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Synthetic Biology @UW

Synthetic Biology @UW | SynBioFromLeukipposInstitute | Scoop.it
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University of Washington #SynBio web portal http://bit.ly/YWPHc8

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Methods for the Preparation of Large Quantities of Complex Single-Stranded Oligonucleotide Libraries

Methods for the Preparation of Large Quantities of Complex Single-Stranded Oligonucleotide Libraries | SynBioFromLeukipposInstitute | Scoop.it
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Yusuf E. Murgha, Jean-Marie Rouillard, Erdogan Gulari


"Custom-defined oligonucleotide collections have a broad range of applications in fields of synthetic biology, targeted sequencing, and cytogenetics. Also, they are used to encode information for technologies like RNA interference, protein engineering and DNA-encoded libraries. High-throughput parallel DNA synthesis technologies developed for the manufacture of DNA microarrays can produce libraries of large numbers of different oligonucleotides, but in very limited amounts. Here, we compare three approaches to prepare large quantities of single-stranded oligonucleotide libraries derived from microarray synthesized collections. The first approach, alkaline melting of double-stranded PCR amplified libraries with a biotinylated strand captured on streptavidin coated magnetic beads results in little or no non-biotinylated ssDNA. The second method wherein the phosphorylated strand of PCR amplified libraries is nucleolyticaly hydrolyzed is recommended when small amounts of libraries are needed. The third method combining in vitro transcription of PCR amplified libraries to reverse transcription of the RNA product into single-stranded cDNA is our recommended method to produce large amounts of oligonucleotide libraries. Finally, we propose a method to remove any primer binding sequences introduced during library amplification."

http://bit.ly/1m8jlvN

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BNL Newsroom | 'Life Redesigned: The Emergence of Synthetic Biology' Lecture on Wednesday, April 30

BNL Newsroom | 'Life Redesigned: The Emergence of Synthetic Biology' Lecture on Wednesday, April 30 | SynBioFromLeukipposInstitute | Scoop.it
Biomedical engineer James Collins of Boston and Harvard universities and the Howard Hughes Medical Institute, will give a BSA Distinguished Lecture, titled "Life Redesigned: The Emergence of Synthetic Biology," at the U.S. Department of Energy's Brookhaven National Laboratory on Wednesday, April 30.
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Functionalized Amphipols: A Versatile Toolbox Suitable for Applications of Membrane Proteins in Synthetic Biology

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Eduardo Antonio Della Pia, Randi Westh Hansen, Manuela Zoonens, Karen L. Martinez

"Amphipols are amphipathic polymers that stabilize membrane proteins isolated from their native membrane. They have been functionalized with various chemical groups in the past years for protein labeling and protein immobilization. This large toolbox of functionalized amphipols combined with their interesting physico-chemical properties give opportunities to selectively add multiple functionalities to membrane proteins and to tune them according to the needs. This unique combination of properties makes them one of the most versatile strategies available today for exploiting membrane proteins onto surfaces for various applications in synthetic biology. This review summarizes the properties of functionalized amphipols suitable for synthetic biology approaches."
http://bit.ly/1h0r7QB

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Will Synthetic Biology Evolve Into the Next Hot Field?

Will Synthetic Biology Evolve Into the Next Hot Field? | SynBioFromLeukipposInstitute | Scoop.it
Five things you should know about this growing segment that aims to modify life itself.
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Question to all Entrepreneurs: 

http://bit.ly/1gWLBtp

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Rapid and tunable post-translational coupling of genetic circuits

Rapid and tunable post-translational coupling of genetic circuits | SynBioFromLeukipposInstitute | Scoop.it

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Arthur Prindle, Jangir Selimkhanov, Howard Li, Ivan Razinkov, Lev S. Tsimring & Jeff Hasty

"One promise of synthetic biology is the creation of genetic circuitry that enables the execution of logical programming in living cells. Such ‘wet programming’ is positioned to transform a wide and diverse swathe of biotechnology ranging from therapeutics and diagnostics to water treatment strategies. Although progress in the development of a library of genetic modules continues apace1, 2, 3, 4, a major challenge for their integration into larger circuits is the generation of sufficiently fast and precise communication between modules5, 6. An attractive approach is to integrate engineered circuits with host processes that facilitate robust cellular signalling7. In this context, recent studies have demonstrated that bacterial protein degradation can trigger a precise response to stress by overloading a limited supply of intracellular proteases8, 9, 10. Here we use protease competition to engineer rapid and tunable coupling of genetic circuits across multiple spatial and temporal scales. We characterize coupling delay times that are more than an order of magnitude faster than standard transcription-factor-based coupling methods (less than 1 min compared with ~20–40 min) and demonstrate tunability through manipulation of the linker between the protein and its degradation tag. We use this mechanism as a platform to couple genetic clocks at the intracellular and colony level, then synchronize the multi-colony dynamics to reduce variability in both clocks. We show how the coupled clock network can be used to encode independent environmental inputs into a single time series output, thus enabling frequency multiplexing (information transmitted on a common channel by distinct frequencies) in a genetic circuit context. Our results establish a general framework for the rapid and tunable coupling of genetic circuits through the use of native ‘queueing’ processes such as competitive protein degradation."

 http://bit.ly/1hGY7NV

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Doctors implant lab-grown vagina

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First International Workshop on Plant Synthetic Biology | May 17-18, 2014 at MIT Stata Center, Cambridge, MA USA

"First International Workshop on Plant Synthetic Biology" #synbio http://t.co/BAbKfZ5efb
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The Predictive Power of Synthetic Nucleic Acid Technologies in RNA Biology

The Predictive Power of Synthetic Nucleic Acid Technologies in RNA Biology | SynBioFromLeukipposInstitute | Scoop.it
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Synthetic and Systems Biology: Toward Achieving Impossible Missions and Deciphering Human Complex Disease Genetics | Open Access |

Synthetic and Systems Biology: Toward Achieving Impossible Missions and Deciphering Human Complex Disease Genetics | Open Access | | SynBioFromLeukipposInstitute | Scoop.it
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Yue Zhang

"Many pioneering works have inspired researchers to stay up-todate on synthetic and system biology. Several cases that were originally thought to be exceptionally difficult, if not impossible, have been carried out successfully, such as Craig Venter’s creation of the world’s first synthetic life form. At a system level, nucleic reprogramming succeeded in frog half a century ago (reviewed in [1]); but doubts about whether or not this was impossible lingered until 40 years later, when a cocktail of four transcriptional factors systematically reprogrammed the somatic cells to stem cells [1-3]. Other cases include that telomerase reactivation may lead to the reversal of tissue degeneration in aged telomerase-deficient mice [4] and muscle-derived stem/progenitor cell dysfunction acts as a healthspan and lifespan limiting factor for murine progeria reversal [5].

 
Here, we focus on the latest impossible or exceptionally difficult missions, plus those of the future, i.e. decoding the complex diseases genetics and their possible modified nutritional, tour and other benign environmental treatments, which most of us could easily have and best exercise. Some complex diseases currently considered “difficult – to be addressed” are largely diseases of aging. For instance, starting for relatively simple neurodegenerative disorders like Parkinson’s disease (PD) , today, no drugs exist to address the underlying pathology; for autoimmune diseases (ADs), no one is even sure what causes such outcomes; and for cancer, though billions of dollars have been invested and millions of articles published, there is still a long way to go to deal with them both theoretically and therapeutically to satisfy researchers and sufficiently match the expectations of patients. Successful creation of disease models and screening of targets are expected to be identified for such diseases and thus help slow or even prevent disease progression.
 "


http://bit.ly/1n9gwbm

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Synthetic gene circuits pump up cell signals

Synthetic gene circuits pump up cell signals | SynBioFromLeukipposInstitute | Scoop.it
(Phys.org) —Synthetic genetic circuitry created by researchers at Rice University is helping them see, for the first time, how to regulate cell mechanisms that degrade the misfolded proteins implicated in Parkinson's, Huntington's and other diseases.
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Mathematicians and Biochemists Synthesize a Temperature-Invariant Biological Genetic Clock at UH and Rice

Mathematicians and Biochemists Synthesize a Temperature-Invariant Biological Genetic Clock at UH and Rice | SynBioFromLeukipposInstitute | Scoop.it
Read about how Mathematicians and Biochemists Synthesize a Temperature-Invariant Biological Genetic Clock at UH and Rice
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Berkeley Lab proposal for an open biofoundry passes crucial first test - Nanowerk

Berkeley Lab proposal for an open biofoundry passes crucial first test - Nanowerk | SynBioFromLeukipposInstitute | Scoop.it
Nanowerk Berkeley Lab proposal for an open biofoundry passes crucial first test Nanowerk This biomanufacturing center would aim to meet the biomanufacturing challenges through three main interrelated components: a one-of-a-kind open collaboration...
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Living organ regeneration 'first'

Living organ regeneration 'first' | SynBioFromLeukipposInstitute | Scoop.it
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The World's Leading Tire Manufacturers Are Turning to Synthetic Biology -- But Not for the Reason You May Think

The World's Leading Tire Manufacturers Are Turning to Synthetic Biology -- But Not for the Reason You May Think | SynBioFromLeukipposInstitute | Scoop.it
Forget sustainability -- 13 of the world's leading tire manufacturers are eyeing Amyris' synthetic biology platform for a completely different reason. - Maxx Chatsko - Energy
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Heuristic for Maximizing DNA Reuse in Synthetic DNA Library Assembly

Heuristic for Maximizing DNA Reuse in Synthetic DNA Library Assembly | SynBioFromLeukipposInstitute | Scoop.it
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Open Biomedical Initiative

Nonprofit Organization for LOW COST, OPEN SOURCE, 3D PRINTABLE Biomedical Technologies
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Scientists Try To Build Heart With 3-D Printer

Scientists Try To Build Heart With 3-D Printer | SynBioFromLeukipposInstitute | Scoop.it
LOUISVILLE, Ky. (AP) -- It may sound far-fetched, but scientists are attempting to build a human heart with a 3-D printer.Ultimately, the goal is to create a new heart for a patient with their own cells that could be transplanted. It is an ambitious project to first, make a heart and then get it to work in a patient, and it could be years — perhaps decades — before a 3-D printed heart would ever be put in a person.The technology, though, is not all that futuristic: Researchers have already used 3-D printers to make splints, valves and even a human ear.
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Synthetic biology: Biocircuits in synchrony

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Ricard Solé & Javier Macía

"Cellular biocircuit design has taken a major step forward. The circuit reuses the cell's own protein-degradation system to synchronize the expression of two synthetic modules throughout an entire bacterial population."




http://bit.ly/1hqOKqu

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Creating body parts in a lab: 'Things are happening now'

Creating body parts in a lab: 'Things are happening now' | SynBioFromLeukipposInstitute | Scoop.it
Scientists grew reproductive organs and nasal cartilage in labs, and later successfully implanted them in patients, according to two studies released Thursday.
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Sign in to read: Pharma to fork: How we'll swallow synthetic biology

Sign in to read: Pharma to fork: How we'll swallow synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
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Bacterial 'FM radio' developed

Bacterial 'FM radio' developed | SynBioFromLeukipposInstitute | Scoop.it
Programming living cells offers the prospect of harnessing sophisticated biological machinery for transformative applications in energy, agriculture, water remediation and medicine. Inspired by engineering, researchers in the emerging field of synthetic biology have designed a tool box of small genetic ...
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Nano-Robots That Compute With DNA Installed Into Living Cockroach

Nano-Robots That Compute With DNA Installed Into Living Cockroach | SynBioFromLeukipposInstitute | Scoop.it
 Gives a whole new meaning to the term "computer bug." 
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Science AMA Series: I’m Mark Hahnel, former stem cell biologist, founder of figshare. Academia is broken. Discuss. Also, AMA. : science

Science AMA Series: I’m Mark Hahnel, former stem cell biologist, founder of figshare. Academia is broken. Discuss. Also, AMA. : science | SynBioFromLeukipposInstitute | Scoop.it
There are very few, if any discoveries each year in academia that come about without building on the concepts and ideas that have been previously publ...
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*Academica is broken*

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 MarkHahnel

"There are very few, if any discoveries each year in academia that come about without building on the concepts and ideas that have been previously published in academic journals. This is the natural progression of research. However, this is often limited to building on top of conclusions or ideas, as opposed to conducting the actual research itself. Current dissemination of research is largely based on making .pdf-based summaries of key findings available, while the actual research outputs and raw data behind the graphs are largely unavailable. This isn’t due to a lack of demand to by researchers to get credit for all of their hard work, it’s because the publication and subsequent reward structure in academia does not support this.

Perhaps the most depressing part of academia is the waste of research outputs. So much funding and researcher time goes into doing experiments that produce null results. This isn’t a bad thing. The problem here is that no single academic can be right all of the time, so when experiments are carried out (often at great costs, both financially and in terms of time) that do not confirm the hypothesis, where does this research go? The simple answer is nowhere."


 http://bit.ly/1gLNpW4

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Summarizing DNA nanotechnology, Synthetic Biology are on the path to realizing visions of nanomedicine and Nanoscale Metamaterial to visible spectrum control

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How these London scientists make body parts in a lab - The Times Herald

How these London scientists make body parts in a lab - The Times Herald | SynBioFromLeukipposInstitute | Scoop.it
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How these London scientists make body parts in a lab
The Times Herald
How these London scientists make body parts in a lab.
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