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PLoS ONE: Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology

PLoS ONE: Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it

by Benjamin A. Blount Tim Weenink, Serge Vasylechko, Tom Ellis

"Yeast is an ideal organism for the development and application of synthetic biology, yet there remain relatively few well-characterised biological parts suitable for precise engineering of this chassis. In order to address this current need, we present here a strategy that takes a single biological part, a promoter, and re-engineers it to produce a fine-graded output range promoter library and new regulated promoters desirable for orthogonal synthetic biology applications. A highly constitutive Saccharomyces cerevisiae promoter, PFY1p, was identified by bioinformatic approaches, characterised in vivo and diversified at its core sequence to create a 36-member promoter library. TetR regulation was introduced into PFY1p to create a synthetic inducible promoter (iPFY1p) that functions in an inverter device. Orthogonal and scalable regulation of synthetic promoters was then demonstrated for the first time using customisable Transcription Activator-Like Effectors (TALEs) modified and designed to act as orthogonal repressors for specific PFY1-based promoters. The ability to diversify a promoter at its core sequences and then independently target Transcription Activator-Like Orthogonal Repressors (TALORs) to virtually any of these sequences shows great promise toward the design and construction of future synthetic gene networks that encode complex “multi-wire” logic functions.

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[Bio]nanotechnology & Programmable Matter - Groups - Autodesk Research

[Bio]nanotechnology & Programmable Matter - Groups - Autodesk Research | SynBioFromLeukipposInstitute | Scoop.it

[Bio]nanotechnology & Programmable Matter
Carlos Olguin
Head of [Bio]nanotechnology & Programmable Matter Group
Nanotechnology, the control of matter on an atomic and molecular scale, is an emerging meta-field growing at an accelerated pace.

It is in our interest to identify the implications of nanotechnology and programmable matter for the industries that are currently supported by Autodesk software. It is equally important to early assess the new design spaces enabled by nanotechnology, in particular in regards to life & materials sciences.

Today, the design paradigm behind programmable matter is one that can be gradually applied to concrete projects across a range of domains and metric scales. The cross-pollination across projects will help create a robust scale-free body of knowledge.

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Berkeley Conference: Unmasking the Bay Area Biolab and Synthetic biology– | Blue Meanie Me .com

Berkeley Conference: Unmasking the Bay Area Biolab and Synthetic biology– | Blue Meanie Me .com | SynBioFromLeukipposInstitute | Scoop.it

Berkeley Conference: Unmasking the Bay Area Biolab and Synthetic biology– Event on 2012-03-29 19:00:00 Location Details: David Brower Center 2150 Allston...

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Reading "Art of Governance of Synthetic Biology

Reading "Art of Governance of Synthetic Biology" http://t.co/q6jZiQ0y via @hilarysutcliffe (thanks!

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Puriney - Apps Collections for Synthetic Biology

"Synthetic biology which is inspired by “plug-and-play” concept is supported by standardized biobricks and also computational tools for analysis and optimization. Here are bio-apps collections for you. Personally Tinkercell and UNAFold are favorite.

Circuit design and simulation
Biojade http://web.mit.edu/jagoler/www/biojade/
Tinkercell http://www.tinkercell.com/Home
Asmparts http://soft.synth-bio.org/asmparts.html
ProMoT http://www.mpimagdeburg.mpg.de/projects/promot
GenoCAD http://www.genocad.org/genocad/
GEC http://research.microsoft.com/gec
TABASCO http://openwetware.org/wiki/TABASCO#TabascoSimulator
Hy3S http://hysss.sourceforge.net/index.shtml

Circuit optimization
Genetdes http://soft.synth-bio.org/genetdes.html
RoVerGeNe http://iasi.bu.edu/∼batt/rovergene/rovergene.htm

DNA and RNA design
Gene Designer https://www.dna20.com/index.php?pageID=220
GeneDesign http://www.genedesign.org
UNAFold http://www.bioinfo.rpi.edu/applications/hybrid/download.php
mfold http://mfold.bioinfo.rpi.edu/download/
DINAMelt http://dinamelt.bioinfo.rpi.edu/
Vienna RNA package http://www.tbi.univie.ac.at/∼ivo/RNA/
Vienna RNA web servers http://rna.tbi.univie.ac.at/
Zinc Finger Tools http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php

Protein design
Rosetta http://www.rosettacommons.org/main.html
RAPTOR http://www.bioinformaticssolutions.com/products/raptor/index.php
HHpred http://toolkit.lmb.uni-muenchen.de/hhpred
Modeler http://salilab.org/modeller/
PFP http://dragon.bio.purdue.edu/pfp/
Autodock 4.2 http://autodock.scripps.edu/
HEX 5.1 http://webloria.loria.fr/∼ritchied/hex/

Integrated workflows
SynBioSS http://synbioss.sourceforge.net/
Clotho http://biocad-server.eecs.berkeley.edu/wiki/index.php/Tools
Biskit http://biskit.sf.net"

Provided and collected by Puriney!
http://bit.ly/FVEVJb
Thanks to them for sharing!

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The mainstream fronts of Synthetic Biology: Guest post | Lab Rat, Scientific American Blog Network

The mainstream fronts of Synthetic Biology: Guest post | Lab Rat, Scientific American Blog Network | SynBioFromLeukipposInstitute | Scoop.it

"“What I cannot build, I cannot understand”.

This phrase by the genius physicist Richard Feynman is cleverly encrypted into the genetic code of the first bacterial cells with an artificial genome that have ever existed.

Actually the quote says “what I cannot create…”, but maybe the scientists at the JCVI –who are behind this tremendous breakthrough- preferred to save some base pairs to avoid the use of the word “create” and its tricky implications. They published this work in 2010 and opened a whole new world of possibilities and made it completely clear to anyone what we mean when we talk about Synthetic Biology and what its ultimate purpose should be: to understand life by building it...."

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BioCurious

BioCurious | SynBioFromLeukipposInstitute | Scoop.it

We believe that innovations in biology should be
accessible, affordable, and open to everyone.

We’re building a community biology lab for
amateurs, inventors, entrepreneurs,
and anyone who wants to
experiment with friends.

Welcome to BioCurious

Visit the BioCurious homepage

http://www.BioCurious.org

BioCurious Community Lab

Opened in Sunnyvale, CA Fall 2011!

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Rapid hierarchical assembly of medium-size... [Nucleic Acids Res. 2012] - PubMed - NCBI

"Synthetic biology applications call for efficient methods to generate large gene cassettes that encode complex gene circuits in order to avoid simultaneous delivery of multiple plasmids encoding individual genes. Multiple methods have been proposed to achieve this goal. Here, we describe a novel protocol that allows one-step cloning of up to four gene-size DNA fragments, followed by a second assembly of these concatenated sequences into large circular DNA. The protocols described here comprise a simple, cheap and fast solution for routine construction of cassettes with up to 10 gene-size components...."

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Video: Creating Transient Cell Membrane Pores Using a Standard Inkjet Printer

Video: Creating Transient Cell Membrane Pores Using a Standard Inkjet Printer | SynBioFromLeukipposInstitute | Scoop.it

"Bioprinting has a wide range of applications and significance, including tissue engineering, direct cell application therapies, and biosensor microfabrication.1-10 Recently, thermal inkjet printing has also been used for gene transfection.8,9 The thermal inkjet printing process was shown to temporarily disrupt the cell membranes without affecting cell viability. The transient pores in the membrane can be used to introduce molecules, which would otherwise be too large to pass through the membrane, into the cell cytoplasm.8,9,11
The application being demonstrated here is the use of thermal inkjet printing for the incorporation of fluorescently labeled g-actin monomers into cells. The advantage of using thermal ink-jet printing to inject molecules into cells is that the technique is relatively benign to cells.8, 12 Cell viability after printing has been shown to be similar to standard cell plating methods1,8. In addition, inkjet printing can process thousands of cells in minutes, which is much faster than manual microinjection. The pores created by printing have been shown to close within about two hours. However, there is a limit to the size of the pore created (~10 nm) with this printing technique, which limits the technique to injecting cells with small proteins and/or particles. 8,9,11
A standard HP DeskJet 500 printer was modified to allow for cell printing.3, 5, 8 The cover of the printer was removed and the paper feed mechanism was bypassed using a mechanical lever. A stage was created to allow for placement of microscope slides and coverslips directly under the print head. Ink cartridges were opened, the ink was removed and they were cleaned prior to use with cells. The printing pattern was created using standard drawing software, which then controlled the printer through a simple print command. 3T3 fibroblasts were grown to confluence, trypsinized, and then resuspended into phosphate buffered saline with soluble fluorescently labeled g-actin monomers. The cell suspension was pipetted into the ink cartridge and lines of cells were printed onto glass microscope cover slips. The live cells were imaged using fluorescence microscopy and actin was found throughout the cytoplasm. Incorporation of fluorescent actin into the cell allows for imaging of short-time cytoskeletal dynamics and is useful for a wide range of applications.13-15..."

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Francisco J. Menéndez González's curator insight, April 10, 2013 3:37 AM

cómo convertir una simple impresora en una 3D Bioprinter....¿Dónde podré comprar los cartuchos?¿podré imprimir desde un word?. No estamos tan lejos.......

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Awakening: Synthetic Biology on the Verge of Revolutionizing Evolution

Awakening: Synthetic Biology on the Verge of Revolutionizing Evolution | SynBioFromLeukipposInstitute | Scoop.it

Some interesting videos!

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Tailored optical material from DNA: Nano spiral staircases modify light

Tailored optical material from DNA: Nano spiral staircases modify light | SynBioFromLeukipposInstitute | Scoop.it

"In the human body genetic information is encoded in double-stranded deoxyribonucleic acid building blocks, the so-called DNA. Using artificial DNA molecules, an international team of scientists headed by the Cluster of Excellence Nanosystems Initiative Munich has produced nanostructured materials that can be used to modify visible light by specification. The researchers present their results in the current issue of the renowned scientific journal Nature...."

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IJISA-V4-N2-7.pdf

Agent-based Models in Synthetic Biology: Tools for Simulation and Prospects

"We describe a multiset of agents based modeling and simulation paradigm for synthetic biology. The multiset of agents –based programming paradigm, can be interpreted as the outcome arising out of deterministic, nondeterministic or stochastic interaction among elements in a multiset object space, that includes the environment. These interactions are like chemical reactions and the evolution of the multiset can emulate the system biological functions. Since the reaction rules are inherently parallel, any number of actions can be performed cooperatively or competitively among the subsets of elements, so that the elements evolve toward equilibrium or emergent state. Practical realization of this paradigm for system biological simulation is achieved through the concept of transactional style programming with agents, as well as soft computing (neural- network) principles. Also we briefly describe currently available tools for agent-based-modeling, simulation and animation..."

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Synthetic biology: genetic engineering on steroids | TechCentral

Synthetic biology: genetic engineering on steroids | TechCentral | SynBioFromLeukipposInstitute | Scoop.it

"Whether or not we agree with it, we’re all pretty used to the idea of genetic engineering. Our food chain is full of GM crops and pretty soon we may be genetically modified ourselves. But synthetic biology takes the idea even further.
Instead of merely modifying existing organisms, synthetic biology aims to create entirely new organisms, often for large-scale industrial or agricultural use. Speaking at this year’s South by South West (SXSW) Interactive festival, a panel of experts discussed the state of this rapidly evolving field...."
Christina Agapakis, a synthetic biology academic from the University of California in Los Angeles, explains that the field is so new that it doesn’t even have a dictionary definition yet. She quotes Jim Collins, a biomedical engineer from Boston University who coined the phrase “genetic engineering on steroids”.

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Scientists develop tools to make more complex biological machines from yeast

"(Nanowerk News) Scientists are one step closer to making more complex microscopic biological machines, following improvements in the way that they can "re-wire" DNA in yeast, according to research recently published in the journal PLoS ONE ("Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology"). The researchers, from Imperial College London, have demonstrated a way of creating a new type of biological "wire," using proteins that interact with DNA and behave like wires in electronic circuitry. The scientists say the advantage of their new biological wire is that it can be re-engineered over and over again to create potentially billions of connections between DNA components. Previously, scientists have had a limited number of "wires" available with which to link DNA components in biological machines, restricting the complexity that could be achieved.
The team has also developed more of the fundamental DNA components, called "promoters," which are needed for re-programming yeast to perform different tasks. Scientists currently have a very limited catalogue of components from which to engineer biological machines. By enlarging the components pool and making it freely available to the scientific community via rapid Open Access publication, the team in this new study aims to spur on development in the field of synthetic biology.
Future applications of this work could include tiny yeast-based machines that can be dropped into water supplies to detect contaminants, and yeast that records environmental conditions during the manufacture of biofuels to determine if improvements can be made to the production process.
Dr Tom Ellis, senior author of the paper from the Centre for Synthetic Biology and Innovation and the Department of Bioengineering at Imperial College London, says: "From viticulture to making bread, humans have been working with yeast for thousands of years to enhance society. Excitingly, our work is taking us closer to developing more complex biological machines with yeast. These tiny biological machines could help to improve things such as pollution monitoring and cleaner fuels, which could make a difference in all our lives."..."

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Life Technologies Launches GeneArt® Precision TALs

Life Technologies Launches GeneArt® Precision TALs | SynBioFromLeukipposInstitute | Scoop.it

Life Technologies Corporation LIFE +0.17% today announced the launch of GeneArt® Precision TALs, generally referred to as TAL effector proteins (TALE), which will allow researchers the ability to edit genomes and control gene activity with unprecedented precision and reliability.

 
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Of Bugs and Biofuels - Can synthetic biology transform renewable energy?

Of Bugs and Biofuels - Can synthetic biology transform renewable energy? | SynBioFromLeukipposInstitute | Scoop.it

The world has an energy problem. And a carbon problem. Amidst the debate about the various forms of renewable energy and efforts to reduce carbon em...

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Leukippos - Synthetic Biology Dry Lab: a new FB group!

a new FB group for all interested in SynBio in silico:
databases, computational tools for analysis, modeling and optimization...... Circuit design and simulation, circuit optimization, DNA and RNA design, protein design, integrated workflows, computer aided design, integration of safety, tools for cloud collaboration.....
http://on.fb.me/xHvMAZ

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Synthetic Biology Newsletter 2.0 is available for the summer!

Synthetic Biology Newsletter 2.0 is available for the summer! | SynBioFromLeukipposInstitute | Scoop.it

"Synthetic Biology Newsletter 2.0 is available for the summer!
The Synthetic Biology Newsletter is an initiative of LIS Consult and the Synthetic Biology Project of the Woodrow Wilson International Center for Scholars. The newsletter is financially supported by the Commission on Genetic Modification and the Rathenau Institute, both in the Netherlands."

http://www.synbioproject.org/process/assets/files/6603/_draft/synthetic_biology_newsletter_02.pdf

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Scientists Manipulate Electrons Into Material Never Seen on Earth

Scientists Manipulate Electrons Into Material Never Seen on Earth | SynBioFromLeukipposInstitute | Scoop.it

"Scientists Manipulate Electrons Into Material Never Seen on Earth
Stanford scientists have created designer electrons that behave as if they were exposed to a magnetic field of 60 Tesla—a force 30 percent stronger than anything ever sustained on Earth. The work could lead to a revolution in the materials that make everything from video displays to airplanes to mobile phones.

"The behavior of electrons in materials is at the heart of essentially all of today's technologies," said Hari Manoharan, associate professor of physics at Stanford and a member of SLAC's Stanford Institute for Materials and Energy Sciences, who led the research. "We're now able to tune the fundamental properties of electrons so they behave in ways rarely seen in ordinary materials.""

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Has blogging changed science writing? — JCOM

Has blogging changed science writing? — JCOM | SynBioFromLeukipposInstitute | Scoop.it

"Rather than crystal ball gazing into the future of science journalism, this essay invites critical discussion over how much, if at all, has the web changed the way science is discussed in public? The short answer is no, or only slightly. Drawing on basic tenants of the social studies of technology, I argue there have always been more options than action when it comes to innovation in science writing. This essay takes three stories of the impact of the web on science journalism which I believe to be overstated, as well as three areas where I do think we can see change. None are clear-cut, as my chief aim here is to argue that our future is up for debate..."

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Data Deluge Drives Demand - Science Careers - Biotech, Pharmaceutical, Faculty, Postdoc jobs on Science Careers

Data Deluge Drives Demand - Science Careers - Biotech, Pharmaceutical, Faculty, Postdoc jobs on Science Careers | SynBioFromLeukipposInstitute | Scoop.it

Reprogramming computer scientists

"With the world’s fastest computers capable of processing quadrillions of calculations per second and the amount of data researchers generate growing by an order of magnitude each year, every field of science is turning to supercomputers to do new, innovative, data-intensive things: analyze genomes, simulate the evolution of dark matter, visualize the structure of proteins, and on and on. Supercomputers also offer a number of time- and money-saving opportunities for companies, which increasingly rely on these powerful machines to design everything from jets to sudsier laundry detergent......."

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On science blogs this week: SynBio | ScienceWriters (www.nasw.org)

"PUTTING THE SIN — AND THE PROZAC YOGURT — INTO SYNTHETIC BIOLOGY. Synthetic biology has as yet no agreed-upon definition even among synthetic biologists. But it already has a nickname, as an event this week is making clear, that is somewhat unfortunate from the standpoint of public relations. The nickname: synbio.

The event was a report issued by 111 environmental and other organizations. They argue that synthetic biology is potentially dangerous and needs more oversight. At ScienceInsider, Elizabeth Pennisi summarizes the call they issued this week. At Patent Docs, Kevin Noonan goes into more detail about the organizations' press conference, the report they issued, and even lists all the participating organizations.

If you're not sure what the term "synthetic biology" means either, you won't get much help. The new report calls it "an extreme form of genetic engineering." Read on, but for now let's go with Pennisi, who says synthetic biology comprises..."

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Synthetic biology in space: considering the broad societal and ethical implicati

"Although the field of synthetic biology is still in its infancy, there are expectations for great advances in the coming decades, both on Earth and potentially in space. Promising applications for long duration space missions include a variety of biologically engineered products and biologically aided processes and technologies, which will undoubtedly be scrutinized for risks and benefits in the broad context of ethical, legal and social realms. By comparing and contrasting features of Earth-based and space-applied synthetic biology, it is possible to identify the likely similarities and differences, and to identify possible challenges ahead for space applications that will require additional research, both in the short and long terms. Using an analytical framework associated with synthetic biology and new technologies on Earth, this paper analyses the kinds of issues and concerns ahead, and identifies those areas where space applications may require additional examination. In general, while Earth- and space-based synthetic biology share many commonalities, space applications have additional challenges such as those raised by space microbiology and environmental factors, legal complications, planetary protection, lack of decision-making infrastructure(s), long duration human missions, terraforming and the possible discovery of extraterrestrial (ET) life. For synthetic biology, the way forward offers many exciting opportunities, but is not without legitimate concerns - for life, environments and society, both on Earth and beyond...."

 
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Informit - Chain Reaction - Synthetic biology and the future bio-economy (Humanities & Social Sciences Collection)

Informit - Chain Reaction - Synthetic biology and the future bio-economy (Humanities & Social Sciences Collection) | SynBioFromLeukipposInstitute | Scoop.it

"In May 2010, Craig Venter announced that he had created "the first self-replicating species that we've had on the planet whose parent is a computer." This was the first time most people had heard of the emerging field known as "synthetic biology," which is attempting to write genetic code, design entire genomes, and even create life from scratch..."

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