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Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition
Research, development and production of antiviral treatments since perspectives evolutionary and synthetic Biology: Study of Systems and Mechanims of evolution viruses through bioinformatics tools for immunomodulation addressed of systems delivery with iRNAs, antivirals and celular signaling regulation.
Curated by Cesar Saldaña
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An adaptor from translational to transcriptional control enables predictable assembly of complex regulation

An adaptor from translational to transcriptional control enables predictable assembly of complex regulation | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it

Chang C Liu,Lei Qi,Julius B Lucks,Thomas H Segall-Shapiro,Denise Wang,Vivek K Mutalik& Adam P Arkin

 

Nature Methods9,1088–1094(2012)doi:10.1038/nmeth.2184

 

Abstract:

 

Bacterial regulators of transcriptional elongation are versatile units for building custom genetic switches, as they control the expression of both coding and noncoding RNAs, act on multigene operons and can be predictably tethered into higher-order regulatory functions (a property called composability). Yet the less versatile bacterial regulators of translational initiation are substantially easier to engineer. To bypass this tradeoff, we have developed an adaptor that converts regulators of translational initiation into regulators of transcriptional elongation in Escherichia coli. We applied this adaptor to the construction of several transcriptional attenuators and activators, including a small molecule–triggered attenuator and a group of five mutually orthogonal riboregulators that we assembled into NOR gates of two, three or four RNA inputs. Continued application of our adaptor should produce large collections of transcriptional regulators whose inherent composability can facilitate the predictable engineering of complex synthetic circuits.

 

http://www.nature.com/nmeth/journal/v9/n11/full/nmeth.2184.html?WT.ec_id=NMETH-201211

 


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Giant viruses coexisted with the cellular ance... [BMC Evol Biol. 2012] - PubMed - NCBI

Giant viruses coexisted with the cellular ance... [BMC Evol Biol. 2012] - PubMed - NCBI | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it
PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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Genome-editing tools storm ahead : Nature Methods : Nature Publishing Group

Genome-editing tools storm ahead : Nature Methods : Nature Publishing Group | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it
The menu of maturing, diversifying methods calls for careful selections in experimental design.

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Fluorescent proteins and in vitro genetic organization for cell-free synthetic biology

Fluorescent proteins and in vitro genetic organization for cell-free synthetic biology | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it

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Socrates Logos's curator insight, March 9, 2013 10:57 AM

by
Roberta Lentini , Michele Forlin , Laura Martini , Cristina Del Bianco , Amy C Spencer , Domenica Torino , and Sheref S Mansy

"To facilitate the construction of cell-free genetic devices, we evaluated the ability of 17 different fluorescent proteins to give easily detectable fluorescence signals in real-time from in vitro transcription-translation reactions with a minimal system consisting of T7 RNA polymerase and E. coli translation machinery, i.e. the PUREsystem. The data were used to construct a ratiometric fluorescence assay to quantify the effect of genetic organization on in vitro expression levels. Synthetic operons with varied spacing and sequence composition between two genes that coded for fluorescent proteins were then assembled. The resulting data indicated which restriction sites and where the restriction sites should be placed in order to build genetic devices in a manner that does not interfere with protein expression. Other simple design rules were identified, such as the spacing and sequence composition influences of regions upstream and downstream of ribosome binding sites and the ability of non-AUG start codons to function in vitro."

http://bit.ly/12DfUo5

see also
Cell-free synthetic biology: Thinking outside the cell http://bit.ly/YjBmWH
Fig taken from this ref.

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Discovery in synthetic biology a step closer to new industrial revolution - Imperial College London

Discovery in synthetic biology a step closer to new industrial revolution - Imperial College London | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it

Parts made up of DNA are re-engineered by scientists and put into cells to make biological factories. However, a major bottleneck in synthetic biology is the lack of parts from which to build new types of factories. To build parts using the current time-consuming method, scientists have to re-engineer DNA in a cell and observe how it works. If it functions according to their specifications, then the scientists store the part specifications in a catalogue.

 

Now, scientists from Imperial College London have devised a much quicker method that does away with the need for them to re-engineer a cell every time they want to make a new part. The team say their work could lead to vast new libraries of off-the-shelf components that could be used to build more sophisticated biological factories.


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US bird flu research to resume under new restrictions

US bird flu research to resume under new restrictions | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it
Back in January 2012, the US government announced it was joining with scientists around the world and temporarily suspending research on the deadly pathogen H5N1, also known as avian flu or "bird...

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Ed Rybicki's curator insight, February 25, 2013 12:08 AM

" "the policy aims to preserve the benefits of life sciences research while minimizing the risk of misuse.""

 

OK - can't argue too hard with that, I suppose?  EXCEPT that it probably limits access to the research of countries where the virus is ACTUALLY a problem.

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Lego-Like Cloning Platform for Transforming Synthetic Biology

Lego-Like Cloning Platform for Transforming Synthetic Biology | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it

Scientists at Oxford Genetics have developed a range of synthetic DNA products that they believe will revolutionize the genetic research sector: the SnapFast.


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Genetic programs constructed from layered logic gates in single cells

Genetic programs constructed from layered logic gates in single cells | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it

Tae Seok Moon,Chunbo Lou,Alvin Tamsir,Brynne C. Stanton& Christopher A. Voigt

Nature491,249–253(08 November 2012)doi:10.1038/nature11516

Received02 February 2012Accepted15 August 2012Published online07 October 2012

 

Abstract:

Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics1. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits and they have been used in various cellular engineering applications, including the implementation of process control in metabolic networks and the coordination of spatial differentiation in artificial tissues. A key limitation is that the circuits are based on biochemical interactions occurring in the confined volume of the cell, so the size of programs has been limited to a few circuits1, 7. Here we apply part mining and directed evolution to build a set of transcriptional AND gates in Escherichia coli. Each AND gate integrates two promoter inputs and controls one promoter output. This allows the gates to be layered by having the output promoter of an upstream circuit serve as the input promoter for a downstream circuit. Each gate consists of a transcription factor that requires a second chaperone protein to activate the output promoter. Multiple activator–chaperone pairs are identified from type III secretion pathways in different strains of bacteria. Directed evolution is applied to increase the dynamic range and orthogonality of the circuits. These gates are connected in different permutations to form programs, the largest of which is a 4-input AND gate that consists of 3 circuits that integrate 4 inducible systems, thus requiring 11 regulatory proteins. Measuring the performance of individual gates is sufficient to capture the behaviour of the complete program. Errors in the output due to delays (faults), a common problem for layered circuits, are not observed. This work demonstrates the successful layering of orthogonal logic gates, a design strategy that could enable the construction of large, integrated circuits in single cells.

 

http://www.nature.com/nature/journal/v491/n7423/full/nature11516.html

 

 


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Fluorescent fusion protein knockout mediated by anti-GFP nanobody - Nature Struct. Mol. Biology

Fluorescent fusion protein knockout mediated by anti-GFP nanobody - Nature Struct. Mol. Biology | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it

http://www.nature.com/nsmb/journal/v19/n1/full/nsmb.2180.html

Caussinus et al (2012)

The use of genetic mutations to study protein functions in vivo is a central paradigm of modern biology. Recent advances in reverse genetics such as RNA interference and morpholinos are widely used to further apply this paradigm. Nevertheless, such systems act upstream of the proteic level, and protein depletion depends on the turnover rate of the existing target proteins. Here we present deGradFP, a genetically encoded method for direct and fast depletion of target green fluorescent protein (GFP) fusions in any eukaryotic genetic system. This method is universal because it relies on an evolutionarily highly conserved eukaryotic function, the ubiquitin pathway. It is traceable, because the GFP tag can be used to monitor the protein knockout. In many cases, it is a ready-to-use solution, as GFP protein-trap stock collections are being generated in Drosophila melanogaster and in Danio rerio.


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aamoros2's curator insight, June 24, 9:39 AM

Proteínas fluorescentes.

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Factory of Life - Science News

Factory of Life - Science News | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it

Synthetic biology was born a little more than a decade ago, an offshoot of traditional genetic engineering but distinct in its ambitions, precision and mind-set.


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How to turn living cells into computers - Nature.com

How to turn living cells into computers - Nature.com | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it

Synthetic biologists have developed DNA modules that perform logic operations in living cells.


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An Infinity of Viruses

An Infinity of Viruses | Evolutionary and Synthetic Biology: Design devices for addressed antiviral inhibition | Scoop.it

When I talk about viruses, I have to struggle with big numbers. 

If you get sick with the flu, for example, every infected cell in your airway produces about 10,000 new viruses. The total number of flu viruses in your body can rise to 100 trillion within a few days. That’s over 10,000 times more viruses than people on Earth.

If there can be so many viruses in a single person, how many viruses are there in total on our planet? I’ve hunted around for a number, and the one I’ve seen most often is 1031. As in, 10000000000000000000000000000000. As in over 10 million times more viruses than there are stars in the universe. As in, if you were to stack one virus on top of another, you’d create a tower that would stretch beyond the moon, beyond the sun, beyond Alpha Centauri, out past the edge of the Milky Way, past neighboring galaxies, to reach a height of 200 million light years.


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jeje y 1000000 por cada litro de agua marina

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Ed Rybicki's curator insight, February 25, 2013 10:19 PM

Definitely a Virus Planet!

Chris Upton + helpers's comment, February 26, 2013 11:50 AM
Lets leave "infinity" to Toy Story and Physics!