Outer-Membrane Protease (OmpT) Based E. coli Sensing with Anionic Polythiophene and Unlabeled Peptide Substrate

E. coli and Salmonella are two of the most common bacterial pathogens involved in foodborne and waterborne related deaths. Hence, it is critical to develop rapid and sensitive detection strategies for near-outbreak applications. Reported is a simple and specific assay to detect as low as 1 CFU mL⁻¹ of E. coli in water within 6 hours by targeting the bacteria's surface protease activity. The assay relies on polythiophene acetic acid (PTAA) as an optical reporter and a short unlabeled peptide (LL37_FRRV) previously optimized as a substrate for OmpT, an outer-membrane protease on E. coli. LL37_FRRV interacts with PTAA to enhance its fluorescence while also inducing the formation of a helical PTAA-LL37_FRRV construct, as confirmed by circular dichroism. However, in the presence of E. coli LL37_FRRV is cleaved and can no longer affect the conformations and optical properties of PTAA. This ability to distinguish between an intact and cleaved peptide was investigated in detail using LL37_FRRV sequence variants.     

Reversible Soft Mechanochemical Control of Biaryl Conformations through Crosslinking in a 3D Macromolecular Network

Tuning the dihedral angle (DA) of axially chiral compounds can impact biological activity, catalyst efficiency, molecular motor performance, or chiroptical properties. Herein, we report gradual, controlled, and reversible changes in molecular conformation of a covalently linked binaphthyl moiety within a 3D polymeric network by application of a macroscopic stretching force. We managed direct observation of DA changes by measuring the circular dichroism signal of an optically pure BINOL-crosslinked elastomer network. Stretching the elastomer resulted in a widening of the DA between naphthyl rings when the BINOL was doubly grafted to the elastomer network; no effect was observed when a single naphthyl ring of the BINOL was grafted to the elastomer network. We have determined that ca. 170 % extension of the elastomers led to the transfer of a mechanical force to the BINOL moiety of 2.5 kcal mol⁻¹ Å⁻¹ (ca. 175 pN) in magnitude and results in the opening of the DA of BINOL up to 130°.     

Dynamic Bio-Barcode Assay Enables Electrochemical Detection of a Cancer Biomarker in Undiluted Human Plasma: A Sample-In-Answer-Out Approach

There is a need for biosensing systems that can be operated at the point-of-care (POC) for disease screening and diagnostics and health monitoring. In spite of this, simple to operate systems with the required analytical sensitivity and specificity in clinical samples, using a sample-in-answer-out approach, remain elusive. Reported here is an electrochemical bio-barcode assay (e-biobarcode assay) that integrates biorecognition with signal transduction using molecular (DNA/protein) machines and signal readout using nanostructured electrodes. The e-biobarcode assay eliminates multistep processing and uses a single step for analysis following sample collection into the reagent tube. A clinically relevant performance for the analysis of prostate specific antigen (PSA) in undiluted and unprocessed human plasma: a log-linear range of 1 ng mL⁻¹–200 ng mL⁻¹ and a LOD of 0.4 ng mL⁻¹, was achieved. The e-biobarcode assay offers a realistic solution for biomarker analysis at the POC.     

The Hodge structure of the coloring complex of a hypergraph

Let G be a simple graph with n vertices. The coloring complex Δ(G) was defined by Steingrímsson, and the homology of Δ(G) was shown to be nonzero only in dimension n−3 by Jonsson. Hanlon recently showed that the Eulerian idempotents provide a decomposition of the homology group H_n−3(Δ(G)) where the dimension of the jth component in the decomposition, , equals the absolute value of the coefficient of λ^j in the chromatic polynomial of G, χ_G(λ).Let H be a hypergraph with n vertices. In this paper, we define the coloring complex of a hypergraph, Δ(H), and show that the coefficient of λ^j in χ_H(λ) gives the Euler Characteristic of the jth Hodge subcomplex of the Hodge decomposition of Δ(H). We also examine conditions on a hypergraph, H, for which its Hodge subcomplexes are Cohen–Macaulay, and thus where the absolute value of the coefficient of λ^j in χ_H(λ) equals the dimension of the jth Hodge piece of the Hodge decomposition of Δ(H). We also note that the Euler Characteristic of the jth Hodge subcomplex of the Hodge decomposition of the intersection of coloring complexes is given by the coefficient of jth term in the associated chromatic polynomial.     

Rank varieties for Hopf algebras

We construct rank varieties for the Drinfeld double of the Taft algebra Λ_n and for u_q(sl₂). For the Drinfeld double when n=2 this uses a result which identifies a family of subalgebras that control projectivity of Λ-modules whenever Λ is a Hopf algebra satisfying a certain homological condition. In this case we show that our rank variety is homeomorphic to the cohomological support variety. We also show that Ext^∗(M,M) is finitely generated over the cohomology ring of the Drinfeld double for any finitely generated module M.     

Classical Cys2His2 zinc finger peptides are rapidly oxidized by either H2O2 or O2 irrespective of metal coordination

ZIF268, a member of the classical zinc finger protein family, contains three Cys(2)His(2) zinc binding domains that together recognize the DNA sequence 5'-AGCGTGGGCGT-3'. These domains can be fused to an endonuclease to make a chimeric protein to target and cleave specific DNA sequences. A peptide corresponding to these domains, named ZIF268-3D, has been prepared to determine if the zinc finger domain itself can promote DNA cleavage when a redox active metal ion, Fe(II), is coordinated. The UV-vis absorption spectrum of Fe(II)-ZIF268-3D is indicative of Fe(II) coordination. Using fluorescence anisotropy, we demonstrate that Fe(II)-ZIF268-3D binds selectively to its target DNA in the same manner as Zn(II)-ZIF268-3D. In the presence of added oxidant, H(2)O(2) or O(2), DNA cleavage is not observed by Fe(II)-ZIF268-3D. Instead, the peptide itself is rapidly oxidized. Similarly, Zn(II)-ZIF268-3D and apo-ZIF268-3D are rapidly oxidized by H(2)O(2) or O(2), and we propose that ZIF268-3D is highly susceptible to oxidation.     

Reduced dimensionality spin-orbit dynamics of CH3 + HCl ⇌ CH4 + Cl on ab initio surfaces

A reduced dimensionality quantum scattering method is extended to the study of spin-orbit nonadiabatic transitions in the CH(3) + HCl ? CH(4) + Cl((2)P(J)) reaction. Three two-dimensional potential energy surfaces are developed by fitting a 29 parameter double-Morse function to CCSD(T)/IB//MP2/cc-pV(T+d)Z-dk ab initio data; interaction between surfaces is described by geometry-dependent spin-orbit coupling functions fit to MCSCF/cc-pV(T+d)Z-dk ab initio data. Spectator modes are treated adiabatically via inclusion of curvilinear projected frequencies. The total scattering wave function is expanded in a vibronic basis set and close-coupled equations are solved via R-matrix propagation. Ground state thermal rate constants for forward and reverse reactions agree well with experiment. Multi-surface reaction probabilities, integral cross sections, and initial-state selected branching ratios all highlight the importance of vibrational energy in mediating nonadiabatic transition. Electronically excited state dynamics are seen to play a small but significant role as consistent with experimental conclusions.     

The role of mineral surface chemistry in modified dextrin adsorption

The adsorption of two modified dextrins (phenyl succinate dextrin--PS Dextrin; styrene oxide dextrin--SO Dextrin) on four different mineral surfaces has been studied using X-ray photoelectron spectroscopy (XPS), in situ atomic force microscopy (AFM) imaging, and captive bubble contact angle measurements. The four surfaces include highly orientated pyrolytic graphite (HOPG), freshly cleaved synthetic sphalerite (ZnS), and two surfaces produced through surface reactions of sphalerite: one oxidized in alkaline solution (pH 9, 1 h immersion); and one subjected to metal ion exchange between copper and zinc (i.e. copper activation: exposed to 1×10(-3) M CuSO(4) solution for 1 h). XPS measurements indicate that the different sphalerite surfaces contain varying amounts of sulfur, zinc, oxygen, and copper, producing substrates for polymer adsorption with a range of possible binding sites. AFM imaging has shown that the two polymers adsorb to a similar extent on HOPG, and that the two polymers display very different propensities for adsorption on the three sphalerite surface types, with freshly cleaved sphalerite encouraging the least adsorption, and copper activated and oxidized sphalerite encouraging significantly more adsorption. Contact angle measurements of the four surfaces indicate that synthetic sphalerite has a low contact angle upon fracture, and that oxidation on the timescale of one hour substantially alters the hydrophobicity. HOPG and copper-activated sphalerite were the most hydrophobic, as expected due to the carbon and di/poly-sulfide rich surfaces of the two samples, respectively. SO Dextrin is seen to have a significant impact on the wettability of HOPG and the surface reacted sphalerite samples, highlighting the difficulty in selectively separating sphalerite from carbonaceous unwanted minerals in flotation. PS Dextrin has the least effect on the hydrophobicity of the reacted sphalerite surfaces, whilst still significantly increasing the wettability of graphite, and thus has more potential for use as a polymer depressant in this separation.     

Highly chemoselective direct crossed aliphatic-aromatic acyloin condensations with triazolium-derived carbene catalysts

It has been shown for the first time that triazolium precatalysts promote (in the presence of base) highly chemoselective crossed acyloin condensation reactions between aliphatic and ortho-substituted aromatic aldehydes. An o-bromine atom can serve as a temporary directing group to ensure high chemoselectivity (regardless of the nature of the other substituents on the aromatic ring) which then can be conveniently removed. The process is of broad scope and is operationally simple as it does not require the preactivation of any of the coupling partners to ensure selectivity. Preliminary data indicate that highly enantioselective variants of the reaction are feasible using chiral precatalysts.     

Dihydropyranone formation by ipso C-H activation in a glucal 3-carbamate-derived rhodium acyl nitrenoid

By using (N-tosyloxy)-3-O-carbamoyl-D-glucal 10, which removes the need for a hypervalent iodine(III) oxidant, we provide evidence for rhodium nitrenoid-mediated ipso C-H activation as the origin of a C3-oxidized dihydropyranone product 3. This system may be especially susceptible to such a pathway because of the ease of forming a cation upon hydride transfer to the rhodium-complexed acyl nitrene.