News

"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 LinkedIn group for synthetic biology centres: The Synbio Network

The Synbio Centres and the Foundries in the UK

The Synbio Centres and the Foundries in the UK

In this Linked-In group present and former members of the UK Synthetic Biology Research Centres, the DNA foundries and the Synbio Innovation and Knowledge Centre can connect with each other. Through this group we aim to maintain and build the network of synbio scientists in and outside the UK. This provides us with a forum through which we can stay in touch, make new connections, stay up to date on developments in the sector, exchange ideas, and build new collaborations. Please join our group and spread the word among your colleagues!

https://www.linkedin.com/groups/13754621/

Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid

OpenPlant PI Chris Howe and colleagues published their work on control of plastid gene expression in the dinoflagellate Amphidinium carterae:

Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid

Richard G.Dorrell, R. Ellen R.Nisbet, Adrian C.Barbrook, Stephen J.L.Rowden, and Christopher J.Howe

Protist 170(4), August 2019, Pages 358-373

Abstract:

The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed “minicircles”. These minicircles may contain genes, or no recognisable coding information. Transcripts produced from minicircles may undergo unusual processing events, such as the addition of a 3' poly(U) tail. To date, little is known about the genetic or transcriptional diversity of non-coding sequences in peridinindinoflagellate plastids. These sequences include empty minicircles, and regions of non-coding DNA in coding minicircles. Here, we present an integrated plastid genome and transcriptome for the model peridinin dinoflagellate Amphidinium carterae, identifying a previously undescribed minicircle. We also profile transcripts covering non-coding regions of the psbA and petB/atpA minicircles. We present evidence that antisense transcripts are produced within the A. carterae plastid, but show that these transcripts undergo different end cleavage events from sense transcripts, and do not receive 3' poly(U) tails. The difference in processing events between sense and antisense transcripts may enable the removal of non-coding transcripts from peridinin dinoflagellate plastid transcript pools.

Transformation of the dinoflagellate chloroplasts to enable studies on coral bleaching

eLife 8:e45292 Figure 5: A chloroplast localization for chloramphenicol acetyl transferase.

eLife 8:e45292 Figure 5: A chloroplast localization for chloramphenicol acetyl transferase.

Dinoflagellate algae are of enormous ecological importance as they form symbiosis with corals, providing fixed carbon to their hosts. Environmental stresses such as raised temperature lead to breakdown of the symbiosis, expulsion of the dinoflagellates, and coral bleaching. Little is known about why the symbiosis breaks down, although the generation of reactive oxygen species in the chloroplast is probably involved. Dinoflagellates have long been resistant to transformation, which has hampered research into bleaching.

With funding from the Gordon and Betty Moore Foundation, Chris Howe’s lab in the Cambridge Biochemistry Department has succeeded in transforming the chloroplast of a model dinoflagellate, Amphidinium carterae (Nimmo IC et al. (2019) Genetic transformation of the dinoflagellate chloroplast. eLife 8:e45292 DOI: https://doi.org/10.7554/eLife.45292). They exploited the highly unusual organisation of the chloroplast genome – fragmented into plasmid-like ‘minicircles’ – to make shuttle vectors for biolistic transformation. This should open the way for studies on how environmental stresses affect dinoflagellate chloroplast function and ultimately lead to coral bleaching. 

Hive BioLab, the first community/DIYBio lab in Ghana, launches @hivebiolab

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Hive BioLab is the first community/DIYBio lab in Ghana dedicated to the rapid prototyping of ideas in biology, research, enterprising bio-startups by helping and providing resources to students and graduates to translate science to businesses.

HiveBioLab is now active on twitter: @hivebiolab

A Biomaker team has made it to the final of the BBSRC Innovator of the Year 2019 Awards

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A Biomaker team with participants from Quadram Institute Bioscience (QIB), the Earlham Institute (EI), the John Innes Centre (JIC) and the University of Oxford, has developed a small scale speed breeding cabinet, which has qualified them for the final of the BBSRC Innovator of the Year 2019 Awards. Read more about this story here:

https://www.jic.ac.uk/news/norwich-research-park-team-in-line-for-early-career-innovator-award/

A specialized metabolic network selectively modulates Arabidopsis root microbiota

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OpenPlant scientists Hans-Wilhelm Nützmann and Anne Osbourn demonstrate that model plant Arabidopsis thaliana produces a range of specialized triterpenes that direct the assembly and maintenance of a specific microbial community within and around its roots. Their work, which was part of a collaborative effort, was recently published in Science:

Ancheng C. Huang, Ting Jiang, Yong-Xin Liu, Yue-Chen Bai, James Reed, Baoyuan Qu, Alain Goossens, Hans-Wilhelm Nützmann, Yang Bai, Anne Osbourn

A specialized metabolic network selectively modulates Arabidopsis root microbiota

Science (2019) Vol. 364, Issue 6440, eaau6389
DOI: 10.1126/science.aau6389

https://science.sciencemag.org/content/364/6440/eaau6389

Abstract

Plant specialized metabolites have ecological functions, yet the presence of numerous uncharacterized biosynthetic genes in plant genomes suggests that many molecules remain unknown. We discovered a triterpene biosynthetic network in the roots of the small mustard plant Arabidopsis thaliana. Collectively, we have elucidated and reconstituted three divergent pathways for the biosynthesis of root triterpenes, namely thalianin (seven steps), thalianyl medium-chain fatty acid esters (three steps), and arabidin (five steps). A. thaliana mutants disrupted in the biosynthesis of these compounds have altered root microbiota. In vitro bioassays with purified compounds reveal selective growth modulation activities of pathway metabolites toward root microbiota members and their biochemical transformation and utilization by bacteria, supporting a role for this biosynthetic network in shaping an Arabidopsis-specific root microbial community.

Cas9-mediated mutagenesis of potato starch branching enzymes generates a range of tuber starch phenotypes

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OpenPlant scientists Aytug Tuncel, Nicola Patron and Alison Smith demonstrate that Cas9-mediated mutagenesis of starch-branching enzymes has the potential to generate new, potentially valuable starch properties.

Aytug Tuncel, Kendall R. Corbin, Jennifer Ahn‐Jarvis , Suzanne Harris, Erica Hawkins, Mark A. Smedley, Wendy Harwood, Frederick J. Warren, Nicola J. Patron, Alison M. Smith

Cas9-mediated mutagenesis of potato starch branching enzymes generates a range of tuber starch phenotypes

Plant Biotechnology Journal https://doi.org/10.1111/pbi.13137

Abstract

We investigated whether Cas9‐mediated mutagenesis of starch‐branching enzymes (SBEs) in tetraploid potatoes could generate tuber starches with a range of distinct properties. Constructs containing the Cas9 gene and sgRNAs targeting SBE1, SBE2 or both genes were introduced by Agrobacterium‐mediated transformation or by PEG‐mediated delivery into protoplasts. Outcomes included lines with mutations in all or only some of the homoeoalleles of SBE genes, and lines in which homoeoalleles carried several different mutations. DNA delivery into protoplasts resulted in mutants with no detectable Cas9 gene, suggesting the absence of foreign DNA. Selected mutants with starch granule abnormalities had reductions in tuber SBE1 and/or SBE2 protein that were broadly in line with expectations from genotype analysis. Strong reduction of both SBE isoforms created an extreme starch phenotype, as reported previously for low‐SBE potato tubers. HPLC‐SEC and 1H NMR revealed a decrease in short amylopectin chains, an increase in long chains and a large reduction in branching frequency relative to wild‐type starch. Mutants with strong reductions of SBE2 protein alone had near‐normal amylopectin chain length distributions and only small reductions in branching frequency. However, starch granule initiation was enormously increased: cells contained many granules of < 4 μm and granules with multiple hila. Thus large reductions in both SBEs reduce amylopectin branching during granule growth, whereas reduction of SBE2 alone primarily affects numbers of starch granule initiations. Our results demonstrate that Cas9‐mediated mutagenesis of SBE genes has the potential to generate new, potentially valuable starch properties without integration of foreign DNA into the genome.

The protosteryl and dammarenyl cation dichotomy in polycyclic triterpene biosynthesis revisited: has this ‘rule’ finally been broken?

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OpenPlant postdoc Michael Stephenson, and group leaders Rob Field and Anne Osbourn at the John Innes Centre in Norwich, reveal novel insights into triterpene biogenesis in their recent paper.

Stephenson MJ,  Field RA,  and  Osbourn A (2019) The protosteryl and dammarenyl cation dichotomy in polycyclic triterpene biosynthesis revisited: has this ‘rule’ finally been broken? Natural Product Reports, DOI: 10.1039/c8np00096d

Abstract

The triterpene alcohols represent an important and diverse class of natural products. This diversity is believed to originate from the differential enzymatically controlled cyclisation of 2,3-oxidosqualene. It is now a well-established presumption that all naturally occurring tetra- and penta-cyclic triterpene alcohols can be rationalised by the resolution of one of two intermediary tetracyclic cations, termed the protosteryl and dammarenyl cations. Here, a discussion of typical key triterpene structures and their proposed derivation from either of these progenitors is followed by comparison with a recently reported novel pentacyclic triterpene orysatinol which appears to correspond to an unprecedented divergence from this dichotomous protosteryl/dammarenyl view of triterpene biogenesis. Not only does this discovery widen the potential scope of triterpene scaffolds that could exist in nature, it could call into question the reliability of stereochemical assignments of some existing triterpene structures that are supported by only limited spectroscopic evidence. The discovery of orysatinol provides direct experimental evidence to support considering more flexibility in the stereochemical interpretation of the biogenic isoprene rule.

Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis

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OpenPlant postdoc Henry Temple, in Prof Paul Dupree’s lab at the University of Cambridge, has published his discovery of a novel role for members of the DUF579 protein family in plant cell wall modification.

Temple H, Mortimer JC, Tryfona T, Yu X, Lopez‐Hernandez F, Sorieul M, Anders N, Dupree P (2019) Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis. Plant Direct, https://doi.org/10.1002/pld3.117

Abstract

All members of the DUF579 family characterized so far have been described to affect the integrity of the hemicellulosic cell wall component xylan: GXMs are glucuronoxylan methyltransferases catalyzing 4‐O–methylation of glucuronic acid on xylan; IRX15 and IRX15L, although their enzymatic activity is unknown, are required for xylan biosynthesis and/or xylan deposition. Here we show that the DUF579 family members, AGM1 and AGM2, are required for 4‐O–methylation of glucuronic acid of a different plant cell wall component, the highly glycosylated arabinogalactan proteins (AGPs).

Postnatural Botany: A creative exploration of botanical diversity, observation and communication skills

“Postnatural Botany” rules booklet, plant discovery cards, and role-playing cars for “Explorer”, “Regulator” and “Artist”. Photo: Karen Ingram

“Postnatural Botany” rules booklet, plant discovery cards, and role-playing cars for “Explorer”, “Regulator” and “Artist”. Photo: Karen Ingram

Guest post by Karen Ingram, Creative Director

Postnatural Bestiary/Botany

This past July, participants of the 2018 OpenPlant Forum went on an expedition where they discovered several new species of plants. Ok- they didn’t REALLY discover the plants, but they played a game that enacted the discovery of 18 new plants, from alpine to outback, at the conference dinner held at the Sainsbury Centre for Visual Arts (SVCA). The game, “Postnatural Botany” was inspired by Medieval Bestiaries, and the notion that explorers would describe the wildlife from their travels to people who had never seen such wildlife, as a means to share with the community.

Image courtesy of Rutgers University Honors College Instagram and Julia Buntaine.

Image courtesy of Rutgers University Honors College Instagram and Julia Buntaine.

“Postnatural Botany” has its origin as a workshop I created for 23 students in the Rutgers University Honors College and Douglass Residential College for women. The workshop took place in early 2018 and was part of a course, “Science/Art/Technology in New/York/City" taught by Julia Buntaine of the SciArt Center.

Originally dubbed “Postnatural Bestiary” and depicting a wide array of animals, I worked with Dr. Nicola Patron from the Earlham Institute to tailor the game to be plant focused, specifically for the Open Plant Forum.

The 2018 Open Plant Forum was hosted in Norwich, at the John Innes Centre. Norwich–which enjoyed great prosperity in the Middle ages–was the perfect backdrop for a game based on medieval bestiaries.

Playing the Game

Each person was assigned a role as an “explorer”, “artist”, or “regulator” and worked in teams to produce artworks of each plant according to the rules of play. Patron selected a wide variety of plant life; Venus Flytrap, Rainbow Eucalyptus, Welwitschia, Jack-in-the-Pulpit, and Java Moss were all “discovered”, described with limited terminology and depicted with magic markers and imaginative minds.

Karen Ingram  introducing the game to attendees of the Open Plant Forum. Photo: Nicola Patron

Karen Ingram introducing the game to attendees of the Open Plant Forum. Photo: Nicola Patron

The “explorer” in each group was given an envelope that contained a card with the plant they had “discovered.” The card displayed a limited amount of information, including an image of the plant, the name, habitat, size, characteristics of its flower (if there was one), and information about a specific “outstanding feature” for each plant.

The “explorer” had to describe the plant they had discovered to an”artist” for visual interpretation. A “regulator” was also part of the game play, in order to ensure all parties followed the rules, of which there were many! Neither the artist nor the regulator were allowed to guess what the plant might be. The artist was not allowed to talk at all, primarily to keep them from guessing what the plant was.

Explorer  Jenny Molloy  gesticulates as she describes a Baobab tree to her team’s artists,  Joanne Kamens  and  Dave Rejeski . Photo: Karen Ingram

Explorer Jenny Molloy gesticulates as she describes a Baobab tree to her team’s artists, Joanne Kamens and Dave Rejeski. Photo: Karen Ingram

Fun with Rules

I created a fictitious human-centric “public” that has no access to robust image catalogues and information we have via the internet, and no knowledge of the sciences. Because of these limitations, “explorers” had to use simplified terminology; leaning on familiar household objects and tools used by humans (purses, for example) and referencing the human body as a measurement unit. Professor George Lomonosoff from the John Innes Center remarked that it was a joy to describe a Rainbow Eucalyptus tree to his team’s “artists” as being “...as tall as twenty men!”

Jim Haseloff  puts the final touches on his drawing. Photo: Nicola Patron

Jim Haseloff puts the final touches on his drawing. Photo: Nicola Patron

Simple explanations, gestures, analogies referencing common household objects, an abbreviated list of plant traits (stems, leaves, flowers, roots), as well as a few select domesticated plants were used in favor of scientific terminology.

The key objectives of the game were not so much to depict the plant correctly, but to work as a team: to communicate carefully on the part of the explorers, and to listen and interpret on the part of artists and regulators, and for everyone to have fun with plants.

An amazingly accurate rendering of a Sturt’s Desert Pea by  Jan Lyczakowski , who exclaimed “I’ve never seen this plant before, but apparently I did a pretty well!” Photo: Nicola Patron

An amazingly accurate rendering of a Sturt’s Desert Pea by Jan Lyczakowski, who exclaimed “I’ve never seen this plant before, but apparently I did a pretty well!” Photo: Nicola Patron

Open Plant Forum attendees marvel over a gallery of colorful creations. Photo: Nicola Patron

Open Plant Forum attendees marvel over a gallery of colorful creations. Photo: Nicola Patron

Colette Matthewman–whose winning drawings of a Jack-in-the-pulpit underwent several iterations before she was satisfied–shared her thoughts: “The OpenPlant Forum attracts a mutidisciplinary crowd, and this was a great game for breaking down barriers of language as we were all restricted to using very every-day words together with gestures to describe and understand the look of the plant – and the plants chosen looked really fantastical! As ‘an artist’ it was fascinating to see how I started to relate the explorer’s description to plants that I knew. This helped me to draw a reasonable likeness, but also limited my ability to take on board specific instructions from the explorer as they didn’t match the image in my head.”

A Note about the Postnatural

The term “Postnatural” is defined as any organism altered by humans via selective breeding or genetic engineering. In the fable of this game, the plants and organisms are newly “discovered” by humans. Through the ages, plant collectors took their findings to new places for breeding and growth in new environments, altering the genetics and epigenetics of the plants forever. This calls to question, at what point of human intervention do organisms become “postnatural”? Once an organism is known and it is integrated into our lexicon; in a Bestiary as it was in the Middle Ages, domesticated to produce products for humans, or its genome sequenced, it is part of our human narrative. Fewer and fewer botanists get to experience the thrill of discovering a new plant species. And yet, through the discoveries of modern biology, humans are experiencing a new kinship with other organisms as we learn more about common biological processes and origins of life on earth. The gameplay of “Postnatural Botany” relies on observation, communication, listening, and interpretation; tools that we can all use to examine the potential impact of this kinship.

Markers down.  Randy Rettberg ,  Roger Castells , and  Ian Small  survey the final pieces as people finish their pieces. Photo: Karen Ingram

Markers down. Randy Rettberg, Roger Castells, and Ian Small survey the final pieces as people finish their pieces. Photo: Karen Ingram

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Sketches show depictions of Venus Flytrap, Corpse flower, Java moss, Jack-in-the-pulpit (the winner), and Vegetable Sheep. Photos: Nicola Patron

Two publications describe focus stacking setup developed through OpenPlant Fund

Dr Jennifer Deegan has built a Focus Stacking system that enables her to take close up photos of really small plant samples, in which the full sample is in focus. In her OpenPlant Fund project, she developed the system further, working with collaborators to try photography of new samples, and built up teaching tools to enable others to replicate the system. Read about her project here: https://www.biomaker.org/projects/focus-stacking-for-teaching-and-publication-in-plant-sciences and in the two publications below:

Part 1: Deegan, J. (2017). Photographing The Fern Gametophyte Developmental Series – The First Attempt. Pteridologist, 6 (4), 263-265. https://doi.org/10.17863/CAM.17067

Part 2: Deegan, J. I., & Deegan, T. (2018).  Macrophotography of Fern Gametophytes Using a Focus Stacking System. Pteridologist, 6 (5), 357-360. https://doi.org/10.17863/CAM.33541

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

OpenPlant postdoc Francisco Navarro, in Prof David Baulcombe’s lab at the University of Cambridge, has published his work on regulation of synthetic gene circuits by miRNA in Chalmydomonas reinhardtii, in ACS Synthetic Biology. This work describes a new mechanism for regulation that can be used in in new synthetic biology applications in this green algae chassis.

Navarro F, Baulcombe DC (2019). miRNA-mediated regulation of synthetic gene circuits in the green alga Chlamydomonas reinhardtii. ACS Synthetic Biology, https://doi.org/10.1021/acssynbio.8b00393. [Epub ahead of print]

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.

Improving homebrewing with the help of arduinos and XOD: Our Biomaker Challenge

We are a small, merry band of newbie Biomakers and amateur homebrewers and have started a project to monitor the progression of our fine brews in real time. By day we are two research scientists and a Biology teacher.

 We are looking to develop a piece of kit which allows us to see how quickly our homebrew is turned from a mixture of sugars in the initial malty extract into alcohol in beer. As sugars are converted to alcohol by the yeast, the density, or Specific Gravity (SG), of the liquid decreases and this is traditionally monitored by the means of a hydrometer. The SG decreases over time until it reaches a final plateau, at which point all of the sugars have been turned into alcohol. We are interested in monitoring how quickly this happens and how we can monitor it in real time.

Sam’s Biomaker Starter Kit arrives “what an exciting package to find on my desk first day back in the lab in 2019!”

Sam’s Biomaker Starter Kit arrives “what an exciting package to find on my desk first day back in the lab in 2019!”

An alcohol meter, testing beer immediately after brewing but before fermentation.  Image by  Jeena  on Wikipedia, shared under  CC BY-SA 3.0

An alcohol meter, testing beer immediately after brewing but before fermentation.

Image by Jeena on Wikipedia, shared under CC BY-SA 3.0

Getting started…

Getting started…

Initial challenges

As two of us have absolutely no prior knowledge of using Arduinos the first challenge has been to work out which end of the lead plugs into the laptop and which end into the Arduino. One of us has much more experience of programming, but not huge experience with Arduinos. It’s pretty much a ragtag skillset, held together with a Whatsapp group, copious mugs of tea, soup, swearing and an overarching dedication to the cause of better homebrew.

Initial thoughts

The learning curve of getting the Arduinos, laptops and components to talk to each other was incredibly steep. A few pointers from the ever-helpful Colette Matthewman helped immensely. Gratifyingly learning the XOD aspect of the project has been pretty straightforward. The online tutorials have stepped us through what we need to do in a logical manner.

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 Our initial design has been modified, from just monitoring the height via the height sensor supplied, to attaching a Hall Sensor to the Arduino and attaching magnets to the hydrometer. We have developed ideas which can spring from this once we’ve got the basics in place and are quite excited (an overused word), about the potential scope of what we’re playing with.

 We are still very much in the early stages of the project, but are learning and have welcomed the opportunities to work towards a common goal (better beer), whilst acquiring new skills. This project has some way to run and will, no doubt, be adapted, modified and changed over time.

Follow our progress (intermittently) via twitter @dewhurst_ben, @popupcamptrout, @LP_Alwyn, @AutoBrewControl

More information about the Biomaker Challenge can be found at www.biomaker.org

[Closes 6 Jan 2019] Post-doctoral researcher position in the Osbourn Group at John Innes Centre

Closing Date: 6 Jan 2019

>>> Apply here <<<

Grade SC6 Starting Salary: £31,250 - £35,400

Expected/Ideal Start Date: 01 Feb 2019

Duration: 17 Months

Main Purpose of the Job

Applications are invited for a Postdoctoral Scientist with expertise in natural product chemistry. The post involves extraction, analysis, purification and structural determination of medicinally important complex triterpene glycosides . The successful candidate will work with other researchers within the Osbourn lab as part of a multi-disciplinary team.

Further details of this project and the laboratory can be found at https://www.jic.ac.uk/scientists/anne-osbourn/.

Key Relationships

The successful applicant will be line-managed by Professor Anne Osbourn. The position is one of four postdoctoral positions funded by a Biotechnology and Biological Sciences Research Council (BBSRC) Super Follow-on Fund award for translational research. The successful applicant will work closely with this team and with John Innes Centre Metabolite Services.

Main Activities & Responsibilities

  • Extraction, analysis, purification and strutcural determination of complex triterpenes (saponins)

  • Prepare results, reports and manuscripts for publication in leading scientific journals and other relevant media

  • Disseminate research findings though presentations to various audiences at internal, national and international meetings

  • Collaborate with colleagues within the Institute in the development of original and world-class research, including contributing to research proposals and grant applications

  • Liaise with industry and other external stakeholders

  • Ensure research and record keeping is carried out in accordance with good practice, Scientific Integrity and in compliance with local policies and any legal requirements

  • Contribute to the smooth running of the group, including the effective use of resources, supervision of visitors to the laboratory and assisting with training others, encouraging scientific excellence

  • Continually strive for excellence, seeking out and acting on feedback and relevant learning and development opportunities

As agreed with line manager, any other duties commensurate with the nature of the role

Speed breeding made accessible and democratic

Scientists at the John Innes Centre, Earlham Institute, and Quadram Institute in Norwich and the University of Queensland have improved the technique, known as speed breeding, adapting it to work in vast glasshouses and in scaled-down desktop growth chambers. The scaled-down chambers are the result of an OpenPlant Fund project to develop a “Bench-top Controlled Environment Growth Chamber for Speed-Breeding and Crop Transformation”.

Two papers have been published detailing the research on speed breeding and the protocols:

Watson A, Ghosh S, Williams MJ, Cuddy WS, Simmonds J, Rey MD, Asyraf Md Hatta M, Hinchliffe A, Steed A, Reynolds D, Adamski NM, Breakspear A, Korolev A, Rayner T, Dixon LE, Riaz A, Martin W, Ryan M, Edwards D, Batley J, Raman H, Carter J, Rogers C, Domoney C, Moore G, Harwood W, Nicholson P, Dieters MJ, DeLacy IH, Zhou J, Uauy C, Boden SA, Park RF, Wulff BBH, Hickey LT. Speed breeding is a powerful tool to accelerate crop research and breeding. Nat Plants. 2018 Jan;4(1):23-29. doi: 10.1038/s41477-017-0083-8.

Ghosh S, Watson A, Gonzalez-Navarro OE, Ramirez-Gonzalez RH, Yanes L, Mendoza-Suárez M, Simmonds J, Wells R, Rayner T, Green P, Hafeez A, Hayta S, Melton RE, Steed A, Sarkar A, Carter J, Perkins L, Lord J, Tester M, Osbourn A, Moscou MJ, Nicholson P, Harwood W, Martin C, Domoney C, Uauy C, Hazard B, Wulff BBH, Hickey LT. Speed breeding in growth chambers and glasshouses for crop breeding and model plant research. Nat Protoc. 2018 Dec;13(12):2944-2963. doi: 10.1038/s41596-018-0072-z.

There has been a lot of interest in the speed breeding technology and in the desktop speed breeding chamber, and the researchers highlighted the work in a piece on BBC Look East. The research is also described in a news article on the John Innes Centre website and through a series of videos.

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

Late night (biological) engineering in London

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By Sami Stebbings

Once a month something amazing happens at the London Science Museum, and last month our collaborative team from OpenPlant, the SAW Trust, the University of East Anglia (UEA) and graphic recorder Rebecca Osborne, got to be part of it.

On the last Wednesday of every month, the London Science Museum opens its doors late into the evening to welcome adults to an engaging and free evening out, as part of the Science Museum Lates.

Each evening is themed around a different science topic, attracts around 4,000 guests per night and offers a relaxed atmosphere where you can walk around with a drink in hand whilst talking science.

This month’s theme was ‘The year of the engineer’ and we brought the synthetic biology edge to the night with our ‘Engineering Natural Products’ stand. With the help of Dr Richard Bowater (University of East Anglia), Hannah Griffiths (John Innes Centre) and of course DNA Dave, visitors were taken on a journey from the discovery of DNA through to how scientists engineer biological systems.

Our enthusiastic public engagement volunteers, Jenni Rant and Sami Stebbings (SAW Trust) and John Innes Centre PhD students' Hannah Griffiths and Shannon Woodhouse.

Our enthusiastic public engagement volunteers, Jenni Rant and Sami Stebbings (SAW Trust) and John Innes Centre PhD students' Hannah Griffiths and Shannon Woodhouse.

Our stand told the story of avenacin, a triterpene that is found in the roots of oat plants and helps make the plant resistant to fungal diseases. By understanding how these plants produce avenacin from the instruction in their DNA, we explored how scientists can engineer other biological systems to mimic their production. For example, can we transfer these genes from oat plants, into other crops, such as wheat which have no natural antifungal protection?

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Guests had a plethora of activities to take part in, from our ‘Fishing for DNA’ activity, Avenacin Pathway puzzle, to getting up close and personal with an avenacin molecule using VR. They also had a chance to get hands on and infiltrate tobacco plants and see fluorescing oat seedlings!

With a steady stream of people throughout the night, the evening was a great success (not only because there was gin bar)! A massive thank you to all our collaborators who helped pull our stand and activities together, as well as the fantastically organised, London Science Museum team.

In was a great event to be part of and we hope to return to another Lates event sometime in the future!

Opening up Global Biotech Innovation: Publication of OpenMTA

The OpenMTA was launched with a commentary published in the journal Nature Biotechnology in October 2018. It provides a new way to exchange materials commonly used in biological research and engineering, complementing existing, more restrictive arrangements. The OpenMTA also promotes access for researchers and individuals working in less privileged institutions and world regions.

Download: OpenMTA Commentary. “Opening options for material transfer”. Linda Kahl, Jennifer Molloy, Nicola Patron, Colette Matthewman, Jim Haseloff, David Grewal, Richard Johnson & Drew Endy. Nature Biotechnology 36:923–927 (2018). https://doi.org/10.1038/nbt.4263


Abstract

Material-transfer agreements (MTAs) underlie the legal frameworks within which biotechnology practitioners define the terms and conditions for sharing biomaterials ranging, for example, from plasmid DNA to patient samples. If MTAs are easy to use and well adapted to the needs of individual researchers, institutions, and broader communities, then more sharing, innovation, and translation can occur. However, the MTA frameworks currently in place were developed in the 1990s—before widespread adoption of the World Wide Web, genome sequencing, and gene synthesis—and are not always well adapted for contemporary research and translation practices or aligned with social objectives.

Here, we introduce a new MTA, the Open Material Transfer Agreement (OpenMTA), that relaxes restrictions on the redistribution and commercial use of biomaterials while maintaining aspects of standard MTAs that support widespread adoption (for example, incorporation into semiautomated administration systems). In developing the OpenMTA, our motivation was to realize a simple, standardized legal tool for sharing biological materials as broadly as possible without undue restrictions, while respecting the rights of creators and promoting safe practices and responsible research. Importantly, we wanted the tool to work within the practical realities of technology transfer and to be sufficiently flexible to accommodate the needs of many groups globally (for example, providing support for international transfers and compatibility with public and philanthropic funding policies).