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DIY Synthetic biology: Redefining Open Source for Synthetic Biology

DIY Synthetic biology: Redefining Open Source for Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it

"Synthetic biology is an emerging technology combining information technology and biology. One notable presumption of synthetic biology is that scientists, with the assistance of computers, can create new life form without using naturally occurring organisms as references. However, it may be an overstatement in practice, because, even a single-base variation in a genome might dictate whether the synthetic organism could survive. Unlike the open source in information technologies, the open-source movement in synthetic biology raises biosafety concerns. The Article proposed a modified version of open source for the development of synthetic biology.

Download article here: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1990113 "

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Making microbes that can do the dirty work

Making microbes that can do the dirty work | SynBioFromLeukipposInstitute | Scoop.it

Ginkgo BioWorks has engineered bacteria to produce fuel using electricity and CO2 

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ACS Synthetic Biology: Volume 1, Issue 1 (ACS Publications)

"About the Cover:
Research in the inaugural issue of ACS Synthetic Biology focuses on advances which utilize genetic engineering, computational analysis, and cellular machinery – three driving forces in the field of synthetic biology. The cover image is an artistic representation of these themes created from stock images. Stock art: Shutterstock."

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Chemists create artificial cell membrane | KurzweilAI

Chemists create artificial cell membrane | KurzweilAI | SynBioFromLeukipposInstitute | Scoop.it
Chemists have taken an important step in making artificial life forms from scratch, creating self-assembling cell membranes, the structural envelopes that...
 
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Trends in Microbiology - Engineering the robustness of industrial microbes through synthetic biology

"Microbial fermentations and bioconversions play a central role in the production of pharmaceuticals, enzymes and chemicals. To meet the demands of industrial production, it is desirable that microbes maintain a maximized carbon flux towards target metabolites regardless of fluctuations in intracellular or extracellular environments. This requires cellular systems that maintain functional stability and dynamic homeostasis in a given physiological state, or manipulate transitions between different physiological states. Stable maintenance or smooth transition can be achieved through engineering of dynamic controllability, modular and hierarchical organization, or functional redundancy, three key features of biological robustness in a cellular system. This review summarizes how synthetic biology can be used to improve the robustness of industrial microbes."

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Science Online 2012: Day Two Blitz - Annotum

"The process of authoring, reviewing, and publishing scholarly articles remains an expensive, time-consuming process that can require significant up-front investment and technical expertise. Coupled with lengthy review processes this can create delays of up to a year before new scientific findings are published. Annotum, a new, open-source, open-access authoring publishing platform based on WordPress, provides an easy-to use alternative to existing publishing systems that supports very rapid expert review and professional online publishing.
In this live demonstration, we will show how Annotum can be used by scholarly authors to collaboratively author articles with rich text formatting, structured figures and equations, and citations. Then we'll show how authors can submit their article to a peer-review process, demonstrate the review and approval workflow, and publish the approved article online as well as in PDF and NLM-compatible XML formats. And did we mention that Annotum is completely free and open source, and available for free on WordPress.com?
Annotum is a product of Solvitor LLC with heavy lifting by Crowd Favorite. Annotum is free..."

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Stanford professor gives up tenure to start Udacity free online university

Stanford professor gives up tenure to start Udacity free online university | SynBioFromLeukipposInstitute | Scoop.it

Inspired by the number of people that the Khan Academy's free video lectures reached, Stanford professor Sebastian Thrun put his own artificial intelligence class online and enrolled 160,000...

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Innovation at the intersection of synthetic and systems biology 10.1016/j.copbio.2011.12.026 : Current Opinion in Biotechnology | ScienceDirect.com

"The promises of modern biotechnology hinge upon the hope that we can understand microscopic cellular complexity and in doing so create novel function. In this regard, the fields of systems and synthetic biology are important for accelerating both our understanding of biological systems and our ability to quantitatively engineer cells. At the nexus of these two fields is a unique synergy that can help attain these goals. Thus, the next greatest advances in biology and biotechnology are arising at the intersection of the top-down systems approach and the bottom-up synthetic approach. Collectively, these developments enable the precise control of cellular state for systems studies and the discovery of novel parts, control strategies, and interactions for the design of robust synthetic function. This review seeks to highlight this activity as well as provide a perspective for future directions. Combining these efforts can provide novel insights into cellular function and lead to robust, novel synthetic design."

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Genetic design automation: engineering fantasy or scientific renewal? 10.1016/j.tibtech.2011.09.001 : Trends in Biotechnology | ScienceDirect.com

"The aim of synthetic biology is to make genetic systems more amenable to engineering, which has naturally led to the development of computer-aided design (CAD) tools. Experimentalists still primarily rely on project-specific ad hoc workflows instead of domain-specific tools, which suggests that CAD tools are lagging behind the front line of the field. Here, we discuss the scientific hurdles that have limited the productivity gains anticipated from existing tools. We argue that the real value of efforts to develop CAD tools is the formalization of genetic design rules that determine the complex relationships between genotype and phenotype."

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The Bio! iGEM History Database

"The second release of the Bio! iGEM History is on its beta version. We have updated it with the iGEM 2011 results and with prize information. Information for some teams is still under development.

The database file may work better as an Excel sheet, using the filter functions to navigate the keyword columns."

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Ribosome-independent biosynthesis of biologically active peptides: application of synthetic biology to generate structural diversity 10.1016/j.febslet.2012.01.017 : FEBS Letters | ScienceDirect.com

"Peptide natural products continue to play an important role in modern medicine as last-resort treatments of many life-threatening diseases, as they display many interesting biological activities ranging from antibiotic to antineoplastic. A large fraction of these microbial natural products is assembled by ribosome-independent mechanisms. Progress in sequencing technology and the mechanistic understanding of secondary metabolite pathways has led to the discovery of many formerly cryptic natural products and a molecular understanding of their assembly. Those advances enable us to apply protein and metabolic engineering approaches towards the manipulation of biosynthetic pathways. In this review we discuss the application potential of both templated and non-templated pathways as well as chemoenzymatic strategies for the structural diversification and tailoring of peptide natural products."

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An Insight into the Use of Genome, Methylome and Gethylome in Synthetic Biology

"The development of new molecular approaches in biology and biotechnology introduced new scientific terms which include genome, genomics, methylome and methylomics. These are currently used in the literature of molecular and synthetic biology to refer various molecular concepts and applications. The present study is about the requirement of new “ome” and “omics” terms. This is because there are unique structural and functional aspects associated with genome and methylome at specific regions in the DNA sequence which are not explained by the two currently used terms methylome and genome. There is a requirement for new ome/omics terms to refer specific structural and functional matters associated with particular specialized zones in the DNA sequences. These genomic regions contain both the fifth base “methyl cytosine” and the other four coding bases. Methylated and non methylated DNA sequences are involved in gene expression of RNA and proteins, beside their role in the structural organization of the DNA sequence and the chromosome. In this study I suggest introducing two words which are derived from the established scientific terms “genome, genomics, methylome and methylomics”. The two new derived words are: gethylome and gethylomics. I suggest that these two words might be useful and could be used to explain various issues related to specific regions in the DNA sequence and chromosomes of eukaryotic organisms which contain the fifth base. Furthermore, gethylomics will help to refer more precisely to new applications in synthetic biology and genomics to design or redesign specific gethylomic circuits."

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German Hackers Building DIY Satellites For New Uncensored Internet

German Hackers Building DIY Satellites For New Uncensored Internet | SynBioFromLeukipposInstitute | Scoop.it

"There’s more than one way to stick it to The Man. There’s civil disobedience, subversive propaganda, political art, outright violent revolt – each possessing its own degree of difficulty and consequence. In a decidedly 21st-century twist, team of German hackers bent on fighting the powers that be has chosen a rather ambitious means of taking the power back: building a hacker-owned-and-operated space program, complete with a constellation of communications satellites beaming uncensored Internet to users on the ground."

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Ribosome-independent biosynthesis of biologically active peptides: Application of synthetic biology to generate structural diversity

"Peptide natural products continue to play an important role in modern medicine as last-resort treatments of many life-threatening diseases, as they display many interesting biological activities ranging from antibiotic to antineoplastic. A large fraction of these microbial natural products is assembled by ribosome-independent mechanisms. Progress in sequencing technology and the mechanistic understanding of secondary metabolite pathways has led to the discovery of many formerly cryptic natural products and a molecular understanding of their assembly. Those advances enable us to apply protein and metabolic engineering approaches towards the manipulation of biosynthetic pathways. In this review we discuss the application potential of both templated and non-templated pathways as well as chemoenzymatic strategies for the structural diversification and tailoring of peptide natural products."

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Membrane Assembly Driven by a Biomimetic Coupling Reaction - Journal of the American Chemical Society (ACS Publications)

"One of the major goals of synthetic biology is the development of non-natural cellular systems. In this work, we describe a catalytic biomimetic coupling reaction capable of driving the de novo self-assembly of phospholipid membranes. Our system features a coppercatalyzed azide–alkyne cycloaddition that results in the formation of a triazole-containing phospholipid analogue. Concomitant assembly of membranes occurs spontaneously, not requiring preexisting membranes to house catalysts or precursors. The substitution of efficient synthetic reactions for key biochemical processes may offer a general route toward synthetic biological systems."

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MIT Mints a Valuable New Form of Academic Currency - Commentary - The Chronicle of Higher Education

MIT Mints a Valuable New Form of Academic Currency - Commentary - The Chronicle of Higher Education | SynBioFromLeukipposInstitute | Scoop.it

"The Massachusetts Institute of Technology has invented or improved many world-changing things—radar, information theory, and synthetic self-replicating molecules, to name a few. Last month the university announced, to mild fanfare, an invention that could be similarly transformative, this time for higher education itself. It's called MITx. In that small lowercase letter, a great deal is contained.

MITx is the next big step in the open-educational-resources movement that MIT helped start in 2001, when it began putting its course lecture notes, videos, and exams online, where anyone in the world could use them at no cost. The project exceeded all expectations—more than 100 million unique visitors have accessed the courses so far.

Meanwhile, the university experimented with using online tools to help improve the learning experience for its own students in Cambridge, Mass. Now MIT has decided to put the two together—free content and sophisticated online pedagogy­—and add a third, crucial ingredient: credentials. Beginning this spring, students will be able to take free, online courses offered through the MITx initiative. If they prove they've learned the materi­al, MITx will, for a small fee, give them a credential certifying as much."

 
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Natural versus Artificial Creation of Base Pairs in DNA: Origin of Nucleobases from the Perspectives of Unnatural Base Pair Studies - Accounts of Chemical Research (ACS Publications)

Natural versus Artificial Creation of Base Pairs in DNA: Origin of Nucleobases from the Perspectives of Unnatural Base Pair Studies - Accounts of Chemical Research (ACS Publications) | SynBioFromLeukipposInstitute | Scoop.it

"Since life began on Earth, the four types of bases (A, G, C, and T(U)) that form two sets of base pairs have remained unchanged as the components of nucleic acids that replicate and transfer genetic information. Throughout evolution, except for the U to T modification, the four base structures have not changed. This constancy within the genetic code raises the question of how these complicated nucleotides were generated from the molecules in a primordial soup on the early Earth. At some prebiotic stage, the complementarity of base pairs might have accelerated the generation and accumulation of nucleotides or oligonucleotides. We have no clues whether one pair of nucleobases initially appeared on the early Earth during this process or a set of two base pairs appeared simultaneously.

Recently, researchers have developed new artificial pairs of nucleobases (unnatural base pairs) that function alongside the natural base pairs. Some unnatural base pairs in duplex DNA can be efficiently and faithfully amplified in a polymerase chain reaction (PCR) using thermostable DNA polymerases. The addition of unnatural base pair systems could expand the genetic alphabet of DNA, thus providing a new mechanism for the generation novel biopolymers by the site-specific incorporation of functional components into nucleic acids and proteins. Furthermore, the process of unnatural base pair development might provide clues to the origin of the natural base pairs in a primordial soup on the early Earth. In this Account, we describe the development of three representative types of unnatural base pairs that function as a third pair of nucleobases in PCR and reconsider the origin of the natural nucleic acids.

As researchers developing unnatural base pairs, they use repeated “proof of concept” experiments. As researchers design new base pairs, they improve the structures that function in PCR and eliminate those that do not. We expect that this process is similar to the one functioning in the chemical evolution and selection of the natural nucleobases. Interestingly, the initial structures designed by each research group were quite similar to those of the latest successful unnatural base pairs. In this regard, it is tempting to form a hypothesis that the base pairs on the primordial Earth, in which the natural purine bases, A and G, and pyrimidine bases, C and T(U), originated from structurally similar compounds, such as hypoxanthine for a purine base predecessor. Subsequently, the initial base pair evolved to the present two sets of base pairs via a keto-enol tautomerization of the initial compounds."

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Victory for crowdsourced biomolecule design : Nature News & Comment

Victory for crowdsourced biomolecule design : Nature News & Comment | SynBioFromLeukipposInstitute | Scoop.it

"Obsessive gamers’ hours at the computer have now topped scientists’ efforts to improve a model enzyme, in what researchers say is the first crowdsourced redesign of a protein.

The online game Foldit, developed by teams led by Zoran Popovic, director of the Center for Game Science, and biochemist David Baker, both at the University of Washington in Seattle, allows players to fiddle at folding proteins on their home computers in search of the best-scoring (lowest-energy) configurations...."

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Startup Makes 'Wireless Router for the Brain' - Technology Review

Startup Makes 'Wireless Router for the Brain' - Technology Review | SynBioFromLeukipposInstitute | Scoop.it

"Optogenetics has been hailed as a breakthrough in biomedical science—it promises to use light to precisely control cells in the brain to manipulate behavior, model disease processes, or even someday to deliver treatments.

But so far, optogenetic studies have been hampered by physical constraints. The technology requires expensive, bulky lasers for light sources, and a fiber-optic cable attached to an animal—an encumbrance that makes it difficult to study how manipulating cells affects an animal's normal behavior."

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Andrew Hessel on Singularity 1 on 1: Don't Fear Synthetic Biology

"Today I am very happy to have Andrew Hessel as my guest on Singularity 1 on 1. During the interview Andrew shares his truly infectious passion about synthetic biology and the unique opportunities that lie ahead of the budding first generation of DIY bio-hackers.

We also discuss a variety of other interesting issues such as the singularity, religion, the promise of personalized medicine as cancer treatment, the risks and benefits of open-source synthetic-biology and the fact that biology is a dual-use technology.

I have to admit that I was so infected by Andrew's passion and his unique, open-source approach that I couldn't help it but buy a 20 dollar share in the Pink Army Cooperative. So, check out the interview and don't hesitate to let me know what you think..."

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Computational tools for the synthetic desi... [Nat Rev Microbiol. 2012] - PubMed - NCBI

"As the field of synthetic biology is developing, the prospects for de novo design of biosynthetic pathways are becoming more and more realistic. Hence, there is an increasing need for computational tools that can support these efforts. A range of algorithms has been developed that can be used to identify all possible metabolic pathways and their corresponding enzymatic parts. These can then be ranked according to various properties and modelled in an organism-specific context. Finally, design software can aid the biologist in the integration of a selected pathway into smartly regulated transcriptional units. Here, we review key existing tools and offer suggestions for how informatics can help to shape the future of synthetic microbiology."

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DIY Synthetic biology: Open source.com : BioCurious? The DIY garage biology movement

DIY Synthetic biology: Open source.com : BioCurious? The DIY garage biology movement | SynBioFromLeukipposInstitute | Scoop.it
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Recombinant protein scaffolds for tissue engine... [Biomed Mater. 2012] - PubMed - NCBI

"New biological materials for tissue engineering are now being developed using common genetic engineering capabilities to clone and express a variety of genetic elements that allow cost-effective purification and scaffold fabrication from these recombinant proteins, peptides or from chimeric combinations of these. The field is limitless as long as the gene sequences are known. The utility is dependent on the ease, product yield and adaptability of these protein products to the biomedical field. The development of recombinant proteins as scaffolds, while still an emerging technology with respect to commercial products, is scientifically superior to current use of natural materials or synthetic polymer scaffolds, in terms of designing specific structures with desired degrees of biological complexities and motifs. In the field of tissue engineering, next generation scaffolds will be the key to directing appropriate tissue regeneration. The initial period of biodegradable synthetic scaffolds that provided shape and mechanical integrity, but no biological information, is phasing out. The era of protein scaffolds offers distinct advantages, particularly with the combination of powerful tools of molecular biology. These include, for example, the production of human proteins of uniform quality that are free of infectious agents and the ability to make suitable quantities of proteins that are found in low quantity or are hard to isolate from tissue. For the particular needs of tissue engineering scaffolds, fibrous proteins like collagens, elastin, silks and combinations of these offer further advantages of natural well-defined structural scaffolds as well as endless possibilities of controlling functionality by genetic manipulation."

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