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 The science business model high impact factor paper, tax money paid position is outdated, however the one, which feed us.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
Rewritable digital data storage in live cells via engineered control of recombination directionality
by Jerome Bonnet, Pakpoom Subsoontorn, and Drew Endy "The use of synthetic biological systems in research, healthcare, and manufacturing often requires autonomous history-dependent behavior and therefore some form of engineered biological memory. For example, the study or reprogramming of aging, cancer, or development would benefit from genetically encoded counters capable of recording up to several hundred cell division or differentiation events. Although genetic material itself provides a natural data storage medium, tools that allow researchers to reliably and reversibly write information to DNA in vivo are lacking. Here, we demonstrate a rewriteable recombinase addressable data (RAD) module that reliably stores digital information within a chromosome. RAD modules use serine integrase and excisionase functions adapted from bacteriophage to invert and restore specific DNA sequences. Our core RAD memory element is capable of passive information storage in the absence of heterologous gene expression for over 100 cell divisions and can be switched repeatedly without performance degradation, as is required to support combinatorial data storage. We also demonstrate how programmed stochasticity in RAD system performance arising from bidirectional recombination can be achieved and tuned by varying the synthesis and degradation rates of recombinase proteins. The serine recombinase functions used here do not require cell-specific cofactors and should be useful in extending computing and control methods to the study and engineering of many biological systems." http://bit.ly/K5n33R Comment Nature, News: Rewritable memory encoded into DNA by Erika Check Hayden "Researchers have encoded a form of rewritable memory into DNA. The arduous work involved in building the system is almost as notable as the achievement itself, says Drew Endy of Stanford University in California who led the work, which is published today in Proceedings of the National Academy of Sciences1. Synthetic biologists have long sought to devise biological data-storage systems because they could be useful in a variety of applications, and because data storage will be a fundamental function of the digital circuits that the field hopes to create in cells. DNA can be programmed to act as a biological data-storage device. Rewritable biological memory circuits have been made previously, for instance from systems of transcription factors, which can be used to shut gene expression on or off in a cell. In such systems, once the memory state of the circuit is set, it can be erased and encoded with a new memory state, as is done in everyday devices such as personal computers. Endy’s group attempted to create a rewritable memory system by splicing genetic elements from a bacteriophage — a bacterium-infecting virus — into the DNA of the bacterium Escherichia coli. ..." http://bit.ly/Ktd2wt
"The Synthetic Biology Engineering Research Center (SynBERC) is a multi-institution research effort to lay the foundation for the emerging field of synthetic biology. SynBERC’s vision is to catalyze biology as an engineering discipline by developing the foundational understanding and technologies to allow researchers to design and build standardized, integrated biological systems to accomplish many particular tasks. In essence, we are making biology easier to engineer.
Just as technicians now assemble electronic devices from commercial, off-the-shelf parts, SynBERC foresees a day when synthetic biologists will design biological systems from scratch and assemble them using well-characterized biological parts, devices, and chasses. SynBERC brings together biologists, engineers, and human scientists from world-class institutions to produce the tools, techniques, and scientific understanding needed to design and construct a broad range of biological tools for health, energy, environment and, ultimately, human welfare." http://bit.ly/iE5zMP
is working to make the engineering of new complex function in cells vastly more efficient, reliable, predictable, and safe. Its breakthroughs will speed the development of biologically engineered solutions to pressing global problems related to health, materials, energy, environment, and security. http://bit.ly/nTAuh0
"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.
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
"The military-industrial complex just got a little bit livelier. Quite literally.
That’s because Darpa, the Pentagon’s far-out research arm, has kicked off a program designed to take the conventions of manufacturing and apply them to living cells. Think of it like an assembly line, but one that would churn out modified biological matter — man-made organisms — instead of cars or computer parts.
The program, called “Living Foundries,” was first announced by the agency last year. Now, Darpa’s handed out seven research awards worth $15.5 million to six different companies and institutions. Among them are several Darpa favorites, 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 is something of a biology superstar: He was among the first scientists to sequence a human genome, and his institute was, in 2010, the first to develop an entirely synthetic organism.
“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......" http://bit.ly/LfrB67
"Andrew Maynard, Ph.D., focuses on the responsible development and use of emerging technologies, and on innovative approaches to addressing emergent risks. An international expert on nanotechnology, he is a professor of risk science and environmental health sciences at University of Michigan School of Public Health." http://bit.ly/Lowedr
Bringing next-generation therapeutics to the clinic through synthetic biology
by Lukasz J Bugaj, David V Schaffer "Highlights ► Synthetic biology tools are being applied towards the clinical development of enhanced therapeutics. ► Engineered genetic circuits can create ‘smart’ drugs with sensing and actuating capabilities. ► Therapeutic devices may be delivered through viral vectors, encapsulated cells, or bacteria. ► With initial clinical trials underway, safety will be the first priority." "Recent advances in synthetic biology have created genetic tools with the potential to enhance the specificity, dynamic control, efficacy, and safety of medical treatments. Interfacing these genetic devices with human patients may thus bring about more efficient treatments or entirely new solutions to presently intractable maladies. Here we review engineered circuits with clinical potential and discuss their design, implementation, and validation." http://bit.ly/LctrVt
"Computation is defining trait of biological systems and a broad framework that captures the complex adaptive nature of molecules, cells and organisms. Computation is also at the core of the genotype-phenotype mapping, since it provides a natural framework to define function in a self-consistent way. The study of existing biological systems (from signalling cas- cades to ant colonies or brains) as well as the evolution of synthetic in silico networks performing computations reveals a number of nontrivial patterns of organization, sometimes in clear conflict with standard view of engineering or optimiza- tion. In spite of our increasing knowledge, there is a lack of a theoretical framework where computation and its pos- sible forms is integrated within a general picture. Synthetic biology provides a new avenue where engineered molecular circuits can be implemented to perform non-standard com- putations. Here we review recent advances in the domain of multicellular synthetic computing and suggest a potential morphospace of computational systems including both stan- dard and non-standard approximations."
"UC Berkeley’s Understanding Science resource website makes excellent use of interactive schemata to reinforce the scientific method. The flow of information facilitates both global and sequential learning. The community analysis sphere (below) deals with quality control—one of two major collaboratory elements to use crowdsourcing. Students are encouraged to review the work of others, both past and present, and the mention of individual scientists reinforces the value of the collective. Further development considerations include smartphone adaptability and 3D visualization. ...."
"The goal of synthetic biology is to make the construction of novel biological systems into a practical and useful engineering discipline. The key is the development of an engineering methodology based on standardized and well-characterized interchangeable parts. Biological systems can be a basis for practical programmable materials, providing an engineering substrate with exquisite control over and response to the chemical world. The consequences of synthetic biology will be as great as the development of chemical engineering from alchemy, with enormous and as perhaps unimaginable implications for materials science and medicine. The range of applications for synthetic biology is vast, encompassing but not limited to: diagnostics, therapeutics, sensors, environmental remediation, energy production, and a host of other biomolecular and chemical manufacturing outputs. Synthetic biology can also help us gain valuable insight into fundamental biological principles and improve our quantitative understanding of the living world.
The mission of the Synthetic Biology Center at MIT is to develop and advance the engineering discipline for this emerging field.
The Center will be structured around three layered Thrusts:
Foundations Thrust, focused on creating an infrastructure of synthetic biology tools and capabilities. Systems Engineering Thrust, for engineering highly sophisticated biological systems rapidly, efficiently, and reliably. Grand Challenge Applications Thrust, for select areas where synthetic biology provides unique opportunities and capabilities." http://bit.ly/MzKXrI
Christopher Voigt "We are developing a basis by which cells can be programmed like robots to perform complex, coordinated tasks for pharmaceutical and industrial applications. We are engineering new sensors that give bacteria the senses of touch, sight, and smell. Genetic circuits - analogous to their electronic counterparts - are built to integrate the signals from the various sensors. Finally, the output of the gene circuits is used to control cellular processes. We are also developing theoretical tools from statistical mechanics and non-linear dynamics to understand how to combine genetic devices and predict their collective behavior."