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Frontiers | Nature Publishing Group and Frontiers form alliance to further open science

Frontiers | Nature Publishing Group and Frontiers form alliance to further open science | SynBioFromLeukipposInstitute | Scoop.it
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*Nature Publishing Group and Frontiers form alliance to further open science*

"Emerging publisher Frontiers is joining Nature Publishing Group (NPG) in a strategic alliance to advance the global open science movement.

NPG, publisher of Nature, today announces a majority investment in the Swiss-based open access (OA) publisher Frontiers. NPG and Frontiers will work together to empower researchers to change the way science is communicated, through open access publication and open science tools. Frontiers, led by CEO and neuroscientist Kamila Markram, will continue to operate with its own platform, brands, and policies. Founded by scientists from École Polytechnique Fédérale de Lausanne (EPFL) in 2007, Frontiers is one of the fastest growing open access publishers, more than doubling articles published year on year. Frontiers now has a portfolio of open access journals in 14 fields of science and medicine, and published over 5,000 OA articles in 2012. Working with NPG, the journal series “Frontiers in” will significantly expand in 2013-2014. Currently, sixty-three journals published by NPG offer open access options or are open access and NPG published over 2000 open access articles in 2012. Bilateral links between nature.com and frontiersin.org will ensure that open access papers are visible on both sites. Frontiers and NPG will also be working together on innovations in open science tools, networking, and publication processes."

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US science to be open to all

US science to be open to all | SynBioFromLeukipposInstitute | Scoop.it
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*US science to be open to all*

by
Richard Van Noorden

"The rumours have been buzzing around Capitol Hill since before last year’s election, and last week, supporters of open-access publication in the United States got most of what they wanted. The White House declared that government-funded research would be made free for all to read, rather than kept behind paywalls. However, those hoping that the government would require papers to be free from the time of publication were disappointed.
In a 22 February memo, John Holdren, director of the White House’s Office of Science and Technology Policy (OSTP), gave federal agencies until 22 August to produce plans for making the data and papers from the research they fund more accessible to the public. The move, he says, would “accelerate scientific breakthroughs and innovation” and boost economic growth. Agencies should aim to make research papers free by 12 months after publication — a concession to publishers, who say that a year’s delay is needed to maintain their revenue from subscriptions....."

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Gordon Research Conferences - 2013 Program - Synthetic Biology

Gordon Research Conferences - 2013 Program - Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
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June 9-14, 2013

Mount Snow Resort  VT 

""Synthetic biology" is an emerging field that is very rapidly gaining currency within the scientific community and society at large. Although in itself not an entirely new concept and having been referred in literature for the first time as early as 1912, the advancements in molecular biology, high-throughput "omics" analysis and on computer and engineering sciences, only now begin to enable a serious, systematic approach to the development and forward engineering of biological circuits and cellular capabilities that may be ultimately translated into processes or products. The core of this concept is that, by drawing on knowledge developed in biology, chemistry, robotics and adapting engineering design and production principles stemming from Information Technologies, it is possible now to set off the creation of artificial (i.e. "synthetic") and hybrid systems using biological engineering design principles with unprecedented power and efficiency. The pursuit of synthetic biology is both the design and fabrication of biological components and systems that do not exist in the natural world as well as the re-design and fabrication of already existing biological systems. Eventually, it is envisioned to build up from scratch - bottom-up approaches - cellular components, compartments and even cells to create living devices and use them either as molecular-scale factories, to detect chemical weapons, clean up pollutants, make simple computations, diagnose disease, deliver vaccines, produce water for water or sunlight, or to create new, hybrid materials. Other on-going efforts - top-down approaches - with ultimately the very same goals focus on simplifying and genetically reprogramming existing cells with simple genomes. This vision has thus tremendous scientific, technological and economical impacts. However, regardless of a number of recent advances in this regard of the extraordinary possibilities, Synthetic Biology is as yet in its infancy, with knowledge being is highly scattered and scarce, and facing many serious scientific, technological and societal challenges ahead. This conference will provide an in-depth discussion forum among practitioners of the various fields underlying Synthetic Biology. It aims to pin-point the challenges, realistically assess the potential and pitfalls and to lay the basis for future developments and consolidation of the field towards fulfilling the envisaged - and ambitious - goals. Because of the lack of a common language among the scientists from the many different fields involved, longer meetings with large blocks of time dedicated to discussions, rather than series of presentations held at 'traditional' conferences, are favored for establishing such a forum. In addition to bringing together a collection of investigators who are at the forefront of their field, this conference will provide opportunities for junior scientists and graduate students to present their work in poster format and exchange ideas with leaders in the field. The collegial atmosphere of this conference, with programmed discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings, provides an avenue for scientists from different disciplines to brainstorm and promotes cross-disciplinary collaborations in the various research areas represented."

http://bit.ly/15UaqUI
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JAK/STAT signalling – an executable model assembled from molecule-centred modules demonstrating a module

JAK/STAT signalling – an executable model assembled from molecule-centred modules demonstrating a module | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Blätke MA, Dittrich A, Rohr C, Heiner M, Schaper F, Marwan W.

"Mathematical models of molecular networks regulating biological processes in cells or organisms are most frequently designed as sets of ordinary differential equations. Various modularisation methods have been applied to reduce the complexity of models, to analyse their structural properties, to separate biological processes, or to reuse model parts. Taking the JAK/STAT signalling pathway with the extensive combinatorial cross-talk of its components as a case study, we make a natural approach to modularisation by creating one module for each biomolecule. Each module consists of a Petri net and associated metadata and is organised in a database publically accessible through a web interface (). The Petri net describes the reaction mechanism of a given biomolecule and its functional interactions with other components including relevant conformational states. The database is designed to support the curation, documentation, version control, and update of individual modules, and to assist the user in automatically composing complex models from modules. Biomolecule centred modules, associated metadata, and database support together allow the automatic creation of models by considering differential gene expression in given cell types or under certain physiological conditions or states of disease. Modularity also facilitates exploring the consequences of alternative molecular mechanisms by comparative simulation of automatically created models even for users without mathematical skills. Models may be selectively executed as an ODE system, stochastic, or qualitative models or hybrid and exported in the SBML format. The fully automated generation of models of redesigned networks by metadata-guided modification of modules representing biomolecules with mutated function or specificity is proposed."

http://bit.ly/ZEynev

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Reading the Human Genome

Reading the Human Genome | SynBioFromLeukipposInstitute | Scoop.it
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"Lab researchers have achieved a major advance in understanding how genetic information is transcribed from DNA to RNA by providing the first step-by-step look at the biomolecular machinery that reads the human genome." Berkeley Lab on G+

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11 Emerging Scientific Fields That Everyone Should Know About

11 Emerging Scientific Fields That Everyone Should Know About | SynBioFromLeukipposInstitute | Scoop.it
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6. *Synthetic Biology*

by
George Dvorsky

"This is the big one, and it's the emerging world-changing scientific discipline that many of us are already familiar with.

 Synthetic biology is the design and construction of new biological parts, devices and systems. It also involves the redesign of existing biological systems for any number of useful purposes. Craig Venter, a leader in this field, shook the biology community in 2008 by announcing that he had manufactured the entire genome of a bacterium by piecing together its chemical components. Two years later his team created "synthetic life" — DNA created digitally, and then printed and inserted into a living bacterium. And last year, synbio scientists created the first complete computational model of an actual organism. Looking ahead, synthetic biologists will sequence and analyze genomes to create custom-designed bootable organisms and biological robots that can produce chemicals from scratch, like biofuels. There's also the potential for pollution devouring cyborg bacteria, and the downloading and printing of recently updated vaccines during a pandemic. The possibilities are almost endless."


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Synthetic biology: A circuit to remember

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Review by

Louisa Flintoft 

"One challenge of synthetic biology is to assemble genetic circuits efficiently that can carry out complex logic processing functions. Another is to combine processing and memory in a single device. ...."

http://bit.ly/ValnOW

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Realizing the promise of biotechnology: Infrastructural-icons in synthetic biology

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Realizing the promise of biotechnology: Infrastructural-icons in synthetic biology

by

Adrian MackenzieThat part of synthetic biology concerned with engineering promises to make good on the potential of biotechnology to address problems of food, energy, health and environment. How do the synthetic biologistsrealize the promise of biology as technology? In analysing realization of promise in synthetic biology, I suggest that we should pay close attention to different rates of realization. Synthetic biologists have consistently focused on making particular kinds of devices such as oscillators, timers and clock that both address problems of control over rates, and that themselves resemble and link to other rate-controlling mechanisms such as the many clocks found in large technical systems. They have also, again in those parts of the field concerned with engineering, expended much effort in developing infrastructures, techniques, methods and systems for rapid assembly of parts and components. The clocks and assembly methods function as both as iconic signs and as infrastructural elements or practices that will realise the promise of biotechnology. The field has not only produced what we might call infrastructural-icons for biology as technology, but almost defined itself in terms of a promise of realisation. In analysing how synthetic biology or any other technological endeavour shows how things could be (icons), and makes operational connections between things (infrastructures), the main goal is not to situate field in social or economic contexts. Rather, it is to open a way to see how synthetic biologists and others -- philosophers, social scientists, historians, artists, designers, scientists engineers, as students or consumers–manage to address the gaps that open up as the promise of biology as technology is realized at different rates.
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Understanding and Exploiting Feedback in Synthetic Biology

Understanding and Exploiting Feedback in Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
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*Understanding and Exploiting Feedback in Synthetic Biology* 

by
Taliman Afroz, Chase L. Beisel

"Synthetic biology employs traditional engineering concepts in the construction of cells and organisms. One of the most fundamental concepts is feedback, where the activity of a system is influenced by its output. Feedback can imbue the system with a range of desirable properties such as reducing the rise time or exhibiting an ultrasensitive response. Feedback is also commonly found in nature, further supporting the incorporation of feedback into synthetic biological systems. In this review, we discuss the common attributes of negative and positive feedback loops in gene regulatory networks, whether alone or in combination, and describe recent applications of feedback in metabolic engineering, population control, and the development of advanced biosensors. The examples principally come from synthetic systems in the bacterium Escherichia coli and in the budding yeast Saccharomyces cerevisiae, the two major workhorses of synthetic biology. Through this review, we argue that biological feedback represents a powerful yet underutilized tool that can advance the construction of biological systems."
http://bit.ly/YyiFP5

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For Autodesk, a Step Into a Nanoscale World

For Autodesk, a Step Into a Nanoscale World | SynBioFromLeukipposInstitute | Scoop.it
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By JOHN MARKOFF

"Autodesk, a quirky software start-up in Marin County, north of San Francisco, rose to prominence in the early 1980s because of AutoCAD, its computer-aided design program that was intended for use on personal computers. Over the next decade, AutoCAD became the standard design tool for architects and engineers.

 This week at the TED conference in Long Beach, Calif., the company will take the first public step toward translating its computer design approach, which has since spilled over from Hollywood to the Maker movement, into the emerging nanoscale world of synthetic biology and materials. For the last two years, a small group of software engineers and molecular biologists have been developing a software system for designing at the molecular level at the company’s research laboratory in downtown San Francisco. At the TED conference, Autodesk will introduce “Project Cyborg,” a Web-based software platform for delivering a range of services like molecular modeling and simulation. The company has quietly begun working with a small group of molecular biologists in the last year. It has not announced when it will commercialize the technology, but it envisions that scientists, engineers and even students and “citizen scientists” will soon be able to use the system on individual projects. There are still many open questions that nanotechnology needs to surmount, ranging from viability to safety. Autodesk executives and the designers of Project Cyborg believe, however, that they can recreate the thriving commercial ecosystems that the company has now evolved in engineering design at a Lilliputian scale. They foresee nanorobots that will be able to attack cancers and other diseases and a new world of molecular materials, as well as a visualization system for an entire universe beyond the range of the unaided human eye. “People are only now being introduced to the fact that this form of science is in fact design, and it has the same paradigms and patterns as designing a factory or designing a car, with different nouns and verbs,” said Jeff Kowalski, Autodesk’s chief technology officer. “That’s our objective – to understand how to take 30 years of technology to transform how design is done in the inert world and empower those who are designing in the living world.” The company will introduce its new nanodesign software vision in two talks to be given by scientists who have been working with the Autodesk research lab. One will be delivered by Skylar Tibbits, an M.I.T. architect and computer scientist who is to discuss biomolecular self-assembly on Tuesday. Jessica Green, a University of Oregon ecologist, is to speak on Thursday about design at the molecular scale. Autodesk took its first commercial step into biological design last year with a partnership with Organovo Holdings, a San Diego start-up that aims to manufacture human tissues and organs. Autodesk software will be used to control a so-called bioprinter being developed by Organovo. It will initially have pharmaceutical testing applications. Autodesk is not alone in seeking to build nanoscale design tools, nor the first to try to commercialize molecular design.Thomas Knight, an M.I.T electrical engineer, introduced the concept of biobricks in 2003. The idea has been to create a library of standard biological parts derived from specific DNA sequences. Ideally they would share a common “interface,” making it possible to use them to construct new biological systems. A striking example of the potential of molecular design was announced in February 2012 by the Wyss Institute for Biologically Inspired Engineering at Harvard. Two scientists at the institute designed a robotic device from DNA that was intended to seek out specific cells and deliver anticancer therapeutics with remarkable precision. The nanoscale robot is shaped like a clamshell and designed to open when it reaches its target, releasing a specific molecule. The Autodesk researchers acknowledge they are far from being able to sell commercially robust engineering tools for the nano world. “Right now we don’t even have the notion of digital prototyping in any mature way in biology,” said Carlos Olguin, head of the Autodesk Bio/Nano/Programmable Matter Group. “People really do all of this by trial and error.” But the company is placing a significant bet that that will not always be the case. If Autodesk is right, it will be a tremendous vindication for K. Eric Drexler, an M.I.T.-trained engineer who in the 1970s began forecasting the emergence of a world engineered by nanoscale machines...." 


http://nyti.ms/15eRpuS

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Can You Feel Me Now? The Sensational Rise of Haptic Interfaces

Can You Feel Me Now? The Sensational Rise of Haptic Interfaces | SynBioFromLeukipposInstitute | Scoop.it
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*Can You Feel Me Now*? *The Sensational Rise of Haptic Interfaces*

by
BY NATHAN HURST

"Your first experience with haptics was probably your phone vibrating in your pocket. Or maybe it was the rumble pack on your N64 controller. But whatever the case, you probably didn’t know it as a haptic interface.

Haptics is to touch the way optics is to sight. It's a user interface that circumvents the cluttered inputs of sight and sound, and it's appearing in an increasing number of objects we interact with daily. Vibration is just the beginning.

......

Unlike the feedback-based, interactive vibrations from Surround Haptics, Cadillac, and RISR, the vibrating insoles Jim Collins is working on don't impart information to the user — at least not consciously. Collins — a bioengineer at Boston University and the Wyss Institute at Harvard — found that random vibrations introduced in the feet of participants helped them sway less, or keep their balance better. "It's not a feedback-based system," says Collins, who has been studying the effect for almost 20 years. "What we're doing is introducing a bias signal, to their sensory neurons, which is basically serving as a pedestal or booster for the signals they normally would detect." That is, small vibrations in the feet cause heightened nerve sensitivity, and thus users — including stroke victims, diabetics, the elderly, but also the young and fit — detect signals they would normally miss. The insoles aren't on the market yet, but Collins envisions additional future applications in sports equipment, like ski boots and golf shoes...."


http://bit.ly/YpWVH7

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Reprogramming human fibroblasts to pluripotency using modified mRNA

Reprogramming human fibroblasts to pluripotency using modified mRNA | SynBioFromLeukipposInstitute | Scoop.it
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by
Pankaj K Mandal& Derrick J Rossi

"Induced pluripotent stem (iPS) cells hold the potential to revolutionize regenerative medicine through their capacity to generate cells of diverse lineages for future patient-specific cell-based therapies. To facilitate the transition of iPS cells to clinical practice, a variety of technologies have been developed for transgene-free pluripotency reprogramming. We recently reported efficient iPS cell generation from human fibroblasts using synthetic modified mRNAs. Here we describe a stepwise protocol for the generation of modified mRNA-derived iPS cells from primary human fibroblasts, focusing on the critical parameters including medium choice, quality control, and optimization steps needed for synthesizing modified mRNAs encoding reprogramming factors and introducing these into cells over the course of 2-3 weeks to ensure successful reprogramming. The protocol described herein is for reprogramming of human fibroblasts to pluripotency; however, the properties of modified mRNA make it a powerful platform for protein expression, which has broad applicability in directed differentiation, cell fate specification and therapeutic applications."
http://bit.ly/Wb3d0X

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Biotechdaily - Automated Liquid Handling Platforms Boost Productivity of Synthetic Biology Researchers

Biotechdaily - Automated Liquid Handling Platforms Boost Productivity of Synthetic Biology Researchers | SynBioFromLeukipposInstitute | Scoop.it
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By BiotechDaily International staff writers

"Use of automated robotic liquid handling workstations is giving a dramatic push to development efforts in the exciting new field of synthetic biology.

 Synthetic biology is the design and construction of new biological entities such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. Synthetic biology builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. "



http://bit.ly/VUWKaA

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Why Synthetic Biology Is the Field of the Future

Why Synthetic Biology Is the Field of the Future | SynBioFromLeukipposInstitute | Scoop.it
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by
Jay 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.

 Synthetic biology is a relatively young field, begun only about ten years ago. But in that time, we have made some astonishing progress. This is due, in part, to the enormous improvements in our ability to synthesize and sequence DNA. But we’ve also gained a much greater understanding of how the various parts of the genome interact. We now can reliably combine various genetic pieces to produce a range of consumer products, from biofuels to cosmetics....."

http://to.pbs.org/Z0UEAQ

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TEDxDeExtinction – Revive & Restore

TEDxDeExtinction – Revive & Restore | SynBioFromLeukipposInstitute | Scoop.it
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In this decade some extinct species will begin to come back.

Rapid advances in molecular biology are converging with new perspectives in conservation biology to create a new field called “de-extinction.”  Now is the time to begin public discussion of how de-extinction projects can best proceed responsibly. On Friday, March 15, National Geographic is hosting the first-ever public exploration of the subject of reviving extinct species at TEDxDeExtinction, a daylong event at Grosvenor Auditorium in Washington, DC. Speakers include: Chris Anderson, Michael Archer, David Burney, George Church, David Ehrenfeld, John Fahey, Alberto Fernández-Arias, Hank Greely, Susan Haig, Kate Jones, Henri Kerkdijk-Otten, Isabella Kirkland, Robert Lanza, Michael Mace, Michael McGrew, Ben Novak, Hendrik Poinar, William Powell, Kent Redford, Oliver Ryder, Joel Sartore, Beth Shapiro, James Tate, Stanley Temple, Carl Zimmer
http://bit.ly/15UdqR7

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The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly

The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Blätke MA, Dittrich A, Rohr C, Heiner M, Schaper F, Marwan W.

"Mathematical models of molecular networks regulating biological processes in cells or organisms are most frequently designed as sets of ordinary differential equations. Various modularisation methods have been applied to reduce the complexity of models, to analyse their structural properties, to separate biological processes, or to reuse model parts. Taking the JAK/STAT signalling pathway with the extensive combinatorial cross-talk of its components as a case study, we make a natural approach to modularisation by creating one module for each biomolecule. Each module consists of a Petri net and associated metadata and is organised in a database publically accessible through a web interface (). The Petri net describes the reaction mechanism of a given biomolecule and its functional interactions with other components including relevant conformational states. The database is designed to support the curation, documentation, version control, and update of individual modules, and to assist the user in automatically composing complex models from modules. Biomolecule centred modules, associated metadata, and database support together allow the automatic creation of models by considering differential gene expression in given cell types or under certain physiological conditions or states of disease. Modularity also facilitates exploring the consequences of alternative molecular mechanisms by comparative simulation of automatically created models even for users without mathematical skills. Models may be selectively executed as an ODE system, stochastic, or qualitative models or hybrid and exported in the SBML format. The fully automated generation of models of redesigned networks by metadata-guided modification of modules representing biomolecules with mutated function or specificity is proposed."

http://bit.ly/Z3Kgtp

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Physical Constraints on Biological Integral Control Design for Homeostasis and Sensory Adaptation

Physical Constraints on Biological Integral Control Design for Homeostasis and Sensory Adaptation | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

 by
Ang J, McMillen DR.

"Synthetic biology includes an effort to use design-based approaches to create novel controllers, biological systems aimed at regulating the output of other biological processes. The design of such controllers can be guided by results from control theory, including the strategy of integral feedback control, which is central to regulation, sensory adaptation, and long-term robustness. Realization of integral control in a synthetic network is an attractive prospect, but the nature of biochemical networks can make the implementation of even basic control structures challenging. Here we present a study of the general challenges and important constraints that will arise in efforts to engineer biological integral feedback controllers or to analyze existing natural systems. Constraints arise from the need to identify target output values that the combined process-plus-controller system can reach, and to ensure that the controller implements a good approximation of integral feedback control. These constraints depend on mild assumptions about the shape of input-output relationships in the biological components, and thus will apply to a variety of biochemical systems. We summarize our results as a set of variable constraints intended to provide guidance for the design or analysis of a working biological integral feedback controller."

http://bit.ly/YK4sTi

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Bacteriophone: Microbial Wallpapers

Bacteriophone: Microbial Wallpapers | SynBioFromLeukipposInstitute | Scoop.it
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by
Christina Agapakis |

"I take a lot of photos of bacteria on my phone, and sometimes I use those pictures as my phone’s wallpaper. These photos are meta-phone bacteria wallpapers: photographs of bacteria that I collected off the surface of my phone (h/t to Nick for the microbial inspiration). To sample the phone’s microbiome I simply placed it on a plate of fresh LB agar and incubated for two weeks at 30 degrees Celsius. Click for higher resolution...."

http://bit.ly/15R9cJX

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A Unifying Mathematical Framework for Genetic Robustness, Environmenta

A Unifying Mathematical Framework for Genetic Robustness, Environmenta | SynBioFromLeukipposInstitute | Scoop.it
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by
Bor-Sen Chen and Ying-Po Lin

"Robust stabilization and environmental disturbance attenuation are ubiquitous systematic properties that are observed in biological systems at many different levels. The underlying principles for robust stabilization and environmental disturbance attenu- ation are universal to both complex biological systems and sophisticated engineering systems. In many biological networks, network robustness should be large enough to confer: intrinsic robustness for tolerating intrinsic parameter fluctuations; genetic robustness for buffering genetic variations; and environmental robustness for resisting environmental disturbances. Network robustness is needed so phenotype stability of biological network can be maintained, guaranteeing phenotype robustness. Synthetic biology is foreseen to have important applications in biotechnology and medicine; it is expected to contribute significantly to a better understanding of functioning of complex biological systems. This paper presents a unifying mathematical framework for investigating the principles of both robust stabilization and environmental disturbance attenuation for synthetic gene networks in synthetic biology. Further, from the unifying mathematical framework, we found that the phenotype robustness criterion for synthetic gene networks is the following: if intrinsic robustness + genetic robustness + environmental robustness  network robustness, then the phenotype robustness can be maintained in spite of intrinsic parameter fluctuations, genetic variations, and environmental disturbances. Therefore, the trade-offs between intrinsic robustness, genetic robustness, environmental robustness, and network robustness in synthetic biology can also be investigated through corresponding phenotype robustness criteria from the systematic point of view. Finally, a robust synthetic design that involves network evolution algorithms with desired behavior under intrinsic parameter fluctuations, genetic variations, and environmental disturbances, is also proposed, together with a simulation example."

http://bit.ly/13lrF1L

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Synthetic Biology as Understanding, Control, Construction, and Creation? Techno-Epistemic and Socio-Political Implications of Different Stances in Talking and Doing Technoscience

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Synthetic Biology as Understanding, Control, Construction, andCreation? Techno-Epistemic and Socio-Political Implications of Different Stances in Talking and Doing Technoscience

by

Karen Kastenhofer,
Systems biology and synthetic biology are said to represent ‘two sides of the same coin,’ with systems biology focussing on understanding and synthetic biology on construction. This notion is based on the implicit assumption that understanding and construction (or science and engineering) are, in themselves, ‘two sides of the same coin.’ Moreover, synthetic biology has been framed as an approach that encompasses understanding as well as control, construction, and creation. In the’ talking’ and ‘doing’ of synthetic biology, one can discern a contemplative, interventionist, constructionist, and creationist stance. It is the aim of this paper to illustrate these stances in detail and to discuss more generally their techno-epistemic and socio-political implications.
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Modeling the effect of cell division on genetic oscillators

Modeling the effect of cell division on genetic oscillators | SynBioFromLeukipposInstitute | Scoop.it
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*Modeling the effect of cell division on genetic oscillators*

by
Gonze D.

"Many genetic oscillators (circadian clocks, synthetic oscillators) continue to oscillate accross the cell division cycle. Since cell divisions create discontinuities in the dynamics of genetic oscillators the question about the resilience of oscillations and the factors that contribute to the robustness of the oscillations may be raised. We study here, through stochastic simulations, the effect of the cell division cycle on genetic oscillations using the Repressilator - a genetic oscillator developed in the context of synthetic biology. We consider intrinsic noise (molecular noise due to the limited number of molecules) and extrinsic noise (variability in the cell division time and in the partition of the molecules into daughter cells, cell-cell variability in kinetic parameters, etc). Our numerical simulations show that, although noisy, oscillations are quite resilient to cell division and that cell-cell heterogeneity may be the main source of variability observed experimentally. Finally, similar simulations performed with another model, the Goodwin model, show that oscillations may be entrained and synchronized by cell division. This highlights the influence of the clock architecture on the robustness of genetic oscillations. Our approach provides a general framework to study the effect of cell division on dynamical systems and several possible extensions are described."

http://bit.ly/ZGXAsy

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Reading and writing omes

Reading and writing omes | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

*Reading and writing ones* 

by
Church GM.

"‘Systems Technologies' are increasingly potent drivers of biological research. Molecular Systems Biology will be illustrating this evolution with a new Reviews Series highlighting key technologies in systems medicine, genome-scale, computational, quantitative and synthetic biology. The series is launched with a review from the Snyder group on reading human omes (Soon et al, 2013) and a companion review on writing genomes from Harvard's Wyss Institute (Esvelt and Wang, 2013)."

http://1.usa.gov/15eSz9H

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4th International Conference on Biomolecular Engineering Tackles New Challenges with Synthetic Biology

4th International Conference on Biomolecular Engineering Tackles New Challenges with Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:
Keynote Presentation: George Church: Microbial and Human Multiplex Genome 
Synthetic Biology: Chris Voighttp://bit.ly/11SUaV0 see alsohttp://bit.ly/XBLVoN
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Lipid Nanotechnology

Lipid Nanotechnology | SynBioFromLeukipposInstitute | Scoop.it
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*Lipid Nanotechnology*

by
Mashaghi S, Jadidi T, Koenderink G, Mashaghi A.

"Nanotechnology is a multidisciplinary field that covers a vast and diverse array of devices and machines derived from engineering, physics, materials science, chemistry and biology. These devices have found applications in biomedical sciences, such as targeted drug delivery, bio-imaging, sensing and diagnosis of pathologies at early stages. In these applications, nano-devices typically interface with the plasma membrane of cells. On the other hand, naturally occurring nanostructures in biology have been a source of inspiration for new nanotechnological designs and hybrid nanostructures made of biological and non-biological, organic and inorganic building blocks. Lipids, with their amphiphilicity, diversity of head and tail chemistry, and antifouling properties that block nonspecific binding to lipid-coated surfaces, provide a powerful toolbox for nanotechnology. This review discusses the progress in the emerging field of lipid nanotechnology.

..."

http://bit.ly/XTppH7
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Interview: Jason Silva - Synthetic Biology

Gerd Moe-Behrens's insight:

Interview: 
*Jason Silva* - *Synthetic Biology* 


http://bit.ly/13AxP9Y

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