SynBioFromLeukipposInstitute

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Simon Ausländer, David Ausländer, Marius Müller, Markus Wieland & Martin Fussenegger
"Synthetic biology has advanced the design of standardized control devices that program cellular functions and metabolic activities in living organisms1. Rational interconnection of these synthetic switches resulted in increasingly complex designer networks that execute input-triggered genetic instructions with precision, robustness and computational logic reminiscent of electronic circuits2, 3. Using trigger-controlled transcription factors, which independently control gene expression4, 5, and RNA-binding proteins that inhibit the translation of transcripts harbouring specific RNA target motifs6, 7, we have designed a set of synthetic transcription–translation control devices that could be rewired in a plug-and-play manner. Here we show that these combinatorial circuits integrated a two-molecule input and performed digital computations with NOT, AND, NAND and N-IMPLY expression logic in single mammalian cells. Functional interconnection of two N-IMPLY variants resulted in bitwise intracellular XOR operations, and a combinatorial arrangement of three logic gates enabled independent cells to perform programmable half-subtractor and half-adder calculations. Individual mammalian cells capable of executing basic molecular arithmetic functions isolated or coordinated to metabolic activities in a predictable, precise and robust manner may provide new treatment strategies and bio-electronic interfaces in future gene-based and cell-based therapies."
http://bit.ly/LhEZpo

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Glykys DJ, Szilvay GR, Tortosa P, Suárez Diez M, Jaramillo A, Banta S.
"The de novo engineering of new proteins will allow the design of complex systems in synthetic biology. But the design of large proteins is very challenging due to the large combinatorial sequence space to be explored and the lack of a suitable selection system to guide the evolution and optimization. One way to approach this challenge is to use computational design methods based on the current crystallographic data and on molecular mechanics. We have used a laccase protein fold as a scaffold to design a new protein sequence that would adopt a 3D conformation in solution similar to a wild-type protein, the Trametes versicolor (TvL) fungal laccase. Laccases are multi-copper oxidases that find utility in a variety of industrial applications. The laccases with highest activity and redox potential are generally secreted fungal glycoproteins. Prokaryotic laccases have been identified with some desirable features, but they often exhibit low redox potentials. The designed sequence (DLac) shares a 50% sequence identity to the original TvL protein. The new DLac gene was overexpressed in E. coli and the majority of the protein was found in inclusion bodies. Both soluble protein and refolded insoluble protein were purified, and their identity was verified by mass spectrometry. Neither protein exhibited the characteristic T1 copper absorbance, neither bound copper by atomic absorption, and neither was active using a variety of laccase substrates over a range of pH values. Circular dichroism spectroscopy studies suggest that the DLac protein adopts a molten globule structure that is similar to the denatured and refolded native fungal TvL protein, which is significantly different from the natively secreted fungal protein. Taken together, these results indicate that the computationally designed DLac expressed in E. coli is unable to utilize the same folding pathway that is used in the expression of the parent TvL protein or the prokaryotic laccases. This sequence can be used going forward to help elucidate the sequence requirements needed for prokaryotic multi-copper oxidase expression. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11693-011-9080-9) contains supplementary material, which is available to authorized users."

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Radoje Drmanac
"Encoded in the DNA sequence of our individual genome is the genetic program to build, maintain, and adapt all our tissues and their functions. Each human genome contains 200,000 coding elements (exons) and millions of regulatory elements (1) defining complex signaling and regulatory networks."
http://bit.ly/JDaZEI

An awesome paper in Science about quantum field theory. I ask myself: Will we get quantum biology? Is quantum theory also valid at the scale of biological structures? What is your opinion?

Quantum Algorithms for Quantum Field Theories

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Stephen P. Jordan, Keith S. M. Lee, John Preskill
"Quantum field theory reconciles quantum mechanics and special relativity, and plays a central role in many areas of physics. We developed a quantum algorithm to compute relativistic scattering probabilities in a massive quantum field theory with quartic self-interactions (ϕ4 theory) in spacetime of four and fewer dimensions. Its run time is polynomial in the number of particles, their energy, and the desired precision, and applies at both weak and strong coupling. In the strong-coupling and high-precision regimes, our quantum algorithm achieves exponential speedup over the fastest known classical algorithm."

http://bit.ly/MkM6V1

Crosstalk between endogenous and synthetic components - synthetic signaling meets endogenous components

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Morey KJ, Antunes MS, Barrow MJ, Solorzano FA, Havens KL, Smith JJ, Medford J.
"Synthetic biology uses biological components to engineer new functionality in living organisms. We have used the tools of synthetic biology to engineer detector plants that can sense man-made chemicals, such as the explosive trinitrotoluene, and induce a response detectable by eye or instrumentation. A goal of this type of work is to make the designed system orthogonal, that is, able to function independently of systems in the host. In this review, the design and function of two partially synthetic signaling pathways for use in plants is discussed. We describe observed interactions (crosstalk) with endogenous signaling components. This crosstalk can be beneficial, allowing the creation of hybrid synthetic/endogenous signaling pathways, or detrimental, resulting in system noise and/or false positives. Current approaches in the field of synthetic biology applicable to the design of orthogonal signaling systems, including the design of synthetic components, partially synthetic systems that utilize crosstalk to signal through endogenous components, computational redesign of proteins, and the use of heterologous components, are discussed."

http://1.usa.gov/LfoAnJ

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Bryan Wei, Mingjie Dai & Peng Yin
"Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape9, 14, 15, 16, 18, 19, 20, 21, 25. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA2, 3, 4, 5, 8, 10, 11, 12, 13, 17, 23 or RNA7, 22 tiles into periodic3, 4, 7, 22 and algorithmic5 two-dimensional lattices, extended ribbons10, 12 and tubes4, 12, 13, three-dimensional crystals17, polyhedra11 and simple finite two-dimensional shapes7, 8. But creating finite yet complex shapes from a large number of uniquely addressable tiles remains challenging. Here we solve this problem with the simplest tile form, a ‘single-stranded tile’ (SST) that consists of a 42-base strand of DNA composed entirely of concatenated sticky ends and that binds to four local neighbours during self-assembly12. Although ribbons and tubes with controlled circumferences12 have been created using the SST approach, we extend it to assemble complex two-dimensional shapes and tubes from hundreds (in some cases more than one thousand) distinct tiles. Our main design feature is a self-assembled rectangle that serves as a molecular canvas, with each of its constituent SST strands—folded into a 3 nm-by-7 nm tile and attached to four neighbouring tiles—acting as a pixel. A desired shape, drawn on the canvas, is then produced by one-pot annealing of all those strands that correspond to pixels covered by the target shape; the remaining strands are excluded. We implement the strategy with a master strand collection that corresponds to a 310-pixel canvas, and then use appropriate strand subsets to construct 107 distinct and complex two-dimensional shapes, thereby establishing SST assembly as a simple, modular and robust framework for constructing nanostructures with prescribed shapes from short synthetic DNA strands...."
http://bit.ly/LLmACs

a great news and views:
Nanotechnology: The importance of being modular
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Paul W. K. Rothemund & Ebbe Sloth Andersen
"DNA is the material of choice for making custom-designed, nanoscale shapes and patterns through self-assembly. A new technique revisits old ideas to enable the rapid prototyping of more than 100 such DNA shapes"
http://bit.ly/JCC7Zn

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Gao CY, Zhao L, Wang MX.

"We report herein the synthesis of a new metal cluster-encapsulated supramolecular capsule, [(C≡C)@Ag(5-6)@(Py6)(2)](CF(3)SO(3))(3-4) (3, Py6 = azacalix[6]pyridine), by use of a bowl-shaped macrocyclic ligand Py6. The multinuclear silver carbide cluster aggregate in 3 is encapsulated by two Py6 ligands through both metal-ligand coordination and cation-π interactions, spotlighting a new synthetic strategy for supramolecular capsules."

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Liang JC, Smolke CD.

"A synthetic gene-regulatory device platform was described by modularly assembling three RNA components encoding distinct functions of sensing, transmission, and actuation. The molecular binding at the sensor component is translated by the transmitter component through a strand-displacement event to modulate activity of the actuator component, which then interacts with cellular transcriptional machinery to affect gene expression levels. Here, we provide some general guidelines on linking RNA components to construct gene-regulatory devices and strategies to tune device regulatory activities through an RNA folding -program for specific cellular applications."

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Leprince A, van Passel MW, Dos Santos VA.

"At the junction between systems and synthetic biology, genome streamlining provides a solid foundation both for increased understanding of cellular circuitry, and for the tailoring of microbial chassis towards innovative biotechnological applications. Iterative genomic deletions (targeted and random) helps to generate simplified, stabilized and predictable genomes, whereas multiplexing genome engineering reveals a broad functional genetic diversity. The decrease in oligo and gene synthesis costs promises effective combinatorial tools for the generation of chassis based on streamlined and tractable genomes. Here we review recent progresses in streamlining genomes through recombineering techniques aiming to generate insights into cellular mechanisms and responses towards the design and assembly of streamlined genome chassis together with new cellular modules in diverse biotechnological applications."

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Liam R. Brunham, Michael R. Hayden
"Rapid advances in DNA sequencing technology have made whole-genome sequencing (WGS) both technically and economically feasible. WGS has been used with great effect in specific settings to clarify molecular diagnosis and even to guide therapy (1, 2). But are we ready for the routine use of WGS in the care of healthy individuals?"
http://bit.ly/JDbq1R

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Neil P. King, William Sheffler, Michael R. Sawaya, Breanna S. Vollmar, John P. Sumida, Ingemar André, Tamir Gonen, Todd O. Yeates, David Baker
"We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nano materials."
http://bit.ly/KGJAGo

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Dror Seliktar
"Hydrogels are polymeric materials distinguished by high water content and diverse physical properties. They can be engineered to resemble the extracellular environment of the body’s tissues in ways that enable their use in medical implants, biosensors, and drug-delivery devices. Cell-compatible hydrogels are designed by using a strategy of coordinated control over physical properties and bioactivity to influence specific interactions with cellular systems, including spatial and temporal patterns of biochemical and biomechanical cues known to modulate cell behavior. Important new discoveries in stem cell research, cancer biology, and cellular morphogenesis have been realized with model hydrogel systems premised on these designs. Basic and clinical applications for hydrogels in cell therapy, tissue engineering, and biomedical research continue to drive design improvements using performance-based materials engineering paradigms."
http://bit.ly/M8ULXT

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Cardinale S, Arkin AP.
"Despite the efforts that bioengineers have exerted in designing and constructing biological processes that function according to a predetermined set of rules, their operation remains fundamentally circumstantial. The contextual situation in which molecules and single-celled or multi-cellular organisms find themselves shapes the way they interact, respond to the environment and process external information. Since the birth of the field, synthetic biologists have had to grapple with contextual issues, particularly when the molecular and genetic devices inexplicably fail to function as designed when tested in vivo. In this review, we set out to identify and classify the sources of the unexpected divergences between design and actual function of synthetic systems and analyze possible methodologies aimed at controlling, if not preventing, unwanted contextual issues."
http://1.usa.gov/KEG2Ex

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Yamamoto A, Ueda A, Brémond P, Tiseni PS, Kishi Y.

"The first total synthesis of halichondrin C has been completed, highlighted by development of the synthetic method to construct the C8-C14 polycycle. Cr-mediated coupling reactions are used seven times to form a new C-C bond. The acid stability of halichondrin C is studied, demonstrating that the macrolactone stabilizes the C8-C14 polycycle, relative to the one present in the C1-C16 model."