Cambridge Consultant Synthetic Biology PhD Studentship

Cambridge Consultants is building an exciting new business in biotechnology, particularly synthetic biology. They’re working to bring together biology, chemistry and engineering to design and build engineered biological systems. As part of this mission, they're looking for a bright, motivated PhD student to join the team on an internship.

No deadline has been given but the advert was posted in Aug 2017.

With a strong background in biochemistry or molecular biology, the successful applicant will work alongside our scientists and engineers to apply their scientific skills and knowledge to our synthetic biology projects.  They’ll learn how new technology is applied in a business context and the challenges this presents.  

This is a three-month internship with flexible timing.

More information >>

[Closes 1 Sep 2017] Plant Synthetic Biology Assistant/Associate Professor (University of Nebraska)

Plant Synthetic Biology Assistant/Associate Professor The University of Nebraska-Lincoln (UNL) is committed to conducting world-class research in plant biochemistry and has recently secured a $20 million Experimental Program to Stimulate Competitive Research (EPSCoR) Grant from the NSF to establish the Center for Root and Rhizobiome Innovation (CRRI). Reflecting the institutional commitment to building infrastructure in plant biochemistry, UNL is seeking applicants for nine-month (academic year) tenure-leading Assistant Professor or Associate Professor faculty position (80% research and 20% teaching) in the Department of Biochemistry and the Center for Plant Science Innovation.

They will address the development and application of synthetic biology tools to address questions central to plant biology that contribute to crop productivity and/or quality.

Required qualifications include a PhD or equivalent in biochemistry, biology, molecular biology, plant physiology or related field; a minimum of two years of postdoctoral experience; and a strong record of original research as evidenced by peer- reviewed publications. For Assistant Professor, the incumbent is expected to develop an internationally recognized research program that attracts federal, commodity, international foundation, and/or industry funding leading to research results published in refereed scientific journals and presented at professional meetings. Applicants at the Associate Professor levels must have an externally supported research program and/or sufficient private sector experience, with publication, patent, and presentation outcomes demonstrating sustained and recognized research productivity. The incumbent will broadly address the development of synthetic biology tools, which may include but are not limited to those involving genome editing, gene stacking, and/or RNA-based control of gene expression and apply these tools for studies of photosynthesis, central carbon metabolism, specialized metabolism or other biochemical or biological processes that lead to improved crop germplasm. The ability to apply computational methods for use of large data sets in synthetic biology tool development is also desired. The university offers state of the art proteomics and metabolomics core facilities in the Center for Biotechnology and high-speed computing resources in the Holland Computing Center. Extensive field facilities, state-of-the-art image-based phenotyping instrumentation, breeding resources, and crop transformation core capacity are available to support translational research. This position is part of the Institute of Agriculture and Natural Resources initiative in Stress Biology, which offers a highly collaborative environment to develop focused research programs linked with modern biochemical methodologies, metabolic engineering, metabolomics, genomics, and computational approaches. A competitive start-up package and appropriate laboratory and office space will be offered.

The incumbent will contribute to the teaching mission of the College of Agricultural Sciences and Natural Resources and in particular will develop and teach undergraduate and graduate courses in the biochemistry core curriculum. It is expected that the incumbent will contribute to recruitment, retention and placement activities; incorporation of outcomes assessment; engagement in instructional improvement; mentoring undergraduate and graduate students; and serve on department, college, and UNL committees as appropriate.

To learn more about the University of Nebraska, the Department of Biochemistry and the Center for Plant Science Innovation see http://biochem.unl.edu ; http://www.unl.edu/psi/ .

How to Apply

To view details of the position and make application, go to http://employment.unl.edu Search for position F_170058. Click on “Apply to this job.”

Postdoctoral Research Fellow on engineering synthetic phage (Jaramillo Lab, Warwick University)

The goal of the Jaramillo lab is to achieve proof of concept for synthetic phages within the next 3 years. By working at the interface of molecular biology, combinatorial optimisation, microfluidics, directed evolution and 3D printing it is hoped that reaching this goal will accelerate more synthetic biology research globally thus enhancing our ability to combat diseases of the future.

There is no closing date listed, but the advert was posted in Aug 2017

From Warwick University:

“Superbugs…these are our babies…now they have body piercings and anger” - House, TV Show

According to the World Health Organisation antibiotic resistance is one of the biggest threats to global health, food security, and development today. The prevalent use of modern antibiotics over the last century has led to a bacterial arms race with increasingly potent infections proving more difficult to treat as each year passes. As the efficacy of our current armoury of antibiotics wanes, hospital stays lengthen, medical costs rise and without urgent action we will soon enter a post-antibiotic world where common infections will kill once again. While there are some new antibiotics in development, none of them are expected to be effective against the most dangerous forms of antibiotic-resistant bacteria of the future.

Is there a possible response that could safeguard humanity? Professor Alfonso Jaramillo thinks so and his lab at the University of Warwick is working hard to provide such a solution. It is a multidisciplinary lab that develops novel automated methodologies for design optimisation using computers, viruses or living cells for use in Phage Therapy. The ambition is the eventual development of synthetic phages, powerful antimicrobials which if their work proves successful will herald a new age in the fight against bacterium. Progress of the lab since 2013 has been steady with the foundations already laid of new technologies (computational and experimental) for the engineering of biomolecules. The key current focus is on the creation of automated algorithms that enable directed evolution in support of the difficult design phase of Synthetic Biology, by developing a general methodology for the de novo engineering of synthetic RNA parts and circuits it is hoped they will work robustly as targeted in a given cellular context.

The goal of the lab is to achieve proof of concept within the next 3 years. By working at the interface of molecular biology, combinatorial optimisation, microfluidics, directed evolution and 3D printing it is hoped that reaching this goal will accelerate more synthetic biology research globally thus enhancing our ability to combat diseases of the future.

This is where you come in, as a Postdoctoral Research Fellow we need your expertise to help build the lab’s research capability. You will form part of a high profile international team with labs in Warwick and ISSB in France. Your contribution to the lab’s body of knowledge in support of the goal of reaching proof of concept will have a direct impact on one of the most urgent health threats facing humanity.

More information >> [PDF] 

[Closes 22 Aug 2017] Research Associate position on open hardware for science (University of Bath)

From University of Bath:

Open source hardware could bring about a step change in science and medicine, by making high quality instruments more widely available and easier to customise. We are looking for a talented researcher with (or soon to be awarded) a PhD in Physics, Engineering, or a related discipline, to work as part of the "Open Lab Instrumentation" project that includes the Universities of Bath and Cambridge as well as our partners STICLab in Tanzania.

Salary: Starting from £32,004, rising to £38,183
Placed On: Monday 24 July 2017
Closing Date: Tuesday 22 August 2017
Interview Date: To be confirmed
Reference: SF5079

This project will enable high quality open-source instrumentation, by characterising and improving the mechanical properties of 3D printed mechanisms, then using these optimised structures, together with readily available electronic and optical components, as building blocks for microscopes, spectrometers, micromanipulators and more. Our first open instrument, the OpenFlexure Microscope, has already been reproduced by a number of groups, and tested in applications from malaria diagnostics to water quality monitoring.

You will build an understanding of how the small-scale structure of 3D printed parts (the "toolpath") affects their properties, then use this understanding to create improved toolpaths that result in stronger or more flexible parts.  This will involve both simulations and lab-based measurements, as well as adapting open-source software tools to generate the optimised toolpaths.  You will then go on to create designs for instrumentation using those optimisations, as well as contributing to software tools that allow others to do the same.  Good programming skills are essential, and experience in instrumentation design, mechanical simulation, and/or 3D printing is highly desirable.   As our goal is open-source hardware, we will contribute to various open source projects as well as starting new ones, and experience of open or collaborative development of either software or hardware would be particularly valuable.

You will be based within the Centre for Photonics and Photonic Materials in the Department of Physics.  This post is funded by an EPSRC project that is part of the Global Challenges Research Fund, announced by the UK Government to support cutting-edge research that addresses the challenges faced by developing countries.  In keeping with the international remit of this funding, there will be opportunities to travel to meet our Tanzanian partners, and to work with the end-users of our new instruments. 

Physics at the University of Bath is a research-led Department, ranked highly in the UK in the latest Research Excellence Framework, and the University recently attained a Gold rating in the Teaching Excellence Framework. Both the Department and the University are committed to providing a supportive and inclusive working environment, with an active Athena Swan programme and opportunities for researchers to receive training, mentorship, and career development.

Informal enquiries are encouraged, and should be directed to Dr. Richard Bowman (r.w.bowman@bath.ac.uk). 

More information >>

UK SynBio Start-Up Survey published showing thriving East of England ecosystem

SynbiCITE have published the first survey of the UK synthetic biology start-up ecosystem, highlighting the changing sources of innovation and entrepreneurship at work in the sector from a macro-level perspective.

The report covers activity between 2000 and 2016 in research and development, technology transfer, industrial sectors, financing and investors. Its key finding were:

  • The UK produced more than 146 synthetic biology start-ups between 2000 and 2016.
  • More than half (54%) of new start-ups are tech transfer start- ups,
  • Synthetic biology start-up activity is concentrated in the South-East, East of England and London (67%). With Oxford, Cambridge and London Universities producing a cluster of activity nucleating in and around London. 
  • Synthetic biology start-up companies have raised over £620m of public (£56m) and private (£564m) investment in the UK since 2010. 

Dr. Stephen Chambers, CEO of SynbiCITE, commented that “Confirming the arrival of a new innovation ecosystem demands evidence: proof that variables ranging from investment, pipeline infrastructure, to talent and education are established and stable. We believe the industry has reached a critical mass of companies, showing a healthy churn of attrition and creation. Roughly 76% of all the start-ups founded in the survey period are still active and with the continuation of an effective national strategy in the future, this ecosystem will undoubtedly thrive, creating jobs and wealth while sustaining the UK’s leading role in the field.”

East of England emerged as the region with the highest number of synthetic biology start-ups after London, with spin-offs concentrated around the OpenPlant partner locations of Cambridge and Norwich. 

Read More >>

Download Report [PDF, 4MB]

 

Plant Science SAW projects at Tunstead primary School

Guest blog from Emma McKechnie-Welsch, a PhD student from the John Innes Centre who spent three months doing an internship in Science Engagement with OpenPlant and the SAW Trust.

 

Plant Science SAW projects at Tunstead primary School

Arabidopsis apical meristem. Image by Emma McKechnie-Welsch

Arabidopsis apical meristem. Image by Emma McKechnie-Welsch

My name is Emma and I am a PhD student working in the Cell and Developmental Biology department at the John Innes Centre. My research looks at genes functioning to facilitate controlled plant growth and development from the shoot apical meristem in Professor Robert Sablowski’s research group. My PhD funding from the BBSRC includes a three month work placement and I was keen to gain experience in science communication and outreach so arranged a joint placement with OpenPlant and the SAW trust.

On my placement I had the opportunity to design two SAW projects to discuss science relevant to my research with primary school children at Tunstead primary school. For the year 1/2 class I worked with writer Julia Webb and artist Lara Nicole and the aim was to get children thinking about the functions of different parts of a plant. For the year 5/6 class I was worked with writer Mike O’Driscoll and artist Chris Hann with a day themed around plant evolution.

 

We used scientific images at the start of the day to catalyse inquisitiveness about the science we were going to explore, and provide inspiration for the poetry and art sessions.

 

Practical Science with Year 1/2

Build a plant game, played with year 1/2 class

Build a plant game, played with year 1/2 class

To start off the lesson we played a “build a plant” game to get more familiar with the main parts of a plant, their function, and what plants use from their environment to grow. Each child also put a cut flower in coloured water to think about the use of the stem. Then the children were given a selection of fruit and vegetables and asked to decide what part of the plant each came from. They were given a flower to look more closely at the reproductive parts and think about how seeds are formed by pollination. Finally, they looked at different types of seeds in a seed kit and we discussed the different types of seed dispersal tactics plants use.

 

Practical Science with Year 5/6

The children dissected plants to look up close at the reproductive parts under the microscope.

The children dissected plants to look up close at the reproductive parts under the microscope.

We began by guessing the number of different plant species on earth and the children suggested why plants are useful. In groups, they were given cards representing each component of photosynthesis and had to arrange them to think about the process. We covered pollination and its importance for increasing genetic variation.

The children dissected plants to look up close at the reproductive parts under the microscope. I covered different types of seed dispersal and the importance of varying environmental conditions for evolution. Then children carried out DNA extraction from strawberries after learning a bit about what DNA was and how important it was in controlling the appearance of the plant, with a single mutation in a gene coding region potentially greatly changing this. Following on from DNA extraction there was a game to match the numbers of genes to different organisms.

 

 

After the morning science sessions the children had poetry and art sessions based on the content. Here are some poems and images from the Year 5/6 group (age 10/11):

Poem 1.png
Yr 6 art work.jpg
Poem 1.png

 

The Year 1/2 children (age 4/5) wrote poems as if they were a seed growing up, and made flower hand puppets after designing a flower:

sock puppets.jpg

The children really engaged with the scientific learning aspect of the day which was great. Lots of the children thought about the questions I asked to the classes and gave insightful answers, as well as wanting to ask questions throughout the lesson/ activities. When asked about their favourite part of the day, at least half the children listed specific sections of the science morning.

The poems produced by the year 5/6 children really showcased the children’s interest in understanding genetics and how growth and development of organisms are controlled. The younger children were enthusiastic about looking at different types of seeds, bringing back different types they had found in their school grounds at break time to show me. It was great for them to think about the different stages of growth a plant goes through from seed to eventually producing a flower, including difficulties different environmental conditions could cause, while writing their poems.

The children were really excited about getting to do an afternoon of art although the activities designed weren’t quite as expected. The art didn’t centre around drawing on paper but producing 3D art pieces. The younger children gave lots of personality to their individual hand puppets and used them to help communicate their poetry whilst the older children focused on the scientific pictures provided and gave interpretations of pollen and seed dispersal, as well as the protective mechanism of the cactus.

From this experience, I could see how integration of science with writing and art can help children associate science more closely with creative thought, rather than a regimented, inflexible learning process, which makes the subject inaccessible to some children. The teachers were impressed with the pieces the children managed to produce and the level of thought about scientific processes they reached, which I think was largely down to the different approach to education SAW days take.

[Closes 31 Aug 2017] Call for Fellows at CRI Research

Information from the website of the Centre Recherches Interdisciplinaires (CRI): https://cri-paris.org 

The CRI collaboratory is recruiting fellows to join their adventure. They are inviting applications for three types of fellows: short (3-6 months), long (1-3 years) and core (5 years): https://cri-paris.org/research/call-for-fellows/


The CRI is broadening its research activities, creating a collaboratory at the crossroads across the life, learning, and digital sciences.

We are developing an open, collaborative research program to tackle the world’s health and education challenges, focusing on the following broad topics, amenable to bridge foundational research and societal impact:

  • Open health – from data-rich research to development of frugal software and hardware solutions.
  • Open learning – from understanding learning to human-machine paradigms
  • Open synthetic and systems biology – from foundational understanding of living systems to open biotech and open pharma solutions.
  • Open transitions – from tracing past major transitions to understanding and shaping current digital transition.
  • Open phronesis – tackling ethical challenges of our time.

The Collaboratory will host short (3-6 months), long (1-3 years) and core (5 years) research fellows alongside with their affiliated postdocs and PhD students. They will be accompanied by associate faculty members from France and abroad that will take part in the selection and mentoring the incoming fellows and students. Anyone capable of carrying an autonomous research project, from young graduates to established researchers (including sabbaticals) is eligible to apply to become a CRI Research Fellow.  We expect a gradual recruitment build-up to reach a 60-70 strong cohort within our dedicated building at the historical heart of Paris (the Marais) that will open its doors within a year. This 6500m2 building will include state-of-the-art wet lab space, makerspace, pedagogic facilities and studio apartments for young researchers.

[Closes 9 Aug 2017] DNA Foundry, Science and Technology Lead

Applications are invited for a DNA Foundry, Science and Technology Lead to join the Engineering Biology Group at the Earlham Institute. Using start-of-the-art laboratory automation and synthetic biology approaches, the Foundry has automated nanoscale pipelines for (i) part-based assembly and bacterial transformation, (ii) quality control of assemblies and (iii) delivery of constructs to chassis organisms. The mission of the Foundry is to bring these capabilities to bear on research in academia and industry. The post holder will establish and manage synthetic biology workflows at the Earlham DNA Foundry. This will include working with automation specialists and technical assistants to develop and execute protocols in DNA assembly, biosynthesis and genome engineering. In addition, they will engage and communicate with researchers in academia and industry to promote the mission of the Earlham Foundry and to establish and develop new collaborations. The ideal candidate will possess a PhD in Molecular Biology, Biotechnology, Synthetic Biology or a related subject. They will have an in depth understanding of molecular biology laboratory techniques and experience of collaborating with internal and external stakeholders on large scale projects. They must possess excellent communication and interpersonal skills. This position is open to applicant of all nationalities.

All applications must be made through the portal link: http://www.earlham.ac.uk/dna-foundry-science-and-technology-lead

Contact: nicola.patron@earlham.ac.uk

OpenPlant and the OpenMTA feature in 'Learning by Sharing' at SB 7.0

Prof Jim Haseloff, Dr Nicola Patron and BioBricks Foundation Legal Director Dr Linda Kahl who pioneers the OpenMTA initiative with which OpenPlant is collaborating, all presented in the 'Learning by Sharing' session at SB 7.0 in Singapore, 13-16 June 2017.

The videos of all talks are now online at the BioBricks Vimeo site.

Prof Jim Haseloff (Director, OpenPlant at University of Cambridge)

Dr Nicola Patron (Earlham Institute)

Dr Linda Kahl (BioBricks Foundation)

OpenPlant researchers advance a translational synthetic biology platform for rapid access to new drug-like molecules

Researchers in Prof Anne Osbourn's lab at the John Innes Centre, including Prof Osbourn and OpenPlant PDRA Dr Michael Stephenson, have published a new paper detailing their advances in rapidly creating and purifying gram-scale quantities of natural products that were previously not possible to synthesise. This has the potential to reinvigorate drug discovery pipelines by opening up whole regions of chemical diversity for testing and production of potentially medicinally important molecules.

OAlogo.png

Reed, J., Stephenson, M.J., Miettinen, K., Brouwer, B., Leveau, A., Brett, P., Goss, R.J., Goossens, A., O’Connell, M.A. and Osbourn, A., 2017. A translational synthetic biology platform for rapid access to gram-scale quantities of novel drug-like moleculesMetabolic Engineering. DOI: 10.1016/j.ymben.2017.06.012

Fig 2 from paper: Generation of gram quantities of triterpene using vacuum infiltration a, Vacuum infiltration of N. benthamiana plants. Plants are retained by a bespoke holder, inverted into a bath containing 10 L of A. tumefaciens suspension, and a vacuum applied. Upon release of the vacuum the infiltration process is complete. b, GFP expression in leaves from a vacuum-infiltrated plant 5 days after infiltration (leaves arranged from top left to bottom right in descending order of their height on the plant). The youngest leaves (top left) were formed post-infiltration. c, β-Amyrin purified from vacuum-infiltrated plants following transient expression.

Fig 2 from paper: Generation of gram quantities of triterpene using vacuum infiltration a, Vacuum infiltration of N. benthamiana plants. Plants are retained by a bespoke holder, inverted into a bath containing 10 L of A. tumefaciens suspension, and a vacuum applied. Upon release of the vacuum the infiltration process is complete. b, GFP expression in leaves from a vacuum-infiltrated plant 5 days after infiltration (leaves arranged from top left to bottom right in descending order of their height on the plant). The youngest leaves (top left) were formed post-infiltration. c, β-Amyrin purified from vacuum-infiltrated plants following transient expression.

Abstract

Plants are an excellent source of drug leads. However availability is limited by access to source species, low abundance and recalcitrance to chemical synthesis. Although plant genomics is yielding a wealth of genes for natural product biosynthesis, the translation of this genetic information into small molecules for evaluation as drug leads represents a major bottleneck. For example, the yeast platform for artemisinic acid production is estimated to have taken >150 person years to develop. Here we demonstrate the power of plant transient transfection technology for rapid, scalable biosynthesis and isolation of triterpenes, one of the largest and most structurally diverse families of plant natural products. Using pathway engineering and improved agro-infiltration methodology we are able to generate gram-scale quantities of purified triterpene in just a few weeks. In contrast to heterologous expression in microbes, this system does not depend on re-engineering of the host. We next exploit agro-infection for quick and easy combinatorial biosynthesis without the need for generation of multi-gene constructs, so affording an easy entrée to suites of molecules, some new-to-nature, that are recalcitrant to chemical synthesis. We use this platform to purify a suite of bespoke triterpene analogs and demonstrate differences in anti-proliferative and anti-inflammatory activity in bioassays, providing proof of concept of this system for accessing and evaluating medicinally important bioactives. Together with new genome mining algorithms for plant pathway discovery and advances in plant synthetic biology, this advance provides new routes to synthesize and access previously inaccessible natural products and analogs and has the potential to reinvigorate drug discovery pipelines.

 

 

Twenty-nine Biomaker Challenge projects funded plus extra deadline for proposals - 21 July 2017

Twenty-nine Biomaker Challenge projects were funded by the SRI, OpenPlant and CamBridgSens covering a huge range of biology and engineering tasks from cell-free synthetic biology to clinical devices to lab automation solutions. Due to late interest, we have added a later deadline of 21 July.

Starting in this summer for the first time, the Biomaker Challenge is a four-month programme challenging interdisciplinary teams to build low-cost sensors and instruments for biology. From colorimeters to microfluidics and beyond, we were looking for frugal, open source and DIY approaches to biological experiments and we found them! The proposals contained a rich set of interdisciplinary project ideas from across the University of Cambridge and Norwich Research Park, with many external collaborators from local industry, the Royal College of Art and further afield.

 The 29 awardees have now been announced (see full list below) and will shortly be documented on GitHub and the Biomaker.org website, where some proposals are already online.

Biomaker Challenge Coordinator Kyata Chihbalabala has recently joined the SRI for ten weeks to manage the programme and arrange training and meetups. The Biomaker Toolkits are now being distributed so watch this space for events coming soon!

Apply by 21 July for Biomaker Challenge Round Two!

Due to a rush of late interest, we have decided to open another round. You still have an opportunity to apply for a Biomaker Toolkit (worth £250) and £750 additional support for your biological instrumentation project.

Find out more about how to apply >>

Acknowledgements

Judging Panel: Dr Emre Ozer (ARM Ltd), Dr Stephanie Reichel (CRUK Cambridge Institute), Dr Dan MacLean (Earlham Institute), Prof Jim Haseloff (Department of Plant Sciences, University of Cambridge), Dr Alexandre Kabla (Engineering Department, University of Cambridge), Dr Oliver Hadeler (Chemical Engineering and Biotechnology, University of Cambridge).

Sponsors: ARM Ltd, New England Biolabs

 

The Funded Projects

  1. A cell-free sensor platform for the quantification of arsenic concentrations in drinking water.
  2. A Device for Real-Time Monitoring of Protein Synthesis.
  3. A low cost reusable microfluidic device for the detection of antibiotic resistant genes in bacteria isolated from patient samples.
  4. A low cost, point-of- care device to measure blood haemoglobin levels, using calorimetry and infrared spectroscopy.
  5. A low-cost colorimeter for accurate detection of colour changes in medical diagnostic tests
  6. A low-cost, pressurized liquid chromatography system for protein purification
  7. A microdroplet incubator to establish 3D organoids cultures from oesophageal adenocarcinoma.
  8. A sensor to improve the accuracy of stereotactic brain biopsies for the diagnosis of brain tumours
  9. An artificial habitat to investigate Boquila trifoliata mimicry
  10. Cheap Do-It- Yourself Small Volume UV Spectrometer for Nucleic Acid and Protein Quantitation
  11. Detecting alterations in ionic concentrations associated with different cellular states
  12. Detecting pathogens in sewage sludge
  13. Developing a self-regulating control system for intravenous drug administration -- using aminoglycosides as an example
  14. Development of an anti-TFF3 functionalized surface to capture of Barrett’s oesophagus cells
  15. DIY bioacoustics
  16. Field portable colorimeter
  17. Functional membrane-based integrated biosensing devices for detection and quantitation of specific nucleic acids and other biomolecules
  18. Handheld syringe pump with heating element
  19. KNOW-FLOW: A low-cost programmable blood flow system
  20. Low Cost Wearable Sensors Strain Sensors for illness identification via Gait, Posture and muscle usage
  21. Low-Cost Multispectral Imagery for UAV-based Vegetation Monitoring
  22. Macrophotography of fern gametophytes using a DIY focus stacking system.
  23. Microfluidic Turntable for molecular diagnostic testing
  24. OptoFlow: Optical flow rate measurement for microfluidics
  25. Puzzle-solving Bacterial Pet: Imaging Platform for Microfluidics-based Reinforced Learning with Motile Bacterial Cells
  26. Remote Environment Controller for Experiments in Extreme Environments
  27. Sci-Fi Cam
  28. Ultrasonic Plant Height System for High- Throughput Plant Phenotyping
  29. Real-Time monitoring of cell proliferation

 

Biomaker Challenge is sponsored by BBSRC/EPSRC through OpenPlant Synthetic Biology Research Centre (www.openplant.org) and the University of Cambridge Research Policy Committee through the Synthetic Biology Strategic Research Initiative (www.synbio.cam.ac.uk) and the Sensors Strategic Research Network (www.sensors.cam.ac.uk).

Call for abstracts for SynBio UK 2017

SynBio UK conference will showcase UK Synthetic Biology research and to create a focal point for the community, embracing its diversity and fostering its growth and engagement. Submit your abstract to the scientific programme now.

The UK is a world leader in science and engineering, and Synthetic Biology has been identified as an important area for our continued success. Key to that success is a cohesive, vibrant and multidisciplinary community, open to collaboration, open to advances, supportive of young talent, and driven to exceptional research with meaningful outcomes.

Synthetic Biology UK is a conference for the UK synthetic biology community and we look forward to seeing a good cohort from the Cambridge Synthetic Biology community attending!

SynBio UK 2017 is hosted by the Manchester SynBio Research Centre, SYNBIOCHEM, which specialises in synthetic biology for fine and speciality chemicals production.

Abstracts must be submitted by Monday 25 September 2017. Oral communication slots are available at this meeting. 

SPEAKERS INCLUDE

  • Anil Wipat (Newcastle University, United Kingdom)
  • Jason Chin (MRC Laboratory of Molecular Biology, United Kingdom)
  • Jens Nielsen (Chalmers University of Technology, Sweden)
  • Luke Alphey (Pirbright, United Kingdom)
  • Perdita Barran (University of Manchester, United Kingdom

[Closes 14 July 2017] Postdoctoral Researcher - Single Cell Genomics

Job Vacancy: Postdoctoral Researcher to lead the development of next-gen sequencing tech to analyse single cells

The Macaulay Group at the Earlham Institute (formerly TGAC) is looking for an enthusiastic Postdoctoral Researcher to lead the development and implementation of next generation sequencing technologies to analyse single cells. This is an exciting opportunity to work on a BBSRC-funded project to explore transcriptional and epigenetic heterogeneity in individual haematopoietic stem and progenitor cells.

More details and application here

My OpenPlant Experience: Outreach, Engagement and 3D printing

Guest blog post by Roger Castells-Graells about his OpenPlant Fund project “Accessible 3D Models of Molecules”. Roger recently won a UEA Engagement Award in recognition of the work he has done both with OpenPlant and beyond.

 

PhD student Roger Castells-Graells in the lab

PhD student Roger Castells-Graells in the lab

My name is Roger and I am a PhD student in Prof. George Lomonossoff’s lab at the John Innes Centre in Norwich. My research project is about the production of virus-like particles to understand viral dynamics for future applications and to generate new bionanotechnological tools. I have a passion for science communication and public engagement and I have had numerous opportunities to communicate my science in Norwich, the UK and abroad since the start of my PhD.

My OpenPlant experience started in September 2016, when I attended a great Co-Lab workshop organized by the Open Science School and funded by an OpenPlant Fund. With this opportunity I had the chance to interact with scientists from different fields and also with designers and artists. It was an enriching experience and we developed a project called VRICKS (Virus Bricks) that aimed to generate tools to explain viruses in educational ways, like for example with paper models.

Following up from this workshop, in October 2016, I organized an activity for the Norwich Science Festival, together with Jenni Rant (The SAW Trust) and Colette Matthewman (OpenPlant), where we recreated the assembly of proteins into a virus protein coat using materials like paper and plastic, which represented the subunits of the virus. The public contributed to the assembly of a virus model, they learnt about related research from the Lomonossoff lab and they took home a build-at-home model. Over one hundred people participated in the activity during the weekend, making it a roaring success.

Presenting the virus activity and engaging with people at the Norwich Science Festival

Presenting the virus activity and engaging with people at the Norwich Science Festival

Following up with the interest to build tools to explain biological processes, such as virus assembly, I decided to apply for and OpenPlant Fund with the project “Accessible 3D Models of Molecules”. The project team is a multidisciplinary team (molecular biology, bioinformatics and engineering) of students from JIC and University of Cambridge and with this fund we are developing models of viruses and proteins using 3D printing technologies.

3D printed virus models for the OpenPlant Fund project

3D printed virus models for the OpenPlant Fund project

Recently I presented some of the virus models in a high school with students aged 12 to 16 years old. The students enjoyed being able to handle and compare representations of real virus structures and were amazed that some of these structures were only discovered this year. When the school teacher was asked about how the use of educational 3D models in the classroom could benefit the learning process he answered that first of all it creates excitement and focuses the attention of the students. It is something completely new! It contributes to the understanding of three-dimensional models and gives the students a better sense of the reality of the object. Furthermore, it allows the students to calculate scale as it is possible to touch, measure and compare different models.

I was invited to speak at the Pint of Science Festival in Norwich in May, and gave a talk entitled “20000 Leagues under the microscope: Viruses & Nanomachines”. At the event, I passed around several models of 3D printed viruses and the public loved having the opportunity to handle them. It was a great experience and we received really positive feedback. I want to thank the organizers of Pint of Science for such a great event!

As a result of all of these activities, I was recently awarded a UEA Engagement Award 2016/17 for contribution to Public & Community Engagement, which I am very proud of.

    Norwich Pint of Science Festival tweets

 

 

Norwich Pint of Science Festival tweets

Roger tweets2b.png

With thanks to my supervisor Prof. George Lomonossoff, OpenPlant and all the people that have helped, encouraged me and opened up opportunities in this last year.

[Closes 30 June 2017] Apply now for the OpenPlant Fund

The OpenPlant Fund is now open to proposals for innovative, open and interdisciplinary projects relevant to plant or in vitro Synthetic Biology. Projects run for six months and can include biological research, hardware prototyping, software, outreach and policy work.

Each project will receive up to £5k, with up to £4k up front and an additional £1k for follow-on and outreach after reporting. PhD students and postdocs are particularly encouraged to apply and external collaborators are welcome. 

The aim of the fund is to promote the development of plant Synthetic Biology as an interdisciplinary field and to facilitate exchange between the University of Cambridge, the John Innes Centre, and the Earlham Institute for the development of open technologies and responsible innovation in the context of Synthetic Biology.

More information can be found here: https://www.openplant.org/openplant-fund/

Cell-free technology startup founded by former OpenPlant Fellow awarded funding by RebelBio.

Cell-Free Tech is a brand new start up company specialising in giving people the ability to do biological research, without the need for expensive tools and infrastructure. Based at the Microbiology Department of the University College Cork, Cell-free Tech is part of RebelBio, an accelerator programme that helps life sciences innovators, academics, biomakers and citizen scientists to change the world with biology.

Former OpenPlant Fellow Thomas Meany has helped found an exciting new startup company based on making cell-free technology more accessible. Meany founded the startup this year in collaboration with Ian McDermott (Chief Scientific Officer Cell-Free Tech), and together they have been awarded funding from the accelerator programme RebelBio and SOSV (a venture capital and investment management firm)to take cell-free technology out of the lab and into the world.

Originally a physicist by trade, Meany undertook a OpenPlant/Wellcome Trust ISSF Interdisciplinary Fellowship, co-supervised in the Haseloff and Hall groups (Department of Plant Sciences and Department of Chemical Engineering and Biotechnology respectively), where he applied his computing and engineering skills to the field of synthetic biology. It was through his involvement in the SynBio SRI activities around cell-free systems, such as our recent workshop ‘Programmable biology in the test tube’, that he realised the potential of cell free systems to provide exciting and simple tools with which to do biological research.

In vitro or cell-free synthetic biology uses cell extracts rather than whole cells, programming them with DNA to produce chemicals or encode logic circuits that respond to their environment. The technology can be used to create vital biomolecules like insulin, or to generate stunning coloured, glow in the dark proteins. Since it doesn’t involve genetic engineering or extensive resources, cell-free technology can be used without the need for expensive facilities or infrastructure. Meany became increasingly fascinated by the concept: “I just loved the idea of doing biology anywhere, being able to make and create things with biology on a tabletop is fascinating.”

It was around this time Meany collaborated with SRI Steering Committee Member Helene Steiner (Royal College of Art and Microsoft Research Cambridge) on a series of cell-free workshops for the Royal College of Art (RCA) Biodesign Challenge,  aimed at making synthetic biology tools accessible to art and design students. It was through these events it became clear there was a great deal of interest in cell-free systems among the public. However, a recurring problem was that there was little scope for people to get involved, due to the lack of availability of affordable tools. Meany realised the potential for providing cheap, effective materials and after meeting Ian McDermott, a biochemist with experience in founding a business startup, they realised they think the same way. “Biology today is like computing in the late 1980s, simply awaiting an explosion of innovation. Technologies are developing faster than ever but some key platform technologies are still missing. People need to be able to access biology at an affordable price, in their own homes or workplaces and without enormous infrastructure” - explained Meany.

After communicating their vision to Bill Liao (Founder of RebelBio and SOSV investment partner) during a RebelBio conference, it was clear that their passion for cell-free technology was shared. Meany and McDermott left their University roles and with investment from RebelBio and SOSV, the team have set about producing the first publicly available low cost bio-prototyping kit at large scale, while directly reaching consumers through active market research. The kits will include a collection of 50 tubes containing individual cell-free extract alongside a set of plasmids that can be added to the extracts to produce colours, fluorescence and odours. Meany hopes universities, students, designers and makers or hobbyists from all backgrounds will be interested. “We are building the platform technology that will allow innovators from all backgrounds to engineer the materials of the future. Our hope is that the community will build on our initial projects to create and share amazing ideas of their own. We want to see biosensors, paper diagnostics and open-source insulin produced using our kits!” - Meany.

If you would like to contact Cell-free Tech to find out more or to get involved, please get in touch. They are eager to work with members of the Cambridge synthetic biology community. For more information on Cell-Free Tech, please click here.

If you are interested in learning more about cell-free technology, the SynBio SRI is currently running a series of events in this area, such as the OpenPlant Forum, OpenPlant Fund, and training workshops. For more information about these initiatives and upcoming events, please click here.

How an open approach to patents could help build a sustainable future

This article by Dr Lecturer in Technology and Innovation Management at the University of Cambridge was originally published at The Conversation on 15 May 2017, licensed under CC-BY-ND 4.0. See the original article here and in The Independent.

Dr Tietze is a co-convenor with the SynBio SRI and OpenPlant of an upcoming CRASSH Faculty Research Group on Open IP in emerging technologies.

File 20170510 21623 1y5wofm Nadezda Murmakova/Shutterstock

To sustain a population of 9.7 billion people by 2050 the world is going to need innovations that make careful use of the available resources, human and environmental. Key industry sectors such as energy, water, agriculture and transport are already under pressure to move to more sustainable methods of production and consumption. However, there are barriers in the way. The Conversation

One of these lies in how the world manages the creation and ownership of inventions and ideas. A protectionist approach to intellectual property is designed to protect and prolong the lifecycle of existing technologies, and allow innovators to capture the profits from their creations. In a paper published with colleagues from universities in Germany and India, we examined how this also makes it harder for new and more sustainable technologies to be developed and adopted. That explains why there are now other approaches being used to move key sectors to more sustainable systems and end this status quo.

Electric car manufacturer Tesla, has been doing just that. Tesla CEO Elon Musk “shocked” the world in 2014 when he announced that his company was joining the open source movement and giving away its patents for free.

It is important to understand the rationale here. Why would a company that had worked so hard to develop and protect its technology from its global car manufacturer competitors suddenly give its technology away for free?

Switching track

Tesla initially developed a patent portfolio to protect its technology. However, Tesla’s concern that it would be overwhelmed once established car makers ramped up their production of electric cars never came to pass.

Instead, it saw the electric car market stagnate at less than 1% of total vehicle sales. So Tesla changed its strategy from trying to prevent others from building electric cars to trying to encourage them into the market.

Part of the reasoning here is that if more electric cars are built, then more battery recharging stations will be built too. This would make electric cars become more visible, and a more conventional choice. Tesla believes that an open intellectual property strategy can strengthen rather than diminish its position by building the size of the electric car market, and as a result, build its own share of the total automotive market.

This kind of careful management of intellectual property at company level, supported by policy-level awareness, can be a powerful way to support the same kinds of transitions to more sustainable technologies in other industries too.

Power companies need to adapt. Chiu Ho-yang/Flickr, CC BY-NC-SA

Energy supply faces an array of difficulties: the depletion of natural resources; air pollution and greenhouse gas emissions; nuclear risks; and security of supply. The water supply sector is restricted by water scarcity, pollutants, extreme environmental events such as flooding and costs associated with supplying water to communities in poor countries and remote communities. The agri-food sector, meanwhile, is under pressure to sustainably produce more food and to address malnutrition in poor countries.

For these industries to navigate a path around these problems, new knowledge and the innovations that follow will be essential. And in knowledge economies, intellectual property can either be an enabler or an inhibitor.

Taking the medicine

If the ownership of intellectual property is fragmented in an industry, it can slow down technology innovation and uptake, such as in the electronics industry where multiple players own complementary patents. However, firms can instead open up their innovation processes and move away from jealously guarded, internal cultures, where intellectual property is used to protect and prolong lifecycles. This change may see knowledge sharing that leads to accelerated innovation cycles and a more rapid uptake of sustainable alternatives throughout a sector: just what Tesla was hoping for in electric vehicles.

This approach to intellectual property, so-called “open IP”, is well advanced and mature in the software industry and healthcare. It has given access to life-saving medicines to millions of people, particularly in developing countries through patent pools, such as the Medicine Patent Pool. This kind of project relies on multinational pharmaceutical companies sharing their intellectual property, but small companies can also play a strategic roles in creating these new, more sustainable systems, and it’s not all about open IP.

Plumpy'Nut is handed out in Kenya. DFID /Flickr, CC BY

As progress in technology is cumulative, there will always be phases of “closed IP” for small companies to build up their portfolio. This can also be a strategy designed to make a social impact. Take Nutriset, which manufacturers food for famine relief. It protects both its invention, Plumpy’Nut, and its entire business model by patents. Plumpy’Nut is a peanut-based paste for the treatment of severe malnutrition and can be administered at home rather than through a supervised hospital treatment. As a result it can treat more patients.

Nutriset says that it uses patents to enable the development of local production plants for Plumpy’Nut and to protect those in emerging nations from being taken over by global manufacturing sites in more developed countries. The local production of Plumpy’Nut helps with creating skills and employment in the regions where Nutriset’s product is most needed.

An open approach to intellectual property has clear advantages in popularising and establishing new and widespread sustainable technologies, but there is a rationale in some cases for sticking to the more traditional approach. The trick now is to discover when and where different sectors and innovators deploy each strategy. The grand open IP gestures in the mould of Tesla can force through rapid structural advances; a small peanut paste supplier shows that patent protection can still help put the building blocks in place.

Frank Tietze, Lecturer in Technology and Innovation Management, University of Cambridge

This article was originally published on The Conversation. Read the original article.

[Closes 6 Jul 2017] DST-NRF Fellowships for UK Early Career Researchers - Synthetic Biology Opportunities in South Africa

This Newton Fund opportunity allows early career UK researchers to spend 3-6 months working with a South African research group.

The SynBio SRI has a network of researchers in South Africa with whom we can connect interested researchers and an invitation from Dr Karl Rumbold at the University of the Witwatersrand, Johannesburg for Fellows who might like to join lab and/or field-based projects including synthetic biology and biocatalysis.

Find out more about the call here >>

Contact us on synbio@hermes.cam.ac.uk if you are interested and would like help making connections in South Africa.

[Closes 21 June 2017] OpenPlant PDRA researching regulatory elements of cyanobacteria

Applications are invited for a Postdoctoral Research Associate position in Prof Christopher Howe's lab as part of the Cambridge OpenPlant Synthetic Biology Centre. OpenPlant is a joint initiative between the University of Cambridge, John Innes Centre, the Sainsbury Laboratory and the Earlham Institute, funded by BBSRC and EPSRC.

This position is aimed at identifying regulatory elements of cyanobacterial genes enabling control of gene expression in response to environmental electrical potential. Prof Howe's group has pioneered the development of 'biophotovoltaic' systems (McCormick et al. (2015) Energy & Environmental Science 8:1092) for the generation of electrical power from photosynthetic microorganisms. This post will analyse the transcriptional responses of cyanobacteria in biophotovoltaic devices.

Experience in the molecular biology of cyanobacteria, and in recombinant DNA techniques applied to microorganisms is essential. A PhD in a relevant subject is essential. Experience of electrochemistry is desirable, but not essential.

The appointee needs to be able to take up the post by 1 Sept 2017.

Fixed-term: The funds for this post are available for 24 months in the first instance.

For more information and to apply see the jobs.cam.ac.uk listing >>