Bio::BioStudio::Basic 1.01 Basic functions for the BioStudio synthetic biology framework - SoftBuz.Com...
SynBioFromLeukipposInstitute
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gBlocks Gene Fragments from Integrated DNA Technologies are double-stranded, sequence-verified genomic blocks up to 500 base pairs. Their high sequence fidelity allows for easy assembly of multiple gene fragments. 
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"The design of biomimetic materials that parallel the morphology and biology of extracellular matrixes is key to the ability to grow functional tissues in vitro and to enhance the integration of biomaterial implants into existing tissues in vivo. Special attention has been put into mimicking the nanostructures of the extracellular matrix of bone, as there is a need to find biomaterials that can enhance the bonding between orthopedic devices and this tissue.
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"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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"In an example of life imitating art, biologists and bioengineers at the University of California, San Diego have created a living neon sign comprising millions of bacterial cells that periodically fluoresce in unison like blinking light bulbs. Their achievement, detailed in “A Sensing Array of Radically Coupled Genetic ‘Biopixels’” published in the journal Nature, involved attaching a fluorescent protein to the biological clocks of the bacteria, synchronizing the clocks of the thousands of bacteria within a colony, then synchronizing thousands of the blinking bacterial colonies to glow on and off in unison. A little bit of art with a lot more bioengineering, the flashing bacterial signs are not only a visual display of how researchers in the new field of synthetic biology can engineer living cells like machines, but will likely lead to some real-life applications...."
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"Synthetic biology is a rapidly emerging biotechnology discipline with a wide range of applications. Despite its emerging status, synthetic biology provides a significant number of near-term commercial opportunities, and the list of new products and applications is continuously growing. These applications include specialty chemicals, enzymes, synthetic genes and other DNA parts, pharmaceuticals, biofuels, and chassis microorganisms. ( http://www.bharatbook.com/detail.asp?id=147795&rt=Synthetic-Biology-Emerging-Global-Markets.html ) The goal for this study is to determine the specific applications and forecast global market demand for synthetic biology products over a 5-year period from 2008 to 2013. Our particular interest is to characterize and quantify the synthetic biology products market potential by technology and end-use market segments. We also analyze the synthetic biology industry structure, competitors, and intellectual property landscape. It is important for companies in industries affected by the developments in synthetic biology to sort through the many potential applications to identify near-term commercial opportunities for product development focus. This report allows companies to prioritize product opportunities, establishing a solid framework for strategic planning. Synthetic biology encompasses a wide range of industries, including life science tools, biotechnology, pharmaceuticals, energy, and chemicals. Because of its wide scope, synthetic biology will play an important role in the future of the industrial economy of the early 21st century. Ongoing advances in enabling technologies, such as microfluidics, DNA synthesis, DNA sequencing, and bioinformatics, as well as a need for renewable feedstocks, are driving the growth of synthetic biology. Rapid developments in these multidisciplinary fields promise to advance the synthetic biology industry and create unique market opportunities. This report analyzes these trends and their impact on the future markets for synthetic biology products..."
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"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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Ginkgo BioWorks has engineered bacteria to produce fuel using electricity and CO2
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"About the Cover:
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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 Museum launches online games about the future of technology The Science Museum has launched a suite of online games designed to raise questions about the future of medicine, robotics and technology. Developed as part of the Talk Science programme, which was initiated to encourage discussion of science in schools, the 'Futurecade' features four titles exploring areas such as geo-engineering and synthetic biology. In Batco-Lab, players must engineer E.coli bacteria to make useful products, while ensuring that no harmful mutant bacteria are accidentally unleashed on the world....."
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"Students and scientists at Duke University have collaborated to produce a free, open-source textbook devoted to marine science, called Cachalot, reported Wired Science. Although Cachalot (sperm whale in French) was designed for a specific class, Marine Megafauna, it’s currently available as an app for anyone with an iPad. Its digital platform, FLOW, was built by Duke University computer science students, and enables Cachalot users to take notes, connect to Twitter, and watch National Geographic videos. Users will also be connected to up-to-date science, with peer-reviewed text, images, and open access studies contributed by marine science experts...."
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"The synthetic reconstruction of natural gene networks and the de novo design of artificial genetic circuits provide new insights into the cell's regulatory mechanisms and will open new opportunities for drug discovery and intelligent therapeutic schemes. We will present how modular synthetic biology tools like repressors, promoters and enzymes can be assembled into complex systems in order to discover small molecules to shut off antibiotic resistance in tubercle bacteria and to design self-sufficient therapeutic networks. The transfer of these synthetic biological modules to the material science field enables the construction of novel drug-inducible biohybrid materials for biomedical applications."
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"What to do about biohackers in the garage? The apparent answer from the US Presidential Commission for the Study of Bioethical Issues, whose first task has been to examine the emerging field of synthetic biology, is “prudent vigilance.” It isn’t just tinkerers who are intrigued by the prospect of building genes and genomes. Many scientists are discovering exciting new ways to use synthetic DNA. Moreover, the exponentially decreasing cost of such DNA has encouraged innovative approaches to making drugs, biofuels, and other materials. As early as next year, synthetic biology may be used to produce flu-vaccine strains in days to weeks, rather than the 12 months now required..."
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“The tools of synthetic biology are galvanizing the development of new forms of architecture that respond to environmental change by incorporating the dynamic properties of living systems, such as growth, repair, sensitivity and replication,” Armstrong and Spiller wrote in a piece published last year in the journal Nature.
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"February sees the launch of the ROADBLOCK project, funded by the EPSRC with the goal of developing artificial and programmable bacterial coatings to protect surfaces against infective agents. While Bioengineering techniques that allow genes to be manipulated have been around for some time, the discipline of Synthetic Biology allows for the more effective design of genetic circuits. The Principle Investigator for this project is Dr Sara Kalvala, who will be applying her expertise in Compiler Design and Formal Logics towards the development of tools which will help assemble genetic networks and model their interactions with host genes...."
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Synthetic Biology, Plants and Sustainable technology http://dnanonymous.wordpress.com/2012/01/29/plant-b-back-to-the-roots/...
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"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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"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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"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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"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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"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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