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Synthetic biology may change everything: Jeff Kowalski, CTO, Autodesk

Synthetic biology may change everything: Jeff Kowalski, CTO, Autodesk | SynBioFromLeukipposInstitute | Scoop.it
Synthetic biology is literally re-programming cells to do fundamentally different things in the way they were naturally created.
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by
Jarshad NK

"As chief technology officer of Autodesk, Jeff Kowalski, 47, is responsible for shaping the US-based design software maker's long-term technology vision and has a ringside view to some cutting-edge technology in the works, including 4D printing. In a telephonic interview to ET's Jarshad NK, Kowalski talks about the pitfalls of predicting the future, the blurring of lines between the living and material world and why 3D printing, an area in which Autodesk is one of the pioneers, is not likely to replace traditional manufacturing. Excerpts:

It is said that the easiest way to be proved foolish is to predict the future. As someone responsible for doing that at Autodesk, how do you avoid such a pitfall? 
The thing is we (Autodesk) keep our awareness pretty open out into the future. We have a process that we use inside the company and specifically by forward-looking groups-we are out in contact with lots of other individuals outside of the company to look at trends and patterns. The interesting thing is we got a relatively good accuracy rate of things that we can predict, but it will be really hard to say precisely when and with what magnitude they will occur. 
What are the criteria on which you decide on what innovation to back and what to let go? 
There is a very nice Venn diagram that a friend showed me just around the time I began my role as CTO. I use that as a sort of guide. The diagram had three circles and they were feasibility, desirability and viability. Feasibility is, is it reasonably possible to make the thing? Is it technically achievable? Desirability is, is anyone actually going to want it once you have made it? And then there is viability, if we can build it and people want it, can it actually be a business or is it that will never really create a return. All three of these circles need to be satisfied. 
What are the innovations that excite you the most right now? 
I have a lot of choices, but if I had to pick one that I think is really provocative-and it's in the really early stages-I have to say that it is design for synthetic biology. And I think so because it touches everything. It has the potential for changing everything from agriculture to medicine. It is literally re-programming cells to do fundamentally different things in the way they were naturally created. 
...."

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Dynamical Systems Theory & Philosophy Study Group - Community - Google+

Dynamical Systems Theory & Philosophy Study Group - Community - Google+ | SynBioFromLeukipposInstitute | Scoop.it
This group is aimed at philosophers (and other interested non-specialists) who want to learn more about the mathematics and science of dynamical systems, with a particular eye toward applying the concepts from that field to contemporary problems in...
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Synthetic Biology Entrepreneurs in London

SynBio Entrepreneurs Dinner

Thursday, Jul 14, 2016, 8:00 PM

Kinkao
176 Brick Lane, London, E1 6RU London, GB

9 Biological Engineers Attending

Hello everyone, It's the 1st  Entrepreneurs Meetup in London is sorted - people from all different backgrounds are welcome to join and share perspectives and experiences on Synthetic Biology. New to the field? This time we're at Kinkao - great Thai food! Liverpool St, Whitechapel and Shoreditch High St are the closest stations. Looking forward to m...

Check out this Meetup →

Hello everyone,
It's the 1st  Entrepreneurs Meetup in London is sorted - people from all different backgrounds are welcome to join and share perspectives and experiences on Synthetic Biology.
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Next generation of viral vectors, called AAV 3.0, for gene therapies and genome editing

Next generation of viral vectors, called AAV 3.0, for gene therapies and genome editing | SynBioFromLeukipposInstitute | Scoop.it
Next generation of viral vectors, called AAV 3.0, for gene therapies and genome editing
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Transcriptional Interference in convergent promoters as a means for Tunable Gene Expression

An important goal of synthetic biology involves the extension and standardization of novel biological elements for applications in medicine and biotechnology. Transcriptional interference, occurring in sets of convergent promoters, offers a promising mechanism for building elements for the design of tunable gene regulation. Here, we investigate the transcriptional interference mechanisms of antisense roadblock and RNA polymerase traffic in a set of convergent promoters as novel modules for synthetic biology. We show examples of elements, including antisense roadblock, relative promoter strengths, inter-promoter distance, and sequence content that can be tuned to give rise to repressive as well as cooperative behaviors, therefore resulting in distinct gene expression patterns. Our approach will be useful towards engineering new biological devices and will bring new insights to naturally occurring cis-antisense systems. Therefore, we are reporting a new biological tool that can be used for synthetic biology.
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Real Leather Grown In A Lab Is Moving Closer To Your Closet

Real Leather Grown In A Lab Is Moving Closer To Your Closet | SynBioFromLeukipposInstitute | Scoop.it
There's no dead cow involved in Modern Meadow's new materialjust science!
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Scientists are now using bacteria as living hard drives

Scientists are now using bacteria as living hard drives | SynBioFromLeukipposInstitute | Scoop.it
Computers are becoming more like living beings. It looks like living beings are becoming more like computers. The latest research has demonstrated a 
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GeNeDA: An Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics

J Comput Biol. 2016 Jun 20. [Epub ahead of print]
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The Internet of Things Goes Nano

The Internet of Things Goes Nano | SynBioFromLeukipposInstitute | Scoop.it
Tiny sensors could take medicine, energy efficiency and many other sectors to a whole new dimension
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Lattice engineering through nanoparticle-DNA frameworks

Lattice engineering through nanoparticle-DNA frameworks | SynBioFromLeukipposInstitute | Scoop.it
Advances in self-assembly over the past decade have demonstrated that nano- and microscale particles can be organized into a large diversity of ordered three-dimensional (3D) lattices. However, the ability to generate different desired lattice types from the same set of particles remains challenging. Here, we show that nanoparticles can be assembled into crystalline and open 3D frameworks by connecting them through designed DNA-based polyhedral frames. The geometrical shapes of the frames, combined with the DNA-assisted binding properties of their vertices, facilitate the well-defined topological connections between particles in accordance with frame geometry. With this strategy, different crystallographic lattices using the same particles can be assembled by introduction of the corresponding DNA polyhedral frames. This approach should facilitate the rational assembly of nanoscale lattices through the design of the unit cell.
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A Robotic Platform for Automated RNA Extraction and Analysis during Reporter Gene–Based Dynamic Characterization of Bacterial Promoters

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In Just 3 Days, AI Solves Biology Mystery: How Flatworms Regenerate into New Organisms

In Just 3 Days, AI Solves Biology Mystery: How Flatworms Regenerate into New Organisms | SynBioFromLeukipposInstitute | Scoop.it
A computer has solved one of biology's biggest mysteries - how a sliced up flatworm can regenerate into new organisms, and it only took it a matter of days. However, years of programming went into the tech.
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The Great Debate - What Is Life?

Richard Dawkins, J. Craig Venter, Nobel laureates Sidney Altman and Leland Hartwell, Chris McKay, Paul Davies, Lawrence Krauss, and The Science ...
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Science Reviews Applications of synthetic gene networks

Applications of synthetic gene networks: synthetic biology https://t.co/kudeZZeBaq #genetics #biology https://t.co/RqP3z9i37h
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Synthesis in Space | PLOS Synthetic Biology Community

Synthesis in Space | PLOS Synthetic Biology Community | SynBioFromLeukipposInstitute | Scoop.it
by CosmoCrops, the University of Copenhagen iGEM team 2016 The Challenge: Space Exploration Ever wondered why humans have not colonized Mars, or traveled
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Design of a synthetic integral feedback circuit: dynamic analysis and DNA implementation.

The design and implementation of regulation motifs ensuring robust perfect adaptation are challenging problems in synthetic biology. Indeed, the design of high-yield robust metabolic pathways producing, for instance, drug precursors and biofuels, could be easily imagined to rely on such a control strategy in order to optimize production levels and reduce production costs, despite the presence of environmental disturbance and model uncertainty. We propose here a motif that ensures tracking and robust perfect adaptation for the controlled reaction network through integral feedback. Its metabolic load on the host is fully tunable and can be made arbitrarily close to the constitutive limit, the universal minimal metabolic load of all possible controllers. A DNA implementation of the controller network is finally provided. Computer simulations using realistic parameters demonstrate the good agreement between the DNA implementation and the ideal controller dynamics.
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MIT Engineers Developed a Super Strong Artificial Skin

MIT Engineers Developed a Super Strong Artificial Skin | SynBioFromLeukipposInstitute | Scoop.it
Engineers from MIT have developed a substance that could be used as an artificial skin, long-lasting contact lens, drug-delivering bandage, and more.
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Transcriptional regulation with CRISPR-Cas9: principles, advances, and applications

Curr Opin Biotechnol. 2016 Jun 23;40:177-184. doi: 10.1016/j.copbio.2016.06.003. [Epub ahead of print] REVIEW
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Build your own lab

Build your own lab | SynBioFromLeukipposInstitute | Scoop.it
Build your own lab » The Journal of Peer Production #opensource #openscience https://t.co/Y6elac0xwL
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Soon we'll cure diseases with a cell, not a pill

Soon we'll cure diseases with a cell, not a pill | SynBioFromLeukipposInstitute | Scoop.it
Current medical treatment boils down to six words: Have disease, take pill, kill something. But physician Siddhartha Mukherjee points to a future of medicine that will transform the way we heal.
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Analog Computers May Be Better at Body Simulations

Analog Computers May Be Better at Body Simulations | SynBioFromLeukipposInstitute | Scoop.it
Qmed (formerly Medical Device Link) is the world's first completely prequalified supplier directory and news source for medical device OEMs. Find medical device suppliers and IVD suppliers who are FDA-registered, ISO 13485- and ISO 9001-certified.
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Scientists want to replace lab workhorse E. coli with the world’s fastest-growing bacterium

Scientists want to replace lab workhorse E. coli with the world’s fastest-growing bacterium | SynBioFromLeukipposInstitute | Scoop.it
<i>Vibrio natriegens</i> could save researchers valuable time
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DNA design helps create novel nanomaterials - Materials Today

DNA design helps create novel nanomaterials - Materials Today | SynBioFromLeukipposInstitute | Scoop.it
A cube, an octahedron and a prism are among the polyhedral structures, or frames, made of DNA that scientists at the US Department of Energy's (DOE) Brookhaven National Laboratory have designed to connect nanoparticles into a variety of precisely structured three-dimensional (3D) lattices. The scientists have also developed a method to integrate nanoparticles and DNA frames into interconnecting modules, expanding the diversity of possible structures.

These achievements, described in papers in Nature Materials and Nature Chemistry, could lead to the rational design of nanomaterials with enhanced or combined optical, electric and magnetic properties.

"We are aiming to create self-assembled nanostructures from blueprints," said physicist Oleg Gang, who led this research at the Center for Functional Nanomaterials (CFN), a DOE Office of Science User Facility at Brookhaven. "The structure of our nanoparticle assemblies is mostly controlled by the shape and binding properties of precisely designed DNA frames, not by the nanoparticles themselves. By enabling us to engineer different lattices and architectures without having to manipulate the particles, our method opens up great opportunities for designing nanomaterials with properties that can be enhanced by precisely organizing functional components. For example, we could create targeted light-absorbing materials that harness solar energy, or magnetic materials that increase information-storage capacity."

Gang's team has previously exploited DNA's complementary base pairing – the highly specific binding of chemical bases known by the letters A, T, G and C that make up the rungs of the DNA double-helix ‘ladder’ – to bring particles together in a precise way. Particles coated with single strands of DNA with a defined sequence of bases link to particles coated with strands with a complementary sequence (A binds with T and G binds with C) while repelling particles coated with non-complementary strands.

They have also designed 3D DNA frames whose corners have single-stranded DNA tethers to which nanoparticles coated with complementary strands can bind. When the scientists mix these nanoparticles and frames, the components self-assemble into lattices that are mainly defined by the shape of the designed frame. The Nature Materials paper describes the most recent structures achieved using this strategy.

"In our approach, we use DNA frames to promote the directional interactions between nanoparticles such that the particles connect into specific configurations that achieve the desired 3D arrays," said Ye Tian, lead author of the Nature Materials paper and a member of Gang's research team. "The geometry of each particle-linking frame is directly related to the lattice type, though the exact nature of this relationship is still being explored."

So far, the team has designed five polyhedral frame shapes – a cube, an octahedron, an elongated square bipyramid, a prism and a triangular bipyramid – but a variety of other shapes could be created.

"The idea is to construct different 3D structures (buildings) from the same nanoparticle (brick)," explained Gang. "Usually, the particles need to be modified to produce the desired structures. Our approach significantly reduces the structure's dependence on the nature of the particle, which can be gold, silver, iron, or any other inorganic material."

To design the frames, the team used DNA origami, a self-assembly technique in which short synthetic strands of DNA (staple strands) are mixed with a longer single strand of biologically-derived DNA (scaffold strand). When the scientists heat and cool this mixture, the staple strands selectively bind with or ‘staple’ the scaffold strand, causing the scaffold strand to repeatedly fold over onto itself. Computer software helps them determine the specific sequence required to ensure the DNA folds into desired shapes.

The folding of the single-stranded DNA scaffold exposes anchoring points that contain free ‘sticky’ ends – unpaired strings of DNA bases – where nanoparticles coated with complementary single-strand tethers can attach. These sticky ends can be positioned anywhere on the DNA frame, but Gang's team chose the corners so that multiple frames could be connected.

For each frame shape, the number of DNA strands linking a frame corner to an individual nanoparticle is equivalent to the number of edges converging at that corner. The cube and prism frames have three strands at each corner, for example. By producing these corner tethers with varying numbers of bases, the scientists can tune the flexibility and length of the particle-frame linkages. The interparticle distances are determined by the lengths of the frame edges, which are tens of nanometers long in the frames designed to date, but the scientists say it should be possible to tailor the frames to achieve any desired dimensions.

The scientists verified the frame structures and nanoparticle arrangements through cryo-electron microscopy (a type of microscopy conducted at very low temperatures) at the CFN and Brookhaven's Biology Department, and through x-ray scattering at the National Synchrotron Light Source II (NSLS-II), a DOE Office of Science User Facility at Brookhaven.

In the Nature Chemistry paper, Gang's team described how they used a similar DNA-based approach to create programmable two-dimensional (2D) square-like DNA frames around single nanoparticles. DNA strands inside the frames provide coupling to complementary DNA on the nanoparticles, essentially holding the particle inside the frame. Each exterior side of the frame can be individually encoded with different DNA sequences. These outer DNA strands guide frame-frame recognition and connection.

Gang likens these DNA-framed nanoparticle modules to Lego bricks. "Each module can hold a different kind of nanoparticle and interlock to other modules in different but specific ways, fully determined by the complementary pairing of the DNA bases on the sides of the frame," he said.

In other words, the frames not only determine if the nanoparticles will connect but also how they will connect. Programming the frame sides with specific DNA sequences means only frames with complementary sequences can link up.

Mixing different types of modules together can yield a variety of structures, similar to the constructs that can be generated from different Lego bricks. By creating a library of the modules, the scientists hope to be able to assemble structures on demand. The selectivity of the connections allows different types and sizes of nanoparticles to be combined into single structures.

The geometry of the connections, or how the particles are oriented in space, is very important for designing structures with desired functions. For example, optically-active nanoparticles can be arranged in a particular geometry to rotate, filter, absorb and emit light – capabilities that are relevant for applications such as display screens and solar panels.

By using different modules from their ‘library’, Gang's team has so far demonstrated the self-assembly of one-dimensional linear arrays, ‘zigzag’ chains, square-shaped and cross-shaped clusters, and 2D square lattices. The scientists have even generated a simplistic nanoscale model of Leonardo da Vinci's Vitruvian Man. "We wanted to demonstrate that complex nanoparticle architectures can be self-assembled using our approach," said Gang.

Again, the scientists used sophisticated imaging techniques – electron and atomic force microscopy at the CFN and x-ray scattering at NSLS-II – to verify that their structures were consistent with the prescribed designs and to study the assembly process in detail.

"Although many additional studies are required, our results show that we are making advances toward our goal of creating designed matter via self-assembly, including periodic particle arrays and complex nanoarchitectures with freeform shapes," said Gang. "Our approach is exciting because it is a new platform for nanoscale manufacturing, one that can lead to a variety of rationally designed functional materials."

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Synthetic biology: from mainstream to counterculture

Existing at the interface of science and engineering, synthetic biology represents a new and emerging field of mainstream biology. However, there also exists a counterculture of Do-It-Yourself biologists, citizen scientists, who have made significant inroads, particularly in the design and development of new tools and techniques. Herein, I review the development and convergence of synthetic biology's mainstream and countercultures.
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Ethical Questions Loom Over Efforts to Make a Human Genome from Scratch

Ethical Questions Loom Over Efforts to Make a Human Genome from Scratch | SynBioFromLeukipposInstitute | Scoop.it
The biggest beneficiary of a plan to fabricate a human genome from scratch could be a Massachusetts startup called Gen9 that has close ties to the authors of the still-secretive proposal.
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