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Scooped by
Gerd Moe-Behrens
March 10, 2012 12:58 PM
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"Instead of using a 3D printer to build up an object in layers, a single sheet of material could morph into just about any structure thanks to a new technique. Devised by Ryan Hayward and colleagues from University of Massachusetts at Amherst, it involves spreading a pattern on a responsive material to control how it deforms when exposed to a stimulus. Although, so far temperature-sensitive materials are the most advanced, the team is also looking at sheets that respond to electric and magnetic fields, as well as chemical cues. The method is inspired by the way adjacent areas in plants can grow into different shapes. Curly edges in leaves or petals form as some cells expand, while neighbouring ones do not. To mimic this strategy, the light-sensitive gel in this video was coated with a mask to restrict the areas exposed to ultraviolet light. The amount of light absorbed by each part of the sheet determines how much it will swell when in contact with water, allowing the gel to be moulded into a specific shape. You can watch it shrink to form a flat disc when heated and then regrow into a buckled 3D shape upon cooling. The team hopes to use the technique to create artificial blood vessels and organs. Recent studies have shown that patterned growth of thin layers of cells are often responsible for the way biological tissues and organs develop. "An area of interest for us is whether synthetic materials with patterned swelling can be used to guide shapes that cultured tissues adopt when grown in the lab," says Hayward."
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Scooped by
Gerd Moe-Behrens
March 10, 2012 12:44 PM
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"....One area I'm really excited about is synthetic biology," Dr. S. Pete Worden, the Center's director, told The Register. "We're convinced that if people go into space for long periods of time they will need some sort of self-replicating machine, and the only ones we know of are biological." NASA is working closely with Craig Venter, who created the first self-replicating semi-synthetic bacterial cell in 2010, and who was in the vanguard of mapping the human genome. Venter is working with NASA to develop programmed microbes that have been hacked to be much more efficient than their current forms, and which can be used in space exploration....."
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Scooped by
Gerd Moe-Behrens
March 9, 2012 6:56 PM
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Bruce is an award winning animation that explores how advances in open-source synthetic biology allow a young man to grow his very own tiny Bruce Willis from a lump of mince. Running at just over three minutes, Bruce pokes at one possible ramification of synthetic biology by positioning it inline with the open-source microprocessor project Arduino.
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Scooped by
Gerd Moe-Behrens
March 9, 2012 8:16 AM
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"In recent years, the term synthetic biology has become very popular. Synthetic biology is a new area of biological research and technology that combines science and engineering. It encompasses a variety of different approaches, methodologies, and disciplines with a variety of definitions. The common goal is the design and construction of new biological functions and systems not found in nature. The advancement of synthetic biology relies on several key enabling technologies, provided at ever increasing speed and lower cost. DNA sequencing, fabrication of genes, modeling the synthetic gene's behavior and ensuring its precise measurements are the essential tools used in synthetic biology.1 Some applications of synthetic biology that benefit society could also be applied in ways that can harm it, or that could be unintentionally dangerous; the use of such technologies in the development of a biological weapon, such as a virus, is an obvious concern. The issue of safety is further complicated because applications of synthetic biology that are considered beneficial by some may be perceived as harmful or dangerous by others. The security and ethical aspects of synthetic biology have been debated in congressional hearings and by the Presidential Commission for the Study of Bioethical Issues and the National Academy of Science, among others. The US government is very supportive of efforts to develop new and improved methods to screen double-stranded DNA sequences for biosecurity purposes. There has been lot said about open source software. Open source refers to a program in which the source code is available to the general public for use and/or modification from its original design free of charge. Open source code is typically created as a collaborative effort in which programmers improve upon the code and share their changes within the community. Open source sprouted in the technological community as a response to proprietary software owned by corporations. Motivations for using and developing open source software are mixed, ranging from philosophical and ethical reasons to purely practical issues and applications. A software package designed to minimize the potential risks of synthetic biology for the purpose of national defense and security is now available to the gene synthesis industry and synthetic biology community in an open-source format. Virginia Tech has licensed GenoTHREAT, a software tool that helps to detect the use of synthetic DNA as bioterrorism agents. The open-source project team is led by Jean Peccoud, associate professor at Virginia Bioinformatics Institute at Virginia Tech. The software is being released using the Apache License Version 2.0 to ensure broad accessibility. So how does GenoTHREAT software work? GenoTHREAT implements the "best match" screening protocol method recommended by the federal government to minimize the risk that unauthorized individuals or those with malicious intent will obtain toxins and other potentially dangerous materials from DNA synthesis providers. The process of developing GenoTHREAT allowed Peccoud's team to conduct a rigorous bioinformatics analysis of the strengths and limitations of the best match method. This was published in the March 2011 issue of Nature Biotechnology. The main aim of the team is to develop a more comprehensive biosecurity solution that can be customized for a variety of users.2....."
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Scooped by
Gerd Moe-Behrens
March 8, 2012 1:41 PM
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The Basics Think the "Central Dogma" involves a kennel of chihuahuas? You need to start here with the basics.
Bare bones biochemistry Basic Molecular Biology Practical DNA What is PCR? Introduction to Biobricks and Basic Cloning This tutorial is best used in conjunction with the sequence editor ApE. Read the section about ApE for a description of how to install it.
Installing ApE Overview of Cloning Introduction to Biobricks Introduction to Refactoring Technical Design Basic Oligo Design (old) Special Case: Single Internal Restriction Sites (old) Construction of short parts Design of composite parts Keeping track of construction files Sequencing Analysis Advanced Technical Design Working with Translational Fusions Circularly Permuted Proteins The "what did they make" game Implementation Implementing the Basic Construction File Introduction to Structural Biology and Part Engineering DeepView Basics Tour of Structural Biology Things you should know Common Pitfalls and Tips Origins of replication The Critical Path
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Scooped by
Gerd Moe-Behrens
March 7, 2012 11:38 AM
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Current Research in Teachable Form Animations
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Scooped by
Gerd Moe-Behrens
March 7, 2012 7:00 AM
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"Christina Agapakis is a synthetic biologist and postdoctoral research fellow at UCLA who blogs about about biology, engineering, biological engineering, and biologically inspired engineering at Oscillator.
A few weeks ago, I saw a retweet that claimed “biohacking is easier than you think” with a link to a post on a blog accompanying a book called Massively Networked. The post included video of Tuur van Balen’s presentation at the NextNature power show a few months earlier. Van Balen is a designer whose work I’ve followed for a couple years now, and his most recent project imagines how synthetic biology might produce and deliver medicines in the future. He demonstrates—using homemade tools, equipment purchased on eBay, and online resources for finding and synthesizing DNA sequences—how someone could engineer a strain of bacteria to produce Prozac-laced yogurt. While he’s not actually making Prozac, his demonstration does show pretty accurately how someone could get DNA into a bacterium (without, of course, the frustrating months of troubleshooting that almost any experiment inevitably requires). I posted my own version of the story, writing that art projects like this can ask important questions about biological design...."
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Scooped by
Gerd Moe-Behrens
March 7, 2012 6:36 AM
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"An Oxford philosopher argues that we are not adequately accounting for technology's risks -- but his solution to the problem is not for Luddites. ........Bostrom: I think the biggest existential risks relate to certain future technological capabilities that we might develop, perhaps later this century. For example, machine intelligence or advanced molecular nanotechnology could lead to the development of certain kinds of weapons systems. You could also have risks associated with certain advancements in synthetic biology......What technology, or potential technology, worries you the most?
Bostrom: Well, I can mention a few. In the nearer term I think various developments in biotechnology and synthetic biology are quite disconcerting. We are gaining the ability to create designer pathogens and there are these blueprints of various disease organisms that are in the public domain---you can download the gene sequence for smallpox or the 1918 flu virus from the Internet......"
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Scooped by
Gerd Moe-Behrens
March 6, 2012 6:20 PM
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"Get ready for a paradigm shift in biotechnology!
Not too long ago, it took millions of dollars and years of development to start a new technology business. But not anymore, as many tech startups get up and running in weeks for under $20K. Biotechnology is poised to follow this trend powered by synthetic biology – genetic engineering done with software-based design tools coupled with low-cost DNA synthesis and assembly. Using synthetic biology, undergraduate students are developing everything from DNA data storage systems to new biofuels or gene therapies in just months; DIYbio enthusiasts are making DNA testing kits, PCR machines and more; and graduate scientists are bootstrapping innovative synbio companies producing custom-made organisms, phage-based diagnostics, and open-source genome design software...."
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Scooped by
Gerd Moe-Behrens
March 6, 2012 9:37 AM
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"Scientists have once again turned to biomimicry for inspiration, this time in Scotland, where a team of researchers at the University of Glasgow have come up with an “electric leaf”. The technique uses photosynthetic bacteria to produce biofuels using electricity. Scientists involved in the Glasgow Solar Fuels project at Glasgow University in Scotland recently revealed at the American Association for the Advancement of Science annual meeting in Vancouver (Canada) that they had made a breakthrough in making biofuels more efficiently using electricity rather than sunlight, which is normally used in the case of algae or bacteria-based biofuels. The team led by Professor Richard Cogdell has been studying photosynthetic organisms that have evolved light-harvesting complexes to concentrate solar energy and accumulate enough charge to perform catalytic reactions such as water splitting and CO2 fixation...."
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Scooped by
Gerd Moe-Behrens
March 6, 2012 8:43 AM
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"The use of microbial consortia for bioprocessing has been limited by our ability to reliably control community composition and function simultaneously. Recent advances in synthetic biology have enabled population-level coordination and control of ecosystem stability and dynamics. Further, new experimental and computational tools for screening and predicting community behavior have also been developed. The integration of synthetic biology with metabolic engineering at the community level is vital to our ability to apply system-level approaches to building and optimizing synthetic consortia for bioprocessing applications. This review details new methods, tools and opportunities that together have the potential to enable a new paradigm of bioprocessing using synthetic microbial consortia."
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Scooped by
Gerd Moe-Behrens
March 6, 2012 8:22 AM
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"Most of the reports on synthetic biology include not only familiar topics like biosafety and biosecurity but also a chapter on 'ethical concerns'; a variety of diffuse topics that are interrelated in some way or another. This article deals with these 'ethical concerns'. In particular it addresses issues such as the intrinsic value of life and how to deal with 'artificial life', and the fear that synthetic biologists are tampering with nature or playing God. Its aim is to analyse what exactly is the nature of the concerns and what rationale may lie behind them. The analysis concludes that the above-mentioned worries do not give genuine cause for serious concern. In the best possible way they are interpreted as slippery slope arguments, yet arguments of this type need to be handled with care. It is argued that although we are urged to be especially vigilant we do not have sufficiently cogent reasons to assume that synthetic biology will cause such fundamental hazards as to warrant restricting or refraining from research in this field."
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Scooped by
Gerd Moe-Behrens
March 6, 2012 7:37 AM
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"Cheap medicines for Africa. Probiotica that detect diseases in your digestive system. Ultra strong and light materials. Land mine detection by plants. The social, economic and industrial potential of synthetic biology seems enourmous. The sky is the limit. However, the past has taught us that scientists are sometimes a bit too optimistic regarding the potential applications of new technologies. There is one important thing they often forget: the society. Public perception of genetic engineering is very negative. Ask a random person on the street about his opinion on DNA modification and the reaction will be more or less along the following lines: “Nature shouldn’t be changed, because nature can’t be improved.” Or: “Messing around with DNA will only bring bad to us.” However, without genetic engineering techniques, no synthetic biology!
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Scooped by
Gerd Moe-Behrens
March 10, 2012 12:51 PM
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Reporter speaks to Professors Paul Freemont (Life Sciences) and Richard Kitney (Bioengineering), who lead the EPSRC Centre for Synthetic Biology and Innovation (CSynBI) at Imperial, to learn what synthetic biology is and how Imperial is leading the way in using engineering and biological principles to systematically design new biological devices and systems.
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Scooped by
Gerd Moe-Behrens
March 9, 2012 7:32 PM
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University of California, San Diego electrical engineers are building a forest of tiny nanowire trees in order to cleanly capture solar energy without using fossil fuels and harvest it for hydrogen fuel generation.
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Scooped by
Gerd Moe-Behrens
March 9, 2012 10:27 AM
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GenoGUARD is a DNA sequence screening software that implements the best match method recommended by the federal government to detect the presence of biosecurity threats in synthetic DNA orders.
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Scooped by
Gerd Moe-Behrens
March 9, 2012 7:10 AM
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"Cells are organized on length scales ranging from ångström to micrometres. However, the mechanisms by which ångström-scale molecular properties are translated to micrometre-scale macroscopic properties are not well understood. Here we show that interactions between diverse synthetic, multivalent macromolecules (including multi-domain proteins and RNA) produce sharp liquid–liquid-demixing phase separations, generating micrometre-sized liquid droplets in aqueous solution. This macroscopic transition corresponds to a molecular transition between small complexes and large, dynamic supramolecular polymers. The concentrations needed for phase transition are directly related to the valency of the interacting species. In the case of the actin-regulatory protein called neural Wiskott–Aldrich syndrome protein (N-WASP) interacting with its established biological partners NCK and phosphorylated nephrin1, the phase transition corresponds to a sharp increase in activity towards an actin nucleation factor, the Arp2/3 complex. The transition is governed by the degree of phosphorylation of nephrin, explaining how this property of the system can be controlled to regulatory effect by kinases. The widespread occurrence of multivalent systems suggests that phase transitions may be used to spatially organize and biochemically regulate information throughout biology."
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Scooped by
Gerd Moe-Behrens
March 8, 2012 1:27 PM
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"The field of synthetic biology has been developing rapidly since the early 2000s, when the human genome was first sequenced. Paul (pictured below left) and Richard (below right right) became interested in the potential that this offered for building biological devices and systems from scratch and, in 2003, heard from colleagues at Massachusetts Institute of Technology (MIT) that similar work had started under the title ‘synthetic biology’. Paul explains: “With our incredibly strong engineering and life sciences departments at Imperial, we knew we had the potential to have a huge impact on the field and were excited that it would provide incredible opportunities for our students.”"
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Scooped by
Gerd Moe-Behrens
March 7, 2012 8:01 AM
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"To build a complex structure does not necessarily need complex Lego pieces. I has been thinking about to use just 2x1 pieces to build models since they are the smallest Lego units that provide connections. Here is a few tries on animal models...."
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Scooped by
Gerd Moe-Behrens
March 7, 2012 6:45 AM
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An interactive guide to some of the latest developments in bionic body parts...
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Scooped by
Gerd Moe-Behrens
March 6, 2012 6:45 PM
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In an ongoing experiment to leverage new educational technologies, the university is launching five free online classes this month.
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Scooped by
Gerd Moe-Behrens
March 6, 2012 5:57 PM
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by Keiji Nishida, Pamela A. Silver "Most organisms are simply diamagnetic, while magnetotactic bacteria and migratory animals are among organisms that exploit magnetism. Biogenic magnetization not only is of fundamental interest, but also has industrial potential. However, the key factor(s) that enable biogenic magnetization in coordination with other cellular functions and metabolism remain unknown. To address the requirements for induction and the application of synthetic bio-magnetism, we explored the creation of magnetism in a simple model organism. Cell magnetization was first observed by attraction towards a magnet when normally diamagnetic yeast Saccharomyces cerevisiae were grown with ferric citrate. The magnetization was further enhanced by genetic modification of iron homeostasis and introduction of ferritin. The acquired magnetizable properties enabled the cells to be attracted to a magnet, and be trapped by a magnetic column. Superconducting quantum interference device (SQUID) magnetometry confirmed and quantitatively characterized the acquired paramagnetism. Electron microscopy and energy-dispersive X-ray spectroscopy showed electron-dense iron-containing aggregates within the magnetized cells. Magnetization-based screening of gene knockouts identified Tco89p, a component of TORC1 (Target of rapamycin complex 1), as important for magnetization; loss of TCO89 and treatment with rapamycin reduced magnetization in a TCO89-dependent manner. The TCO89 expression level positively correlated with magnetization, enabling inducible magnetization. Several carbon metabolism genes were also shown to affect magnetization. Redox mediators indicated that TCO89 alters the intracellular redox to an oxidized state in a dose-dependent manner. Taken together, we demonstrated that synthetic induction of magnetization is possible and that the key factors are local redox control through carbon metabolism and iron supply..." http://bit.ly/zQC1Kb
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Scooped by
Gerd Moe-Behrens
March 6, 2012 9:19 AM
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First time accepted submitter awjourn writes "During his years working in pharma R&D, Tomasz Sablinski was frustrated by the industry's need for secrecy and its utter inability to design patient-friendly drug trials.
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Scooped by
Gerd Moe-Behrens
March 6, 2012 8:38 AM
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"Metabolic engineering is the enabling science of development of efficient cell factories for the production of fuels, chemicals, pharmaceuticals, and food ingredients through microbial fermentations. The yeast Saccharomyces cerevisiae is a key cell factory already used for the production of a wide range of industrial products, and here we review ongoing work, particularly in industry, on using this organism for the production of butanol, which can be used as biofuel, and isoprenoids, which can find a wide range of applications including as pharmaceuticals and as biodiesel. We also look into how engineering of yeast can lead to improved uptake of sugars that are present in biomass hydrolyzates, and hereby allow for utilization of biomass as feedstock in the production of fuels and chemicals employing S. cerevisiae. Finally, we discuss the perspectives of how technologies from systems biology and synthetic biology can be used to advance metabolic engineering of yeast...."
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Scooped by
Gerd Moe-Behrens
March 6, 2012 8:19 AM
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"The Gram-negative bacterium Campylobacter jejuni encodes an extensively characterised N-linked protein glycosylation system that modifies many surface proteins with a heptasaccharide glycan. In C. jejuni the genes that encode the enzymes required for glycan biosynthesis and transfer to protein are located at a single pgl gene locus. Similar loci are also present in genome sequences of all other Campylobacter species, though variation in gene content and organisation are evident. In this study we have demonstrated that only Campylobacter species closely related to C. jejuni produce glycoproteins that interact with both a C. jejuni N-linked glycan specific antiserum and a lectin known to bind to the C. jejuni N-linked glycan. In order to further investigate the structure of Campylobacter N-linked glycans we employed an in vitro peptide glycosylation assay combined with mass spectrometry to demonstrate that Campylobacter species produce a range of structurally distinct N-linked glycans with variation in number of sugar residues (penta-, hexa- and heptasaccharides), presence of branching sugars and monosaccharide content. These data considerably expand our knowledge of bacterial N-linked glycan structure and provide a framework for investigating the role of glycosyltransferases and sugar biosynthesis enzymes in glycoprotein biosynthesis with practical implications for synthetic biology and glycoengineering."
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