"Chang AL, Wolf JJ, Smolke CD Curr Opin Biotechnol. 2012 Feb 3;
The engineering of biological systems offers significant promise for advances in areas including health and medicine, chemical synthesis, energy production, and environmental sustainability. Realizing this potential requires tools that enable design of sophisticated genetic systems. The functional diversity of RNA makes it an attractive and versatile substrate for programming sensing, information processing, computation, and control functions. Recent advances in the design of synthetic RNA switches capable of detecting and responding to molecular and environmental signals enable dynamic modulation of gene expression through diverse mechanisms, including transcription, splicing, stability, RNA interference, and translation. Furthermore, implementation of these switches in genetic circuits highlights the potential for building synthetic cell systems targeted to applications in environmental remediation and next-generation therapeutics and diagnostics."
"(PhysOrg.com) -- A Rice University undergraduate will depart with not only a degree but also a possible patent for his invention of an efficient way to create protein libraries, an important component of biomolecular research...
Libraries are particularly useful for scientists who study the rules governing the adaptation of proteins during molecular evolution; they also are useful for designing biosensors and molecular switches with novel functions for synthetic biology...."
Last week, taken aback by the revelation of Elsevier’s deep support for the Research Works Act, an anti open-access piece of US legislation, I declined to review a manuscript for the publisher and wrote about my reasons for doing so. My blogpost received an unusual amount of traffic. It seemed to have caught a wave – started elsewhere – that is sweeping through the scientific blogosphere. Mentioned in Research Fortnight, the post even drew comment from Elsevier. In a follow-up piece Benoit Bruneau explored the impact on scientific societies of a radical shift to OA models of scholarly publishing...."
is part of the broader Slow Movement. It is based on the belief that science should be a slow, steady, methodical process, and that scientists should not be expected to provide "quick fixes" to society's problems. Slow Science supports curiosity-driven scientific research and opposes performance targets."
More than one report from an august body of experts has gathered dust in Washington, D.C. But the Woodrow Wilson International Center for Scholars, a public policy think tank based in the U.S.
"This talk describes Foldit and EteRNA, a series of remarkable new scientific discovery games Adrien Treuille has helped create. These games lead us to wonder: how many unknown "Kasparovs" are out there on the Internet -- potential experts at tasks they never knew existed? Is this the future of expertise?
Adrien is an Assistant Professor of computer science and robotics at Carnegie Mellon. He researches scientific challenges through multi-player on-line games such as Foldit (protein folding) and EteRNA (nano-engineering)."
Solve for X is a forum to encourage and amplify technology-based moonshot thinking and teamwork.
For thousands of years the imagination of storytellers has been a guiding light for people trying to change the world. In the last decade or two science fiction has almost fallen behind the work of technologists and entrepreneurs. For the sake of a more interesting tomorrow, we need to get the proverbial horse back out in front of the cart with our imagination professionals building a vision of the future to inspire the builders of the new world.
Neal Stephenson is the author of the three-volume historical epic "The Baroque Cycle" (Quicksilver, The Confusion, and The System of the World) and the novels Cryptonomicon, The Diamond Age, Snow Crash, and Zodiac.
"The field of synthetic biology is rapidly expanding and has over the past years evolved from the development of simple gene networks to complex treatment-oriented circuits. The reprogramming of cell fate with open-loop or closed-loop synthetic control circuits along with biologically implemented logical functions have fostered applications spanning over a wide range of disciplines, including artificial insemination, personalized medicine and the treatment of cancer and metabolic disorders. In this review we describe several applications of interactive gene networks, a synthetic biology-based approach for future gene therapy, as well as the utilization of synthetic gene circuits as blueprints for the design of stimuli-responsive biohybrid materials. The recent progress in synthetic biology, including the rewiring of biosensing devices with the body's endogenous network as well as novel therapeutic approaches originating from interdisciplinary work, generates numerous opportunities for future biomedical applications."
"What if every scientist could share their data as easily as they tweet about their lunch? Michael Nielsen calls for scientists to embrace new tools for collaboration that will enable discoveries to happen at the speed of Twitter."
"Michael Nielsen is one of the pioneers of quantum computation. Together with Ike Chuang of MIT, he wrote the standard text in the field, a text which is now one of the twenty most highly cited physics books of all time. He is the author of more than fifty scientific papers, including invited contributions to Nature and Scientific American. His research contributions include involvement in one of the first quantum teleportation experiments, named as one of Science Magazine's Top Ten Breakthroughs of the Year for 1998. Michael was a Fulbright Scholar at the University of New Mexico, and has worked at Los Alamos National Laboratory, as the Richard Chace Tolman Prize Fellow at Caltech, as Foundation Professor of Quantum Information Science at the University of Queensland, and as a Senior Faculty Member at the Perimeter Institute for Theoretical Physics. Michael left academia to write a book about open science, and the radical change that online tools are causing in the way scientific discoveries are made."
"Cracking the encryption: Parallel computing with molecular finite-state automata and fluorescently labeled DNA molecules has been used to decipher two different images encrypted onto a single DNA chip (see picture). The images were deciphered by a mixture of input molecules that were processed by biomolecular automata, a strategy that potentially offers a huge diversity of encrypted images."
Video "Professor Giuseppe Battaglia takes a debate by a molecular biology as well as dungeon biology laboratories during a University of Sheffield as well as explains a purpose of a dilettante analytic apparatus accessible to students as well as researchers to capacitate world-class training as well as research."
"There are no hospitals in space. The closest E.R. is back on Earth, and astronauts can't exactly jump in a cab to get there. So what happens if the sun burps out a massive blast of radiation while an astronaut is space-amblin' by?
The NASA Biocapsule—made of carbon nanotubes—will be able to "diagnose" and instantly treat an astronaut without him or her even knowing there's something amiss. It would be like having your own personal Dr. McCoy—implanted under your skin. It represents one of the most significant breakthroughs in the history of medicine, and yes, it'll work on Earth, too. Out of all the amazing things we saw during our NASA visits, nothing blew our minds as much as this tiny little bundle of carbon. The Space Biosciences Division at NASA Ames creates medical technology for astronauts. They essentially provide healthcare for outer space. Dr. David Loftus is the man who invented the NASA Biocapsule and has been awarded a patent for it...."
"Synthetic biology can significantly advance metabolic engineering by contributing tools (minimal hosts, vectors, genetic controllers, characterized enzymes). The development of these tools significantly reduced the costs and time to develop the antimalarial drug artemisinin, but the availability of more tools could have reduced these costs substantially."
Life may be the software that makes its own hardware, but where is the compiler? If we plan to start programming life itself, we are going to need a radically different and better tool kit than the one available to geneticists today. Omri lays out a concrete vision for how such a tool would work and for how it would be used to create the bio-products our future needs so badly.
Omri is the founder & CEO of Genome Compiler Corp, a Synthetic Biology venture. His background is in biochemical and structural studies of membrane protein complexes involved in bio-energetics.
Amazon.com: Living Architecture: How Synthetic Biology Can Remake Our Cities and Reshape Our Lives (Kindle Single) (TED Books) eBook: Rachel Armstrong: Kindle Store (RT@TEDFellow: What will cities of the future look like?
"The 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...."
Turning a standard technique into an unbiased screen for diagnostic biomarkers
"Screening for antibody biomarkers of disease to facilitate diagnosis has been fraught with failure, despite its logical approach: stick proteins onto a microscope slide and then pour over a patient’s serum, full of disease-specific antibodies, and see what sticks. Compare the results to the serum of a healthy person, and you’ve got an antibody-protein pair that should signal disease. But of the proteins IDed employing that method, “none of them are even close” to clinical diagnosis, says Thomas Kodadek, at the Scripps Research Institute in Jupiter, Florida. Kodadek and his colleagues figured that the antibodies in the serum of an ill individual wouldn’t be likely to bind to normal biological proteins. The immune system recognizes the foreign proteins of an invading pathogen or the markers of a dying cell precisely because they are different from the body’s normal proteins. A cell involved in a disease like cancer or Alzheimer’s is more likely to produce altered proteins, either because of genetic mutations or because the disease process changes the cytoplasmic environment, causing unexpected posttranslational changes. But trying to guess what those chemical alterations might be is difficult. “We have absolutely no freakin’ idea what those events are,” says Kodadek. So instead of coating the slide with known proteins, Kodadek coated a glass slide with a fairly random assortment of unrelated synthetic small molecules that bind serum antibodies simply because of their chemical shapes, allowing for a broad and unbiased search. “The difference is what you’re fishing with,” he says."
A molecular biology portal for molecular protocols and methods, listings for bioinformatic tools and product information, the latest news and views on research topics, and articles for many biology fields.
"Ania Truszczynski invited me to give a little talk on the use of various collaborative tools for scientists. I enjoyed presenting this as a chalk-talk, but alas no slides to link so here’s a list of reference. Rather than the impossible attempt to be comprehensive, this is restricted to resources I use regularly and have found to be the best of their class. All are freely available.
TOOLS Science Blogs (e.g. Arsenic Life & peer review) ressearchblogging.org Preprint servers (arXiv, Nature Precedings) Twitter (a Scientist’s intro), also see (Eysenbach 2011) Mendeley — social reference manager Github — social coding WordPress — collaborative website (WP for scientists) Google Docs, Dropbox (but try WordPress or github) Stackoverflow and similar Q&A sites RSS readers (all the above can create RSS feeds of updates) Open Notebook Science A few tools I didn’t mention: Increase your impact: share your science. Dryad (published data), FigShare (Figures and data), Slideshare (slides)"
"Biological systems are characterised by highly complex genetic and cellular networks that are locked together by feedback interactions that give rise to properties of self-organisation, repair and reproduction. They are capable of assembling functional structures that are many orders of magnitude more complex than the most sophisticated man-made artefacts, and they do this in a renewable fashion and cheaply.
Synthetic Biology is an emerging field that employs engineering principles to reprogram living systems. Recent scientific advances allow us to use imaging techniques to monitor activities within living organisms, and to precisely reconstruct cellular dynamics, in order to re-design biological circuits, in a way that has become routine in other fields of engineering.
These scientific advances are contributing to a new wave of opportunities for improved sustainability and production of biomass, fuels, food, polymers and drugs, and are already finding uses in the biotechnology sector. Our talk will focus on the prospects for this potentially disruptive technology and its anticipated impact on the field of biotechnology.
Dr Jim Haseloff, is a plant biologist working at the Department of Plant Sciences, University of Cambridge. His scientific interests are focused on the engineering of plant morphogenesis, using microscopy, molecular genetic, computational and synthetic biology techniques (www.haseloff-lab.org). As well as running a research lab, Jim teaches Synthetic Biology and promotes its wider potential as a tool for engineering biological systems and underpinning sustainable technologies. (www.synbio.org.uk)"
"Life on Earth demonstrates that a single example of complicated chemistry known as biology proves the possibility of life, but not its probability of happening. Our Generation 1.0 is currently seeing synthetic biology begetting Generation 2.0 --a new tree of life --what Harvard's Dimitar Sasselov says "is a historic watershed that proves that ordinary matter has an inherent capability to self-organize, to create diversity from a single biochemistry, and ultimately to amplify that diversity by spawning multiple biochemistries."
It is a watershed observes Sasselov in The Life of Super-Earths, because it could be a recipe for amplification of diversity on the scale of the Milky Way and on timescales that last billions of years and because it suggests the existence of a new generation of life --what life-science expert Juan Enriquez (in the video below) calls Homo evolutis. Generation 2.0 may already exist in the Milky Way and other galaxies, according to Sasselov. As of 1995, we began to read the full gene sequence of bacteria, insects, plants, animals, and humans. It is written in a four-letter code (A, T, C, G) . . . If you change this code, just as if you change the code in a floppy disk or on a CD, you change the message, the product, and the outcome. We are beginning to acquire direct and deliberate control over the evolution of all life forms on the planet including ourselves, according to Enriquez.
Enriquez has co-authored, with Steve Gullans, Homo Evolutis: A Short Tour of Our New Species. The book takes you into a world where humans increasingly shape their environment, their own selves, and other species. By the end of the video below, you will see a broad, and sometimes scary, map of life- science-driven change, a Homo evolutis, who directly and deliberately controls its own evolution and that of many other species."
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