SynBio Cambridge http://www.synbio.org.uk/ Sat, 02 Mar 2013 05:44:20 GMT FeedCreator 1.8.1 (obRSS 1.8.11) http://www.synbio.org.uk/images/ SynBio Cambridge http://www.synbio.org.uk/ Resources for Synthetic Biology at the University of Cambridge from the www.synbio.org.uk website. How will synthetic biology and conservation shape the future of nature? http://www.synbio.org.uk/synthetic-biology-index/2713-how-will-synthetic-biology-and-conservation-shape-the-future-of-nature.html 1. What is synthetic biology and what does it have to do with conservation?
2. What is biodiversity and how might it be affected by synthetic biology?
3. The practice of conservation and how it might be affected by synthetic biology
4. Implications of synthetic biology for wider social and economic change relevant to future conservation
5. What aspects of synthetic biology should conservationists worry about and/or be excited about? And what areas of conservation should synthetic biologists worry about and/or be excited about?
6. The public landscape of synthetic biology and conservation - how can we move forward?

ConservationBee13

Synthetic biology promises to change the world in significant ways, yet it is largely unrecognized within the field of conservation. This conference will bring together the synthetic biology and the conservation practitioner communities to discuss the implications that synthetic biology may have for the natural world and conservation and develop new thinking and new strategies to cope with the potential challenges and opportunities.

Conference: April 9-11, 2013. Clare College Cambridge, England

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[email protected] (Jim Haseloff) 2013-02-22T20:51:22+00:00 http://www.synbio.org.uk/synthetic-biology-index/2713-how-will-synthetic-biology-and-conservation-shape-the-future-of-nature.html
Scientists Create Living Crystals http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2694-scientists-create-living-crystals.html

Sometimes, science follows science fiction. Take, for example, the case of 'living crystals,' which sounds like a race of alien beings. But thanks to science, theyre now real.

Physicists Jérémie Palacci and Paul Chaikin of New York University had created microscopic cubes of hematite - a compound consisting of iron and oxygen, sheathed in a spherical polymer coat with one corner exposed - that behave as if they were alive.

Under certain wavelengths of blue light, hematite conducts electricity. When the particles are placed in a hydrogen peroxide bath under blue light, chemical reactions catalyze around the exposed tips.

As the hydrogen peroxide breaks down, concentration gradients form. The particles travel down these, aggregating into crystals that also follow the gradients.
Random forces pull the crystals apart, but eventually they merge again. The process repeats again and again, stopping only when the lights go out.

The ultimate goal of the work is to study how complicated collective behaviors arise from simple individual properties, perhaps informing molecular self-assembly projects, but it’s hard not to think about the origin-of-life implications.

‘Here we show that with a simple, synthetic active system, we can reproduce some features of living systems,’ Palacci said. ‘I do not think this makes our systems alive, but it stresses the fact that the limit between the two is somewhat arbitrary.’

Chaikin notes that life is difficult to define, but can be said to possess metabolism, mobility, and the ability to self-replicate. His crystals have the first two, but not the last.

Brandon Keim of Wired has the story and video clip: Link

Scientists Create Living Crystals

(Via Neatorama.)

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[email protected] (Jim Haseloff) 2013-02-12T01:11:38+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2694-scientists-create-living-crystals.html
Novozymes Says Biofuel May Supply 90% of Its Revenue by 2030 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2679-novozymes-says-biofuel-may-supply-90-of-its-revenue-by-2030.html

Novozymes A/S, the world’s biggest maker of enzymes used in laundry soap, may get 90 percent of its revenue from biofuel makers by 2030 if more governments start promoting renewable energy, the company’s next CEO said.

Novozymes Says Biofuel May Supply 90% of Its Revenue by 2030

(Via Bioenergy News - RenewableEnergyAccess.com.)

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[email protected] (Jim Haseloff) 2013-01-26T15:33:31+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2679-novozymes-says-biofuel-may-supply-90-of-its-revenue-by-2030.html
The Tortoise Beetle - Amazing Metallic Arthropods http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2664-the-tortoise-beetle-amazing-metallic-arthropods.html

image credit: Seabrook Leckie cc

They look almost manufactured. Many tortoise beetles have transparent cuticles, the tough but flexible outer covering which gives the insect family its name protects the delicate creature within.

The living tissue is often metallic in color and can in some species even change color. The combination is as diverse as it is extraordinary - many look like tiny robots assembled to infiltrate, the ultimate bug. Take a look in at the amazing variations of tortoise beetle our world holds.

(thanks Robert-John)

The Presurfer

The Tortoise Beetle - Amazing Metallic Arthropods

(Via The Presurfer.)

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[email protected] (Jim Haseloff) 2013-01-26T12:41:56+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2664-the-tortoise-beetle-amazing-metallic-arthropods.html
Scientists Attempt to Artificially Recreate Photosynthesis in Order to Develop Efficient ... http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2658-scientists-attempt-to-artificially-recreate-photosynthesis-in-order-to-develop-efficient-renewable-energy.html photosynthesis, leaves, university of east anglia, microbes, renewable energy, hydrogen, electricity

When it comes to harnessing the power of the sun, nothing can quite compare to leaves. Using chlorophyll to convert light into usable chemical energy, photosynthesis has long been a source of inspiration for those looking to generate efficient renewable energy. With fossil fuels dwindling and polluting our environment, scientists are turning to the biological processes of nature to create clean electricity that can be used on demand. Researchers at the University of East Anglia, University of Leeds, and the University of Cambridge in the UK have been granted £800,000 to develop technology that mimics photosynthesis, with hopes of producing more efficient forms of renewable energy.

photosynthesis, leaves, university of east anglia, microbes, renewable energy, hydrogen, electricity sun, solar power, panels, leaves, photosynthesis, university of east anglia, research, renewable energy

Read the rest of Scientists Attempt to Artificially Recreate Photosynthesis in Order to Develop Efficient Renewable Energy

(Via INHABITAT.)

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[email protected] (Jim Haseloff) 2013-01-26T11:25:44+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2658-scientists-attempt-to-artificially-recreate-photosynthesis-in-order-to-develop-efficient-renewable-energy.html
The light fantastic: Harnessing Nature's glow http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2654-the-light-fantastic-harnessing-natures-glow.html
Dinoflagellates

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Bioluminescence describes the light that some living creatures such as fireflies and jellyfish emit from their cells. Harnessing these reactions has already transformed key areas of clinical diagnosis and medical research.

But scientists are now looking at whether this "living light" could help enhance food crops, detect pollution or even illuminate our journeys home.

On a night in January 1832, off the coast of Tenerife, a young Charles Darwin wandered up on to the deck of the HMS Beagle.

As the young naturalist looked out to sea, he was struck by the unearthly glow emanating from the ocean.

"The sea was luminous in specks and in the wake of the vessel, of a uniform, slightly milky colour," he wrote.

"When the water was put into a bottle, it gave out sparks for some minutes after having been drawn up."

'Natural light'

Fluorescence: Energy from an external source of light is absorbed and re-emitted. Fluorescence can only occur in the presence of this light source; it cannot happen in complete darkness.

Bioluminescence: The energy for light production comes from a chemical reaction in living cells, as opposed to the absorption of photons as happens in fluorescence.

Darwin was almost certainly describing the light emitted by tiny marine organisms called dinoflagellates. His accounts of this phenomenon, known as bioluminescence, were unearthed by Prof Anthony Campbell in hand-written notebooks stored at Cambridge University.

While Darwin was one of the first modern scientists to document the phenomenon, it would be more than a century before it was put to practical use. Prof Campbell, from Cardiff University, carried out pioneering research throughout the 1970s and 1980s leading to the discovery that living creatures produce this light using special proteins called luciferases. The proteins take part in a chemical reaction in the cells, which is responsible for the light emission.

"When I started researching bioluminescence 40 years ago at the [Cardiff University] medical school, a lot of people raised their eyebrows and said: 'What the devil is this guy doing working on animals in the sea? He was brought from Cambridge to do medical research'," Prof Campbell explains.

But he was able to spot the phenomenon's potential. Having discovered the proteins involved in bioluminescence, he realised that by combining luciferases with other molecules, it was possible to harness this light emission to measure biological processes.

Jellyfish

This would pave the way for something of a revolution in medical research and clinical diagnosis.

For example, by attaching a luminescent protein to an antibody - a protective molecule produced by the body's immune system - it could be used to diagnose disease. This allowed clinicians to dispense with the radioactive markers that had previously been used in such tests.

"This market is now worth about £20bn. If you go into a hospital and have a blood test which measures viral proteins, cancer proteins, hormones, vitamins, bacterial proteins, drugs, it will almost certainly use this technique," Prof Campbell told BBC News.

Bioluminescent proteins are also tools in drug discovery and have found widespread applications in biomedical research, where they are used to study biological processes in live cells.

"If you've got a university department that doesn't use these techniques, they are not at the cutting edge," says Campbell.

Other applications are on the horizon. At the University of Lausanne in Switzerland, Prof Jan van der Meer has developed a test for the presence of arsenic in drinking water using genetically modified bacteria.

Arsenic contamination of groundwater is a pernicious problem in some parts of the world, especially in Bangladesh, India, Laos and Vietnam.

Prof van der Meer's microbes have been engineered to emit light when they come into contact with arsenic-containing compounds. Potentially contaminated water is injected into vials, activating the dormant GM bacteria. The extent to which the microbes emit light is then measured to provide an indication of arsenic concentrations in the water.

Glowing trees   Cambridge iGEM

The work is now being commercialised by the German firm Arsolux. Prof van der Meer says the bacterial-based kits cope well with multiple samples, require fewer materials than standard chemical testing field kits, and are easy to prepare.

But regulatory hurdles remain to the take-up of bacteria-based tests in these countries. And, Prof van der Meer adds: "In the end it comes down to market things… things you cannot control as a scientist."

So called rainbow proteins (a spin-off from work into bioluminescence), which change colour in response to particular compounds, are also an option for detecting environmental toxins, or the potential agents of terrorism.

There are already several consumer applications of bioluminescence: one US firm has made use of it to manufacture luminous drinks for sale in nightclubs.

And researchers have even modified plants so that they emit light. Bioluminescent crops could indicate when they require water and nutrients, or warn of disease and infestation. However, the controversy surrounding GM foods has so far prevented these ideas from taking hold.

A few years ago, a team of undergraduates at Cambridge University researched the idea of luminescent trees that would act as natural "street lamps".

"What we achieved in that project was to put together some DNA which allowed bioluminescence, to show that it worked in [the bacterium] E. coli, and to submit it to the 'parts registry' which holds this DNA so anyone else can use it in future," team member Theo Sanderson told BBC News.

"We were approached about a year ago and offered funding to continue developing the project, but we have all gone on to other things and so it wasn't really an option."

Previous efforts to create light-emitting plants in the lab have made use of a luciferase gene derived from fireflies. But these plants can only glow when supplemented with an expensive chemical called luciferin. The method used by the Cambridge team is attractive because it is based on bacterial systems which produce their own fuels for luminescence and so can be fed normal nutrients.

Firefly

In 2010, a separate team published a study in which they were able to demonstrate that such methods could be used to create plants that glowed without the need for chemical supplements. The US-Israeli team of scientists inserted light-emitting genes from bacteria into the plants' chloroplasts - the structures in their cells which convert light energy from the Sun into chemical fuel.

Mr Sanderson, who now works at the Sanger Institute near Cambridge, said this was a good choice because chloroplasts are essentially bacteria that have become incorporated into plant cells, so they can easily express the microbe-derived gene without the need for other modifications.

But researchers will need to find ways to boost the light emission from such lab organisms if GM trees are ever to light our way through the urban jungle.

Prof Campbell says the potential of luminescent proteins in drug discovery and medical research has not yet been fully exhausted and he is currently collaborating on a project to use luciferases to research Alzheimer's disease.

Bioluminescent creatures might also provide a convenient means of studying environmental changes in the sea. Some animals obtain the light-emitting chemicals they need from the organisms they eat. So studying the interactions between these species might allow scientists to detect changes in marine food webs.

Despite the impact on clinical diagnosis and research, Prof Campbell points out that he has only ever received one grant to research bioluminescence. Nevertheless, he says it is a "beautiful example of how curiosity - quite unexpectedly - has led to major discoveries in biology and medicine. And it has created several billion dollar markets".

[email protected]

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[email protected] (Jim Haseloff) 2013-01-25T22:08:24+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2654-the-light-fantastic-harnessing-natures-glow.html
These Spiders Are Frightening and Beautiful At the Same Time http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2618-these-spiders-are-frightening-and-beautiful-at-the-same-time.html Click here to read These Spiders Are Frightening and Beautiful At the Same Time

If you have a fear of spiders, you might not want to click through. But if you have a love for bright, colorful objects, then go right ahead! More »

(Via Gizmodo.)

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[email protected] (Jim Haseloff) 2013-01-19T16:37:39+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2618-these-spiders-are-frightening-and-beautiful-at-the-same-time.html
The Brazilian Treehopper may be the strangest creature we've ever laid eyes on http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2610-the-brazilian-treehopper-may-be-the-strangest-creature-weve-ever-laid-eyes-on.html Click here to read The Brazilian Treehopper may be the strangest creature weve ever laid eyes on

Because holy crap, just look at that headgear. Everyone, meet Bocydium globulare. Better known as the Brazilian treehopper, B. globulare excels at living a solitary life, hanging out on the leaves of glory bushes, and head-sphering its way into your nightmares. More »

(Via io9.)

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[email protected] (Jim Haseloff) 2013-01-19T14:54:32+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2610-the-brazilian-treehopper-may-be-the-strangest-creature-weve-ever-laid-eyes-on.html
New challenges and opportunities for industrial biotechnology. http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2578-new-challenges-and-opportunities-for-industrial-biotechnology.html New challenges and opportunities for industrial biotechnology.

Related Articles

New challenges and opportunities for industrial biotechnology.

Microb Cell Fact. 2012 Aug 20;11(1):111

Authors: Chen GQ

Abstract
ABSTRACT: Industrial biotechnology has not developed as fast as expected due to some challenges including the emergences of alternative energy sources, especially shale gas, natural gas hydrate (or gas hydrate) and sand oil et al. The weaknesses of microbial or enzymatic processes compared with the chemical processing also make industrial biotech products less competitive with the chemical ones. However, many opportunities are still there if industrial biotech processes can be as similar as the chemical ones. Taking advantages of the molecular biology and synthetic biology methods as well as changing process patterns, we can develop bioprocesses as competitive as chemical ones, these including the minimized cells, open and continuous fermentation processes et al.

PMID: 22905695 [PubMed - as supplied by publisher]

(Via pubmed: "synthetic biology".)

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[email protected] (Jim Haseloff) 2013-01-14T19:59:15+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2578-new-challenges-and-opportunities-for-industrial-biotechnology.html
The PLOS ONE Synthetic Biology Collection: Six Years and Counting. http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2577-the-plos-one-synthetic-biology-collection-six-years-and-counting.html The PLOS ONE Synthetic Biology Collection: Six Years and Counting.

Related Articles

The PLOS ONE Synthetic Biology Collection: Six Years and Counting.

PLoS One. 2012;7(8):e43231

Authors: Peccoud J, Isalan M

Abstract
Since it was launched in 2006, PLOS ONE has published over fifty articles illustrating the many facets of the emerging field of synthetic biology. This article reviews these publications by organizing them into broad categories focused on DNA synthesis and assembly techniques, the development of libraries of biological parts, the use of synthetic biology in protein engineering applications, and the engineering of gene regulatory networks and metabolic pathways. Finally, we review articles that describe enabling technologies such as software and modeling, along with new instrumentation. In order to increase the visibility of this body of work, the papers have been assembled into the PLOS ONE Synthetic Biology Collection (www.ploscollections.org/synbio). Many of the innovative features of the PLOS ONE web site will help make this collection a resource that will support a lively dialogue between readers and authors of PLOS ONE synthetic biology papers. The content of the collection will be updated periodically by including relevant articles as they are published by the journal. Thus, we hope that this collection will continue to meet the publishing needs of the synthetic biology community.

PMID: 22916228 [PubMed - in process]

(Via pubmed: "synthetic biology".)

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[email protected] (Jim Haseloff) 2013-01-14T19:56:39+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2577-the-plos-one-synthetic-biology-collection-six-years-and-counting.html
Industrial pitches in Cambridge http://www.synbio.org.uk/synthetic-biology-index/2576-industrial-pitches-in-cambridge.html IfMpitchevent2013

The Cambridge University Institute for Manufacturing’s Open Innovation Forum is holding an “Innovation Pitching Event” on 11 March 2013. Over 15 major global players in the Food and FMCG industries (including Global brand owners Unilever, GlaxoSmithKline, Mars, Bacardi and General Mills; Packaging suppliers: Crown, MeadWestvaco; Ingredients and materials suppliers: DSM, Cargill, Imerys and Tate & Lyle and Process equipment suppliers Siemens and Domino) will be in Cambridge to find Innovative solutions for opportunities they have identified from Life sciences (Including ingredients, health, food safety, preservatives and synthetic biology); Materials (Including packaging materials, waste reduction and sustainability); Manufacturing (Including customisation, batch-of-one and novel food processing); IT / electronics (Including smart packaging, communications, tagging & ID and E-science) and Marketing and business models (Including social media, digital marketing and new business models). You can find more information and a web entry form at http://www.ifm.eng.cam.ac.uk/events/oipitching/

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[email protected] (Jim Haseloff) 2013-01-14T19:17:49+00:00 http://www.synbio.org.uk/synthetic-biology-index/2576-industrial-pitches-in-cambridge.html
Top 10 Innovations 2012 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2572-top-10-innovations-2012.html

The Scientist’s 5th installment of its annual competition attracted submissions from across the life science spectrum. Here are the best and brightest products of the year.

By The Scientist Staff | December 1, 2012

© PAUL EDMONDSON/CORBIS

Innovation has been a buzzword since at least the early 1990s. A Wall Street Journal article published earlier this year bemoaned the more recent overuse of the word, citing its appearance in product descriptions by soup makers, bubble-wrap manufacturers, and dried cranberry producers among more than 33,000 companies whose 2011 quarterly and annual reports featured the word. Such ubiquitous usage may be diluting the very meaning of innovation. But as the global economy searches for ways out of its current morass, the word is again fresh on many lips—innovation economy, innovation strategies, innovation officers, and the foreboding-sounding innovation gap.

With The Scientist’s fifth installment of our annual Top 10 Innovations competition we refocus on the core meaning of  “innovation”—to whit: a new idea, method, or device, according to the Merriam-Webster dictionary. And this year’s crop of winning products speaks directly to this simple definition.

From a 3-D system for culturing cells and tissues and a synthetic gene service to a laboratory organization Web and iPad app (one that is coincidentally featured in this month’s Careers article “Lab 2.0” on page 67) and products that showcase the latest in rapid, cheap genome sequencing, this year’s winners exemplify true innovation. And to celebrate that spirit of inventive creativity, in which researchers and product developers push the technological envelope in order to propel science and our exploration of life, we present The Scientist’s Top 10 Innovations of 2012.


BioFab

GEN9

Modern pharmaceutical, chemical, and fuel companies increasingly depend on synthetic biology to produce DNA tailor-made to suit their production needs. Making synthetic genes to program microorganisms used to require a lot of time, in addition to expensive robots and other equipment, but Gen9 has developed BioFab, a new system that can quickly and cheaply produce tens of thousands of double-stranded DNA fragments of between 500 and 1,000 base pairs in length. The company’s system for “biological fabrication” couples inexpensively made small DNA fragments with patented or patent-pending chemical processes that accurately assemble them into larger DNA strands, which the platform can do in bulk. Though pricing varies with the amount of synthetic DNA and the modifications a customer needs, the cost can be less than 10 cents per base pair, which is as little as 1/5 of what some competitors charge, according to Gen9 President and CEO Kevin Munnelly. “The ability to synthesize large numbers of genes in parallel at low cost could transform the field of computational protein design,” says molecular engineer David Baker of the University of Washington, who is a customer and a member of the Gen9 advisory board.

The company, which launched this summer, currently has about 20 customers—half from industry, half from academia. Gen9’s high-throughput manufacturing process allows the company to reduce both the cost and the production time of synthetic DNA. By 2013, Gen9 hopes to singlehandedly surpass the world’s current capacity to manufacture synthetic DNA.

WILEYBrings the cost and speed of DNA synthesis down to the point where entire vectors can be designed and assembled from scratch. A critical component needed to make synthetic biology a reality.


Ion Proton System

Life Technologies

Human-scale genome sequencing just got a whole lot more accessible. Twelve years ago, it cost $1 billion to sequence a single human genome. By next year, using Life Technologies’ Ion Proton machine, it will take less than a day and cost $1,000 (not including analysis costs, of course).

Launched in September, Ion Proton is driven by the same semiconductor technology—which converts chemical information directly into digital data—that powers the successful Personal Genome Machine (PGM). For now, the Proton I chip sequences a human exome in a few hours. But in early 2013, Life Technologies will release the Proton II chip, designed to handle an entire human genome, from sample prep to full sequence, in 8 hours. The Ion Proton costs $244,000, and each disposable one-run chip goes for $1,000.

“We’ve piggybacked on over a decade of investment in semiconductor technology to bring a dramatic reduction in cost and increase in speed,” says Maneesh Jain, VP of business development and marketing at Ion Torrent, the sequencing technology start-up acquired by Life Technologies in 2010. By making large-scale sequencing more widely available, this machine will enable a new era of discovery, he adds.  

“This will give us the capacity to quickly go after the whole exome, whereas on the PGM we were looking at 20 to 50 genes at a time,” says Christopher Corless, medical director at Oregon Health and Science University’s Knight Diagnostic Laboratories in Portland, who plans to use the Ion Proton to look for mutations in tumors that can be targeted by new pharmaceuticals. “That will be a big jump forward.”

MAZARThis opens up all sorts of possibilities for interpretation of animal experiments, clinical trials, and the evaluation of new therapeutic interventions.


MyCell Services

Cellular Dynamics International

This October, Shinya Yamanaka shared the 2012 Nobel Prize in Physiology or Medicine for his discovery that injecting a few transcription factors into a differentiated adult cell can render that cell pluripotent once again. The technology revolutionized biomedical research, allowing scientists to create induced pluripotent stem cell (iPSC) models for a variety of diseases. Now, Cellular Dynamics International (CDI) is utilizing that technology to offer, via the company’s MyCell Services, iPSC lines from any patient of interest, as well as differentiated cell lines derived from the iPSCs.

“[Customers] don’t have to be stem-cell biologists to leverage this technology,” says Chris Parker, CDI’s chief commercial officer. “They can simply be interested in a disease state and get the human cells they need to answer appropriate questions.”

Paul Watkins, for example, director of The Hamner–University of North Carolina Institute for Drug Safety Sciences, is using MyCell Services to create iPSC-derived hepatocytes from patients who have survived severe liver reactions to drugs, comparing them to iPSC-derived hepatocytes from healthy donors. Ultimately, he says, the goal is to identify specific genetic profiles that indicate susceptibility to adverse drug reactions. “We have the whole exome sequence [for these patients], and we will have [the] whole genome sequence, so we know the variations that exist and have various hypotheses,” Watkins says. “But this [technology] will allow us to test, directly, those hypotheses.”

The iPSC lines are derived from CD34 cells in blood samples sent in by customers, and returned as 96-well plates of a cell type of interest. To create an iPSC line from a patient sample costs $15,000 and takes about 6 months, Parker says, but once the iPSC lines are established, it takes just 1 to 2 months to order more specific cell types derived from that line. The cost per plate for differentiated cells is approximately $1,500, with a minimum order of 20 plates.

CHANDLERThe ability to produce induced pluripotent stem cells “on demand” with high quality and purity has high potential to transform both numerous fields of life sciences research and open the door to potential medical applications.


Labguru

BioData

Vanishing are the days when grad students and postdocs scribble their experimental setups and data in splotched black-and-white notebooks. Labs across the world are going digital, and Labguru is a new product that could change the way that labs chart their progress.

Labguru (coincidentally featured in this month’s Careers article “Lab 2.0”) is a digital platform, accessible via an Internet browser or as an iPad app, that stores data from different investigators in a lab, tracks reference materials, logs logistical information such as reagent inventory, and can be used to share experimental protocols and other useful tidbits. “Our biggest concern is to get labs to run more efficiently and to be more productive,” says Jonathan Gross, founder of BioData Ltd., the Israel-based company that created Labguru.

Gustavo Valbuena, a research pathologist at University of Texas Medical Branch at Galveston who studies the pathogenesis of Rocky Mountain spotted fever among other phenomena, has used Labguru in his lab for the past 9 months. After trying other software and electronic lab notebooks to organize activity and data in his lab, he found Labguru to be most effective in upping his students’ and technicians’ productivity and accountability. “What I see is that people in the lab are more consistently entering their data there,” says Valbuena, who pays about $100 per user per year for the upgraded version of Labguru. Use of the basic iPad app and Web version is free.

WILEYThis could finally start to bring experimental biologists out of the paper age and into the computer age.


MiSeq

Illumina

Illumina has incorporated its ubiquitous sequencing by synthesis (SBS) technology into a stripped down “personal sequencer” called MiSeq—a faster, cheaper, and simpler benchtop machine that aims to bring next-gen sequencing into the mainstream.

For a 2-square-foot device it packs a lot of throughput, supporting 2x250 base pair runs and generating up to 8.5 gigabases per run. And MiSeq’s intuitive interface makes it very user-friendly. “We’ve taken what Illumina has done over the past 5 years and condensed [everything] into a really simple package,” says Jeremy Preston, Illumina’s director of product marketing. Just prepare the DNA, load the cartridge, and press “Go.”

It’s fast, too: users can prepare samples in 90 minutes and sequence an entire microbial genome in a day or less. And at $125,000 per machine—with individual runs costing from $400 to $750—MiSeq is affordable enough to use in clinical settings.

The FDA has already tapped MiSeq for use in its efforts to track food-borne pathogens. Over the next 2 years, it will also be used to track superbug outbreaks in hospitals, says Derrick Crook, a microbiologist at the University of Oxford, U.K., and coauthor of a recent pilot study into the use of MiSeq for the surveillance of C. difficile and MRSA in several UK hospitals, published in BMJ Open. “You get really high-quality sequencing in a very short turnaround time,” he says. “It’s a huge step forward.”

MAZARFast, small footprint, expands ability of preclinical and clinical researchers to get genomic sequence data that can then be rapidly correlated with drug response, etc.


ONIX Microfluidic Platform

CellASIC

The CellASIC ONIX Microfluidic Perfusion Platform is putting a new spin on live-cell imaging. The setup looks like a rearranged 96-well plate with a glass bottom. Cells placed in inlet wells flow into a culture chamber, where they are subject to a dynamic environment designed by the user. In other plate wells, researchers can put various media, drugs, and other variables. Then, the plate is placed under a microscope and hooked up to a machine that can be programmed to control the flow of the wells’ contents via microchannels into and out of the culture chamber.

“You pipette in all your chemistry—your media, your cells—and then you go to the software and program all your automated steps,” says Alex Mok, a product manager at CellASIC, now part of EMD Millipore. “The researcher has the ability to control exactly what’s going in and what’s coming out of that chamber. . . [and] you don’t have to come in on weekends to watch your cells.”

The system, originally released in 2009, got a makeover this year, with completely revamped hardware and software, and the ability to control the temperature and gas pressure in the chamber, in addition to the chemistry. The system is perfect for use in core facilities, says Jennifer Waters, microscopy director at the Nikon Imaging Center at Harvard Medical School, which acquired an ONIX system last fall. “Because it works by pneumatics, it’s just air flowing through . . . [so] we don’t have to worry about our ONIX system being contaminated in any way with the user sample.” Plus, with several different plate types tailored to specific applications, “you can image anything from bacterial to mammalian cells,” she says.

The entire ONIX setup costs $23,000 and comes with five starter plates. Additional plates are sold in five-packs for $400.

MAZARIf utilized in conjunction with 3-D systems, this platform could provide a tremendous opportunity to study the dynamics and pharmacology of drug delivery.


NanoLuc Luciferase Technology

Promega

Luminescence reporter assays have become indispensable tools for immunologists, cell and molecular biologists, geneticists, and other researchers seeking to shine a light on the molecular dynamics of a cell. Into the mix of luminescence options, which includes firefly luciferase and green fluorescent protein (GFP), Promega has now introduced a new fluorescent reporter enzyme called NanoLuc Luciferase, derived from an enzyme found in a deep-sea shrimp of genus Oplophorus.

The new tool offers several improvements over other luminescent reporters. Its small size—about 2/3 as large as GFP—makes NanoLuc less likely to disrupt the cellular processes researchers are using it to probe. It can also shine up to 240 times as brightly as firefly luciferase. “Bioluminescence has become one of the fundamental measurement technologies used in life science,” says Promega head of research Keith Wood. “We think with NanoLuc we’ve advanced that technology in a number of ways.”

NanoLuc user Samuel Hasson, a pharmacology research fellow at the National Institute of Neurological Disease and Stroke, agrees. Without the small size and brighter glow of NanoLuc, Hasson says that his in vitro studies of mitochondrial dysfunction’s role in Parkinson’s disease would not even be possible. “The signal that you get from the NanoLuc is much brighter,” he says. “So when you have cases of low gene expression, the level of signal you get is much higher” than with a firefly luciferase. Plus, “you perturb the natural process less when you have a smaller reporter tagged onto the mitochondrial protein.”

The DNA plasmid containing the genetic content needed to produce NanoLuc runs about $320, and the substrate used to detect the molecule’s glow is another $125, according to Kevin Kopish, global product manager for NanoLuc. Researchers can expect to pay recurring reagent costs.

CHANDLERThe increased sensitivity, small size of the protein, and the high stability could result in dramatic changes in reporter assays across many systems.


xSCELL Digital Scientific Camera

Photonis

The new Photonis xSCell Digital Scientific Camera combines low-light capability, high speed, and high resolution. The camera can connect easily to a microscope—via a C-mount—shoot at 1024x1024 pixel resolution, capture images at 1000 frames per second, quickly switch to streaming video at full resolution, store up to 16GB of data, and (depending on the model) be cooled to -30 °C.

“There is a push for higher speed in modern fluorescence microscopy techniques, especially super-resolution microscopy,” says xSCell user and Yale School of Medicine cell biologist Joerg Bewersdorf. “High sensitivity down to the single-molecule level is required. The new xSCell camera, with its dramatically improved speed, represents another large step in this direction, and will help to advance the field of biomedical microscopy.”

Photonis director of imaging products Marc Neglia points out that the camera will be useful in a wide range of applications, including astronomy as well as spectroscopy and any high-throughput screening, particularly because the high-end model can be cooled to -30 °C, which helps reduce the snow-like effect on images caused by the camera’s sensors getting too hot—a common problem with digital photography.

The xSCell digital camera sells for a little more than $40,000. Having just started shipping this new model, the company has sold about 10 so far this year and expects to sell 50 in 2013.

WILEYThis camera offers a revolutionary combination of speed, resolution, and sensitivity. This should be a great boost to developing ultra-resolution microscopy technologies, which are normally limited by the slow speed of high-resolution cameras.


Photo-Morpholinos

Gene Tools

Morpholino oligomers (oligos) are molecules that bind to RNA and are commonly used to disrupt gene expression. To have better control over when and where target RNAs are knocked down, biotech company Gene Tools devised Photo-Morpholinos, photo-cleavable morpholinos that can be used to turn gene expression on and off in an organism or tissue culture at particular times using light.  When sense Photo-Morpholinos bind to antisense morpholino oligos, the Photo-Morpholino acts as a cage to prevent the antisense morpholino oligo from interacting with its target RNA and reducing gene expression. But shine a little UV light on the system, and the Photo-Morpholino pops off, initiating gene knockdown. Or, antisense Photo-Morpholinos can directly bind the sense RNA target, but the knockdown is reversible with illumination, which cleaves and inactivates the morpholino oligo.

The technique allows researchers to look at the effects of genes in specific tissues of an organism or during different periods of development. George Eisenhoffer, a postdoc in Jody Rosenblatt’s lab at the University of Utah’s Huntsman Cancer Institute, and his colleagues used Photo-Morpholinos to knock down the gene for a stretch-activated channel called Piezo1, which they hypothesized to play a role in the extrusion of live cells from epithelial membranes as cells become overcrowded. When Eisenhoffer used a traditional morpholino for Piezo1, zebrafish embryos died very early in development. But with Photo-Morpholinos, he was able “to bypass those defects early in development,” knocking down Piezo1 only after it was not lethal to the animals. Sure enough, inhibiting Piezo1 expression later in development led to cell masses on the zebrafish’s sides, indicating their membranes had failed to properly extrude epithelial cells (Nature, 484:546-49, 2012).

The company, located in Philomath, Oregon, has sold about 30 custom-made Photo-Morpholinos since the product was launched this past summer, says Jon Moulton, a researcher at Gene Tools. At $700 for 300 nanomoles—enough to inject more than 1,000 zebrafish, for example—the product is not a blockbuster, but “we never saw this one as a big moneymaker,” he says. “It was one that our customers really, really wanted.”

CHANDLERThis could potentially dramatically change how genetic manipulation experiments are done in cell cultures as well as numerous organisms.


HubioGEM + the Wiggler

Vivo Biosciences + Global Cell Solutions

For scientists researching new therapies and conducting toxicity screening, biologically realistic 3-D cell constructs are important. But they’re also tricky. Enter HubioGEM, a product jointly developed by Vivo Biosciences (which makes HuBiogel, a human-derived biogel matrix) and Global Cell Solutions (which makes the GEM magnetic microcarrier).

Unlike animal-derived matrices, the biogel supports cells in an environment that approximates human tissue biology. Meanwhile, the microcarriers—made up of a semi-porous hydrogel filled with magnetic particles—provide magnetic control of cell clusters during collection or media exchange without interfering with analysis or screening. Together in a single mixture, they offer a better way to generate and manage 3-D tumor or stem-cell constructs that accurately mimic in vivo metabolic function.

Throw in the Wiggler—a bioreactor system from Global Cell Solutions designed to grow and maintain more robust cultures than conventional multiwell plate or mixing-flask methods, launched this October—and you have a new platform for predictive bioassays. “We’ve stacked several advantageous traits into a single solution,” says Uday Gupta, CEO of Global Cell Solutions. “The end result is healthier, longer-lasting, more manageable, and physiologically relevant cell cultures.”

Such qualities have proven “extremely valuable” for Eric Murphy, who works on cancer pharmacology at the Genomics Institute of the Novartis Foundation in San Diego, California. “We do a lot of our drug combination screens in this format now, and we’re seeing a lot of therapeutics you would have skipped over in our traditional screens,” he says. “I think it’s getting us closer to predicting what will happen in vivo.”

MAZARThe platform proposed herein sounds like it will overcome the challenges of 2-D systems, which can be poor predictors of in vivo activity and inaccurate in their representation of tumor cell–microenvironment interactions.



MEET THE JUDGES

ANDREW MAZAR is the entrepreneur-in-residence in the Chemistry of Life Processes Institute and serves as the managing director of the Center for Developmental Therapeutics (CDT) at Northwestern University. He has spent 23 years working on drug discovery and development at the interface of academia and industry, and is also recognized for his basic research work on the role of the urokinase plasminogen activator (uPA) system in tumor progression and angiogenesis. Mazar is also the chair of the National Cancer Institute’s Nano Alliance Animal Model Working Group and a charter member on the NCI Developmental Therapeutics study section.GABRIEL POPESCU is an assistant professor at the University of Illinois at Urbana-Champaign (UIUC) in the Department of Electrical and Computer Engineering and holds a full faculty appointment with the Beckman Institute for Advanced Science and Technology. He is also an affiliate faculty member in the Bioengineering Department. Popescu received the 2009 National Science Foundation CAREER Award, was the 2012 Innovation Discovery Finalist selected by the Office of Technology Management Office, UIUC, and was elected as the 2012–2013 Fellow of the Center for Advanced Studies at UIUC. He is an associate editor of Optics Express and Biomedical Optics Express, and an editorial board member of the Journal of Biomedical Optics.VICKI CHANDLER is chief program officer for the Gordon and Betty Moore Foundation’s Science Program, which invests in technology development and supports top research scientists and new scientific partnerships. That investment portfolio includes the Marine Microbiology Initiative, plant science collaboration with Howard Hughes Medical Institute, the Data-Driven Discovery Initiative, and the Thirty Meter Telescope project. Previously Chandler led research programs in epigenetics at the University of Oregon and the University of Arizona.H. STEVEN WILEY is currently a Senior Research Scientist and Laboratory fellow at Pacific Northwest National Laboratory. He published some of the earliest computer models of receptor regulation (early 1980s) and is known for developing a variety of quantitative biochemical and optical assays as a basis for validating computational models of cell processes. His current research is focused on the integration of multiple types of high-throughput data to reconstruct cell regulatory networks. Wiley is also a frequent contributor to The Scientist.

 

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[email protected] (Jim Haseloff) 2012-12-09T22:17:56+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2572-top-10-innovations-2012.html
Design, implementation and practice of JBEI-ICE: an open source biological part registry ... http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2562-design-implementation-and-practice-of-jbei-ice-an-open-source-biological-part-registry-platform-and-tools.html Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

Nucleic Acids Res. 2012 Jun 19;

Authors: Ham TS, Dmytriv Z, Plahar H, Chen J, Hillson NJ, Keasling JD

Abstract
The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

PMID: 22718978 [PubMed - as supplied by publisher]

(Via pubmed: "synthetic biology".)

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[email protected] (Jim Haseloff) 2012-08-29T18:21:31+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2562-design-implementation-and-practice-of-jbei-ice-an-open-source-biological-part-registry-platform-and-tools.html
Gprize 2012 for Synthetic Biology http://www.synbio.org.uk/synthetic-biology-index/2548-gprize-2012-for-synthetic-biology.html GprizeIcon

Gen9 has developed a unique technology to synthesize DNA constructs and has used it to build a novel fabrication capability for next-generation gene synthesis known as the BioFab® platform. The BioFab® platform has the capacity to generate tens of thousands of synthetic gene fragments per year in just a few square feet of laboratory space. Today, Gen9 is manufacturing and shipping double-stranded GeneBits™ DNA constructs, or gene fragments, from 500 to 1,024 base pairs long.

The inaugural G-Prize contest, conceived and exclusively sponsored by Gen9, was launched to foster creative and innovative approaches for using synthetic DNA libraries to constructively advance industries such as pharmaceuticals, chemicals, biofuels and agriculture.

If you also believe in the potential of synthetic biology, tell us how you want to revolutionize an industry through your research. Winners of the inaugural G-Prize will receive a free library of up to 500 GeneBits™ DNA constructs! Each GeneBits™ construct is a double-stranded gene fragment from 500 to 1,024 base-pairs in length, with error rates better than 1:2,500 when shipped as linear DNA, confirmed by consensus sequencing.
The G-Prize contest is open to academic and non-profit scientists only. Deadline for entries is September 30, 2012. More details at: http://gen9bio.com/g-prize/

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[email protected] (Jim Haseloff) 2012-07-23T17:35:18+00:00 http://www.synbio.org.uk/synthetic-biology-index/2548-gprize-2012-for-synthetic-biology.html
Strategic roadmap for Synthetic Biology in the UK http://www.synbio.org.uk/synthetic-biology-index/2547-strategic-roadmap-for-synthetic-biology-in-the-uk.html SynBioSIG

A strategic roadmap for synthetic biology was published in July 2012 with the key purpose of developing 'a roadmap that defines the likely timeframe and actions required to establish a world leading Synthetic Biology industry within the UK.’ The roadmap, produced by an independent panel of experts for the government's Department for Business Innovation and Skills, sets out a shared vision for realising the potential of synthetic biology in the UK.

Five core themes for the roadmap emerged from this work:
1. Foundational science and engineering: the need for sufficient capabilities for the UK to maintain a leading edge
2. Continuing responsible research and innovation: including the need for awareness, training and adherence to regulatory frameworks
3. Developing technology for commercial use
4. Applications and markets: identifying growth markets and developing applications
5. International cooperation

To achieve this, the roadmap outlines five key recommendations:
1. Invest in a network of multidisciplinary centres to establish an outstanding UK synthetic biology resource.
2. Build a skilled, energised and well-funded UK-wide synthetic biology community [via the Synthetic Biology Special Interest Group].
3. Invest to accelerate technology responsibly to market.
4. Assume a leading international role.
5. Establish a leadership council

The roadmap report and an A3 schematic representation of the timelines are available online, after registration at: https://connect.innovateuk.org/web/guest

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[email protected] (Jim Haseloff) 2012-07-23T06:39:07+00:00 http://www.synbio.org.uk/synthetic-biology-index/2547-strategic-roadmap-for-synthetic-biology-in-the-uk.html
Starbucks Swaps Crushed Parasitic Beetle Food Coloring for Tomat-O-Red Dye in Strawberry Drinks http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2529-starbucks-swaps-crushed-parasitic-beetle-food-coloring-for-tomat-o-red-dye-in-strawberry-drinks.html Tomatored, Lycored, starbucks, cochineal, carmine, natural dye

We were recently shocked to learn that Starbucks’ strawberry drinks are colored with ‘carmine’ – a dye made from crushed parasitic beetles. Those of us on an insect-free diet can now breathe a sigh of relief, as Starbucks just announced that their products from now on will get that extra splash of red from the vegan-friendly Tomat-O-Red dye. The all-natural color is produced by Israel-based company ‘Lycored’ and it’s – in contrast to carmine – claimed to be a healthy colorant full of antioxidants.

Tomatored, Lycored, starbucks, cochineal, carmine, natural dye Tomatored, Lycored, starbucks, cochineal, carmine, natural dye Tomatored, Lycored, starbucks, cochineal, carmine, natural dye Tomatored, Lycored, starbucks, cochineal, carmine, natural dye


Read the rest of Starbucks Swaps Crushed Parasitic Beetle Food Coloring for Tomat-O-Red Dye in Strawberry Drinks

(Via INHABITAT.)

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[email protected] (Jim Haseloff) 2012-07-07T23:17:49+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2529-starbucks-swaps-crushed-parasitic-beetle-food-coloring-for-tomat-o-red-dye-in-strawberry-drinks.html
Genetic switchboard for synthetic biology applications. http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2491-genetic-switchboard-for-synthetic-biology-applications.html Publication Date: 2012 Mar 27 PMID: 22454498
Authors: Callura, J. M. - Cantor, C. R. - Collins, J. J.
Journal: Proc Natl Acad Sci U S A

A key next step in synthetic biology is to combine simple circuits into higher-order systems. In this work, we expanded our synthetic riboregulation platform into a genetic switchboard that independently controls the expression of multiple genes in parallel. First, we designed and characterized riboregulator variants to complete the foundation of the genetic switchboard; then we constructed the switchboard sensor, a testing platform that reported on quorum-signaling molecules, DNA damage, iron starvation, and extracellular magnesium concentration in single cells. As a demonstration of the biotechnological potential of our synthetic device, we built a metabolism switchboard that regulated four metabolic genes, pgi, zwf, edd, and gnd, to control carbon flow through three Escherichia coli glucose-utilization pathways: the Embden-Meyerhof, Entner-Doudoroff, and pentose phosphate pathways. We provide direct evidence for switchboard-mediated shunting of metabolic flux by measuring mRNA levels of the riboregulated genes, shifts in the activities of the relevant enzymes and pathways, and targeted changes to the E. coli metabolome. The design, testing, and implementation of the genetic switchboard illustrate the successful construction of a higher-order system that can be used for a broad range of practical applications in synthetic biology and biotechnology.

post to: CiteULike

Genetic switchboard for synthetic biology applications.

(Via PNAS.)

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[email protected] (Jim Haseloff) 2012-04-04T23:20:34+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2491-genetic-switchboard-for-synthetic-biology-applications.html
Video: Cambridge Researchers Use Legos to Build Artificial Bone in the Lab http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2476-video-cambridge-researchers-use-legos-to-build-artificial-bone-in-the-lab.html

Lego Mindstorms in the Lab

Researchers at Cambridge University are building artificial bone in the lab, and they're doing so with what might be considered an unorthodox partner: Lego. The tedious process of building up a sample of artificial bone requires a lot of repetitive dipping of samples into various substances, rinsing, and repeating. So to automate sample creation, the researchers built a couple of inexpensive laboratory robots using Lego Mindstorms.

The robots, as you will see in the video below, handle the sample creation duties, freeing up the human researchers to focus on other laboratory tasks. Which is pretty clever. Lego, for its part, sees an expanding role for itself in the laboratory and in education in general. The company has teamed up with Google for the 2012 Google Science Fair, which is a pretty cool initiative that encourages kids 13 to 18 to solve answer any question that's been bothering them any which way they can.

[via Slashdot]

Video: Cambridge Researchers Use Legos to Build Artificial Bone in the Lab

(Via Popular Science -.)

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[email protected] (Jim Haseloff) 2012-04-04T17:26:40+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2476-video-cambridge-researchers-use-legos-to-build-artificial-bone-in-the-lab.html
How Traditional Publishing Hurts Scientific Progress http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2457-how-traditional-publishing-hurts-scientific-progress.html

A battle that has raged for over a decade between advocates of open science and publishers of traditional scientific journals is coming to a head.

From the Fields is a periodic Wired Science op-ed series presenting leading scientists’ reflections on their work, society and culture.

 

Michael Eisen

Michael Eisen is a molecular biologist at UC Berkeley and an Investigator of the Howard Hughes Medical Institute. His lab studies how genome sequences encode the complex patterns of gene expression that underlie animal development. He is also a strong proponent of open science, and a co-founder of the open access publisher Public Library of Science (PLoS). He blogs at www.michaeleisen.org.

Eighty five percent of published papers remain locked behind subscription pay walls, accessible only to those affiliated with universities and other large research institutions. But new journals that make everything they publish freely available are growing rapidly. And government efforts to make the results of all publicly funded scientific and medical research accessible to everyone are expanding, despite industry-backed legislative efforts to end them.

Backed into a corner, traditional publishers have launched a public relations campaign of sorts, attempting to justify their business practices by highlighting the value they add by overseeing peer review and editorial selection. Charging for access to their content, they argue, is the only way they can recoup their costs.

This argument resonates with many interested parties. Most scientists value peer review, believing it protects and improves the papers they publish and read. They also place great stock in the sorting of papers into journals organized on the basis of audience and importance, which plays a major role in determining who succeeds in science. The public, in turn, values peer review, believing it determines which scientific results they can trust.

Never mind that publishers are on shaky ground when they take credit for peer review, as reviewers and many editors volunteer their time.

The real problem with the “value added” argument is that value is a net proposition. To calculate the actual impact of traditional scientific publishing, whatever value peer review adds must be balanced against the value lost by continuing to use a subscription based business model to pay for it.

The most obvious cost is financial. Science, technology and medical publishers take in close to $10 billion every year (pdf). Some of this goes to pay editorial and production staff and to fund essential publishing processes. But a lot of money is wasted marketing journals to subscribers and managing access, and there are tremendous inefficiencies in maintaining over 10,000 distinct titles in an era of electronic dissemination.

Subscription journals are also monopolies. If you think a journal is charging too much for a paper, you cannot shop around for a better deal (papers are not interchangeable). For decades publishers have exploited this situation to raise and raise prices, even as one of their largest costs – printing and distribution – has all but disappeared. It is no coincidence that Elsevier – the biggest player in the industry – posted profits of over $2 billion last year.

But it’s not just about money. Even if we paid only $1 a year, we would still be getting a bad deal. Because no matter how much value peer review adds, it cannot make up for the myriad ways in which traditional scientific publishing retards scientific progress.

If you think that scientific research makes the world a better place through treatments for disease, technologies that improve our lives, or just knowledge about the world around us – that is, if you believe in science – then you have to also believe that delaying scientific advances costs lives and diminishes the quality of our society.

When a paper describing a new idea, method or observation spends months bouncing around from journal to journal in the name of “peer review,” any major advance to which it might someday contribute is put off by months as well. The effect of these delays is compounded when you count all the steps – one group of scientists building on the work of others – there are along the path to most great discoveries.

And the access restrictions that are a central part of traditional publishing make things worse. There are many great scientists at research institutions that lack anything like comprehensive access to the literature. Imagine the discoveries that are never made because these researchers are not fully plugged in to what their colleagues are doing.

Open access publishers like PLoS (which I co-founded) and BioMed Central have shown that it is possible to build thriving businesses that provide immediate free access to everything they publish. Many of their journals (e.g. PLoS ONE and most BMC journals) only assess the technical merits of submitted works. But many open access journals engage in traditional peer review and selection too. And in this effort to only publish papers they deem of sufficient import, they inevitably delay publication both of papers they ultimately deem worthy, and those they do not.

To build a system of scientific publishing that optimally serves researchers, health care workers, teachers and the public, we have to sever the acts of publication and assessment. Research works should be made available to scientists and the public as soon as they are finished – following an initial screen to ensure they are legitimate works of science. The same volunteer reviewers and editors would decide how important they are, and to whom they are important, but they would do so alongside and after – rather than before — publication.

There will be some false starts and a bit of chaos. And we will have to give up some deeply ingrained ideas and practices. But in the last century scientists wiped out viruses like smallpox and polio, landed people on the moon and sequenced the human genome. Surely we can build a system for communicating and assessing our ideas and discoveries that actually adds value.

Image: Johan Larsson/Flickr

Op-Ed: How Traditional Publishing Hurts Scientific Progress: "

(Via Wired Science.)

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[email protected] (Jim Haseloff) 2012-04-04T14:39:04+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2457-how-traditional-publishing-hurts-scientific-progress.html
The State of the 2012 Advanced Biofuels Industry http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2454-the-state-of-the-2012-advanced-biofuels-industry.html The State of the 2012 Advanced Biofuels Industry: " Intrigued by the prospects for advanced biofuels, but lack the time to wade through a 200-page industry forecast? Our 15-Minute "state of the industry primer" presented this week at World Biofuels Markets, may be just the right size."

(Via Bioenergy News - RenewableEnergyAccess.com.)

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[email protected] (Jim Haseloff) 2012-04-04T13:39:42+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2454-the-state-of-the-2012-advanced-biofuels-industry.html
In planta cytometry http://www.synbio.org.uk/synthetic-biology-index/2425-in-planta-cytometry.html NatMethCart1 (275)

Integrated genetic and computation methods for in planta cytometry
Fernán Federici, Lionel Dupuy, Laurent Laplaze, Marcus Heisler & Jim Haseloff
Nature Methods, Advance publication April 2012 (DOI 10.1038/nmeth.1940)

There is a critical need for improved techniques for the quantitative measurement of biological parameters within living systems. This new publication describes the integrated use of advanced genetic and imaging techniques for automated quantitative analysis of cell growth and genetic activity in living plant tissues. With this new technique, fluorescent protein markers can be used to identify cells, map cell geometries and provide ratiometric measurement of gene expression within intact tissues. The procedure, which we term in planta cytometry, allows the measurement of cellular properties in intact tissue, while retaining the cellular context for further studies.

The routine consists of four steps. (i) A genetic marker is used for the specific labeling of nuclei and cell membranes in transgenic plants. (ii) Fluorescence microscopy and image processing allows the counting of cells and extraction of positional information using a particle search algorithm (iii) Identified nuclei are used to initiate an active contour segmentation algorithm that uses a fluorescent signal located at the plasma membrane to extract information regarding size, shape and topology of cells. (iii) Cell-specific gene expression is quantified by ratiometric measurement of spectrally distinct nuclear fluorescent proteins expressed under the control of different regulated promoters. This new cytometry technique allows one to quantitatively measure cell activities within living organisms, and to precisely reconstruct cellular dynamics - and to produce a numerical description that can be used to inform computer models.

University of Cambridge.

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[email protected] (Jim Haseloff) 2012-04-03T19:37:02+00:00 http://www.synbio.org.uk/synthetic-biology-index/2425-in-planta-cytometry.html
Beached Firefly Squid Light Up the Japanese Coast http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2446-beached-firefly-squid-light-up-the-japanese-coast.html Click here to read Beached Firefly Squid Light Up the Japanese Coast

The Firefly Squid (Watasenia scintillans) inhabits the Western Pacific and is famously found in Toyama Bay, Japan. The 3-inch long creatures employ bioluminescent glands in each tentacle to attract and hunt prey. Surprisingly, this is the only species of of cephalopod that is suspected of having color vision. [Sparkling Enope Wiki via Buzzfeed - Composite Image (clockwise from left): Slutgarden, seavenger, pinktentacle] More »

Beached Firefly Squid Light Up the Japanese Coast

(Via Gizmodo.)

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[email protected] (Jim Haseloff) 2012-04-03T19:32:42+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2446-beached-firefly-squid-light-up-the-japanese-coast.html
Wellcome Trust - MIT postdoctoral fellowships http://www.synbio.org.uk/synthetic-biology-index/2424-wellcome-trust-mit-postdoctoral-fellowships.html WT MITpostdocs2012Wellcome Trust–Massachusetts Institute of Technology (MIT) Postdoctoral Fellowships provide four years’ support for recently qualified postdoctoral researchers to gain experience of research at the interfaces between biology/medicine and mathematics, engineering, computer, physical or chemical sciences.

This scheme offers opportunities for postdoctoral scientists to undertake research at the interfaces between biology/medicine and mathematics, engineering, computer, physical or chemical sciences, firstly at MIT and then at a UK institution. Candidates will be expected to identify an important biomedical research question and to propose a personal interdisciplinary training programme to achieve their research aims.

The aim is to support those who will train in a new research area that is complementary to, but distinct from, their current field of expertise, to enable an interdisciplinary approach to their research question - e.g. you might be a physicist wanting to work on a biology-based programme, or a biologist wanting to undertake a bio-engineering project. For more information see: www.wellcome.ac.uk/mit/wn Deadline: 11 June 2012.

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[email protected] (Jim Haseloff) 2012-03-28T18:11:50+00:00 http://www.synbio.org.uk/synthetic-biology-index/2424-wellcome-trust-mit-postdoctoral-fellowships.html
Top 10 emerging technologies http://www.synbio.org.uk/synthetic-biology-index/2423-top-10-emerging-technologies.html WEFlogo

Synthetic Biology and metabolic engineering were placed at Number 2 in the list of top ten technologies that will have major global impacts in 2012. 

Emerging technologies are critical to building a sustainable and resilient future. But without new understanding, tools and capabilities, their safe and successful development is far from guaranteed. At the Summit on the Global Agenda 2011, the World Economic Forum asked some of the world’s leading thinkers which technology trends would have the greatest social, economic and environmental impacts on the state of the world in the near future. They were listed in order of greatest potential:

1. Informatics for adding value to information
2. Synthetic biology and metabolic engineering
The natural world is a testament to the vast potential inherent in the genetic code at the core of all living organisms. Rapid advances in synthetic biology and metabolic engineering are allowing biologists and engineers to tap into this potential in unprecedented ways, enabling the development of new biological processes and organisms that are designed to serve specific purposes – whether converting biomass to chemicals, fuels and materials, producing new therapeutic drugs or protecting the body against harm.
3. Green Revolution 2.0 – technologies for increased food and biomass
4. Nanoscale design of materials
5. Systems biology and computational modelling/simulation of chemical and biological systems
6. Utilization of carbon dioxide as a resource
7. Wireless power
8. High energy density power systems
9. Personalized medicine, nutrition and disease prevention
10. Enhanced education technology

For the full article see: (http://forumblog.org/2012/02/the-2012-top-10-emerging-technologies/)

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[email protected] (Jim Haseloff) 2012-03-21T09:44:14+00:00 http://www.synbio.org.uk/synthetic-biology-index/2423-top-10-emerging-technologies.html
Alan Turing’s School Grades http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2421-alan-turings-school-grades.html

As an adult, Alan Turing proved to be a genius. Among other accomplishments, he was a pioneer in computer science. But when he was a teenager, Turing was less impressive. Here’s what his English instructor said about his work:

Without being lazy, he seems to do his work rather perfunctorily. I should like to see rather more life in him.

And his math teacher:

Works well. He is still very untidy. He must try to improve in this respect.

And his science teacher:

He is keen & has a natural bent for science, but his work is badly spoilt by extreme untidiness.

One headmaster wrote about his integration into the school community:

His ways sometimes tempt persecution: though I don’t think he is unhappy. Undeniably he is not a ‘normal’ boy: not the worse for that, but probably less happy.

Link -via Marginal Revolution | Photo: Sherborne School

Alan Turing’s School Grades

(Via Neatorama.)

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[email protected] (Jim Haseloff) 2012-03-19T08:26:31+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2421-alan-turings-school-grades.html
Newspaper: America’s Fastest Shrinking Industry http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2418-newspaper-americas-fastest-shrinking-industry.html  

Are you working for the fastest shrinking industry in the United States? You are, if you're working for a newspaper according to this study by LinkedIn and the Council of Economic Advisors.

The fastest-growing industries include renewables (+49.2%), internet (+24.6%), online publishing (+24.3%), and e-learning (+15.9%). Fastest-shrinking industries were newspapers (-28.4%), retail (-15.5%), building materials (-14.2%), and automotive (-12.8%).

Instead of the growth in percentage terms, we also examined the volume of job gain / loss by industry, as indicated by the largest bubbles in the figure above. Our data show that even through the recession, the industries with the largest volume of employment growth (the largest circles on the figure above) were internet, hospitals & healthcare, health, wellness & fitness, oil & energy, IT and renewables. On the other side of the story, retail, construction, telecommunications, banking, and automotive had the largest volume of job losses between 2007 and 2011.

Link - via The Atlantic

Newspaper: America’s Fastest Shrinking Industry

(Via Neatorama.)

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[email protected] (Jim Haseloff) 2012-03-19T07:44:38+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2418-newspaper-americas-fastest-shrinking-industry.html
The best new scientific idea in years [Video] http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2417-the-best-new-scientific-idea-in-years-video.html Click here to read The best new scientific idea in years

Crowdfunding site Kickstarter has now successfully helped more than one project earn over $1 million, turning the traditional model of media production on its ear. What if we could do the same thing for science? With government spending for the sciences on the decline, entrepreneur Matt Salzberg saw an opportunity. He'd create a crowdfunding site for scientists, where researchers could get funding directly from the public. Last week, he and his team launched Petridish.org, and they've already got reputable researchers whose projects are almost funded after just a few days. Could this be the future of publicly funded science? More »

This slime mold conquered (a miniature map of) America [Mad Urbanism]

(Via io9.)

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[email protected] (Jim Haseloff) 2012-03-19T06:54:35+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2417-the-best-new-scientific-idea-in-years-video.html
Allylix bags BASF investment http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2409-allylix-bags-basf-investment.html The flavors and fragrance (F&F) market seem to be benefiting from renewable chemicals developments from players such as Amyris, Allylix and Blue Marble Biomaterials...and chemical firms also supplying the F&F market are taking notice.

BASF announced on Monday that its venture capital business has invested $13.5m in Allylix, which BASF said allows them to leverage their aroma chemicals, nutrition and cosmetic chemicals competency. BASF is one of the biggest global producer of aroma chemicals by the way.

According to a study released last year by US accounting firm Marcum LLP and the Samuel Curtis Johnson Graduate School of Management at Cornell University, the market for aroma chemicals and essential oils are [either] both a rapidly expanding market segment [or] and a highly profitable product segment.

"The highest growth companies in the study, those that experienced over 6% growth year-over-year, generated 20% of their overall revenue from the sale of aroma chemical and essential oils while "low-growth" companies (those with 1-2% growth year-over-year) generated half as much of their revenue from this product segment."

Meanwhile, US market research firm Freedonia reported that the US market for F&F is forecast to rise 3%/year to $5.5bn in 2014. Among the major product segments, essential oils and natural extracts are projected to achieve the most rapid gains.


US FLAVORS & FRAGRANCES DEMAND
(million dollars)
% Annual Growth
2004
2009
2014
2004-2009
2009-2014
Flavor & Fragrance Demand
3910
4750
5500
4.0
3.0
Food
1436
1740
1990
3.9
2.7
Cosmetics & Toiletries
980
1270
1500
5.3
3.4
Cleaning Products
500
570
650
2.7
2.7
Environmental Fragrance Goods
397
470
560
3.4
3.6
Beverages
364
430
500
3.4
3.1
Other
233
270
300
3.0
2.1

© 2011 by The Freedonia Group, Inc.

 


Back to Allylix, the company said it will soon launch its rare and highly valuable terpene that is structurally related to beta-vetivone, one of the key component of vetiver oil - an essential oil. Beta-vetivone has never been commercialized because it cannot be produced synthetically in a cost-effective process, according to Allylix.

Trademarked Epivone, Allylix' product is expected to gain annual  revenue between $20m and $200m based on revenues for similar terpene molecules used in fragrance applications.

Allylix expects to start production of Epivone in commercial quantities in the third quarter 2012 in applications such as cologne, hair care and personal care fragrance.

Allylix bags BASF investment

(Via ICIS Green Chemicals.)

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[email protected] (Jim Haseloff) 2012-03-19T05:37:01+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2409-allylix-bags-basf-investment.html
Synchronized Pipetting http://www.synbio.org.uk/component/content/article/128-cambridge-news/2400-synchronized-pipetting.html by Mary Abraham and Jochen Rink

Department of Biochemistry, University of Cambridge

We investigated the effect of using music to enhance the sub-optimal system of undergraduate laboratory research assistants (Researcheria virginium). Many aspects of the interaction between the undergraduate and the laboratory bench leave much to be desired. We focused on the simplest — yet easily quantifiable — laboratory skill, the noble art of accurate pipetting.

Background

Many publications have documented the beneficial effects of music on mind and body, a phenomenon known as the Mozart effect.[1] Intelligence improves whilst one listens to music. It is also known that classical music causes significant increases in the milk yield of Holstein cows (Bovus holsticus). We merely attempted to see if music could be successfully applied in a similar way on a different problem.

Theoretical Pretext for this Research

Our premise was that pipetting errors must originate somewhere within the sensory motor axis of the undergraduate. Thus our investigation plumbs the depths of the undergraduate central nervous system (CNS), such as it is.

Our Findings

First we discovered that when a student pipetted to musical accompaniment, his or her speed, accuracy and final experimental success rates were transformed. We witnessed dazzling refinements in all aspects of pipetting that came under our scrutiny (data not shown). The authors’ personal recommendation for a piece of music ideally suited for this purpose is Strauss’ “The Blue Danube.”

Suggestive as these preliminary findings were, our most significant discovery was unexpected, and momentous. There is a synergistic effect when music is used to synchronise the pipetting of all the workers on a bench.

We completely shattered world records for experimental success rates (data not shown).

Moreover, it is our conviction that no display of synchronized motion in the natural world can rival the heavenly vision of a symmetrical row of researchers rhythmically pipetting. The majestic beauty of such a sight has moved several (two of two) of the investigators to tears.

We believe that this combination of laboratory procedure and music points, somehow, to the missing link between science and art, with the power to transform lives.[2]

Future studies

Our subjects, damn them, showed a marked reluctance to provide sufficient volume of CNS tissue samples us to do a proper physiological and biochemical analysis. Therefore the molecular basis, if any, for the effect remains unknown.

Pipetting to the Oldies


(YouTube link)

References

1. F.H. Rauscher, G.L. Shaw, and K.N. Ky, Nature, vol. 365, no. 611, 1993.
2. Twelfth Night, W. Shakespeare.

_____________________

This article is republished with permission from the July-August 2001 issue of the Annals of Improbable Research. You can download or purchase back issues of the magazine, or subscribe to receive future issues. Or get a subscription for someone as a gift!

Visit their website for more research that makes people LAUGH and then THINK.

Synchronized Pipetting

(Via Neatorama.)

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[email protected] (Jim Haseloff) 2012-03-03T16:14:58+00:00 http://www.synbio.org.uk/component/content/article/128-cambridge-news/2400-synchronized-pipetting.html
DNA2.0 offers BIOFAB parts http://www.synbio.org.uk/synthetic-biology-index/2390-dna20-offers-biofab-parts.html GD2SplashScreen small

 The gene synthesis company DNA2.0 has provided direct access to a collection of biological building blocks characterized by the BIOFAB. Gene Designer is free graphically-rich computer-aided design tool that enables bioengineers to easily manipulate and visualize DNA elements such as promoters, terminators, fusion tags and vector components. BIOFAB DNA parts are now embedded within the application. This provides the first “app store” for molecular biology and biotechnology. By embedding a marketplace of third-party, pretested parts, the process of creating optimized or novel genes can be enhanced. Further, the creation of a marketplace offers the scientific community a place to develop and share new biological parts. For more information see: https://www.dna20.com/ and http://biofab.org

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[email protected] (Jim Haseloff) 2012-02-25T15:39:19+00:00 http://www.synbio.org.uk/synthetic-biology-index/2390-dna20-offers-biofab-parts.html
gBlocks for Synthetic Biology http://www.synbio.org.uk/synthetic-biology-index/2389-gblocks-for-synthetic-biology.html idtlogo2010IDT (Integrated DNA Technologies) have rolled out their £69 ($99) gBlocks - low cost synthetic DNA fragments of up to 500 bp in length that can be shipped in 3–4 working days for gene construction and modification.These are useful for production of short synthetic promoters and genes using Gibson Assembly. Error rates may be an issue for assembly of longer sequences, as average sequence fidelity of the gBlocks is around 90% - still potentially very useful. A User Guide is available at: http://www.idtdna.com/pages/docs/synthetic-biology/gblocks-user-guide.pdf

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[email protected] (Jim Haseloff) 2012-02-25T15:16:29+00:00 http://www.synbio.org.uk/synthetic-biology-index/2389-gblocks-for-synthetic-biology.html
Arsenic Biosensors for Nepal http://www.synbio.org.uk/synthetic-biology-index/2388-arsenic-biosensors-for-nepal.html ArsenicBiosensor1Do you have a PhD in molecular microbiology or related field and interested in working on a robust whole-cell arsenic biosensor for field use in Nepal? Looking for a job?

Applications are invited for two Postdoctoral Research positions (for 3 years) as part of collaborative Wellcome Trust Translational Research grant between the laboratories of Dr Jim Ajioka (Cambridge) and Dr Chris French (Edinburgh).  One post will be in Cambridge, one in Edinburgh. Previous experience in synthetic biology, Bacillus subtilis genetics/development and microbial biosynthesis pathway analysis would be advantageous.

Informal inquiries can be made to Dr Jim Ajioka ([email protected]) and Dr Chris French ([email protected]).

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[email protected] (Jim Haseloff) 2012-02-23T15:06:09+00:00 http://www.synbio.org.uk/synthetic-biology-index/2388-arsenic-biosensors-for-nepal.html
Analyzing and engineering cell signaling modules with synthetic biology. http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2361-analyzing-and-engineering-cell-signaling-modules-with-synthetic-biology.html Signaling pathways lie at the heart of cellular responses to environmental cues. The ability to reconstruct specific signaling modules ex vivo allows us to study their inherent properties in an isolated environment, which in turn enables us to elucidate fundamental design principles for such motifs. This synthetic biology approach for analyzing natural, well-defined signaling modules will help to bridge the gap between studies on isolated biochemical reactions-which can provide great mechanistic detail but do not capture the complexity of endogenous signaling pathways-and those on entire networks of protein interactions-which offer a systems-level view of signal transduction but obscure the mechanisms that underlie signal transmission and processing. Additionally, minimal signaling modules can be tractably engineered to predictably alter cellular responses, opening up possibilities for creating biotechnologically and biomedically useful cellular devices.

Analyzing and engineering cell signaling modules with synthetic biology.: "Publication Date: 2012 Feb 8 PMID: 22325791
Authors: O'Shaughnessy, E. C. - Sarkar, C. A.
Journal: Curr Opin Biotechnol

post to: CiteULike"

(Via Current Opinion in Biotechnology.)

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[email protected] (Jim Haseloff) 2012-02-15T16:31:48+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2361-analyzing-and-engineering-cell-signaling-modules-with-synthetic-biology.html
New international plant science network http://www.synbio.org.uk/synthetic-biology-index/2352-new-international-plant-science-network-.html era-caps-logoA new European Commission-funded network launched at the end of January will coordinate plant science research across Europe and beyond. 26 partners from 23 countries will pool their resources and expertise in order to fund plant science research programmes to help address global challenges such as ensuring food security and providing sustainable bioenergy.

The network, (ERA-NET for Coordinating Action in Plant Sciences - ERA-CAPS) will run until 2014 and is expected to fund two calls for collaborative research projects as well as organising strategic workshops for identifying common priorities and activities around data sharing and open access.

The collaborative projects are expected to investigate fundamental plant biology and science that may have applications including improved crops for food, energy and industrial biotechnology. Projects funded by the network will involve scientists from three or more partner nations with each country funding researchers from their own national institutions. In addition to the 17 European nations, the network will include Canada, India, Israel, Japan, New Zealand and the USA. This will allow many of the best plant science researchers from across the world to collaborate to solve problems in plant biology.

Steve Visscher, BBSRC Deputy Chief Executive, said "Plant science research can help us address many global challenges. However the scale of these challenges means that no nation can combat them alone. By working together through this network the scientists of many nations will be able to draw on one another's strengths, with the synergies enabling more rapid progress and enhancement of the research outputs . The network will also help each nation get better value from its investment in plant science by providing focus, direction and opportunities for sharing."

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[email protected] (Jim Haseloff) 2012-02-15T03:13:35+00:00 http://www.synbio.org.uk/synthetic-biology-index/2352-new-international-plant-science-network-.html
Synthetic Biology Project: Scorecard http://www.synbio.org.uk/synthetic-biology-index/2335-synthetic-biology-project-scorecard.html WW SynBioProjectThe Synthetic Biology Project at the Woodrow Wilson Center is launching a new web-based Synthetic Biology Scorecard, designed to track federal and non-federal efforts to improve the governance of synthetic biology research and development so risks are minimized and broad social and economic benefits can be realized. The Scorecard, unveiled today, monitors the progress made toward implementing the recommendations in New Directions: The Ethics of Synthetic Biology and Emerging Technologies, a December 2010 report from the Presidential Commission for the Study of Bioethical Issues. The report contains 18 recommendations covering a range of topics from risk assessment to ethics education and public engagement. More than a year has passed since the release of the Commission’s report. What progress has been made? The Scorecard seeks to answer that question: In addition to tracking the progress of various federal and non-federal initiatives, the website encourages broad participation in achieving the goals set forth by the Commission and invites public comment on the recommendations and implementation efforts.

“The Commission’s report was a landmark document and lays out a framework with broad applicability to many emerging technologies, but, like many reports of this type, no mechanisms were put in place to track progress,” David Rejeski, director of the Synthetic Biology Project, said. “Our goal is ensure that this report -- and others like it – can drive change.”

Following the launch of the Scorecard, the Synthetic Biology Project will update the website to reflect new initiatives and publish a bi-annual summary of federal and non-federal activities that fulfill the recommendations. Additions to the Scorecard are welcome and encouraged.

The Synthetic Biology Scorecard can be found here: http://www.synbioproject.org/scorecard/

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[email protected] (Jim Haseloff) 2012-02-08T21:22:33+00:00 http://www.synbio.org.uk/synthetic-biology-index/2335-synthetic-biology-project-scorecard.html
Singularity University Launchpad http://www.synbio.org.uk/synthetic-biology-index/2333-singularity-university-launchpad.html LaunchPad

Singularity University is partnering with Triple Ring Technologies to mentor and develop select synthetic biology teams between May and August 2012. They are looking for promising biotechnology entrepreneurs who we can help to incorporate and develop products and services that can be made and tested in a short amount of time (three months), and with little capital (on average less than $50k).

Needs more assembly than breakthrough invention (development, not research); Can be advanced to a working demo in 3 months (seeing is believing); Is understandable to general audiences (non-experts); Has identifiable customers and markets; Has few or no regulatory barriers; Catches people’s attention, usually in a positive way; High profit and growth potential. We will provide: Access to a professional biology lab; DIYbio and maker facilities; Summer Funding (May through August); Incorporation; Business mentorship; Technical mentorship; Insights into exponential technologies; A community of other entrepreneurs like you; Support and inspiration.

What They’re looking for: Emerging, passionate bio-entrepreneurs who are ready to work hard and have fun. Completion of a short application that tells us who you are, explains your big idea, and outlines what you need to be successful. If your idea and team are promising, one or more interviews as a next step in the process. If accepted, a detailed summary that will help you hit the ground running. Relocation to the SF Bay Area to develop your idea and company between May and August 2012. More details: http://singularityu.org/launchpad/

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[email protected] (Jim Haseloff) 2012-02-08T16:15:07+00:00 http://www.synbio.org.uk/synthetic-biology-index/2333-singularity-university-launchpad.html
Plants: biofactories for a sustainable future? http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2330-plants-biofactories-for-a-sustainable-future.html Depletion of oil reserves and the associated effects on climate change have prompted a re-examination of the use of plant biomass as a sustainable source of organic carbon for the large-scale production of chemicals and materials. While initial emphasis has been placed on biofuel production from edible plant sugars, the drive to reduce the competition between crop usage for food and non-food applications has prompted massive research efforts to access the less digestible saccharides in cell walls (lignocellulosics). This in turn has prompted an examination of the use of other plant-derived metabolites for the production of chemicals spanning the high-value speciality sectors through to platform intermediates required for bulk production. The associated science of biorefining, whereby all plant biomass can be used efficiently to derive such chemicals, is now rapidly developing around the world. However, it is clear that the heterogeneity and distribution of organic carbon between valuable products and waste streams are suboptimal. As an alternative, we now propose the use of synthetic biology approaches to 're-construct' plant feedstocks for optimal processing of biomass for non-food applications. Promising themes identified include re-engineering polysaccharides, deriving artificial organelles, and the reprogramming of plant signalling and secondary metabolism.

PMID: 21464074 [PubMed - in process]

Plants: biofactories for a sustainable future?:

Plants: biofactories for a sustainable future?

Philos Transact A Math Phys Eng Sci. 2011 May 13;369(1942):1826-39

Authors: Jenkins T, Bovi A, Edwards R

(Via pubmed: "synthetic biology".)

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[email protected] (Jim Haseloff) 2012-02-05T00:45:21+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2330-plants-biofactories-for-a-sustainable-future.html
14-Million-Year-Old Organisms? http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2317-14-million-year-old-organisms.html

By Mark Brown, Wired UK

After 20 years of drilling, a team of Russian researchers is close to breaching the prehistoric Lake Vostok, which has been trapped deep beneath Antarctica for the last 14 million years.

Vostok is the largest in a sub-glacial web of more than 200 lakes that are hidden 4 km beneath the ice. Some of the lakes formed when the continent was much warmer and still connected to Australia.

The lakes are rich in oxygen (making them oligotrophic), with levels of the element some 50 times higher than what would be found in your typical freshwater lake. The high gas concentration is thought to be because of the enormous weight and pressure of the continental ice cap.

If life exists in Vostok, it will have to be an extremophile — a life form that has adapted to survive in extreme environments. The organism would have to withstand high pressure, constant cold, low nutrient input, high oxygen concentration and an absence of sunlight.

The conditions in Lake Vostok are thought to be similar to the conditions on Jupiter’s moon Europa and Saturn’s tiny moon Enceladus. In June, NASA probe Cassini found the best evidence yet for a massive saltwater reservoir beneath the icy surface of Enceladus. This all means that finding life in the inhospitable depths of Vostok would strengthen the case for life in the outer solar system.

Back on planet Earth, the team at Vostok are running short on time. Antarctica’s summer will soon end and the researchers need to leave their remote base while they still can. Temperatures will drop as low as -80C, grounding planes and trapping the team.

They missed their chance last year. “Time is short, however. It’s possible that the drillers won’t be able to reach the water before the end of the current Antarctic summer, and they’ll need to wait another year before the process can continue,” we wrote in January 2011. The drill halted in February.

Meanwhile, Russian engineers are planning to venture into the lake itself, with swimming robots. In the Antarctic summer of 2012 to 2013, they plan to send a robot into the lake to collect water samples and sediments from the bottom. An environmental assessment of the plan will be submitted at the Antarctic Treaty’s consultative meeting in May 2012.

Image: Wikipedia/NASA

Source: Wired.co.uk

Russian Drill Nears 14-Million-Year-Old Antarctic Lake

(Via Wired: Science.)

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[email protected] (Jim Haseloff) 2012-02-02T20:58:57+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2317-14-million-year-old-organisms.html
2012 Dyson Awards Call for Entries, Seeking Solutions from Youthful Minds http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2312-2012-dyson-awards-call-for-entries-seeking-solutions-from-youthful-minds.html 02012dysawa.jpg

Attention student designers: The 2012 James Dyson Award is now open for entry, seeking solutions from design or engineering students from Australia, Austria, Belgium, Canada, France, Germany, Italy, Ireland, Japan, Malaysia, the Netherlands, New Zealand, Russia, Singapore, Spain, Switzerland, UK and the US.

If you students were to enter most world-class design competitions, you'd undoubtedly be at a disadvantage for lacking the resources and experience of, say, a legacy design firm. Alternatively there's always an abundance of small-scale student design competitions, if you don't mind designing your ass off for a chance to win a gift certificate to Houlihan's. But the Dyson comp carries a US $15,000 purse and is geared towards you specifically because you're young and have little experience. In Dyson's own words,

Young people have an unsullied view of the world. Budding engineers and designers can use their fresh perspective to develop wonderfully simple solutions to baffling problems. Original ideas and rigorously engineered projects will attract the attention of the judges. I challenge applicants to think big and use the award as a springboard for your idea.

You've gotta love the six-word brief—"Design something that solves a problem"—and lack of a registration fee. Also, even recent students can enter; anyone who was an undergrad design or engineering student anytime in the last four years is eligible.

Details are here.

(more...)

2012 Dyson Awards Call for Entries, Seeking Solutions from Youthful Minds (Via Core77.)

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[email protected] (Jim Haseloff) 2012-02-02T20:00:11+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2312-2012-dyson-awards-call-for-entries-seeking-solutions-from-youthful-minds.html
Cambridge: the UK’s most successful city http://www.synbio.org.uk/component/content/article/128-cambridge-news/2278-cambridge-the-uks-most-successful-city.html Cambridge: the UK’s most successful city Cambridge has come first in a report comparing cities across the country by Jonny Barlow Wednesday 25th January 2012, 18:21 GMT Cambridge’s economy has ranked first in an annual Cities Outlook report, suggesting that that Cambridge could play a significant role in driving the country’s economic successes amidst a bleak national picture.

This is in light of the publication of the think-tank Centre for Cities’ annual Cities Outlook report on 64 cities last Monday, in which Cambridge performed well across a range of measures pertaining to education, employment and inequality.

Of particular note was the city’s proficiency in terms of innovation, with over four times as many patents granted in Cambridge than in second-placed Aldershot.

Moreover, this was just one of six measures (out of fifteen) in which Cambridge is the highest-performing city in the country, well ahead of London’s three. These successes encompass a wide range of accolades, including having the lowest percentage of people on Jobseeker’s Allowance (JSA), and the lowest percentage of residents with no qualifications.

Though the report provides encouraging news for Cambridge, the forecast for the country as a whole is mixed.

Cambridge’s success is relative, and must be placed in a context of economic gloom.

In particular, Leader of Cambridge City Council Cllr Sian Reid is keen to avoid complacency on unemployment.

Leader of Cambridge City Council, Cllr Sian Reid She notes that “Cambridge and South Cambridgeshire Local Strategic Partnership has agreed that getting young people into work should be one of its top priorities for spending its last round of grants money, about £100,000.”

Nonetheless, though unemployment in Cambridge rose by 0.1 of a percentage point, to 1.8% last year, the city still had the lowest unemployment level within the survey.

Cambridge: the UK’s most successful city | Varsity Online

(Via .)

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[email protected] (Jim Haseloff) 2012-02-01T00:47:41+00:00 http://www.synbio.org.uk/component/content/article/128-cambridge-news/2278-cambridge-the-uks-most-successful-city.html
Integrating Anaerobic Digestion Into Our Culture: Stats, Reality and the Future http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2274-integrating-anaerobic-digestion-into-our-culture-stats-reality-and-the-future.html "North America is at an inflection point in managing organic materials. Just as paper, metal and plastics were the darlings of the recycling industry a couple decades ago, our society is defining a new relationship with organic materials: one that harnesses the full carbon, energy and nutrient potential of organics. In order to help shape that new relationship, industry leaders are cultivating North America's awareness and understanding of anaerobic digestion's features, benefits and potential role in society.

Integrating Anaerobic Digestion Into Our Culture Part 2: Stats, Reality and the Future:

(Via Renewable Energy News - RenewableEnergyAccess.com.)

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[email protected] (Jim Haseloff) 2012-01-31T23:46:53+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2274-integrating-anaerobic-digestion-into-our-culture-stats-reality-and-the-future.html
Innovation at the intersection of synthetic and systems biology. http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2270-innovation-at-the-intersection-of-synthetic-and-systems-biology.html The promises of modern biotechnology hinge upon the hope that we can understand microscopic cellular complexity and in doing so create novel function. In this regard, the fields of systems and synthetic biology are important for accelerating both our understanding of biological systems and our ability to quantitatively engineer cells. At the nexus of these two fields is a unique synergy that can help attain these goals. Thus, the next greatest advances in biology and biotechnology are arising at the intersection of the top-down systems approach and the bottom-up synthetic approach. Collectively, these developments enable the precise control of cellular state for systems studies and the discovery of novel parts, control strategies, and interactions for the design of robust synthetic function. This review seeks to highlight this activity as well as provide a perspective for future directions. Combining these efforts can provide novel insights into cellular function and lead to robust, novel synthetic design.

Innovation at the intersection of synthetic and systems biology.: "Publication Date: 2012 Jan 19 PMID: 22265125
Authors: Lanza, A. M. - Crook, N. C. - Alper, H. S.
Journal: Curr Opin Biotechnol

(Via Current Opinion in Biotechnology.)

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[email protected] (Jim Haseloff) 2012-01-31T23:06:32+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2270-innovation-at-the-intersection-of-synthetic-and-systems-biology.html
Psychedelic Petri dishes turn lab work into a freakout session http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2258-psychedelic-petri-dishes-turn-lab-work-into-a-freakout-session.html NewImage

 

KLARI REIS SCI ART BY ROBERT T. GONZALEZ

Psychedelic Petri dishes turn lab work into a freakout session Can you guess the subject of this photograph? It's a bloodshot alien eyeball! Just kidding, although all that red totally resembles vasculature don't you think?

Don't worry, the real answer is just as awesome: believe it or not, this is actually a Petri dish, created by artist Klari Reis.

Reis uses individually-crafted dishes like the one up top (although each one is incredibly unique-looking), and combines them into much bigger installation pieces like the one you see below. This particular collection of dishes is described on her website - definitely check out her blog

NewImage

Colored life forms dance across the wall in this installation project comprised of groups of 150, 60, or 30 hand painte"

 

(Via .)

NewImage

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[email protected] (Jim Haseloff) 2012-01-31T21:07:06+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2258-psychedelic-petri-dishes-turn-lab-work-into-a-freakout-session.html
Neil deGrasse Tyson lays bare the decline of American science in 180 seconds http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2257-neil-degrasse-tyson-lays-bare-the-decline-of-american-science-in-180-seconds.html Click here to read Watch Neil deGrasse Tyson lay bare the decline of American science in 180 seconds

The United States has long been recognized as one of the most scientifically productive countries on Earth. But when you're discussing progress, where you've been is not nearly as important as

a) where you are today, and
b) where you stand to go from there

What this presentation from astrophysicist Neil deGrasse Tyson makes abundantly clear is that America's scientific future is shaping up to look very different from its scientific past. "This is the changing landscape of the world," he explains. "As everyone else understands the value of innovative investments in science and technology in ways that [the U.S.] does not, we slowly fade."

When the Supercommittee responsible for trimming 1.5-trillion dollars from the U.S. federal budget failed to reach an agreement last November, it triggered a 1.2-trillion dollar budget-slashing measure that threatens to place the future of scientific research on even rockier terrain than it already is.

Cuts to science, said Michael Lubell (head of public affairs with the American Physical Society)in an interview with io9, will be discouraging for young scientists trying to establish themselves:

The message to students and graduate students will be: if you want to be a scientist, you might want to look at other countries - and that would not be good.

...If you want a high-tech work force, if you want science that drives the economy, [you must increase science funding]. If you don't, the country will suffer. We will not be innovative. We will not be building a better America. And that is what we're looking at.

It's unsettling to think about how strongly Lubell's sentiments resonate with those of Tyson's, especially when you realize that Tyson delivered the above presentation last May — almost two months before the joint Supercommittee on deficit reduction was even created.

Watch Neil deGrasse Tyson lay bare the decline of American science in 180 seconds

(Via io9.)

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[email protected] (Jim Haseloff) 2012-01-31T21:00:56+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2257-neil-degrasse-tyson-lays-bare-the-decline-of-american-science-in-180-seconds.html
Renewables funding going strong http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2239-renewables-funding-going-strong.html It looks like a good start for 2012 with several companies closing some good funding this month.

New Zealand-based LanzaTech announced this week that it has bagged a total of US $55.8m in its series C round of financing led by the Malaysian Life Sciences Capital Fund. New investors include PETRONAS Technology Ventures Sdn Bhd and Dialog Group. Existing investors such as Khosla Ventures, Qiming Venture Partners and K1W1 -- I like this name =) -- participated in the round as well. LanzaTech said the compay raised a total of more than $85m to date.

The company also gave a small update on their $5m acquisition of a US cellulosic ethanol facility now dubbed "Freedom Pines Biorefinery" located in Soperton, Georgia, which was previously owned by Range Fuels. LanzaTech said, the facility will produce renewable fuels and chemicals from waste wood using their proprietary processing technology (industrial waste gas-to-fuel/chemicals via fermentation).

Another recent news is advanced fuel developer KiOR closing a $75m four-year term loan with a lender group comprised of  an affiliate of Vinod Khosla and two Canadian corporations owned by pension fund clients of Alberta Investment Management Corp.

Waste CO2-to-fuel/chemicals developer Joule has also closed a $70m funding this month bringing a total funding round of more than $110m to date. The company did not disclose funding sources.

The proceeds will be applied towards the build-out and operation of a Joule facility located in Hobbs, New Mexico and slated for commissioning in the summer of 2012. Joule was founded by venture capital firm Flagship Ventures in 2007.

Zeachem also announced yesterday that it has been selected by the US Department of Agriculture (USDA) for a $232.5m loan guarantee under the 9003 Biorefinery Assistance Program. The conditional loan enables the financing and construction of ZeaChem's first commercial-scale cellulosic biorefinery in Boardman, Oregon, with a capacity of 25m gal/year enabling the production of cellulosic ethanol and acetic acid/ethyl acetate using woody biomass.

On Wednesday, Canadian renewable chemical firm EcoSynthetix secured a $2.1m funding from Sustainable Development Technology Canada (SDTC). The funding will support EcoSynthetix's project for further development of its EcoMer® bio-based monomer platform.

The blog also received news from Bioformix CEO Adam Malofsky that the company closed a $13m funding from GM Ventures this month and is waiting to close another funding from a big Japanese multinational company soon.

Also this year, we had BASF investing $30m in cellulosic sugar developer Renmatix; Agilyx secured $25m in its series C funding; DSM investing $250m in cellulosic ethanol via its joint venture with US developer POET;  US biodiesel company Renewable Energy Group targeting $100m via its IPO filing; DuPont investing in biomass sorghum developer NextSteppe (undisclosed amount); and another sorghum developer Chromatin has been awarded $5.7m grant from the US DOE.

I've compiled a rough list of last year's financing rounds and IPOs. Hopefully, this will be useful to you.

2011 Renewable Chemicals Financing
IPO Companies Capital Raised
2/9/2011 Gevo $123.3m
5/27/2011 Solazyme $227.2m
6/24/2011 KiOR $150m
8/4/2011 EcoSynthetix $101.6m

 

 

IPO Companies Filed Target
5/2011 Myriant $125m
8/2011 Genomatica $100m
9/2011 Elevance $100m
10/2011 BioAmber $150m
12/2011 Coskata $100m
9/2011 Fulcrum BioEnergy $115m
7/2011 Cathay Industrial withdrawn in August

 

Companies Financing Amount
Agilyx $47m (series B and C)
Avantium $35.9m
BioAmber $45m (series B)
Cereplast $12.5m (private)
Cobalt Technologies $20m (series D)
Dyadic $3m (private)
Elevance $50m (private)
Enerkem $105m (series C)
Fulcrum Bioenergy $75m (series C)
Genomatica $45m (series D)
Gevo $17m (Lanxess)
$5m (USDA grant)
Global Bioenergies $1.98m (Synthos)
$9.3m (IPO)
LS9 $9m (DOE grant)
Materia $17m
Metabolix $6m (DOE grant)
Myriant $60m (PTTGC)
NatureWorks $150m (PTTGC)
NextSteppe $14m (series B)
OPXBio $41.2m (series C)
Plaxica $7.8m
Rivertop Renewables $3.5m (MonTEC grant)
$1.5m (venture capital)
Siluria $20m (series B)
Verenium $16m (loan)
Zeachem $24m (series C)
$40m (USDA grant)


Source: Company Reports

Renewables funding going strong: "

(Via ICIS Green Chemicals.)

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[email protected] (Jim Haseloff) 2012-01-30T10:12:27+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2239-renewables-funding-going-strong.html
Sainsbury Undergraduate Studentships http://www.synbio.org.uk/synthetic-biology-index/2184-sainsbury-undergraduate-studentships.html These prestigious studentships are offered to up to seven students each year.

The total amount of the award is £4,000. This is broken down into £1000 payable to the student on commencement of the studentship after a successful interview. If the student opts to work in a lab over summer then £1500 is payable to the student in June/July with £500 going towards lab costs. The final £1000 is payable to the student upon satisfactory reports (or presentation of poster at the Network Meeting) in the December.

The scheme is designed to be flexible. A student can propose to:
- work in a research laboratory over the summer vacation (not in a lab run by their mentor or at their place of study) to gain valuable experience. Research projects can be in any area of plant science.
- provide an opportunity to travel to, and attendance at, plant-related conferences
- purchase books or subscriptions to journals/scientific magazines
- fund the cost of field work.

Successful students are eligible to compete for a Sainsbury PhD Studentship starting in October 2013 and will be invited to attend the 2012 Gatsby Plant Science Network meeting and the 2013 Gatsby training weekend.

Please supply a covering letter (including why you are interested in plant science, what you intend to do with the funding and what you ultimately hope to achieve) and your cv, to Julian Hibberd at jmh65(at)cam.ac.uk by 15th February 2012.

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[email protected] (Jim Haseloff) 2012-01-24T17:17:19+00:00 http://www.synbio.org.uk/synthetic-biology-index/2184-sainsbury-undergraduate-studentships.html
Synthetic biosystems for the production of high-value plant metabolites. http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2177-synthetic-biosystems-for-the-production-of-high-value-plant-metabolites.html Synthetic biosystems for the production of high-value plant metabolites.: "Publication Date: 2011 Dec 29 PMID: 22209518
Authors: Facchini, P. J. - Bohlmann, J. - Covello, P. S. - De Luca, V. - Mahadevan, R. - Page, J. E. - Ro, D. K. - Sensen, C. W. - Storms, R. - Martin, V. J.
Journal: Trends Biotechnol

Plants display an immense diversity of specialized metabolites, many of which have been important to humanity as medicines, flavors, fragrances, pigments, insecticides and other fine chemicals. Apparently, much of the variation in plant specialized metabolism evolved through events of gene duplications followed by neo- or sub-functionalization. Most of the catalytic diversity of plant enzymes is unexplored since previous biochemical and genomics efforts have focused on a relatively small number of species. Interdisciplinary research in plant genomics, microbial engineering and synthetic biology provides an opportunity to accelerate the discovery of new enzymes. The massive identification, characterization and cataloguing of plant enzymes coupled with their deployment in metabolically optimized microbes provide a high-throughput functional genomics tool and a novel strain engineering pipeline.

post to: CiteULike"

(Via Trends in biotechnology.)

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[email protected] (Jim Haseloff) 2012-01-22T23:56:50+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2177-synthetic-biosystems-for-the-production-of-high-value-plant-metabolites.html
Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor ... http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2175-production-of-amorphadiene-in-yeast-and-its-conversion-to-dihydroartemisinic-acid-precursor-to-the-antimalarial-agent-artemisinin-applied-biological-sciences.html Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin [Applied Biological Sciences]: "Malaria, caused by Plasmodium sp, results in almost one million deaths and over 200 million new infections annually. The World Health Organization has recommended that artemisinin-based combination therapies be used for treatment of malaria. Artemisinin is a sesquiterpene lactone isolated from the plant Artemisia annua. However, the supply and price of artemisinin fluctuate greatly, and an alternative production method would be valuable to increase availability. We describe progress toward the goal of developing a supply of semisynthetic artemisinin based on production of the artemisinin precursor amorpha-4,11-diene by fermentation from engineered Saccharomyces cerevisiae, and its chemical conversion to dihydroartemisinic acid, which can be subsequently converted to artemisinin. Previous efforts to produce artemisinin precursors used S. cerevisiae S288C overexpressing selected genes of the mevalonate pathway [Ro et al. (2006) Nature 440:940–943]. We have now overexpressed every enzyme of the mevalonate pathway to ERG20 in S. cerevisiae CEN.PK2, and compared production to CEN.PK2 engineered identically to the previously engineered S288C strain. Overexpressing every enzyme of the mevalonate pathway doubled artemisinic acid production, however, amorpha-4,11-diene production was 10-fold higher than artemisinic acid. We therefore focused on amorpha-4,11-diene production. Development of fermentation processes for the reengineered CEN.PK2 amorpha-4,11-diene strain led to production of > 40 g/L product. A chemical process was developed to convert amorpha-4,11-diene to dihydroartemisinic acid, which could subsequently be converted to artemisinin. The strains and procedures described represent a complete process for production of semisynthetic artemisinin."

(Via PNAS - RSS feed of Early Edition articles.)

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[email protected] (Jim Haseloff) 2012-01-22T23:30:05+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2175-production-of-amorphadiene-in-yeast-and-its-conversion-to-dihydroartemisinic-acid-precursor-to-the-antimalarial-agent-artemisinin-applied-biological-sciences.html
A transcription activator-like effector toolbox for genome engineering http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2169-a-transcription-activator-like-effector-toolbox-for-genome-engineering.html A transcription activator-like effector toolbox for genome engineering: "

A transcription activator-like effector toolbox for genome engineering

Nature Protocols 7, 171 (2012). doi:10.1038/nprot.2011.431

Authors: Neville E Sanjana, Le Cong, Yang Zhou, Margaret M Cunniff, Guoping Feng & Feng Zhang

Transcription activator-like effectors (TALEs) are a class of naturally occurring DNA-binding proteins found in the plant pathogen Xanthomonas sp. The DNA-binding domain of each TALE consists of tandem 34–amino acid repeat modules that can be rearranged according to a simple cipher to target new

(Via Nature Protocols.)

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[email protected] (Jim Haseloff) 2012-01-22T18:43:47+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2169-a-transcription-activator-like-effector-toolbox-for-genome-engineering.html
Synthetic biological approaches to natural product biosynthesis. http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2160-synthetic-biological-approaches-to-natural-product-biosynthesis.html Synthetic biological approaches to natural product biosynthesis.: "Publication Date: 2012 Jan 3 PMID: 22221832
Authors: Winter, J. M. - Tang, Y.
Journal: Curr Opin Biotechnol

Small molecules produced in Nature possess exquisite chemical diversity and continue to be an inspiration for the development of new therapeutic agents. In their host organisms, natural products are assembled and modified using dedicated biosynthetic pathways. By rationally reprogramming and manipulating these pathways, unnatural metabolites containing enhanced structural features that were otherwise inaccessible can be obtained. Additionally, new chemical entities can be synthesized by developing the enzymes that carry out these complicated chemical reactions into biocatalysts. In this review, we will discuss a variety of combinatorial biosynthetic strategies, their technical challenges, and highlight some recent (since 2007) examples of rationally designed metabolites, as well as platforms that have been established for the production and modification of clinically important pharmaceutical compounds.

post to: CiteULike"

(Via Current Opinion in Biotechnology.)

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[email protected] (Jim Haseloff) 2012-01-22T16:23:19+00:00 http://www.synbio.org.uk/component/content/article/115-synthetic-biology-news/2160-synthetic-biological-approaches-to-natural-product-biosynthesis.html