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The ‘reading’ of DNA is a solved technological problem but what about ‘writing’ DNA? Could we program or reprogram biological systems and even generate new life forms? In this Friday Evening Discourse at the Ri, Paul Freemont explores how the powerful fusion of molecular biology, design and engineering could lead to a ‘Biotechnological Revolution’ and considers the implications of the extraordinary field of synthetic biology.
Scientists launch company to develop the therapeutic potential of gene-snipping enzymes
A showcase of the best infographics from around the web
byPorcar M, Peretó J."Synthetic Biology is a singular, revolutionary scenario with a vast range of practical applications but, is SB research really based on engineering principles? Is it contributing to the artificial synthesis of life or using approaches "sophisticated" enough to fall outside the scope of biotechnology or metabolic engineering? We have reviewed the state of the art on synthetic biology and we conclude that most research projects actually describe an extension of metabolic engineering. We draw this conclusion because the complexity of living organisms, their tight dependence on evolution and our limited knowledge of the interactions between the molecules they are made of, actually make life difficult to engineer. We therefore propose the term synthetic biology should be used more sparingly."
They look like beans, but these ghostly little organs are alive.
by+Jonny Serfaty "Sunny Allen was always interested in science, but overwhelming workloads and lack of encouragement led her to study linguistics instead. Five years of waitressing later, she decided to go back to school and start a second degree in biology and programming, which led her into the world of DIY bio. Now she is helping to get a new DIY bio lab started in the Bay area and working on a huge project to make affordable bioreactors available to the public.
Low Cost Synthesis of Tuberculosis Drugs Using Synthetic Biology http://t.co/8LjmiGkOq1 #GCCgrantee #rcanconf
Biologist-turned-artist Britt Wray, keynote speaker at a Concordia round table, explains the potential and the pitfalls.
"From helping produce more energy-efficient biofuels to increasing global access to life-saving medications, the emerging field of synthetic biology has the potential to provide solutions for many of humanity’s problems. At Concordia, the Centre for Applied Synthetic Biology (CASB) — Canada’s first dedicated research centre — is leading the way. It brings biologists, engineers, computer scientists and social scientists together to develop tools and technologies with practical applications in environmental and health management. On November 26, the university held a round table to explore new interdisciplinary approaches to the research and teaching of this vast and ethically complex discipline. “Synthetic Biology: Interdisciplinary Perspectives” was hosted by the Individualized Program at the School of Graduate Studies. Academics from all four faculties — Arts and Science, Fine Arts, Engineering and Computer Science, and the John Molson School of Business — attended, including CASB co-directors Vincent Martin, the Canada Research Chair in Microbial Genomics, and Nawwaf Kharma, an associate professor in Electrical and Computer Engineering. The event’s keynote speaker was Brittany Wray, a filmmaker, radio documentary producer and self-described “biologist-turned-artist” who has been researching synthetic biology for three years. She completed Concordia’s graduate diploma in Communication Studies in 2010. In an interview before Tuesday’s round table, Wray explained the basics. What exactly is synthetic biology? Brittany Wray: Synthetic biology is the field of science where an engineering mindset gets applied to biology in an attempt to build things out of nature from an intentional design perspective. It is always a tricky discipline to define because it takes many forms, from work that aims to make genetic devices that modify an organism in a specific way, to whole genome engineering where the entire genetic information in an organism is organized by a scientist from the bottom up. What are some practical examples? BW: Synthetic biology is being developed largely for biofuels and medicine. For example, a company has recently made a synthetic yeast that creates biofuel as a product of its metabolism. Another recent development has been the invention of the cheapest anti-malarial drug to hit the medical world. Synthetic biology can also be used to create synthetic versions of some coveted food ingredients, like vanilla or saffron. The applications are far ranging — from biosensors, to cell communication and protein transfer devices, to strategies for interspecies communication. What impact can this emerging field have on society? BW: Synthetic biology is often propped up as the big fix to some of the big problems we face around sustainability, and the deep environmental trenches we've gotten ourselves into after many decades of industrialized life. It garners a lot of excitement because of its potential to produce fuel in far more sustainable ways. But the question remains, of course, can it do so on such a large scale? It also has the potential to help us see health problems before it is too late. A synthetic biosensor could test for meat spoilage before it goes to markets. There are any other number of scenarios where invisible issues arise — and sometimes go wrong — when things are not examined on the level of their biology. Synthetic biology may also be able to provide far greater numbers of people with accessible pharmaceuticals, because it would lower the manufacturing costs of medications. But synthetic biology is not regarded as a magic bullet. To go back to the example of cheap pharmaceuticals, many argue that synthetic biology will have detrimental effects on societies in the places like the global south. In those countries, many farmers’ livelihoods depend on growing the non-synthetic versions of artemisia — a pre-cursor to the malaria vaccine — or vanilla, and they will not be able to compete with corporately manufactured synthetic versions of their crops. Why is an interdisciplinary approach important in synthetic biology? BW: There is a very exciting and diverse set of interests that are focused on synthetic biology at the moment. Do-it-yourself biologists are interested in making the tools to access and use biotechnology more openly. Ethicists, anthropologists and other natural scientists are trying to understand the moral issues involved in doing this type of work, and the impacts it will have on human and non-human communities for years to come. Essentially, there's a Pandora's box at play in terms of how this technology could be used. The more interested, critical and thoughtful minds we have working on it at once, the more productive a deliberation we can have. And hopefully that will give rise to the responsible insight we need in order to use synthetic biology as beneficially as possible with the least amount of harm. "
byPolka JK, Silver PA."The elaborate spatial organization of cells enhances, restricts, and regulates protein-protein interactions. However, the biological significance of this organization has been difficult to study without ways of directly perturbing it. We highlight synthetic biology tools for engineering novel cellular organization, describing how they have been, and can be, used to advance cell biology." http://1.usa.gov/1aiQPfC
Garg N, Manchanda G, Kumar A.
"Bacterial quorum sensing (QS) systems are cell density-dependent regulatory networks that coordinate bacterial behavioural changes from single cellular organisms at low cell densities to multicellular types when their population density reaches a threshold level. At this stage, bacteria produce and perceive small diffusible signal molecules, termed autoinducers in order to mediate gene expression. This often results in phenotypic shifts, like planktonic to biofilm or non-virulent to virulent. In this way, they regulate varied physiological processes by adjusting gene expression in concert with their population size. In this review we give a synopsis of QS mediated cell-cell communication in bacteria. The first part focuses on QS circuits of some Gram-negative and Gram-positive bacteria. Thereafter, attention is drawn on the recent applications of QS in development of synthetic biology modules, for studying the principles of pattern formation, engineering bi-directional communication system and building artificial communication networks. Further, the role of QS in solving the problem of biofouling is also discussed."
"Engineering radically altered genetic codes will allow for genomically recoded organisms that have expanded chemical capabilities and are isolated from nature. We have previously reassigned the translation function of the UAG stop codon; however, reassigning sense codons poses a greater challenge because such codons are more prevalent, and their usage regulates gene expression in ways that are difficult to predict. To assess the feasibility of radically altering the genetic code, we selected a panel of 42 highly expressed essential genes for modification. Across 80 Escherichia colistrains, we removed all instances of 13 rare codons from these genes and attempted to shuffle all remaining codons. Our results suggest that the genome-wide removal of 13 codons is feasible; however, several genome design constraints were apparent, underscoring the importance of a strategy that rapidly prototypes and tests many designs in small pieces."
Elsevier Store: Article
FREE access to select content from Open-Source Lab: How to Build Your Own Hardware and Reduce Research Costshttp://bit.ly/1a5wkmI
by+Douglas Densmore and +Swapnil Bhatia "Synthetic biology promises to usher in a new era of scientific innovation and discovery . Applications of this technology are broad and diverse . Although applications frequently dominate the headlines, of equal importance are the engineering design principles. If these principles are developed rigorously, they will lay the foundation for the field and enable long-term growth and accessibility. A crucial engineering principle is design automation. Design automation is the process of applying tools (software, hardware, and wetware) to remove manual processes. Often, design automation transforms a high-level system objective ‘input’ (e.g., optimize this metabolic pathway) into a physically realized artifact ‘output’ (e.g., DNA, microbial strain, or protein). In order for design automation to be broadly applied it requires solutions to be based on sound definitions, tractable algorithms, and standardized data formats. Design automation promises to lower costs, increase design reuse, improve design reproducibility, reduce design error, and enable complex designs.
byHelen Shen"Scientists launch company to develop the therapeutic potential of gene-snipping enzymes.Instead of taking prescription pills to treat their ailments, patients may one day opt for genetic 'surgery' — using an innovative gene-editing technology to snip out harmful mutations and swap in healthy DNA.The system, called CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), has exploded in popularity in the past year, with genetic engineers, neuroscientists and even plant biologists viewing it as a highly efficient and precise research tool. Now, the gene-editing system has spun out a biotechnology company that is attracting attention from investors as well.
Scientists have finally turned human stem cells into lung cells, and say the breakthrough paves the way for using a patient's own cells for lung transplant.
byZhang M, Wang F, Li S, Wang Y, Bai Y, Xu X."Transcription activator-like effectors (TALEs), first identified in Xanthomonas bacteria, are naturally occurring or artificially designed proteins that modulate gene transcription. These proteins recognize and bind DNA sequences based on a variable numbers of tandem repeats. Each repeat is comprised of a set of ∼34 conserved amino acids; within this conserved domain, there are usually two amino acids that distinguish one TALE from another. Interestingly, TALEs have revealed a simple cipher for the one-to-one recognition of proteins for DNA bases. Synthetic TALEs have been used to successfully target genes in a variety of species, including humans. Depending on the type of functional domain that is fused to the TALE of interest, these proteins can have diverse biological effects. For example, after binding DNA, TALEs fused to transcriptional activation domains can function as robust transcription factors (TALE-TFs), while fused to restriction endonucleases (TALENs) can cut DNA. Targeted genome editing, in theory, is capable of modifying any endogenous gene sequence of interest; this can be performed in cells or organisms, and may be applied to clinical gene-based therapies in the future. With current technologies, highly accurate, specific, and reliable gene editing cannot be achieved. Thus, recognition and binding mechanisms governing TALE biology are currently hot research areas. In this review, we summarize the major advances in TALE technology over the past several years with a focus on the interaction between TALEs and DNA, TALE design and construction, potential applications for this technology, and unique characteristics that make TALEs superior to zinc finger endonucleases." http://bit.ly/IErZ3z
byJacqueline Vanacek"In April 2013, we celebrated the 10th anniversary of the completion of the Human Genome Project. Led by the National Institutes of Health, the Human Genome Project (HGP) was completed 2.5 years ahead of schedule and well under budget. “For the first time, anyone could freely read the fundamental instruction set needed to make a human body.”But it took years and billions of dollars to reach this point. How did we get here? And where are we headed? While those in the field point to “next gen sequencing” as a primary accelerator for the HGP, I wanted to explore what that meant.So I visited the nexus of the HGP — the National Human Genome Research Institute – to hear the history and tour the laboratory with NIH Intramural Sequencing Center (NISC) Director Jim Mullikin, PhD and Head of IT Systems Don Preuss from the National Center for Biotechnology Information (NCBI).The NIH Intramural Sequencing Center delivers high throughput DNA sequencing to support NHGRI’s basic research into both cause and treatments for genetic diseases. NISC experts “manufacture” high outputs of usable genomics data from samples of purified DNA or RNA for clinical investigators. And NCBI provides the advanced software tools and databases to study these “biologically important molecules.” The NISC tour included a look at past and present DNA sequencers with Jim Mullikin.“First Generation” DNA SequencingNHGRI defines DNA sequencing as a “laboratory technique used to determine the exact sequence of bases (A, C, G and T) in a DNA molecule. The DNA base sequence carries the information a cell needs to assemble protein and RNA molecules” which govern how our bodies are built and function.While recently deceased genomics pioneer and Nobel Laureate Frederick Sanger developed rapid DNA sequencing chemical methods in the 1970s, it was not until ten years later, in 1986, that the first fully automated DNA sequencing instrument appeared on the market.These early automated sequencers were used in the Human Genome Project and could decipher about 700-1000 base-pair long DNA fragments at a time. There was no ability or expectation to decipher and map a full human genome back then. And with 3 billion DNA building blocks making up a single human genome, the HGP required thousands of scientists mapping thousands of fragments to eventually be reconstructed into one complete sequence.Back then, each DNA sequencer cost about $1 million. And when one considers how labor-intensive this early work was, it’s easy to understand why it took 13 years and cost about $3.5 billion in total to map the 99% of the Human Genome DNA blueprint that is identical for all of us.“Next Generation” DNA SequencingWhen Dr. Francis Collins, then Director of NHGRI, challenged the genomics community to reduce the cost of mapping a personal genome from $100 million to $1000, advances in DNA sequencers skyrocketed.The subsequent miniaturization of sequencers has allowed for smaller DNA sample sizes, less chemical reagents and the ability to run multiple DNA samples in parallel. All of these factors have dramatically reduced the time and cost of analysis.Today, a variety of sequencers exists, ranging from those that can survey a full human genome in eleven days to jumpstart a research investigation — to solid state sequencers that can do a partial analysis in just a day for quality control or to zero in on a specific chromosome.Where DNA Sequencing Is HeadedEven with so many advances in DNA sequencing, there is another wave yet to come! For example, Jim Mullikin talked about the Genome in a Bottle Consortium’s collaboration with the National Institute of Standards. NIST will develop whole genome reference materials to ensure accuracy of high throughput DNA sequencing done in a clinical setting. Recent studies show that false positives or negatives in genetic variants or mutations could arise from different sequencing and bioinformatics analysis methods. The reference materials would ensure that any risk is minimized.Finally, Don Preuss described the emerging genome-in-a-box concept, with a myriad of vendor approaches. For example, from Harvard Medical School, George Church’s Knome company is offering a “plug-and-play” human genome interpretation system. It combines hardware and genomic interpretation software to simplify getting “useful medical information from a patient’s DNA.” This approach supports data privacy and regulatory compliance.Genomics leader Illumina’s “lab in a box” model permits customers to “upload their DNA sequences to a cloud-based data storage and analysis system for interpretation.” And Bina Technologies offers a pay-per-use Genomic Analysis Platform or on premise appliance that can process a whole human genome in only 4 hours......" http://onforb.es/IJzvuR
byTanaya Joshi"Being from a very different background than my fellow bloggers, it can be a challenge to find a topic to write about. I mean, I’m an Industrial Design major and that’s pretty far from science and labs and stuff, right? WRONG!
Gregory Radick School of Philosophy, Religion and History of Science, University of Leeds, Leeds LS2 9JT This piece will appear in the December 2013 issue of STUDIES IN HISTORY AND PHILOSOPHY OF BI...
Britt Wray is a biologist-turned-artist. She researches biotechnologically-driven change in the human and non-human living world, and uses radio, video, and ...
*Researchers find a missing component in effort to create primitive, synthetic cells*byAnonymous"A team of Massachusetts General Hospital (MGH) investigators working to create "protocells" – primitive synthetic cells consisting of a nucleic acid strand encased within a membrane-bound compartment – have accomplished an important step towards their goal. In the November 28 issue of Science, the investigators describe a solution to what could have been a critical problem – the potential incompatibility between a chemical requirement of RNA copying and the stability of the protocell membrane.
byAdrian Mackenziea"Synthetic biology provides a vivid and richly entangled contemporary example of a science being made public. A science, however, can be made public in different ways. A public could validate, legitimate, de-legimate, object to, verify, confirm or dissent from science. Practically, scientists could publicise science—in the mass media—or they could make science public. The contrast between high-profile, media scientists such as J. Craig Venter, and community-based participatory mechanisms such as OpenWetWare allows us to see how these alternatives play out in practice. While it is easy to criticise and dismiss the public-relations oriented promotion of synthetic biology by figures such as Venter, how should we evaluate the open participatory mechanisms of a social media effort such as OpenWetWare? I suggest, drawing on the work of Isabelle Stengers and Michael Warner, that the case of synthetic biology is interesting because many synthetic biologists commit themselves to making it public, and making its public-ness part of how it is done. They place hope in publics to make the science viable. At the same time, however, the publics who are welcomed into OpenWetWare are largely confined to validating the coordination mechanisms on which the claim to public-ness rests. Whether publics can do more than validate synthetic biology, then, remains a question both for publics outside and inside this emerging scientific field. And whether the alternatives of validation or participation themselves adequately frame what is at stake in the emergence of fields such as synthetic biology remains debatable."http://bit.ly/1fPFg80
byMichael Eisenstein"Bacteria's ability to withstand broad genomic editing offers a potential route toward more robust and useful genetically modified organisms.
Big Data, Cardiovascular Disease, Public Policy & Synthetic Biology: new Strategic Research Initiatives at Cambridge: http://t.co/lRCP4mZUu9