SynBioFromLeukipposInstitute

By JP Mangalindan

"Want to keep track of every piece of personal data in your life? There's probably a tool for you.

If you want something done, do it yourself, the old saying goes. It's a philosophy that fuels the "quantified self," a growing movement toward tracking one's life with the help of technology. It extends far beyond Nike's (NKE) groundbreaking Nike+ running app: Devotees can dutifully track fitness routines, eating habits, even medical conditions. And companies are developing tools for nearly every scenario imaginable. Here are just a few.FitnessRunKeeper employs a phone's GPS to track activities like running and cycling, and through its Health Graph lets users compare performance. Devices like the Fitbit apply a data-tracking method called actigraphy to gauge movements during sleep.MedicineThe Spiroscout sensor, an inhaler attachment, uses satellite data to show asthmatics locations that may worsen their condition. The Boozerlyzer, built to measure blood alcohol levels, can be doctored to track drug intake and side effects.LifestyleWith GreenGoose's sticker-size sensors, everyday items  -- toothbrushes, toys, even pets -- transmit data back to an egg-shaped base station. Users can keep track of information such as how often they've brushed their teeth or if someone walked the dog...."

http://bit.ly/W2saJn

"World's FIRST citizen science project to sequence the human microbiome. Available INTERNATIONALLY in 196 countries. Learn about your health & change the world!

Scientists recently discovered an important new organ in the human body. Incredibly, this organ isn’t made of human cells: It’s microbes! In fact, there are so many of these microbes in your body that they outnumber human cells 10 to 1. This is your microbiome. It's another world inside your body. Thousands of species, trillions and trillions of tiny organisms. We barely know who they are, let alone what they're doing -- or importantly, how they affect our health. It's been described as the greatest scientific mystery of our day.  By joining uBiome, you can explore your own microbiome and participate in the exciting scientific discovery to unlock this mystery. In order for it to work, we need lots of samples and a little bit of money. By pulling together as a group, we can do cutting-edge biomedical research at a fraction of the normal cost. It's called citizen science."

http://bit.ly/Tk5rH2

talk by
Ellen Jorgensen

"We have personal computing, why not personal biotech? That's the question biologist Ellen Jorgensen and her colleagues asked themselves before opening Genspace, a nonprofit DIYbio lab in Brooklyn devoted to citizen science, where amateurs can go and tinker with biotechnology. Far from being a sinister Frankenstein's lab (as some imagined it), Genspace offers a long list of fun, creative and practical uses for DIYbio."

http://bit.ly/UQLBS4

By Alexandra Witze

"Synthetic biologists reinvent nature with parts, circuits.

Quietly, on the top floor of a non- descript commercial building overlooking Boston Harbor, the future is being born.

Rows of young scientists tap intently in front of computer monitors, their concentration unbroken even as the occasional plane from Logan Airport buzzes by. State-of-the-art lab equip- ment hums away in the background. This office, in Boston’s Marine Industrial Park, is what California’s Silicon Valley was four decades ago — the vanguard of an industry that will change your life.Just as researchers from Stanford provided the brains behind the semi- conductor revolution, so are MIT and Harvard fueling the next big transfor- mation. Students and faculty cross the Charles River not to build computer chips, but to re-engineer life itself...."

free PDF
http://bit.ly/S1S7Z4

"Rss, Creative Common, Reddit are just some of the web-revolution that Aaron help to develop.Then Openlibrary and Demand Progress against the bills Sopa/Pipa.

Aaron was 26 years old. .... Here's what happened. In the fall of 2010 Aaron wrote a script to download via the MIT wireless network, nearly five million academic articles stored on the Digital Library JSTOR. It was discovered by MIT and arrested by the Massachusetts attorney for computer fraud. He was released only after payment of a deposit of 100 thousand dollars. In the summer of 2011 JSTOR declare he didn't want to pursue Aaron, who had returned all the downloaded materials , and asked the government to drop the charges (and two days before the suicide of Swartz, JSTOR also announced that it would make available free of charge different million articles). "The death of Aaron is not only a personal tragedy. But the product of criminal justice", openly writes the family on the site in memory of the young: "The decisions taken by officials from the prosecutor's office of Massachusetts and MIT have contributed to his death. The prosecutor's office has accused him of an exceptional sequence of criminal charges that could have led to more than 30 years in prison for an alleged crime he did not victims. And in the meantime, unlike JSTOR, MIT has refused to defend Aaron."   We need to stop to hunt people, who are trying to help to move into the digital age."At the time of his death, Swartz, if convicted, faced a maximum of $1 million in fines and more than 35 years in prison after the government increased the number of felony counts against him from 4 to 13....." ...." 

*The One and Only Popular Synthetic Biology Book*

by
Eric Sawyer

"Three months ago, the first popular synthetic biology book was released. Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves is the work of Harvard biologist George Church and science writer Ed Regis, who team up to tell the story of life on Earth and speculate about the roles technologies like synthetic biology might play in its narrative. I had the pleasure of reading it over my winter holiday.

 Each chapter carries the name of a stretch of geological time, which serves as a jumping off point for the contents. Of particular intrigue are the recurring ideas that humans can (and in his view should) alter the biochemistry of our industrial microbes, and eventually ourselves. The simplest approach to this would be to tweak the genetic code, which dictates how sequences of nucleotides (A, C, G, T/U) in DNA and RNA are translated into the set of 20 amino acids used in proteins. Viruses, whether they are human pathogens or E. coli pathogens, take over their hosts by exploiting the universality of the code. Tweaking the code or making a new one entirely would bestow total invulnerability to viral infection. To my surprise, we actually have a lot of the pieces needed to accomplish this, though putting them together is another matter. The potential of genome-wide engineering extends beyond viral resistance. Church offers them as a practical alternative to the whole genome synthesis approach of the J. Craig Venter Institute: one genome could be evolved into another in the laboratory. This could mean introducing exotic genes that make humans a hardier species, perhaps for safer space travel. And, he suggests, extinct species with surviving DNA but no surviving cells could be resurrected from living relatives, perhaps avoiding ecosystem collapses. Church also proposes using this technology to bring back the Neanderthals, with the stated goal of bringing more genetic diversity into the human gene pool. However, it's not entirely clear why he specifically suggests this, since diversity presumably could be introduced into humans directly without the need of the Neanderthals. Nevertheless, perhaps human society would benefit from a relaxed self-importance that would likely result from the reawakening of the Neanderthals...."

http://bit.ly/10s9jMd

*The Growing Pains and Pleasures of a Synthetic Biology Start-Up* 

BY JEFFREY MARLOW

"On the southeastern outskirts of Denver, Colorado, where snow-dusted prairie meets freshly laid asphalt and barbed wire fences restrain the tumbleweed, a nondescript office building in a business park houses Gevo.  From these innocuous facilities – and a growing number of production plants and test sites around the world – the fledgling biotech company is reimagining a handful of industries from plastic bottle production to renewable fuels.

 The common link in Gevo’s ambitious reach is isobutanol, a four-carbon alcohol packed with energetic potential and useful for several industrial applications.  The company’s primary thrust – and most far-reaching opportunity – is the integration of isobutanol into the fuel industry, which could provide a continuous bridge (isobutanol works as a gasoline additive and is compatible with existing infrastructure) toward renewable fuels. Gevo was founded by Frances Arnold, the Caltech professor who employs directed evolution to improve target enzymes, co-opting biological machinery for industrial purposes.  The original goal was to produce methanol from methane, but as Gevo President and Chief Operating Officer Chris Ryan puts it, “technologically it was a very challenging problem.”  Arnold’s researchers couldn’t get the methane processing enzymes to behave no matter how much they altered the underlying amino acid code.  This technical roadblock, along with the fact that methanol has questionable profitability margins, led the fledgling company to pursue isobutanol instead...."

http://bit.ly/XtttQn

by
+Eugenio Battaglia 

"I'm totally supporting this potential system theorized some days ago by Micah Allen and his friend Hauke on Allen's Neuroconscience blog . They discuss a quick and reliable strategy to share papers behind a paywall.

The proposed system is really easy and accessible by everyone, since it uses particular twitter's #hashtags for query and response.I strongly believe that what started after Aaron Swartz's dead with #pdftribute, and continued with #sharecredentials (unfortunately and strangely still not so shared on twitter), and now followed by #icanhazpdf / #papester  will quickly lead to a massive weaken of paywall systems. Therefore, this will push people to understand and to propose alternative ways that are more ethically correct and also apt to current science needs.  Also, i don't believe that this ways are so illegal to warn people not to use them, and even if they are is just because old rules simply doesn't fit anymore with the actual need of a more open and accessible science. Finally, i could suggest you to leave the army and join the pirates! Because no one will be interested in fighting for your right of research. We are facing really big issues nowadays, and without a coordinated network strategy we won't be able to solve this topics together. Instead we would leave this solutions to big institutions and corporations, that to this date are too biased by market logics and profitable goals.Concluding, i think this battle has to be fight by those who believe that knowledge has to be definitely accessible to everyone on Earth. I don't want to necessarily appear as a criminal, and of course I'm aware that editors have to make profits in order to produce a quality service, but the results of paywalls are pretty clear. A recent article on Cyberpsychology, behavior and social networking journal, argue:"In a national online longitudinal survey, participants reported their attitudes and behaviors in response to the recently implemented metered paywall by the New York Times. Previously free online content now requires a digital subscription to access beyond a small free monthly allotment. Participants were surveyed shortly after the paywall was announced and again 11 weeks after it was implemented to understand how they would react and adapt to this change. Most readers planned not to pay and ultimately did not. Instead, they devalued the newspaper, visited its Web site less frequently, and used loopholes, particularly those who thought the paywall would lead to inequality."[1]Finally, I want share the interesting idea of Allen and his friend Hauke:"Yesterday my friend Hauke and I theorized about a kind of dream scenario- a totally distributed, easy to use, publication liberation system. This is perhaps not feasible at this point [1]. Today we’re going to present something that will be useful right now. The essential goal here is to make it so that anyone, anywhere, can access the papers they need in a timely manner. The idea is to take advantage of existing strategies and tools to streamline paper sharing as much as possible. Folks already do this- every day on twitter or in private, requests for papers are made and fulfilled. Our goal is to completely streamline this process down to a few clicks of your mouse. That way a small but dedicated group of folks – the Papester Collective – can ensure that #icanhazpdf requests are fulfilled almost instantly. This is a work in progress. Leave comments on how to improve and further streamline this system and join the collective!  SHORT VERSION: HOW TO GET A PAPER BEHIND A PAYWALL QUICKLY Tweet (for example): “#icanhazpdf http://dx.doi.org/10.1523/JNEUROSCI.4568-12.2013” Show your support for the papester collective by tweeting: “Thanks to #papester, my #icanhazpdf request was fufilled in seconds! Join: http://bit.ly/W7fa2T #pdftribute”Click: Here you can find more detailed instructions. HOW TO JOIN THE COLLECTIVE AND START SERVING REQUESTSSHORT INSTRUCTIONS AND REQUIRED SOFTWARE:Twitter:  Monitor #icanhazpdf #requests Zotero and zotero browser plugin: after clicking on DOI link or abstract page just click on ‘Save to Zotero’ button to auto-grabs PDFs  Zotfile: automatically copies new Zotero pdfs files saved to public Dropbox folder  Dropbox: Cloud storage system to seamlessly share files with anyone without login. Dropbox linker: automatically adds links from public folder to your clipboard Reply to request tweets: paste URL from clipboard and if you want #papester That’s it! Now you can just click request links, click the Zotero get PDF button, and CTRL+V a dropbox direct download link in response! Click: Here you can find more detailed instructions.  1.The fundamental problem: uploading huge repositories of scientific papers is not sensible for now. It’s too much data (50 million papers * 0.5-1.5 megabytes together make up ~ 25-75 Terrabytes) and the likelihood for every paper to be downloaded is more uniformly distributed than with files traditionally shared like music. For instance, there are 100 million songs x 3.5 mb songs, and it is difficult to find exotic songs online – some songs have decent availability now because there are only a few favourites – not so with favourite papers. Also, fewer people will share papers than songs, so this makes it more even more difficult to sustain a complete repository. Thus, we need a system that fufills requests individually. Disclaimer: Please make sure you only share papers with friends who also have the copyrights to the papers you share." From Michah Allen's Neuroscience BlogAs you can see I reported the disclaimer of Allen's Blog. I don't agree with that, and also i don't see how my #sharecredentials is far more illegal in this sense! Free your paper, Free your credentials and share your knowledge for free! use the #sharecredentials to share your credentials for limited-access data-bases use the #pdftribute to share your papers by using the bookmarklet here http://aaronsw.archiveteam.org/ and your JSTOR account you can "liberate" one paperTweet #icanhazpdf  ARTICLE_URL or DOI;  more info hereCook, J., & Attari, S. (2012). Paying for What Was Free: Lessons from the PaywallCyberpsychology, Behavior, and Social Networking, 15 (12), 682-687 DOI: 10.1089/cyber.2012.0251

http://bit.ly/VPtKyC

As we move into personalized medicine, we need to rethink who owns and administrate an maybe analyze your personal medical data. Maybe it is you!

*Identifying Personal Genomes by Surname Inference*

by
Melissa Gymrek, Amy L. McGuire, David Golan, Eran Halperin, Yaniv Erlich

"Sharing sequencing data sets without identifiers has become a common practice in genomics. Here, we report that surnames can be recovered from personal genomes by profiling short tandem repeats on the Y chromosome (Y-STRs) and querying recreational genetic genealogy databases. We show that a combination of a surname with other types of metadata, such as age and state, can be used to triangulate the identity of the target. A key feature of this technique is that it entirely relies on free, publicly accessible Internet resources. We quantitatively analyze the probability of identification for U.S. males. We further demonstrate the feasibility of this technique by tracing back with high probability the identities of multiple participants in public sequencing projects."

http://bit.ly/13M0ef9

see also:
Genetic genealogy
http://bit.ly/WmGzh5

by
OLIVIA JUDSON

"Intelligent design. That’s one goal of synthetic biology, a field that was catapulted into the news last week with the announcement that a group of biologists had manufactured a genome that exists nowhere in nature and inserted it into a bacterial cell. The dream is that, one day, we’ll be able to sit and think about what sort of life-form we’d like to make — and then design and build it in much the same way we make a bridge or a car.

 Realizing this dream is still some way off. But before I get to that, let me briefly describe the state of play. Synthetic biology is predicated on the fact that, to a large extent, organisms can be broken down into a set of parts. For example, the information contained in DNA comes in discrete chunks — namely, genes. Genes contain the instructions for making proteins — molecules that come in different shapes and sizes — as well as information about where and when those proteins should be used. Proteins interact with each other, driving many of the functions of the cell. Some genes are essential: without the proteins they encode, the organism cannot exist. But many genes are “optional” — in the laboratory at least, the organism gets on fine without them.  Likewise, having an “extra” gene or two isn’t usually a problem. Already, we have exploited this fact to insert new genes into organisms as diverse as petunias and goats. Since the 1980s, human insulin has been mass-produced by bacterial cells genetically engineered to make it....."

http://nyti.ms/Sdf5wk

by
Raymond Kapral

"Self-propelled nanomotors use chemical energy to produce directed motion. Like many molecular motors they suffer strong perturbations from the environment in which they move as a result of thermal fluctuations and do not rely on inertia for their propulsion. Such tiny motors are the subject of considerable research because of their potential applications, and a variety of synthetic motors have been made and are being studied for this purpose. Chemically powered self-propelled nanomotors without moving parts that rely on asymmetric chemical reactions to effect directed motion are the focus of this article. The mechanisms they use for propulsion, how size and fuel sources influence their motion, how they cope with strong molecular fluctuations, and how they behave collectively are described. The practical applications of such nanomotors are largely unrealized and the subject of speculation. Since molecular motors are ubiquitous in biology and perform a myriad of complex tasks, the hope is that synthetic motors might be able to perform analogous tasks. They may have the potential to change our perspective on how chemical dynamics takes place in complex systems."


http://bit.ly/SPm8wO

July 9-11
Imperial College, London, UK
- registration is now open

"The BioBricks Foundation SB6.0 Conference is made up of plenary and workshop sessions over three days.  Your conference registration includes breakfast, lunch, snacks, happy-hour poster sessions, awards ceremony and closing reception.  Each day will begin with breakfast at 8 am, sessions will conclude by 6 pm, followed by happy hour poster sessions on day one and two and a closing reception on day three.

Lodging during the conference will be available at Imperial College and at hotels close by.

Be sure to sign up for the BioBricks mailing list below.

The conference program is currently in development.  Themes you can expect to see will be evolution, materials, human therapeutics, plants, cell-free systems and global health and sustainability.

A sample of the confirmed speakers are Jason Chin, Jim Collins, Victor de Lorenzo, Domitilla Del Vecchio, Martin Fusseneger, Jay Keasling, Suzanne Lee, Anne Osbourn, Chris Voigt, Pam Silver, Sven Panke, Sang Yup Lee and many more to be announced.

For more information, contact us at sb6-info@biobricks.org."

http://bit.ly/W9Nx9i

by
RACHEL Z. ARNDT

I"n 2013 we will sequence DNA faster and cheaper than ever, design radios that intelligently find open spectrum amid the crowded airways, and charge EVs without plugging them in. Consider this your cheat sheet for the year in tech.
*Nanopore Sequencing*
Back in 2008 it took four months and nearly $1.5 million to sequence the complete genome of DNA co-discoverer James Watson. Now, with the commercialization of nanopore sequencing on the horizon, it should take only 15 minutes. Decoding a genome requires linking together several of Oxford Nanopore Technologies' $30,000 sequencers. Each sequencer pulls a strand of DNA through a 1-nanometer—wide hole—about 100,000 times smaller than the diameter of a human hair—and monitors the distinctive changes in an electric current that reveal which of the four DNA bases is passing through the opening. Oxford Nanopore Technologies is also releasing a single-use sequencer that plugs into a computer like a USB key and costs less than $900....."

http://bit.ly/ZWQ47G

by
Jeffrey M Perkel

"Researchers are injecting ever more conscious design into their bioengineering workflow.

Yogurt. Comedian George Carlin wouldn’t touch it; Spaceballs villain “Dark Helmet” “hated” it—even with strawberries. But Boston University biomedical engineer James Collins, a Howard Hughes Medical Institute Investigator, has recently been giv- ing the fermented dairy treat a great deal of thought. Not how his preferred flavor, vanilla, tastes atop granola, nor how plain yogurt and dill pair perfectly with salmon. For Collins, yogurt—or, more precisely, the lactobacilli that make yogurt yogurt—could potentially be the answer to a vexing public health problem: cholera.Collins is a pioneer in the burgeoning field of synthetic biology, the science of reprogramming cells with novel biological functions, from biosensors to antimicrobi- als to biofuels. The field, writes Harvard Medical School geneticist George Church, capitalizes on the fact that biological organisms are effectively programmable manufacturing systems. In this context, cells serve as miniature computers, pro- grammed toward a new purpose with externally supplied genetic instructions. Church notes that “making small changes in their genetic software a bioengineer can effect big changes in their output”....."

free PDF
http://bit.ly/XD3lCN

by
Zheng-jun Guan, Markus Schmidt, Lei Pei, Wei Wei and Ke-ping Ma

"The International Genetically Engineered Machines (iGEM) competition is one of the largest and most visible activities in synthetic biology. iGEM serves to introduce synthetic biology to students—the pool of talent for the future of synthetic biology. Although its participants have tried to construct useful genetic devices and systems in a playful way, iGEM has also been recognized for its important role in raising students’ awareness of biosafety issues. In the present study, we analyzed how the iGEM teams have quantitatively and qualitatively dealt with new safety requirements in recent years and what suggestions were made to further improve biosafety. We found an increase in the number of teams reporting safety aspects and a general improvement in the safety assessment of their projects. Although the students’ safety awareness has improved, certain gaps must still be filled before iGEM can fully live up to its role as an educational competition."


http://bit.ly/103F3WR