[Closes 5 Jan 2018] Two post-doctoral fellowships in plant synthetic biology at Colorado State University

The Antunes and Medford Research groups at Colorado State University are looking for two (2) post-doctoral fellows to work on a new plant synthetic biology project to produce useful, living biomaterials

 A Ph.D. in plant molecular biology, cell biology, synthetic biology or a related field is required. Ideal applicants will have experience in molecular biology, plant cell biology and gene cloning. Experience in synthetic biology, design of synthetic genes and gene circuits, and basic mathematical modeling is desired; however, strong candidates without experience in one of these areas may be considered. Experience in moss culture and transformation is valued. Experience with transgenic plants is helpful but not essential.

Well-developed skills in written and verbal communication are desirable. The incumbents are expected to interact with other post-docs, graduate students, lab technicians and undergraduate students in a positive and professional manner.

Duties include applying a variety of molecular biology techniques, gene expression studies, synthetic gene construction, production and analysis of transgenic plants, planning experimental approaches based on research literature, and interpreting results. The successful individuals will be self-motivated and capable of independent thought and research.

More information and to apply >>

Deadline is January 05, 2018.

Report highlights opportunities and risks associated with synthetic biology and bioengineering

Human genome editing, 3D-printed replacement organs and artificial photosynthesis – the field of bioengineering offers great promise for tackling the major challenges that face our society. But as a new article out today highlights, these developments provide both opportunities and risks in the short and long term.

Rapid developments in the field of synthetic biology and its associated tools and methods, including more widely available gene editing techniques, have substantially increased our capabilities for bioengineering – the application of principles and techniques from engineering to biological systems, often with the goal of addressing 'real-world' problems.

In a feature article published in the open access journal eLife, an international team of experts led by Dr Bonnie Wintle and Dr Christian R. Boehm from the Centre for the Study of Existential Risk at the University of Cambridge, capture perspectives of industry, innovators, scholars, and the security community in the UK and US on what they view as the major emerging issues in the field. The participants included several OpenPlant researchers and members of the management team.

Dr Wintle says: “The growth of the bio-based economy offers the promise of addressing global environmental and societal challenges, but as our paper shows, it can also present new kinds of challenges and risks. The sector needs to proceed with caution to ensure we can reap the benefits safely and securely.”

The report is intended as a summary and launching point for policy makers across a range of sectors to further explore those issues that may be relevant to them.

Among the issues highlighted by the report as being most relevant over the next five years are:

Artificial photosynthesis and carbon capture for producing biofuels

If technical hurdles can be overcome, such developments might contribute to the future adoption of carbon capture systems, and provide sustainable sources of commodity chemicals and fuel.  

Enhanced photosynthesis for agricultural productivity

Synthetic biology may hold the key to increasing yields on currently farmed land – and hence helping address food security – by enhancing photosynthesis and reducing pre-harvest losses, as well as reducing post-harvest and post-consumer waste.

Synthetic gene drives

Gene drives promote the inheritance of preferred genetic traits throughout a species, for example to prevent malaria-transmitting mosquitoes from breeding. However, this technology raises questions about whether it may alter ecosystems, potentially even creating niches where a new disease-carrying species or new disease organism may take hold.

Human genome editing

Genome engineering technologies such as CRISPR/Cas9 offer the possibility to improve human lifespans and health. However, their implementation poses major ethical dilemmas. It is feasible that individuals or states with the financial and technological means may elect to provide strategic advantages to future generations.

Defence agency research in biological engineering

The areas of synthetic biology in which some defence agencies invest raise the risk of ‘dual-use’. For example, one programme intends to use insects to disseminate engineered plant viruses that confer traits to the target plants they feed on, with the aim of protecting crops from potential plant pathogens – but such technologies could plausibly also be used by others to harm targets.

In the next five to ten years, the authors identified areas of interest including:

Regenerative medicine: 3D printing body parts and tissue engineering

While this technology will undoubtedly ease suffering caused by traumatic injuries and a myriad of illnesses, reversing the decay associated with age is still fraught with ethical, social and economic concerns. Healthcare systems would rapidly become overburdened by the cost of replenishing body parts of citizens as they age and could lead new socioeconomic classes, as only those who can pay for such care themselves can extend their healthy years.

Microbiome-based therapies

The human microbiome is implicated in a large number of human disorders, from Parkinson’s to colon cancer, as well as metabolic conditions such as obesity and type 2 diabetes. Synthetic biology approaches could greatly accelerate the development of more effective microbiota-based therapeutics. However, there is a risk that DNA from genetically engineered microbes may spread to other microbiota in the human microbiome or into the wider environment.

Intersection of information security and bio-automation

Advancements in automation technology combined with faster and more reliable engineering techniques have resulted in the emergence of robotic 'cloud labs' where digital information is transformed into DNA then expressed in some target organisms. This opens the possibility of new kinds of information security threats, which could include tampering with digital DNA sequences leading to the production of harmful organisms, and sabotaging vaccine and drug production through attacks on critical DNA sequence databases or equipment.

Over the longer term, issues identified include:

New makers disrupt pharmaceutical markets

Community bio-labs and entrepreneurial startups are customizing and sharing methods and tools for biological experiments and engineering. Combined with open business models and open source technologies, this could herald opportunities for manufacturing therapies tailored to regional diseases that multinational pharmaceutical companies might not find profitable. But this raises concerns around the potential disruption of existing manufacturing markets and raw material supply chains as well as fears about inadequate regulation, less rigorous product quality control and misuse.

Platform technologies to address emerging disease pandemics

Emerging infectious diseases—such as recent Ebola and Zika virus disease outbreaks—and potential biological weapons attacks require scalable, flexible diagnosis and treatment. New technologies could enable the rapid identification and development of vaccine candidates, and plant-based antibody production systems.

Shifting ownership models in biotechnology

The rise of off-patent, generic tools and the lowering of technical barriers for engineering biology has the potential to help those in low-resource settings, benefit from developing a sustainable bioeconomy based on local needs and priorities, particularly where new advances are made open for others to build on.

Dr Jenny Molloy comments: “One theme that emerged repeatedly was that of inequality of access to the technology and its benefits. The rise of open source, off-patent tools could enable widespread sharing of knowledge within the biological engineering field and increase access to benefits for those in developing countries.”

Professor Johnathan Napier from Rothamsted Research adds: “The challenges embodied in the Sustainable Development Goals will require all manner of ideas and innovations to deliver significant outcomes. In agriculture, we are on the cusp of new paradigms for how and what we grow, and where. Demonstrating the fairness and usefulness of such approaches is crucial to ensure public acceptance and also to delivering impact in a meaningful way.”

Dr Christian R. Boehm concludes: “As these technologies emerge and develop, we must ensure public trust and acceptance. People may be willing to accept some of the benefits, such as the shift in ownership away from big business and towards more open science, and the ability to address problems that disproportionately affect the developing world, such as food security and disease. But proceeding without the appropriate safety precautions and societal consensus—whatever the public health benefits—could damage the field for many years to come.”

The research was made possible by the Centre for the Study of Existential Risk, the Synthetic Biology Strategic Research Initiative (both at the University of Cambridge), and the Future of Humanity Institute (University of Oxford). It was based on a workshop co-funded by the Templeton World Charity Foundation and the European Research Council under the European Union’s Horizon 2020 research and innovation programme. 

Reference
Wintle, BC, Boehm, CR et al. A transatlantic perspective on 20 emerging issues in biological engineering. eLife; 14 Nov 2017; DOI: 10.7554/eLife.30247

Link to original piece on University News

Hear OpenPlant Coordinator Dr Jenny Molloy discuss the work on BBC Radio 4 'Inside Science' 

The text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

Image Credit: Reaching for the Sky
Susanne Nilsson

Open technology and democratisation of synthetic biology features on BBC Radio 4 'Inside Science'

The OpenPlant Cambridge Coordinator Dr Jenny Molloy appeared on BBC Radio 4's 'Inside Science' last week following the publication of a bioengineering horizon scanning exercise co-organised by the Centre for the Study of Existential Risk and SynBio SRI, (both University of Cambridge) and the Future of Humanity Institute (University of Oxford) in Dec 2016.

In an interview with host Adam Rutherford, Jenny discussed the potential democratised future of synthetic biology and the importance of open tools and technologies for engineering biology, such as those generated by OpenPlant and the SRI's activities such as the Biomaker Challenge.

Topics covered included the ways in which synthetic biology is getting cheaper, faster and more distributed with increasing activity within institutions and education but also in community labs like Cambridge's Biomakespace. Changing ownership models in biotechnology was highlighted in the horizon scan as a long term trend that is likely to be a major issue in the next 15 years; it can potentially lead to greater equity in access to technology for public benefit but democratisation also raises questions of responsible governance and regulation. Jenny pointed to the work of the Woodrow Wilson Centre in demonstrating that the DIY biology community are typically very proactive in self-governance and drawing up community codes of ethics and engaging with law enforcement and regulators.

You can download or take a listen to the episode online. The synthetic biology segment starts at 14 min.

More information on the biological engineering horizon scan >>

Wintle, Bonnie C., Christian R. Boehm, Catherine Rhodes, Jennifer C. Molloy, Piers Millett, Laura Adam, Rainer Breitling et al. "A transatlantic perspective on 20 emerging issues in biological engineering." eLife 6 (2017).

[Closes 31 Dec 2017] Applications for the 2018 EUSynBioS Steering Committee are now open !

EUSynBioS is a community for students and postdocs in European synthetic biology. Applications to join their 2018 Steering Committee are now open until 31 December 2017, where you can help facilitate horizontal connections across the synthetic biology community and convene joint events with fellow communities around the globe.

Christian Boehm, who recently completed his PhD at the University of Cambridge is the current EUSynBioS Chair and sends this message:

"Dear EUSynBioS community,

As you know, this initiative is run entirely by dedicated students and postdocs keen to make a difference in European synthetic biology. Over the previous year, we have had a fantastic group of people on the Steering Committee: they have amplified our social media presence, represented our voice in the UN Convention on Biological Diversity's discussions on synthetic biology, organised the EUSynBioS Social in Manchester and of course our EUSynBioS Symposium at CNB-CSIC Madrid.
The fourth year of EUSynBioS shall facilitate horizontal connections across the community, further strengthen our interface to industry, and bring about more joint events with fellow communities around the globe.

Do these challenges sound appealing to you ?
Do you have an idea which would really make a difference to the community ?
Do you have what it takes to be a leader in European synthetic biology ?

Then be a part of the 2018 EUSynBioS Steering Committee!
Applications are now open until 31. December 2017. We will be in touch with you soon thereafter, and aim to announce our 2018 Steering Committee in early January."

More information and to apply >>

Technology for development and design for co-creation workshops

The Cambridge Global Challenges Initiative is running the following events for post-graduates and early career researchers in the New Year and a Global Challenges Round Table on 8th December. Book now to secure your place!

Global Challenges Round Table - 8th December

GCI will run Round Tables twice a year to give Cambridge researchers the opportunity to talk about research relating to the UN Sustainable Development Goals (SDGs). The programme of the December 2017 edition, which includes data-driven modelling of airborne diseases, digital design for development aid and innovative bacterial testing, has been shared. You are still very welcome to register to participate in the discussions that will follow the short talks and/or to share research projects to be presented in forthcoming editions of the Round Tables. 

Co-creation for Global Challenges

The following events are part of the focus of Global Challenges Initiative in facilitating the dialogue and co-creation between Cambridge researchers and end-users in the developing world. 

• • Workshop on User-Centred Design in Developing World Contexts – 10th January (application deadline: 15th December). This workshop will introduce the principles of user-centred design and explore the specific challenges and opportunities that commonly arise when using this approach to co-create innovative responses to global challenges. The workshop is open to post-graduates and early career researchers, from different research backgrounds, interested in user-centred design for the benefit of the bottom half of the world’s population. To apply please send a CV (max. 2 pages) and a letter of motivation outlining your interest and how you hope to apply learnings from the workshop to Sophie Mower (sophie.mower@centreforglobalequality.org). 

• Masterclass in Design Methods for Global Challenges – 11th January. This Masterclass will explore the similarities and differences between particular disciplinary approaches to co-creation with end-users in developing world contexts. One-to-one discussions between expert practitioners from different disciplinary and practitioner communities and established Cambridge researchers in fields within the EPSRC remit will be organized. To register for the event, please complete the online form.

Please note that a Technology for Development Graduate Sandpit – 15th January (application deadline: 11th December), aimed at Graduate students and Early Career Researchers, will take place after these two co-creation-oriented events. Winning teams of the competition sandpit will be awarded bursaries to undertake field trips to develop and test their ideas in real developing world situations. Please apply by completing the application form and submitting a CV (max. 2 pages) to winton@phy.cam.ac.uk.

[Closes Dec 2017] Eligo Bioscience seeking synthetic biologist and related positions

Eligo Bioscience are recruiting a new cohort of amazing scientists and executives to work with us on one of the most exciting synthetic biology-based drug-development platforms. To build the next generation of targeted drugs, they are looking for the most talented microbiologists, genome architects, bioengineers, and DNA hackers to join one of their R&D teams

Eligo Bioscience are recruiting a new cohort of amazing scientists and executives to work with us on one of the most exciting synthetic biology-based drug-development platforms. To build the next generation of targeted drugs, they are looking for the most talented microbiologists, genome architects, bioengineers, and DNA hackers
to join one of their R&D teams

Synthetic Biologist / Geneticist

To be able to translate our research to the clinic, we need to genetically engineer our producer strains to enable the packaging of synthetic circuits into our eligobiotics, and also to optimize the genetic circuits themselves to perform well in in-vivo models.

We are looking for excellent molecular biologists / synthetic biologists excited to tackle the ambitious challenges of diving into phage genetics and engineering bacterial strains.

The ideal candidate is passionate about genetic engineering. You’ll work hand-in-hand with Eligo microbiologists, phage biologists, and animal model scientists to optimize the engineering and validation of eligobiotics

Microbiologist

Eligo is building a platform technology to produce an arsenal of eligobiotics to target a wide range of bacterial species. With such a capability, Eligo is poised to lead the new generation of precision microbiome engineering companies. To build our library of delivery vectors based on phage capsids, we need to turn wild-type bacterial strains into engineered producer strains.

We are looking for excellent microbiologists excited to tackle the challenge of engineering and optimizing bacterial strains (aerobic/anaerobic, gram pos/gram neg, etc) to enable the production of species-specific eligobiotics. The ideal candidate is passionate about microbiology and molecular biology.

You’ll work hand-in-hand with Eligo phage biologists, synthetic biologists, and animal models scientists to optimize the engineering and validation of eligobiotics candidates for clinical trials.candidates for clinical trials.

Phage Biologist

To build our library of delivery vectors based on phage capsids, we need not only to discover and characterize a large number of phages with unique capabilities, but also validate their in-vivo activity.

We are looking for phage experts excited to tackle the challenge of both screening environmental samples and bacterial collections to discover unknown phages and characterizing them once isolated. Our whole process is now highly automatized thanks to our robotic pipeline.

The ideal candidate is passionate about phage biology and phage therapy. You’ll work hand-in-hand with Eligo microbiologists, genetic engineers, and animal model scientists to optimize the engineering and validation of eligobiotics candidates for clinical trials.

RebelBio opens call for London life-sciences accelerator - deadline 1 Dec 2017

RebelBio, the world’s first early-stage life-sciences accelerator, is seeking applications from ambitious scientists and entrepreneurs for its 2018 programmes. Science graduates, PhDs, postdocs and academics who feel a strong urge to commercialise their research or who need to advance their existing companies are particularly welcome.

More information from RebelBio 

Our investment  is given with the aim to develop a life-sciences product, commercialise research, or accelerate existing companies that can give the world something it needs.

RebelBio will invest up to $250K*, along with extensive business and scientific mentoring during the three-month period of the program, which take place in London from January 8th to April 8th 2018 & Corks programme from May - July.

During this time, RebelBio will provide laboratory space and supplies designed to allow our founders to move forward technically and business development. The program will culminate with a demo day and is part of an ongoing relationship that applicants will have with the world’s premier early-stage venture-capital fund, SOSV.

This relationship will provide many benefits including access to RebelBio’s vast network of investors, corporates and other like-minded entrepreneurs.

Application Information:

• Apply here - https://goo.gl/jXSzx1
• Review overview deck containing additional information on our programme - https://goo.gl/jXSzx1
• More details - https://goo.gl/XaN4yh

Deadlines:

• The closing date for the London programme is December 1st 2017
• The closing date for the Cork programme will be announced in early 2018.

Informal inquiries through contacting steven.oconnell@sosv.com.  

*Subject to performance

Biomaker Fayre showcases 40 open source, low-cost biological instruments

There was a real buzz in the air on Saturday 21 October, as 40 interdisciplinary teams exhibited their prototypes for the 2017 Biomaker Challenge at the Department of Engineering.

Projects covered everything from spectrometers for measuring the colour of penguin guano, microfluidics for tissue culture, to ultrasonic systems for measuring plant height and 3D printed modular microscopes. Each group was given a £1000 grant and four months to turn their big ideas for open source and DIY research tools into reality and over 100 people came along to the final event.

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

Winners of the 3D-printed awards were:

Best Technology: A low-cost chromatography system for protein purification

Stéphanie Polderdijk (Cambridge Institute for Medical Research) and Wolfgang Schmied (MRC LMB) set out to lower the cost of column chromatography: a routine technique for the separation of components from complex mixtures.

In biochemistry and molecular biology, proteins frequently need to be purified by gravity flow, centrifugation, which are time-consuming or by using expensive automated systems that use pumps to force solutions over a column. They produced a lower cost, modular, open-source alternative to these commercial systems for performing simple, routine purifications.

Best Biology: PiRMA: A low-cost rodent physiology monitoring bed for pre-clinical experiments

Marcel Gehrung, Dominick McIntyre and Lina Hacker (all from CRUK Cambridge Institute) developed a low-cost rodent physiology monitor which is suitable for a wide range of experiments and imaging applications such as Magnetic Resonance Imaging (MRI) and Computed Tomography (CT). Parameters such as Heart Rate (HR), Respiratory Rate (RR), and Temperature can be measured which are important to reduce data artefacts. Existing solutions are in the cost range of several thousand pounds and do not support the holistic workflow required in animal experiments.

Maker Spirit: A DIY focus stacking system for macrophotography of developing ferns 

Jennifer Deegan (Department of Plant Sciences) and team Matthew Couchman (John Innes Centre), Tim Deegan (CohoData) and Richard Mortier (Computer Lab) developed a  very low-budget  focus stacking system for microphotography in order to take a series of photographs showing the development of the fern gametophyte from the very earliest feasible stage to the appearance of the first sporophyte leaf. 

Dr Jenny Molloy, co-organiser of the Biomaker Challenge and Fayre reported that “the judging panel were hugely impressed by the progress the teams made over just four months and we're excited to see where people go next with these open source designs, that are free for anyone to download, replicate and build on in their own labs”.

See more photos from the day here >>

Biomaker Challenge 2017 was jointly funded by OpenPlant, a BBSRC/EPSRC Synthetic Biology Research Centre Grant BB/L014130/1 and the Isaac Newton Trust.

The Biomaker Challenge and Biomaker Fayre were coordinated by University of Cambridge's Synthetic Biology Strategic Research Initiative and the CambridgeSens Network.

Thank you also to our sponsors ARM Ltd and New England Biolabs.

Expressions of interest open for BrisSynBio 4 Day MBA (9 - 13 April 2018)

BrisSynBio will be running their successful 4 day MBA again in April 2018 and are likely to be able to offer significantly discounted (or even free) tickets to postdocs and PhD students from the UK Synthetic Biology Research Centres, including OpenPlant

Details of the 2017 course are available here: http://www.bristol.ac.uk/brissynbio/innovation/innovation-training-and-events/

Early expressions of interest should go to Andy Boyce: Andy.Boyce@bristol.ac.uk  

[Closes 30 Nov 2017] PhD Internship available: BrisSynBio Innovations Officer

BrisSynBio are looking for an enthusiastic individual to support some of BrisSynBio's innovation activities in 2018. They will develop, organise and participate in the BrisSynBio 4-Day More Business Acumen (MBA) course

This hands-on programme provides entrepreneurship and business training to synthetic biologists and culminates in a dragons’ den pitching event with venture capitalists and £10,000 of prizes. They will also support the broader activities of the innovation programme including industrial networking and translational funding as required.

The post will be located in the Life Sciences Building on the University of Bristol campus, but may also include travel within Bristol and the UK. Applicants should have good organisational, communication, and interpersonal skills and be available to start in February 2018.

Deadline: 30 November 2017 

https://pipsadverts.wordpress.com/2017/10/20/bristol-centre-for-synthetic-biology-brissynbio/

[Closes 27 Nov 2017] PhD on plant gene regulation

PhD available with Dr Nicola Patron of the Earlham Institute on design principles for synthetic gene regulation - understanding how cis-regulatory functions are encoded in plant DNA.

Plants are emerging as commercially-relevant production systems for high-value natural products. This requires suites of non-homologous, characterised regulatory elements for applications such as balancing components within a responsive circuit and preventing the build-up of toxic intermediates along a biosynthesis pathway. Plant regulatory sequences are comprised of complex arrangements of protein binding motifs and cis-regulatory elements. Both the primary DNA sequence and secondary DNA structure contribute to regulating gene-expression by recruiting proteins and dictating nucleosome architecture. This project will apply an original synthetic-biology approach to study the relationship between sequence and function utilising comparative genomic approaches to inform the design of synthetic regulatory sequences. This will enable us to understand how cis-regulatory function is encoded in specific DNA sequences. The project will focus on the identification and characterisation of cis-regulatory elements conserved across plants to inform the design of minimal synthetic elements that function across species. Comparative analysis of genome sequences will be used to inform iterative 'design-build-test-learn' cycles in which the function of libraries of designed, synthetic sequences will be analysed. The student will be trained in bioinformatics and comparative genomics analyses, synthetic biology approaches and low and high-throughput plant molecular biology and biotechnology techniques.

More information and application >>

[Closes 12 Jan 2018] Synthetic Biology Centre for Doctoral Training 2018 Cohort is now open for applications

The Synthetic Biology Centre for Doctoral Training (CDT) is a collaboration between the Universities of Bristol, Oxford and Warwick. It offers a four-year training programme leading to a PhD. The programme is designed for students with both physical and life sciences backgrounds.

More information and to apply >>

The first two terms are in Oxford, taught by staff from all three institutions, and devoted to acquiring the necessary theoretical and technical skills, through a combination of intensive lecture courses, practicals, seminars, project work and training in research and communication skills.

Over the third term and summer period at the end of the first year, students will undertake two extended projects, each lasting about 10 weeks. These are similar in scope to a master's-level project and serve as both advanced training and to help students  choose their research topic for the final three years of the course.

After completing these projects, students will undertake substantive PhD research projects in synthetic biology in their home participating university.

The Synthetic Biology CDT will produce internationally excellent researchers with key skills desired by prospective employers in the nascent field of synthetic biology.

[Closes 24 Nov 2107] Apply now to 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, policy work and training.

For this round applications focused on training and knowledge exchange are especially encouraged.

The deadline is 24 Nov 2017 for projects led from University of Cambridge or Norwich Research Park with external collaborators welcome.

Apply now by 24 Nov 2017 >>>

Download: Poster | Info Sheet

Each successful project will receive up to £5k, with £4k up front and an additional £1k for follow-on and outreach after reporting. PhD students and postdocs are particularly encouraged to apply.
 
A wealth of tools, technologies and methodologies have been developed for plant and cell free Synthetic Biology, including those developed through OpenPlant, the OpenPlant Fund, the Biomaker Challenge and complementary efforts. In the current OpenPlant Fund call, we are encouraging applications for projects that will provide training or knowledge exchange to broaden the use of plant and cell-free synthetic biology tools, techniques and technologies. Information about previous OpenPlant Fund projects are available on www.biomaker.org.
 
For more information see https://www.openplant.org/fund/ and join the upcoming mixer event on Thursday 9 Nov 2017. If you are interested in submitting a proposal or have any questions, please email colette.matthewman@jic.ac.uk.
 

Want to learn more and find collaborators?

OpenPlant Fund mixer and a light-hearted look at training!
4pm on Thursday 9 November, The Rec Centre Bar, John Innes Centre, Norwich
RSVP to this event here >>
 
This event provides an introduction to the opportunities and a chance to present your initial proposals and to meet potential collaborators over drinks and pizza. We will also have a light-hearted look at training, including different models and effective communication of technical details. Come along to learn some tips and tricks in this fun and informative training session, and to network and meet potential collaborators. More details to follow.

Cafe Synthetique: Towards engineering circadian rhythms
6pm on Monday 20 November, The Panton Arms, 43 Panton Street, Cambridge
RSVP to this event here >>

Help will be on hand to answer any questions you might have as the deadline for applications approaches and to find last minute partners for your teams!
 

Eligibility

Applicants should be graduate students or postdoctoral workers at the University of Cambridge, the John Innes Centre or The Sainsbury Laboratory. The team must be interdisciplinary, must contain members from both Norwich and Cambridge and may contain external collaborators of any type. Applicants must have agreement from their research supervisor and cost-code sponsor that the proposed project and management of the allocated funding will fit with their existing work. All proposals must lead to tangible, publicly documented and open outcomes, which could include (but are not limited to) the following:

• Design files and prototype for a hardware project
• Software development and documentation
• White paper arising from a workshop
• Educational resource
• Synthesis and sharing of useful DNA parts or vectors.

For more information and to apply see the OpenPlant Fund webpage

[Closes 27 Nov 2017] PhD on plant gene regulation

PhD available with OpenPlant PI Dr Nicola Patron of the Earlham Institute on design principles for synthetic gene regulation - understanding how cis-regulatory functions are encoded in plant DNA.

Plants are emerging as commercially-relevant production systems for high-value natural products. This requires suites of non-homologous, characterised regulatory elements for applications such as balancing components within a responsive circuit and preventing the build-up of toxic intermediates along a biosynthesis pathway. Plant regulatory sequences are comprised of complex arrangements of protein binding motifs and cis-regulatory elements. Both the primary DNA sequence and secondary DNA structure contribute to regulating gene-expression by recruiting proteins and dictating nucleosome architecture. This project will apply an original synthetic-biology approach to study the relationship between sequence and function utilising comparative genomic approaches to inform the design of synthetic regulatory sequences. This will enable us to understand how cis-regulatory function is encoded in specific DNA sequences. The project will focus on the identification and characterisation of cis-regulatory elements conserved across plants to inform the design of minimal synthetic elements that function across species. Comparative analysis of genome sequences will be used to inform iterative 'design-build-test-learn' cycles in which the function of libraries of designed, synthetic sequences will be analysed. The student will be trained in bioinformatics and comparative genomics analyses, synthetic biology approaches and low and high-throughput plant molecular biology and biotechnology techniques.

More information and application >>

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

Former OpenPlant Fellow Dr Fernan Federici, former OpenPlant PDRA Dr Tim Rudge and colleagues have recently published a pre-print for their low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering, supported by the OpenPlant Fund.

Nuñez, Isaac, Tamara Matute, Roberto Herrera, Juan Keymer, Tim Marzullo, Tim Rudge, and Fernan Federici. "Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering." bioRxiv (2017): 194324

Examples of images of bacterial colonies and cell-free systems using the microscope. Credit: Federici Lab

Abstract

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates.

We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information.

To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential for STEM teaching in a high school environment, using it to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for STEM education, scientific research and bioengineering. All the resources developed here are available under open source license

[Closes 30 Nov 2017] GapSummit 2018 open for applications

GapSummit is 'The world’s first global and intergenerational leadership summit in biotechnology' from Global Biotech Revolution and will take place 16-18 April 2018 at St Johns College, Cambridge.

The GapSummit welcomes 100 future bio-leaders (Leaders of Tomorrow) from around the world for a 3-day conference, which aims to "provide the bio-leaders of tomorrow with a comprehensive overview of current and future biotechnology trends and issues, inciting discussion about world challenges that can be met by biotechnological application."

 The GapSummit 2018 will attract more than 60 world leaders and pioneers from the biotech, pharmaceutical & healthcare industry to the University of Cambridge.

APPLY NOW

Deadline 30 Nov 2017

Cafe Synthetique tackles DNA-based Information Storage and DNA Synthesis

Cafe Synthetique on 18 Sep 2017 commanded a full house with plenty of interesting discussion around Pierre Murat's research on DNA-based information storage and Jiahao Huang's work on long chain DNA synthesis.

Pierre Murat from the Department of Chemistry spoke about his research on encoding and decoding synthetic strands of DNA. He presented data to show how he turned (the encoded word) 'Black to 'White', Pierre has also successfully encoded images of Darwin ,Franklin and and Turin! By exploiting differential kinetics of hydrolytic deamination reactions of cytosine and its naturally occurring derivatives, he demonstrated how multiple layers of information can be stored in a single DNA template. He explained how controlled redox reactions allow for interconversion of these DNA-encoded layers of information, encoding a single strand with multiple 'messages'.

Discussion focussed in part, on the challenges of sequencing the complex encoded DNA, including the ultimate test: an outsider successfully decoding a message hidden in DNA from Murat's lab - a challenge many attendees might relish.

Jiahao Huang covered the interesting history of DNA synthesis since it's advent in the 1970's before talking about the exciting work going on at Nuclera Nucleics where heand his colleaguesare developing a next-generation DNA synthesis using engineered terminal deoxynucleotidyl transferases, or TdT. With tehability to synthesise strands tens of bases long already, he hopes to be able to accurately produce long chain DNA strands by the end of this decade, and ultimately whole genomes. Discussion covered, accuracy, large scale production and lead to the inevitable question of cost. With research moving at a rapid pace Jiahao anticipates that a long chain sample will eventually become less than the cost of sending it by FedEx!

OpenPlant Fund supported project publishes on better DNA transfer from Escherichia coli to Bacillus subtilis

Dr Mario Juhas and OpenPlant PI  Dr Jim Ajioka from the Department of Pathology at the University of Cambridge have contributed to creating reliable and efficient systems for the transfer of synthetic DNA between E. coli and B. subtilis, supported by the OpenPlant Fund.

The majority of the good DNA editing techniques have been developed in Escherichia coli; however, Bacillus subtilis is better host for a plethora of synthetic biology and biotechnology applications. 

Using synthetic biology approaches, such as streamlined lambda Red recombineering and Gibson Isothermal Assembly, the team integrated genetic circuits  encoding the lysis genes of bacteriophages MS2, ΦX174 and lambda, the thermosensitive repressor and the T7 RNA polymerase into the E. coli chromosome.

In this system the T7 RNA polymerase regulated by the thermosensitive repressor drives the expression of the phage lysis genes. T7 RNA polymerase significantly increases efficiency of cell lysis and transfer of the plasmid and bacterial artificial chromosome-encoded DNA from the lysed E. coli into B. subtilis. The T7 RNA polymerase-driven inducible cell lysis system is therefore suitable for the efficient cell lysis and transfer of the DNA engineered in E. coli to other naturally competent hosts, such as B. subtilis.

The research obtained support from the SynBio Fund and OpenPlant Fund

The full article can be read here.

Image attribution: Debivort at the English language Wikipedia
This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.

Cafe Synthetique highlights graduate student work in synthetic biology: algae, arsenic testing and automated labs

Cafe Synthetique this August gave the floor to a talented collection of graduate students working on synthetic biology projects around the University of Cambridge and primarily from OpenPlant Labs. It was an excellent insight into some cutting edge science and how these early career researchers view the future of biological engineering.

Jan Lyczakowski (Department of Biochemistry) from Prof Paul Dupree’s lab described his efforts to engineer the structure of the plant sugar xylan in order to extract more biofuel from woody biomass. By using an enzyme from the plant model organism Arabidopsis thaliana, several times more xylose sugar could be extracted and fermented into ethanol using engineered E.coli bacteria. Jan also brought along some 3D-printed models of xylan to provide a hands-on demonstration of the structure!

Algal synthetic biology featured heavily as Aleix Gorchs Rivera, Stefan Grossfurthner and Patrick Hickland from Prof Alison Smith’s Lab, in the Department of Plant Sciences, presented different approaches to engineering algae to generate valuable products, such as pigments and medicinal compounds.

Patrick’s work focuses on tools to engineer the brown alga Phaeodactylum tricornutum, which is not a common lab organism but has useful features like a rapid growth rate and high accumulation of lipids like omega 3 fatty acids. Specifically, Patrick has engineered an inducible on/off genetic switch in the alga and is now applying it to manipulate metabolic pathways and boost production of useful compounds.

Aleix and Stefan are both working with the more common model alga Chlamydomonas reinhardtii. Aleix presented his work building inducible genetic circuits to express in the algal chloroplast, which is a major site of protein production. He aims to tightly dose expression of interesting metabolic genes and even antibodies. Stefan is constructing a metabolic pathway for engineering and manipulating cytosolic production of sesquiterpenes, an interesting family of compounds including the anti-malarial drug artemisinin. He presented his current progress during the first year of his PhD and future plans.

From eukaryotes to cell-free biochemical systems, Tess Skyrme represented the Sensors Centre for Doctoral Training (Department of Chemical Engineering and Biotechnology), where 12 students have spent the summer designing and prototyping an arsenic biosensor. Their sensor produces glucose oxidase in the presence of arsenic which is detected electrochemically on a device that can send data from remote field locations such as wells in Bangladesh and Nepal, where arsenic contamination has been described as the ‘largest mass poisoning of a population in history’ (WHO, 2002). The team built an arsenic sensitive genetic circuit, tested multiple electrochemistries, and designed an open source potentiometer that is 10% the cost of commercially available options for almost equivalent functionality. They are now focused on integrating the device components ahead of Sensors Day on 20 Oct 2017.

Looking to the future and calling for a revolution in the way that biological experiments are performed, Clayton Rabideau provided an introduction to the current state of the art in machine learning and automation in synthetic biology. His presentation marked the first appearance of Mario Brothers at Cafe Synthetique, with a demonstration of how machine learning over many generations can result in large efficiency gains compared.

Efficiency was also a key driver for the increase in labs moving to automated liquid handling through open source lab robots like OpenTrons, new technologies such as the Labcyte Echo, which is available in Cambridge as part of the OpenPlant Synthetic Biology Centre, and fully automated ‘cloud labs’. However, Clayton also highlighted the ‘reproducibility crisis’ in experimental science and how increased use of machines to minimise human error might help. He ended by predicting that in the coming decades graduate students would spend far less time in the lab. This went down well with an audience whose most automated lab experience so far was reportedly ‘multi-channel pipettes’.

It’s the first time that Cafe Synthetique has featured a full line up of graduate students and we hope to repeat the successful format in the near future. If you are a graduate student working on a synthetic biology related topic and would like to present at the next Cafe Synthetique Grad Talks, get in touch!

New Royal Society Report: Synthetic Biology - does industry get it?

On 8 February 2017, the Royal Society hosted a conference that posed the question Synthetic biology – does industry get it? It brought together nearly 200 experts from academia, industry and government to provide an honest and open appraisal of how industry is using synthetic biology, acknowledging successes and strengths but also looking at what barriers still need to be overcome.

A report from the meeting has now been published, summarising the discussions that took place and the key points raised.

Issues including the global energy challenge, regulation and public acceptance of synthetic biology, and finding the right talent and skills were all raised and great industrial interest in synthetic biology was demonstrated.

In answer to the question, “Does industry get it?”, the Royal Society report that:

"there was a clear sense that industry is very interested in synthetic biology but that there remains a conservativism that holds back its wider implementation. Industry speakers encouraged synthetic biologists to look at solving the unmet needs of industry and demonstrate the benefits that future products will bring. Researchers should avoid the risk of overselling their new and exciting science - there needs to be a balance between ambitious, long-term scientific targets and working within the existing product development lifetimes in industry...Synthetic biology stands on the cusp – as the costs of processes fall, the moment where rapid growth in industrialisation will take place is nearly upon us."

The full report can be read here.