SynBioFromLeukipposInstitute

by
Ariadna Martos, Mercedes Jiménez, Germán Rivas, Petra Schwille

"The components of the bacterial division machinery assemble to form a dynamic ring at mid-cell that drives cytokinesis. The nature of most division proteins and their assembly pathway is known. Our knowledge about the biochemical activities and protein interactions of some key division elements, including those responsible for correct ring positioning, has progressed considerably during the past decade. These developments, together with new imaging and membrane reconstitution technologies, have triggered the ‘bottom-up’ synthetic approach aiming at reconstructing bacterial division in the test tube, which is required to support conclusions derived from cellular and molecular analysis. Here, we describe recent advances in reconstituting Escherichia coli minimal systems able to reproduce essential functions, such as the initial steps of division (proto-ring assembly) and one of the main positioning mechanisms (Min oscillating system), and discuss future perspectives and experimental challenges."

http://bit.ly/TD7d6I

by
Siegfried Schloissnig,Manimozhiyan Arumugam,Shinichi Sunagawa,Makedonka Mitreva, Julien Tap,Ana Zhu,Alison Waller,Daniel R. Mende,Jens Roat Kultima,John Martin, Karthik Kota,Shamil R. Sunyaev,George M. Weinstock& Peer Bork

"Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake."

http://bit.ly/10W4SIr

"Mission:

http://bit.ly/UJd2Q2

by

 http://bit.ly/MbNeVW

by
MARY ANN GIORDANO

"The largest and most sophisticated rover landed safely on Mars and the world’s most famous Moon visitor died, but the space event that most captured the public’s imagination in 2012 involved a journey to Earth.

On Oct. 14, YouTube counted 52 million streams of the Austrian daredevil Felix Baumgartner’s supersonic, record-breaking jump from a balloon 24 miles above the New Mexico desert. YouTube called it “one of the most-viewed live events ever,” and it landed at No. 10 on the video-sharing site’s year-end trending list — the first time a science-related subject made the list, a YouTube spokeswoman said. (Google listed the leap as No. 7 in its Zeitgeist 2012 of trending events.)

And it was far from the only science story to go viral. To put it in 140 characters or less, social media and science found each other in 2012.

In surprising numbers, people posted, viewed and searched for science-related topics last year — sharing news from space and undersea, commenting on new discoveries and uploading photos and video in a full-out embrace of the ability to communicate with thousands of others about global subjects in real time.

The first Twitter message on Aug. 5 from @MarsCuriosity, NASA’s official rover handle — “Gale Crater I Am in You!!!” — was retweeted more than 72,000 times. Photos of the space shuttle Endeavour flying over the West Coast, on its way to its final resting place, ricocheted across the planet. And the director James Cameron’s claim to have sent the “deepest tweet” — from the Mariana Trench, about seven miles below the surface of the Pacific — was rated one of Twitter’s “moments of serendipity and just plain awesomeness” (though it was actually sent by a friend above water). Four science-related events made that list, with the Mars landing at No. 1.In an age of despair over math and science acuity, it appears that what was once considered uninteresting or unfathomable has become cool and exciting.
......"
http://nyti.ms/WYurni

by
Hwangbeom Kim, Hyojun Han, Jinwoo Ahn, Joongoo Lee, Namjin Cho, Hoon Jang, Hyoki Kim, Sunghoon Kwon, and Duhee Bang

"We developed a highly scalable ‘shotgun’ DNA synthesis technology by utilizing microchip oligonucleotides, shotgun assembly and next-generation sequencing technology. A pool of microchip oligonucleotides targeting a penicillin biosynthetic gene cluster were assembled into numerous random fragments, and tagged with 20bp degenerate barcode primer pairs. An optimal set of error-free fragments were identified by high-throughput DNA sequencing, selectively amplified using the barcode sequences, and successfully assembled into the target gene cluster...."

http://1.usa.gov/UAxLqd

*World University*
*Synthetic Biology*

A new open course initiative!

http://bit.ly/Wvs49G

by
Le Cong, F. Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D. Hsu, Xuebing Wu, Wenyan Jiang, Luciano Marraffini, Feng Zhang

"Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats) adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Finally, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the CRISPR technology..."
http://bit.ly/RvcPjN

comment in MIT news:
*Editing the genome with high precision* 

by
Anne Trafton

"Researchers at MIT, the Broad Institute and Rockefeller University have developed a new technique for precisely altering the genomes of living cells by adding or deleting genes. The researchers say the technology could offer an easy-to-use, less-expensive way to engineer organisms that produce biofuels; to design animal models to study human disease; and  to develop new therapies, among other potential applications.

http://bit.ly/XnultA ;

by Paola Antonelli

"When the materials of design are not plastics, wood, ceramics or glass, but rather living beings or living tissues, the implications of every project reach far beyond the form/function equation and any idea of comfort, modernity or progress. Design transcends its traditional boundaries and its implications aim straight at the heart of the moral sphere, toying with our deepest-seated beliefs. The figure of the mad scientist playing God in order to create a new being that turns into a harbinger of Armageddon does not, however, apply to most bio-designers. Some work with visible organisms such as plants and animals, others with bacteria and cells, others still tinker with DNA to create new beings, but they never work alone in an ethical vacuum, preferring instead teams that also comprise physicists, mathematicians, computer scientists, engineers, chemists and bio-ethicists, and sometimes even economists and philosophers. Their work is encouraged and celebrated in a few centres of "irradiation" of these new ideas, such as the indomitable Design Interactions programme at the Royal College of Art in London, the Science Gallery at Trinity College in Dublin, and the Paris-based Le Laboratoire gallery and research centre founded in 2007 by David Edwards, a professor of Biomedical Engineering at Harvard, which has helped designer Mathieu Lehanneur propel himself in this realm. Many of them were featured in MoMA's 2008 exhibition Design and the Elastic Mind and are now part of the museum's collection..."

 http://bit.ly/vpMIOC

CONVERSATION
Serge Schmemann
Susan Greenfield
Maria Popova

"SINCE broadband began its inexorable spread at the start of this millenium, Internet use has expanded at a cosmic rate. Last year, the number of Internet users topped 2.4 billion — more than a third of all humans on the planet. The time spent on the screen was 16 hours per week globally — double that in high-use countries, and much of that on social media. We have changed how we interact. Are we also changing what we are?

We put that question to three people who have written extensively on the subject, and brought them together to discuss it with Serge Schmemann, the editor of this magazine. The participants: Susan Greenfield, professor of synaptic pharmacology at Oxford. She has written and spoken widely on the impact of new technology on users’ brains. Maria Popova, the curator behind Brain Pickings, a Web site of “eclectic interestingness.” She is also an M.I.T. Futures of Entertainment Fellow and writes for Wired and The Atlantic. Evgeny Morozov, the author of The Net Delusion: The Dark Side of Internet Freedom . He is a contributing editor to The New Republic ...."

http://nyti.ms/VXOz63