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Engineering and Control of Biological Systems: A New Way to Tackle Complex Diseases

Engineering and Control of Biological Systems: A New Way to Tackle Complex Diseases

by
Menolascina F, Siciliano V, di Bernardo D.
"The ongoing merge between engineering and biology has contributed to the emerging field of Synthetic Biology. The defining features of this new discipline are abstraction and standardisation of biological parts, decoupling between parts to prevent undesired cross-talking, and the application of quantitative modelling of synthetic genetic circuits in order to guide their design. Most of the efforts in the field of synthetic biology in the last decade have been devoted to the design and development of functional gene circuits in prokaryotes and unicellular eukaryotes. Researchers have used synthetic biology not only to engineer new functions in the cell, but also to build simpler models of endogenous gene regulatory network to gain knowledge of the "rules" governing their wiring diagram. However, the need for innovative approaches to study and modify complex signalling and regulatory networks in mammalian cells and multicellular organisms has prompted advances of Synthetic Biology also in these species, thus contributing to develop innovative ways to tackle human diseases. In this work, we will review the latest progress in synthetic biology and the most significant developments achieved so far, both in unicellular and multicellular organisms, with emphasis to human health."
http://1.usa.gov/JE4h3m

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- SCI-TECH and HEALTH

- SCI-TECH and HEALTH | SynBioFromLeukipposInstitute | Scoop.it

"Tel Aviv, May 15: Now, there's a quick check for synthetic chemicals and poisons that contaminate water or food supplies and generate bodily reactions from minor illness to painful death.

Yosi Shacham-Diamand, professor of engineering at Tel Aviv University, and Shimshon Belkin of the Hebrew University of Jerusalem, have married biology and engineering to design a biosensor called the "Dip Chip," which detects toxicity quickly and accurately.

The Dip Chip contains microbes designed to exhibit a biological reaction to toxic chemicals, duplicating the biological responses of humans or animals. The bio-reaction is converted into an electronic signal that can be read by the user....."
http://bit.ly/IVylW2

 
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Crowd funding - a novel concept for financing science

Crowd funding: A new exiting option for financing biomedical research!

Crowd funding
Kicksatrter
http://www.kickstarter.com/
IndieGoGo
http://www.indiegogo.com/
RocketHub
http://www.rockethub.com/
Microryza
http://thenextweb.com/apps/2012/04/12/meet-microryza-crowd-funding-for-scientific-research/?utm_source=GooglePlus
https://www.microryza.com/
Crowdfunding is the future of science
http://scifundchallenge.org/blog/2012/05/09/crowdfunding-is-the-future-of-science/

Jobs act
http://watch.bnn.ca/#clip674892
http://watch.bnn.ca/#clip674899
http://watch.bnn.ca/#clip674902

 
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Science at Cal - Terry Johnson - Synthetic Biology: Beating the Cell at its Own Game

Science at Cal - Terry Johnson - Synthetic Biology: Beating the Cell at its Own Game

Video
"Your body routinely produces 200 billion red blood cells every day, yet you could spend years at a lab bench attempting to artificially synthesize all of the raw materials that those cells are made of. Your cells manage to do that - and to assemble new cells out of those raw materials - with relative ease. Synthetic biology aims to design and construct biological systems to make valuable products or perform constructive tasks. The tremendous diversity in the natural world provides us with a versatile and complex set of biological tools. We'll discuss how synthetic biologists apply and hone these tools, and to what ends."
http://bit.ly/Jz6IEo

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Synthetic Life, Blood Vessel Printing, Jaw Transplants, and other Medical Breakthroughs

Synthetic Life, Blood Vessel Printing, Jaw Transplants, and other Medical Breakthroughs | SynBioFromLeukipposInstitute | Scoop.it

byJohn Niman

"Today I want to talk about three broad categories: Synthetic or engineered medical research or treatments, biological (DNA) research and procedures, and various transplants that have been performed or are being researched.

Synthetic Medical Advances:

A lot of research recently has been targeted at creating synthetic life. These are not robotic solutions (so, for these purposes at least, synthetic does not mean artificial intelligence or cyborgs) but instead largely biological entities that have been tinkered with.

For example, Kurzweilai.net reports that chemists have created cells with self-assembling, artificial membranes. Because creating truly artificial life will require both an artificial membrane and an artificial genome (which has also been created) this is an important step towards creating entirely new organisms. The best part: it seems to be easy and cheap to create these new artificial membranes, so we should see a lot of movement in this area in the near future.

Once we have entirely synthetic cells, how could we make more?........"
http://bit.ly/KlM1hU

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Biohack

game

"We've all played physics-based games before. But have you ever tried one based on biochemical kinetics? BioHack is a simulation game where you must solve challenging design problems. This Lite version of the game includes the first 15 levels from the full game. No science background necessary!"

http://www.fileplanet.com/216253/210000/fileinfo/BioHack-Lite

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Living Photography | Oscillator, Scientific American Blog Network

Living Photography | Oscillator, Scientific American Blog Network | SynBioFromLeukipposInstitute | Scoop.it

By Christina Agapakis

"Plants don’t always seem particularly charismatic, but hidden from us in their slow-motion and chemical activities are incredible mechanisms that sense and respond to the world around them. Plants move in response to light, bending and stretching to get maximum sunlight. This phototropism extends all the way down to much smaller photosynthetic organisms. Like other bacteria, many species of photosynthetic cyanobacteria can swim and swarm to move towards areas where more food–sunlight–is available. Shading some regions will quickly clear them of bacteria, reproducing which areas were bright and which were dark, creating a living photographic image."
http://bit.ly/M7IgNL

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Is a new form of life really so alien?

"The idea of discovering a new form of life has not only excited astronomers and astrobiologists for decades, but also the wider public. The notion that we are the only example of a successful life form in the galaxy has, for many, seemed like an unlikely statistic, as we discover more and more habitable planetary bodies and hear yet more evidence of life's ability to survive in extreme conditions. A new essay, published May 8 in the online, open-access journal PLoS Biology, examines what really constitutes 'life' and the probability of discovering new life forms. Accompanying the article is an interview with the author in the latest edition of the PLoS Biology Podcast."

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How Can Compressive Sensing and Advanced Matrix Factorizations enable Synthetic Biology ?

Videos

eg TEDxCaltech J.Craig Venter - Future Biology

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Northwestern University professors recognized got awards from Grand Challenges Explorations for their #synbio work

2 Grand Challenges Explorations grants for global health

"The innovative research of three Northwestern University professors who are making a big difference in the highly promising area of synthetic biology has been recognized with two early-stage discovery awards from Grand Challenges Explorations, an initiative funded by the Bill & Melinda Gates Foundation.
The global health projects will focus on creating new compounds to combat malaria and on producing biosensors for low-cost, in-home diagnoses.
The prestigious awards are two of 107 Grand Challenges Explorations (GCE) grants announced this week. The funding supports scientists, researchers and entrepreneurs worldwide who are testing unconventional ideas that show great promise to improve the health of people in the developing world.
Northwestern now has received a total of three GCE grants as part of the Gates Foundation's call to "Apply Synthetic Biology to Global Health Challenges." (Synthetic biology is the design and construction of new types of biological systems.) To date, only 30 synthetic biology grants have been awarded as part of this initiative, acknowledging Northwestern as being at the forefront of its use to address global health issues.
"The Gates Foundation support allows us to pursue high-risk, high-reward projects that are utilizing cutting-edge techniques to engineer biological systems," said Keith Tyo, an investigator on all three grants. "Success on any one of these projects could result in a dramatic improvement in quality of life for millions of suffering people."
Tyo is an assistant professor of chemical and biological engineering in the McCormick School of Engineering and Applied Science.
Andreas Matouschek, professor of molecular biosciences in the Weinberg College of Arts and Sciences, and Tyo will develop synthetic compounds that target essential proteins in the Plasmodium parasite for destruction by its own protein degradation mechanisms. This strategy could lead to new treatment modalities as well as small molecule drug development efforts to combat malaria.
In the other project, Tyo and Joshua Leonard, an assistant professor of chemical and biological engineering, will work to engineer yeast-based biosensors that identify protein biomarkers in samples like blood and urine. An array of yeast strains could serve as a low-cost, in-home device providing patients with a panel of diagnostics to improve treatment and diagnosis in resource-poor settings...."
http://bit.ly/JIX83m

 
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The Inner Life of the Cell

Harvard University selected XVIVO to develop an animation that would take their cellular biology students on a journey through the microscopic world of a cell, illustrating mechanisms that allow a white blood cell to sense its surroundings and respond to an external stimulus. This award winning piece was the first topic in a series of animations XVIVO is creating for Harvard's educational website BioVisions at Harvard.
http://www.xvivo.net
http://multimedia.mcb.harvard.edu/

 
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Engineering synthetic TAL effectors with orthogonal target sites

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Garg A, Lohmueller JJ, Silver PA, Armel TZ.
"The ability to engineer biological circuits that process and respond to complex cellular signals has the potential to impact many areas of biology and medicine. Transcriptional activator-like effectors (TALEs) have emerged as an attractive component for engineering these circuits, as TALEs can be designed de novo to target a given DNA sequence. Currently, however, the use of TALEs is limited by degeneracy in the site-specific manner by which they recognize DNA. Here, we propose an algorithm to computationally address this problem. We apply our algorithm to design 180 TALEs targeting 20 bp cognate binding sites that are at least 3 nt mismatches away from all 20 bp sequences in putative 2 kb human promoter regions. We generated eight of these synthetic TALE activators and showed that each is able to activate transcription from a targeted reporter. Importantly, we show that these proteins do not activate synthetic reporters containing mismatches similar to those present in the genome nor a set of endogenous genes predicted to be the most likely targets in vivo. Finally, we generated and characterized TALE repressors comprised of our orthogonal DNA binding domains and further combined them with shRNAs to accomplish near complete repression of target gene expression.2
http://1.usa.gov/LNkZhA
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Synthetic biology: We can rebuild you

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Andrew Jermy
"The complex regulatory systems that control the expression of gene clusters in bacteria can make it difficult to alter the functional properties of such clusters or to transfer them between organisms. Now Temme et al.Klebsiella oxytoca and replaced them with synthetic genetic components."http://bit.ly/Jj7XJx

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Berkeley Lab Scientists Generate Electricity From Viruses « Berkeley Lab News Center

Berkeley Lab Scientists Generate Electricity From Viruses « Berkeley Lab News Center | SynBioFromLeukipposInstitute | Scoop.it

New approach is a promising first step toward the development of tiny devices that harvest electrical energy from everyday tasks

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DNA origami puts a smart lid on solid-state nanopore sensors

DNA origami puts a smart lid on solid-state nanopore sensors | SynBioFromLeukipposInstitute | Scoop.it

"The latest advance in solid-state nanopore sensors – devices that are made with standard tools of the semiconductor industry yet can offer single-molecule sensitivity for label-free protein screening – expands their bag of tricks through bionanotechnology. Researchers at the Technische Universitaet Muenchen have enhanced the capabilities of solid-state nanopores by fitting them with cover plates made of DNA. These nanoscale cover plates, with central apertures tailored to various "gatekeeper" functions, are formed by so-called DNA origami – the art of programming strands of DNA to fold into custom-designed structures with specified chemical properties...."

http://bit.ly/LIPjtE
additional ref
DNA Origami Gatekeepers for Solid-State Nanopores
by
Ruoshan Wei, Thomas G. Martin, Ulrich Rant, Hendrik Dietz
http://bit.ly/LIPjtE

 
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TEDxNYU - Christopher Bradley - Synthetic Biology: This Will Change Everything

In this fascinating talk Christopher Bradley shows us that our world is about to change radically thanks to the promise of Synthetic Biology. About Christopher Bradley Christopher is a student at NYU ...

http://bit.ly/JbcFLx

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Next Generation 3-D Printing: Higher Resolution, Tastier, and Super Cute

Next Generation 3-D Printing: Higher Resolution, Tastier, and Super Cute | SynBioFromLeukipposInstitute | Scoop.it

BY JOSEPH FLAHERTY

Food printers, medical printers......

"For desktop designers, consumer-grade 3-D printers are nothing short of revolutionary. But the technology is still fairly crude, limited to producing “low-resolution” shapes made out of plastic. What’s next? There are a host of new tools coming down the pike that promise to radically improve both the form and function of the stuff you can print, from chess pieces to chocolate...."

http://bit.ly/K7VSCe

 
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GENtle 2 by Synbiota

a great rethink of the original GENtle by Magnus Manske http://gentle.magnusmanske.de/ for the web. http://bit.ly/Jvicsr

 
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Synbiota | About

Synbiota | About | SynBioFromLeukipposInstitute | Scoop.it

Synbiota is building a bio-lab in a browser. Synthetic Biology promises to revolutionize the world in ways we have yet to imagine. Synbiota is working towards this revolution by developing powerful, standards-based, open and free tools for synthetic biology design. We need your help!

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Distributed computation: the new wave of synthetic biology devices

Distributed computation: the new wave of synthetic biology devices | SynBioFromLeukipposInstitute | Scoop.it

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Javier Macía, Francesc Posas, Ricard V. Solé
"Synthetic biology (SB) offers a unique opportunity for designing complex molecular circuits able to perform predefined functions. But the goal of achieving a flexible toolbox of reusable molecular components has been shown to be limited due to circuit unpredictability, incompatible parts or random fluctuations. Many of these problems arise from the challenges posed by engineering the molecular circuitry: multiple wires are usually difficult to implement reliably within one cell and the resulting systems cannot be reused in other modules. These problems are solved by means of a nonstandard approach to single cell devices, using cell consortia and allowing the output signal to be distributed among different cell types, which can be combined in multiple, reusable and scalable ways."
http://bit.ly/J7wk8y

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May 21 - Building Biology: A symposium on synthetic biology - NOW - Concordia University

This symposium will act as a cornerstone for the creation of a synthetic biology research hub at and for Concordia University (May 21 - Building Biology: A symposium on synthetic biology: http://t.co/3JUVMCOT #biology...
 
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Application of targeted proteomics to metabolically engineered Escherichia coli

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Singh P, Batth TS, Juminaga D, Dahl RH, Keasling JD, Adams PD, Petzold CJ.
"As synthetic biology matures to compete with chemical transformation of commodity and high-value compounds, a wide variety of well-characterized biological parts are needed to facilitate system design. Protein quantification based on selected-reaction monitoring (SRM) mass spectrometry compliments metabolite and transcript analysis for system characterization and optimizing flux through engineered pathways. By using SRM quantification, we assayed red fluorescent protein (RFP) expressed from plasmids containing several inducible and constitutive promoters and subsequently assessed protein production from the same promoters driving expression of eight mevalonate pathway proteins in Escherichia coli. For each of the promoter systems, the protein level for the first gene in the operon followed that of RFP, however, the levels of proteins produced from genes farther from the promoter were much less consistent. Second, we used targeted proteomics to characterize tyrosine biosynthesis pathway proteins after removal of native regulation. The changes were not expected to cause significant impact on protein levels, yet significant variation in protein abundance was observed and tyrosine production for these strains spanned a range from less than 1 mg/L to greater than 250 mg/L. Overall, our results underscore the importance of targeted proteomics for determining accurate protein levels in engineered systems and fine-tuning metabolic pathways."
http://1.usa.gov/JndoGi

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The Saccharomyces cerevisiae SCRaMbLE system and... [Bioeng Bugs. 2012] - PubMed - NCBI

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Dymond J, Boeke J.
"We have recently reported the first partially synthetic eukaryotic genome. Saccharomyces cerevisiae chromosomes synIXR and semi-synVIL are fully synthetic versions of the right arm of chromosome IX and the telomeric segment of the left arm of chromosome VI, respectively, and represent the beginning of the synthetic yeast genome project, Sc2.0, that progressively replaces native yeast DNA with synthetic sequences. We have designed synthetic chromosome sequences according to principles specifying a wild-type phenotype, highly stable genome, and maintenance of genetic flexibility. Although other synthetic genome projects exist, the Sc2.0 approach is unique in that we have implemented design specifications predicted to generate a wild-type phenotype until induction of "SCRaMbLE," an inducible evolution system that generates significant genetic diversity. Here we further explore the significance of Sc2.0 and show how SCRaMbLE can serve as a genome minimization tool."

http://1.usa.gov/LwUJru

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