SynBioFromLeukipposInstitute
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The sweet spot integrating neurobiology, robotics and synthetic biology - Joseph Ayers

"Prof. Joseph Ayers' presentation at the 4th New Phytologist Workshop (Synthetic Biology). More videos and information from the Workshop can be found at: http://www.newphytologist.org/synthetic/default.htm

Abstract:
The adaptive capabilities of underwater organisms result from layered exteroceptive reflexes responding to gravity, impediment, and hydrodynamic and optical flow. In combination with taxic responses to point sources of sound or chemicals, these reflexes allow reactive autonomy in the most challenging of environments. We are developing a new generation of lobster and lamprey-based robots that operate under control by synaptic networks rather than algorithms. The networks are based on the command neuron, coordinating neuron, central pattern generator architecture, code sensor input as labeled lines and activate shape memory alloy-based artificial muscle through a simple neuromuscular interface. In a separate project, we are developing an electronic nervous system to control the flight of RoboBee. In all systems, the behavioral set results from chaining sequences of exteroceptive reflexes released by sensory feedback from the environment. In parallel we are exploring principles of synthetic biology to develop biohybrid robots and sensors and actuators that can interface to electronic nervous systems. Cyberplasm combines an aVLSI electronic nervous system with engineered cellular sensors and engineered muscle that responds to light generated by oLEDs gated by neuron action potentials. In the ONR MURI we are integrating programmable bacteria with RoboLobster and RoboLamprey to enhance chemosensory capabilities."
http://bit.ly/NhwmiR

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Richard Ryan - Notes Toward a Biohacking Handbook in The Quantified Self

Filmed on February 22, 2012 at the NY Quantified Self Show&Tell #15 at Fahrenheit 212.
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Synthetic Biology Speed Debate

Synthetic Biology Speed Debate | SynBioFromLeukipposInstitute | Scoop.it
This summer we're planning to build artificial islands by taking on plastic pollution with genetically modified microorganisms. We're inviting you to voice your opinion at an evening of speed debating.

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Tuesday, August 7, 2012 from 7:00 PM to 10:00 PM London, United Kingdom http://bit.ly/OGukbg

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3D-Printed "Magic Arms"

Two-year-old Emma wanted to play with blocks, but a condition called arthrogryposis meant she couldn't move her arms. So researchers at a Delaware hospital 3...

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Novel technologies for the formation of 2-D and 3-D droplet interface bilayer networks

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Elani Y, Demello AJ, Niu X, Ces O.

"Droplet interface bilayer (DIB) networks have vast potential in the field of membrane biophysics, synthetic biology, and functional bio-electronics. However a technological bottleneck exists in network fabrication: existing methods are limited in terms of their automation, throughput, versatility, and ability to form well-defined 3-D networks. We have developed a series of novel and low-cost methodologies which address these limitations. The first involves building DIB networks around the contours of a microfluidic chip. The second uses flow rate and droplet size control to influence droplet packing geometries within a microfluidic chamber. The latter method enables the controlled formation of various 3-D network arrays consisting of thousands of interconnected symmetric and asymmetric lipid bilayers for the first time. Both approaches allow individual droplet position and composition to be controlled, paving the way for complex on-chip functional network synthesis."

http://1.usa.gov/N60Oya

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3ders.org - First open source powder-based 3D printer | 3D Printing news

3ders.org - First open source powder-based 3D printer | 3D Printing news | SynBioFromLeukipposInstitute | Scoop.it

The University of Twente, the Netherlands brought their Pwdr Model 0.1 to the open source community, an open source powder-based rapid prototyping machine.

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Modular Biological Complexity

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Christof Koch

"It has been argued that the technological capability to fully simulate the human brain on digital computers will exist within a decade. This is taken to imply that we will comprehend its functioning, eliminate all diseases, and “upload” ourselves to computers (1). Although such predictions excite the imagination, they are not based on a sound assessment of the complexity of living systems. Such systems are characterized by large numbers of highly heterogeneous components, be they genes, proteins, or cells. These components interact causally in myriad ways across a very large spectrum of space-time, from nanometers to meters and from microseconds to years. A complete understanding of these systems demands that a large fraction of these interactions be experimentally or computationally probed. This is very difficult."

http://bit.ly/RrY5x4

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Systems biology: A cell in a computer

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Mark Isalan

"The small genomes of some bacteria could provide the first complete understanding of a biological system. A new computer model brings this goal closer, by calculating every process in a dividing Mycoplasma cell...."

http://bit.ly/OMmShb

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Timelines, roadmaps, and tools: navigating the futures of synthetic biology | Oscillator, Scientific American Blog Network

Timelines, roadmaps, and tools: navigating the futures of synthetic biology | Oscillator, Scientific American Blog Network | SynBioFromLeukipposInstitute | Scoop.it

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Christina Agapakis

"Earlier this summer I got a travel fellowship from the SynBERC Student & Postdoc Association and Practices Thrust to attend the Six Parties Symposium on Synthetic Biology. The theme of the symposium was “Synthetic Biology for the Next Generation” and was jointly run by the National Academies of Science and Engineering from the US, the UK, and China. The fellows were asked to write a short perspective about the symposium and how we see the field advancing in the future. I’m posting my essay below, and you can see the perspectives of the other fellows here.

What is the future of synthetic biology? How do we get there? The recent Six Parties Symposium on Synthetic Biology brought together scientists, engineers, policy makers, and social scientists from the US, the UK, and China to think about the future. Panels focused on the grand challenges that we face, the potential for synthetic biology to address some of these challenges, and the tools—technical and otherwise—necessary to see this potential through to real world applications...."

http://bit.ly/Mmpl3K

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Episode 30: Dr. Jordan Miller on the use of 3D printing to make blood vessels | The Weekly Weinersmith

Podcast: Today Zach and Kelly talk to Dr. Jordan Miller, a postdoctoral student in Dr. Christopher Chen’s Tissue Microfabrication Lab at the University of Pennsylvania, about his recent breakthrough using 3D printing to create blood vessels.

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James J. Collins, Ph.D. » Biomedical Engineering | Boston University

James J. Collins, Ph.D. » Biomedical Engineering | Boston University | SynBioFromLeukipposInstitute | Scoop.it

Congratulations to Jim Collins, BU Innovator of the Year & father of synthetic biology http://t.co/5gaFLnDt...

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Amazon.com: Synthetic Gene Networks: Methods and Protocols (Methods in Molecular Biology) (9781617794117): Wilfried Weber, Martin Fussenegger: Books

Synthetic Gene Networks: Methods and Protocols (Methods in Molecular Biology) [Wilfried Weber, Martin Fussenegger] on Amazon.com. *FREE* super saver shipping on qualifying offers.
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Futurity.org – Really, really small robots that swim

Futurity.org – Really, really small robots that swim | SynBioFromLeukipposInstitute | Scoop.it

- Maybe an inspiration for #syntheticbiology

http://bit.ly/Nhv8Ei

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Synthetic Biology and Gene Synthesis: Malaria vaccine comes closer to reality

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19 new transcription factors break bottleneck that limited synthetic biology complexity

comment on: Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK and Collins JJ. A synthetic biology framework for programming eukaryotic transcription functions. Cell 150: 647-658 (2012).

PDF can be found here: http://www.bu.edu/abl/files/cell_khalil.pdf
http://bit.ly/MmoVo1

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"DNA as a Future Component of Electronics"

Our electronic devices are getting smaller and smaller while doing more and more, so much so that we will soon reach the practical limit of current materials. The electronics of tomorrow require alternatives, such as nanowires made of DNA that can serve as conductive paths and nanotransistors for miniature circuits. In the journal Angewandte Chemie, German scientists have now described a new method for the production of stable, conducting DNA nanowires.

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Wisdom of crowds for robust gene network inference

 http://bit.ly/Oy5DRb

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Researchers build a toolbox for synthetic biology - MIT News Office

Researchers build a toolbox for synthetic biology - MIT News Office | SynBioFromLeukipposInstitute | Scoop.it

Engineers design new proteins that can help control novel genetic circuits in cells.

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Cell - A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

Important paper!

*A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions*

by
Ahmad S. Khalil, Timothy K. Lu, Caleb J. Bashor, Cherie L. Ramirez, Nora C. Pyenson, J. Keith Joung, James J. Collins

*Highlights*
- Zinc fingers can be used to wire orthogonal connections in yeast synthetic circuits
- Zinc finger TF design permits adjustable component properties for modulating outputs
- Protein-protein interactions can be used to engineer cooperativity in zinc finger TFs
- TF component properties can be combinatorially adjusted to reshape signal integration

*Summary*
Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks."

http://bit.ly/MBzzZD

Comment
*Researchers expand synthetic biology's toolkit: New method could enable reprogramming of mammalian cells*

"Through the assembly of genetic components into "circuits" that perform logical operations in living cells, synthetic biologists aim to artificially empower cells to solve critical problems in medicine, energy and the environment. To succeed, however, they'll need far more reliable genetic components than the small number of "off-the-shelf" bacterial parts now available.
Now a new method developed by Boston University biomedical engineers Ahmad S. Khalil and James J. Collins -- and collaborators at Harvard Medical School, Massachusetts General Hospital and MIT -- could significantly increase the number of genetic components in synthetic biologists' toolkit and, as a result, the size and complexity of the genetic circuits they can build. The development could dramatically enhance their efforts not only to understand how biological organisms behave and develop, but also to reprogram them for a variety of practical applications. Described in the August 2 online edition of Cell, the method offers a new paradigm for constructing and analyzing genetic circuits in eukaryotes -- or organisms whose cells contain nuclei, which include everything from yeasts to humans. Instead of constructing these circuits with off-the-shelf parts from bacteria and porting them into eukaryotes, as most synthetic biologists do, Khalil and his collaborators have engineered these circuits using modular, functional parts from the eukaryotes themselves...."
http://bit.ly/Np2iiF

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PLoS ONE: Design and Construction of “Synthetic Species”

PLoS ONE: Design and Construction of “Synthetic Species” | SynBioFromLeukipposInstitute | Scoop.it

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Moreno E.

"Synthetic biology is an area of biological research that combines science and engineering. Here, I merge the principles of synthetic biology and regulatory evolution to create a new species with a minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic population arises with small eyes and a different venation pattern that fulfils the criteria of a new species according to Mayr's Biological Species Concept. The population described here is the first transgenic organism that cannot hybridize with the original wild type population but remains fertile when crossed with other identical transgenic animals. I therefore propose the term "synthetic species" to distinguish it from "natural species", not only because it has been created by genetic manipulation, but also because it may never be able to survive outside the laboratory environment. The use of genetic engineering to design artificial species barriers could help us understand natural speciation and may have practical applications. For instance, the transition from transgenic organisms towards synthetic species could constitute a safety mechanism to avoid the hybridization of genetically modified animals with wild type populations, preserving biodiversity...."

http://bit.ly/M4HZM7

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DNA2.0 Sponsors Singularity University Launchpad | Virtual-Strategy Magazine

DNA2.0 Sponsors Singularity University Launchpad | Virtual-Strategy Magazine | SynBioFromLeukipposInstitute | Scoop.it

Accelerator to Launch Synthetic Biology Startups | Virtual Strategy Magazine is an online publication devoted entirely to virtualization technologies.

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