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

[Closes 13 Feb 2019] Postdoc position in engineering complex traits in plants

postdoctoral-research-scientist-engineering-complex-traits-plants-patron-lab-jan-2019-social.png

Applications are invited for a Postdoctoral Research Scientist to join the Laboratory of Dr Nicola Patron to work on a project to engineer plant responses to nitrogen availability. The aim of this project is to deploy genome engineering tools to introduce multiplexed targeted mutations in specific coding and non-coding regions of a group of plant genes predicted to coordinate large-scale transcriptional responses to environmental nitrogen availability. The post-holder will be based in the Patron Lab at the Earlham Institute, (Norwich Research Park, UK) and will work in collaboration with the Brady and Segal Labs (UCDavis).

Salary on appointment will be within the range £31,250 to £38,100 per annum depending on qualifications and experience. This is a fulltime post for a contract of 23 months from 1st April 2019.

http://www.earlham.ac.uk/postdoctoral-research-scientist-engineering-complex-traits-plants

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.

[Closes 10 Feb 2019] Post-doc position in Field lab at JIC: Enzymes for scalable carbohydrate synthesis

Currently advertised is a post-doctoral position in the lab of Prof Rob Field at the John Innes Centre, in Enzymes for scalable carbohydrate synthesis.

Deadline for applications in 10 February 2019. For more information and to apply click here.


Main Purpose of the Job

Postdoctoral Researchers work with limited supervision to carry out individual and collaborative research projects relevant to the enzymatic synthesis of glycans, sugar nucleotides and sugar phosphates using chemical and enzymatic approaches.

Key Relationships

Internal: Line manager, group members and, as necessary, other researchers, research support staff and students across the Institute.

External: Collaborators at Keele, Manchester and Iceni Diagnostics 

Main Activities & Responsibilities

  • Identify, plan, carry out and modify experiments to meet the objectives of the project

  • 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 stakeholders5Ensure 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 the line manager, any other duties commensurate with the nature of the post, for example, contributing to the work of Institute committees

[Closes 1 Mar 2019] CSIRO Synthetic Biology Future Science Fellowships scheme

The third round of the CSIRO Synthetic Biology Future Science Platform Future Science Fellowships scheme is open – please see details below. These Fellowships provide an opportunity for early-to-mid career researchers (academic rank A-C in the Australian system) to develop their careers in synthetic biology research through collaboration with their Australasian host university (or other eligible host organisation) and CSIRO, Australia’s peak scientific research organisation. Applications close 5pm Australian Eastern Standard Time, Friday 1st March 2019.

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

The 2019 priority Application Domains are Health & Medicine, and Maximising Impact (social sciences). Applications in other Application Domains will also be accepted. We also have a technical priority area: BioFoundry use (high throughput robotic engineering; Foundry facilities are available). Further details can be found in the Priority Areas (see section under ‘Projects’ in the Instructions to Applicants).

Fellowship Enquiries: SynBioFSP@csiro.au

Foundry Enquiries: SynBioFoundry@csiro.au


2019 CSIRO Synthetic Biology Future Science Fellowships

CSIRO’s Synthetic Biology Future Science Platform (SynBio FSP) is pleased to announce the opening of the third round of CSIRO Synthetic Biology Future Science Fellowships.

The scheme aims to attract outstanding national and international early- to mid-career postdoctoral researchers (equivalent to Australian 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. Research projects must demonstrate an ability to build Australian capacity in synthetic biology.

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. Fellows will have a Visiting Scientist appointment at CSIRO and may spend a portion of time physically located within a CSIRO research group if appropriate for the Fellowship project.

How to apply?

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

Applications must be submitted by 5pm Australian Eastern Standard Time, Friday 1st March 2019.

The SynBio FSP strongly supports women and other minorities in STEM disciplines. We welcome applications from such individuals and greatly value the diversity they bring to the SynBioFSP. We recognise that women are less likely to apply for engineering-related Fellowships and Fellowships in general, and would therefore like to encourage applications from women. Processes are in place to recognise and properly assess output relative to opportunity, and opportunities for flexible working arrangements and career interruptions are embedded in the Fellowship rules.

Further enquiries can be directed to: SynBioFSP@csiro.au

[Closes 24 Jan 2019] OpenPlant Programme Manager job

Apply here >>> https://www.jic.ac.uk/vacancies/openplant-programme-manager-osbourn-group/

Main Purpose of the Job

Applications are invited for the position of an OpenPlant Programme Manager to be based at the John Innes Centre in Norwich. This position is part of the £13 M OpenPlant Synthetic Biology Research Centre, a large collaborative project led jointly by the John Innes Centre and the University of Cambridge (http://www.openplant.org). The successful applicant will work closely with Professor Anne Osbourn (Director, OpenPlant, Norwich) and other scientists at the John Innes Centre and the Earlham Institute to co-ordinate, integrate, trouble-shoot, evaluate and report on the progress of the overall programme. A key part of the responsibilities of the post holder will be (with Professor Osbourn) to liaise with Professor Jim Haseloff (Director, OpenPlant, Cambridge) and his team to enable the successful delivery of the scientific and strategic goals of this large and complex project. The post holder will also be expected to take an active role in OpenPlant engagement activities.

Further details 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 and will work closely with scientists within OpenPlant at the John Innes Centre and the Norwich-based Earlham Institute to co-ordinate and enable the successful delivery of the Norwich-based parts of the OpenPlant programme. A key part of the responsibilities of the post holder will be (with Professor Osbourn) to liaise closely with Professor Jim Haseloff and his team to co-ordinate, integrate, trouble-shoot, evaluate and report on the progress of the overall programme. The post holder will also be expected to take an active role in OpenPlant engagement activities.

Main Activities & Responsibilities

  • Oversee the day-to-day running of the OpenPlant Lab (Norwich) - co-ordinate, integrate, trouble-shoot, evaluate and assist with reporting on the progress of the overall programme

  • Liaise closely with Professor Jim Haseloff, the Cambridge-based OpenPlant Project Manager, and scientists in the OpenPlant Lab (Cambridge) to ensure effective integration of the two-site Programme and to maximise opportunities for synergy

  • Organise meetings, workshops, training courses, engagement activities and other events on behalf of OpenPlant

  • Undertake other science engagement/social science activities relevant to OpenPlant

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

[Closes 22 Jan 2019] Tenure-track assistant professor position in Plant Genome Engineering

The department of Genetics Development and Cell Biology at Iowa State University (ISU) is inviting applications for a tenure-track assistant professor position in Plant Genome Engineering. They’re looking for a plant biologist who uses and/or develops genome editing technologies in their research.

Apply here >>> https://www.iastatejobs.com/postings/37758

GDCB seeks to hire a plant biologist who addresses fundamental or applied questions in the mechanisms of plant function and/or development at the cellular and molecular level using genome engineering such as CRISPR/Cas gene editing. Scientists developing resources that potentially reshape specific plant characteristics for the benefit of the environment and the human condition are strongly encouraged to apply.

Areas of interest will address or integrate Signature Themes at ISU in Biological Systems, Datarich Environments, and Environmental Sustainability, including but not limited to: molecular and cellular processes integral to plant health or disease, genome dynamics, phenomics, plant development, epigenetics, genetic and metabolic regulatory networks, and plant responses to environmental signals and stresses. Interdisciplinary or collaborative research is encouraged.

Responsibilities include building a nationally recognized research program that competes successfully for extramural funding, advancing the discipline through high-quality publications, mentoring students, and effective teaching of undergraduate and graduate courses. The successful candidate will demonstrate excellent communication and leadership skills and will share the university’s commitment to an inclusive environment that supports diversity.

GDCB and ISU provide an interactive, collegial environment of world-class scientists studying biological questions of fundamental importance, with particular strengths in plant sciences. Our faculty use experimental and computational approaches in an array of organisms, and participate in interdisciplinary graduate training programs in Plant Biology, Genetics and Genomics, Molecular, Cellular and Developmental Biology, Bioinformatics and Computational Biology, and an NSF Research Traineeship in Predictive Plant Phenomics.

Required Qualifications:

  • Ph.D. in life sciences or related

  • Published record of high-quality research

Preferred Qualifications:

  • Demonstrated ability or clear potential to secure extramural funding

  • Evidence of ability to develop a research program with potential for national distinction

  • Research plan that enhances existing strengths at ISU

  • Engagement in interdisciplinary or collaborative research

  • Postdoctoral research experience

  • Demonstrated ability or potential to excel in scholarly teaching

  • Evidence of commitment to an inclusive climate that supports diversity and enableshonest and respectful exchange of ideas

Please visit https://www.iastatejobs.com/postings/37758 to view the entire vacancy and apply electronically. For full consideration, submit the application by January 22, 2018.

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

[EoI deadline 15 Jan 2019] BBSRC/EPSRC Interdisciplinary Grants: Building Collaboration at the Physics of Life Interface

Expression of interest deadline: 15 January 2019, 16:00

Application deadline: 12 February 2019, 16:00

Full details at: https://bbsrc.ukri.org/funding/filter/2018-physics-of-life/

Summary

This is the first of two calls for proposals from the UK Research and Innovation (UKRI) Physics of Life Strategic Priority Fund to support internationally leading research that requires collaborative, interdisciplinary working to address key challenges at the interface of physics and the life sciences. This call will fund high-quality proposals that demonstrate deep integration of cutting edge experimental, theoretical and/or computational physics with life sciences research to advance our understanding of living systems in biological or biomedical contexts.

This UK Research and Innovation (UKRI) call, led by EPSRC with support from BBSRC and MRC, is making available up to £15 million, to include £13.2 million of resource funding and £1.8 million of capital funding. This call is open to staff of UK institutions who are eligible to receive funding from UK Research and Innovation (UKRI) as well as Public Sector Research Establishments (PSREs). Multi-institution applications are permitted.

Applicants interested in applying to this call must complete the intention to submit form on the call website by 16:00 on 15 January 2019. This information will primarily be used to manage potential conflicts when selecting the panel. Applicants will receive an email from UK Research and Innovation (UKRI) by 16:00 on Friday 18 January 2019 confirming our expectation that they will submit a full proposal. Full proposals must be submitted by 16:00 on 12 February 2019 and will be assessed directly by an interdisciplinary expert peer review panel from across the physics and life sciences communities.

We envisage high demand for funding, therefore we strongly discourage the premature submission of proposals which may benefit from further development in anticipation of the second Physics of Life call, which will be of a similar scale.

OpenPlant researcher characterises pathway for active chemical in catnip

News article below has been copied with permission from the John Innes Centre website. The original article can be found here.

Benjamin R. Lichman, Mohamed O. Kamileen, Gabriel R. Titchiner, Gerhard Saalbach, Clare E. M. Stevenson, David M. Lawson & Sarah E. O’Connor. Uncoupled activation and cyclization in catmint reductive terpenoid biosynthesis. Nature Chemical Biologyvolume 15, pages71–79 (2019)


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Researchers at John Innes Centre have shed light on how catnip – also known as catmint – produces the chemical that sends cats into a state of wanton abandon.

The remarkable effect catnip has on cats is well known thanks to the scores on online videos showing pets enjoying its intoxicating highs.

The substance that triggers this state of feline ecstasy is called nepetalactone, a type of chemical called a terpene. This simple, small molecule is part of an unusual chain of events, not previously seen by chemists.

The researchers believe that understanding the production of these nepetalactones could help them recreate the way that plants synthesise other chemicals like vinblastine, which is used for chemotherapy. This could lead to the ability to create these useful medicines more efficiently and quickly than we are currently able to harvest them from nature.

Usually in plants, for example peppermint, terpenes are formed by a single enzyme. In their paper published online this week in Nature Chemical Biology, the researchers report that in catnip terpenes are formed in a two-step process; an enzyme activates a precursor compound which is then grabbed by a second enzyme to produce the substance of interest.

This two-step process has previously never been observed, and the researchers also expect something similar is occurring in the synthesis of anti-cancer drugs vincristine and vinblastine from Madagascan periwinkle, Catharanthus roseus, and elsewhere in olive and snapdragon.

In the publication, the team describe the process by which catmint produces nepetalactone in microscopic glands on the underside of its leaves. The study also identifies three new enzymes with unusual activity.

Dr Benjamin Lichman, who conducted the work while a post-doc at John Innes Centre and who is now a lecturer at the University of York, says: “We have made significant progress in understanding how catnip makes nepetalactones, the chemicals that sends cats crazy. Catnip is performing unusual and unique chemical processes, and we plan to use these to help us create useful compounds that can be used in treatment of diseases such as cancer. We are also working to understand the evolution of catnip to understand how it came to produce the cat-active chemicals.”

Professor Sarah O’Connor, project leader at the John Innes Centre, says: “Nepetalactones have potential use in agriculture as they participate in certain plant-insect interactions. In future work we will explore the roles that these compounds have in plants.”

This research is funded by National Science Foundation Grant #1444499 and the UK Biotechnological and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC) joint-funded OpenPlant Synthetic Biology Research Centre (BB/L014130/1).

[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

[Closes 15 Jan 2019] Postdoctoral researcher post in bioinformatics and computational protein design

Job number: ACAD103712

Division/School: School of Chemistry

Contract type: Open Ended

Working pattern: Full time

Salary: £33,199 - £42,036 per annum

Closing date for applications: 15-Jan-2019

>>> Apply here <<<

A 2-year, BBSRC/EPSRC-funded, postdoctoral position is available to develop bioinformatics and computational tools for protein analysis and design. The post is in the protein design laboratory of Prof Dek Woolfson (Chemistry and Biochemistry, Bristol; https://woolfsonlab.wordpress.com/).

The post has two aspects: The first project involves the development of computational tools (bioinformatics and virtual reality (VR)) to facilitate in silico protein design. This is in collaboration with Dr Dave Glowacki (Chemistry and Computer Science, Bristol). Protein designs will be tested experimentally in the Woolfson lab. The second project involves the construction of a database for collating and interrogating atomic structures of protein-protein interactions (PPIs). This is in collaboration with Prof Andy Wilson (Chemistry, Leeds). This work will underpin experimental studies across the POPPI consortium of academic and industrial researchers (https://poppi.website/).

The protein-design work builds on the Woolfson group’s expertise in computational and experimental protein design. See: Thomson et al. (2014) Science 346, 485-488, DOI:10.1126/science.1257452; and Wood et al. (2017) Bioinformatics 33, 3043–3050, DOI:10.1093/bioinformatics/btx352. The aim is to combine this with expertise in VR and machine learning in the Glowacki group to create accessible, user-friendly tools for protein design. See: O’Connor et al. (2018) Science Advances 4, DOI: 10.1126/sciadv.aat2731.

The work on protein-protein interactions will contribute to an on-going computational and experimental effort to understand PPIs better. This understanding will be exploited in the design of peptide and small-molecule inhibitors of PPIs important to fundamental cellular processes and implicated in disease. See: Fletcher et al. (2018) Chem Sci 9, 7656-7665, DOI:10.1039/C8SC02643B. The aim is to generate a searchable database of PPIs of use to informaticians and experimentalists to interrogate and exploit PPIs.

The position is best suited to a talented and ambitious researcher with an interest in applying bioinformatics and computational biochemistry to protein science. Essential skills for this post include: an ability to program fluently in one or more computer languages, and ideally in Python; and experience with applications of bioinformatics, databases, or computer science in biochemistry or chemistry, and ideally in protein science. Desirable skills include: experience with computational protein design, databases for protein-structure analysis, molecular modelling in virtual reality environments, and in machine learning methods applied to protein science.

For informal enquiries, please contact: d.n.woolfson@bristol.ac.uk

The closing date for applications is Tuesday 15th January 2019.

We appreciate and value difference, seeking to attract, develop and retain a diverse mix of talented people that will contribute to the overall success of Bristol and help maintain our position as one of the world’s leading universities.

[Closes 14 Feb 2019] Four senior/lectureship posts available in Biological Sciences at Bristol University

Job number: ACAD103726

Division/School: School of Biological Sciences

Contract type: Open Ended

Working pattern: Full time

Salary: £43,267 - £51,630 per annum

Closing date for applications: 14-Feb-2019

>>> Apply here <<<

The School of Biological Sciences seeks four new academics at lecturer or senior lecturer level. Successful applicants will be research leaders with proven international track records commensurate with experience. They will drive influential research programmes that span the long-standing research strengths of the School: behavioural ecology and sensory biology, ecology and environmental change, evolutionary biology and plant and agricultural science.

Successful applicants will have strong interdisciplinary research portfolios and evidence of academic leadership along with strong commitment and aptitude for teaching at undergraduate and postgraduate level and roles across the spectrum of academic life.

A good fit to existing University Research Institutes and the Faculty of Life Sciences would also be an advantage.

For informal enquiries please contact Prof Claire Grierson (headofschool-biology@bristol.ac.uk).

The closing date for applications is 11:59pm on Thursday 14th February 2019. It is anticipated that interviews will be held during week commencing 1st April 2019.

[Close 18 Jan 2019] Two postdoc positions on AI and SynBio in Edinburgh Genome Foundry

The Edinburgh Genome foundry are looking for two post-doctoral researchers to work with the School of Engineering at the University of Edinburgh.

Research Associate in Mammalian Synthetic Biology

Closing Date: 18-Jan-2019

>>> Apply here <<<

Vacancy Ref: #046305

Contact Person: Dr Filippo Menolascina (Filippo.Menolascina@ed.ac.uk)

A 3 year, fixed term postdoctoral appointment is available within the School of Engineering at the University of Edinburgh to work on the automatic (re)design of synthetic promoters, primarily for mammalian cells, focusing on the control Chimeric Antigen Receptors expression.

As part of this project, the successful candidate will develop a microfluidics-based platform to perform high-throughput cell screening and will liaise with the Edinburgh Genome Foundry to build, and automatically model, large libraries of synthetic inducible promoters.

They will combine machine learning and computational optimisation to predict promoter strength, leakiness and automatically optimise promoter design to meet set specifications (e.g. maximise fold induction, minimise response time). They will also build a promoter to maximise sensitivity/specificity of transgene expression.

The ideal candidate should have a PhD with a background in Engineering or Computer Science and previous experience with techniques/protocols in Cell Biology and Microscopy. Experience with microfluidic device fabrication is desirable.

Research Associate in Microbial Synthetic Biology

Closing Date: 18-Jan-2019

>>> Apply here <<<

Vacancy Ref: #046306

Contact Person: Dr Filippo Menolascina (Filippo.Menolascina@ed.ac.uk)

A 2 year, fixed term postdoctoral appointment is available within the School of Engineering at the University of Edinburgh to work on the automatic engineering of synthetic microbial promoters.

As part of this project, the successful candidate will develop a microfluidics-based platform to perform high-throughput cell screening and will liaise with the Edinburgh Genome Foundry to build, and automatically model, large libraries of synthetic inducible promoters.

They will combine machine learning and computational optimisation to predict promoter strength, leakiness and automatically optimise promoter design to meet set specifications (e.g. maximise fold induction, minimise response time). They will also build a promoter to maximise sensitivity/specificity of transgene expression.

The ideal candidate should have a PhD with a background in Engineering or Computer Science and previous experience with techniques/protocols in Cell Biology and Microscopy. Experience with microfluidic device fabrication is desirable.

Loop assembly: a simple and open system for recursive fabrication of DNA circuits

A new DNA assembly method has been developed by the Haseloff lab in Cambridge, in collaboration with the Patron lab at the Earlham Institute in Norwich and Fernan Federici in Chile. The method provides a simple solution for working with standardised DNA parts, e.g. those developed with the type IIS common syntax, and the system is openly shared under the OpenMTA.

Pollak B, Cerda A, Delmans M, Álamos S, Moyano T, West A, Gutiérrez RA, Patron N, Federici F, Haseloff J. Loop assembly: a simple and open system for recursive fabrication of DNA circuits. New Phytol. 2018 Dec 6. doi: 10.1111/nph.15625.

Abstract

High efficiency methods for DNA assembly have enabled routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customisation, elaborate vector sets or serial manipulations for the different stages of assembly. We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardised level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly enables efficient and versatile DNA fabrication for plant transformation. We show construction of plasmids up to 16 genes and 38 Kb with high efficiency (>80%). We have characterized Loop assembly on over 200 different DNA constructs and validated the fidelity of the method by high-throughput Illumina plasmid sequencing. Our method provides a simple generalised solution for DNA construction with standardised parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.

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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.

Birth of a Photosynthetic Chassis: Microalga Chlamydomonas reinhardtii

An European collaboration that has included researchers in the OpenPlant labs of Prof. David Baulcombe, Prof. Alison Smith and Prof. Jim Haseloff has resulted in the publication of a key paper in ACS Synthetic Biology aiming to establish Chlamydomonas reinhardtii as a chassis for synthetic biology. As part of this effort, the authors have developed and characterised 119 openly distributed genetic parts.

Full Text

Crozet P, Navarro FJ, Willmund F, Mehrshahi P, Bakowski K, Lauersen KJ, Pérez-Pérez ME, Auroy P, Gorchs Rovira A, Sauret-Gueto S, Niemeyer J, Spaniol B, Theis J, Trösch R, Westrich LD, Vavitsas K, Baier T, Hübner W, de Carpentier F, Cassarini M, Danon A, Henri J, Marchand CH, de Mia M, Sarkissian K, Baulcombe DC, Peltier G, Crespo JL, Kruse O, Jensen PE, Schroda M, Smith AG, Lemaire SD. Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii. ACS Synth Biol. 2018 Sep 21;7(9):2074-2086. doi: 10.1021/acssynbio.8b00251.

Abstract

Microalgae are regarded as promising organisms to develop innovative concepts based on their photosynthetic capacity that offers more sustainable production than heterotrophic hosts. However, to realize their potential as green cell factories, a major challenge is to make microalgae easier to engineer. A promising approach for rapid and predictable genetic manipulation is to use standardized synthetic biology tools and workflows. To this end we have developed a Modular Cloning toolkit for the green microalga Chlamydomonas reinhardtii. It is based on Golden Gate cloning with standard syntax, and comprises 119 openly distributed genetic parts, most of which have been functionally validated in several strains. It contains promoters, UTRs, terminators, tags, reporters, antibiotic resistance genes, and introns cloned in various positions to allow maximum modularity. The toolkit enables rapid building of engineered cells for both fundamental research and algal biotechnology. This work will make Chlamydomonas the next chassis for sustainable synthetic biology.

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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

Visual method for triterpene production in Nicotiana benthamiana

OpenPlant post-doc Michael Stephenson in Prof. Anne Osbourn’s lab at the John Innes Centre, has starred in a video supporting a protocols paper in the Journal of Visual Experimentation:


Abstract

The triterpenes are one of the largest and most structurally diverse families of plant natural products. Many triterpene derivatives have been shown to possess medicinally relevant biological activity. However, thus far this potential has not translated into a plethora of triterpene-derived drugs in the clinic. This is arguably (at least partially) a consequence of limited practical synthetic access to this class of compound, a problem that can stifle the exploration of structure-activity relationships and development of lead candidates by traditional medicinal chemistry workflows. Despite their immense diversity, triterpenes are all derived from a single linear precursor, 2,3-oxidosqualene. Transient heterologous expression of biosynthetic enzymes in N. benthamiana can divert endogenous supplies of 2,3-oxidosqualene towards the production of new high-value triterpene products that are not naturally produced by this host. Agro-infiltration is an efficient and simple means of achieving transient expression in N. benthamiana. The process involves infiltration of plant leaves with a suspension of Agrobacterium tumefaciens carrying the expression construct(s) of interest. Co-infiltration of an additional A. tumefaciens strain carrying an expression construct encoding an enzyme that boosts precursor supply significantly increases yields. After a period of five days, the infiltrated leaf material can be harvested and processed to extract and isolate the resulting triterpene product(s). This is a process that is linearly and reliably scalable, simply by increasing the number of plants used in the experiment. Herein is described a protocol for rapid preparative-scale production of triterpenes utilizing this plant-based platform. The protocol utilizes an easily replicable vacuum infiltration apparatus, which allows the simultaneous infiltration of up to four plants, enabling batch-wise infiltration of hundreds of plants in a short period of time.

Stephenson MJ, Reed J, Brouwer B, Osbourn A. Transient Expression in Nicotiana Benthamiana Leaves for Triterpene Production at a Preparative Scale. J Vis Exp. 2018 Aug 16;(138). doi: 10.3791/58169.