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A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells

A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells | SynBioFromLeukipposInstitute | Scoop.it
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Müller K, Engesser R, Metzger S, Schulz S, Kämpf MM, Busacker M, Steinberg T, Tomakidi P, Ehrbar M, Nagy F, Timmer J, Zubriggen MD, Weber W "Growth and differentiation of multicellular systems is orchestrated by spatially restricted gene expression programs in specialized subpopulations. The targeted manipulation of such processes by synthetic tools with high-spatiotemporal resolution could, therefore, enable a deepened understanding of developmental processes and open new opportunities in tissue engineering. Here, we describe the first red/far-red light-triggered gene switch for mammalian cells for achieving gene expression control in time and space. We show that the system can reversibly be toggled between stable on- and off-states using short light pulses at 660 or 740 nm. Red light-induced gene expression was shown to correlate with the applied photon number and was compatible with different mammalian cell lines, including human primary cells. The light-induced expression kinetics were quantitatively analyzed by a mathematical model. We apply the system for the spatially controlled engineering of angiogenesis in chicken embryos. The system's performance combined with cell- and tissue-compatible regulating red light will enable unprecedented spatiotemporally controlled molecular interventions in mammalian cells, tissues and organisms."


http://bit.ly/YeQgQl

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A robust and sensitive synthetic sensor to monitor the transcriptional output of the cytokinin signaling network in plants

A robust and sensitive synthetic sensor to monitor the transcriptional output of the cytokinin signaling network in plants | SynBioFromLeukipposInstitute | Scoop.it
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Zürcher E, Tavor-Deslex D, Lituiev D, Enkeli K, Tarr PT, Müller B  "Cytokinins are classic plant hormones that orchestrate plant growth, development, and physiology. They affect gene expression in target cells by activating a multistep phosphorelay network. Type-B response regulators, acting as transcriptional activators, mediate the final step in the signaling cascade. Previously, we have introduced a synthetic reporter, TCS (Two Component signaling Sensor)::GFP, which reflects the transcriptional activity of type-B response regulators. TCS::GFP was instrumental in uncovering novel roles of cytokinin, and deepening our undestanding of existing functions. However, TCS-mediated expression of reporters is weak in some developmental contexts, where cytokinin signaling has a documented role, such as in the shoot apical meristem, or in the vasculature of Arabidopsis thaliana. In addition, we observed that GFP expression becomes rapidly silenced in TCS::GFP transgenic plants. Here, we present an improved version of the reporter, TCS new (TCSn), which, compared to TCS, is more sensitive to phosphorelay signaling in Arabidopsis and maize cellular assays, while retaining its specificity. Transgenic Arabidopsis TCSn::GFP plants exhibit strong and dynamic GFP expression patterns consistent with known cytokinin functions. In addition, GFP expression has been stable over generations, allowing crosses with different genetic backgrounds. Thus, TCSn represents a significant improvement to report the transcriptional output profile of phosphorelay signaling networks in Arabidopsis, maize, and likely other plants that display common response regulator DNA-binding specificities."

http://bit.ly/WyTdJt
#syntheticbiology #synbio

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Biosciences - Meeting on Future Perspectives in Synthetic Biology ...

Biosciences - Meeting on Future Perspectives in Synthetic Biology ... | SynBioFromLeukipposInstitute | Scoop.it
By: Caroline Channing January 23, 2013 3:37 PM. The Manchester Institute of Biotechnology is hosting a joint Academia/Industry discussion meeting on the topic of "Future Perspectives in Synthetic Biology" on Friday 8th February 2013.
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DNA Hacking, Bio-punks, and the Future of Synthetic Biology

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talk by

Jameson Dungan 

Recorded at Ignite Hampton Roads #3 at Nauticus in Norfolk Virginia by Ethan O'Toole and Leroy Baynum.

(video)
http://bit.ly/Wsntsm

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Systems as the Driver for Synthetic Biology

Systems as the Driver for Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:


Synthetic Biology is a practical application of Systems Biology

*Video*: *Systems as the driver for synthetic biology*

"We now possess the ability to read and write DNA. These tools are not only revolutionizing biotechnology but also the basic life sciences as well. The challenge is that we are still learning the grammar. In other words, we often do not know which genetic perturbations to make in order to alter the behavior of an organism. As a result, synthetic biology still involves much trial and error. Moreover, we are still far from the point where we can engineer new organisms from scratch – rather, we need to alter the physiology of existing ones. Even then, we still need to understand how these organisms function in an integrated manner. In this talk, I will discuss the application systems biology to synthetic biology as a general strategy for overcoming many of these challenges. I will first review some of our previous work applying comparative genomics to inform biological design. I will then discuss our work applying systems biology approaches to improve organisms for fuel and chemical production. I will conclude by discussing our recent work developing tools for engineering non-model organisms with unique properties.

 Dr. Christopher Rao is an associate professor of chemical and biomolecular engineering at the University of Illinois, Urbana-Champaign, a Robert W. Schaefer Professional Scholar, and a member of the Energy Biosciences Institute. He received his B.S. degree in Chemical Engineering from Carnegie Mellon University in 1994 and his Ph.D. degree in Chemical Engineering from the University of Wisconsin in 2000 under the guidance of Dr. James Rawlings. Prior to joining UIUC in 2005, he was a postdoctoral fellow at the Howard Hughes Medical Institute and University of California, Berkeley working under the guidance of Dr. Adam Arkin. Dr. Rao has authored and co-authored 58 research articles. In addition, he has given invited lectures in more than 55 international meetings and institutions. Dr. Rao has received numerous research and teaching awards and honors, including American Institute of Chemical Engineers (AIChE) Computing and Systems Technology Outstanding Young Research Award (2012), Petit Scholar from UIUC College of Liberal Arts and Sciences (2011), International Federation of Automatic Control (IFAC) High Impact Paper Award (2010), UIUC School of Chemical Sciences Excellence in Teaching Award (2008), American Institute of Chemical Engineers (AIChE) Computing and Systems Technology W. David Smith Award (2007), and National Science Foundation CAREER Award (2007). Dr. Rao is an editor for PLoS Computational Biology and PLoS One. The goal of his research is to understand how cells employ feedback control in decision-making processes. In addition, he develops experimental and computational tools for synthetic biology." 


 http://bit.ly/Wslswi

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Synthetic Biology is on its Way to Treating Human Disease

Synthetic Biology is on its Way to Treating Human Disease | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by 
Eric Sawyer

"Synthetic biology has definitely gotten generous helpings of hype recently, so much so that it's easy to confuse speculation with data-backed results. I recently read a review of the clinical applications of synthetic biology1 and was surprised by how much progress has already been made!

Human health applications are particularly difficult because bringing new technology into the clinic lies at the end of a long, arduous journey involving clinical trials, government certification, and care provider education. Here's a "review of a review" on the most impressive steps synthetic biology has made toward improving human health.*

Bacteria and the human body are both friend and foe. Some bacteria conspire against us to cause severe illness; others live harmlessly inside us, even playing crucial roles in maintaining our health. Perhaps the most pressing challenge in our fight against pathogens is the arms race between modern medicine and antibiotic resistant bacteria. Ordinary natural selection, aided by poor healthcare management and patient noncompliance, has created a global crisis where pathogens are evolving resistance to our treatments.

Part of the problem is that invading bacteria collude to build protective biofilms that create a physical barrier to antibiotics. In a project from Collins's own lab, investigators successfully engineered the T7 phage, a virus that infects E. coli, to degrade biofilms. The viruses invade E. coli cells and hijack their protein synthesis machinery, churning out viral proteins. The engineered version of T7 also contains a gene coding for the enzyme DspB, a molecular wrecking ball that destroys biofilm. With their fortress destroyed, a whopping 99.997% of the E. coli in Collins's experiments were killed by the engineered phages...."

http://bit.ly/UwT1wJ

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Strange behavior: new study exposes living cells to synthetic protein

Strange behavior: new study exposes living cells to synthetic protein | SynBioFromLeukipposInstitute | Scoop.it
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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 ;

 

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Barcoding cells using cell-surface programmable DNA-binding domains

Barcoding cells using cell-surface programmable DNA-binding domains | SynBioFromLeukipposInstitute | Scoop.it



Gerd Moe-Behrens's insight:

*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

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Big medical data

Big medical data | SynBioFromLeukipposInstitute | Scoop.it

.

Gerd Moe-Behrens's insight:

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

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Recap and Top Tweets: Programming Nature, a MIT/Stanford VLAB Event on Synthetic Biology | Innov8Social - Exploring Social Innovation

Recap and Top Tweets: Programming Nature, a MIT/Stanford VLAB Event on Synthetic Biology | Innov8Social - Exploring Social Innovation | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

"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


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Half a Million DVDs in Your DNA

Half a Million DVDs in Your DNA | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Robert F. Service 

"Paleontologists routinely resurrect and sequence DNA from woolly mammoths and other long extinct species. Future paleontologists, or librarians, may do much the same to pull up Shakespeare's sonnets, listen to Martin Luther King Jr.'s "I have a dream" speech, or view photos. Researchers in the United Kingdom report today that they've encoded these works and others in DNA and later sequenced the genetic material to reconstruct the written, audio, and visual information.

 The new work isn't the first example of large-scale storage of digital information in DNA. Last year, researchers led by bioengineers Sriram Kosuri and George Church of Harvard Medical School reported that they stored a copy of one of Church's books in DNA, among other things, at a density of about 700 terabits per gram, more than six orders of magnitude more dense than conventional data storage on a computer hard disk. Now, researchers led by molecular biologists Nick Goldman and Ewan Birney of the European Bioinformatics Institute (EBI) in Hinxton, U.K., report online today in Nature that they've improved the DNA encoding scheme to raise that storage density to a staggering 2.2 petabytes per gram, three times the previous effort."


http://bit.ly/SGkrk1


original paper
http://bit.ly/W2oB6w

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Alpha males and “adventurous human females”: gender and synthetic genomics

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By Christina Agapakis 


"In May of 2010, two influential Science papers changed the way that we think about the past and future of genomes. The decoding of the Neandertal genome showed that humans and Neandertals interbred some time before Neandertals went extinct some 30,000 years ago. A couple weeks later, the J. Craig Venter Institute announced their chemical synthesis of a complete bacterial genome and its “booting up” in a closely related cell. The coincidence of the announcement of ancient and synthetic genomes, as well as the recent publication of technologies for large scale bacterial genome engineering from George Church’s lab led some people to ask whether it would be possible to clone Neandertals by a combination of gene synthesis, human genome editing, and stem cell cloning. While the New Scientist article about the implications of the Neandertal genome was pessimistic on the short-term prospect of “resurrecting” Neandertals, George Church himself has more recently made news by suggesting how such a future scenario might work in his recent book Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. In the book’s introduction, Church (with science writer Ed Regis) writes: You’d start with a stem cell genome from a human adult and gradually reverse-engineer it into the Neanderthal genome or a reasonably close equivalent. These stem cells can produce tissues and organs. If society becomes comfortable with cloning and sees value in true human diversity, then the whole Neanderthal creature itself could be cloned by a surrogate mother chimp–or by an extremely adventurous human female...."


http://bit.ly/WmSLxU

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­Lost in translation: Harvard geneticist denies plans to clone Neanderthals

­Lost in translation: Harvard geneticist denies plans to clone Neanderthals | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

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

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Scaffold technologies for controlling cell behavior in tissue engineering

Scaffold technologies for controlling cell behavior in tissue engineering | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Lee SJ, Atala A.

"Scientists in the field of tissue engineering are now applying the principles of cell biology, material science and biomedical engineering to create biological substitutes that will restore and maintain normal function in diseased and injured tissues/organs [1-3]. Tissue-engineered scaffolds should (i) facilitate the localization and delivery of tissue-specific cells to precise sites in the body, (ii) maintain a three-dimensional architecture that permits the formation of new tissues, and (iii) guide the development of new tissues with appropriate function. ..."

http://1.usa.gov/Xd9ZyP

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Gerd Moe-Behrens's comment, January 29, 2013 10:17 AM
(Photo source http://en.wikipedia.org/wiki/Scaffold)
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Synthetic Biology Special Interest Group - Plant Synthetic Biology Workshop, 21-22 May 2013, University of Nottingham - Articles - Open Innovation

Synthetic Biology Special Interest Group - Plant Synthetic Biology Workshop, 21-22 May 2013, University of Nottingham - Articles - Open Innovation | SynBioFromLeukipposInstitute | Scoop.it
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Plant Synthetic Biology Workshop, 21-22 May 2013, University of Nottingham http://bit.ly/WqF6bH

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What Does the Future Of Innovation Look Like? Thought Leaders At 'The Intersection' Give Us a Glimpse

What Does the Future Of Innovation Look Like? Thought Leaders At 'The Intersection' Give Us a Glimpse | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

Steve Jurvetson, a leading Silicon Valley venture capitalists: "we’ll see remarkable progress in…synthetic biology" 

*What does the future of innovation look like*? *Thought leaders at the intersection give us a glimpse*

by

 Hamdan Azhar


"Writing and data science both involve telling stories and there are many stories to be told in Silicon Valley. In these articles, I attempt to convey a human portrait of the tech world by offering a personal account of some of the events that I attend. Recently, I went to The Intersection, a conference on innovation and social change.

 MOUNTAIN VIEW, Calif. – “I want you to go up to that lady in red and ask her if she knows what a maglev train is.” Josiah, an outgoing and precocious 18-year old, ...

Steve Jurvetson, one of Silicon Valley’s leading venture capitalists, then had a session on the science of innovation. Citing typical Kurzweilian arguments about semi-conductors, he argues that the pace of innovation was expanding exponentially. “In the coming years, we’ll see remarkable progress in artificial intelligence, synthetic biology, space exploration, and 3D-printing,” he predicts."



http://bit.ly/VtASme

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We travel the road to 'mastery of our biological destiny'

We travel the road to 'mastery of our biological destiny' | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Tom Beal 

"Genomics, the topic of this year's lecture series at the University of Arizona's College of Science, is not an inherently controversial topic.

 It is the realm of scientists who sequence and assemble the entire set of DNA contained in each cell of an organism. Genomics provides a road map for researchers in a variety of endeavors - biology, evolution, immunology, pharmacology, medicine, agriculture and more. It has the potential to unlock the mysteries of our ancestry, feed the world, improve health, cure disease and lengthen productive lives. In the public realm it also raises fears about the misuse of medical information, the danger of synthetic biology and concerns about our food supply, expressed in terms like "super weeds" and "Frankenfoods." That is partly the reason for the lecture series, said Dr. Fernando Martinez, the pediatrician and asthma researcher who heads the UA's Bio5 Research Institute and will give the initial lecture Wednesday. "The time has come for society to understand the genome," said Martinez. He predicts that within the next 10 years, a personalized genome map will be made available to the parents of each child born in the United States....."


http://bit.ly/14p025M

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Italian Research: opinion from italian scientists (Teaser)

www.sciencetogrok.om
Gerd Moe-Behrens's insight:

How does science change in the digital age?
How will the publication system change?
How do we deal with the big amount of data scientist generate?

+Eugenio Battaglia has interviewed a number of italian scientist about the situation of science and what might be necessary to change. Eugenio made a great series of videos about the situation of Science. The video below is a teaser for this awesome material. It touches some local questions.

However, it is mainly about the challenges science meets in general. As we are on the dawn of the digital age, science is in the process of major changes.

The way scientist used to published their data is obvious not longer well dapped to our new digital reality. The traditional scientific journal is dying. Novel models of publishing are under discussion.

Moreover, scientist have to deal l with an enormous storage and processing capacity.  "We talk about a magnitude in the “petabyte” scale, which is equivalent to 1000 terabytes (TB) = 1 quadrillion bytes = 10E+15 bytes. Google processes about 24 petabytes per day. Within the last decade or so, scientific research (such as research in biology, bioinformatics, and medicine, to name a few) has increasingly produced vast amounts of data from high throughput experiments. We have also witnessed an exponential increase in the number and/or size of data sets, in particular in biology and bioinformatics research. For example, the 1000 Genomes Project has so far produced 200 TB publicly available data sets since its inception. Moreover, the output in scientific literature has become so vast and complex, that it has become difficult to read, assimilate and process such research production." (see http://bit.ly/TtuNOP ;)

Moreover,  many scientist participate in social networks. These platforms provide the potential option of planetary scale connectivity among researchers and the ability to organize research projects solely in the cloud.

I was so fortunate to have the opportunity to watch the whole material. I can promise you some awesome contributions to the discussion where science stands for the moment and what problems we face and need to solve.

http://bit.ly/X3yg8N

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Synthetic Biology Center @ MIT | Research

Synthetic Biology Center @ MIT | Research | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:
*Genetic Programming* bySBC@MIT Our goal is to create a programming language for living cells that is similar to languages used to program computers and robots. This requires the development of a high-level language that allows a programmer to describe a desired function and computational methods that convert this language into a linear DNA sequence. The sequence is then built and inserted into an organism, which runs the program. Examples of programs built by the SBC include an edge detection program that gives bacteria to identify the light-dark interfaces in an image, a program that forms two-dimensional patters, and one that enables bacteria to count. http://bit.ly/SVyQsT
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Molecular assembler finally created

Molecular assembler finally created | SynBioFromLeukipposInstitute | Scoop.it
An artificial molecular assembler has been designed and fabricated at the University of Manchester.
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Brazil and the “next industrial revolution:” Synthetic Biology

Brazil and the “next industrial revolution:” Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
  Synthetic Biology is the hot new ticket in Life Sciences and beyond, with research establishments in developed and developing countries piling aboard the new discipline. No surprise then, t...
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Preparing synthetic biology for the world

Preparing synthetic biology for the world | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Gerd H. G. Moe-Behrens, Rene Davis and Karmella A. Haynes

"Synthetic Biology promises low-cost, exponentially scalable products and global health solutions in the form of self-replicating organisms, or “living devices.” As these promises are realized, proof-of-concept systems will gradually migrate from tightly regulated laboratory or industrial environments into private spaces as, for instance, probiotic health products, food, and even do-it-yourself bioengineered systems. What additional steps, if any, should be taken before releasing engineered self-replicating organisms into a broader user space? In this review, we explain how studies of genetically modified organisms lay groundwork for the future landscape of biosafety. Early in the design process, biological engineers are anticipating potential hazards and developing innovative tools to mitigate risk. Here, we survey lessons learned, ongoing efforts to engineer intrinsic biocontainment, and how different stakeholders in synthetic biology can act to accomplish best practices for biosafety."

http://bit.ly/W8eV9J

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DIY Bioprinter

DIY Bioprinter | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

*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

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DNA storage a reality

DNA storage a reality | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

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

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Greenwich researcher named alongside Beyonce as inspiring woman

Greenwich researcher named alongside Beyonce as inspiring woman | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

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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
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