SynBioFromLeukipposInstitute

*DIY* - *Bio* 

*Bioprinter lets build structures from living cells*

By
JOSEPH FLAHERTY

"A new bioprinter developed at a hackerspace can print living cells for less than the cost of an iPod touch.

 3-D bioprinters have the potential to change the way medical research is conducted, even print living tissue and replacement organs, but they are expensive and highly specialized. They literally build living structures, like blood vessels or skin tissue, cell by cell, revolutionizing biomedical engineering. Unfortunately, they’re expensive, rare, and require a Ph.D. (or two) to operate successfully. Frustrated by their cost and exclusivity, a group of makers at the DIYbio hackerspace BioCurious are developing a system open to anyone with a soldering iron and a serious passion for cell biology. The plans to build your own have been thoroughly documented as an Instructable by Patrik D’haeseleer, a genomics, bioinformatics, and computational biology researcher who has worked in labs at the Harvard Medical School and is now at the Lawrence Livermore National Lab. The printer can’t yet produce a replacement pancreas, but it spawns new possibilities for hackers and scientists. Instead of laboriously hand-placing cultures in a petri dish with a pipette, researchers could prepare their experiments in software scripts, print out sheets of cells, and run experiments with the output — all on a post-doc’s budget. For $150, more than half of which is Arduino boards and shields, anyone who took AP bio can set up sophisticated experiments and evolve their hypothesis as quickly as printing a photo. ..."

http://bit.ly/WQKkeQ

Great news about DNA storage:

*Towards practical, high-capacity, low-maintenance information storage in synthesized DNA*  

by
Nick Goldman,Paul Bertone,Siyuan Chen,Christophe Dessimoz,Emily M. LeProust, Botond Sipos& Ewan Birney

"Digital production, transmission and storage have revolutionized how we access and use information but have also made archiving an increasingly complex task that requires active, continuing maintenance of digital media. This challenge has focused some interest on DNA as an attractive target for information storage1 because of its capacity for high-density information encoding, longevity under easily achieved conditions2, 3, 4 and proven track record as an information bearer. Previous DNA-based information storage approaches have encoded only trivial amounts of information5, 6, 7 or were not amenable to scaling-up8, and used no robust error-correction and lacked examination of their cost-efficiency for large-scale information archival9. Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information10 of 5.2 × 106 bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade."

http://bit.ly/149vRzv

by
Sarah Shaffi

"A university researcher has found herself named alongside the likes of international superstar Beyonce in a list of most inspiring women.

 Dr Rachel Armstrong, a researcher at the Advanced Virtual and Technological Architecture Research Laboratory in the University of Greenwich’s School of Architecture, Design & Construction, features in women’s lifestyle and technology website Chip Chick’s Top Nine Inspiring Women of 2012. Chip Chick says Dr Armstrong, who is a trained architect and a synthetic biologist, “is a great role model for both women and men worldwide”. She is also the co-director of Avatar, a research group which explores how advanced technology can be used in architecture. The website praises Dr Armstrong’s work in new technologies such as synthetic biology, which combines science and engineering to create new materials which can have a positive impact on the environment and help build sustainable structures. Dr Armstrong’s Kindle short book, Living Architecture: How Synthetic Biology Can Remake Our Cities and Reshape Our Lives, has also been nominated in the non-fiction category of the British Science Fiction Association awards. She said: “It is very flattering to be listed in such grand company and it’s especially nice to see the book recog.."
http://bit.ly/VjQzfz

Entrepreneurs are transforming synthetic biology into real dollars

 When: Tuesday,  January 22, 2013 6:00 - 7:00pm  Networking and Refreshments 7:00 - 8:30pm  Panel Discussion and Q&A WhereCemex Auditorium at Knight Management Center (Parking and Directions) Event Description: Synthetic biology was once-upon-a-time reserved for big pharma and the multimillion dollar chemical manufacturing industry. But today, startups and hackers in their garages and basements are using cloud based services and low cost labs, tools, and equipment to manipulate organisms to produce materials and products of economic value. Startups like Lygos are altering the DNA of yeast and e-coli to produce nylon, polyester, and polypropylene for clothing. RefactoredMaterials is transforming proteins to create materials that mimic spider silk. All of this is possible because cloud-based services and low cost tools are enabling these companies to quickly and cheaply build and iterate through multiple DNA blueprints to discover the right formula to produce these materials. Come to our event on January 22, 2013 at the Stanford Graduate School of Business to learn: What are the tools and cloud services that enable synthetic biology for startups?What are the keys to low cost innovation that will democratize synthetic biology and create profitable ventures?How do movements like Biohacking and Biocurious help shape this new movement?Can backyard biologists have the same impact that the homebrew computer clubs did in the 1980s?Is there a Moore's law equivalent for this space and what do investors see as the next big opportunities?Join us to Learn More. Moderator:  Megan Palmer, Deputy Director,  Stanford University, Synthetic Biology Engineering Research Center (SynBERC) Panelists:  Dan Widmaier, CEO, Refactored Materials  Nathan J. Hillson, Founder and Chief Scientific Officer, Teselagen Warren Hogarth, Partner, Sequoia Capital   Sasha Kamb, Senior Vice President, Amgen      http://bit.ly/141eoKs ;

Toward the synthetic biology for robotics and informatics in vivo

by
Tomonori Kawano, François Bouteau and Stefano Mancuso

"The automata theory is the math- ematical study of abstract machines commonly studied in the theoretical computer science and highly interdisci- plinary fields that combine the natural sciences and the theoretical computer science. In the present review article, as the chemical and biological basis for natural computing or informatics, some plants, plant cells or plant-derived mol- ecules involved in signaling are listed and classified as natural sequential machines (namely, the Mealy machines or Moore machines) or finite state automata. By defining the actions (states and transition functions) of these natural automata, the similarity between the computational data processing and plant decision-mak- ing processes became obvious. Finally, their putative roles as the parts for plant- based computing or robotic systems are discussed.

IntroductionNatural computing is the recently grow- ing field of research that investigates models and computational techniques inspired by nature and, dually, attempts to understand the world around us in terms of information processing.1 It is a highly interdisciplinary field that combines the natural sciences and the theoretical com- puter science. The automata theory is the mathematical study of abstract machines commonly studied in the theoretical computer science.2 Using these abstract machines called automata (singular,automaton), the computational prob- lems can be properly solved. A finite-state automaton (FSA), known as the finite- state machine is a behavioral model used to design the computer programs, which is composed of a finite number of states asso- ciated to transitions. A transition is a set of actions allowed starting from one state and ending in the same or another state, which is started by a triggering event or condition. In biology and artificial intel- ligence researches, finite-state machine are sometimes used to describe the neurologi- cal systems.In the present review article, as the chemical and biological basis for natural computing or informatics, some plants, plant cells or plant-derived molecules behaving as natural sequential machines or automata are listed and classified as natural sequential machines (namely the Mealy machines or Moore machines) or FSA. By defining the actions (states and transition functions) of these natural automata, the similarity between the com- putational data processing and plant deci- sion-making processes became obvious. Finally, their putative roles as the parts for plant-based computing or robotic systems are discussed....."

http://bit.ly/13ZQJtO

Peter Diamandis identifies eight technologies ripe for major change

*On why innovation will take off*

"We're going from, in 2010, just shy of two billion people connected on the Internet, to, by 2020, five billion people. Three billion new minds are coming online who have never been able to help contribute ideas, solve problems and challenges. And those three billion people are coming online when education and health care are going to make them better educated and healthier. I think it's going to be driving tens of trillions of dollars in the global economy.…Add artificial intelligence on top of that, and we're going to start seeing a rate of innovation that will scare all of us."

*On Eight Explosive Technologies*

"1. Biotechnology. It's the field where we're going to see the next $100 billion companies. Synthetic biology in particular, when you start to think of life as a programming language. Craig Venter [decoder of the human genome] just published that he increased the efficiency of photosynthesis 300%. What's that going to do for food production?

2. Computational systems. One of the things that computational systems give us is the ability to model almost anything. Anywhere on the planet you can hire, from cloud computing, 100, 1,000 computers for a minute, an hour, a day, and begin to model things.

3. Networks and sensors. Networks and sensors will give us huge amounts of data that we can begin to mine literally for anything we need, anything you want. It's a matter of asking the right question. We're looking at launching an earthquake prediction X PRIZE. 4. Artificial intelligence. AI has transformed almost every industry and will continue to do so. Imagine an individual with a software shell around them. I'm going to give it permission to listen to every conversation I have, to read everything about me, to scan my genome, to literally deep-dive into everything I've ever produced. It's going to start to literally finish my sentences for me. These AI's are going to become the most powerful assistants we have.

5. Robotics. Robotics will be everywhere. In five years, we'll have conferences like this and people will be beaming in if they can't physically be there. 6. Digital manufacturing. Three-D printing, digital manufacturing, will transform global manufacturing. I think about the woman going to a gala that evening who goes online and sees a beautiful dress designed in Bangladesh and prints it out in her closet. The notion is being able to print what you want, where you need it, on demand. 7. Medicine. Medicine is becoming an information technology. We launched a competition to build a hand-held mobile device that any mom could use at 2 a.m. to diagnose themselves or their kid, no matter where they are. We announced it, and a year later, we have 265 teams in 33 countries around the world competing for this.

8. Nanotechnology. We really look at nanomaterials versus nanotechnology. We're working on an X PRIZE on the future of mobility. We're looking at a battery X PRIZE for being able to increase battery energy and power storage densities 300% to 500%."

http://on.wsj.com/WBI23m

byArizona State University, Press release "One approach to understanding components in living organisms is to attempt to create them artificially, using principles of chemistry, engineering and genetics. A suite of powerful techniques—collectively referred to as synthetic biology—have been used to produce self-replicating molecules, artificial pathways in living systems and organisms bearing synthetic genomes.  In a new twist, John Chaput, a researcher at Arizona State University’s Biodesign Institute and colleagues at the Department of Pharmacology, Midwestern University, Glendale, Ariz. have fabricated an artificial protein in the laboratory and examined the surprising ways living cells respond to it.  “If you take a protein that was created in a test tube and put it inside a cell, does it still function,” Chaput asks. “Does the cell recognize it? Does the cell just chew it up and spit it out?”  This unexplored area represents a new domain for synthetic biology and may ultimately lead to the development of novel therapeutic agents.  The research results, reported in the advanced online edition of the journal ACS Chemical Biology, describe a peculiar set of adaptations exhibited by Escherichia coli bacterial cells exposed to a synthetic protein, dubbed DX. Inside the cell, DX proteins bind with molecules of ATP, the energy source required by all biological entities.  “ATP is the energy currency of life,” Chaput says. The phosphodiester bonds of ATP contain the energy necessary to drive reactions in living systems, giving up their stored energy when these bonds are chemically cleaved. The depletion of available intracellular ATP by DX binding disrupts normal metabolic activity in the cells, preventing them from dividing, (though they continue to grow). " http://bit.ly/WgTpQ8 ;

 

*Barcoding cells using cell-surface programmable DNA-binding domains*

by
Mali P, John Aach J, Lee J, Levner D, Nip L, Church GM 

Submitted

for more info see:

*Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA*

by
Chenxiang Lin,Ralf Jungmann,Andrew M. Leifer,Chao Li,Daniel Levner,George M. Church, William M. Shih& Peng Yin

"The identification and differentiation of a large number of distinct molecular species with high temporal and spatial resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here, we used (deoxy)ribonucleic acid (DNA)-origami technology to construct submicrometre nanorods that act as fluorescent barcodes. We demonstrate that spatial control over the positioning of fluorophores on the surface of a stiff DNA nanorod can produce 216 distinct barcodes that can be decoded unambiguously using epifluorescence or total internal reflection fluorescence microscopy. Barcodes with higher spatial information density were demonstrated via the construction of super-resolution barcodes with features spaced by ∼40 nm. One species of the barcodes was used to tag yeast surface receptors, which suggests their potential applications as in situ imaging probes for diverse biomolecular and cellular entities in their native environments."
http://bit.ly/Qc4o7O


*Researchers at Harvard’s Wyss Institute Engineer Novel DNA Barcode*

*New technology could launch biomedical imaging to next level*

by
Kristen Kusek

"Researchers have created a new kind of barcode that uses DNA origami technology. Colored dots can be arranged into geometric patterns or fluorescent linear DNA barcodes, and the combinations are almost limitless -- substantially increasing the number of distinct molecules or cells scientists can observe in a sample. [Credit: Chenxiang Lin, Ralf Jungmann, Andrew M. Leifer, Chao Li, Daniel Levner, George M. Church, William M. Shih, Peng Yin, Wyss Institute for Biologically Inspired Engineering, Harvard Medical School]"

"Much like the checkout clerk uses a machine that scans the barcodes on packages to identify what customers bought at the store, scientists use powerful microscopes and their own kinds of barcodes to help them identify various parts of a cell, or types of molecules at a disease site. But their barcodes only come in a handful of "styles," limiting the number of objects scientists can study in a cell sample at any one time.

 Researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University have created a new kind of barcode that could come in an almost limitless array of styles -- with the potential to enable scientists to gather vastly more vital information, at one given time, than ever before. The method harnesses the natural ability of DNA to self-assemble, as reported today in the online issue of Nature Chemistry."

http://hvrd.me/TCzOvu

Big data is one of the key challenges for contemporary science. We will move into an area of data driven science. This leads to a paradigm shift where systemics will be a key concept - see systems biology and it`s practical application synthetic biology. see http://bit.ly/OkBAMt

*Big medical data*

by
Larry Hardesty

"At the intersection of medicine and computer science, researchers look for clinically useful correlations amid mountains of information. With the recent launch of MIT’s Institute for Medical Engineering and Science, MIT News examines research with the potential to reshape medicine and health care through new scientific knowledge, novel treatments and products, better management of medical data, and improvements in health-care delivery. 

At the end of 2012, the National Public Radio show "Fresh Air" featured a segment in which its linguistics commentator argued that “big data” should be the word of the year. The term refers not only to the deluge of data produced by the proliferation of Internet-connected, sensor-studded portable devices but also to innovative techniques for analyzing that data; and big data has received a good deal of credit for Barack Obama’s victory in the last presidential election.

Certainly, the term was in heavy use around MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL), which in 2012 launched a new big-data initiative called bigdata@CSAIL. Several of the researchers affiliated with bigdata@CSAIL are developing new techniques for processing medical data, to make it more accessible to both physicians and patients and to find correlations that could improve diagnosis or choice of therapies. ...."

http://bit.ly/W6tFXr

"Under the umbrella of social innovation are the many emerging technologies that have the potential to create a meaningful, positive impact on society and the environment. Synthetic biology falls squarely into this category.

 A Steve Jobs Perspective "One of the very few silver linings about me getting sick is that Reed's gotten to spend a lot of time studying with some very good doctors...His enthusiasm for it is exactly how I felt about computers when I was his age. I think the biggest innovations of the twenty-first century will be the intersection of biology and technology. A new era is beginning, just like the digital one when I was his age." - Steve Jobs These words, captured by Walter Isaacson and said in a moment of reflection, are both profound and prophetic. So what would Silicon Valley luminary and chief innovator, Steve Jobs, have said about a room full of the sharpest, brightest, most innovative minds in the field of synthetic biology talking about the future of the field? MIT/Stanford VLAB Hosts "Programming Nature", a Panel Discussion on Synthetic Biology That is what the scene was this week at the MIT/Stanford Venture Lab (VLAB) event titled, "Programming Nature" held at the Stanford School of Business Knight Center.  Hundreds of attendees filled the auditorium to listen in on experts in the field share their insights and predictions. You can check back on VLAB's YouTube Channel to watch the entire event once it is posted. A (R)evolution? The discussion was moderated by Megan Palmer, Deputy Director of the Practices Thrust at the Synthetic Biology Engineering Research Center (SynBERC), which is housed within the Stanford University School of Bioengineering. At SynBERC, a multi-university initiative to promote synthetic biology, Megan recently organized the Synthetic Biology Leadership Accelerator Program (LeAP). Beyond organizing and creating opportunities for others in the field, she is herself a tried and true synthetic biologist. She holds a Ph.D. in Biological Engineering from MIT and a B.Sc.E. in Engineering Chemistry from Queen's College in Canada. Megan provided an effective guided tour into the field of synthetic biology, highlighting the key features that make it applicable across sectors. She introduced synthetic biology as a disruptive technology---asking the audience about what the potential could be if biology could be programmed just like computer program code. She posed the advances in synthetic biology as a either an evolution or revolution since the field has been active for some time. And, Megan spoke to her experience of spending 6 years to test one single aspect of a hypothesis as an example of how the lengthy life cycles of bioengineering can impact the time it takes to see results. Synthetic biology seeks to make the design, build, test cycle for bioengineering faster, cheaper, and better. An Infusion of Innovation The panelists provided unique perspectives and infused the discussion with examples of innovation in the field. Panelist Dan Widmaier, CEO and Founder of Refactored Materials in San Francisco, spoke about his company's project of simulating spider silk fibers and mass-producing. The fibers, known for their strength, durability, and extensibility, have the potential for building cars and airplanes that are aerodynamic and light, creating durable  performance apparel and gear, developing medical devices that the body may be more apt to accept, creating new offerings in cosmetics, and revolutionalizing entire industries.

http://bit.ly/Wj95CS

As I discussed on the original post: 
https://plus.google.com/115722829851477319854/posts/Z2Giw8NwRhg?hl=en
This is the outcome, when sensation press takes over, when few people interpreting the world. As this example shows: It works much better, when like comments and shares define the agenda of the public discussion. Journalism has changed for good.

*Lost in translation*: *Harvard geneticist denies plans to clone Neanderthals*

Soon after the news about a Harvard professor hoping to revive the extinct Neanderthal species blasted the web, the scientist himself sharply denied the reports, saying they have likely been caused by mistranslation.“The real story here is how these stories have percolated and changed in different ways,” said the internationally-recognized scholar, Professor of Harvard Medical School George Church, suggesting that the initial article reporting his cloning plans published in Britain’s Daily Mail was based on his interview to Germany’s Der Spiegel.Earlier this week the media exploded with the news that the professor was looking for an ‘adventurous woman’ who would agree to become a surrogate mother for a Neanderthal embryo. Reports suggested that Church would reconstruct Neanderthal DNA from fossil remains, put DNA into stem cells and inject them into a human embryo.Church explained that he was talking about the theoretical possibility of such an operation, but never said he intended to perform one.“I’m saying, if it is technically possible someday, we need to start talking about it today,” he told the Boston Herald.Of some 500 interviews given about his research projects this is the first one that triggered massive speculation and he is going to use it “as an educational moment to talk about journalism and technology,” the professor said.He pointed out that his current project has nothing to do with cloning ancient species.Church is a pioneer in synthetic biology and was at the origins of the Human Genome Project in the 1980s. In the meantime he is working on the use of genetics and DNA in improving healthcare.

 http://bit.ly/XzTSKv

by
Philip Whiterow

"Biome Technologies (LON:BIOM) is mulling a move into the emerging area of bio-based materials through the use of synthetic biology.

The bioplastics group has been developing new applications for its intellectual property following the sale of its half of its Biotec joint venture in October.Biome said it has a small number of early stage collaborations with both academic and industrial partners in the bio-based materials area. It has applied for government funding to accelerate this in 2013.Overall, Biome said its financial performance in 2012 was in line with expectations.Development of a high performance single-use food service product is progressing well and was market tested in the fourth quarter of 2012 with a full launch now underway with some 40 tonnes delivered already. A multi-layer sealing film for single-use coffee capsules has also been launched..."

http://bit.ly/10vtKC9

by
Kevin M Esvelt & Harris H Wang

"Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targetedgene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering."

http://bit.ly/141cmtE

*MITOPENCOURSEWARE*: 

*Intro to Nanotechnology* 

Published on Jan 16, 2013MIT 2.57 Nano-to-Micro Transport Processes, Spring 2012View the complete course: http://ocw.mit.edu/2-57S12Instructor: Gang Chen License: Creative Commons BY-NC-SAMore information at http://ocw.mit.edu/termsMore courses at http://ocw.mit.edu

http://bit.ly/T5b3bf