SynBioFromLeukipposInstitute

Global synthetic biology market is estimated to reach $38.7 billion by 2020
http://bit.ly/1D4gt9B

by
Anonymous

"Best known as a gene-editing system, CRISPR/Cas9 is also being used to edit the epigenome, turning on specific gene promoters and enhancers. The trick is to silence CRISPR/Cas9’s DNA-cutting mechanism. Instead, the CRISPR/Cas9 machinery is used to deliver an enzyme, an acetyltransferase, which adds artificial epigenetic marks to the DNA packaging proteins known as histones.

 http://bit.ly/1CgdQyI

by
Heidi Ledford

"Discovery expands potential CRISPR toolbox for treating genetic diseases in humans.

 http://bit.ly/1EKDX79

*Design criteria for synthetic riboswitches acting on transcription*

by
Wachsmuth M, Domin G, Lorenz R, Serfling R, Findeiß S, Stadler PF, Mörl M.

"Riboswitches are RNA-based regulators of gene expression composed of a ligand-sensing aptamer domain followed by an overlapping expression platform. The regulation occurs at either the level of transcription (by formation of terminator or antiterminator structures) or translation (by presentation or sequestering of the ribosomal binding site). Due to a modular composition, these elements can be manipulated by combining different aptamers and expression platforms and therefore represent useful tools to regulate gene expression in synthetic biology. Using computationally designed theophylline-dependent riboswitches we show that 2 parameters, terminator hairpin stability and folding traps, have a major impact on the functionality of the designed constructs. These have to be considered very carefully during design phase. Furthermore, a combination of several copies of individual riboswitches leads to a much improved activation ratio between induced and uninduced gene activity and to a linear dose-dependent increase in reporter gene expression. Such serial arrangements of synthetic riboswitches closely resemble their natural counterparts and may form the basis for simple quantitative read out systems for the detection of specific target molecules in the cell."


http://bit.ly/1OZEe9c

*Engineering a Bacterial Tape Recorder*

by
Alexander Prokup andAlexander Deiters

"A method has been developed to produce and integrate single-stranded DNA into genomic locations in bacteria in response to exogenous signals. The system functions similarly to a cellular tape recorder by writing information into DNA and reading it at a later time. Much like other cellular memory platforms, its operation is based on DNA recombinase function. However, the scalability and recording capacity have been improved over previous designs. In addition, memory storage was reversible and could be recorded in response to analogue inputs, such as light exposure. This modular memory writing system is an important addition to the genomic editing toolbox available for synthetic biology."


http://bit.ly/1aeVV4X


Image from:
Bacteria become 'genomic tape recorders', recording chemical exposures in their DNA http://bit.ly/1HhoWqM

by
Stuart Mason Dambrot 

"a quick overview:

by
Erika Check Hayden

"Synthetic biologists have a vision. Researchers in this young field, who build ‘devices’ from engineered genes and other molecular components, imagine a future in which products such as drugs, chemicals, fuels and food are manufactured by microbes. These devices could even be wired up to create cellular computers, much as electronic transistors are wired up to make microprocessors (see Nature http://doi.org/3fz; 2013).

But if the dream is to be realized, those components need to perform more consistently and be more reproducible than they are now, especially as they move from the lab bench to the biofactory. Unlike silicon-based electronic devices, synthetic organisms assembled from genetic components do not always have predictable properties — at least not yet.

On 31 March, representatives from industry, academic institutions and government met at Stanford University in California to launch the Synthetic Biology Standards Consortium, an initiative led by the US National Institute of Standards and Technology (NIST) to address issues preventing the field from reaching its potential.

“It’s the signal of a maturing industry,” says Patrick Boyle, who oversees the organism-design pipeline at Ginkgo BioWorks, a synthetic-biology company in Boston, Massachusetts. “As we get better at synthetic biology, we want to make sure we are comparing apples to apples.”

The standards push comes at a pivotal point for synthetic biology. Ginkgo BioWorks is one of several ‘foundries’ set up to mass produce organisms for various uses. ....."


http://bit.ly/1FrkvqW

by
Drew Endy

"Time Lapse Movie by Jerome Bonnet et al. (Stanford) showing brightfield (left), control signal change over time (middle) and gate output (right) in individual cells operating a transcriptor-based genetic amplifier. "

http://bit.ly/1GLzr7l


ref to 
*Amplifying Genetic Logic Gates*
http://bit.ly/1Fhukgv

by
Masoumeh Emadpour, Daniel Karcher and Ralph Bock

"Riboswitches are RNA sensors that regulate gene expression in response to binding of small molecules. Although they conceptually represent simple on/off switches and, therefore, hold great promise for biotechnology and future synthetic biology applications, the induction of gene expression by natural riboswitches after ligand addition or removal is often only moderate and, consequently, the achievable expression levels are not very high. Here, we have designed an RNA amplification-based system that strongly improves the efficiency of riboswitches. We have successfully implemented the method in a biological system for which currently no efficient endogenous tools for inducible (trans)gene expression are available: the chloroplasts of higher plants. We further show that an HIV antigen whose constitutive expression from the chloroplast genome is deleterious to the plant can be inducibly expressed under the control of the RNA amplification-enhanced riboswitch (RAmpER) without causing a mutant phenotype, demonstrating the potential of the method for the production of proteins and metabolites that are toxic to the host cell."

 http://bit.ly/1bPDRP7

by
Nicole Rusk

"Synthetic small RNA transcriptional activators can regulate gene transcription in Escherichia coli.

'Learn from nature and copy what it does' is one of the guiding principles in the laboratory of Julius Lucks at Cornell University, but in their recent work, the researchers developed a strategy that seemingly expands what nature has to offer.

“We want to leverage our ability to model and measure RNA structures to make gene networks,” says Lucks. His team focuses on transcriptional control, and they aim to have RNA inputs control RNA outputs without involving proteins such as transcription factors. “The big conceptual advantage of RNA over proteins is that you can do design,” explains Lucks. “We know a lot more about RNA folding than we do about protein folding.”

The strategy of the Lucks team has been to observe RNA design principles in nature, characterize their structure and then apply these designs to the engineering of genetic circuits. The limitation is that whereas nature very efficiently uses small RNAs to repress transcription, there are to date no known instances of small RNAs alone activating transcription. “But,” says Lucks, “if you want to build networks, you need to turn things on as well as off.”

Melissa Takahashi, a graduate student in the lab, first focused on characterizing the function of a natural RNA transcriptional repressor mechanism: a special sequence upstream of a gene's coding region that can form RNA structures that allow or prevent progression of the RNA polymerase. These structures are switchable: in one case transcription is stopped by a transcriptional terminator RNA hairpin, and in the other case transcription is allowed by an antiterminator sequence that sequesters the terminator and prevents the formation of the blocking hairpin. Takahashi looked at the structural transitions needed in order to undergo the switch from active to inactive transcription; she then came up with a strategy to invert this repression mechanism into one that activates transcription by adding yet another layer of structural transitions using a small transcription activating RNA (STAR)...."

http://bit.ly/1OZAWTi

Comment to:
Creating small transcription activating RNAs

by
James Chappell, Melissa K Takahashi & Julius B Lucks

"We expanded the mechanistic capability of small RNAs by creating an entirely synthetic mode of regulation: small transcription activating RNAs (STARs). Using two strategies, we engineered synthetic STAR regulators to disrupt the formation of an intrinsic transcription terminator placed upstream of a gene in Escherichia coli. This resulted in a group of four highly orthogonal STARs that had up to 94-fold activation. By systematically modifying sequence features of this group, we derived design principles for STAR function, which we then used to forward engineer a STAR that targets a terminator found in the Escherichia coli genome. Finally, we showed that STARs could be combined in tandem to create previously unattainable RNA-only transcriptional logic gates. STARs provide a new mechanism of regulation that will expand our ability to use small RNAs to construct synthetic gene networks that precisely control gene expression."
http://bit.ly/1HjhZW7