Urine utilisation by Microbial Fuel Cells; energy fuel for the future

Another approach to green energy, or yellow in this case. Essentially the authors created a microbial fuel cell that uses molecules in urine (uric acid, creatinine, small peptides, etc.) to generate electricity. Imagine the grad student who had to come in to work and urinate in his fuel cell every morning for two years...

Nutty, but interesting science.

A Small Molecule Modulates Circadian Rhythms through Phosphorylation of the Period Protein

This paper is a cool example of one advantage of Chemical Biology over Genetics. They reported the application in behavioral studies of the small molecule inhibitor of CKIdelta to overcome the limitation of lethality induced by CKIdelta knock-down mutations.

They identified the small molecule LH846 after a Luciferase cell-based assay of 500 000 compounds. The probe was then functionalized with a PEG linker and used in pull-down assays, they identified casein kinase 1 delta (CKIdelta) as the target. This is a known protein kinase that regulates the circadian clock. LH846 is a relatively potent and selective CKIdelta inhibitor that could provide insights into the role of circadian rhythms as well as new treatments for circadian disorders.

Structure-switching biosensors: inspired by Nature

This paper discusses biomolecular switches used as chemosensors. Biomolecules undergo binding-induced conformational changes to transduce chemical information into biochemical outputs. The efforts here are aimed at generating artificial chemical sensors that change their conformations upon ligand binding. These biomolecular switches allow for rapid and selective transduction of binding events in a single step. Their application has implications for the diagnosis of genetic and infectious diseases.

Correlated Optical and Electrical Single-Molecule Measurements Reveal Conformational Diffusion from Ligand Binding to Channel Gating in the Nicotinic

This communication looks at the kinetics of gate and channel opening with the use of fluorophores. By irradiating the fluorophore with light focused on the cell surface, electrical responses can be obeserved. Analyzing these responses showed that the ligand binds to the channel receptor, explores multiple confomational energy states, then proceeds through a quick gating event. I found the article interesting because of the experimental set up, which focused light on the cell surface where fluorophores were added and subsequent electrical responses were recorded.

Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’

This is another Tabor paper that involves quorum sensing in E. coli as a means to communicate logic gate outputs of engineered bacteria. Here, they expand upon their earlier work in making functional logic gates by successfully creating the more complex XOR gate and EQUALS function. Also, their colonies are arranged in a manner like a circuit board with the molecular outputs of the logic gates playing the roles of wires. So, desired computational outcomes can be generated by the system by calculated addition or subtraction of distinct E. coli colonies with one discrete gate function.

A Chemical Reporter for Protein AMPylation

AMPylation is a post-translational modification which is not well-understood. Current methods for detecting AMPylation include radioactive ATP, targeted mass spectrometry, and specific antibodies. The authors of this paper have developed a new method for detection of AMPylation using click chemistry. Native AMPylators are able to utilize N6-propargyl ATP as a substrate. This small molecule will be able to be utilized by more labs than radioactive ATP and can be modified with a variety of molecules including fluorophores for detection and biotin for purification.

Transducing Methyltransferase Activity into Electrical Signals in a Carbon Nanotube-DNA Device

This paper reminded me of the lecture presented by the PLU speaker last year.  They are able bind DNA to two carbon nanotubes and detect the conductivity of the DNA.  With this setup they can detect whether the DNA has been methylated or not.  The methylated DNA along with M. Sssl causes a conformational change that decreases the conductivity of the DNA. 

A synthetic library of RNA control modules for predictable tuning of gene expression in yeast.

This paper describes RNA-based control modules that allow for the tuning of protein expression levels in yeast. The Rnt1p substrate library described can be used to predictably tune gene expression, in this case gene regulation, in concert with any promoter. Two design strategies were implemented. First, a 'clamp' region was added to the base of each Rnt1p hairpin. Second, only sequences that formed predicted hairpin structures at the lowest free energies were included within the Rnt1p control module set. This prevents any flanking sequences from disrupting the desired folding of the control modules which could vary function in a genetic context. The Rnt1p library provides a key tool for synthetic biology applications in yeast.

Light Activation of a Cysteine Protease Inhibitor: Caging of a Peptidomimetic Nitrile with Ru

A photocaged protease inhibitor was designed using a synthesized peptidomimetic molecule with a nitrile group used for attachment to the 'cage', a ruthinium-based complex in this case. The aim is to develop this technology as a cancer drug that can be activated in proximity to the cancerous tissue with light. The protease inhibitor is meant to target a cysteine cathepsin, which is overexpressed in many cancers. Additionally, the ruthinium molecule also has potential bioactivity since it can covalently bind DNA. This complex showed excellent stability in the dark and rapid release of the inhibitor upon irradiation with light.

Manipulating the munchies in mice

This "news and views" paper gives a summary of this article about using a bump-and-hole method to create ion channels which are activated by drugs rather than by their native substrates. (We were talking in class today about how difficult it is to make a protein with this degree of orthogonality.) The ligand-binding extracellular domain was linked to cation- or anion-selective transmembrane and intracellular domains so that nerve cells could be selectively inhibited or excited. I chose this article mainly because I thought it had a funny title, but also because it was a good summary of the research that had been done.

DNA hybridization of pathogenicity island of vancomycin-resistant Enterococcus faecalis with discretely functionalized gold nanoparticles in organic solvent mixtures

Researchers joined short DNA sensors to gold nanoparticles in an organic solvent mixture.  The 10 base-pair DNA fragments were able to anneal to the target DNA and label it.  Such technology could be used in disease detection.  The researchers went on to see the effects changes to the solvent had on the annealing.  The study is lacking in a couple of areas, but the overall idea seems as though it could prove useful

Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase

This paper analyzes with the hydrophobic in an attempt to better model it.  Current modeling of the hydrophobic effect for biological application is incomplete and these researchers find it may be partially wrong.  They find that the effect stretches further than just the water molecules adjacent to the hydrophobic components and also analyze the effects on the binding pocket.

Architecture of human telomerase RNA

I was at an RNA symposium this weekend and Qi Zhang presented an interesting structural analysis of the telomerase RNA. This article discusses how the structure of the RNA component of telomerase core domain is important for template recognition. The core domain has a 39 degree angle of motion that correlates well with moving across the template DNA during telomere extension. It is a nice example of using structural information to understand the mechanism of action for biologically relevant enzymes. Additionally, the structural data could be used to develop specific SM inhibitors as we previously learned.

Rapid Multitarget Immunomagnetic Separation through Programmable DNA Linker Displacement

The authors describe a technique for magnetic selection of multiple targets in less time than previous studies.  Antibodies on the magnetic beads selectively bind their targets and then a first sort can occur.  The magnetic beads can then be selectively cleaved in a short amount of time and additional sorts can be used to sort all targets from one another.  The purity was high, but the yield of each target was low.  For sorting of four different groups this process took 1.5 hours compared to 5 hours by the standard method.

Cytocompatible click-based hydrogels with dynamically tunable properties through orthogonal photoconjugation and photocleavage reactions

The authors present a hydrogel network with two orthogonal light controlled functions. Thiol containing molecules can be covalently attached by the radical mediated thiol-ene reaction with visible light. The gel matrix can also be degraded by photocleaving at a nitrobenzyl moiety using UV light. These reactions are bioorthogonal and spatiotemporally controlled, allowing the material's properties to be regulated in real time. They demonstrated the utility of this matrix by encapsulating human mesenchymal stem cells. The cells were allowed to grow through regions of the hydrogel that had been modified by the thiol-ene reaction to contain integrin binding peptide ligands. The photocleaving reaction was then used to liberate cells at specific areas of the gel. Also, the authors encapsulated a cell-laden fibrin clot. Cell migration from the clot was controlled by both of the the photochemical reactions.

Metabolic engineering of microorganisms for isoprenoid production

This 2008 article gives a nice (if somewhat dated, now) overview of isoprenoid engineering advances. In Dr. Williams course we recently looked at mevalonate pathway optimization for increased amorpha-4,11-diene production and I touched upon taxadiene production as well. Both drug precursors rely on isoprenoid engineering for useful semisynthetic production versus extraction from plants, which is costly, time consuming, and environmentally adverse (in the case of Taxol). Though not the thorough review of Keasling's work that Dr. Williams hopes that one of us turns up, this could serve as a starting point for further investigation of isoprenoid production in microbial hosts.

Structure-Based Identification and Neutralization Mechanism of Tyrosine Sulfate Mimetics That Inhibit HIV-1 Entry

HIV-1 entry occurs when CD4 binds to the HCV-1 gp120 glycoprotein on the cell surface which induces a conformational change to trigger additional co-receptor CCR5 to interact. In this paper, P.D. Kwong and co-workers identified CCR5-N terminus mimetic small molecule inhibitors using in silico screening and further characterized in viral entry inhibition assay.  

RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites

This paper describes the development of a new independent E. Coli strain JX 33 that allows to reassign the stop codon UAG into a sense codon, in order to facilitate the introduction of unnatural amino acids in live cells.In JX33, the release factor 1 has been knocked-out to overcome the current issues associated with low level of incorporation. Also, their method can be used to incorporate several unnatural amino acids at different sites within the same protein. They tested the incorporation of up to 6 mutations in the EGFP gene and obtained similar level of fluorescence among all mutants.

This is an interesting article. It may open up the possibility to introduce different unnatural amino acids within the same protein with high level of incorporation.