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byanonymous"A team of students from the University of Exeter are making their final preparations before taking part in a prestigious international synthetic biology competition.
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New 'GenoCAD' modelling helping design synthetic biological systems NDTV Known as 'GenoCAD', the open-source software would help synthetic biologists capture biological rules to engineer organisms that produce useful products or health-care...
byMackay JL, Sood A, Kumar S."The ability to independently assemble multiple cell types within a three-dimensional matrix would be a powerful enabling tool for modeling and engineering complex tissues. Here we introduce a strategy to dynamically pattern distinct subpopulations of cells through genetic regulation of cell motility. We first describe glioma cell lines that were genetically engineered to stably express constitutively active or dominant negative Rac1 GTPase mutants under the control of either a doxycycline-inducible or cumate-inducible promoter. We culture each population as multicellular spheroids and show that by adding or withdrawing the appropriate inducer at specific times, we can control the timing and extent of Rac1-dependent cell migration into three-dimensional collagen matrices. We then report results with mixed spheroids in which one subpopulation of cells expresses dominant negative Rac1 under a doxycycline-inducible promoter and the other expresses dominant negative Rac1 under a cumate-inducible promoter. Using this system, we demonstrate that doxycycline and cumate addition suppress Rac1-dependent motility in a subpopulation-specific and temporally-controlled manner. This allows us to orthogonally control the motility of each subpopulation and spatially assemble the cells into radially symmetric three-dimensional patterns through the synchronized addition and removal of doxycycline and cumate. This synthetic biology-inspired strategy offers a novel means of spatially organizing multiple cell populations in conventional matrix scaffolds and complements the emerging suite of technologies that seek to pattern cells by engineering extracellular matrix properties." http://bit.ly/1e0zDC3
byDenisa Kera"Typically nanotechnology and synthetic biology are discussed in terms of novel life forms and materials created in laboratories, or by novel convergences of technologies (ICTs and biological protocols) and science paradigms (engineering and biology) they initiated. Equally inspiring is their ability to generate novel institutions and global communities around emergent sciences, which radicalize the forms of public engagement and ethical deliberation. We are starting to witness alternative (iGEM competitions) and almost underground R&D engagements with Synthetic Biology (DIYbio movement), which inspired the emerging bottom-up involvements in nanotechnologies in projects, such as the NanoSmanoLab in Slovenia. These bottom-up involvements use tinkering and design as models for both research and public engagement. They democratize science and initiate a type of grassroots “science diplomacy”, supporting research in developing countries. We will discuss several recent examples, which demonstrate these novel networks (“Gene gun” project by Rüdiger Trojok from the Copenhagen based hackerspace, Labitat.dk, the “Bioluminescence Project” by Patrik D'haeseleer from Biocurious biotech hackerspace in Sunnyvale, CA, and the “Biodesign for the real world” project by members of the Hackteria.org). They all use design prototypes to enable collaborative and global tinkering, in which science and community are brought together in open biology laboratories and DIYbio hackerspaces, such as Hackteria.org or Biocurious. In these projects research protocols encompass broader innovative, social and ethical norms. Hackerspaces represent a unique opportunity for a more inclusive, experimental, and participatory policy that supports both public and global involvements in emergent scientific fields." http://bit.ly/1aOnQ5p
Compute Midwest 2013: Andrew Hessel, Genomic Futurist @ Autodesk , Speaks About The Next Generation Of Computing: Programming Living Things. About Compute Mi...
“DIYbio” is the name given to the growing movement of people who are interested in performing science outside of traditional academic and corporate pharma.
byKyrie Vala-Webb"he group you hear tinkering away in your neighbor’s garage may be making molecules, not music. DIY biology, also known as “DIYbio” is the name given to the growing movement of people who are interested in performing science outside of traditional academic and corporate pharma environments.
A quantum computer is a serious piece of hardware. My colleagues and I build quantum computers from superconducting systems, quantum dots, lasers operating on nonlinear crystals,... Read Full Postelse
byOrlando de Lange, Andreas Binder, Thomas Lahaye"Whether rice, yeast, or fly there is barely a model organism not yet reached by transcription activator like effectors (TALEs) and their derivative fusion proteins. Insights into fundamental biology are now arriving on the back of work in the last years to develop these proteins as tools for molecular biology. This began with the publication of the simple cipher determining base-specific DNA recognition by TALEs in 2009 and now encompasses a huge variety of established fusion proteins mediating targeted modifications to transcriptome, genome, and recently, epigenome. Straightforward design and exquisite specificity, allowing unique sites to be targeted even within complex eukaryote genomes, are key to the popularity of this system. Synthetic biology is one field that is just beginning to make use of these properties with a number of recent publications demonstrating TALE-mediated regulation of synthetic genetic circuits. Intense interest has surrounded the CRISPR/Cas9 system within the last twelve months and it is already proving its mettle as a tool for targeted gene modifications and transcriptional regulation. However, questions over off-target activity and means for independent regulation of multiple Cas9-guide RNA pairs will have to be resolved before this method enters into the synthetic biology toolbox. TALEs are already showing promise as regulators of synthetic biological systems, a role that will likely be developed further in the coming years." http://bit.ly/1gnIM4O
This study establishes a proof-of-concept that a tattoo device can target intra-dermal drug delivery against cutaneous leishmaniasis (CL). The selected drug is oleylphosphocholine (OlPC) formulated as liposomes, particles known to be prone to macrophage ingestion. We first show that treatment of cultured Leishmania-infected macrophages with OlPC-liposomes results in a direct dose-dependent killing of intracellular parasites. Based on this, in vivo efficacy is demonstrated using a 10 day tattooing-mediated treatment in mice infected with L. major and L. mexicana. In both models this regimen results in rapid clinical recovery with complete regression of skin lesions by Day 28. Parasite counts and histopathology examination confirm high treatment efficacy at the parasitic level. Low amount of drug required for tattooing combined with fast clinical recovery may have a positive impact on CL patient management. This first example of tattoo-mediated drug delivery could open to new therapeutic interventions in the treatment of skin diseases.
*This forthcoming tome looks like it oughta be pretty happening. *It's a press release. *******************************************************************
byBruce Sterling"Synthetic Aesthetics
byMartyn Dade-Robertsona, Carolina Ramirez Figueroaa, Meng Zhang"This paper discusses the role that material ecologies might have in the emerging engineering paradigm of Synthetic Biology (hereafter SB). In this paper we suggest that, as a result of the paradigm of SB, a new way of considering the relationship between computation and material forms is needed, where computation is embedded into the material elements themselves through genetic programming. The paper discusses current trends to conceptualize SB in traditional engineering terms and contrast this from design speculations in terms of bottom up processes of emergence and self organization. The paper suggests that, to reconcile these positions, it is necessary to think about the design of new material systems derived from engineering living organisms in terms of a state space of production. The paper analyses this state space using the example of biomineralization, with illustrations from simple experiments on bacteria induced calcium carbonate. The paper suggests a framework involving three interconnected state spaces defined as: cellular (the control of structures within the cell structures within a cell, and specifically DNA and its expression through the process of transcription and translation); chemical (considered to occur outside the cell, but in direct chemical interaction with the interior of the cell itself); physical (which constitutes the physical forces and energy within the environment). We also illustrate, in broad terms, how such spaces are interconnected. Finally the paper will conclude by suggesting how a material ecologies approach might feature in the future development of SB." http://bit.ly/PkQNl6
A new microscope can be printed on a flat piece of paper and assembled in less than 10 minutes. And the parts to make it cost less than a dollar.
Original Article from The New England Journal of Medicine — Gene Editing of CCR5 in Autologous CD4 T Cells of Persons Infected with HIV
byChurch GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R."Synthetic biology, despite still being in its infancy, is increasingly providing valuable information for applications in the clinic, the biotechnology industry and in basic molecular research. Both its unique potential and the challenges it presents have brought together the expertise of an eclectic group of scientists, from cell biologists to engineers. In this Viewpoint article, five experts discuss their views on the future of synthetic biology, on its main achievements in basic and applied science, and on the bioethical issues that are associated with the design of new biological systems." http://bit.ly/1imeRy4
Move over, nanotechnologists, and make room for the biggest of the small. Scientists at the Harvard's Wyss Institute have built a set of self-assembling DNA cages one-tenth as wide as a bacterium. The structures are some of the largest and most complex structures ever constructed solely from DNA, they ...
(Phys.org) —Researchers at Virginia Tech and the Massachusetts Institute of Technology have used a computer-aided design tool to create genetic languages to guide the design of biological systems.
byRoderic D. M. Page"Following on from the previous post on putting GBIF data onto Google Maps, I'm now going to put DNA barcodes onto Google Maps. You can see the result at http://iphylo.org/~rpage/bold-map/, which displays around 1.2 million barcodes obtained from the International Barcode of Life Project (iBOL) releases. Let me describe how I made it..........
byCynthia Challener,"The complexity of both small-molecule and large-molecule drugs is increasing as pharmaceutical companies seek therapeutics with new mechanisms of action. In small-molecule therapeutics, increasing complexity often translates to larger numbers of stereocenters. Because only the isomer of a chiral drug that exhibits activity must be produced in high purity, much effort has been invested over the past 20 to 30 years in the development of tools for the asymmetric synthesis of pharmaceutical intermediates. Classical resolution and other methods for the separation of isomers, including large-scale chiral chromatography, and advanced chemocatalysts that mediate a wide variety of enantioselective transformations and enable more rapid and efficient synthesis of complex pharmaceutical intermediates and APIs are widely used today. More recently, technology for the development and commercialization of a diverse array of enzymes that can catalyze stereoselective reactions has led to their increasing use for pharmaceutical synthesis. While advances continue to be made in chemocatalysis, the area of chiral chemistry generating the most excitement is synthetic biology, or the use of multiple enzymes in one-pot reactions (and ultimately in a single organism) to carry out sequential reactions that result in the production of an advanced intermediate or even an API.
As the costs of DNA sequencing and synthesis drop precipitously, a host of computer science-meets-biotech startups are cropping up in Silicon Valley...
A tattoo may make a statement, but can it also help fight disease? Find out...
This Article addresses copyright as a viable form of intellectual property protection for living, organic creations of science and art. The United States Supreme Court’s decision in Association for Molecular Pathology v. Myriad Genetics, Inc. narrowed patent-eligible protection over living components of humans or other organisms. Synthetic biologists are expected to look with renewed focus on copyright law for the intellectual property protection of biological creations. The contribution of this Article is to reveal that the same issues are raised with regard to the copyrightability of the works of synthetic biology as are raised by pictorial, graphic, and sculptural arts that use and produce living media as their works. The current contours of copyrightability present four identical questions that are particularly relevant to and difficult to answer in the context of science and art that purports to create works of living media: Is living media copyrightable subject matter? What is authorship (or who is an author) of living media? What does it mean to create a fixed and tangible work of living media? What constitutes an original creation of living media under the originality doctrines of merger and scenes a faire? This Article will provide an analytical framework for rethinking the contours of copyright so as to answer these questions by comparing contemporary scientific methods of creation with artistic methods in order to determine the copyright narratives and metaphors of subject matter, authorship, creation, and originality that best address the concerns underlying these four questions and allow copyright protection over the works.  Association for Molecular Pathology v. Myriad Genetics, Inc., 133 S. Ct. 2107 (Jun. 13, 2013) (isolated DNA sequences not patentable).
byChiarabelli, Cristiano; Luisi, Pier Luigi"Although both the most popular form of synthetic biology (SB) and chemical synthetic biology (CSB) share the biotechnologically useful aim of making new forms of life, SB does so by using genetic manipulation of extant microorganism, while CSB utilises classic chemical procedures in order to obtain biological structures which are non-existent in nature. The main query concerning CSB is the philosophical question: why did nature do this, and not that? The idea then is to synthesise alternative structures in order to understand why nature operated in such a particular way. We briefly present here some various examples of CSB, including those cases of nucleic acids synthesised with pyranose instead of ribose, and proteins with a reduced alphabet of amino acids; also we report the developing research on the “never born proteins” (NBP) and “never born RNA” (NBRNA), up to the minimal cell project, where the issue is the preparation of semi-synthetic cells that can perform the basic functions of biological cells." http://bit.ly/1crgtqj
byJay Keasling "Most Americans may not be familiar with synthetic biology, but they may come to appreciate its advances someday soon. Synthetic biology focuses on creating technologies for designing and building biological organisms. A multidisciplinary effort, it calls biologists, engineers, software developers, and others to collaborate on finding ways to understand how genetic parts work together, and then to combine them to produce useful applications.