended up focussing on writing up three activities based on work carried out by Dr Paolo Bombelli (plant microbial fuel cells), Dr Nicola Patron (genetic circuits) and Roger Castells-Graells (virus structures), which I was lucky enough to showcase at the OpenPlant Forum. This gave me the chance to receive feedback from other researchers and educators about how the materials could be made more accessible for students and provide more support for teachers and technicians. These suggestions helped shape the basic write-up template, which now includes additional investigations, sources and links to other experiments. 

This was a hugely valuable experience for me - I got to explore new topics, meet people with exciting and original ideas and even got to try my hand at some design work! Although I’m now back doing my PhD, the SynBio 4 Schools project definitely doesn’t end there - we want as many people as possible to get involved.

Currently, there is a growing list of activities that cover a variety of topics from plant natural products to computational biology. But we want to showcase even more research from Norwich and Cambridge! If you have developed a resource that you would like to see included in the SynBio 4 Schools project, or you think your research could translate into an educational setting, please do get in touch! Email Colette.Matthewman@jic.ac.uk

MRes Biotechnology and Biodesign

University of Newcastle are offering a new MSc program in Biotechnology and Biodesign. The course provides a foundation into how design and engineering approaches are used in the creation of new biotechnological processes and products.

More information and to apply>>>

About this course

Advances in biotechnology, computing, and laboratory automation are being coupled with design thinking approaches to engineer biological systems that may produce more sustainable products than traditional manufacturing. Examples include:

  • the production of synthetic meat substitutes
  • dairy-free milk
  • adaptive building materials
  • petroleum-replacement products
  • designer antimicrobial compounds
  • smart drug delivery systems

Our Biotechnology and Biodesign MRes:

  • provides a foundation in design thinking approaches
  • covers recent developments in applied biotechnology
  • provides an opportunity to develop and refine your laboratory skills
  • provides the opportunity to develop your own research project

The training forms an excellent foundation for students opting to follow a research orientated career path and for those looking for successful careers in the biotechnology industry.

The course is interdisciplinary. You'll be suitable for this course if you are:

  • a science graduate
  • looking to develop your knowledge and research skills

You'll gain the skills allowing you to address critical global challenges in:

  • sustainability
  • food security
  • the environment
  • healthcare

Engineering plant production systems to synthesise terpenoids

  Nicotiana benthamiana by Aymeric Leveau (John Innes Centre);  NRP-103

Nicotiana benthamiana by Aymeric Leveau (John Innes Centre); NRP-103

Researchers at the John Innes Centre, including OpenPlant PI Prof Anne Osbourn have recently published a review describing strategies developed in the lab to engineer terpenoid biosynthesis in plant-based production systems.

Terpenoids are the most structurally diverse class of plant natural products with a huge range of commercial and medical applications. Exploiting this enormous potential has historically been hindered due to low levels of these compounds in their natural sources, making isolation difficult, while their structural complexity frequently makes synthetic chemistry approaches uneconomical.

Reed, J. & Osbourn A. (2018), Engineering terpenoid production through transient expression in Nicotiana benthamiana. Plant Cell Rep. https://doi.org/10.1007/s00299-018-2296-3

Abstract

Terpenoids are the most structurally diverse class of plant natural products with a huge range of commercial and medical applications. Exploiting this enormous potential has historically been hindered due to low levels of these compounds in their natural sources, making isolation difficult, while their structural complexity frequently makes synthetic chemistry approaches uneconomical. Engineering terpenoid biosynthesis in heterologous host production platforms provides a means to overcome these obstacles. In particular, plant-based production systems are attractive as they provide the compartmentalisation and cofactors necessary for the transfer of functional pathways from other plants. Nicotiana benthamiana, a wild relative of tobacco, has become increasingly popular as a heterologous expression platform for reconstituting plant natural product pathways, because it is amenable to Agrobacterium-mediated transient expression, a scalable and highly flexible process that enables rapid expression of genes and enzymes from other plant species. Here, we review recent work describing terpene production in N. benthamiana. We examine various strategies taken to engineer this host for increased production of the target metabolite. We also look at how transient expression can be utilised for rapid generation of molecular diversity, including new-to-nature products. Finally, we highlight current issues surrounding this expression platform and discuss the future directions and developments which will be needed to fully realise the potential of this system.

[Closes 30 May 2018] Co-ordinator for Synthetic Biology Centre

We're looking to hire a Cambridge-based coordinator for the OpenPlant SynBio Research Centre and the Cambridge SynBio Strategic Research Initiative. Application deadline is 30 May 2018.

Full details of the post can be found at http://www.jobs.cam.ac.uk/job/17351/


The role-holder would work 50% to support the OpenPlant Synthetic Biology Research Centre and 50% with the Synthetic Biology Strategic Research Initiative (SynBio SRI). The purpose of the role is to help develop and implement a strategy that will enable both initiatives to become known leaders in the field and sustainable in the longer term.

OpenPlant (http://openplant.org) is a consortium funded by BBSRC and EPSRC comprising 20 labs spanning the University of Cambridge, John Innes Centre and the Earlham Institute (Norwich). The work of the Research Centre is intended to promote novel research on tools and applied traits for plant synthetic biology, open sharing of foundational technologies, and responsible innovation. The role-holder will work with the OpenPlant Directors and Management Group, including the OpenPlant Project Manager based in Norwich, to co-ordinate a variety of activities within the Research Centre.

The SynBio SRI (http://synbio.cam.ac.uk) aims to catalyse interdisciplinary exchange between engineering, physics, biology and social sciences to advance Synthetic Biology at the University of Cambridge. The role-holder will work with the SRI Co-Chairs and Steering Committee to develop, plan and deliver the SRI's vision and strategy. They will facilitate efforts to promote development of open technologies, build shared resources, and provide a hub for networking and discussion.

Responsibilities will also include co-ordinating seed funding competitions such as the Biomaker Challenge and OpenPlant Fund; organising formal and informal scientific meetings and forums; developing and managing relationships with stakeholders within and external to the University; seeking small and large-scale funding for future activities. The role-holder is additionally responsible for ensuring that synthetic biology activities in Cambridge are actively communicated and promoted, and is supported by the part-time SynBio SRI Events and Communication Co-ordinator.

The successful candidate will have a PhD in a relevant field and knowledge of Synthetic Biology research, policy and practice. They will have the ability to foster relationships with and between academics at all levels in an interdisciplinary context, and build partnerships with companies, funders and policy makers. A successful track record in attracting research funding would be advantageous. Excellent organisational and communications skills are essential, together with proven problem-solving skills and initiative.

Fixed-term: The funds for this post are available until 30 September 2019 in the first instance.

Cell-free protein synthesis - try it with your favourite protein!

Quentin Dudley, a postdoc at the Earlham Institute, did a PhD in the Jewett lab (Northwestern University, Illinois) focused on the use of cell-free systems for the reconstitution of metabolic pathways and bioproduction of monoterpenes. Now he is using an OpenPlant Fund Award to establish cell-free platforms for protein synthesis in Norwich. Read more about this work below, and on www.biomaker.org

As part of this project he is recruiting participants for a workshop on cell-free protein synthesis to be held in mid-June in Norwich. It is an opportunity to try to express your favourite protein using a low-cost, high-throughput platform. Download the poster for details and contact quentin.dudley@earlham.ac.uk for details and questions.


Cell-free protein synthesis

2018-05-10 CFPS graphic png.png

Cell-free protein synthesis (CFPS) uses crude lysates of E. coli, wheat germ, and other organisms to recapitulate transcription and translation in a test tube (Carlson et al., 2012). This enables protein production at higher throughput, shorter timescales, and simpler troubleshooting compared to expression in cells. While CFPS has several pros/cons, it is particularly powerful when testing many different protein variants/mutations with an output assay that works directly in the crude cell-free reaction.

While CFPS is getting easier to implement, buying commercial kits can get expensive and troubleshooting the first time can be challenging. In response, I’m leading a project sponsored by the OpenPlant fund to establish an in-house E. coli CFPS system (~£1 / rxn) at Norwich/Cambridge and want to compare it to a commercial wheat germ kit (£12 / rxn) for expressing proteins. We are testing a range of different proteins from various plants. If you have an interesting protein you’d like to try expressing in a cell-free system, please contact quentin.dudley@earlham.ac.uk for details!)

I’ve previously worked with CFPS as a graduate student with Michael Jewett at Northwestern University. The Jewett lab is working to develop new CFPS platforms using yeast (S. cerevisiae), chloroplasts, and CHO cells. They also are improving existing E. coli-based systems to synthesize “tricky” proteins that require complex folding environments (membrane proteins, antibodies) or contain nonstandard amino acids. During my time in the lab, I used CFPS to manufacture enzyme homologs which could then be combined to prototype metabolic pathways, for example biosynthesis of monoterpenoids.

It is a very exciting time for cell-free systems. Protein yields have increased to 2 mg/mL and a commercial company (Sutro Biopharma) has reported reaction volumes at 100 L (Zawada et al., 2011). Additionally, cell-free reactions can be freeze-dried on paper and retain full activity; several groups are using this feature to develop on-demand pharmaceuticals or simple, color-changing diagnostics for diseases such as Zika virus (Pardee et al., 2016). As this cell-free technology matures, its flexibility and programmability make it an attractive opportunity for Biomaker projects and future applications will be limited only by the creativity of researchers and developers.

2018-05-01 CFPS flyer FINAL.png

REFERENCES

Carlson, E. D., Gan, R., Hodgman, C. E., & Jewett, M. C. (2012). Cell-free protein synthesis: applications come of age. Biotechnology Advances, 30(5), 1185-1194.

Zawada, J. F., Yin, G., Steiner, A. R., Yang, J., Naresh, A., Roy, S. M., ... & Murray, C. J. (2011). Microscale to manufacturing scale‐up of cell‐free cytokine production—a new approach for shortening protein production development timelines. Biotechnology and Bioengineering, 108(7), 1570-1578.

Pardee, K., Green, A. A., Takahashi, M. K., Braff, D., Lambert, G., Lee, J. W., ... & Collins, J.J. (2016). Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell, 165(5), 1255-1266.

OpenPlant Fund project publishes on droplet-based microfluidics for rapid phenotyping of plant systems

Droplet isolated protoplast.png

Researchers from the University of Cambridge have this month published the results of a collaborative project, supported by the OpenPlant Fund, to develop droplet-based microfluidics systems for rapid prototyping in plant systems. The paper describes how they have achieved on-chip encapsulation and analysis of protoplasts isolated from the emergent plant model Marchantia polymorpha. We caught up with the team to find out more about their OpenPlant Fund project. Read on to find out more...

 

Yu Z, Boehm CR, Hibberd JM, Abell C, Haseloff J, Burgess SJ, et al. (2018) Droplet-based microfluidic analysis and screening of single plant cells. PLoS ONE 13(5): e0196810.

 

Publication abstract

Droplet-based microfluidics has been used to facilitate high-throughput analysis of individual prokaryote and mammalian cells. However, there is a scarcity of similar workflows applicable to rapid phenotyping of plant systems where phenotyping analyses typically are time-consuming and low-throughput. We report on-chip encapsulation and analysis of protoplasts isolated from the emergent plant model Marchantia polymorpha at processing rates of >100,000 cells per hour. We use our microfluidic system to quantify the stochastic properties of a heat-inducible promoter across a population of transgenic protoplasts to demonstrate its potential for assessing gene expression activity in response to environmental conditions. We further demonstrate on-chip sorting of droplets containing YFP-expressing protoplasts from wild type cells using dielectrophoresis force. This work opens the door to droplet-based microfluidic analysis of plant cells for applications ranging from high-throughput characterisation of DNA parts to single-cell genomics to selection of rare plant phenotypes.

 

Interview with the OpenPlant Fund team

A brief overview of the project

A current limitation for plant synthetic biology involves high-throughput screening of genetic parts in plants. Current approaches require testing circuits in individual plants, through transient or stable transgenics. Applying these techniques to hundreds of different circuits is not feasible at a laboratory scale. In this project, we use droplet based microfluidics to isolate and characterise both gene expression activity and chlorophyll content on single plant protoplasts at a high throughput scale. Our device can potentially analyse protoplasts at a processing rate of > 100,000 cells per hour.  We use this system to quantify the stochastic properties of a heat-inducible promoter across a population of transgenic Marchantia polymorpha protoplasts to demonstrate its potential for assessing gene expression activity in response to environmental conditions. In addition, we managed to sort droplets containing YFP-expressing protoplasts from wild type cells using dielectrophoresis force.  This work opens the door to droplet-based microfluidic analysis of plant cells for applications ranging from high-throughput characterisation of DNA parts to single-cell genomics to selection of rare plant phenotypes.

 

 A schematic of the droplet based microfluidics setup

A schematic of the droplet based microfluidics setup

 

What inspired the project?

Part of our research is focused on identifying DNA regulatory elements that could be used for designing synthetic promoters in plants. To achieve this, we would normally create a reporter construct containing the element of interest and then test its activity on individual plants through transient or stable genetic transformation. This approach can be very time consuming and impedes the researcher to test more than a handful of constructs at the time. Based on this we consider there was a need to develop methods that could accelerate the process. We knew Droplet-based microfluidics has been used to facilitate high throughput analysis of individual prokaryote and mammalian cells so we thought implementing this method in plants will be very useful.  

How did this project develop links between Cambridge and Norwich?

During the early stages of the project we teamed up with Oleg Raitskin from the Patron lab at the Earlham Institute. Oleg was very kind to share his experiences with protoplast isolation and also he showed us his method for protoplast transformation in tobacco leaves.

 

 Microscopy images of protoplasts captured in droplets and sorted by fluorescence

Microscopy images of protoplasts captured in droplets and sorted by fluorescence

 

What was your favourite aspect of the project?

We really enjoyed learning more about each other’s area of expertise. This project spans the disciplines of physical chemistry optomechatronics and biology so it gave us an opportunity to approach disciplines in which we were not very familiar.

 Sorting of M. polymorpha protoplasts: Microscopy images of microdroplets sorted into positive and negative channels based on their fluorescence intensity.

Sorting of M. polymorpha protoplasts: Microscopy images of microdroplets sorted into positive and negative channels based on their fluorescence intensity.

What is the biggest challenge the team faced?

Preparing high quality protoplast preparations from Marchantia was one of the greater challenges we encountered.

Is there something that came out of the project that you never expected at the beginning?

Being able to perform the sorting was unexpected at the beginning. Protoplasts are very sensitive cells that can burst spontaneously. The fact that we manage not just to isolate and measure but also sort opens a lot of possibilities for further applications.

How did the OpenPlant Fund enable the development of the project?

We could have never done this kind of project without the OpenPlant Fund. Apart of the funding which played a primal role in the development of the project, the OpenPlant fund offered great support across the whole process. For instance, our collaboration was established during a fund mixer organized by the synbio fund. Thanks to the Open Plant initiative we showed our project in various Open Plant meetings which resulted in very useful comments from various colleagues. Finally the costs derived from publishing the paper and making it open access were also covered by the grant.

What are the future opportunities to take this project forward?

Now that the system is set up, the next step could be to expand it to on-chip protoplast transformation (as has been done for other cell types). Protoplast transformation currently requires large amounts of materials (cells and DNA) and is low throughput, so this would be a big plus.

Researchers find first land plants were parasitised by microbes

The following blog was first published on the website of The Sainsbury Laboratory, Cambridge, and has been reproduced with the permission. The original can be found here.

image.png

Sainsbury Laboratory researchers have found that the relationship between plants and filamentous microbes not only dates back millions of years, but that modern plants have maintained this ancient mechanism to accommodate and respond to microbial invaders.

Why do some plants welcome some microbes with open arms while giving others the cold-shoulder? Like most relationships, it’s complicated, and it all goes back a long way.

By studying liverworts – which diverged from other land plants early in the history of plant evolution – researchers from the Sainsbury Laboratory at the University of Cambridge have found that the relationship between plants and filamentous microbes not only dates back millions of years, but that modern plants have maintained this ancient mechanism to accommodate and respond to microbial invaders.

Liverworts

 Close up of a liverwort.

Close up of a liverwort.

Liverworts are small green plants that don’t have roots, stems, leaves or flowers. They belong to a group of plants called Bryophytes, which also includes mosses and hornworts. Bryophytes diverged from other plant lineages early in the evolution of plants and are thought to be similar to some of the earliest diverging land plant lineages. Liverworts are found all over the world and are often seen growing as a weed in the cracks of paving or on the soil of potted plants. Marchantia polymorpha, which is also known as the common liverwort or umbrella liverwort, was used in this research.

Published today in the journal Proceedings of the National Academy of Sciences, a new study shows that aggressive filamentous microbial (fungi-like) pathogens can invade liverworts and that some elements of the liverwort’s response are shared with distantly related plants. The first author of the paper, Dr Philip Carella, said the research showed that liverworts could be infected by the common and devastating microorganism Phytophthora: “We know a great deal about microbial infections of modern flowering plants, but until now we haven’t known how distantly related plant lineages dealt with an invasion by an aggressive microbe. To test this, we first wanted to see if Phytophthora could infect and complete its life cycle in a liverwort."

 

   A healthy Marchantia polymorpha liverwort (left) and one that has been infected by Phytophthora palmivora (right).

A healthy Marchantia polymorpha liverwort (left) and one that has been infected by Phytophthora palmivora (right).

We found that Phytophthora palmivora can colonise the photosynthetic tissues of the liverwort Marchantia polymorpha by invading living cells. Marchantia responds to this by deploying proteins around the invading Phytophthora hyphal structures. These proteins are similar to those that are produced in flowering plants such as tobacco, legumes or Arabidopsis in response to infections by both symbiont and pathogenic microbes.”

 

   Microscopy image of a cross-section of a Marchantia polymorpha thallus showing the Phytophthora infection (red) in the upper photosynthetic layer of the liverwort plant.

Microscopy image of a cross-section of a Marchantia polymorpha thallus showing the Phytophthora infection (red) in the upper photosynthetic layer of the liverwort plant.

These lineages share a common ancestor that lived over 400 million years ago, and fossils from this time period show evidence that plants were already forming beneficial relationships with filamentous microbes. Dr Carella added: “These findings raise interesting questions about how plants and microbes have interacted and evolved pathogenic and symbiotic relationships. Which mechanisms evolved early in a common ancestor before the plant groups diverged and which evolved independently?”

Phytophthora

  Phytophthora  growing on  Marchantia thallus

Phytophthora growing on Marchantia thallus

Phytophthora is a water mould. Although it looks like it, it is not a fungus at all. Instead it belongs to the oomycetes and is a type of filamentous microbe. Phytophthora pathogens are best known for devastating crops, such as causing the Irish potato famine through potato late blight disease as well as many tropical diseases. This research used the tropical species, Phytophthora palmivora, which causes diseases in cocoa, oil palms, coconut palms and rubber trees.

Dr Sebastian Schornack, who led the research team, says the study indicates that early land plants were already genetically equipped to respond to microbial infections: “This discovery reveals that certain response mechanisms were already in place very early on in plant evolution.”

“Finding that pathogenic filamentous microbes can invade living liverwort cells and that liverworts respond using similar proteins as in flowering plants suggests that the relationship between filamentous pathogens and plants can be considered ancient. We will continue to study whether pathogens are exploiting mechanisms evolved to support symbionts and, hopefully, this will allow us to establish future crop plants that both benefit from symbionts whilst remaining more resistant to pathogens.

“Liverworts are showing great promise as a model plant system and this discovery that they can be colonised by pathogens of flowering plants makes them a valuable model plant to continue research into plant-microbe interactions.”

Read the full paper online.

This research was funded by the Gatsby Charitable Foundation, the Royal Society, the BBSRC OpenPlant initiative and the Natural Environment Research Council.

 

Photo Credits: Images by Philip Carella.

Collaboration including OpenPlant researchers discovers that C4 photosynthesis has co-opted an ancient C3 regulatory code

C4Maize_Ninghui Shi_CC BY-SA 3.0.jpg

A new publication in Molecular Biology and Evolution has resulted from a collaboration of OpenPlant PI Prof. Julian Hibberd and researcher Dr Ivan Reyna-Llorens with colleagues in Portugal at the Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, and the Instituto de Biologia Experimental e Tecnológica in Portugal. The paper shows that C4 photosynthesis has co-opted an ancient C3 regulatory code:

Borba AR, Serra TS, Górska A, Gouveia P, Cordeiro AM, Reyna-Llorens I, Kneřová J, Barros PM, Abreu IA, Oliveira MM, Hibberd JM, Saibo NJM (2018). Synergistic binding of bHLH transcription factors to the promoter of the maize NADP-ME gene used in C4 photosynthesis is based on an ancient code found in the ancestral C3 state. Molecular Biology and Evolution, msy060, https://doi.org/10.1093/molbev/msy060

Abstract

C4 photosynthesis has evolved repeatedly from the ancestral C3 state to generate a carbon concentrating mechanism that increases photosynthetic efficiency. This specialised form of photosynthesis is particularly common in the PACMAD clade of grasses, and is used by many of the world’s most productive crops. The C4 cycle is accomplished through cell-type specific accumulation of enzymes but cis-elements and transcription factors controlling C4 photosynthesis remain largely unknown. Using the NADP-Malic Enzyme (NADP-ME) gene as a model we tested whether mechanisms impacting on transcription in C4 plants evolved from ancestral components found in C3 species. Two basic Helix-Loop-Helix (bHLH) transcription factors, ZmbHLH128 and ZmbHLH129, were shown to bind the C4NADP-ME promoter from maize. These proteins form heterodimers and ZmbHLH129 impairs trans-activation by ZmbHLH128. Electrophoretic mobility shift assays indicate that a pair of cis-elements separated by a seven base pair spacer synergistically bind either ZmbHLH128 or ZmbHLH129. This pair of cis-elements is found in both C3 and C4 Panicoid grass species of the PACMAD clade. Our analysis is consistent with this cis-element pair originating from a single motif present in the ancestral C3 state. We conclude that C4 photosynthesis has co-opted an ancient C3 regulatory code built on G-box recognition by bHLH to regulate the NADP-ME gene. More broadly, our findings also contribute to the understanding of gene regulatory networks controlling C4 photosynthesis.


Image by Ninghui Shi: Cross section of a C4 plant. Specifically of a maize leaf. Vascular bundles shown. Drawing based on microscopic images courtesy of Cambridge University Plant Sciences Department. Image is shared under licence CC BY-SA 3.0

[Close 22 Apr 2018] Two Sr / Research Assocaite positions in Protein Design

Two positions are available in the laboratory of Professor Dek Woolfson, University of Bristol

For more information on the Woolfson group see: http://www.chm.bris.ac.uk/org/woolfson/index.html

For informal enquiries please contact: d.n.woolfson@bristol.ac.uk

Senior Research Associate / Research Associate in Protein Design for Biotechnology

http://www.jobs.ac.uk/job/BIT158/senior-research-associate-research-associate-in-protein-design-for-biotechnology/

A position for a postdoctoral research associate is available to work on a protein design in biotechnology project in the laboratory of Professor Dek Woolfson.  The group is internationally leading in the development of protein design for applications in chemical and synthetic biology.  The successful applicants will join a vibrant research team that combines bioinformatics and computational design, peptide and protein chemistry, biophysics and structural biology, and cell biology.  Expertise in peptide chemistry and biophysical methods would be a distinct advantage for this particular post, and applicants from these areas are particularly encouraged to apply.  However, we are keen to receive applications from ambitious and energetic individuals across the chemical and biochemical sciences or bioengineering with an interest in advancing protein design and its applications generally.

This post in protein design for biotechnology is for one year, and it is funded by a European Research Council Proof-of-Concept grant.  The project will explore the use of a-helical barrels recently discovered and developed in the Woolfson lab (Thomson et al. (2014) Science 346:485-488) in the area of biosensing. Researchers with a background in peptide chemistry, surface chemistry and/or fluorescence spectroscopy/microscopy are strongly encouraged to apply.  An active interest in driving the translation of this basic research into biotechnology applications of societal benefit would be an advantage.

Senior Research Associate / Research Associate in Protein Design

http://www.jobs.ac.uk/job/BIP002/senior-research-associate-research-associate-in-protein-design

A position for a postdoctoral research associate is available to work on protein design in the laboratory of Professor Dek Woolfson.  The group is internationally leading in the development of protein design for applications in chemical and synthetic biology.  The successful applicant will join a vibrant research team that combines bioinformatics and computational design, peptide and protein chemistry, biophysics and structural biology, and cell biology.  Expertise in computational biochemistry and/or structural biology would be a distinct advantage for this post, and applicants from these areas are particularly encouraged to apply.  However, we are keen to receive applications from ambitious and energetic individuals across the chemical and biochemical sciences or bioengineering with an interest in advancing protein design and its applications generally.

The post is available for an initial two-year period and is extendable to a further two years upon a successful start to the project.  This is funded by a grant from the Biotechnology and Biological Research Council of the UK.  The post-holder would be joined in year 2 by an expert in machine learning and virtual reality (VR) working in the laboratory of Dr David Glowacki (Chemistry, Bristol).  Together, these two post-doctoral research associates will develop VR methods to aid and advance the computational design of completely new proteins building on research programmes across the two labs (Thomson et al. (2014) Science 346:485-488; Wood et al. (2017) Bioinformatics 33:3043-3050; https://arxiv.org/pdf/1801.02884.pdf).  There will also be considerable opportunity to work with the international experimental and computational protein design and engineering communities.

PuntSeq; a toolbox and workflow to facilitate realtime monitoring of algal, bacterial and viral diversity in aquatic field work situations.

The PuntSeq team were awarded an OpenPlant Fund grant to develop a toolbox and workflow to facilitate realtime monitoring of algal, bacterial and viral diversity in aquatic field work situations. We caught up with them to find out how the project is progressing.

Full details of the project can be found on the biomaker.org website.

PuntSeq will be talking about their project at the Cambridge Pint of Science Festival. Get your tickets now to hear more about this project: https://pintofscience.co.uk/event/the-technology-behind-mainstream-headlines

Please give us a brief overview of your project (200 words max)

 Water sampling from the River Cam

Water sampling from the River Cam

Year by year, Cambridge rowers, swimmers and punters obtain serious infections associated with pathogens obtained from the Cam river’s water. While an information and research framework that targets the involved microbial culprits is still lacking, our project PuntSeq is a citizen science effort that will provide an in-depth resolution of the Cam river pathogen landscape - with minimum expense!

Led by a small group of graduate students at different Life Science Departments of the University of Cambridge, we have designed a workflow for the hand-sized Oxford Nanopore MinIONTM DNA sequencing device. We are adapting software for processing large volumes of biological data from different spots of the Cam, and try to match our bacterial findings with physical measurements of the same water samples. A do-it-yourself Arduino station that combines signals from pH, temperature, turbidity and other sensors will ultimately help us understand how certain pathogens prefer to reside within particular environmental locations of the Cam.

We regularly communicate our efforts and findings through Twitter (@puntseq) and presentations at scientific conferences. Moreover, a video featuring our research ideas is also currently being produced in collaboration with Wolfson College, Cambridge.

What inspired the project?

 Sampling from aboard a punt on the River Cam

Sampling from aboard a punt on the River Cam

Over the past years, we learned about sections of the river where people appear to often catch infections, by regularly talking to rowers and swimmers in frequent contact with the Cam. Despite the general knowledge of these unsafe areas of our river, the actual cause of the infection (i.e. the bacterial strain) remains unclear in many cases.

Up to now, taking a snapshot of the bacterial population living in a water body has required a laboratory with expensive equipment. Compared to previous sequencing machines, the Oxford Nanopore MinION dramatically reduces running expenses and is also very small, which makes it an ideal instrument for fieldwork applications. For us, this offers the opportunity to explore a new technology as well as to work interdisciplinarily by diving into a whole set of different fields from electrical engineering (Arduino measuring tool), to environmental research and the vision of personalised, data-driven health care.

How did the team meet?

Most of our members have known each other through their PhDs and previous degrees at Cambridge University. Many of us have worked together in other research projects and we share a passion for genomics research and citizen science. With an interdisciplinary combination of expertise in conservation biology, bioinformatics, engineering and physics, in situ sequencing of the Cam appeared as a really cool project for all of us to join in!


How has this project developed links between Cambridge and Norwich?

Our PuntSeq team started a collaboration with Prof. Rob Field’s laboratory at the John Innes Centre (JIC), Norwich. Amongst other environmental phenomenon, the Field lab studies algal blooms of the haptophyte Prymnesium parvum that has been associated with mass die-offs of fish in the Norfolk Broads. While the lab succeeded in associating the toxic algal blooms with infection of P. parvum by the DNA-virus PpDNAV (Wagstaff et al., 2017, Viruses), a quick monitoring system has been lacking.

Here, PuntSeq’s aim of establishing a fast metagenomics surveillance of water sources fit in perfectly. Two of our team members attended the Norfolk Broads stakeholder meeting of 2018, where we learned more about the algal blooms, exchanged our experience with DNA extraction methodology, and presented our own project of assessing the microbial community of the Cam. At this meeting, we started a collaboration with members of Rob Field’s lab to test if our approach was applicable to monitor the presence of P. parvum and PpDNAV in water in a cheap and fast manner. We hence combined our knowledge in DNA sequencing using the MinION technology, in subsequent data analysis and in engineering of environmental measurement tools to perform a metagenomics analysis on a sample of Norfolk’s Hickling Broad. As a preliminary result, we were able to draw a map of the bacterial and fungal community of the Broad, and we found a species of the toxic algae and also evidence of the virus.

 The PuntSeq team joined a Norfolk Broads Stakeholder meeting, held at the John Innes Centre, Norwich  
  
   16.00 
  
  
   
  
    
  
   Normal 
   0 
   
   
   
   
   false 
   false 
   false 
   
   EN-GB 
   X-NONE 
   X-NONE 
   
    
    
    
    
    
    
    
    
    
   
   
    
    
    
    
    
    
    
    
    
    
    
    
    
  
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
  
   
 
 /* Style Definitions */
 table.MsoNormalTable
	{mso-style-name:"Table Normal";
	mso-tstyle-rowband-size:0;
	mso-tstyle-colband-size:0;
	mso-style-noshow:yes;
	mso-style-priority:99;
	mso-style-parent:"";
	mso-padding-alt:0cm 5.4pt 0cm 5.4pt;
	mso-para-margin-top:0cm;
	mso-para-margin-right:0cm;
	mso-para-margin-bottom:8.0pt;
	mso-para-margin-left:0cm;
	line-height:107%;
	mso-pagination:widow-orphan;
	font-size:11.0pt;
	font-family:"Calibri",sans-serif;
	mso-ascii-font-family:Calibri;
	mso-ascii-theme-font:minor-latin;
	mso-hansi-font-family:Calibri;
	mso-hansi-theme-font:minor-latin;
	mso-bidi-font-family:"Times New Roman";
	mso-bidi-theme-font:minor-bidi;
	mso-fareast-language:EN-US;}

The PuntSeq team joined a Norfolk Broads Stakeholder meeting, held at the John Innes Centre, Norwich

What has been your favourite aspect of the project so far?

Through our public outreach on Twitter and by regularly featuring our project at different events, we were able to discuss PuntSeq with peers and leaders in the field, for example to Prof. Nick Loman whose lab has been using the MinION to track the 2015 Ebola outbreak. We received very positive feedback and useful advice from members of the Field lab at the JIC and colleagues at the University of East Anglia (Dr Ben Wagstaff (JIC), Dr Jennifer Pratscher (UEA), Mr Elliot Brooks UEA) as well as from Alina Ham from Oxford Nanopore Technologies, which have already resulted in improvements to our DNA extraction and sequencing workflow.

Apart from this very well-received general interest in our project, we really enjoyed seeing that our first proper MinION run with the sample from the Norfolk Broads worked out - and that the results nicely confirmed our approach.

 

What is the biggest challenge the team have faced?

We have found it extremely challenging to extract high concentrations of DNA from river surface water, and it took us several iterations to significantly improve our low-cost protocol. Starting a MinION sequencing experiment without a laptop that fulfills the high RAM and storage requirements is very challenging and may lead to significant data loss: fortunately, Ms Lara Urban and Mr Jack Monahan from EBI have joined us and could both help with their high-performance institute machines. Since we had to do two overnight MinION runs and Lara couldn't fully dispense her computer for a full working day, the laptop-connected sequencing instrument needed to travel from our lab to her home - via Taxi! Last, waiting for >2 consecutive days of non-rain during a British spring, to only sample the Cam surface water under baseflow condition, hasn't necessarily led to a significant speed-up of our project...

 PuntSeq MinION1

PuntSeq MinION1

Is there something that came out of the project that you never expected at the beginning?

A working DNA extraction protocol, a working MinION and a working Arduino platform!


How has the OpenPlant Fund enabled the development of the project?

Through the generous funding of the OpenPlant grant, we have been able to purchase the MinION starter kit for $1000, different water DNA extraction kits, basic lab equipment and our set of Arduino sensors and wires. Moreover, Dr Colette Matthewman and Dr Jenny Molloy from OpenPlant have kindly brought us in touch with algal expert Dr. Ben Wagstaff, helping us to establish an ideal Cambridge-Norwich collaboration which will help us immensely in expanding the applicability of our approach to algal contamination of freshwater waterways. The Fund's excellent outreach network has helped us in amplifying results and messages of our project through social media channels, mainly via twitter, in addition to their kind provision of facilities for a MinION metagenome sequencing workshop that we will hold in Cambridge very soon.


How do you feel the project is progressing?

Since our PuntSeq project received its first financial funding around half a year ago, it has progressed very quickly. In these few months, our team has been able to learn about all steps that are necessary to perform metagenomics surveillance analyses, from environmental measurements over DNA extraction and MinION sequencing to bioinformatic post-processing of the data. Hereby, it is great to see how much we have learned from each other, but also entirely from scratch by reading subject literature, talking to experts and simply by trial and error. We are now at a stage where we have optimised all individual protocols to perform a major water sampling and sequencing effort at various locations of our river Cam. We expect to be able to provide a profound overview of the microbial community of the Cam by the end of Spring.

Overall, our outreach activities have been very successful although we did not present much data yet. Both scientific and non-scientific communities have shown strong interest in our project, we received a lot of positive feedback, won multiple best-poster-prizes at conferences and motivated many people to follow our progresses via Twitter (@puntseq). We are confident that this already large interest will further increase with our first results about the river Cam being released, and we are currently strengthening our public engagement efforts, e.g. by taking part in events like “A Pint of Science”, by producing a professional movie clip and conducting an online-survey on infection rates through direct contact with the Cam.

What are the future opportunities to take this project forward?

We founded PuntSeq to inform the general public about the merits of DNA sequencing, especially about the direct impact it might have on peoples' health. In future, we would ideally like to sample from multiple rivers of the greater Cambridgeshire area and beyond, producing a map of microbial communities along the length of respective waterway trajectories. We hope to share our findings with relevant environmental authorities in Cambridge and East Anglia, and to influence environmental conservation through genomics. Our team is also further streamlining the process from extraction of the aquatic DNA to sequencing with the MinION and automatic identification of potential pathogens in the field, so that non-specialists can perform these experiments and gain a deep insight into the beautiful science of microbiology.


PuntSeq team members are: Mr Maximilian Stammnitz (Department of Veterinary Medicine, University of Cambridge); Ms Meltem Gürel (Cancer Research UK Cambridge Institute); Dr Philipp Braeuninger-Weimer (Centre of Advanced Photonics and Electronics, University of Cambridge); Mr Daniel Elías Martin-Herranz (European Bioinformatics Institute); Mr Daniel Kunz (Wellcome Trust Sanger Institute); Mr Christian Schwall (Sainsbury Laboratory, University of Cambridge); Ms Lara Urban (European Bioinformatics Institute); Mr Jack Monahan (European Bioinformatics Institute); Ms Surangi Perera (Department of Physiology, Development and Neuroscience, University of Cambridge); Ms Eirini Vamva (Department of Medicine, University of Cambridge); Ms Astrid Wendler (Department of Clinical Neuroscience, University of Cambridge).

Full details of the project are at biomaker.org website. Follow the team on twitter @PuntSeq

Plant powered camera trap - are you able to take on the challenge?

With the help of funding from the OpenPlant Fund, University of Cambridge researcher Dr Paolo Bombelli together with Ms Rachael Kemp and Mr Alasdair Davies of the Zoological Society of London have launched a competition to design and manufacture a prototype of a plant powered camera trap. Deadline for proposals is 30th April 2018.

 An artistic representation of a plant-microbial fuel cell

An artistic representation of a plant-microbial fuel cell

Camera trapping has been transformed by technology to become a major tool for conservationists, playing a crucial role in helping to better understand the effects of threats such as climate change and habitat loss, and supply data that can be used to inform policy and practice.

However, the current popular power sources such as battery packs and solar panels, are proving inadequate in more remote areas or in less than optimum conditions, for example in tropical forest canopies.

To overcome these challenges and further develop this area of conservation technology, this interdisciplinary team are running The Plant-Powered Camera Trap Challenge, looking to power camera traps and environmental sensors, using plant-microbial fuel cells.

Are you an architect, engineer, designer or a scientist? Are you able to design and manufacture a prototype open source plant-BES (bio electrochemical system) to power a camera trap to be used in tropical rainforests? All prototypes should be able to deliver 5v and produce 5000mC of charge per day. Submit your concepts by April 30th to receive an award of £10,000 from the Arribada Initiative and OpenPlant to build and deploy your device in the field.

If you think you can take on the challenge click here to register and find out more.

OpenPlant Fund supports project to deliver report on genetic resources in the age of the Nagoya Protocol

Dr Deborah Scott and Dr Dominic Berry of the Engineering Life project (The University of Edinburgh) have published a report "Genetic resources in the age of the Nagoya Protocol and gene/genome synthesis", based on the results of an interdisciplinary workshop held in Cambridge and involving several OpenPlant colleagues and part-funded throught the OpenPlant Fund. The workshop was dedicated to exploring emerging questions and discussions around the practice of synthesising DNA in the context of global biological diversity use and regulation, in relation to the Nagoya Protocol.

 Map showing parties to the Nagoya Protocol and Biological Diversity Convention. Image by L. Tak, CC BY-SA 4.0.

Map showing parties to the Nagoya Protocol and Biological Diversity Convention. Image by L. Tak, CC BY-SA 4.0.

Researchers in law, synthetic biology, social science and history were brought together to consider the implications of the Nagoya Protocol for Synthetic Biology and modern biotechnology. The report summarises the presentations and discussions that took place, including conversations on drivers and implications of ABS legislation, and benefit sharing and proprietary technologies.

The latter half of the report reflects on the workshop in light of the December 2016 UN Biodiversity Convention, and considers similarities and differences in the deliberations addressed at the two events.

The report ‘serves to highlight issues not yet addressed in formal negotiations and to provide additional texture to conversations already underway’.  

Click to download the full report (1.4 MB PDF, 64 pages)

Opportunity to join an exciting new start-up to develop insect tracking and quantification device via IoT

An exciting opportunity is available to work with a young up-and-coming start-up company.  As part of their research development, they are interested in creating an IoT demo device for insect tracking and quantification and could use some engineering help.

They are looking to make a device that can:

  1. Use vision tech to classify broad categories of insects
  2. Combine cloud-based hyper-localized data (weather conditions, time, etc.) with pollinator data. 
  3. Develop an IoT edge device
  4. Design a chemical release mechanism controlled electronically

The position is temporary to begin with, with a view to develop a permanent position in the future if the fit is right. The position would be based in London, but the company are open to applicants who aren't based in London, but are happy to travel on occasion.

ABOUT POM:

Insect pollinators provide a vital ecosystem service for crop pollination in wild plants, and over 75% of crops worldwide benefit from insect pollination through increased yields at harvest. The number of wild pollinators, especially bees is steadily declining. This documented decline poses a significant risk to the production of many crops and threatens food security.

POM encourages flies to be more efficient pollinators, in scenarios where bees are no longer as viable. Flies are already adept pollinators, being the main pollinators in urban environments, and in total, accounting for over 30% of all pollination.

POM provides horticultural growers with information on pollinators and environmental conditions and uses chemical volatiles to manage pollinating fly species, thereby increasing crop productivity, and ensuring sustainable food harvests for the future.

KEY RESPONSIBILITIES:

We are looking to find an experienced Engineer who is interested in working with a young and exciting start-up that has recently taken on investment to develop an insect tracking IoT device.

The individual should have experience with working on Raspberry Pi, Cloud computing and IoT data connectivity. The position will report weekly developments to the POM team in our London office, and reports to the Senior Engineer remotely throughout the week.

This position is a two month contract with the potential to continue with the company after
the achievement of key milestones. Project Salary: £2,300+ per month

Click here to download the job description.

Interested? Contact hello@flypollination.com

www.flypollination.com

[Closes 26 Apr 2018] Bioinformatician - Single Cell Analysis at Earlham Institute

The Core Bioinformatics Group at the Earlham Institute (EI, Norwich, UK) is looking for an enthusiastic and dedicated Bioinformatician to support developments in single cell genomics at the institute. Apply here: http://www.earlham.ac.uk/bioinformatician-single-cell-analysis

The role:

This is a collaborative project with the successful candidate joining the group of Dr. David Swarbreck and working closely with wet and dry lab scientists in the groups of Dr. Iain Macaulay and Dr. Wilfried Haerty. The post-holder will establish and implement pipelines and processes for the analysis of single genome, epigenome and transcriptome data from a wide variety of biological systems. Delivering single cell data analysis in conjunction with faculty groups, the genomic pipelines team and external collaborators.

[Closes 26 Apr 2018] Bioinformatician - Genomics Pipelines at Earlham Institute

This position is within the Core Bioinformatics group working in collaboration with Ksenia Krasileva (University of California, Berkeley). Apply here: http://www.earlham.ac.uk/bioinformatician-genomics-pipelines

The role:

This group member will be working with the latest wheat genomic data and building a toolbox for functional analyses. Specifically, the candidate will be involved in developing software tools to help understand how new variation in NLR immune receptors is generated, updating variant calling pipelines to examine natural and induced variation in complex wheat genomes and integrating this information to enable functional characterization of wheat genes. The candidate will work independently and with members of the Swarbreck (EI) and Krasileva (UC Berkeley) Groups to develop computational tools and pipelines to analyse large datasets and interpret them in a variety of biological contexts.

[Closes 19 Apr 2018] Genomics Pipelines Senior Research Assistant (Automation) at Earlham Institute

Applications are invited for Senior Research Assistant to join the Genomics Pipelines Group at the Earlham Institute. Apply at http://www.earlham.ac.uk/genomics-pipelines-senior-research-assistant-automation

The role:

The SRA will support the automation of high-throughput workflows for the Genomics Pipelines group and the DNA Foundry at the Earlham Institute. The SRA will play a key role in automating, troubleshooting and streamlining both current and future pipelines in a rapidly changing and technology-led environment. The SRA will also assist production teams with the preparation of next-generation sequencing libraries and the building and testing of engineered organisms as required by customers’ and collaborators’ projects.

The SRA will work closely with other laboratory staff in Genomics Pipelines and DNA Foundry to plan, execute and deliver scheduled high throughput and/or novel techniques. The SRA will transition complex, and cutting-edge laboratory processes onto EI’s installed base of liquid handling robotics platforms, as well as ensuring the smooth day-to-day running of laboratory automation, and deliver training to other RAs using automated protocols for deployment into production.

The SRA will ensure efficient, effective and safe operations of the automation they are responsible for. They will train Research Assistants on using automated protocols until they are handed over for production.

The SRA’s work will support Earlham’s strategic science programmes and the National Capability in Genomics and Single Cell Analysis, and DNA foundry.