SynBioFromLeukipposInstitute
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Gerd Moe-Behrens's insight:
by Madec M, Gendrault Y, Lallement C, Haiech J. 
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Get details for Engineering Living Cells with New Capabilities: A Science@Cal Event, including date, start time, driving directions and more. Find other - Talks & Lectures events in Berkeley, CA.
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Storing information in DNA http://econ.st/UHmNPe
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A CRISPR-Cas system is harnessed to introduce template-driven mutations in S. pneumoniae and E. coli at high efficiency without requiring selectable markers.
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Congratulation +David Bikard
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Gerd Moe-Behrens's insight:
via +Christopher de la Torre
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A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells
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by 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."
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by 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
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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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talk by
Jameson Dungan
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Lightning Talks:
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Gerd Moe-Behrens
January 31, 2013 6:36 PM
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Gerd Moe-Behrens's insight:
"Scientists report that they have developed a method that cuts down the time it takes to make new ‘parts’ for microscopic biological factories from two days to only six hours.
The scientists, from Imperial College London, say their research brings them another step closer to a new kind of industrial revolution, where parts for these biological factories could be mass-produced. These factories have a wealth of applications including better drug delivery treatments for patients, enhancements in the way that minerals are mined from deep underground and advances in the production of biofuels.
Professor Paul Freemont, Co- Director of the Centre for Synthetic Biology and Innovation at Imperial College London and principle co-investigator of the study, which is published today in the journal Nucleic Acids Research, says:
“Before the industrial revolution most items were made by hand, which meant that they were slower to manufacture, more expensive to produce and limited in number. We are at a similar juncture in synthetic biology, having to test and build each part from scratch, which is a long and slow process. We demonstrate in our study a new method that could help to rapidly scale up the production and testing of biological parts.”
Parts made up of DNA are re-engineered by scientists and put into cells to make biological factories. However, a major bottleneck in synthetic biology is the lack of parts from which to build new types of factories. To build parts using the current time-consuming method, scientists have to re-engineer DNA in a cell and observe how it works. If it functions according to their specifications, then the scientists store the part specifications in a catalogue....."
bit.ly/WVPVkx
comment to:
Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology
by
James Chappell, Kirsten Jensen and Paul S. Freemont
"A bottleneck in our capacity to rationally and predictably engineer biological systems is the limited number of well-characterized genetic elements from which to build. Current characterization methods are tied to measurements in living systems, the transformation and culturing of which are inherently time-consuming. In order to address this we have validated a completely in vitro approach for the characterization of DNA regulatory elements using E. coli extract cell-free systems. Importantly, we demonstrate that characterization in cell-free systems correlates and is reflective of performance in vivo for the most frequently used DNA regulatory elements. Moreover, we devise a rapid and completely in vitro method to generate DNA templates for cell-free systems, bypassing the need for DNA template generation and amplification from living cells. This in vitro approach is significantly quicker than current characterization methods and is amenable to high-throughput techniques, providing a valuable tool for rapidly prototyping libraries of DNA regulatory elements for synthetic biology."
PDF can be found on the bottom of
bit.ly/WVPVkx
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Gerd Moe-Behrens
January 30, 2013 3:35 AM
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Gerd Moe-Behrens's insight:
LIVING MACHINES - exhibition Science Gallery Dublin http://bit.ly/128JX5u
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Gerd Moe-Behrens
January 29, 2013 9:19 AM
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Gerd Moe-Behrens's insight:
by
Lim WA, Lee CM, Tang C.
"A challenge in biology is to understand how complex molecular networks in the cell execute sophisticated regulatory functions. Here we explore the idea that there are common and general principles that link network structures to biological functions, principles that constrain the design solutions that evolution can converge upon for accomplishing a given cellular task. We describe approaches for classifying networks based on abstract architectures and functions, rather than on the specific molecular components of the networks. For any common regulatory task, can we define the space of all possible molecular solutions? Such inverse approaches might ultimately allow the assembly of a design table of core molecular algorithms that could serve as a guide for building synthetic networks and modulating disease networks."
http://bit.ly/WM9c7Z
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Gerd Moe-Behrens
January 29, 2013 9:01 AM
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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
Gerd Moe-Behrens's comment,
January 29, 2013 10:17 AM
(Photo source http://en.wikipedia.org/wiki/Scaffold)
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January 29, 2013 8:38 AM
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Plant Synthetic Biology Workshop, 21-22 May 2013, University of Nottingham http://bit.ly/WqF6bH
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January 29, 2013 8:31 AM
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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
"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.
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."
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Gerd Moe-Behrens
January 28, 2013 9:26 AM
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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.
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Gerd Moe-Behrens
January 28, 2013 8:36 AM
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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
"Gene expression in chloroplasts is highly regulated during translation by sequence and secondary-structure elements in the 5′ untranslated region (UTR) of mRNAs. These chloroplast mRNA 5′ UTRs interact with nuclear-encoded factors to regulate mRNA processing, stability, and translation initiation. Although several UTR elements in chloroplast mRNAs have been identified by site-directed mutagenesis, the complete set of elements required for expression of plastid mRNAs remains undefined. Here we present a synthetic biology approach using an arrayed oligonucleotide library to examine in vivo hundreds of designed variants of endogenous UTRs from Chlamydomonas reinhardtii and quantitatively identify essential regions through next-generation sequencing of thousands of mutants. We validate this strategy by characterizing the relatively well-studied 5′ UTR of the psbD mRNA encoding the D2 protein in photosystem II and find that our analysis generally agrees with previous work identifying regions of importance but significantly expands and clarifies the boundaries of these regulatory regions. We then use this strategy to characterize the previously unstudied psaA 5′ UTR and obtain a detailed map of regions essential for both positive and negative regulation. This analysis can be performed in a high-throughput manner relative to previous site-directed mutagenesis methods, enabling compilation of a large unbiased data set of regulatory elements of chloroplast gene expression. Finally, we create a novel synthetic UTR based on aggregate sequence analysis from the libraries and demonstrate that it significantly increases accumulation of an exogenous protein, attesting to the utility of this strategy for enhancing protein production in algal chloroplasts."
http://bit.ly/YozAGa ;