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.