Developing a frugal and medium throughput method for assessing protein-DNA binding affinity

What are we doing?

Project collaborators Dr Susana Sauret-Gueto and Dr Eftychios Frangedakis, from the University of Cambridge.

Project collaborators Dr Susana Sauret-Gueto and Dr Eftychios Frangedakis, from the University of Cambridge.

We live in an era in which we can thoroughly investigate all the genetic material that makes up an organism, at the level of the whole genome. Understanding gene regulation, the set of processes that control the decoding of DNA, is an essential part of modern synthetic biology. Although the expression of a gene can be regulated at different levels, transcription is one of the most important steps in this complex multistage process. Transcription is the process of creating messenger sequences, known as RNA, which allow the translation machinery of the cell to build proteins according to the DNA instructions. The efficiency of transcription determines of how much of these messenger RNAs are produced.

Transcription is triggered by a collection of functional proteins known as transcription factors (TFs), which bind onto the DNA sequence in front of the part of the gene that encodes a protein (the coding sequence). This section of DNA is called the promoter. Previous research has demonstrated that the strength of a binding event between a TF and the part of a DNA sequence in the promoter that it can ‘recognise’, is pivotal in affecting the transcription of the associated gene. The strength of this binding event between a TF and its binding site (TFBS) is referred to as binding affinity. Our OpenPlant funded project, based at the Earlham Institute and the University of Cambridge, is focused of finding out how much variation in binding affinity exists in nature, and subsequently creating synthetic promoters with varying binding affinities. We aim to develop a new method to test how variation in TFBS sequence might affect binding affinity. With the knowledge gained, we can then build promoter sequences that activate transcription at the level we design, in the place in a plant we want.

Methods of assessing the binding affinity of TFs and DNA sequences already exist, but have limited scope for asking questions such as ours, either due to low throughput or high cost. One such method, which has been established for decades, is the Electrophoretic Mobility Shift Assay (EMSA). EMSA is based on visualising the travel of the bound TF-DNA complex through a jelly like matrix, or gel. Because each sequence and TF have to be made, and then individually ‘run’ through the EMSA gel, this method is difficult to scale up.

Figure 1: Comparing current protein-DNA binding assays.

Figure 1: Comparing current protein-DNA binding assays.

Another option for testing the binding affinity of TFBS is based on a high-density DNA chip, also known as DNA microarray. This is essentially a glass slide with hundreds of thousands of short DNA sequences attached to the surface. The TF of interest can be synthesised in the lab and then hybridised with the chip. Hybridisation is just letting the binding between TF and TFBS occur as is would in the cell and, following this, the amount of TF bound on to each DNA sequence can be detected. However, the process of creating and reading such a chip is expensive and needs specific devices (Figure 1).

The aim of our work is to design and test a methodology which overcomes the shortcomings of available methods for testing TF binding affinity. Our goal is to provide a medium-throughput test of binding affinity, and we are designing our methodology to be easily replicable using affordable, readily available components. Approaching the problem from both synthetic and evolutionary backgrounds, we want to be able to test a range of binding sites for affinity, with enough replication to validate hypotheses. To do this we have developed the transcription factor relative affinity measurement pipeline (TRAMP).

Where did the ideas come from?

Inspired by the design of the DNA chip-based methods described above, we set out to design a method for assessing TF-DNA binding with as high a throughput as possible, whilst avoiding the high cost and specific requirements of the chip-based assay. We use a simple and cheap commercially available product to immobilise DNA onto the widely available lab workhorse; the 96-well plate. We have also used a recently developed method to tag our TF protein with a small peptide that, when bound to another peptide, gives off a signal. This signal is detectable in a plate reader, a piece of equipment widely used in modern labs. This new method allows us to easily quantify the amount of TF binding at a given TFBS, by measuring the brightness of the glow given off by the cumulative amount of the signal. These two components have allowed us to create a biochemical method of assaying protein-DNA binding affinity (Figure 2).

Figure 2: Assaying protein-DNA binding affinity using the transcription factor relative affinity measurement pipeline (TRAMP)

Figure 2: Assaying protein-DNA binding affinity using the transcription factor relative affinity measurement pipeline (TRAMP)

To maximise the efficiency of selecting TFBS to test in the assay we are designing, we have developed a novel computational tool. This allows us to leverage naturally occurring genetic variation in TFBS sequences gathered from publicly available population wide datasets. Instead of assaying thousands of random DNA sequences before finding a desirable one, we use several analytical methods to categorise natural variation along several parameters. We have been able to use a computational approximation of the binding event itself to score potential affinity. We also model the shape of the DNA double helix where the TFBS lies, allowing us to investigate the role of this physical property of DNA that has been suggested to be important in the efficiency of binding events.

These methods allow us to rapidly generate a set of suggested TFBS that should exhibit a range of binding affinities. This set of TFBS can be passed into the plate-based assay to be tested, and the findings used to test and further develop our understanding of binding affinity.

 

Where can this assay be applied?

We think that our work will be of interest to a wide range of biologists looking to understand the role of TF binding affinity in gene regulation. We hope by using TRAMP, we can find DNA sequences that exhibit different binding affinities to their corresponding TFs. Our aim is to be able to then replace the native TFBS in a promoter with the sequences we discover. We will use this approach to validate our findings, by linking the predictions and lab assays we have conducted back to transcription, the biological function we are interested in understanding.

It is our hope that our synthetic promoters will allow us to alter the activity of the promoter, meaning that when transcription occurs, the target gene will generate a different amount of messenger-RNA. If we can do this, we think our work will help scientists who want to use very specific gene expression patterns as part of synthetic biology strategies to synthesise valuable compounds like medicines. Our pipeline could also be useful for testing the effect of variation in TFBS between individuals, populations, or species.

By Dr Yaomin Cai and Dr Will Nash, Postdoctoral researchers at the Earlham Institute.

www.earlham.ac.uk

@EarlhamInst

[Closes 28th April 2019] Biomaker Challenge Africa Coordinator (Fixed Term), Department of Plant Science, University of Cambridge.

 The Global Challenges Research Fund is supporting a pump-priming programme to take the Biomaker Challenge to centres in Africa. Biomaker is an interdisciplinary programme that brings together multiple teams to build low-cost sensor devices and instruments for biology (https://www.biomaker.org). The Biomaker Africa programme is co-organised by the Synthetic Biology Strategic Research Initiative, the BBSRC-EPSRC OpenPlant, Centre for Global Equality, and OpenBioeconomy Lab in Cambridge. We are looking for a Challenge Coordinator for 12 weeks during May-Jul 2019 to take responsibility for coordinating participating teams and managing online communications and social media. This includes organising and publicising events and highlighting interesting projects online through writing and multimedia presentations, coordinating training and connecting teams who might be able to share knowledge and skills.


The appointee will form part of a team to deliver:

  • A set of informational and training materials for biologists, engineers and interested public (e.g. the Maker community)

  • Blog posts, photos, videos and social media content about Biomaker Africa

The position will provide an opportunity to travel to sites in Africa to help organise starter and training events, and to build a wide range of contacts in this area.


Skills gained include:

  • Coordination, planning and organisation

  • Networking skills between academia and industry, including sponsor liaison

  • Communications including writing, photography, video production and social media

  • Public speaking and presentations

  • Introduction to technologies such as 3D-printing, electronics and DIY approaches to scientific instrumentation

The placement would suit someone with an interest in electronics, biology, and maker technologies e.g. 3D printing. Experience in other coordination and communication roles (paid or voluntary) is desirable. 

For full job description.

For enquiries, please email Alexandra Ting at synbio@hermes.cam.ac.uk.

To apply, send a covering letter explaining your interests and suitability for the role and a CV to synbio@hermes.cam.ac.uk

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

The next call for OpenPlant Fund applications is announced!

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

A summary of the important dates can be found below:

Call Opens: Monday 8 April

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

Call closes: Monday 13 May

Challenge Begins: Friday 24 May

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

Challenge Closes/Open Technology Workshop: Saturday 2 November

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Cambridge Science Festival

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

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

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

Students recieve CRISPR training thanks to OpenPlant-funded project.

Thanks to the support of OpenPlant 4K fund, summer student Nandor Hegyi (University of Aberdeen) and final year undergraduate student Darius Zarrabian (University of Cambridge) received hands-on CRISPR training from Dr Gonzalo Mendoza Ochoa in the lab of Alison Smith (Cambridge).

 

Host species  Chlamydomonas reinhardtii

Host species Chlamydomonas reinhardtii

The OpenPlant-funded project entitled “Site-directed integration of transgenes into the nuclear genome of algae and plants using CRISPR/Cpf1/ssDNA” aimed to solve drawbacks associated with current methods for nuclear transformation, which results in random integration of transgenic DNA. The plan was to firstly develop the method for the green alga and biotech host Chlamydomonas reinhardtii, and then try to adapt this specific method for land plants and compare it with similar methods being developed.

 

The students quickly learned that research can present unexpected challenges. Nonetheless, they remained determined to tackle the problem! Having achieved half of the tasks of the project, Nandor returned to Aberdeen to continue his degree with the thought “I wish I would have had more time to work on this interesting project”. Darius came to the rescue soon after and, with equal enthusiasm, took up where Nandor left off. He is currently in the final stage of his final year research project and is gathering data that indicate that single-stranded DNA fixes nuclease-induced DNA cuts (via homologous recombination) better than exogenous double-stranded DNA.

 

Darius’s words “I have really enjoyed making progress with the project and learning about CRISPR, despite the inevitable multitude of 96-well plates I have had to face!” capture both the joy and hard work of scientific research.

 

We thank again OpenPlant for the support and will be sharing progress in the near future.

By Dr Gonzalo Mendoza (University of Cambridge)

New OpenPlant Programme Manager at the John Innes Centre in Norwich

Hi all,

Dieuwertje van der Does, OpenPlant Programme Manager

Dieuwertje van der Does, OpenPlant Programme Manager

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

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

The 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

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

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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.

DwO0r8nWsAEjfqo.jpg

 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)


catnip - no rights.jpg

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