Enhanced Hydrolytic Stability of Short‐Chain Poly[(R)‐3‐hydroxybutyrate] Conjugated to Native E. coli Cytoplasmic Proteins

Many prokaryotic and eukaryotic proteins are modified by post‐translational conjugation to short‐chain poly[(R)‐3‐hydroxybutyrate] (cPHB). The relative lability of ester bonds raises the concern that the cPHB may be substantially degraded by chemical hydrolysis during protein purification, thus increasing the difficulty of its detection and measurement. Here, we compare rates of acid‐ and base‐catalyzed hydrolysis of cPHB conjugated to native and denatured proteins at room temperature. E. coli cytoplasmic proteins, native or denatured by addition of guanidium hydrochloride, were treated with aqueous solutions of H₂SO₄ or NaOH at concentrations ranging from 0.1–2.0n . The loss of cPHB was measured as a function of time by a chemical assay. We find that cPHB conjugated to native proteins is surprisingly resistant to both acid‐ and base‐catalyzed hydrolysis, whereas cPHB conjugated to denatured proteins is proficiently degraded at rates proportional to acid or base concentration. The results suggest that cPHB occupies a highly protective environment within native proteins.     

Human Group IIA Phospholipase A2—Three Decades on from Its Discovery

Phospholipase A₂ (PLA₂) enzymes were first recognized as an enzyme activity class in 1961. The secreted (sPLA₂) enzymes were the first of the five major classes of human PLA₂s to be identified and now number nine catalytically-active structurally homologous proteins. The best-studied of these, group IIA sPLA₂, has a clear role in the physiological response to infection and minor injury and acts as an amplifier of pathological inflammation. The enzyme has been a target for anti-inflammatory drug development in multiple disorders where chronic inflammation is a driver of pathology since its cloning in 1989. Despite intensive effort, no clinically approved medicines targeting the enzyme activity have yet been developed. This review catalogues the major discoveries in the human group IIA sPLA₂ field, focusing on features of enzyme function that may explain this lack of success and discusses future research that may assist in realizing the potential benefit of targeting this enzyme. Functionally-selective inhibitors together with isoform-selective inhibitors are necessary to limit the apparent toxicity of previous drugs. There is also a need to define the relevance of the catalytic function of hGIIA to human inflammatory pathology relative to its recently-discovered catalysis-independent function.     

The aqueous reference for ESR oximetry

The interaction of molecular oxygen with derivatives of nitroxide EPR spin labels has been investigated using nuclear spin-relaxation spectroscopy in aqueous and nonaqueous solvents. The proton spin-lattice relaxation rate induced by oxygen provides a measure of the local concentration of oxygen, which we find is dependent on solvent. In water, the hydrophobic effect increases the local concentration of oxygen in the nonpolar portions of solute molecules. For nitroxides reduced to the hydroxylamine in aqueous solutions, we find that the local concentration of oxygen is approximately twice that associated with a free diffusion hard sphere limit, while in octane, this effect is absent. These results show that nitroxide based ESR oximetry may suffer a reference concentration shift of order a factor of two if the aqueous nitroxide spectrum or relaxation is used as the reference.     

Experimental characterization of intermolecular multiple-quantum coherence pumping efficiency in solution NMR

The behavior of intermolecular multiple-quantum coherences in a variety of simple liquids with different chemical and magnetic properties is investigated experimentally and modeled by numerical simulations based on modified Bloch equations. The effects of spin concentration, temperature, intramolecular conformational flexibility, chemical exchange, and spin-spin coupling on the formation of high-order coherences are examined. It is shown that any process that makes the Larmor frequency time-dependent may interfere with the formation of these coherences. Good agreement is achieved between experiments and simulation, using independently known values of the magnetization density, the rate constants for translational diffusion, spin-spin and spin-lattice relaxation, and radiation damping.     

Photophysical and computational investigations of bis(phosphine) organoplatinum(II) metallacycles

A series of endohedral and exohedral amine-functionalized ligands were synthesized and used in the construction of supramolecular D(2h) rhomboids and a D(6h) hexagon. These supramolecular polygons were obtained via self-assembly of 120° dipyridyl donors with 180° or 120° diplatinum precursors when combined in 1:1 ratios. Steady-state absorption and emission spectra were collected for each ligand and metallacycle. Density functional theory (DFT) and time-dependent DFT calculations were employed to probe the nature of the observed optical transitions for the rhomboids. The emissive properties of these bis(phosphine) organoplatinum metallacycles arise from ligand-centered transitions involving π-type molecular orbitals with modest contributions from metal-based atomic orbitals. The D(2h) rhomboid self-assembled from 2,6-bis(4-pyridylethynyl)aniline and a 60° organoplatinum(II) acceptor has a low-energy excited state in the visible region and emits above 500 nm, properties which greatly differ from those of the parent 2,6-bis(4-pyridylethynyl)aniline ligand.     

Contact line extraction and length measurements in model sediments and sedimentary rocks

The mechanisms that govern the transport of colloids in the unsaturated zone of soils are still poorly understood, because of the complexity of processes that occur at pore scale. These mechanisms are of specific interest in quantifying water quality with respect to pathogen transport (e.g. Escherichia coli, Cryptosporidium) between the source (e.g. farms) and human users. Besides straining in pore throats and constrictions of smaller or equivalent size, the colloids can be retained at the interfaces between air, water, and grains. Theories competing to explain this mechanism claim that retention can be caused by adhesion at the air-water-interface (AWI) between sediment grains or by straining at the air-water-solid (AWS) contact line. Currently, there are no established methods for the estimation of pathogen retention in unsaturated media because of the intricate influence of AWI and AWS on transport and retention. What is known is that the geometric configuration and connectivity of the aqueous phase is an important factor in unsaturated transport. In this work we develop a computational method based on level set functions to identify and quantify the AWS contact line (in general the non-wetting-wetting-solid contact line) in any porous material. This is the first comprehensive report on contact line measurement for fluid configurations from both level-set method based fluid displacement simulation and imaged experiments. The method is applicable to any type of porous system, as long as the detailed pore scale geometry is available. We calculated the contact line length in model sediments (packs of spheres) as well as in real porous media, whose geometry is taken from high-resolution images of glass bead packs and sedimentary rocks. We observed a strong dependence of contact line length on the geometry of the sediment grains and the arrangement of the air and water phases. These measurements can help determine the relative contribution of the AWS line to pathogen retention.     

New ways of probing surface nuclear relaxation and microdynamics of water and oil in porous media.

The microdynamics of water and oil in macroporous media with SiO2 or CaCO3 surfaces has been probed at various temperatures by magnetic field-cycling measurements of spin-lattice relaxation rates. These measurements and an original theory of surface diffusion allow us to obtain surface dynamical parameters such as surface correlation times, residence times and diffusion coefficients. A coefficient of affinity of the liquids for the pore surface is deduced.     

Synthesis of DTPA analogues derived from piperidine and azepane: potential contrast enhancement agents for magnetic resonance imaging.

Two DTPA derivatives (PIP-DTPA and AZEP-DTPA) as potential contrast enhancement agents in MRI are synthesized. The T1 and T2 relaxivities of their corresponding Gd(III) complexes are reported. At clinically relevant field strengths, the relaxivities of the complexes are comparable to that of the contrast agent, Gd(DTPA) which is in clinical use. The serum stability of the (153)Gd-labeled complexes is assessed by measuring the release of (153)Gd from the ligands. The radiolabeled Gd chelates are found to be kinetically stable in human serum for up to at least 14 days without any measurable loss of radioactivity.     

Algorithmic Aspects of Tree Amalgamation

The amalgamation of leaf-labeled trees into a single (super)tree that “displays” each of the input trees is an important problem in classification. We discuss various approaches to this problem and show that a simple and well-known polynomial-time algorithm can be used to solve this problem whenever the input set of trees contains a minimum size subset that uniquely determines the supertree. Our results exploit a recently established combinatorial property concerning the structure of such collections of trees.