DNA Dave school workshop

The first ever DNA Dave “Build Your Own” School Workshop took place this month!

DNA Dave was first created in 2016 and designed to be used as an interdisciplinary, educational tool to teach the concept of DNA transcription and translation at various science festivals. He was such a hit with audiences and teachers who attended, that a plan to take him into schools was formed.

The workshop welcomed students from schools across Norfolk to learn the biology and coding behind DNA Dave in a bid to create their own educational robot.

Each school taking part received a “DNA Dave Starter Kit” worth £100 that included all the know-how and BBC micro:bit gadgets to build their own robot which they will then present at a celebration event to be held later in the year.

You can find out more about DNA Dave here.

New Cambridge Coordinator

A big thank you to the OpenPlant team for welcoming me onboard! My name is Stephanie Norwood and, as of 3rd Feb 2020, I will be taking over the role of Coordinator for OpenPlant and the Synthetic Biology Interdisciplinary Research Centre in Cambridge. Based in the Department of Plant Sciences at the University of Cambridge, I will be working with the OpenPlant team and SynBio network to organise events and support researchers working on these fantastic initiatives.

Stephanie Norwood: Coordinator for OpenPlant and the Synthetic Biology Interdisciplinary Research Centre in Cambridge.

Previously, I obtained my PhD in Developmental Biology from the Gurdon Institute at the University of Cambridge. Most recently, I have worked for the Babraham Institute on ORIONOpen Science, a European Horizon 2020 project focused on promoting the principles of Open Science and Responsible Research and Innovation in life science institutes. My interests lie in communicating bioscience research, working at the intersection of science and society, and encouraging interaction between different areas of research and the wider world of industry, policy and the public. I’m excited about the opportunity to work on OpenPlant, and look forward to meeting you all soon!

Snapshot of OpenPlant achievements

Over the past 5 years OpenPlant has made significant advances in the field of Plant Synthetic Biology by working at the intersection of Biology, Engineering, Chemistry, and Medicine.

At present, some of the major OpenPlant achievements are:

Successful development of cutting-edge foundational DNA tools and technologies for research and industry. OpenPlant has been pioneering the development of open tools and innovation in agri-tech research, industrial biotechnology and bioengineering services.

Production of high value plant molecules for medicinal or industrial applications. Scientists are now able to produce high value molecules at gram scale in plants. These molecules include for example anti-cancer and anti-malaria drugs for pharmaceutical uses, and pigments for food coloring.

Development and fine-tuning of plant production systems for vaccines. Scientists have developed a system to produce virus-like particles in plants, which has enabled the production of vaccines.

OpenPlant Biomaker for global outreach and capacity building. OpenPlant has surveyed the potential benefits and bottlenecks for application of new technologies in the development of bioeconomies across Africa. It has developed the Biomaker programme to harness frugal and open technologies for interdisciplinary project-based learning and capacity building, and supported numerous projects across the UK and Africa.

Moreover, OpenPlant has catalyzed a number of commercial success stories.

The infographic provides a snapshot of OpenPlant in numbers. For further information please visit the OpenPlant website and have a look at our publications and reports.

Bioluminescent aquatic organisms and their application to three-dimensional flow visualisations of pressure fields.

Bioluminescence on Vilingili beach. Photo credit: Ali Nashan, 2013.

OpenPlant funded a team of eight engineers and scientists to start the LunaFlow project. The aim of the project is to study the behaviour of a strain of bioluminescent organisms, so-called dinoflagellates (Pyrocystis Lunula), in their application to the visualisation of aqueous fluid flows.

Dinoflagellates naturally respond to rapid variations of tension that occur within a flow field by emitting visible blue light. These light emissions are rare sights in the natural world, but not uncommon to the United Kingdom. Dinoflagellates blooms are occasionally reported during summer nights along the British and Welsh coasts and exhibit wondrous glowing patterns as the organisms are pulled and stretched by waves breaking against the shorelines.

The evolutionary reason behind their light emission remains unclear but is often attributed to be a defensive mechanism against predators. The biophysics of the light emissions are also mysterious. They are closely tuned to their circadian cycle and indeed, dinoflagellates require extended periods of darkness to shine. They can be trained to adapt their bioluminescent responses to twelve-hour shifts of light and dark and the team exploited this property to use them in the laboratory.

The dinoflagellates’ natural piezometric responsiveness and relatively small size, c. 20 m, offer an attractive opportunity for their use as a flow tracer. Traditional techniques that measure piezometric properties (albeit pressures, strains and forces) use instrumentation such as Pitot tubes, pressure transducers or force balances. They are recognised to be intrusive (disruptive) to the observed flow and are limited to a local measurement. Artificially lighted particulate flow tracers, on the other hand, are often used to simultaneously measure velocity fields that exhibit complex spatial variations.

Measurement of velocities is achieved using image processing algorithms based on either optical flow techniques, particle tracking velocimetry (PTV) or particle image velocimetry (PIV) techniques. Dinoflagellates offer an opportunity to modify these techniques and measure simultaneous and spatially-distributed piezometric properties. The team set out to assess and demonstrate the feasibility of this application. 

The project

The LunaFlow team: Duncan Scott, Shivani Maharaj, Karla Cervantes Barron, Alessandra Luna Navarro, Edoardo Gianni, Nicholas Wise, Francesco Ciriello and Fernando Guzman Chavez.

The LunaFlow team set itself a two-fold challenge for the competition: to develop (i) a bespoke low-cost incubator to grow the organisms and (ii) a three-dimensional low-cost camera system to study them. The team was composed of three mechanical & civil engineers, two data scientists, two chemists and a biologist. The Biomaker Challenge provided the opportunity for the team to meet and form the group and the support of the OpenPlant organisers provided a technical and financial platform to test and nurture the idea.

Outcomes: Incubator

The incubator design was led by Dr Duncan Scott and was a sheer collective effort of design, build, wiring and testing. The volume required for the incubator was significant, c. 0.2 cubic metres (200 litres). The design was improved through several iterations of modelling and prototyping. Cooling was a major challenge due the incubator volume and the team tested both an air Peltier heat pump system (successfully in a small 20-40L volume, but not so, in a larger 100-200L one) and a mixed water-cooling air-heat-dissipation Peltier heat pump (with improved performance).

The temperature control system was actuated using the Biomaker OpenSmart Arduino board and sensors provided in the competition kits. The kits allowed the team to rapidly develop algorithms and test them for rapid deployment. The Arduino system was set up to communicate by serial communication to a Raspberry Pi Zero in order to feed a remote monitoring system. The control of the remote monitoring system was set up using a ThingSpeak channel that continuously streamed temperature data and sent out email-based emergency alerts. Fully detailed description and instructions for the build are documented on our Hackster page.

Outcomes: Camera system

The camera system design was led by Dr Francesco Ciriello. The primary objective for the system was to create a synchronised multi-camera system with low-cost hardware that was scalable to use with many cameras. Increasing the number of cameras improves the potential of better resolving the three-dimensional structures within the observed flows.

Francesco Ciriello with the LunaFlow design

The hardware architecture works with different commercially available hardware boards (tested with Raspberry Pi 3B+ & 4 and NVIDIA Jetson Nano boards). Communication between devices is set up over a private network that runs on a local DHCP server and uses an MQTT protocol as middleware for synchronised acquisition. Three-dimensional reconstructions were implemented using algorithms from the MATLAB Computer Vision Toolbox and set up so that the cameras automatically calibrated their extrinsics using feature-based registration. The team developed a full end-to-end workflow for acquisition and packaged it into a suite of MATLAB apps that can be executed either in MATLAB desktop, online environments or as a
standalone application. The concept worked well, and the team is now looking at how to expand the middleware to use MQTT within ROS-based architectures. Software and examples are released on GitHub.

About the author

Following the Biomaker Challenge, Francesco Ciriello moved from his Postdoctoral position at Cambridge University Engineering Department and joined the MathWorks Education Customer Success team. He now travels the United Kingdom promoting better teaching practices in higher education. The experience from the competition makes him a firm promoter of reverse classroom approaches based on project-based learning and he whole-heartedly recommends it to all students and staff.

Acknowledgements

Special thanks and congratulations to all LunaFlow team members: Duncan Scott, Shivani Maharaj, Karla Cervantes Barron, Alessandra Luna Navarro, Edoardo Gianni, Nicholas Wise and Fernando Guzman Chavez.

Special thanks to Biomaker organisers Jim Haseloff, Alexandra Ting and Dieuwertje van der Does.

A novel international research initiative born out of Biomaker

Rarely does the opportunity arise to translate academic research to positively influence policy and capacity in a developing country. To this end, we developed the UK-Kenya Phytoplasma Research Initiative with the aim of building local capacity in East-Central Africa to mitigate the risks imposed by emerging and re-emerging phytoplasma-associated crop diseases.

Through a successful OpenPlant-Biomaker Challenge bid, we conceived the initiative and built the partnerships required to impact local Kenyan communities while contributing to international research.

[left] Partners of the UK-Kenya Phytoplasma Research Initiative. From left: James Canham (Postgraduate student, John Innes Centre, Norwich, UK), Florence Munguti (Officer-in-charge, KEPHIS, Nairobi, Kenya), Dr Isaac Macharia (Managing Director, KEPHIS, Nairobi, Kenya), Dr Rose Kigathi (Research Scientist, Pwani
University, Kilifi, Kenya). [Top/bottom right] KEPHIS station in Muguga, Kenya.

The Kenya Plant Health Inspectorate Service (KEPHIS) is a government parastatal under the Ministry of Agriculture, Livestock, Fisheries and Irrigation (MoAFI) and the National Plant Protection Organization (NPPO) of Kenya. During a BBSRC PIPs placement at Pwani University, Kenya, I met with officials from KEPHIS as a part of a nationwide exploration of plant health-related research.

During these meetings, KEPHIS staff described several threats they were monitoring, one of
which appeared to be phytoplasma-related. Given that several colleagues in my lab at the John Innes Centre (Hogenhout lab; https://www.jic.ac.uk/people/saskia-hogenhout/) work on phytoplasma, I was aware of associated diseases and our capacity to study this plant pathogen and hence the Phytoplasma Research Initiative was born.

“Our aim is to establish rapid diagnostic and surveillance tools, expertise and capacity and influence agricultural policy based on our findings. We are optimistic that the initiative will enable us to achieve our aim and help address the challenges of emerging pests”.

- Dr Isaac Macharia, Managing Director, KEPHIS

Along with the Pwani University Bioscience laboratory (PUBReC) staff, we identified the OpenPlant-Biomaker Challenge as an excellent platform to help kick-start the initiative and attract more expertise. We recruited researchers at EBI, Cambridge and Cambridge University as well as an entomologist based at the Museum of Wales and research staff at CIRAD, France. With this team, we believe we are very well placed to build the technical capacity required to help local researchers and stakeholders.

KEPHIS staff surveying agricultural and pastoral land in Kenya to assess the occurrence of plant pathogenic phytoplasma.

What has been achieved so far?

Once the partnership was in place, we moved ahead designing and testing workflows. The PUBReC staff and KEPHIS team started to survey crops with disease symptoms along the breadth of the Kenyan coastline. Samples were transported to PUBReC where Prof. Santie de Villiers and her staff would process them.

In order to build long term capacity and impact, Pwani University used the initiative to develop an MSc. project and two undergraduate studentship projects. To support these students, we provided the Kenya-based staff with reagents to perform gold-standard, PCR-based characterisation of isolates as well as share our experience of sample collection, storage and processing. Additionally, we recently won an internal JIC grant that will fully fund a Kenyan PhD student for 9 months to visit the JIC labs to study the molecular basis of phytoplasma-host plant interactions.

Newly recruited students, John and Hesbon working on projects within the initiative at Pwani University, Kilifi, Kenya.

We have discovered that current diagnostic tools may lead to misidentification of the pathogens and are in the process of re-tooling and optimizing protocols to ensure more accurate characterisation going forward.   

What is next for the project?

All partners are now working toward generating whole-genome sequence data which will allow us to further understand how distinct phytoplasma isolates colonise their plant and insect hosts.

Whilst mitigating actions, resulting from our positive identifications may require a hammer, we hope that with a greater understanding of the pathogen, in future, a chisel will suffice.

We have big plans for the initiative, including several grant applications that will allow us to move the project forward. We are deeply grateful to the OpenPlant-Biomaker Challenge for the platform that allowed us to form effective partnerships and promote our project to a broad, interdisciplinary audience.

Watch this space! 

James Canham (PhD student, John innes Centre)

Bristol Biodesign 2020: one-day international symposium in synthetic biology and biodesign

A one-day international symposium in synthetic biology and biodesign, followed a conference dinner at Bristol Harbour Hotel.

Where: School of Chemistry, University of Bristol

When: May 6th 2020

Registration deadline : April 24th 2020

For more event information

Research Technologist Vacancy - Edinburgh's Genome Foundry

Applications are invited for a Research Technologist position at Edinburgh’s Genome Foundry, based within the School of Biological Sciences at the University of Edinburgh.

The Research Technologist will work with customers to plan, execute and deliver DNA assemblies for Foundry customers in a manner suitable for large-scale automation.

Application deadline: February 3rd 2020

Fixed-term - 2 years with the possibility for extension.

Further information

Post-doctoral Research Associate Vacancy - Sainsbury Lab Cambridge

Applications are invited for a Post-doctoral Research Associate position in the group of Dr James Locke at the Sainsbury Laboratory, to carry out fundamental research in the field of plant systems biology.

The project will focus on using microscopy to study dynamic gene regulation during plant development. The project requires both experimental and quantitative skills.

Application deadline: 26th January 2020

Fixed-term: The funds for this post are available until 31 August 2022 in the first instance.

Further information

Post-doctoral Research Associate Vacancy - Sainsbury Lab Cambridge

Applications are invited for a Post-doctoral Research Associate position in the group of Dr James Locke at the Sainsbury Laboratory, to carry out fundamental research in the field of microbial systems biology.

Fixed-term: The funds for this post are available until 31 August 2022 in the first instance.

Apllication deadline: 26th January 2020

Further Information

Post-doctoral Research Associate Vacancy - Sainsbury Lab Cambridge

Applications are invited for a Post-doctoral Research Associate position in the group of Dr Sebastian Schornack at the Sainsbury Laboratory Cambridge University (SLCU) to investigate the processes underlying the intracellular colonisation of land plants by filamentous microorganisms.

Application closing date: 2nd February 2020

Fixed-term: funding for this post is available for 2 years in the first instance.

Further Information

Prof Anne Osbourn has been awarded an Order of the British Empire for services to plant science

We are excited to announce that Professor Anne Osbourn, one of our OpenPlant directors, has been awarded an Order of the British Empire for services to plant science. Earlier this year, Professor Osbourn was elected as a Fellow of the Royal Society, the 30th FRS in the history of the John Innes Centre.

Please join us in congratulating her!

Read more about this topic here.

Biomaker Fayre

The Biomarker Challenge is an annual competition that funds creative interdisciplinary projects at the interface of biology and engineering.

Each of the 20(+) teams that took part this year, have been supported to produce low cost, open access resources and instruments, for biology. This year, a whole array of innovative and creative projects returned to Cambridge to showcase their final products.

The event also hosted inspiring talks from; Karen Sarkisan (Imperial College) on his start-up company Planta, where they are creating self-luminous plants, Oscar Gonzalez (Quadram Institute) on his team’s speed breeding chamber and Harrison Steel (Oxford University), who spoke of his innovative robotic platform Chi:Bio.

Best Biomaker Spirit awarded to the OpenCM biomaker team

As usual, awards were given out to three outstanding projects. This year the Best Technology prize was given to the LunaFlow team for their incubator which uses a tomographic camera system to measure the luminescent response of pressure sensitive diatoms.

The Best Biology award was given to the team behind creating an Open and Affordable 3D Bioprinter, which provides temperature controlled printing of bacteria and algae.  Lastly, the OpenCM team was given the Best Biomaker Spirit award, for their project which judges stated was a great example of the combined use of open technologies.

Congratulations to the three winning teams and to all the teams who made it to the fayre to exhibit their exciting projects.

For more information on the projects check out the Biomaker hackster page to see what the teams have been up to this year.

LunaFlow winners of this year’s Best Technology award.

Open and Affordable 3D Bioprinter team, winners of this year’s Best Biology award

IoHeat: a nice oasis in the cold room

The problem

Temperature is a crucial, yet often overlooked condition that affects the growth efficiency of mammalian and bacterial cell cultures. To achieve maximal growth rate, the temperature of the culture media needs to be maintained at the optimal level throughout the experiment.

While during a culture the media are maintained at the optimal for the organism level, their composition often dictates that they are stored at a lower (~2-8 °C) temperature. A typical culture medium for mammalian cells is composed of a complement of amino acids, vitamins, inorganic salts, glucose, and serum as a source of growth factors, hormones, and attachment factors; in addition to nutrients, the medium also helps maintain pH and osmolality. Many of these components are not stable for extended periods of time at elevated temperatures.

Sustaining mammalian cell cultures requires regular changes of the medium and/or subcultures (passages) into fresh culture medium. In many cases, the survival of the cells during these processes depends on the thorough pre-conditioning of the media at the desired temperature. Oftentimes, this means pre-incubating the media in a water bath for more than an hour, before they are ready to use.

This can impose time restrictions when experiments need to run at different time-points or need to be carried out early in the day or during out-of-hours, as access can be limited at these periods. Time optimization is needed. 

The Idea

Our project was focusing on developing a remotely-controlled heated compartment, which can be kept in a cold environment.

Schematic of a remotely-controlled heated compartment prototype

The device can be used in laboratories to control specific working temperature (37 °C) of cell culture medium or reagents, shortly before use.

Specifically, the heating device finds application in the laboratories where microbiological or cell culture work are carried out.

The function of incubator is to maintain optimal temperature, humidity and other conditions such as the CO (CO2) and oxygen content of the atmosphere inside. Incubators are essential for a lot of experimental work in cell biology, microbiology and molecular biology and are used to culture both bacterial as well as eukaryotic cells.

With our mini-incubator we aimed to achieve the proper functionality of an incubator, but with the time optimization improvement due to the remote controls of temperature.

In May 2019, we had the great opportunity to take part in the OpenPlant Biomaker Challenge to develop our first prototype. For the first challenge we built an insulator polyester box mimicking the incubator and remotely controllable by the Telegram interface. This represented our proof of concept.

We then developed a set of scripts to locally control the electronic components, designing each command to work with a file-lock system that avoids collision when multiple users operate the device. The scripts allow to start the heating cycle, to report the current status of the device (temperature, humidity, heating status). To allow remote control of the device, a Telegram bot has been developed. The bot has a simple authentication system to allow only white-listed users to operate the device, a queue system allows to schedule multiple heating cycles, and the queue can be queried, and new tasks can be added, through the bot.

Following a series of successful tests our next task was to down-scale the device. We developed a customized 3D printed structure that allows us to efficiently organize the electrical components. In addition, 3D designed incubators can be customized to accommodate a range of different vessels and types of samples.

We also decided to organize a workshop for scientists at the Norwich Research Park. The main aim was to let the participants familiarizing with the programming in RasbperryPi, stressing that behind any problem there is a solution that can be achieved with a multidisciplinary approach.

What’s next?

We think that Biomaker Challenge was a great experience and a big opportunity for develop our idea. Now that we are able to obtain a proof of concept, we are aiming to further optimize our device and hopefully make it available as lab equipment to be used by researchers.

Blog written by IoHeat Team.

Plant genome engineer vacancy with Phytoform Labs

Phytoform Labs enables plant breeding innovation in specialty crops and focuses on sustainability in agriculture.

The company, based at Rothamsted Research centre in Harpenden, is currently looking for a plant genome engineer to join their multidisciplinary team. Offering the right individual a competitive salary in a fast-paced start-up environment.

For more information on the position visit their website or contact Nicolas Kral of Phytoform Labs.

Plant molecular biologist vacancy with Phytoform Labs

Phytoform Labs enables plant breeding innovation in specialty crops and focuses on sustainability in agriculture.

The company, based at Rothamsted Research centre in Harpenden, is currently looking for a plant molecular biologist to join their multidisciplinary team. Offering the right individual a competitive salary in a fast-paced start up environment.

For more information on the position visit their website or contact Nicolas Kral of Phytoform Labs.

PhD studentship available in Prof. Cathie Martin's lab

To divide or not divide? The importance of division to hair formation in plants.

The project aims to compare regulation of multicellular hair development in tomato with single-celled hair development in Arabidopsis and to establish how the induction of DNA replication without cell division (endoreduplication) came to be the key regulatory step in hair development in Brassica species like Arabidopsis.

Application deadline: 25th November 2019.

Project start date: 1st October 2020.

Read more about this position here.

Group Leader Vacancies

Group leader positions currently available at the John Innes Centre.

John Innes Centre would particularly welcome applicants who are working in the areas of population genetics, chemistry and biology of plants and microbial natural products, cell biology, biotic interactions of plants and the interface of agriculture and the natural environment.

Entry deadline is December 16th 2019.

For more more information visit the website.

An efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat (Triticum aestivum L.)

Dr Sadiye Hayta and Prof Wendy Harwood from the John Innes Centre published their work on an efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat, which has important implications for synthetic biology approaches to crop improvements:

Hayta et al. (2019) Fig 6: Transgenic plants showing GUS expression

An efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat (Triticum aestivum L.)

Sadiye Hayta, Mark A. Smedley, Selcen U. Demir, Robert Blundell, Alison Hinchliffe, Nicola Atkinson & Wendy A. Harwood

Plant Methods Volume 15, Article number: 121 (2019)

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0503-z

Abstract:

Background

Despite wheat being a worldwide staple, it is still considered the most difficult to transform out of the main cereal crops. Therefore, for the wheat research community, a freely available and effective wheat transformation system is still greatly needed.

Results

We have developed and optimised a reproducible Agrobacterium-mediated transformation system for the spring wheat cv ‘Fielder’ that yields transformation efficiencies of up to 25%. We report on some of the important factors that influence transformation efficiencies. In particular, these include donor plant health, stage of the donor material, pre-treatment by centrifugation, vector type and selection cassette. Transgene copy number data for independent plants regenerated from the same original immature embryo suggests that multiple transgenic events arise from single immature embryos, therefore, actual efficiencies might be even higher than those reported.

Conclusion

We reported here a high-throughput, highly efficient and repeatable transformation system for wheat and this system has been used successfully to introduce genes of interest, for RNAi, over-expression and for CRISPR–Cas9 based genome editing.

Combining Transient Expression and Cryo-EM to Obtain High-Resolution Structures of Luteovirid Particles

OpenPlant PI George Lomonossoff and colleagues published their work on combining transient expression and cryo-EM to obtain high-resolution structures of luteovirid particles:

Byrne et al. (2019) Graphical abstract

Combining Transient Expression and Cryo-EM to Obtain High-Resolution Structures of Luteovirid Particles

Matthew J. Byrne, John F.C.Steele, Emma L. Hesketh, Miriam Walden, Rebecca F. Thompson, George P. Lomonossoff, and Neil A. Ranson

Structure (2019) https://doi.org/10.1016/j.str.2019.09.010

Abstract:

The Luteoviridae are pathogenic plant viruses responsible for significant crop losses worldwide. They infect a wide range of food crops, including cereals, legumes, cucurbits, sugar beet, sugarcane, and potato and, as such, are a major threat to global food security. Viral replication is strictly limited to the plant vasculature, and this phloem limitation, coupled with the need for aphid transmission of virus particles, has made it difficult to generate virus in the quantities needed for high-resolution structural studies. Here, we exploit recent advances in heterologous expression in plants to produce sufficient quantities of virus-like particles for structural studies. We have determined their structures to high resolution by cryoelectron microscopy, providing the molecular-level insight required to rationally interrogate luteovirid capsid formation and aphid transmission, thereby providing a platform for the development of preventive agrochemicals for this important family of plant viruses.