Wednesday, April 2, 2014

OpenPlant Get £12 Million Funding for Synthetic Biology

Cambridge and Norwich win major boost for synthetic biology


Plant scientists at Cambridge and Norwich have been awarded £12 million funding for a new UK synthetic biology centre – OpenPlant.

Inspired by the way open source data has stimulated innovation in computing, OpenPlant will create a climate of openness in synthetic biology, helping young researchers and entrepreneurs develop and share new tools and libraries of plant DNA.

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OpenPlant is a collaboration between the University of Cambridge and the John Innes Centre on Norwich Research Park. The funding will be shared equally between the two institutions. It is one of three new UK centres for synthetic biology announced today by science minister David Willetts. Over the next five years the three centres will receive more than £40 million in funding from the BBSRC and EPSRC.

Sitting at the boundary between sciences, synthetic biology uses engineering principles – including standardisation and modularisation – to make new biological parts and systems. Using knowledge about the biological properties of plants and microbes, synthetic biology can improve their use as factories, food and fuel. As well as helping improve crops across the world, synthetic biology could be used to develop new medicines, chemicals and green energy sources.

Minister for Universities and Science David Willetts, said: "Synthetic biology is one of the most promising areas of modern science, which is why we have identified it as one of the eight great British technologies of the future. Synthetic biology has the potential to drive economic growth but still remains relatively untapped and these new centres will ensure that the UK is at the forefront when it comes to commercialising these new technologies."

While US researchers are at the cutting edge of synthetic biology in microbes, the UK has the edge in plants. To fulfil its potential, however, researchers and small companies need greater freedom to operate, freedom that in key areas of computing has driven innovation, and created new jobs, software and products.

According to Dr Jim Haseloff of the University of Cambridge: "The field needs a new two-tier system for intellectual property so that new tools including DNA components are freely shared, while investment in applications can be protected."

"This will enable greater participation in innovation for sustainable agriculture and innovation."

Dr Nicola Patron, Head of Synthetic Biology at The Sainsbury Laboratory, another key partner organisation in Norwich, said: "Current intellectual property practices threaten to stifle innovation in plant technology. By creating DNA resources and tools that are free to use, OpenPlant will foster the kind of innovation seen at the emergence of other new technologies such as microelectronics and computer software."

OpenPlant unites two leaders in the field. The University of Cambridge has played an important role in many key scientific discoveries in biology, from the structure of the double helix to next generation DNA sequencing. The John Innes Centre is a world-leader in plant and microbial research that benefits farmers, the environment, humans and economies worldwide. Scientific discoveries about synthetic DNA systems will feed future innovation by researchers at both institutions.

JIC scientists have also pioneered innovative engagement between scientists and the public such as through the Science, Art and Writing (SAW) initiative. Social scientists on the OpenPlant project will help map feasible technical approaches to challenges, such finding a less energy-intensive alternative to nitrogen fertilisers, considering the economic and social implications for different scenarios.
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Case studies

Medicinal plants

Scientists at the John Innes Centre will discover how Chinese medicinal plants such as the coneflower create natural colours and compounds with beneficial effects. The discoveries can be applied to refine their properties and scale up production. Photo of coneflower available.

Plants as factories

A new system for producing useful compounds in plants, such as proteins to make vaccines, is currently used by over 200 academic institutions around the world. The technology developed at the John Innes Centre is licensed to commercial organisations, including Canadian company Medicago, who have used it develop a vaccine against swine flu. Photo available of plant being inoculated with a protein.

Advanced photosynthesis

Crops use photosynthesis to convert sunlight and water into carbohydrates and the way they do this divides them into either C3 or C4 plants. C4 plants are around 50% more efficient than C3 plants but major crops such as rice are C3. By discovering how C4 photosynthesis works and how it evolved, it might be possible one day to engineer a major change to crop productivity. Microscope images available.

A simple test bed for engineering

The liverwort, Marchantia polymorpha, is a descendant of the earliest terrestrial plants. Its small size, rapid growth, simple architecture and genome make the plant a powerful new model for Synthetic Biology. OpenPlant scientists will use the system to develop new DNA circuits and tools to visualise and engineer new forms of plant growth. (See http://www.marchantia.org). Pic available of liverwort.

News Release Source :   Cambridge and Norwich Win Major Boost for Synthetic Biology

Bioscientists develop 'grammar' to design useful synthetic living systems

Bioscientists develop 'grammar' to design useful synthetic living systems


Researchers use software developed at Virginia Tech to design synthetic living systems

Researchers at Virginia Tech and the Massachusetts Institute of Technology have used a computer-aided design tool to create genetic languages to guide the design of biological systems.

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Known as GenoCAD, the open-source software was developed by researchers at the Virginia Bioinformatics Institute at Virginia Tech to help synthetic biologists capture biological rules to engineer organisms that produce useful products or health-care solutions from inexpensive, renewable materials.

GenoCAD helps researchers in the design of protein expression vectors, artificial gene networks, and other genetic constructs, essentially combining engineering approaches with biology.

Synthetic biologists have an increasingly large library of naturally derived and synthetic parts at their disposal to design and build living systems. These parts are the words of a DNA language and the "grammar" a set of design rules governing the language.

It has to be expressive enough to allow scientists to generate a broad range of constructs, but it has to be focused enough to limit the possibilities of designing faulty constructs.

MIT's Oliver Purcell, a postdoctoral associate, and Timothy Lu, an associate professor in the Department of Electrical Engineering and Computer Science, have developed a language detailed in ACS Synthetic Biology describing how to design a broad range of synthetic transcription factors for animals, plants, and other organisms with cells that contain a nucleus.

Meanwhile, Sakiko Okumoto, an assistant professor of plant pathology, physiology, and weed science at the Virginia Tech College of Agriculture and Life Sciences, and Amanda Wilson, a software engineer with the Synthetic Biology Group at the Virginia Bioinformatics Institute, developed a language describing design rules for expressing genes in the chloroplast of microalgae Their work was published in the Jan. 15 issue of Bioinformatics.

"Just like software engineers need different languages like HTML, SQL, or Java to develop different kinds of software applications, synthetic biologists need languages for different biological applications," said Jean Peccoud, an associate professor at the Virginia Bioinformatics Institute, and principal investigator of the GenoCAD project. "From its inception, we envisioned GenoCAD as a framework allowing users to capture their expertise of a particular domain in languages that they could use themselves or share with others."

The researchers said encapsulating current knowledge by defining standards will become increasingly important as the number and complexity of components engineered by synthetic biologists increases.

They propose that grammars are a first step toward the standardization of a broad range of synthetic genetic parts that could be combined to develop innovative products.

"Developing a grammar in GenoCAD is a little like writing a review paper," Purcell said. "You start with the headings and you progressively dig deeper in the details. At the end of the process, you have a much better appreciation for what you know and what you don't know about a particular domain."

Lu added, "Our group has a recognized expertise in synthetic transcription factors. We hope that this work will help a broad range of scientists use our results in their own projects."

"GenoCAD exemplifies the kind of cyberinfrastructure the institute is known for," said Dennis Dean, the director of the Virginia Bioinformatics Institute. "This type of portal can enable collaborations across disciplines and institutions to foster a team approach to today's most pressing scientific challenges."

Peccoud is chief scientific officer of GenoFAB LLC, a company providing products and services derived from GenoCAD.
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More resources are available on the VT News website.

News Release Source :  Bioscientists develop 'grammar' to design useful synthetic living systems

Synthetic Biologists Shine Light on Genetic Circuit Analysis

Rice synthetic biologists shine light on genetic circuit analysis


Bioengineers invent 'light tube array,' 'bioscilloscope' to test, debug genetic circuits

In a significant advance for the growing field of synthetic biology, Rice University bioengineers have created a toolkit of genes and hardware that uses colored lights and engineered bacteria to bring both mathematical predictability and cut-and-paste simplicity to the world of genetic circuit design.

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"Life is controlled by DNA-based circuits, and these are similar to the circuits found in electronic devices like smartphones and computers," said Rice bioengineer Jeffrey Tabor, the lead researcher on the project. "A major difference is that electrical engineers measure the signals flowing into and out of electronic circuits as voltage, whereas bioengineers measure genetic circuit signals as genes turning on and off."

In a new paper appearing online today in the journal Nature Methods, Tabor and colleagues, including graduate student and lead author Evan Olson, describe a new, ultra high-precision method for creating and measuring gene expression signals in bacteria by combining light-sensing proteins from photosynthetic algae with a simple array of red and green LED lights and standard fluorescent reporter genes. By varying the timing and intensity of the lights, the researchers were able to control exactly when and how much different genes were expressed.

"Light provides us a powerful new method for reliably measuring genetic circuit activity," said Tabor, an assistant professor of bioengineering who also teaches in Rice's Ph.D. program in systems, synthetic and physical biology. "Our work was inspired by the methods that are used to study electronic circuits. Electrical engineers have tools like oscilloscopes and function generators that allow them to measure how voltage signals flow through electrical circuits. Those measurements are essential for making multiple circuits work together properly, so that more complex devices can be built. We have used our light-based tools as a biological function generator and oscilloscope in order to similarly analyze genetic circuits."

Electronic circuits -- like those in computers, smartphones and other devices -- are made up of components like transistors, capacitors and diodes that are connected with wires. As information -- in the form of voltage -- flows through the circuit, the components act upon it. By putting the correct components in the correct order, engineers can build circuits that perform computations and carry out complex information processing.

Genetic circuits also process information. Their components are segments of DNA that control whether or not a gene is expressed. Gene expression is the process in which DNA is read and converted to produce a product -- such as a protein -- that serves a particular purpose in the cell. If a gene is not "expressed," it is turned off, and its product is not produced. The bacteria used in Tabor's study have about 4,000 genes, while humans have about 20,000. The processes of life are coordinated by different combinations and timings of genes turning on and off.

Each component of a genetic circuit acts on the input it receives -- which may be one or more gene-expression products from other components -- and produces its own gene-expression product as an output. By linking the right genetic components together, synthetic biologists like Tabor and his students construct genetic circuits that program cells to carry out complex functions, such as counting, having memory, growing into tissues, or diagnosing the signatures of disease in the body.

For example, in previous research, Tabor and colleagues designed genetic circuits that allowed bacteria to change their color based on incoming light. The technique allowed the team to create bacterial colonies in Petri dishes that could behave like photo paper and reproduce black and white images.

In the new study, Tabor and Olson realized that light could be used to create time-varying gene-expression signals that rise and fall, similar to those used in electronic engineering.

"In electronics, two of the key tools are function generators and oscilloscopes," said Olson, a graduate student in applied physics. "The function generator sends a known signal into the circuit being characterized. The oscilloscope is a device with a screen that the engineer uses to see the circuit output. By twisting the knobs on the function generator and viewing the corresponding output on the oscilloscope, the engineer can infer what various parts of the circuit are doing.

"The system of fluorescent reporter genes is our version of the oscilloscope," he said. "It lets us view both the circuit's input and output, and because it uses light to report on what's happening, it provides a very clean signal."

With their "bioscilloscope" in hand, the team needed a corresponding function generator. Olson, the lead author of the Nature Methods paper, put his electronics skills to work in late 2011 and invented the "light tube array," a programmable, eight-by-eight set of LED lights that will fit under a standard 64-well tray of test tubes. With the addition of some light-blocking foam around each test tube, the team had a way to send individually programmed light signals into each test tube in the array. By varying the signals and measuring the corresponding outputs with their bioscilliscope, the team was able to determine exactly how its test circuit performed.

"The precision of light allows us to create exceptionally clean gene expression signals, which we can use to extract far more information about gene circuits than was possible before," Tabor said.

"We found there was a seven-minute delay between the gene expression going into and coming out of the genetic circuit," Olson said. "We also found we could program the circuit to follow specific patterns. For example, to rise by a specific amount over a set amount of time, stop and stay at another level for a predetermined length of time and then drop down to a third level for another interval of time."

Olson said the light tube array and bioscilliscope will be useful tools for biologists to probe how nature's cells work, as well as for synthetic biologists who want to build and analyze their own circuits and networks.

"It's really about having a clean input signal, a clean output signal and the tools required to measure them," Olson said.

Tabor added, "You just never see data this clean in biology. It's remarkable."
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The research was supported by the National Science Foundation, the Office of Naval Research and NASA. Study co-authors include bioengineering graduate students Lucas Hartsough and Brian Landry and former undergraduate Raghav Shroff.

VIDEO is available at: http://youtu.be/74m-wJfaFHA

High-resolution IMAGES are available for download at:

http://news.rice.edu/wp-content/uploads/2014/02/0310-TABOR-LTA002-lg.jpg

CAPTION: Jeffrey Tabor (left) and Evan Olson with their 64-well "light tube array," a programmable platform for controlling and measuring gene expression in living cells via a combination of light and light-sensing proteins.

CREDIT: Jeff Fitlow/Rice University

http://news.rice.edu/wp-content/uploads/2014/03/einstein.jpg

CAPTION: In previous research, Rice synthetic biologist Jeff Tabor and colleagues created colonies of light-sensitive bacteria that exhibited complex patterns when exposed to images, like this portrait of Albert Einstein. In a new study, Tabor and colleagues realized that light could be used to create time-varying gene-expression signals that rise and fall, similar to those used in electronic engineering.

CREDIT: Matt Good and Jeff Tabor

A copy of the Nature Methods paper is available at:

http://dx.doi.org/10.1038/nmeth.2884

Follow Rice News and Media Relations via Twitter @RiceUNews

Located on a 300-acre forested campus in Houston, Rice University is consistently ranked among the nation's top 20 universities by U.S. News & World Report. Rice has highly respected schools of Architecture, Business, Continuing Studies, Engineering, Humanities, Music, Natural Sciences and Social Sciences and is home to the Baker Institute for Public Policy. With 3,920 undergraduates and 2,567 graduate students, Rice's undergraduate student-to-faculty ratio is 6.3-to-1. Its residential college system builds close-knit communities and lifelong friendships, just one reason why Rice has been ranked No. 1 for best quality of life multiple times by the Princeton Review and No. 2 for "best value" among private universities by Kiplinger's Personal Finance.

News Release Source :  Rice synthetic biologists shine light on genetic circuit analysis

UK Establishes Three New Synthetic Biology Research Centers

UK establishes 3 new synthetic biology research centers


Three new multidisciplinary research centres in synthetic biology will be established in Bristol, Nottingham and through a Cambridge/Norwich partnership, thanks to funding from the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC).

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The £40M+ investment will be formally announced by Minister for Universities and Science David Willetts tonight at a BBSRC event in London to mark the achievements and impact of UK bioscience over the last 20 years.

The BBSRC/EPSRC Synthetic Biology Research Centres will receive funding over five years to boost national synthetic biology research capacity and ensure that there is diverse expertise to stimulate innovation in this area. The centres will: offer a strong collaborative culture; provide essential state-of-the-art equipment, facilities, trained researchers and technical staff; drive advancement in modern synthetic biology research; and develop new technologies.

Minister for Universities and Science David Willetts, said: "Synthetic biology is one of the most promising areas of modern science, which is why we have identified it as one of the eight great British technologies of the future. Synthetic biology has the potential to drive economic growth but still remains relatively untapped and these new centres will ensure that the UK is at the forefront when it comes to commercialising these new technologies."

£10M was allocated to the synthetic biology research centres following the announcement of £600M capital investment for Research Councils in the autumn 2012 statement. BBSRC will fund just over 70% of the remaining costs and EPSRC is providing nearly 30%.

Synthetic biology is a revolutionary new way of doing bioscience which applies engineering principles to biology to make new biological parts, devices and systems. Synthetic biology builds on our knowledge of DNA sequencing and could be used to develop new medicines, chemicals and green energy sources as well as improving food crops across the world. Specific applications are already emerging, but its long-term potential for a range of industrial sectors remains largely untapped.

At this evening's BBSRC event, David Willetts will highlight how the development of the biosciences over the last two decades has given the UK a world-leading position in this area, a strong basis for advancing future scientific knowledge, and an engine for economic growth.

Professor Jackie Hunter, BBSRC Chief Executive, said: "Our continued substantial investment in synthetic biology highlights the potential of this important area of science. We must find new solutions to the major global challenges that we face today and these research centres will seek more sustainable ways of producing important industrial materials, food and fuels, while advancing diagnostics and medicines."

Professor David Delpy, EPSRC Chief Executive, said: "Synthetic biology is a very rapidly moving field, bringing together the basic physical sciences with engineering innovation and applying these in the life sciences. It has enormous potential to help us tackle many of the big issues facing the world as well as resulting in new industries. These new centres are building on a solid foundation of investment from both Research Councils that has drawn together skills and knowledge from across all scientific and engineering disciples."
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The new BBSRC/EPSRC Synthetic Biology Research Centres are:

Bristol Centre for Synthetic Biology (BrisSynBio): Led by Professor Dek Woolfson at the University of Bristol, this £14M centre will bring together scientists from a range of different research backgrounds to develop new techniques, technologies and reagents that will allow biologically-based products to be made easily, quickly and cheaply, and in sufficient quantities to make them useful. Researchers hope to develop new antibiotics; assemble virus-like particles to present new routes to vaccines; build simple cells from scratch; use red blood cells to deliver complex molecules like anti-cancer drugs directly to tumours; and reprogram bacteria to perform useful tasks like sensing environmental pollutants.

Synthetic Biology Research Centre Nottingham (SBRC Nottingham): Professor Nigel Minton at the University of Nottingham will develop a £14.3M centre to provide sustainable routes to important chemicals. They will use synthetic biology to engineer microorganisms that can be used to manufacture the molecules and fuels that modern society needs in a cleaner and greener way. They aim to use bacteria to convert gasses that are all around us (such as carbon monoxide (CO), carbon dioxide (CO2) and methane (CH4)) into more desirable and useful molecules, reducing our reliance on petrochemicals.

OpenPlant Synthetic Biology Research Centre: Scientists lead by Prof. David Baulcombe and Dr Jim Haseloff at the University of Cambridge and Prof. Dale Sanders and Prof. Anne Osbourn at the John Innes Centre will collaborate in a £12M effort to develop open technologies for plant synthetic biology. The OpenPlant initiative will establish internationally-linked DNA registries for sharing information about plant specific parts and simple testbeds. The development and exchange of new foundational tools and parts will directly contribute to the engineering of new traits in plants. OpenPlant will also provide a forum for technical exchange and wider discussion of the potential impact of plant synthetic biology on conservation and sustainability.