Newsletter

"Plants can tell time even without a brain"

James Locke and Mark Greenwood (University of Cambridge) recently published their work on the coordination of circadian rhythms between different plant organs in PLOS Biology. This research paper has now been featured in The Conversation.

The article describes how the circadian timing in different plant organs is influenced both by local organ-specific input, as well as by inter-organ communication, allowing the expression of clock proteins to move through the plant in spatial waves.

Read more about the topic using the links above.

Building a CO2-concentrating mechanism

A new blog for the PLOS Synbio Community, written by Steven Burgess (former PDRA in one of the OpenPlant labs), describes the research of Alistair McCormack and colleagues on reconstructing an algal CO2-concentrating mechanism (CCM) into higher plants.

The work is part of an international collaboration that aims to test predictions that increasing the CO2 in plant leaves, with a system adapted from algae, will enhance photosynthetic performance, and water and nutrient use efficiency.

View the blog by Steven Burgess and the paper in the Journal of Experimental Botany.

New publications from the Baulcombe lab

OpenPlant PI David Baulcombe and colleagues recently published two papers: (1) on the miRNA-Argonaute machinery in the unicellular green alga Chlamydomonas reinhardtii, and (2) on the application of miRNAs for regulation of synthetic gene systems in this organism:

Chung  et al . (2019): “Figure 1: Structural features of  Chlamydomonas  Argonautes.”

Chung et al. (2019): “Figure 1: Structural features of Chlamydomonas Argonautes.”

Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression

Betty Y.-W. Chung, Adrian Valli, Michael J. Deery, Francisco J. Navarro, Katherine Brown, Silvia Hnatova, Julie Howard, Attila Molnar & David C. Baulcombe

Sci Rep. 2019; 9: 11091. doi: 10.1038/s41598-019-47415-x

https://www.nature.com/articles/s41598-019-47415-x.pdf

Abstract:

The unicellular green alga Chlamydomonas reinhardtii is evolutionarily divergent from higher plants, but has a fully functional silencing machinery including microRNA (miRNA)-mediated translation repression and mRNA turnover. However, distinct from the metazoan machinery, repression of gene expression is primarily associated with target sites within coding sequences instead of 3′UTRs. This feature indicates that the miRNA-Argonaute (AGO) machinery is ancient and the primary function is for post transcriptional gene repression and intermediate between the mechanisms in the rest of the plant and animal kingdoms. Here, we characterize AGO2 and 3 in Chlamydomonas, and show that cytoplasmically enriched Cr-AGO3 is responsible for endogenous miRNA-mediated gene repression. Under steady state, mid-log phase conditions, Cr-AGO3 binds predominantly miR-C89, which we previously identifed as the predominant miRNA with efects on both translation repression and mRNA turnover. In contrast, the paralogue Cr-AGO2 is nuclear enriched and exclusively binds to 21-nt siRNAs. Further analysis of the highly similar Cr-AGO2 and Cr-AGO 3 sequences (90% amino acid identity) revealed a glycine-arginine rich N-terminal extension of ~100 amino acids that, given previous work on unicellular protists, may associate AGO with the translation machinery. Phylogenetic analysis revealed that this glycine-arginine rich N-terminal extension is present outside the animal kingdom and is highly conserved, consistent with our previous proposal that miRNA-mediated CDS-targeting operates in this green alga.

Navarro and Baulcombe (2019): “Figure 1: Construction of a synthetic circuit to measure miRNA-dependent gene repression.”

Navarro and Baulcombe (2019): “Figure 1: Construction of a synthetic circuit to measure miRNA-dependent gene repression.”

miRNA-mediated regulation of synthetic gene circuits in the green alga Chlamydomonas reinhardtii

Francisco J. Navarro and David C. Baulcombe

ACS Synth Biol. 2019 February 15; 8(2): 358–370. doi:10.1021/acssynbio.8b00393.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396871/pdf/emss-81902.pdf

Abstract:

microRNAs (miRNAs), small RNA molecules of 20–24 nts, have many features that make them useful tools for gene expression regulation — small size, flexible design, target predictability and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3’UTRs, miRNA decoys and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga.

Genome-wide transcription factor binding in leaves from C3 and C4 grasses

OpenPlant PI Julian Hibberd and colleagues published their work on the transcription factor binding repertoire associated with C3 and C4 photosynthesis:

Burgess et al. (2019): “Fig 6: Hyper-conserved cis-elements in grasses recruited into C4 photosynthesis.”

Burgess et al. (2019): “Fig 6: Hyper-conserved cis-elements in grasses recruited into C4 photosynthesis.”

Genome-wide transcription factor binding in leaves from C3 and C4 grasses

Steven J Burgess, Ivan Reyna-Llorens, Sean Ross Stevenson, Pallavi Singh, Katja Jaeger, and Julian M Hibberd

Plant Cell. 2019. pii: tpc.00078.2019. doi: 10.1105/tpc.19.00078.

http://www.plantcell.org/content/plantcell/early/2019/08/19/tpc.19.00078.full.pdf

Abstract:

The majority of plants use C3 photosynthesis, but over sixty independent lineages of angiosperms have evolved the C4 pathway. In most C4 species, photosynthesis gene expression is compartmented between mesophyll and bundle sheath cells. We performed DNaseI-SEQ to identify genome-wide profiles of transcription factor binding in leaves of the C4 grasses Zea mays, Sorghum bicolor and Setaria italica as well as C3 Brachypodium distachyon. In C4 species, while bundle sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that impact gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C4 photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C4 photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.

Joint OpenPlant Fund/ Biomaker call opens Monday 8 April and closes Monday 13 May

The next call for OpenPlant Fund applications is announced!

This year’s OpenPlant Fund call is joined with the Cambridge-Norwich Biomaker Challenge. More information on this joint call can be found at: https://www.biomaker.org/cambridge-norwich-challenge.

A summary of the important dates can be found below:

Call Opens: Monday 8 April

Mixer event in Cambridge: Thursday 25 April (Transport Norwich - Cambridge can be provided)

Call closes: Monday 13 May

Challenge Begins: Friday 24 May

Progress reports and presentations: Monday 29 July (OpenPlant Forum Event)

Challenge Closes/Open Technology Workshop: Saturday 2 November

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Cambridge Science Festival

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For this year's Cambridge Science Festival, Alex Ting (Cambridge OpenPlant coordinator) teamed up with Biomakespace, SciArt in Cambridge, and independent events producer Sophie Weeks to host The Art & Science Soirée. The event brought together scientists, engineers, artists and designers engaged in DIY science for an exciting evening of speed meets, snap-talks, hands-on demos, and unexpected encounters. 

The event opened with slam poetry by Peter Bickerton (Science Communicator, Earlham Institute) followed by a talk by Jim Ajioka (Co-founder, Colorifix) and Giulia Tomasello (Interaction Designer specialising in women's healthcare.) Inside the house, Biomaker Challenge teams exhibited their low-cost, open-source projects. The aim of the event was to provide inspiration for open science projects (talks and demos), showcase the tools available to pursue such projects (Biomaker Challenge), and highlight a community-access space for biology and prototyping (Biomakespace). We hope that the event will inspire and provide an avenue for artists, designers, and other non-scientists to get involved in open science. 

Photos of the event can be found here: https://www.flickr.com/photos/synbiosri/albums/72157679436063798

New OpenPlant Programme Manager at the John Innes Centre in Norwich

Hi all,

Dieuwertje van der Does, OpenPlant Programme Manager

Dieuwertje van der Does, OpenPlant Programme Manager

My name is Dieuwertje van der Does and since February this year I am replacing Colette Matthewman as OpenPlant Programme Manager at the John Innes Centre in Norwich.

Previously, I obtained my PhD in the Netherlands, and worked as postdoctoral fellow at the Sainsbury Laboratory in Norwich to study the plant immune system. Before joining OpenPlant I spent two years at the BecA-ILRI Hub in Nairobi, Kenya, where I was Programme Lead for the 2Blades Foundation to aid the implementation of biotechnological solutions to crop diseases in East Africa. I am very excited to be able to contribute to the OpenPlant mission and accelerate the adoption of synthetic biology innovations in the real world. I am looking forward to our work together!

The Biomaker Challenge Winners and ways to get involved

The 2018 Summer Biomaker Challenge was wrapped up in October with a showcase event, but it not all over. Biomaker activities are still going strong! Below is a summary of activities as well as a write up of the Biomaker Fayre and the winning teams….


Biomaker Activities

Winter Software Challenge (apply by 16 December 2018): Interested in programming? Low-cost hardware for science? Learning new skills with a team? We provide the hardware, you develop software nodes for integrating hardware with new graphical programming interface, XOD. More information at www.biomaker.org/apply-now - a quick, rolling application process so you can receive your kit and start playing ASAP!

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Norwich Biomakers - An interdisciplinary network exploring the cross-over of biology with design, technology, engineering, electronics, software, art and much more. A place to learn about the latest technologies, share ideas and skills and shape projects. We meet up on a monthly basis.

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Cambridge Synthetic Biology meetups - A clearing house for a wide variety of regular open meetings like Cafe Synthetique, Science Makers and the SRI Forums - with a particular focus on building tools and interdisciplinary research.

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Cambridge Biomakespace - Scientists, engineers, students and entrepreneurs are developing the new Cambridge Biomakespace - an innovation space for building with biology in the historic MRC Laboratory of Molecular Biology building.


The Biomaker Fayre

On Saturday 29 October, over 100 attendees came together in the University of Cambridge Department of Engineering to showcase and celebrate open-source technologies in research and education. The day consisted of a morning of talks followed by the Biomaker Fayre, where this year's ten Biomaker Challenge teams exhibited their projects alongside industry leaders and independent makers.

We started the day with some inspiring talks: Paolo Bombelli & Alasdair Davies on open tools for animal conservation and the "Powered by Plants" project, Grey Christoforo on hacking 3D printers to create better solar cells, Helene Steiner on OpenCell and teaching the next generation of designers to work with scientists, Richard Hayler on citizen science and education with Raspberry Pi and Julian Stirling on open instrumentation for Africa.

After a coffee break and lunch, we headed upstairs for the Biomaker Fayre. There was a festive feel to the space- gold balloons marked each exhibit, 3D-printed trophies were on display to be given out at the end of day, and attendees filled the space, excited to get involved and try out some hands-on demos.

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Exhibits covered everything from a cartesian coordinate robot for dispensing fruit fly food to a wearable biosensor for monitoring vaginal discharge and a temperature-controlled container for sample transportation. Among the exhibitors were the ten Biomaker Challenge teams. In June, each team were given a £1000 grant and four months to turn their ideas for open source and DIY research tools into a reality.

The Biomaker Challenge judges were very impressed by each one of the projects and ended up deliberating for over an hour. In the end, the 3D-printed trophies (low-cost and DIY of course) were presented to the following teams:

Best Technology

Dual-View Imaging in a Custom-Built Light Sheet Microscope

Stephanie Hohn, Hannah Sleath, Rashid Khashiev, Francesco Boselli, Karen Lee

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"The large variety of Biomaker projects was very inspiring. We had a lot of fun during the challenge and the feedback from people in different fields was really helpful. It was great to get in touch with programmers, engineers and designers. We received a great confidence boost for future more technical projects."

Stephanie Hohn (University of Cambridge)




Best Biology

Spectre, Low-cost whole-cell biosensors for environmental and medical surveillance.

Feng Geng, Boon Lim, Xiaoyu Chen, Jimmy Chen

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"The Biomaker Challenge has provided us a great opportunity to extend our research into real-world application. As most of us come from a biological background, we faced a lot of difficulties on assembling the electronics and programming our Arduino kit. With three months of perseverance and constant guidance from our advisor Tony, we managed to come up with a customised, miniaturised spectrophotometer which can be used in conjunction with our whole-cell biosensor. We received an Arduino kit and sufficient funding to get us through the proof-of-concept stage of our project and from here, we are planning to further develop and optimise our device into a start-up company. It is amazing to think that it all starts with a small Biomaker Challenge Summer Project!"

Boon Lim, University of Oxford

Maker Spirit

Wearable biosensor for monitoring vaginal discharge

Tommaso Busolo, Giulia Tomasello, Michael Calabrese, James Che

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"We all really enjoyed the multidisciplinary nature of the challenge, working with people from all sorts of backgrounds. We feel we now have a much clearer, hands-on insight into how the more diverse a collaboration is, the more relevant, impactful and exciting the results of ideas brainstorming can be!"

Michael Calabrese, University of Cambridge









Biomaker Challenge and Open Technology Workshop aimed to show the value of open, low-cost and DIY technologies as convening points for interactions between biologists and engineers. They are also important educational tools for those who are interested in developing technical skills and have great potential for improving the quality of science and increasing productivity in the lab for lower costs. With the proliferation of digital designs for 3D-printing and easily available consumer electronics like Arduino which has a huge community of users and lots of online help, designing your instrumentation around your experiment rather than vice versa has never been more possible.

Check out more photos from the day!

The descriptions of all prototypes are available at www.hackster.io/biomaker and anyone who would like to be involved in next year’s competition should write to biomaker@hermes.cam.ac.uk to be kept up to date with developments.


Biomaker Challenge 2018 was funded by OpenPlant, a BBSRC/EPSRC Synthetic Biology Research Centre Grant BB/L014130/1. The Biomaker Challenge and Open Technology Workshop were coordinated by University of Cambridge's Synthetic Biology Strategic Research Initiative

[Closes 3 April 2017] Postdoctoral Researcher - Plant Synthetic Biology

Opportunity for an outstanding post-doctoral scientist to work on a collaborative project between the Patron Group at the Earlham Institute (EI) and the O'Connor group at The John Innes Centre (JIC). The project aims to improve plant production chassis for heterologous bioproduction of proteins (including vaccines) and metabolites and to contribute to our understanding of how the rich endogenous metabolism of plants detoxifies foreign molecules. The post-holder will have access to facilities at the Earlham DNA Foundry, interact with stakeholders at LeafSystems® and have the opportunity to work and collaborate with scientists in the Cambridge-Norwich OpenPlant Synthetic Biology Research Centre.

For details see: http://www.nature.com/naturejobs/science/jobs/606787-postdoctoral-researcher or http://www.earlham.ac.uk/postdoctoral-researcher-plant-synthetic-biology-0

[Closes 27 Mar 2017] CSIRO Synthetic Biology Fellowships

The CSIRO Future Science Platform in Synthetic Biology has released a call for national and international applicants for CSIRO Synthetic Biology Future Science Fellowships. See below and https://research.csiro.au/synthetic-biology-fsp/ for more information:

 

Synthetic Biology Fellowships

Applications are now open for the CSIRO Synthetic Biology Future Science Fellowships, an initiative of CSIRO's new Synthetic Biology Future Science Platform (SynBio FSP).

The scheme aims to attract outstanding national and international early-career post-doctoral researchers (equivalent to Academic Levels A and B, or in exceptional circumstances, Level C) to expand Australian research capacity in synthetic biology. A key element of the SynBio FSP is establishment of a collaborative community of practice extending across CSIRO and Australia more broadly, and linking into international efforts in the field. The SynBio FSP is built on a philosophy of responsible development of synthetic biology technology, striving for ethical outcomes and working within the bounds of social acceptance.

Fellowships will be hosted at a Host Organisation (usually an Australian University, but other Australian research organisations may also be eligible) and will be a partnership between the Fellow, CSIRO, and the Host Organisation. Fellows will be employed by the Host Organisation but will maintain a strong linkage to CSIRO through a partnering CSIRO Mentor(s) and various joint activities designed to support development of a synthetic biology community of practice across Australia

How to apply?

Further information and application instructions for the Fellowships are available at: https://research.csiro.au/synthetic-biology-fsp/

Applications must be submitted by 5pm Australian Eastern Standard Time, 27th March 2017.

Enquiries can be directed to: SynBioFSP@csiro.au