Cambridge Consultants: Senior Scientist – Synthetic Biology

From the Cambridge Consultants website:

We are looking for an outstanding molecular biologist to drive this work forward.  With current expert knowledge in molecular biology techniques you will form the core of the team carrying out work in our labs and delivering answers to our clients.

As Senior Scientist – Synthetic Biology you will play a key role in establishing our technical ability in this new field.

Working with the Head of Synthetic Biology, your main purpose will be to establish the Cambridge Consultants biology lab as a centre for engineering biological systems in bacteria and yeast and use this facility to perform client projects.  You will help build a capability that can design, build and test biological systems in a rapid and cost-effective way.

You will do this by:

• Providing expert scientific knowledge in molecular biology and genetics, particularly the functions and processes within cells and the current methods and techniques used in the lab to characterise nucleic acids, proteins and metabolites
• Designing DNA constructs to meet specific phenotypic or metabolomic requirements
• Designing and executing experimental protocols to transform, culture and characterise cells
• Providing oversight and management of the biology lab, particularly for biological health and safety matters and for data management within the lab.

The successful candidate will be a hands-on, experienced, senior scientist, who wants to build their technical capabilities, create an efficient lab for engineering biology and deliver excellent solutions to client problems.  You will be used to working in multidisciplinary teams alongside other scientific and technical experts.

Read more and apply >>>

[Closes 29 April 2016] PDRA in Sustainable PoLymers from Algae Sugars and Hydrocarbons (University of Cambridge)

Applications are invited for a fixed term Postdoctoral Research Associate position to join an EU FP7 Collaborative Project SPLASH (Sustainable PoLymers from Algae Sugars and Hydrocarbons). The post holder will verify the function of the putative genes from B. braunii using a synthetic biology pipeline.

For more details and to apply see the Department of Plant Sciences page >>

Applications are invited for a fixed term Postdoctoral Research Associate position to join an EU FP7 Collaborative Project SPLASH (Sustainable PoLymers from Algae Sugars and Hydrocarbons). This multidisciplinary project brings together over 20 different partners from academia and industry to investigate the possibility of making plastics from extracellular polysaccharides and hydrocarbons produced by the oleaginous green alga Botryococcus braunii. A major aspect of the work is to sequence the genome of B. braunii, and to carry out transcriptomic / proteomic / metabolomics analysis to identify putative genes encoding enzymes involved in synthesis of these polymers.

The post holder will be based in central Cambridge and work in the group of Prof Alison Smith to verify the function of the putative genes from B. braunii by expression in a heterologous host, namely Chlamydomonas reinhardtii. The approach taken will involve a synthetic biology pipeline, using standard parts and workflow already developed in Prof. Smith's lab.

The successful candidate must have a PhD in an appropriate field, and research experience in molecular biology (ideally including synthetic biology approaches), and genetic engineering of microorganisms, together with a good knowledge of regulation of gene expression and metabolism. Experience with laboratory handling of microalgae or microbiology, and/or analysis of RNA seq data, is highly desirable.

• Salary: £28,982-£37,768
• Closing date: 29 April 2016
• Fixed-term: The funds for this post are available for 1 year in the first instance.
• Download: Further details.
• You can apply online for this vacancy. You will need to register an account (if you have not already) and log in before completing the online application form.
• Please quote reference PD08762 on your application and in any correspondence about this vacancy.

The interviews are scheduled to be held in the week beginning 2 May 2016 as the position is available for an immediate start. For more information contact Alison Smith (algae@plantsci.cam.ac.uk).

The University values diversity and is committed to equality of opportunity.  The University has a responsibility to ensure that all employees are eligible to live and work in the UK.

OpenPlant Fellow wins 2016 Wellcome Trust Image Award

Fernán Federici, OpenPlant Fellow at the University of Cambridge and Director of the Synthetic Biology Lab at Pontificia Universidad Católica in Chile has been awarded a Wellcome Trust Image Award for his micrograph of maize leaves, shot in the Department of Plant Sciences in collaboration with Professor Jim Haseloff.

Fernán has enjoyed considerable success with his artistic images of bacteria and plants using microscopy, winning Wellcome Trust awards in 2011 and 2012. His image has appeared in multiple media outlets, including Nature News, the BBC and The Guardian.

More on the image via the Wellcome Trust >>

Looking inside a cluster of leaves from a young maize (corn) plant reveals lots of details and organised structure. Each curled leaf is made up of lots of small cells (small green square and rectangle shapes), and inside each cell is a nucleus (orange circle), the part of the cell which stores genetic information. Maize is one of the most widely grown cereal crops in the world. It is used as a staple food, in livestock feed, and as a raw material – such as for processing into high-fructose corn syrup. Genetically modified maize crops are being grown to be resistant to pests and herbicides.

Although seeming boring when viewed with the naked eye, maize leaves have such a delicate and intricate structure under the microscope, captured so wonderfully by this picture. The level of detail as demonstrated by the image reminds us how complex even relatively simple organisms are when seen on this scale.

James Cutmore, Picture Editor of BBC Focus

The image has been made freely available to use under a Creative Commons CC-BY-NC-ND 4.0 license.

OpenPlant’s showstopper; synthetic biology! – Public reaction at the Cambridge Science Festival

In March a team from the John Innes Centre brought the premise of synthetic biology to the public. As an annual event growing every year Cambridge Science Festival attracts people from across the city to learn about new developments in science and technology.

Stall activities ranged from the extraction of DNA from Strawberries (University of Cambridge) to investigating evolution first hand with primate skulls (Wellcome Genome Campus). OpenPlant’s stall featured a glimpse into synthetic biology.

A disassembled phone explained the idea that by knowing how each of the individual simple components work (a dialling pad to input your desired number, a vibrating receiver coil to change the electrical signal into a sound wave) you can build more elaborate systems.

A disassembled (and retro) telephone, showing simple components forming a complex system

You can then use this concept in a biological setting. Firstly you understand how genes work, then you break these into smaller components each with their individual job, for example a sequence to tell you when to switch on a biological system. Finally this can be combined in a living organism to produce a desirable trait.

At the Science Festival, the public used this idea to make weird and wonderful new lifeforms! A cat whose nose turns purple when a disease is nearby. Useful for medical diagnosis? Or how about sprouts that taste of strawberries when it snows, which many would no doubt relish at Christmas time? Or a personal favourite provided by one dad – a plant whose leaves turn gold when you water it.

A biological dream; leaves which turn gold when you water it

Obviously most of our new inventions that day were unlikely, no matter how much scientists persevere with them; I think a money tree is still a few years off. But the solid basis for such work is undertaken in laboratories throughout the world, and the public were undoubtedly positive about synthetic biology. Although everybody (well apart from a young girl who wished to use squids to inflict harm on unsavoury characters) was clear that it should be only used for good and moral solutions to problems. The OpenPlant team was able to stress ethical procedures are in place for this which many found comforting as sometimes the public can find scientists secretive at best.

The Cambridge Science Festival is a vibrant, thriving and free event. Not only do people gain a glimpse of the developments in science but it’s also rewarding to the scientists giving up their time to share their knowledge and discussing their subject area. And synthetic biology is a hot topic which everyone should be talking about.

Written by Nicola Capstaff – outplantish.wordpress.com

Cartoon is credited to Erin Zess, a PhD student at the John Innes Centre

The 2017 Cambridge Science Festival will take place on 13-26th March 2017 – www.sciencefestival.cam.ac.uk

CUTEC Bio-Hackathon - apply now!

With support from the University of Cambridge SynBio Fund, CUTEC is hosting the UK’s first ever bio-focused “hackathon” in the University of Cambridge. Interdisciplinary teams will take on some of the greatest challenges facing biology.

This event is about putting together diverse teams to tackle a unique biological problem. If you are a scientist (from ANY discipline), an artist, an economist or have any unique experience and set of skills we want to hear from you! You will spend four days in a University synthetic biology lab where you will have access to hardware, software and biology prototyping tools. The challenge will be revealed to our teams on Tuesday. The final day of the competition will be a pitch at our annual Technology Ventures Conference with over 300 investors, VCs, startups, academics and students. Judges from industry will decide on the most novel solutions. We also will offer the most commercial solution as much help as we can to take it to the next stage. The winning team gets a £1500 cash prize!

The event will run from Tuesday 21st June 6pm to Saturday 25th June 12am. Solutions will be judged on innovative nature and commercial viability. Teams will present their solutions on stage at CUTEC’s flagship Technology Ventures Conference (TVC) in front of investors, academics, students, and incubators.

Individuals who are interested in taking part will apply via the website (www . biohackathon . co . uk) application deadline May 30th) and teams of 3-5 will be assembled. A well-rounded group of researchers from different disciplines is strongly encouraged. Anyone in the UK can apply individually (team assembled by our committee) or as a team. Scholarships are available to those from outside the Cambridge/London area to cover accommodation and travel.

A £1500 cash prize is awarded to the winning team, as well as support to commercialise your ideas through in-kind funding.

In your team you will be introduced to the challenge by an expert in the field then led through a brainstorming session. You will then have four days to refine your solution before presenting to a panel of judges from industry, government, start-ups and academia for feedback on the feasibility of your solution. Winning teams will present their solution on stage at the TVC on June 25th.

Who should apply?

Undergraduates and Post-graduates at any UK University, school, company or otherwise. All fields are encouraged we need: Biology, Chemistry, Physics, Engineering, Computing, Business, International Relations, Anthropology, Art, Design, Marketing, and others! Whatever you do, if you are interested in working on a diverse team to create sustainable solutions to real problems, apply!

Applicants may be individuals. If there is a partner that you would prefer to be placed on a team with, please state this in your application. We want to encourage participants to meet and work with new people but if you already have a team then you may do so but applicants may not apply in teams of more than 5 people.

Why should I apply?

Do you want to challenge yourself intellectually in a collaborative environment?

Do you want to meet new friends and potential future work/research partners?

Are you interested in entrepreneurship but don’t have an idea or a team and just don’t know where to start?

This challenge will foster a community of like-minded researchers and entrepreneurs who want to create a better world. The main focus is solving a problem together; however, if a suitable technology is developed during the project, CUTEC will provide resources for the team to turn that idea into a start-up venture. Our panel of judges providing feedback at the end of the event and who attend our Technology Venture Conference are always looking for bright, fresh talent to enhance their businesses, labs, and initiatives.

How do I apply?

Application forms will be available on our website: www . biohackathon . co . uk

Scholarships

A number of scholarships are available to individuals and teams to cover costs of travel, housing and expenses. Teams outside the Cambridge/London area will be given preference. Please indicate if you can approach other sponsors (societies, university department or other) to help support expenses.

We thank the Synthetic Biology Strategic Research Initiative of the University of Cambridge for funding.

When/Where will it occur?

Applications are due midnight May 30th. Teams will be announced on June 1st.

Entries are accepted either by teams or individuals and assembled into teams by the committee.

The event will run from Tuesday 21st June 6pm to Saturday 25th June 12am in the Department of Plant Sciences University of Cambridge. Judging will occur and presentations awarded at the annual Technology Ventures Conference (TVC) where teams will have the opportunity to pitch and present their solutions.

Enter!

Ethics, Openness, Outreach and the Media course – SAW session

Above: Nicotiana benthamiana by Aymeric Leveau (JIC), image NRP-103: licenced under CC-BY 4.0.

Below: Artwork created by a scientists, inspired by above image of Nicotiana benthamiana

As part of a workshop for post docs on ethics, the media, openness and outreach the participants were treated to an after-dinner Science Art and Writing session at St Andrews Brewhouse in Norwich. The session began with a discussion about communicating with the public and then focused in on specialised communication, something scientists do very well! Writer Mike O’Driscoll then introduced the group to other styles of communication and encouraged them to write poetry to explore new ways of getting messages across. 

Artist Chris Hann then led an art activity on the theme of plants to encourage creative interpretation and sharing of science. This activity not only introduced new ways of approaching outreach but also gave the scientists time to reflect on the key messages and aims of their work and how they might express that and also sitting around the table exercising their artistic sides led to a vibrant level of creative exchange which was very refreshing.

Short poems from scientists

OpenPlant Plant Fund 2016 - Pitches on Mon 14 March announced!

We've got a fantastic line-up of teams pitching for the OpenPlant Fund - £5000 grants to support innovative, open and interdisciplinary projects to engineer plant biology. All are welcome to hear the teams 13:00-16:30 on Mon 14 March in the Large Lecture Theatre, Department of Plant Sciences, University of Cambridge. We'll be sticking strictly to time, so feel free to drop in even if you can only make it for a couple of pitches.

Pitch Timetable

14 March 2016, 13:00 - 16:30 Large Lecture Theatre, Department of Plant Sciences, University of Cambridge

Time	Project Title
13:00	Opening remarks
13:15	Hot Tomato: Complementation of the Capsaicin Biosynthetic Pathway to Engineer Spicy Tomatoes
13:30	​Synthetic Biology for Schools: A multidisciplinary approach
13:40	Implementation of a synthetic transcriptional AND gate in the chloroplast of Chlamydomonas reinhardtii
13:50	Co-lab OpenPlant - interdisciplinary workshops of science art and design
14:00	Desktop plant experiment box
14:10	Environmental sensor networks based on plant electrical signalling.
14:20	Coffee Break
14:50	Plant electro-mechanics
15:00	Advancing the ability to image single RNA molecules at the cellular level
15:10	Establish a Procedure for Rapid Identification of Genetic Parts for Use in Algal Biotechnology
15:20	Establishing 3D Printed Microfluidics for Molecular Biology Workflows
15:30	Universal precise large area colony scanning stage with measurement and selection tool integration
15:40	Development of an Open Source Autonomous Imaging Station for Distribution in High Schools, Universities, and Emerging DIY Scientific Communities.
15:50	Printable SynBioLab - a feasability study
16:00	A synthetic biology approach to investigating arbuscular mycorrhizal symbiosis in Marchantia paleacea
16:10	Closing remarks

EUSynBioS Symposium: Registration Open!

EUSynBioS is an organisation for students and postdocs in synthetic biology research in Europe, founded by University of Cambridge plant synthetic biologist Christian Boehm, is holding its first EUSynBioS Symposium, themed Engineering Biology for a Better Future at Imperial College London, 9-10 April 2016.

From EUSynBioS:

The Symposium kicks off with a Visionary keynote address from none other than synthetic biology pioneer Tom Knight (Ginkgo Bioworks)! A former professor at MIT and one of the very first synthetic biology entrepreneurs, Tom will give us an insight into the early days of synthetic biology and talk about what the future holds. Next up we have a session of scientific presentations exclusively by early career synbio researchers, i.e. you! We want the symposium to provide graduate students and early career post-docs a platform where they present their research to peers and senior scientists. I’m sure other members and PIs attending can’t wait to see more cutting edge synthetic biology research, so register and submit your abstracts until the 1st of April!

Post-lunch the symposium breaks up into smaller breakout sessions on various topics from biodiversity to design and public engagement. Led by excellent fellow members, these sessions are a great opportunity to express your views and hear others on important issues in synbio today. We then have two inspiring speakers, Luke Alphey (Oxitec) and Emily LeProust (Twist BioSciences) talking about their career paths to setting up world changing synbio companies. A must for all budding synbio entrepreneurs! We hear about efforts to regulate synbio technologies from gene synthesis to gene editing regularly. Michele Garfinkel (former Policy Analyst at the J.Craig Venter Institute, and currently at EMBO) will talk next, guiding us through the world of policy making and talk about how we can make a difference in how synbio is legislated in the future.

And finally, we close the symposium with an Open Discussion on a topic chosen by you: Gene Drives! Gene Drives have gotten a lot of press in the last few months and we have none other than the scientist who coined the term, Austin Burt (Imperial College London), joined by Michele Garfinkel and Luke Alphey, giving us an introduction to what this fascinating technology holds for the future. This session is a forum for you the express your views and get answers from experts about gene drives: How do they work? Will they change the world for the better? Is it ethical to do so? ...and many more questions, we’re sure!

If any of these topics (or indeed all!) interest you, or if you want to meet and interact with other synthetic biologists, this symposium is made for you!

Register for the event here, and we hope to see you all in April!

Your EUSynBioS Steering Committee

http://www.eusynbios.org/ sc.eusynbios@gmail.com

Open Source Hardware in Synthetic Biology

Source: Open Source Hardware from the PLOS SynBio Community, licensed under CC-BY 4.0

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by Tobias Wenzel, who received an OpenPlant Fund grant to develop DokuBricks

Open Source Hardware is an exciting new trend

Figure 1: OpenFlexture Microscope by Richard Bowman, UK, 3D printed and operated with a Raspberry Pi computer.

 “This microscope is one of the cleverest pieces of open source hardware for laboratory use that I have seen so far” said Prof. Jim Haseloff in the Plant Science Department at the University of Cambridge, as he learned about a design by Richard Bowman. Richard, a fellow in the Department of Physics, was frustrated about the difficulty of working with conventional technologies for some of his experiments. For example fitting a growth chamber into a microscope can be a major challenge. Many conventional scientific instruments are designed to be incompatible to possible extensions and are not co-developed by the user community, leading to impractical designs. Thus he built his own digital microscope from a 3D printed chassis and a simple Raspberry Pi computer. The main challenge to solve for high-quality microscopy results was to position and stabilise the sample. He solved this with a one-piece 3D printed flexing mechanism in plastic. Now the microscope is ready for all sorts of adaption, it can even be placed inside commercial incubators or used in education and field uses – all at a tiny fraction of the price of conventional digital microscopes. What a great demonstration of the uses that are enabled by rapid prototyping methods! Increasingly available methods are e.g. 3D printing and laser cutting along with accessible electronic units such as Arduino microcontrollers or Raspberry Pi computers.

Figure 2: OpenTrons pipetting robot for open source liquid handling, designed by junior MIT scientists, USA

Richard is not alone in his desire to make experiments more reproducible, and customisable as well as automated. In the last few years, Open Ephys and Backyard Brains started providing tools for electrophysiology measurements, OpenTrons and open syringepump designs target the automation of liquid handling, the electrochemical potentiostat Cheapstat was a creation of an iGEM team and was published in 2011, a different iGEM team in 2015 created a fluorescence microscope adaptation of Richard’s initial design to join the ranks of another popular fluorescence microscope by Tom Baden and Andre Chagas from the University of Tuebingen, Germany. The last mentioned scientists also curate the PLOS Open Source Hardware collection where many other examples can be discovered.

Sharing equipment plans is an opportunity for experimental science, especially Synthetic Biology

Another noteworthy collection that demonstrates the fast raising popularity of Open Source Hardware is Joshua Pearce’s Appropedia and his book Open-source Lab. He illustrates the benefits of open scientific information sharing to the reader in depth. Beyond the arguments of openness, Open Source Hardware works well in science since many experimental set-ups are prototypes that are suitable for manual or rapid manufacturing methods and because technical training is widely available in science. Furthermore, it is a job requirement to demonstrate impact in this profession. Extending the publication-like sharing philosophy to hardware has worked well for the pioneers.

Synthetic Biology specifically can benefit from the open community engineering approach to bring the users and designers of complex interdisciplinary equipment closer together. The exchange of designs and protocols comes hand in hand with an increase of reproducibility of experiments, which is a major challenge of the field. The reproducibility is further enhanced by the additional number of eyes that can spot errors in protocols and improve processes without additional development cost. Open Source Hardware works well in businesses too, when equipment is expensive and specialised as is the case for most synthetic biology instruments. For example: OpenIOlabs is a young Cambridge company that (among others) is in the process of open sourcing many expensive equipment parts from the supply chain, in order to make their key products more accessible and IO Rodeo offers open source laboratory equipment for which the user can decide how many parts he wants to buy and what to build on their own. Users then often contribute improvements for free, which has most prominently driven the development cycles of 3D printers.

Many designs come from the DIY community. Are the bio laboratory designs good enough?

Figure 3: NinjaPRC, a thermocycler design for open source DNA amplification, by Shingo Hisakawa, Japan

A lot of existing open source designs come from the do-it-yourself (DIY) and maker community, as the trend only recently reached academia and business more widely. A group of scientists and makers in Cambridge, UK, tried to replicate open source designs for biology laboratory equipment to kickstart a DIY biolab and evaluate the designs along the criteria of safety, quality, adaptability and ease of build. Funded by a mini-grant of the Synthetic Biology Strategic Research Initiative, they attempted designs for electrophoretic gel boxes, a centrifuge, PCR thermocyclers, tube holders, syringe pumps and a 3D printer (more to be found online, soon). Unfortunately, the team discovered more problems than solutions: even in the documentation sets that looked good, essential parts were missing. Some designs referred to specific parts that are not generally available and that had to be shipped from the US for high costs. Most design files where difficult to adapt to other sizes of e.g. acrylic sheets when build from a metric rather than US-imperial material stock. Assembly sets that could be ordered commercially were complete and had decent to good assembly instructions, but the documentations were usually not sufficient to build the hardware without buying the set, thus not fully deserving the label ‘Open Source Hardware’.

Open Source Hardware + good documentation; it just got easier with DocuBricks

There is a lesson to be learned from the incompleteness of commercial assembly-set documentations: Open Source Hardware is more than an assembly instruction. It is also about documenting design files and decisions along its functionality and in a modular fashion, complete with testing and calibration instructions. A good documentation enables the project to grow and improve without the doing of the inventor. Only in this way most projects can enfold their benefit well to society and technology companies. To be sure, documenting a hardware project is not easy and requires time. For this reason a handful scientists at the University of Cambridge (including the author), all with a background in technology and biology, recently started the DocuBricks initiative. DocuBricks is an open source and free software that makes documenting hardware and usage procedures easier. The name is a reference to modularity in the same way as Lego or BioBricks. As the name suggests, the editor part of the software guides the user through a modular documentation structure with relevant fields in a standardised, yet general format. The user can create a hierarchy of documentation bricks, explaining their function, implementation and assembly while referring to a parts library. The result is a XML document and a folder with construction and media files that is displayed with the viewer part of the software (a style sheet and script to enable interactivity).

Figure 4: DocuBricks* logo, the new open source tool for easy generation of high-quality hardware and procedure documentations. (*Image rights: Tobias Wenzel)

Over the database with the same name, DocuBrick.com, the projects can be shared and found. The team puts emphasis on impact tracking and acknowledgement, to make engagement in Open Source Hardware not only easier, but also more promising to the scientific community. Projects can also be cited via DOI’s, which are internationally curated short links and the standard way of referencing scientific literature. The new initiative is growing fast: Richard Bowman’s microscope from the beginning of this article can already be found. The wireless communication designs of Shuttleworth Fellow and collaborator Luca Mustafa will be released soon, just like several projects of the OpenPlant Initiative in Cambridge and a number of other scientific interest groups. Even a journal on Open Source Hardware from the Ubiquity Press will be launched and intends to use DocuBricks as the preferred documentation format. When will you join the effort to make science more open and reproducible?

Tobias Wenzel is a PhD candidate at the University of Cambridge and DocuBricks founder. This blog is a summary of a presentation given at Cafe Synthetique in November 2015. 

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[Closes 17 Mar 2016] Postdoctoral Research Fellow in SynBio Governance

The Innogen Institute is advertising for a research fellow to take up a 2-year post to work in collaboration with two large science projects in the University of Edinburgh, the UK Centre for Mammalian Synthetic Biology (CMSB) and Implantable Micro-systems for Personalised Anti-Cancer Therapy (IMPACT).

You will conduct social/policy research for two science projects, UK Centre for Mammalian Synthetic Biology (CMSB) and Implantable Micro-systems for Personalised Anti-Cancer Therapy (IMPACT), investigating the governance processes in place for the relevant technologies and how they will influence future innovative value chains.

This is a fixed term, full time post tenable for a 24 month period from a flexible start date of 2 May 2016. This post attracts an annual salary of £31,656 to £37,768 per annum based on 35 hours each week (pro rata).

Closing Date: 5pm (GMT) on Thursday 17th March 2016.

Read more >>>

Plant Artificial Chromosome Technology

AMELIA FRIZELL-ARMITAGE of The Global Plant Council introduces future directions for Plant Artificial Chromosome Technology:

Plant artificial chromosomes (PACs) have many advantages over traditional transformation systems. For example, to confer complex traits such as disease resistance and tolerance to abiotic stresses such as heat and drought, multiple genes are required. This is not easy with current methods of modification.

Read more >>>

There's also mention of the recent workshop on the CRISPR-CAS system of genome editing held in September 2015 by GARNet and OpenPlant at the John Innes Centre in Norwich! You can read the full meeting report here.