Engineering whole-cell biosensors with no antibiotic markers for monitoring aromatic compounds in the environment.

Gene regulation is one of the foci of synthetic biology research. This paper provides further insight into the engineering of components of a gene regulatory network for whole-cell biosensors’ physical and chemical signals. Its aim is to increase the sensitivity of a particular genetic circuit towards XylR inducers. XylR is a transcriptional regulator of the TOL pathway of Pseudomonas putida mt-2. The TOL plasmid encodes a pathway for the catabolism of toluene and xylenes.

Parts-Based Assembly of Synthetic Transmembrane Proteins in Mammalian Cells

This Synthetic Biology paper looks at membrane targeting using a "parts" approach. It was determined that the only necessary part was a transmembrane helix to target proteins to membranes. I found this article interesting because part of my proposal depended on the ability to target proteins to the outside of the cells. It will be interesting to see how these studies progress to investigate signaling and orientation of assembled parts.

Optimized clinical performance of growth hormone with an expanded genetic code

I thought this paper was pretty interesting... This paper describes the incorporation of an unnatural amino acid into human growth hormone. This incorporation allows for a PEG group to be site specifically attached to the HGH. The PEG group improves efficacy and potency and is as safe as normal HGH. Baseball players though probably want something that is potent and out of the system quick... Either way this pretty interesting application of UAA mutagenesis!

Inducible gene expression from the plastid genome by a synthetic riboswitch

I think this is a really cool paper. Currently very few synthetic riboswitches exist in eukaryotic systems. This is because eukaryotic transcription and translation is a lot more complex than a prokaryotic system and hence harder to manipulate. The author is able to get around this problem by targeting the chloroplast (plastids) in plants. Chloroplasts have their own transcription/ translation machinery which is largely prokaryotic. Therefore, the author is able to screen these riboswitches in E. coli and then transfer them to the chloroplasts. In this article, the author feels that this would be a great tool for synthetic biology and the manufacture of natural products. This is because chloroplasts have the ability to store large amounts of products with out becoming toxic to the cell. The picture above shows six different riboswitches expressed in the presence or the absence of their ligand. As you can see the only switch that worked was the synthetic theophylline switch.

An Origin of Life on Mars

I thought this article was kind of interesting and related to class when we talked about how life could evolve differently.  The article discusses what information about life found on Mars could tell us about evolution and also makes some speculations about what it would be like.  It's a quick read and will provide some variety to the papers you read

Functional Detection of Proteins by Caged Aptamers

The research presented in this paper uses caged aptamers as a way to detect analyte proteins, followed by elution under mild conditions and qPCR. The advantage of this technique over immuno-PCR, which employs antibodies attached to a short DNA strand, is that the aptamer both binds the target and is the template for quantification. Because light is used to free the analyte, no damage is done to either the aptamer or the target protein, so further analysis is possible.

Reversible Covalent Chemistries Compatible with the Principles of Constitutional Dynamic Chemistry: New Reactions to Create More Diversity

While preparing my slides on unnatural nucleotides, I came across the idea of dynamic combinatorial chemistry. Essentially, one creates a dynamic combinatorial library, where individual components are reversibly bonding to one another creating interchanging products under thermodynamic control. Upon addition of a target molecule, the equilibrium changes based on Le Chatalier's rules, enriching the multimers with the highest affinity to the target.

This review covers some of the best examples of reactions that are suited for DCC.

20 years of DNA-encoded chemical libraries

DNA-encoded chemical library is a technology that advances the identification of ligands and small molecules for protein targets. The use of a DNA-encoded library makes the connection between genotype and pheontype easier to identify through amplification of the DNA "barcode". This review discussed the growth of the technology and enhanced methods that have been developed. Applications through the years are also presented.

Small Molecules from Spiders Used as Chemical Probes

Acylpolyamine toxins from spiders have been characterized to selectively block calcium-permeable iGlu receptors in neurons, belonging to the AMPA class of neurons. Variations of these chemicals from other species have been used to selectivly block potassium, sodium and calcium voltage-gated channels in mammals. In additon to acting as a precise tool for chemical genetics, some therapeutic applications may be on the horizon.