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Gerd Moe-Behrens
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Gerd Moe-Behrens

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Arithmetic logic unit in a biological microprocessor

AND gate

An AND gate can be based on the transcriptor (T), an asymmetric transcription terminator, which can block RNA polymerase flows one directional. If both terminators are flipped, induced by their respective input signal (a and b), RNA polymerase flows unhindered (full length RNA output). http://bit.ly/YI13bF
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Three developments that will help synthetic biology live up to its promise

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Dominic Basulto 

"Using synthetic biology techniques, researchers have created everything fromnew flavors and fragrances to new types of biofuels and materials. While the innovation potential of combining biology and engineering is unquestionable, now comes the hard part of proving that it is possible to design and build engineered biological systems on a cost-effective industrial scale, thereby creating true “bio-factories.”

For that scenario to become a reality, here are three developments in the synthetic biology space to keep an eye on in 2015:

1. New efforts to catalogue synthetic biology innovations

On April 29, the Wilson Center in Washington, D.C. launched a new crowdsourcing initiative of its Synthetic Biology Project (which dates back to 2008): a first-of-its-kind inventory to track the dizzying array of new synthetic biology products.

2. New initiatives to embrace industry-wide standards

Synthetic biology has the reputation for being a bit of freewheeling industry where anything goes and results are hard to replicate, so it’s no surprise that the push is growing for standards so that companies and researchers can compare apples with apples and oranges with oranges. On March 31, the U.S. National Institute of Standards and Technology (NIST) convened a working group at Stanford University to launch the Synthetic Biology Standards Consortium.

3. The entry of innovation champions such as DARPA into the synthetic biology field

After announcing the launch of its new Biological Technologies Office in April 2014, DARPA is finally moving off the sidelines and getting into the game. If DARPA brings the same innovation know-how to synthetic biology that it has brought to fields such as robotics, the Internet and autonomous vehicles, this could be big."

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Meet the latest phase of genetic engineering: synthetic biology

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AMANDA RUGGERI

"In a corner of Istanbul’s Design Biennial late last year, photographs of bizarre creatures sat alongside more conventional displays of product design and typefaces. Diaphanous globes, like transparent balloons, clung to the mossy trunk of an oak tree. Rust-coloured patterns ran across green leaves, as if the foliage had been decorated with henna. On the forest floor, a slug-like creature slithered, its back dotted with gold markings; in another photograph, what looked like a porcupine without a head crawled over the dirt, its quills tipped blood-red.

But as strange as the creatures looked, what they actually are is even stranger. Not quite living things, not quite machines, these imagined prototypes inhabit a dystopic, future world – a world in which they had been created to solve the problems of the living. The porcupine, for example, is an Autonomous Seed Disperser, described as a device that would collect and disperse seeds to increase biodiversity. The slug would be programmed to seek out acidic soils and neutralize them by dispersing an alkali hygroscopic fluid.
..."



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Smartphone-based portable biosensing system using impedance measurement with printed electrodes for TNT detection http://bit.ly/1LLzAsn
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A biological microprocessor

The the general purpose silicon computer system can be used as a template for biocomputers. "Such a template consists of four units: the input and output device (I/O), the arithmetic logic unit, the control unit and the memory.

The first three units collectively build the central processing unit (CPU), typically constructed on a single integrated circuit called a microprocessor. The control unit coordinates the various system components. It decodes the program instructions, and transforms them into control signals, which activate other system parts. This finally results in a change of the system state. Historically the control unit was defined as a distinct part, whereas in modern design this unit is an internal part of the CPU. Busses (often made of groups of wires) interconnect these units. Each unit contains a huge number of small electrical circuits. Switches can turn these circuits on (1) or off (0). A logic gate can perform a logic operation on one or more of such logic inputs and produce a single logic output. Thus, basic elements of any biocomputer unit are switches and logic gates."

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For the first time a biocomputer, based on DNA, was built in 1994 by Leonard Adleman


This system was able to solve a complex, combinatorial mathematical problem, the directed Hamiltonian path problem. This problem is in principle similar to the following: Imagine you wish to visit 7 cities connected by a set of roads. How can you do this by stopping in each city only once? The solution of this problem, a directed graph was encoded in molecules of DNA. Standard protocols and enzymes were used to perform the “operations” of the computation.

ref
Molecular computation of solutions to combinatorial problems
by
LM Adleman
http://bit.ly/1SGyVgD

A PDF of this groundbreaking paper can be found here:
http://bit.ly/1FHRytR
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Input/Output (I/O) device in a biological microprocessor:

A switch, which produce an on (induced) or off (not induced) state: The figure gives an example of a switch in a synthetic gene network. Off (no detectable EGFP expression): LAcl repressor proteins, which are constitutively expressed, bind to two introns with lac operator (lacO) sites, inducing transcriptional repression of EGFP and TetR respectively. Repression of TetR allows transcription of shRNA, which can subsequently bind to its target sequence, and repress it’s shRNA target. On (EGFP expression induced): isopropyl-b-thiogalactopyrano (IPTG) binds to Lacl proteins. As a consequence, the repressor proteins are inactive, as they change their conformation. Thus, TetR, which represses shRNA, and EGFP get transcribed. http://bit.ly/YI13bF
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Startup Weekend IMMIGRATION,

San Francisco, CA
29-31 May

This event is for anyone who wants to make something cool and pay it forward to future of generations of immigrants, whether you’re an immigrant yourself or just passionate about this issue.

http://bit.ly/1cl8Ou5
  === Check out the Event Website for complete details === This event is for anyone who wants to make something cool and pay it forward to future of generations of immigrants, whether you’re an immigrant yourself or just passionate about this issue. Need some inspiration? Check out Immigration Startup Ideas (promo code inside) WHAT is "Startup Weekend"? Startup Weekends are weekend-long (non-profit) events where anyone with an idea can for...
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Study reveals flaws in gene testing; results often conflict

By MARILYNN MARCHIONE

"The first report from a big public-private project to improve genetic testing reveals it is not as rock solid as many people believe, with flaws that result in some people wrongly advised to worry about a disease risk and others wrongly told they can relax.

Researchers say the study shows the need for consumers to be careful about choosing where to have a gene test done and acting on the results, such as having or forgoing a preventive surgery.

"We have very clear documentation that there are differences in what patients are getting" in terms of how tests on the same gene variations are interpreted, said the study leader, Heidi Rehm, genetics lab chief at Brigham and Women's Hospital in Boston.

When deciding to get tested, either through a doctor's office or by sending in a swab to a private company, "patients need to choose labs that are sharing their data" with the broader research community so scientists can compare and learn from the results and make testing more accurate for everyone, she said.

Dozens of companies now offer gene tests to gauge a person's risk of developing various disorders. One of the newest tests on the market costs $250 and checks about 20 genes that can affect breast cancer risk.

But not all gene mutations, or variants, are equal. Some raise risk a lot, others just a little, and some not at all. Most are of unknown significance — a quandary for doctors and patients alike. And most variants are uncommon, making it even tougher to figure out which ones matter and how much.

To solve these mysteries and give patients better information, the U.S. government several years ago helped form and fund ClinVar, a database for researchers around the world to pool gene findings, coded to keep patients' identities confidential. More than 300 labs contribute to it, including universities such as Harvard and Emory and some private companies such as Ambry Genetics and GeneDX.

On Wednesday, the group made its first report at a conference in Washington. The study also was published online by the New England Journal of Medicine.

So far, the project has tracked more than 172,000 variants in nearly 23,000 genes, a small portion of the millions known to exist but some of the more common ones that have been identified.

More than 118,000 of these variants have an effect on the risk for a disease — and 11 percent have been analyzed by more than one lab so results can be compared. In 17 percent of those cases, labs interpreted the findings differently, as either raising the risk of a disease, having no effect on it or having an unknown effect.

At least 415 gene variants now have different interpretations that could sway a medical decision, such as whether to have healthy breasts or ovaries removed to lower the risk of cancer, or to get a medical device such as an implanted defibrillator to cut the risk of sudden cardiac death.

"The magnitude of this problem is bigger than most people thought," said Michael Watson, executive director of the American College of Medical Genetics and Genomics, one of the study's authors and a partner in the data pooling project.

And it can harm patients. Rehm described a woman who had genetic testing and wrongly was told she did not have elevated risks for breast cancer. She later developed the disease but could have had preventive surgery had the right gene analyses been done.

An independent expert, Dr. Eric Topol, director of the Scripps Translational Science Institute in La Jolla, California, commended the study leaders and the database project for "cleaning up the mess" from labs that have not shared data in the past.

"We need millions of people sequenced, sharing all the data," to make things better, he said. With more sharing, the mystery gene variant problem " will largely go away, but that's going to take a few years at least.".."


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Susana M. originally shared to Science News:
 
Circulating tumor cells (CTCs) are cells that break away from a tumor and move through a cancer patient's bloodstream. Single CTCs are extremely rare, typically fewer than 1 in 1 billion cells. These cells can take up residence in distant organs, and researchers believe this is one mode by which cancer spreads.

Researchers have developed a microfluidic chip that can capture rare clusters of circulating tumor cells, which could yield important new insights into how cancer spreads. The work was funded by the National Institute of Biomedical Imaging and Bioengineering (NIBIB), part of the National Institutes of Health.

Research article:
A microfluidic device for label-free, physical capture of circulating tumor cell clusters
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3404.html
Nanowerk is the leading nanotechnology portal, committed to educate, inform and inspire about nanotechnologies, nanosciences, and other emerging technologies
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Leukippos Institute - Dedicated to Synthetic Biology - Science in the Cloud
Introduction

PhD, interested in synthetic biology dry lab work, Apple developer, director of the Leukippos Institute for synthetic biology

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Synthetic Biology Research
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  • Leukippos Institute
    Director, present