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Cell-free biology: Exploiting the interface between synthetic biology and synthetic chemistry

Cell-free biology: Exploiting the interface between synthetic biology and synthetic chemistry | SynBioFromLeukipposInstitute | Scoop.it

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D. Calvin Harris, Michael C Jewett

"Just as synthetic organic chemistry once revolutionized the ability of chemists to build molecules (including those that did not exist in nature) following a basic set of design rules, cell-free synthetic biology is beginning to provide an improved toolbox and faster process for not only harnessing but also expanding the chemistry of life. At the interface between chemistry and biology, research in cell-free synthetic systems is proceeding in two different directions: using synthetic biology for synthetic chemistry and using synthetic chemistry to reprogram or mimic biology. In the coming years, the impact of advances inspired by these approaches will make possible the synthesis of nonbiological polymers having new backbone compositions, new chemical properties, new structures, and new functions..."

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ScienceDirect.com - Current Opinion in Biotechnology - Synthetic genomics: potential and limitations

ScienceDirect.com - Current Opinion in Biotechnology - Synthetic genomics: potential and limitations | SynBioFromLeukipposInstitute | Scoop.it

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Michael G Montague, Carole Lartigue, Sanjay Vashee
"Technologies to synthetically assemble chromosome sized fragments of DNA as well as to enable making thousands of simultaneous changes to existing genomes are now available. These capacities are collectively termed synthetic genomics. The implications of synthetic genomics extend beyond the limited pathway and gene engineering of the past to include the engineering or whole metabolisms, regulatory networks, and even ecosystems. However, in order for those potentials to be met, certain limitations and barriers must be overcome. These barriers no longer include DNA modification and assembly, but instead are based in the limited organisms that many synthetic genomics methods function in, and the limited software for designing custom genomic sequences."
http://bit.ly/HukV2B

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Synthetic Biology - Michael Elowitz, California Institute of Technology | Somerco

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Major networking opportunity: IMEx Consortium brings interactomes to light

Major networking opportunity: IMEx Consortium brings interactomes to light | SynBioFromLeukipposInstitute | Scoop.it

"Like people bustling around busy cities, the thousands of molecules inside our cells are constantly interacting with each other: turning each other on or off, working together, splitting up and networking. Understanding the countless ways in which they do so is a major challenge in biology, but it is fundamental to understanding life. Scientists at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) and colleagues in the International Molecular Exchange (IMEx) consortium are rising to the challenge by offering researchers a freely available set of experimental interaction data that can be queried from a single interface. Reporting in Nature Methods, IMEx partners describe the advantages of their service and invite others to join the effort.
To make it easier to create a picture of an organism’s ‘interactome’ – the interactions between all of its molecules – IMEx partners have been working since 2004 to create a one-stop-shop for interaction data. A single standard for curating protein interaction data now makes it much simpler for scientists to identify which protein interactions are supported by the strongest evidence.

“There are over 100 interaction databases available, but none of them holds enough information to describe the interactome of any organism,” explains Sandra Orchard of the EMBL-European Bioinformatics Institute (EMBL-EBI) in the UK. “In addition to the problem of repeated data entries in these databases, only around 1% of the 151 million binary pairs available are reliable data from published experimental work.” The remaining data are theoretical, or the product of text mining; as such, they are far less dependable.

“We’ve now made it easier to find information about proteins that interact with a given molecule, and to compare new experimental results with publicly available, curated experimental data,” says Gianni Cesareni of the University of Rome ‘Tor Vergata’ in Italy.

“IMEx web services now display curated, experimental data from several reputable resources so that a clearer picture of interactions between proteins can begin to emerge,” says Henning Hermjakob, head of Proteomics Services at EMBL-EBI. “We are in effect optimising the return on public investment in interaction databases by co-ordinating global annotation efforts. We are certainly looking forward to having more curated data resources join the consortium.”

IMEx partners currently include DIP (the Database of Interacting Proteins at UCLA in the US), I2D (at the Ontario Cancer Institute in Canada), InnateDB (Simon Fraser University and the University of British Columbia in Canada and the Teagasc Bioscience Department in Ireland), IntAct (at EMBL-EBI); MatrixDB (at CNRS / Lyon1 University in France), MINT; Molecular Connections (in Bangalore, India); MPIDB (at the J. Craig Venter Institute in the US); observer BioGRID (the Biological General Repository for Interaction Datasets) and the most recent member, the Swiss-Prot group from the SIB Swiss Institute of Bioinformatics, representing the UniProt consortium. IMEx is an outcome of PSIMEx, which is funded under the Health Theme of the European Commissions Seventh Framework Programme...."

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Cyberplasm synthetic-biology microscale biohybrid robot

Cyberplasm synthetic-biology microscale biohybrid robot | SynBioFromLeukipposInstitute | Scoop.it
By Edwin Kee
"You know for sure that to describe the Cyberplasm is going to be a mouthful – it is called the synthetic-biology microscale biohybrid robot. Sounds out of this world for sure, but then again, sometimes science needs to make advances in a very different manner in order to break open the new frontier. Cyberplasm integration is achieved through a combination of nano/microscale fabrication as well as matching the synthetic biology with materials development. The latter will be an iterative process, where the Cyberplasm’s will obviously feature a bunch of functions.

At its core lies a hydrogel with tunable mechanical properties and a microbial fuel cell, and the hydrogel is capable of being modified thanks to microscale patterning of PEI in order to pave the way for adhesion of myotubes. In the words of the creative team behind the Cyberplasm, “Additionally, mechanical properties of the hydrogel will be tuned via cross-linking to allow maximum motile propulsion of myotubes. The force that myotubes exert on the hydrogel will be assessed by the displacement of embedded fluorescent beads followed by subsequent finite element analysis. We plan to develop a new microbial fuel cell technology to power Cyberplasm electronics.” It would be great to read about a real life application of Cyberplasm, but it is pretty much geeky stuff at the moment..."

 
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MIT crowdsources and gamifies brain analysis | ExtremeTech

MIT crowdsources and gamifies brain analysis | ExtremeTech | SynBioFromLeukipposInstitute | Scoop.it

"Understandably, neuroscientists really want to investigate these neurons and synapses to work out how they play such a vital role in our human makeup. Unfortunately, these 100 trillion connections are crammed into a two-pound bag of soggy flesh, making analysis rather hard. At the moment we know that neurons trigger an electrical signal, and that hormones affect the speed at which signals cross between synapses, and that somehow this results in a mental image of a naked Kristen Bell from her Veronica Mars period, but that’s about it.

MIT wants to change all that by tasking thousands of people with analyzing a 0.3-millimeter slice of mouse retinal tissue. Using a new site called Eyewire, MIT will ask users to track a neuron’s path by coloring in each axon (tendril). In the future, MIT will roll out another “game” which challenges users to find the synapses. The end result will be the connectome (a tome of connections) of the mouse’s retina."

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SynBERC | Synthetic Biology Engineering Research Center

SynBERC | Synthetic Biology Engineering Research Center | SynBioFromLeukipposInstitute | Scoop.it
The Synthetic Biology Engineering Research Center (SynBERC) is a multi-institution research effort to lay the foundation for the emerging field of synthetic biology. SynBERC’s vision is to catalyze biology as an engineering discipline by developing the foundational understanding and technologies to allow researchers to design and build standardized, integrated biological systems to accomplish many particular tasks. In essence, we are making biology easier to engineer.

Just as technicians now assemble electronic devices from commercial, off-the-shelf parts, SynBERC foresees a day when synthetic biologists will design biological systems from scratch and assemble them using well-characterized biological parts, devices, and chasses. SynBERC brings together biologists, engineers, and human scientists from world-class institutions to produce the tools, techniques, and scientific understanding needed to design and construct a broad range of biological tools for health, energy, environment and, ultimately, human welfare.

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The Science and Applications of Synthetic and Systems Biology - NCBI Bookshelf

The Science and Applications of Synthetic and Systems Biology - NCBI Bookshelf | SynBioFromLeukipposInstitute | Scoop.it

"Excerpt

Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine’s (IOM’s) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. Through invited presentations and discussion, participants explored the ways in which synthetic and systems biology are contributing to drug discovery, development, and production; vaccine design and development; and infectious disease detection and diagnostics. In addition, workshop participants considered how synthetic biology could be used to engineer, or reengineer, microbial host cells to detect environmental toxins, produce carbon-neutral fuels, and produce novel raw materials."

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Nnimmo Bassey Interviewed On Synthetic Biology In Nigeria & The US, IMF And World Bank

Nnimmo Bassey is interviewed on March 28, 2012 in Berkeley, California about the introduction of synthetic biotech into Nigeria. He also discusses the role of the US government and the role of the IMF and World Bank as well as the recent mass protest that also involved the labor movement in Nigeria. Nnimmo Bassey is a Nigerian environmentalist activist and poet, elected chair of Friends of the Earth International and Executive Director of Environmental Rights Action of Nigeria. He was attending the first international conference on "Unmasking the Bay Area Bio Lab and Synthetic Biology: Health, Justice and Communities at Risk: A Public Forum. More information can be found at www.symbiowatch.org and more information about Nnimmo Bassey at http://www.eraction.org/

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what’s MyOpenArchive?

what’s MyOpenArchive? | SynBioFromLeukipposInstitute | Scoop.it

MyOpenArchive is an international Non-Profit Organization that advocates Open Access for never-before-published research papers on the web and provides Self-Archiving platform to enable better knowledge sharing in a way that’s easy to publish. One of our goals is to advocate “Open Access” mind as widely as possible.

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SOBA: Data Visualization and Data Journalism in Science

SOBA: Data Visualization and Data Journalism in Science | SynBioFromLeukipposInstitute | Scoop.it

Inaugural ScienceOnline Bay Area (SOBA) Event: Data Visualization and Data Journalism in Science SOBA is a monthly discussion series on how science is carried out and communicated online.

Thursday, April 19, 2012 from 7:00 PM to 8:30 PM (PT)
San Francisco, CA

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Experiment and mathematical modeling of gene expression dynamics in a cell-free system

by Stögbauer T, Windhager L, Zimmer R, Rädler JO.

"Cell-free in vitro expression is increasingly important for high-throughput expression screening, high yield protein production and synthetic biology applications. Yet its potential for quantitative investigation of gene expression and regulatory circuits is limited by the availability of data on composition, kinetic rate constants and standardized computational tools for modeling. Here we report on calibration measurements and mathematical modeling of a reconstituted in vitro expression system. We measured a series of GFP expression and mRNA transcription time courses under various initial conditions and established the translation step as the bottle neck of in vitro protein synthesis. Cell-free translation was observed to expire after 3 h independent of initial template DNA concentration. We developed a minimalistic rate equation model and optimized its parameters by performing a concurrent fit to measured time courses. The model predicts the dependence of protein yield not only on template DNA concentration, but also on experimental timing and hence is a valuable tool to optimize yield strategies."

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Nano-sized ‘factories’ churn out proteins - MIT News Office

Nano-sized ‘factories’ churn out proteins - MIT News Office | SynBioFromLeukipposInstitute | Scoop.it

Tiny particles could manufacture cancer drugs at tumor sites.

by
Anne Trafton

"Drugs made of protein have shown promise in treating cancer, but they are difficult to deliver because the body usually breaks down proteins before they reach their destination.

To get around that obstacle, a team of MIT researchers has developed a new type of nanoparticle that can synthesize proteins on demand. Once these “protein-factory” particles reach their targets, the researchers can turn on protein synthesis by shining ultraviolet light on them.

The particles could be used to deliver small proteins that kill cancer cells, and eventually larger proteins such as antibodies that trigger the immune system to destroy tumors, says Avi Schroeder, a postdoc in MIT’s David H. Koch Institute for Integrative Cancer Research and lead author of a paper appearing in the journal NanoLetters.

“This is the first proof of concept that you can actually synthesize new compounds from inert starting materials inside the body,” says Schroeder, who works in the labs of Robert Langer, MIT’s David H. Koch Institute Professor, and Daniel Anderson, an associate professor of health sciences and technology and chemical engineering.

Langer and Anderson are also authors of the paper, along with former Koch Institute postdocs Michael Goldberg, Christian Kastrup and Christopher Levins...."

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Synthetic Biology - Orion Weiner, University of California, San Francisco | Somerco

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Is the future one of abundance or scarcity?

Is the future one of abundance or scarcity? | SynBioFromLeukipposInstitute | Scoop.it

"Abundance by Peter Diamandis and Steven Kotler argues that technology brings prosperity. How do their predictions of bounty sit with environmentalists' talk of planetary boundaries?

A fascinating new book – Abundance by Peter Diamandis and Steven Kotler – suggests we are about to begin an era of unprecedented bounty and human flourishing.

The authors have backgrounds in science and innovation (Diamandis is behind the X-Prize and the Singularity University). They argue that coming technological advances – in pervasive digital, nanomaterials and synthetic biology - will allow us to exceed the basic needs of everyone on the planet. In their words, "abundance for all is actually within our grasp".

This is, of course, a challenging concept for environmentalists: our science talks of planetary boundaries; our story is one of resource shortages.

So, are the Abundance authors just Panglossian techno-optimists, peddling a re-heated Whig interpretation of history?....."

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Exclusive Video: Surviving Progress Looks at Technology’s Human Toll

Exclusive Video: Surviving Progress Looks at Technology’s Human Toll | SynBioFromLeukipposInstitute | Scoop.it

By Scott Thill

"“We’re entering an increasingly dangerous period of our history. But I’m an optimist,” says Stephen Hawking in the exclusive clip above from new documentary Surviving Progress.

The theoretical physicist’s balanced perspective is a philosophical template for directors Mathieu Roy and Harold Crooks’ meditative movie, which opens Friday in New York. A brilliant cyborg himself, Hawking is something like living proof of the visually impressive documentary’s existential meditation.

Filled with sweeping footage ranging from flaring rockets and swarming schools of fish to pulsing global metropoles and their inhabitants, Surviving Progress asks the question: Can our evolving humanity achieve a moral symbiosis with exponential technological progress? The moviemakers seem intent on making the asking of this question as engrossing as the complicated answers, and the result is an intelligent analysis of humanity at a crucial crossroads, in search of an exit from self-created dystopia.

“We always have been the initiators of this experiment; we’ve unleashed it, but we’ve never really controlled it,” author Ronald Wright says in Wired’s second exclusive clip below...."

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Cyberplasm, the synthetic-biology microscale biohybrid robot.

Cyberplasm, the synthetic-biology microscale biohybrid robot. | SynBioFromLeukipposInstitute | Scoop.it

by Bruce Sterling

"Given the principles of “synthetic biology,” I can see why an attempt to develop this bizarre nano-gizmo makes good solid research sense. A great deal could be learned from this effort. “Synthetic actuators,” “optoelectronic interfaces”…

*This effort is sure a new on on me, though. Little teensy robots in the human bloodstream are something of a science-fiction staple, but this “biohybrid” thing is the robotic equivalent of a white blood cell. A thing the size of a cell, as gooey as a cell, that’s a little computer-guided machine made mostly of repurposed cell structures. It has a very Rachel Armstrong feeling about it, somehow.

*At least they don’t replicate. By themselves, that is.

http://cyberplasm.net/

System_Integration

“Cyberplasm integration will be accomplished via a combination of nano/microscale fabrication and matching the synthetic biology with materials development (an iterative process). The body of Cyberplasm will have several functions. Its core will consist of a hydrogel with tunable mechanical properties and a microbial fuel cell. The hydrogel will be modified using microscale patterning of PEI to allow for adhesion of myotubes..."

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"High Cotton" - (Podcast) with author Mike Brennan

PODCAST: Intel Futurist, Brian David Johnson, speaks with writer Charles Walbridge about his story contribution to "The Tomorrow Project Anthology", stories of science fiction based on science fact - including the reading of an excerpt from the story as well.

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BioBricks Foundation | Biotechnology in the Public Interest

BioBricks Foundation | Biotechnology in the Public Interest | SynBioFromLeukipposInstitute | Scoop.it

The BBF’s mission is to ensure that the engineering of biology is conducted in an open and ethical manner to benefit all people and the planet.

We believe fundamental scientific knowledge belongs to all of us and must be freely available for ethical, open innovation. This is a new paradigm.

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Chemical Synthetic Biology :: ChemViews Magazine :: ChemistryViews

Chemical Synthetic Biology :: ChemViews Magazine :: ChemistryViews | SynBioFromLeukipposInstitute | Scoop.it

Book covering a dynamic new area of research at the interface of science and engineering is reviewed by S. Brakmann, TU Dortmund .

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Comprehensive Environmental Assessment and Its Application to Synthetic Biology Applications

Comprehensive Environmental Assessment and Its Application to Synthetic Biology Applications | SynBioFromLeukipposInstitute | Scoop.it

A workshop was held to test a Comprehensive Environmental Assessment framework for its ability to identify important research questions to support future ecological risk assessments of synthetic biology applications, using a case study of cyanobacteria engineered to produce industrial products. It brought together engineers and ecologists in a one-day workshop to systematically consider: 1)possible pathways of entry of these cyanobacteria into the environment, 2) what organisms or entities might be exposed, and 3) potential environmental impacts from such exposure. Anticipated products from the workshop include:

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Research on Aging: Consumer Genomics/What Do People Do With Their Genomes?

(Visit: http://www.uctv.tv/) Consumer genomics is certainly a hot topic, but what does it mean for the end user -- you? Genetic testing holds much promise for understanding a person's risk for certain diseases. Does this mean we should all get a DNA test? What are the benefits and limitations of genetic screenings? What if your genome scan shows you a have a gene variation related to a common disease? Is it possible to lower the risk of getting sick by simple lifestyle changes? Join Dr. Cinnamon Bloss with the Scripps Translational Science Institute as she makes sense of it all. Series: "Stein Institute for Research on Aging" [4/2012] [Health and Medicine] [Show ID: 23249]

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End-to-end assembly of gold nanorods via oligopeptide linking and surfactant control

by

Jain T, Roodbeen R, Reeler NE, Vosch T, Jensen KJ, Bjørnholm T, Nørgaard K.

"We report two novel approaches for fabricating self-assembled chains of end-to-end linked Au nanorods separated by a nanogap. In one approach, bi-functional cysteine end-capped oligopeptides of different lengths are used as the linking agent. The widths of the produced nanogaps scale with the length and tertiary structure of the peptide linker. Functionalized oligopeptides containing an acetylene group are also employed as a linker, and the functional group is uniquely identified using surface-enhanced Raman spectroscopy. The development of an oligopeptide-linking platform is motivated by the ease of synthesis and high modularity of peptides; these features enable the possibility to integrate diverse functionality into molecular nanogap junctions - synthesized in water. The stepwise nanochain formation is followed via the evolution of the longitudinal plasmon absorption band in combination with transmission electron microscopy. The reaction rate and extent is tuned by controlling the concentration of the stabilizing CTAB surfactant in the solution. At very low surfactant concentrations, spontaneous end-to-end linking of the Au nanorods is observed even in the absence of linking peptide. The assembled AuNRs may act as next-generation electrodes in a platform for molecular electronics and synthetic biology."

 

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Pamela Silver: Synthesizing a new biology

Interview by Caitlin Sedwick

"Pamela Silver is a strong believer in the potential of synthetic biology and is a leader in this young and rapidly developing field (1, 2). Although she's now interested in designing novel biological systems, she began as a more conventional scientist, coming to the discipline after forging a successful career studying nuclear (3, 4) and RNA (5) biology. We called her at her office at Harvard's Department of Systems Biology to discuss how she arrived at this new frontier and what she sees coming up on her horizon......"

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