Plant-Microbial Fuel Cells to power remote field sensors

Sketch of potential use within project

We would like to apply to the OpenPlant Fund to organise and run a competition where teams of plant biologists, designers and electrical engineers would be invited to design and test robust, transportable prototypes of plant-MFC for delivering a low-cost, environmentally friendly power supply to sensors operating in remote field locations. The project operates on a simple three steps logic: 1) the plant microbial fuel cell (Plant-MFC) charges a capacitor; 2) the trap camera takes a photo; 3) the photo is transmitted. The aim is that these prototypes contribute to the development of solutions that solve battery maintenance challenges associated with deployments of conservation technology, releasing conservationists from this time-bind and ultimately allowing us to better monitor and assess the status of our natural resources worldwide.

Plant-MFCs can be described as biological solar panels. In this case, the photosynthetic plants are used for feeding heterotrophic soil bacteria living in the rhizosphere of the plant. Then those bacteria produce electrons that can be collected by an anode. Current research in plant-MFC exploits several different vascular plants including both rice and moss.

If you are interested in finding out more about this project, please contact colette.matthewman@jic.ac.uk.

Virtual Reality to explore molecules

Our plan is to use Virtual Reality to explore molecules. We have already done some work on this, stemming from the 2016 NRP-UEA iGEM project – some details are here:

http://2016.igem.org/Team:NRP-UEA-Norwich/Practices/VirtualReality

More recently we have developed the VR activity to be more interactive and to focus on exploring the structure of molecules. Up to now we have stayed with proteins, but my idea for the synthetic biology aspect of OpenPlant would be to extend the idea to DNA. As we develop this activity we are keeping in mind 2 distinct approaches for different audiences:

- festivals and events with young children: the VR activity can work well at an entertainment level, and this could be enhanced by incorporating some sort of game element (an idea that comes to my mind is that the players could be looking for some specific bases or mutations, depending on what we feel able to explain)

- Open Days and events with older children/adults: the VR activity can work well for highlighting specific points about molecular structure and function

For the OpenPlant Fund, I think it would be possible to develop one of these approaches. We have the expertise and equipment to develop the VR side of the project, so I think we would be most interested to link up with people who have specific interests about DNA structure, or specific sequences within DNA. But we would also be happy to develop the project in different directions, if there are any good ideas out there.

If anyone wishes to find out more they can contact Richard Bowater at R.Bowater@uea.ac.uk

Cell-free expression of plant proteins using E. coli S30 lysates

Heterologous expression is an important tool for functional characterization of proteins. However, expression in living organisms and subsequent purification often requires significant time and effort which can reduce the number of proteins to be characterized in a single experiment. I am proposing to obtain the reagents for expressing plant proteins using cell-free protein synthesis (CFPS) powered by E. coli crude lysates. This platform would be able to produce 0.5-10 µg of protein in a single 15 µL reaction in 24 hr by simply adding plasmid/linear DNA to the reaction mix. I have years of experience working with CFPS from my doctoral work, but am looking for collaborators that have plant proteins of compelling interest that might be amenable to cell-free expression.

Contact Quentin Dudley (Quentin.Dudley@earlham.ac.uk) if you are interested in potentially collaborating.

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Image: Cell-free expression of fluorescent protein and biosynthesis of violacein by Fernan Federici

Focus stacking microscope for deep focus photography of plants

Jennifer Deegan is working on a project to build a focus stacking microscope that takes deep focus photographs of plants anywhere between about 2.5mm and 1cm tall. At the moment she is concentrating on gametophyte ferns and Utricularia gibba traps.

If anyone has any more plant subjects that are photographically interesting at this scale, she would be really pleased to hear from them. Email Jennifer at jic24@cam.ac.uk

Her microscope setup is shown here: https://www.hackster.io/jendeegan/focus-stacking-system-for-gametophyte-ferns-1bc883

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Image reproduced with permission from Jennifer Deegan

Stably transformed actin-reporter Medicago lines

Medicago is a main model plant to study root nodule symbiosis and arbuscular mycorrhiza. Since recently more and more research groups use Medicago for plant-pathogen, plant-pest and seed development research. Therefore Medicago is gaining popularity. The main disadvantage of Medicago is time consuming genetics. Medicago is transformable but it's not so easy. To generate a transgenic line is a lot of time and efforts. It always imposes some limitations on any project.

An example is actin related research. Usually postdocs working on a project about actin functionality in plant-microbe interactions do not have time to generate stable transgenic line expressing actin fluorescent reporter and have to use chemical staining or other methods, which are full of artifacts. My idea is to generate Medicago line expressing GFP fusions to the actin-binding domain 2. It is a powerful tool to decipher the role of the actin cytoskeleton in plant development and plant-microbe interactions. Publicly available seeds of this line will help a lot to all researchers who studies actin functionality during symbiosis development or pathogenesis. I can design and create several vectors with constitutive expression of actin reporter or driven by symbiotic specific promoters.

Targeting bacteria through host induced gene silencing

Host induced gene silencing (HIGS) is a powerful technique which expresses interfering RNAs from a plant which, for example, have been used to knockdown genes responsible for aflatoxin production in Aspergillius flavis. Nobody however has used HIGS to target bacteria, neither symbiotes living in the rhizosphere or pathogens such as Streptomyces scabies. I am hoping to employ a lethal host induced gene silencing strategy to achieve three things; to aid my research in understanding the rhizospheric microbial ecology by targeting possible keystone species with lethal RNAi, to generate strains of Solanum tuberosum insusceptible to infection by S. scabies and potentially to manipulate plant associated microbiomes to benefit crop yields and disease resistance.

Contact colette.matthewman@jic.ac.uk if you would be interested in joining a team for this proposal.

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Image: Streptomyces coelicolor by Matt Hutchings, University of East Anglia. Shared under CC BY 4.0 on the Norwich Research Park Image Library.

Insulating sequences for novel synthetic promoters

Background

In synthetic biology, one of the main tasks is to rewire cells at transcription level to function as we desire. Novel synthetic promoters are fundamental tools to reprogram the cells transcription. Although a couple of synthetic promoters which recognize orthogonal signals have been developed, novel synthetic promoters recognizing endogenous signals, such as endogenous transcription factors, are still highly demanded. However, designing of synthetic promoters based on transcription factor binding sites (TFBS) derived from traditional position weight metrics (PWM) cannot achieve the accuracy as orthogonal promoters do. This is partially due to the cross binding of TFBS to a group TFs with similar DNA binding domain (DBD), but different transcriptional activities. Several group have conducted some analysis to understand the mechanism that govern th specificity of TFBSs in yeast and mammalian cells1. These analyses indicated that 1) TFs with similar DBD can bind to a set ofendogenous promoters exclusively. 2) mechanisms other than chromatin accessibility contribute to the differential in vivo DNA binding by TFs. 3) the flanking sequences outside the TFBS core motif are elements influence the TFs binding specificity. 4) DNA features, such as groove width, can be computed from its sequences and may underlie the mechanism by which TF bind to a
selective TFBS1-3. In this proposal, we are intended to identify a set of DNA sequences which can “insulate” designated TFBS from cross binding. We will start from identify exclusive TFBSs (including core motif and flanking sequences) for a group of TFs with similar DBD, following by analysis of features in the flanking sequences before creating “insulate” sequences for a designated TF. Finally, we will validate these “insulate” sequences in experiment.

Output

1) a set of “insulate” sequences to increase TFBS specificity (open source, exchangeable DNA element).

2) an optimized algorithm for identifying insulate sequences in plants (open source, software)

If you are interested in collaborating on this project, please contact Yaomin Cai.

References

1. Gordân, R. et al. Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape. Cell Rep. 3, 1093–1104 (2013).
2. Zhou, T. et al. Quantitative modeling of transcription factor binding specificities using DNA shape. PNAS. 122:15, 4653-4659 (2015)
3. Zhou, T. et al. DNAshape: a method for the high-throughput prediction of DNA tructural features on a genomic scale. Nucleic Acids Research. 41:W1, W56-W62 (2013)

Open Resources for Practical Biology with Kumasi Hive's Lab13 Ghana project

This project will aim to make educational materials from OpenPlant projects more available and accessible for use in low-resource settings by simplifying the materials required for experiments to still achieve a useful outcome. Resources will be trialled through Kumasi Hive's Lab13 Ghana project, teaching practical science in eight schools in Ghana's Ashanti region. The educational resources developed may include YouTube videos, worksheets, lists of physical materials required for each activity, and advice on how to source less common materials.

Contact colette.matthewman@jic.ac.uk if you would be interested in joining a team for this proposal.

TReND in Africa: synthetic biology course at Bingham University, Nigeria

TReND in Africa would like to collaborate on a course at Bingham University, Nigeria covering DNA assembly and genetic engineering in plants and animal models. They intend to demonstrate that good science can still be done with limited resources, including DIY recipes and 3D-printed equipment. One session will also cover the value of scientific outreach and how to do outreach work around these topics. TReND courses are open to early stage faculty from across Africa.

Contact colette.matthewman@jic.ac.uk if you would be interested in joining a team for this proposal.