Pawelczyk S, Scott KA, Hamer R, Blades G, Deane CM, Wadhams GH.
"Phosphosignalling pathways are an attractive option for the synthetic biologist looking for a wide repertoire of modular components from which to build. We demonstrate that two-component systems can be used in synthetic biology. However, their potential is limited by the fact that host cells contain many of their own phosphosignalling pathways and these may interact with, and cross-talk to, the introduced synthetic components. In this paper we also demonstrate a simple bioinformatic tool that can help predict whether interspecies cross-talk between introduced and native two-component signalling pathways will occur and show both in vitro and in vivo that the predicted interactions do take place. The ability to predict potential cross-talk prior to designing and constructing novel pathways or choosing a host organism is essential for the promise that phosphosignalling components hold for synthetic biology to be realised."
Richard Van Noorden "Ethanol has dominated the biofuel industry’s attention over the past few years. But synthetic-biology companies are now scaling up production of what some say is a superior fuel: butanol, an alcohol with four carbon atoms to ethanol’s two. Compared to ethanol, butanol stores more energy per litre, is less corrosive to pipelines, is more easily separated from water and can be blended into gasoline (petrol) at higher concentrations before vehicle engines are damaged....." http://bit.ly/KLDmQC
Dongsheng Li, Michael H. Nielsen, Jonathan R. I. Lee, Cathrine Frandsen, Jillian F. Banfield, James J. De Yoreo "The oriented attachment of molecular clusters and nanoparticles in solution is now recognized as an important mechanism of crystal growth in many materials, yet the alignment process and attachment mechanism have not been established. We performed high-resolution transmission electron microscopy using a fluid cell to directly observe oriented attachment of iron oxyhydroxide nanoparticles. The particles undergo continuous rotation and interaction until they find a perfect lattice match. A sudden jump to contact then occurs over less than 1 nanometer, followed by lateral atom-by-atom addition initiated at the contact point. Interface elimination proceeds at a rate consistent with the curvature dependence of the Gibbs free energy. Measured translational and rotational accelerations show that strong, highly direction-specific interactions drive crystal growth via oriented attachment." http://bit.ly/LjFWll
"Embryologists have classically approached the ideas in Turing's "The chemical basis of morphogenesis" in two ways: (a) they have modelled embryos in silico to see if Turing patterning could make a particular pattern in principle; and (b) they have sought evidence, from gene expression patterns and knockout phenotypes, for Turing patterning in vivo.
We are taking a third approach, effectively a hybrid of the other two and of synthetic biology: we seek to assemble a synthetic Turing patterning system in cultures of living cells. Here, we will present our design, how it behaves in models, and will describe the state of our construction at the time of the meeting.
Presented by Professor Jamie Davies, Physiology Department, the University of Edinburgh
Recorded on Friday 11 May 2012 at the Informatics Forum, The University of Edinburgh.
The Turing Research Symposium was organised by the Royal Society of Edinburgh and the University of Edinburgh School of Informatics in partnership with SICSA and supported by Cambridge University Press." http://bit.ly/JJMjtV
A team of researchers at the Council for Scientific and Industrial Research (CSIR) is the first in Africa to establish groundbreaking biomedical stem cell technology, which could hold the key to finding cures for some of Africa’s most prevalent...
BY WILL MENDELSON "Keith Tyo specializes in synthetic biology, engineering cells that can provide inexpensive diagnosis and treatment for disease.
Keith Tyo applies synthetic biology - genetically reprogramming cells - to combat global health crises such as malaria.
Malaria strikes nearly 500 million people and causes a million deaths every year, according to the World Health Organization.
Tyo, a chemical and biological engineer at Northwestern University, recently received a $100,000 grant from the Bill & Melinda Gates Foundation for his work. His global health projects focus on creating new compounds to treat a host of diseases, including HIV and tuberculosis. He plans to produce low-cost biosensors for underprivileged countries desperately in need of basic medical diagnostic equipment....."
Just read this statement by +Eric Schmidt in wired uk http://www.wired.co.uk/news/archive/2012-05/23/eric-schmidt-science-education "the scientific method of hypothesise, test, revise and repeat must remain paramount", adding "careful and repeatable experimentation is the crux of science". I see this quite different: contemporary “science” has moved from the hypothesis method as it fail in respect to the challenges we face today. We have a paradigm change form hypothesis to data driven science. A reductionistic science moves to a holistic systemics (for review see: http://www.leukippos.org/Leukippos_Institute/Video.html ) This is a complicated question to answer and requires knowledge in history of philosophy, formal logic and philosophy of science. The cited review gives you a brief introduction to this subject. Some of the major points: The hypothesis method is reductionistic. It can deal with single correlations, but not with complex systems, because it is impossible to deduce an empirical consequence in multi factor systems. Our move into the digital age has also fundamental impact on the way we perform science. The enormous amount of data we have online access to, has a fundamental impact on the science paradigm. We have now access to huge data amounts, which build complex data systems. This data flooding problem can not be solved by normal science. The hypothesis method failed in this context. Contemporary research has come to a point where we change the perspective from reduction to holism. The reductionistic approach has successfully identified many components and interactions, but does not provide convincing explanation for how a complex system, such as a living being work. Today we are in the situation that we have huge amounts of data from high throughput experiments, but we do not understand the whole picture. Moreover, huge amounts of data and facts available mean lesser need for models. The word science has it’s indo-european root in the word scy. This means separating. Scy belongs to a reductionistic world of thinking. Science is a synonym with reductionism based on a materialistic concept. Heinz Foerster (1911-2002), an architect of cybernetics, saw an end to a 2000 years movement started with Aristotle. He stated: “If you take in account all system theory and systems researchers, which appear today in art and science I would not call this science any longer I would call it systemics. Contemporary science moved to a position, which sees thing together, short systemics. Thus: From science to systemics. This is how I see the steps today.” Beside Norbert Wiener, William Ross Ashby, and Ludwig Bertalanffy is Heinz Foerster one of the key figures, who developed a new theory for dealing with huge data amounts and complex systems: Systems Theory. Systems theory is the basis for Systems Biology and it’s practical application Synthetic Biology, two key sciences of the 21st century which already have moved form the hypothesis method to sytemics.
Hussein R, Lim HN. "Small RNAs (sRNAs) and proteins acting as transcription factors (TFs) are the principal components of gene networks. These two classes of signaling molecules have distinct mechanisms of action; sRNAs control mRNA translation, whereas TFs control mRNA transcription. Here, we directly compare the properties of sRNA and TF signaling using mathematical models and synthetic gene circuits in Escherichia coli. We show the abilities of sRNAs to act on existing target mRNAs (as opposed to TFs, which alter the production of future target mRNAs) and, without needing to be first translated, have surprisingly little impact on the dynamics. Instead, the dynamics are primarily determined by the clearance rates, steady-state concentrations and response curves of the sRNAs and TFs; these factors determine the time delay before a target gene's expression can maximally respond to changes in sRNA and TF transcription. The findings are broadly applicable to the analysis of signaling in gene networks, and we demonstrate that they can be used to rationally reprogram the dynamics of synthetic circuits."
"Darpa notes, even the most cutting-edge synthetic biology projects “often take 7+ years and tens to hundreds of millions of dollars” to complete." http://bit.ly/JpJKSV
I think this is ridiculous. We do not really need 7 years to do a scientific project. The main reason for this is that we still do science in the old fashioned way. Basically we have with the internet got a tool to do this much quicker and some projects have done so e.g. see Linux development or the iGem competition. In this last projects students can do in 3 month what a post doc before did in 3 years. Collaborative intelligence and cloud collaboration have a huge potential to seed up. However, fear for our career held many scientist back to adapt to science2.0. The science business model high impact factor paper, tax money paid position is outdated, however the one, which feed us. As a consequence it take 1 to 2 years to get grants, 3 years to do the project as a single post doc (scientific collaboration is mostly on the papers for grant applications), and 2 years to get it published with many rounds of meaningless rejections ad revisions. Thus you end up with a typically time use of about 7 years instead of 3 month. Cloud collaboration will change this, hopefully soon.
"Architect Neri Oxman is the founder of MATERIALECOLOGY, an interdisciplinary design initiative expanding the boundaries of computational form-generation and material engineering. Named one of Fast Company's "100 Most Creative People in Business," Oxman investigates the material and performance of nature in an effort to define form itself."
A life scientist, an engineer and a social scientist walk into a lab: ...engagement and education in #syntheticbiology
by Edwards B, Kelle A. "The discussion of dual-use education is often predicated on a discrete population of practicing life scientists exhibiting certain deficiencies in awareness or expertise. This has lead to the claim that there is a greater requirement for awareness raising and education amongst this population. However, there is yet to be an inquiry into the impact of the 'convergent' nature of emerging techno-sciences upon the prospects of dual-use education. The field of synthetic biology, although often portrayed as homogeneous, is in fact composed of various sub-fields and communities. Its practitioners have diverse academic backgrounds. The research institutions that have fostered its development in the UK often have their own sets of norms and practices in engagement with ethical, legal and social issues associated with scientific knowledge and technologies. The area is also complicated by the emergence of synthetic biologists outside traditional research environments, the so called 'do-it-yourself' or 'garage biologists'. This paper untangles some of the complexities in the current state of synthetic biology and addresses the prospects for dual-use education for practitioners. It provides a short overview of the field and discusses identified dual-use issues. There follows a discussion of UK networks in synthetic biology, including their engagement with ethical, legal, social and dual-use issues and limited educational efforts in relation to these. It concludes by outlining options for developing a more systematic dual-use education strategy for synthetic biology."
Cartwright JH, Mackay AL. "We argue for a convergence of crystallography, materials science and biology, that will come about through asking materials questions about biology and biological questions about materials, illuminated by considerations of information. The complex structures now being studied in biology and produced in nanotechnology have outstripped the framework of classical crystallography, and a variety of organizing concepts are now taking shape into a more modern and dynamic science of structure, form and function. Absolute stability and equilibrium are replaced by metastable structures existing in a flux of energy-carrying information and moving within an energy landscape of complex topology. Structures give place to processes and processes to systems. The fundamental level is that of atoms. As smaller and smaller groups of atoms are used for their physical properties, quantum effects become important; already we see quantum computation taking shape. Concepts move towards those in life with the emergence of specifically informational structures. We now see the possibility of the artificial construction of a synthetic living system, different from biological life, but having many or all of the same properties. Interactions are essentially nonlinear and collective. Structures begin to have an evolutionary history with episodes of symbiosis. Underlying all the structures are constraints of time and space. Through hierarchization, a more general principle than the periodicity of crystals, structures may be found within structures on different scales. We must integrate unifying concepts from dynamical systems and information theory to form a coherent language and science of shape and structure beyond crystals. To this end, we discuss the idea of categorizing structures based on information according to the algorithmic complexity of their assembly." http://1.usa.gov/Koubt7
Yadav VG, De Mey M, Lim CG, Ajikumar PK, Stephanopoulos G.
"Industrial biotechnology promises to revolutionize conventional chemical manufacturing in the years ahead, largely owing to the excellent progress in our ability to re-engineer cellular metabolism. However, most successes of metabolic engineering have been confined to over-producing natively synthesized metabolites in E. coli and S. cerevisiae. A major reason for this development has been the descent of metabolic engineering, particularly secondary metabolic engineering, to a collection of demonstrations rather than a systematic practice with generalizable tools. Synthetic biology, a more recent development, faces similar criticisms. Herein, we attempt to lay down a framework around which bioreaction engineering can systematize itself just like chemical reaction engineering. Central to this undertaking is a new approach to engineering secondary metabolism known as 'multivariate modular metabolic engineering' (MMME), whose novelty lies in its assessment and elimination of regulatory and pathway bottlenecks by re-defining the metabolic network as a collection of distinct modules. After introducing the core principles of MMME, we shall then present a number of recent developments in secondary metabolic engineering that could potentially serve as its facilitators. It is hoped that the ever-declining costs of de novo gene synthesis; the improved use of bioinformatic tools to mine, sort and analyze biological data; and the increasing sensitivity and sophistication of investigational tools will make the maturation of microbial metabolic engineering an autocatalytic process. Encouraged by these advances, research groups across the world would take up the challenge of secondary metabolite production in simple hosts with renewed vigor, thereby adding to the range of products synthesized using metabolic engineering."
Jane Calvert "Synthetic biology is in the process of inventing itself and its ownership regimes. There are currently two dominant approaches to ownership and sharing in the field. The work of the J. Craig Venter Institute is grounded in molecular biology and in gene patenting. Parts-based approaches to synthetic biology, in contrast, are inspired by engineering, open source software and distributed innovation, and they are building new communities to help further this agenda. Despite these differences, the two approaches make very similar use of informational and computational metaphors. They both also have a place in a vision for the future of synthetic biology as a ‘diverse ecology’ of the open and the proprietary. It remains to be seen whether such a diverse ecology will be sustainable, whether synthetic biology will go down the patenting route taken by previous biotechnologies or whether different forms of ownership and sharing will emerge. Which path is taken will depend on the success of synthetic biology in achieving both its technical objectives and its social innovations." http://bit.ly/JCQVs0
"In the fields of proteomics, metabolic engineering and synthetic biology there is a need for high-throughput and reliable cloning methods to facilitate construction of expression vectors and genetic pathways. Here, we describe a new approach for solid-phase cloning in which both the vector and the gene are immobilized to separate paramagnetic beads and brought into proximity by magnetic force. Ligation events were directly evaluated using fluorescent-based microscopy and flow cytometry. The highest ligation efficiencies were obtained when gene- and vector-coated beads were brought into close contact by application of a magnet during the ligation step. An automated procedure was developed using a laboratory workstation to transfer genes into various expression vectors and more than 95% correct clones were obtained in a number of various applications. The method presented here is suitable for efficient subcloning in an automated manner to rapidly generate a large number of gene constructs in various vectors intended for high throughput applications."
"In April, the White House released a policy paper what was styled the "National Bioeconomy Blueprint." Its presumptions are based on the idea that the portion of the economy "fueled by research and innovation in the biological sciences" is a "large and rapidly growing segment of the world economy that provides substantial public benefit." This has caused innovation in the biological sciences to become a priority of the Obama Administration, promising not only economic development but to "live longer, healthier lives, reduce our dependence on oil, address key environmental challenges, transform manufacturing processes, and increase the productivity and scope of the agricultural sector while growing new jobs and industries." Successes of the bioeconomy touted by the Blueprint include $76 billion in revenues from genetically engineered crops and $100 billion in revenues from "industrial biotechnology" (including "fuels, materials, chemicals, and industrial enzymes derived from genetically modified systems"). The Blueprint identifies genetic engineering technology, DNA sequence analysis and "automated high-throughput manipulations of biomolecules" as "foundational technologies," while identifying "synthetic biology," proteomics and bio-informatics as "emerging technologies."
The result of the "bioeconomy" becoming an Administration "priority" is a directive (Executive Memorandum (M-10-30)) to all Federal agencies to "support research to establish the foundations for a 21st century bioeconomy," an effort that the Blueprint says has made "significant early progress." While these efforts also "raise important ethical and security issues that are also top priorities for the Administration," discussions of these concerns are expressly deemed to be outside the scope of the Blueprint itself.
The first chapter of the Blueprint sets out the broad goals, citing the National Research Council's 2009 report, A New Biology for the 21st Century, ...."
"Twenty-first century society draws from a world that is less determined by objects and increasingly shaped by connectivity. The clear either/or distinctions that formerly informed experience are being replaced by a much more fluid understanding of the world. Identity is not fixed, but shaped by networks where people and ‘things’ can coherently exist in many states. This ‘complex systems’* view extends to the characterization of nature, which is made up of many interacting bodies. Some of these are human, others living and many other participating agencies that are dynamic, yet are not thought of as being alive. Yet the animal, plant and mineral kingdoms represent different kinds of organizing networks that are entwined and constitute our living world.
The study of complex systems has become an important scientific study that requires interdisciplinary collaboration to characterize their properties. Networks, which share patterns of organization, are at the heart of complex systems. This helps us understand poorly understood complex systems, such as metabolic networks, by making analogies with well-known ones, such as the Internet..."
"During the past couple months I’ve been thinking and writing a lot about space colonies for some reason, and I recently had the pleasure of talking with a group of iGEM students that spent last summer designing synthetic microbes that would help astronauts build a community on Mars. The Brown-Stanford joint team worked with NASA scientists on a two-pronged project. Their first project, REGObricks, uses bacteria to break down urea into chemicals that can be used to form crystals that can bond Martian sand into a strong building material. The second project is PowerCell–engineering photosynthetic bacteria that can convert sunlight into the chemical energy (like sugar) needed to power other living things. Their short teaser video is a great introduction to their team...." http://bit.ly/MKxm0I
text2genome: Annotating genes and genomes with DNA sequences extracted from open-access biomedical articles
text2Genome is using a unique way to map scientific articles to genomic locations: From a full-text scientific article and it's supplementary data files, all words that resemble DNA sequences are extracted and then mapped to public genome sequences. They can then be displayed on genome browser websites and used in data-mining applications.
Updates: In 2012, the database of articles is extended at UCSC, see the UCSC Genocoding project for current developments and progress with non-open-access publishers and more recognized keywords. Our efforts have been covered by a news article written by Richard van Noorden for the journal Nature in March 2012, see also the editorial.
DARPAs Living Foundries project was first announced by the agency last year. Darpa has handed out seven research awards worth $15.5 million to six different companies and institutions including the University of Texas at Austin and the California Institute of Technology. Two contracts were also issued to the J. Craig Venter Institute. Dr. Venter was among the first scientists to sequence a human genome, and his institute was, in 2010, the first to create a cell with entirely synthetic genome.
“Living Foundries” aspires to turn the slow, messy process of genetic engineering into a streamlined and standardized one. Of course, the field is already a burgeoning one: Scientists have tweaked cells in order to develop renewable petroleum and spider silk that’s tough as steel. And a host of companies are investigating the pharmaceutical and agricultural promise lurking — with some tinkering, of course — inside living cells.
7+ years for a scientific project - We can do better!
"Darpa notes, even the most cutting-edge synthetic biology projects “often take 7+ years and tens to hundreds of millions of dollars” to complete." http://bit.ly/JpJKSV I think this is ridiculous. We do not really need 7 years to do a scientific project.
The main reason for this is that we still do science in the old fashioned way.
Basically we have with the internet got a tool to do this much quicker and some projects have done so e.g. see Linux development or the iGem competition. In this last projects students can do in 3 month what a post doc before did in 3 years. Collaborative intelligence and cloud collaboration have a huge potential to seed up. However, fear for our career held many scientist back to adapt to science2.0. The science business model high impact factor paper, tax money paid position is outdated, however the one, which feed us. As a consequence it take 1 to 2 years to get grants, 3 years to do the project as a single post doc (scientific collaboration is mostly on the papers for grant applications), and 2 years to get it published with many rounds of meaningless rejections ad revisions. Thus you end up with a typically time use of about 7 years instead of 3 month. Cloud collaboration will change this, hopefully soon.
Johansson EM, Bradley M. "Polymeric styrene microspheres have a great potential at the interface of chemistry and biology. The progress of the synthetic development of multifunctional microspheres and their use as delivery agents of different biomolecules into cells is discussed. Their multifunctional properties open a wide range of applications from intracellular real-time sensors, to the use of microspheres as catalysts performing exogenous chemistry within cells." http://1.usa.gov/JCFsCg
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