SynBioFromLeukipposInstitute

*Open call for  exhibition on Synthetic Biology*

http://bit.ly/115uptu

Advances in synthetic biology akin to new "industrial revolution"http://bit.ly/10WQxvV

by
Giuraniuc CV, Macpherson M, Saka Y.

"onstruction of synthetic genetic networks requires the assembly of DNA fragments encoding functional biological parts in a defined order. Yet this may become a time-consuming procedure. To address this technical bottleneck, we have created a series of Gateway shuttle vectors and an integration vector, which facilitate the assembly of artificial genes and their expression in the budding yeast Saccharomyces cerevisiae. Our method enables the rapid construction of an artificial gene from a promoter and an open reading frame (ORF) cassette by one-step recombination reaction in vitro. Furthermore, the plasmid thus created can readily be introduced into yeast cells to test the assembled gene's functionality. As flexible regulatory components of a synthetic genetic network, we also created new versions of the tetracycline-regulated transactivators tTA and rtTA by fusing them to the auxin-inducible degron (AID). Using our gene assembly approach, we made yeast expression vectors of these engineered transactivators, AIDtTA and AIDrtTA and then tested their functions in yeast. We showed that these factors can be regulated by doxycycline and degraded rapidly after addition of auxin to the medium. Taken together, the method for combinatorial gene assembly described here is versatile and would be a valuable tool for yeast synthetic biology."
http://bit.ly/15Rc64b

by
Anne Trafton

"MIT engineers have transformed bacterial cells into living calculators that can compute logarithms, divide, and take square roots, using three or fewer genetic parts.

 Inspired by how analog electronic circuits function, the researchers created synthetic computation circuits by combining existing genetic “parts,” or engineered genes, in novel ways. The circuits perform those calculations in an analog fashion by exploiting natural biochemical functions that are already present in the cell rather than by reinventing them with digital logic, thus making them more efficient than the digital circuits pursued by most synthetic biologists, according to Rahul Sarpeshkar and Timothy Lu, the two senior authors on the paper, describing the circuits in the May 15 online edition of Nature. “In analog you compute on a continuous set of numbers, which means it’s not just black and white, it’s gray as well,” says Sarpeshkar, an associate professor of electrical engineering and computer science and the head of the Analog Circuits and Biological Systems group at MIT"

http://bit.ly/16hy2FF

SB6.0 digital conference - a great alternative if you  can not travel to London to this major SynBio event. http://bit.ly/10ohQxq

*SBOL Designer is a synthetic biology design tool using Synthetic Biology Open Language (SBOL)* 

http://bit.ly/16vrfaX

*Collecting synthetic biology – an iGEM of an idea* 

by anonymous / Science Museum’

"Collecting stuff is generally the bit I like most about my job. That’s probably why I’ve got a bit over excited about the new acquisitions we’ve made related to synthetic biology – from no other than Tom Knight widely described as the “father” of the discipline.

 Synthetic biology is research that combines biology and engineering. Sounds like genetic engineering by another name? Well yes, but it goes much further. It looks to create new biological functions not found in nature, designing them according to engineering principles.  Some see the field as the ultimate achievement of knowledge, citing the engineer-mantra of American physicist Richard Feynman, “What I cannot create, I do not understand”...."

http://bit.ly/10Cn1XC

*Is This Virtual Worm the First Sign of the Singularity?*

by
ALEXIS C. MADRIGAL

"For all the talk of artificial intelligence and all the games of SimCity that have been played, no one in the world can actually simulate living things. Biology is so complex that nowhere on Earth is there a comprehensive model of even a single simple bacterial cell. 

 And yet, these are exciting times for "executable biology," an emerging field dedicated to creating models of organisms that run on a computer. Last year, Markus Covert's Stanford lab created the best ever molecular model of a very simple cell. To do so, they had to compile information from 900 scientific publications. An editorial that accompanied the study in the journal Cell was titled, "The Dawn of Virtual Cell Biology." In January of this year, the one-billion euro Human Brain Project received a decade's worth of backing from the European Union to simulate a human brain in a supercomputer. It joins Blue Brain, an eight-year-old collaboration between IBM and the Swiss Federal Institute of Technology in Lausanne, in this quest. In an optimistic moment in 2009, Blue Brain's director claimed such a model was possible by 2019. And last month, President Obama unveiled a $100 million BRAIN Initiative to give "scientists the tools they need to get a dynamic picture of the brain in action." An entire field, connectomics, has emerged to create wiring diagrams of the connections between neurons ("connectomes"), which is a necessary first step in building a realistic simulation of a nervous system. In short, brains are hot, especially efforts to model them in silico.  But in between the cell-on-silicon and the brain-on-silicon simulators lies a fascinating and strange new project to create a life-like simulation of Caenohabditis elegans, a roundworm. OpenWorm isn't like these other initiatives; it's a scrappy, open-source project that began with a tweet and that's coordinated on Google Hangouts by scientists spread from San Diego to Russia. If it succeeds, it will have created a first in executable biology: a simulated animal using the principles of life to exist on a computer..."

http://bit.ly/YRkcEK

*New Mechanism of Self-Assembly from DNA-Tethered Nanorods*

by
Karen McNulty Walsh, Peter Genzer

"Approach could be useful in fabricating new kinds of materials with engineered properties

UPTON, NY—Scientists at the U.S. Department of Energy's Brookhaven National Laboratory have discovered that DNA "linker" strands coax nano-sized rods to line up in a way unlike any other spontaneous arrangement of rod-shaped objects. The arrangement—with the rods forming "rungs" on ladder-like ribbons linked by multiple DNA strands—results from the collective interactions of the flexible DNA tethers and may be unique to the nanoscale. The research, described in a paper published online in ACS Nano, a journal of the American Chemical Society, could result in the fabrication of new nanostructured materials with desired properties. "This is a completely new mechanism of self-assembly that does not have direct analogs in the realm of molecular or microscale systems," said Brookhaven physicist Oleg Gang, lead author on the paper, who conducted the bulk of the research at the Lab's Center for Functional Nanomaterials (CFN)...."

http://1.usa.gov/112nMrZ

by

Zhen Gu †‡§¶, Alex A. Aimetti †‡§, Qun Wang †‡,Tram T. Dang †‡, Yunlong Zhang †‡§, Omid Veiseh†‡§, Hao Cheng †‡#, Robert S. Langer †‡§, andDaniel G. Anderson †‡§*

 

"Diabetes mellitus, a disorder of glucose regulation, is a global burden affecting 366 million people across the world. An artificial “closed-loop” system able to mimic pancreas activity and release insulin in response to glucose level changes has the potential to improve patient compliance and health. Herein we develop a glucose-mediated release strategy for the self-regulated delivery of insulin using an injectable and acid-degradable polymeric network. Formed by electrostatic interaction between oppositely charged dextran nanoparticles loaded with insulin and glucose-specific enzymes, the nanocomposite-based porous architecture can be dissociated and subsequently release insulin in a hyperglycemic state through the catalytic conversion of glucose into gluconic acid. In vitro insulin release can be modulated in a pulsatile profile in response to glucose concentrations. In vivostudies validated that these formulations provided improved glucose control in type 1 diabetic mice subcutaneously administered with a degradable nano-network. A single injection of the developed nano-network facilitated stabilization of the blood glucose levels in the normoglycemic state (<200 mg/dL) for up to 10 days."

*Secret of efficient photosynthesis is decoded*

by
David L. Chandler

"Purple bacteria are among Earth’s oldest organisms, and among its most efficient in turning sunlight into usable chemical energy. Now, a key to their light-harvesting prowess has been explained through a detailed structural analysis by scientists at MIT.

 A ring-shaped molecule with an unusual ninefold symmetry is critical, the researchers found. The circular symmetry accounts for its efficiency in converting sunlight, and for its mechanical durability and strength. The new analysis, carried out by professors of chemistry Jianshu Cao and the late Robert Silbey, postdoc Liam Cleary, and graduate students Hang Chen and Chern Chuang, has been published in the Proceedings of the National Academy of Sciences."

http://bit.ly/10BAqyi

comment to:

*Optimal fold symmetry of LH2 rings on a photosynthetic membrane*

by

Liam Cleary, Hang Chen, Chern Chuang, Robert J. Silbey, and Jianshu Cao

*An intriguing observation of photosynthetic light-harvesting systems is the N-fold symmetry of light-harvesting complex 2 (LH2) of purple bacteria. We calculate the optimal rotational configuration of N-fold rings on a hexagonal lattice and establish two related mechanisms for the promotion of maximum excitation energy transfer (EET). (i) For certain fold numbers, there exist optimal basis cells with rotational symmetry, extendable to the entire lattice for the global optimization of the EET network. (ii) The type of basis cell can reduce or remove the frustration of EET rates across the photosynthetic network. We find that the existence of a basis cell and its type are directly related to the number of matching points S between the fold symmetry and the hexagonal lattice. The two complementary mechanisms provide selection criteria for the fold number and identify groups of consecutive numbers. Remarkably, one such group consists of the naturally occurring 8-, 9-, and 10-fold rings. By considering the inter-ring distance and EET rate, we demonstrate that this group can achieve minimal rotational sensitivity in addition to an optimal packing density, achieving robust and efficient EET. This corroborates our findings i and ii and, through their direct relation to S, suggests the design principle of matching the internal symmetry with the lattice order.*
http://bit.ly/1490KnO

Synthetic biology and the World Wide Web are teaming up to modernize our flu vaccines

by
Taylor Kubota

"Four years ago, the H1N1 swine flu emerged, launching the United States into its first influenza pandemic in 40 years. By the spring of 2010, the Centers for Disease Control and Prevention (CDC) estimated that at least 43 million Americans had been infected with the virus. Even after this landmark flu season ended, its impact inspired Dr. Philip Dormitzer and his colleagues to make some radical changes to the way we create flu vaccines. When the H1N1 season reached its peak in late October of 2009, the vaccines were only just becoming available. In general, vaccines aren’t obtainable until about five or six months after a virus is first identified. Now, Dormizter, the leader of viral research at the private pharmaceutical lab Novartis, is using downloadable DNA sequences and custom-made synthetic viruses to give vaccine production a long-awaited speed boost."

http://bit.ly/10Qpq5S

A new major paper about biological computing:

Synthetic analog computation in living cells

"A central goal of synthetic biology is to achieve multi-signal integration and processing in living cells for diagnostic, therapeutic and biotechnology applications1. Digital logic has been used to build small-scale circuits, but other frameworks may be needed for efficient computation in the resource-limited environments of cells2, 3. Here we demonstrate that synthetic analog gene circuits can be engineered to execute sophisticated computational functions in living cells using just three transcription factors. Such synthetic analog gene circuits exploit feedback to implement logarithmically linear sensing, addition, ratiometric and power-law computations. The circuits exhibit Weber’s law behaviour as in natural biological systems4, operate over a wide dynamic range of up to four orders of magnitude and can be designed to have tunable transfer functions. Our circuits can be composed to implement higher-order functions that are well described by both intricate biochemical models and simple mathematical functions. By exploiting analog building-block functions that are already naturally present in cells3, 5, this approach efficiently implements arithmetic operations and complex functions in the logarithmic domain. Such circuits may lead to new applications for synthetic biology and biotechnology that require complex computations with limited parts, need wide-dynamic-range biosensing or would benefit from the fine control of gene expression."
http://bit.ly/YWXbm2

by
Susan Young 

"Advanced genetic engineering is already changing vaccine development and could make inroads into other branches of medicine.

Synthetic biology is breathing new life into the old-fashioned world of vaccine production, raising hopes that manufacturers could release vaccines much more quickly when outbreaks occur. At a meeting on synthetic biology held at MIT, the drug company Novartis said it has synthesized hybrid flu genomes in a process that could shave weeks off the time required to produce vaccines. When new flu strain emerges, government agencies normally send samples to vaccine manufacturers, who grow large numbers of the pathogen in chicken eggs as starting material for vaccines, says Philip Dormitzer, leader of viral vaccine research for Novartis. This process can take months and can miss the peak of an outbreak. But Novartis, working with synthetic biologists, has developed a way of chemically synthesizing virus genomes and growing them in tissue culture cells. That saves time and may produce more effective vaccines. The idea is to build a synthetic virus based on sequence data that can be distributed much more quickly than actual viral material harvested at the site of an outbreak. The synthetic viral genome combines a genomic backbone common to many flu viruses with genes specific to the strains seen in a new outbreak. In 2011, the team tested its method in response to a mock outbreak of a bird-flu virus (one closely related to the H7N9 virus currently spreading in China). Starting at 8 a.m. on Monday that year, the team began to chemically synthesize a viral genome based on sequence data, says Dormitzer.  By noon the following Friday, the team had confirmed that it had live virus growing in cell culture......"

http://bit.ly/YHG0lS