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Protein gets in on DNA's origami act

Protein gets in on DNA's origami act | SynBioFromLeukipposInstitute | Scoop.it
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*Protein gets in on DNA's origami act* 

by
Mark Peplow

"Engineered bacteria make self-assembling tetrahedra.

Practitioners of DNA origami have spent the better part of the past decade folding the molecule into minuscule smiley faces, boxes, letters of the alphabet and dozens of other intricate shapes. Proteins, on the other hand, have been rather late in joining the origami party — even though nature is adept at moulding them into a dazzling array of functional shapes, including molecular-recognition systems and catalysts. Now Roman Jerala, a biochemist at the National Institute of Chemistry in Ljubljana, Slovenia, is making up for lost time. He and his colleagues have designed and built a protein that folds itself into a tetrahedron — a pyramid with a triangular base — and he says that the strategy could be used to make a wide range of other shapes. Whereas examples of DNA origami often look pretty, few of these creations have any practical use. Proteins, on the other hand, are much better suited to performing useful tasks, such as delivering drugs, according to Jerala..."

http://bit.ly/ZY2FYs

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*Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments*
byHelena Gradišar, Sabina Božič, Tibor Doles, Damjan Vengust, Iva Hafner-Bratkovič, Alenka Mertelj, Ben Webb, Andrej Šali, Sandi Klavžar & Roman Jerala

"Protein structures evolved through a complex interplay of cooperative interactions, and it is still very challenging to design new protein folds de novo. Here we present a strategy to design self-assembling polypeptide nanostructured polyhedra based on modularization using orthogonal dimerizing segments. We designed and experimentally demonstrated the formation of the tetrahedron that self-assembles from a single polypeptide chain comprising 12 concatenated coiled coil–forming segments separated by flexible peptide hinges. The path of the polypeptide chain is guided by a defined order of segments that traverse each of the six edges of the tetrahedron exactly twice, forming coiled-coil dimers with their corresponding partners. The coincidence of the polypeptide termini in the same vertex is demonstrated by reconstituting a split fluorescent protein in the polypeptide with the correct tetrahedral topology. Polypeptides with a deleted or scrambled segment order fail to self-assemble correctly. This design platform provides a foundation for constructing new topological polypeptide folds based on the set of orthogonal interacting polypeptide segments."
http://bit.ly/17tJn2A

and

*Self-Assembling Cages from Coiled-Coil Peptide Modules*

by
 Jordan M. Fletcher et al

"An ability to mimic the boundaries of biological compartments would improve our understanding of self-assembly and provide routes to new materials for the delivery of drugs and biologicals, and the development of protocells. We show that short designed peptides can be combined to form unilamellar spheres approximately 100 nanometers in diameter. The design comprises two, noncovalent, heterodimeric and homotrimeric coiled-coil bundles. These are joined back-to-back to render two complementary hubs, which when mixed form hexagonal networks that close to form cages. This design strategy offers control over chemistry, self-assembly, reversibility, and size of such particles."
http://bit.ly/11SATOV
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Genomics pioneer J. Craig Venter to give free talk at CU-Boulder on Sept. 29 | University of Colorado Boulder

Genomics pioneer J. Craig Venter to give free talk at CU-Boulder on Sept. 29 | University of Colorado Boulder | SynBioFromLeukipposInstitute | Scoop.it
Pioneering genomics researcher J. Craig Venter—best known for leading the privately funded team that sequenced the first human genome—will give a keynote talk at the University of Colorado Boulder on Sept. 29 about the scientific potential of and future products derived from “synthetic life.” 
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How Will Synthetic Biology Change the Way We Live? | Arizona SciTech

How Will Synthetic Biology Change the Way We Live? | Arizona SciTech | SynBioFromLeukipposInstitute | Scoop.it
Free public presentation about how synthetic biology will change our life! 9/23 @HeardMuseum #ASU #Biology #Phoenix http://t.co/GKyMkU0JL7
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Synthetic Biology

Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
The Boston University Center of Synthetic Biology (CoSBi) ICE Repository http://cidarlab.org/wp-content/uploads/2014/08/PaigeICEIWBDA2014.pdf (The #Boston University Center of #Synthetic #Biology (CoSBi) ICE Repository by @legomics
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Hydrogel scaffolds to study cell biology in four dimensions

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http://1.usa.gov/1ti0lxp

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Synthetic Biology - Springer

Synthetic Biology - Springer | SynBioFromLeukipposInstitute | Scoop.it
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http://bit.ly/1wohYuQ

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What is Synthetic Biology? [Video]

How to create life from scratch, as explained by SciAm editor David Biello (RT @dbiello: @mdichristina that's what we (@sciam) said ;) http://t.co/9c88oPCZAo)...
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Oxford iGEM - Our very own Timothy Ang featured on the... | Facebook

Our very own Timothy Ang featured on the great new blog "Humans and Synthetic Biology" by Cornell iGEM.... (Our very own Timothy Ang featured on the great new blog "Humans and Synthetic Biology" by Cornell iGEM....
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Drew Endy: The iGEM Revolution - The Long Now

Drew Endy: The iGEM Revolution - The Long Now | SynBioFromLeukipposInstitute | Scoop.it
hey sf, anyone interested in the long now talk tonight on synthetic biology? http://t.co/XPmHFx3UIQ I’ve got a spare ticket. DM/message me
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I See Your Smart Phone and Raise You Smart Bacteria

I See Your Smart Phone and Raise You Smart Bacteria | SynBioFromLeukipposInstitute | Scoop.it
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by

jtozer

"“Smart” bacteria that sense, track, pursue, fight and defeat infectious and other biological agents afflicting the warfighter might be closer to reality.

Building on earlier work focused on understanding how bacteria sense their nearest neighbors (including pathogens), a DTRA CB/JSTO-funded research team managed by DTRA CB’s Dr. Ilya Elashvili and led by Dr. William E. Bentley has paired with the Italian synthetic biology team headed by Dr. Sheref Mansy. The joint team created artificial cells that translate non-native signals into native signals that manipulate a local bacterial population.
These new tools have the potential to offer a means to localize bacteria and take actions to identify pathogens, other maladies (e.g., cancer cells), and synthesize drugs for local delivery and treatment.
Synthetic biology holds great promise to enable the engineering of “smart” bacteria that execute high order functions, such as those needed to sense, track, pursue, and fight pathogens. The Bentley lab focuses on minimally rewiring native cell processes so as not to “over engineer” these designer cells.
For example, they have built modules that recognize a pathogen’s signals and that rewire metabolic pathways to synthesize a pathogen-targeted drug. However, as these modules are pieced together and new modules are added, they impede other needed functions, such as swimming to or away from desired locales.
One way to counter unanticipated “side effects” is to employ small populations of orchestrated cells that act collectively to accomplish their task. Their plans, for example, call for “sentinel” and “dirigible” cells that find pathogens and call for backup.
In a recent Nature Communications article, “Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour,” the American-Italian joint team showed they were able to induce desired activity of native cells through communication with artificial cells.
The artificial cells, in turn, read a chemical cue foreign to the native cells and synthesized another compound recognized by the native cells. In this way, the artificial cells served as a translator. To the authors’ knowledge, this is the first artificial, cell-like system capable of translating unrecognized signals into a chemical language that natural cells can recognize.
The artificial non-living cell was built with a phospholipid vesicle containing isopropyl β-D-1-thiogalactopyranoside (IPTG), DNA, and transcription–translation machinery. The DNA template codes for a previously selected ribo-switch that activates translation in response to the presence of a model chemical signal molecule, theophylline.
Theophylline is added to the mixture, diffuses into the vesicle, and triggers the synthesis of the pore forming protein α-hemolysin (αHL). Therefore, only in the presence of theophylline a pore forms that releases entrapped IPTG.
Released IPTG will increase the transcription of a variety of genes induced by the lac operon in E. coli. IPTG is a model signal molecule in the current study, but it is a surrogate for a pathogen-modulating compound that would otherwise be held in abeyance in the vesicle in future studies.
E. coli alone does not respond to theophylline, and IPTG does not cross the vesicle membrane of the artificial cell in the absence of the pore. The ability of E. coli to receive the chemical message (IPTG) sent by the artificial cells was assessed in two ways.
First, a recombinant E. coli transformed with a plasmid, synthesized green fluorescent protein in response to IPTG; this was assayed using flow cytometry. Second, a natural or “wild type” E. coli was tested via reverse transcription quantitative polymerase chain reactions (RT-qPCR) that confirmed the up-regulation of the lac operon genes (more than a 20-fold increase).
The integration of artificial translator cells with natural cells represents a new strategy to introduce synthetic features to a biological system and at the same time, lessens the need for direct genetic manipulation...."



http://1.usa.gov/1BJMH8Q

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100% Design 2014 - Talks with 100% Design

100% Design 2014 - Talks with 100% Design | SynBioFromLeukipposInstitute | Scoop.it
The theme for the year’s 100% Design is serendipity.
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I need your help with this survey

Hi!

Can you do me a favor and fill out this…

I need your help with this survey<br/><br/>Hi!<br/><br/>Can you do me a favor and fill out this… | SynBioFromLeukipposInstitute | Scoop.it
I need your help with this survey

Hi!

Can you do me a favor and fill out this survey.


https://www.surveymonkey.com/s/YTPJW9G


It would also be great… - Cellular Computing - Google+
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*I need your help with this survey*
Hi!
Can you do me a favor and fill out this survey. 
It would also be great to send it to your friends
Thanks so much in advance.
Have a great weekend.
Best Gerd
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IChemE | Events | Biochemical Engineering Special Interest Group | Synthetic Biology 2014

This event will feature important advances in synbio from leading companies in the field, ranging from industrial to healthcare applications. (RT @AmyElizaTayler: I'm going to the @IChemE SynBio symposium on 22nd Sept.
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Synthetic Biology Market (Synthetic DNA, Synthetic Genes, Synthetic Cells, XNA, Chassis Organisms, DNA Synthesis, Oligonucleotide Synthesis) - Global Industry Analysis, Size, Share, Growth, Trends ...

SYS-CON Media, NJ, The world's leading i-technology media company on breaking technology news.
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Synthetic Biology and Metabolic Engineering for Marine Carotenoids: New Opportunities and Future Prospects

Synthetic Biology and Metabolic Engineering for Marine Carotenoids: New Opportunities and Future Prospects | SynBioFromLeukipposInstitute | Scoop.it
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by
Chonglong Wang , Jung-Hun Kim and Seon-Won Kim

"Carotenoids are a class of diverse pigments with important biological roles such as light capture and antioxidative activities. Many novel carotenoids have been isolated from marine organisms to date and have shown various utilizations as nutraceuticals and pharmaceuticals. In this review, we summarize the pathways and enzymes of carotenoid synthesis and discuss various modifications of marine carotenoids. The advances in metabolic engineering and synthetic biology for carotenoid production are also reviewed, in hopes that this review will promote the exploration of marine carotenoid for their utilizations."


 http://bit.ly/1rlWA9K

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Theispot.com - Stuart Bradford: Synthetic Biology

Theispot.com - Stuart Bradford: Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
Stuart Bradford: Synthetic Biology. Stuart Bradford created a series of illustrations for Harvard Alumni magazine on synthetic biology, wherein scientists alter genetic structure to create tiny machines, tinkering like engineers.
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Synthetic Biology

Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
Kristala L. J. Prather (MIT) Part 1: Introduction to Synthetic Biology a...
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Bioengineers develop a toolkit for designing more successful synthetic molecules

Bioengineers develop a toolkit for designing more successful synthetic molecules | SynBioFromLeukipposInstitute | Scoop.it
(Phys.org) —Ever since Robert Hooke first described cells in 1665, scientists have been trying to figure out what is going on inside.
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Synthetic biology at the interface of functional genomics

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http://bit.ly/ZonkM3

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Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour

Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour | SynBioFromLeukipposInstitute | Scoop.it
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by
Roberta Lentini et al

"Previous efforts to control cellular behaviour have largely relied upon various forms of genetic engineering. Once the genetic content of a living cell is modified, the behaviour of that cell typically changes as well. However, other methods of cellular control are possible. All cells sense and respond to their environment. Therefore, artificial, non-living cellular mimics could be engineered to activate or repress already existing natural sensory pathways of living cells through chemical communication. Here we describe the construction of such a system. The artificial cells expand the senses of Escherichia coli by translating a chemical message that E. coli cannot sense on its own to a molecule that activates a natural cellular response. This methodology could open new opportunities in engineering cellular behaviour without exploiting genetically modified organisms."

 http://bit.ly/Xx7v4m

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Zócalo Public Square: How Will Synthetic Biology Change the Way We Live?

Zócalo Public Square: How Will Synthetic Biology Change the Way We Live? | SynBioFromLeukipposInstitute | Scoop.it
Biologist and entrepreneur J. Craig Venter visits Zócalo to talk with Arizona State University President Michael M.
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Legomics - Timeline Photos | Facebook

Legomics - Timeline Photos | Facebook | SynBioFromLeukipposInstitute | Scoop.it
Design and Build Biological Systems with @legomics #Synthetic #Biology #IGEM (RT @legomics: Design and Build Biological Systems with @legomics #Synthetic #Biology #IGEM http://t.co/nFieFQ4h8b)...
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How Synthetic Biology Will Reconsider Natural Bioluminescence and Its Applications

How Synthetic Biology Will Reconsider Natural Bioluminescence and Its Applications | SynBioFromLeukipposInstitute | Scoop.it
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by
Benjamin Reeve, Theo Sanderson, Tom Ellis, Paul Freemont

"As our understanding of natural biological systems grows, so too does our ability to alter and rebuild them. Synthetic biology is the application of engineering principles to biology in order to design and construct novel biological systems for specific applications. Bioluminescent organisms offer a treasure trove of light-emitting enzymes that may have applications in many areas of bioengineering, from biosensors to lighting. A few select bioluminescent organisms have been well researched and the molecular and genetic basis of their luminescent abilities elucidated, with work underway to understand the basis of luminescence in many others. Synthetic biology will aim to package these light-emitting systems as self-contained biological modules, characterize their properties, and then optimize them for use in other chassis organisms. As this catalog of biological parts grows, synthetic biologists will be able to engineer complex biological systems with the ability to emit light. These may use luminescence for an array of disparate functions, from providing illumination to conveying information or allowing communication between organisms."


 http://bit.ly/1oRmdKB

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Certificate in Synthetic Biology | Synberc | CodonOps

Certificate in Synthetic Biology | Synberc (Certificate in Synthetic Biology | Synberc http://t.co/GkOeIVksGi #synbio)
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Certificate in Synthetic Biology | Synberc

Certificate in Synthetic Biology | Synberc | SynBioFromLeukipposInstitute | Scoop.it
Certificate in Synthetic Biology | Synberc http://t.co/YLGFqgEwMw, see more http://t.co/IcOOX7d7AA
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BCom Student Will Travel to Boston with iGEM uOttawa to Present Their Synthetic Biology Project - Telfer School of Management

BCom Student Will Travel to Boston with iGEM uOttawa to Present Their Synthetic Biology Project - Telfer School of Management | SynBioFromLeukipposInstitute | Scoop.it
BCom student will travel to Boston with @uOttawaiGEM to present their synthetic biology project - http://t.co/G3n4TJ52Li #Telfer #uOttawa
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