"Jason Kelly was in Manhattan Thursday to meet with a prospective customer in the perfume business. Kelly, a founder of Boston-based Ginkgo Bioworks , sells custom-crafted organisms — mostly yeast, bacteria, and algae — and one of the jobs they can do is make synthetic scents that might one day go into a fragrance that you spray or dab on.
Custom-crafted organisms? Yep, designed and produced in a lab that overlooks Boston Harbor.
If textile mills represented the cutting edge of Massachusetts manufacturing in the early 1800s, this is one example of the extremely advanced manufacturing that could thrive in the 21st century. This month, Ginkgo announced that it had raised its first venture capital funding since it spun out from MIT in 2008 — $9 million — and it put the finishing touches on a production facility it calls Foundry1, full of automated machines that can cost hundreds of thousands of dollars each.
Ginkgo is part of a field called “synthetic biology” that holds immense promise — but also freaks people out. It involves writing genetic code and inserting it into simple organisms to change their function. Boosters point to the possibility of vats of algae cranking out fuels or industrial chemicals that today come from petroleum, or to bespoke bacteria that could diagnose diseases sooner than we can today. But others worry about terrorists producing ultra-potent pathogens, or someone accidentally spawning a fast-replicating organism that damages the environment.
How do bacteria sense their environment? How can we describe the genetic mechanisms behind this process? How can we use this knowledge to develop useful appl...
by Moore R, Spinhirne A, Lai MJ, Preisser S, Li Y1, Kang T1 Bleris L
"Controllable gene delivery via vector-based systems remains a formidable challenge in mammalian synthetic biology and a desirable asset in gene therapy applications. Here, we introduce a methodology to control the copies and residence time of a gene product delivered in host human cells but also selectively disrupt fragments of the delivery vehicle. A crucial element of the proposed system is the CRISPR protein Cas9. Upon delivery, Cas9 guided by a custom RNA sequence cleaves the delivery vector at strategically placed targets thereby inactivating a co-expressed gene of interest. Importantly, using experiments in human embryonic kidney cells, we show that specific parameters of the system can be adjusted to fine-tune the delivery properties. We envision future applications in complex synthetic biology architectures, gene therapy and trace-free delivery."
by Mitchell R. O’Connell,Benjamin L. Oakes,Samuel H. Sternberg,Alexandra East-Seletsky, Matias Kaplan& Jennifer A. Doudna
"The CRISPR-associated protein Cas9 is an RNA-guided DNA endonuclease that uses RNA–DNA complementarity to identify target sites for sequence-specific double-stranded DNA (dsDNA) cleavage1, 2, 3, 4, 5. In its native context, Cas9 acts on DNA substrates exclusively because both binding and catalysis require recognition of a short DNA sequence, known as the protospacer adjacent motif (PAM), next to and on the strand opposite the twenty-nucleotide target site in dsDNA4, 5, 6, 7. Cas9 has proven to be a versatile tool for genome engineering and gene regulation in a large range of prokaryotic and eukaryotic cell types, and in whole organisms8, but it has been thought to be incapable of targeting RNA5. Here we show that Cas9 binds with high affinity to single-stranded RNA (ssRNA) targets matching the Cas9-associated guide RNA sequence when the PAM is presented in trans as a separate DNA oligonucleotide. Furthermore, PAM-presenting oligonucleotides (PAMmers) stimulate site-specific endonucleolytic cleavage of ssRNA targets, similar to PAM-mediated stimulation of Cas9-catalysed DNA cleavage7. Using specially designed PAMmers, Cas9 can be specifically directed to bind or cut RNA targets while avoiding corresponding DNA sequences, and we demonstrate that this strategy enables the isolation of a specific endogenous messenger RNA from cells. These results reveal a fundamental connection between PAM binding and substrate selection by Cas9, and highlight the utility of Cas9 for programmable transcript recognition without the need for tags."
"Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a "body of knowledge" from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community."
Synthetic Aesthetics: Investigating Synthetic Biology's Designs on Nature, Endy, in gekoo.co - Search, Find, Compare and Buy it Now - Deals and Offers Online - Discounts and Promotions
MIT 7.91J Foundations of Computational and Systems Biology, Spring 2014 View the complete course: http://ocw.mit.edu/7-91JS14 Instructor: Ron Weiss This gues...
Legendary biologist Edward O. Wilson explores three realms of ultimate biology from which we should expect major breakthroughs over the next several decades....
Bioengineers at The University of Texas at Dallas have created a novel gene-delivery system that shuttles a gene into a cell, but only for a temporary stay, providing a potential new gene-therapy strategy for treating disease.
Deep in the heart of synthetic biology are the proteins that make it tick. Protein engineering is the crucial pulse of the booming, relatively new scientific discipline.
*Programmable materials and the nature of the DNA bond*
by Matthew R. Jones, Nadrian C. Seeman2, Chad A. Mirkin
"BACKGROUND
Nucleic acids are ubiquitous in biology because of their ability to encode vast amounts of information via canonical Watson-Crick base-pairing interactions. With the advent of chemical methods to make synthetic oligonucleotides of an arbitrary sequence, researchers can program entire libraries of molecules with orthogonal interactions, directed to assemble in highly specific arrangements. Early attempts to use DNA to make nanostructures led to topologically defined architectures, but ones that were too conformationally flexible to be used to guide the construction of well-defined nanoscale materials from the bottom up. In this Review, we discuss the key discoveries that have overcome this limitation and distill common design principles that have since led to a revolution in materials sophistication based on DNA-directed assembly.
ADVANCES
The experimental realization of DNA-based constructs that are sufficiently rigid so as to impart directionality to hybridization interactions marks a major milestone in the development of programmable materials assembly. This feat was accomplished simultaneously by the Mirkin Group and Seeman Group in 1996, but through chemically and conceptually distinct pathways. In one approach, rigidity is derived from multiple strand crossover events and the hybridization that stabilizes them to create a conformationally restricted DNA tile. In the other approach, a rigid non-nucleic acid–based nanoparticle (inorganic or organic) core acts as a template to organize functionalized DNA strands in a surface-normal orientation. It is appealing to draw the analogy between DNA-based constructs of this sort with the concepts of “bonds” and “valency” found in atomic systems. Just as understanding the nature of atomic bonding is crucial for chemists to manipulate the formation of molecular and supramolecular species, so too is an understanding of the nature of these DNA bonding modes necessary for nanoscientists to build complex and functional architectures to address materials needs.
OUTLOOK
The interest in nanoscale materials constructed by using DNA bonds has continued to grow steadily, but has seen a noteworthy explosion in relevance over the past several years. This is due in large part to the development of methods to move beyond simple clusters and crystals to more sophisticated nanostructured materials that are dynamic and stimuli responsive, are macroscopic in spatial extent, and exhibit emergent physical properties that arise from specific arrangements of matter. These techniques offer perhaps the most versatile way of organizing optically active materials into architectures that exhibit unusual and deliberately tailorable plasmonic and photonic properties. In addition, prospects include the use of these materials in biological settings, being that they are constructed, in large measure, from nucleic acid precursors. The ability to manipulate gene expression, deliver molecular payloads via DNA-based binding events, and detect relevant markers of disease with nanoscale spatial resolution represent some of the most fruitful avenues of future research."
A bacterium has been used to wish people a Merry Xmas. Grown by Dr Munehiro Asally, an Assistant Professor at the University of Warwick, the letters used to spell MERRY XMAS are made of Bacillus subtilis, a non-pathogenic bacterium which is found in soil and also human gut.
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Scott Kirsner
"Jason Kelly was in Manhattan Thursday to meet with a prospective customer in the perfume business. Kelly, a founder of Boston-based Ginkgo Bioworks , sells custom-crafted organisms — mostly yeast, bacteria, and algae — and one of the jobs they can do is make synthetic scents that might one day go into a fragrance that you spray or dab on.
http://bit.ly/1N1dNhm