Environmental Degradation of Microbial Polyhydroxyalkanoates and Oil Palm-Based Composites

This paper investigates the degradation of polyhydroxyalkanoates and its biofiber composites in both soil and lake environment. Time-dependent changes in the weight loss of films were monitored. The rate of degradation of poly(3-hydroxybutyrate) [P(3HB)], poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-23?mol% 4HB)] and poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-4-hydroxybutyrate) [P(3HB-co-9?mol% 3HV-co-19?mol% 4HB)] were investigated. The rate of degradation in the lake is higher compared to that in the soil. The highest rate of degradation in lake environment (15.6?% w/w week^?1) was observed with P(3HB-co-3HV-co-4HB) terpolymer. Additionally, the rate of degradation of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-38?mol% 3HV)] was compared to PHBV biofiber composites containing compatibilizers and empty fruit bunch (EFB). Here, composites with 30?% EFB displayed the highest rate of degradation both in the lake (25.6?% w/w week^?1) and soil (15.6?% w/w week^?1) environment.     

Direct Infusion Electrospray Ionization – Ion Mobility – High Resolution Mass Spectrometry (DIESI-IM-HRMS) for Rapid Characterization of Potential Bioprocess Streams

Direct infusion electrospray ionization?-?ion mobility?-?high resolution mass spectrometry (DIESI-IM-HRMS) has been utilized as a rapid technique for the characterization of total molecular composition in "whole-sample" biomass hydrolysates and extracts. IM-HRMS data reveal a broad molecular weight distribution of sample components (up to 1100 m/z) and provide trendline isolation of feedstock components from those introduced "in process." Chemical formulas were obtained from HRMS exact mass measurements (with typical mass error less than 5 ppm) and were consistent with structural carbohydrates and other lignocellulosic degradation products. Analyte assignments are supported via IM-MS collision-cross-section measurements and trendline analysis (e.g., all carbohydrate oligomers identified in a corn stover hydrolysate were found to fall within 6% of an average trendline). These data represent the first report of collision cross sections for several negatively charged carbohydrates and other acidic species occurring natively in biomass hydrolysates.     

Bivariate interpolation based on univariate subdivision schemes

The paper presents a bivariate subdivision scheme interpolating data consisting of univariate functions along equidistant parallel lines by repeated refinements. This method can be applied to the construction of a surface passing through a given set of parametric curves. Following the methodology of polysplines and tension surfaces, we define a local interpolator of four consecutive univariate functions, from which we sample a univariate function at the mid-point. This refinement step is the basis to an extension of the 4-point subdivision scheme to our setting. The bivariate subdivision scheme can be reduced to a countable number of univariate, interpolatory, non-stationary subdivision schemes. Properties of the generated interpolant are derived, such as continuity, smoothness and approximation order.     

Comparison of coupled motions in Escherichia coli and Bacillus subtilis dihydrofolate reductase

Hybrid quantum/classical molecular dynamics simulations are used to compare the role of protein motion in the hydride transfer reaction catalyzed by Escherichia coli and Bacillus subtilis dihydrofolate reductase (DHFR). These two enzymes have 44% sequence identity, and the experimentally determined structures and hydride transfer rates are similar. The simulations indicate that the tertiary structures of both enzymes evolve in a similar manner during the hydride transfer reaction. In both enzymes, the donor-acceptor distance decreases to approximately 2.7 Angstroms at the transition state configurations to enable hydride transfer. Zero point energy and hydrogen tunneling effects are found to be significant for both enzymes. Covariance and rank correlation analyses of motions throughout the protein and ligands illustrate that E. coli and B. subtilis DHFR exhibit both similarities and differences in the equilibrium fluctuations and the conformational changes along the collective reaction coordinate for hydride transfer. A common set of residues that play a significant role in the network of coupled motions leading to configurations conducive to hydride transfer for both E. coli and B. subtilis DHFR was identified. These results suggest a balance between conservation and flexibility in the thermal motions and conformational changes during hydride transfer. Homologous protein structures, in conjunction with conformational sampling, enable enzymes with different sequences to catalyze the same hydride transfer reaction with similar efficiency.     

Hydrogen bonding pathways in human dihydroorotate dehydrogenase

Dihydroorotate dehydrogenase (DHOD) catalyzes the only redox reaction in the pathway for pyrimidine biosynthesis. In this reaction, a proton is transferred from a carbon atom of the substrate to a serine residue, and a hydride is transferred from another carbon atom of the substrate to a cofactor. The deprotonation of the substrate is postulated to involve a proton relay mechanism along a hydrogen bonding pathway in the active site. In this paper, molecular dynamics simulations are used to identify and characterize potential hydrogen bonding pathways that could facilitate the redox reaction catalyzed by human DHOD. The observed pathways involve hydrogen bonding of the active base serine to a water molecule, which is hydrogen bonded to the substrate carboxylate group or a threonine residue. The threonine residue is positioned to enable proton transfer to another water molecule leading to the bulk solvent. The impact of mutating the active base serine to cysteine is also investigated. This mutation is found to increase the average donor-acceptor distances for proton and hydride transfer and to disrupt the hydrogen bonding pathways observed for the wild-type enzyme. These effects could lead to a significant decrease in enzyme activity, as observed experimentally for the analogous mutant in Escherichia coli DHOD.     

Dynamics on the microsecond timescale in microporous aluminophosphate AlPO-14 as evidenced by 27Al MQMAS and STMAS NMR spectroscopy

Multiple-quantum magic angle spinning (MQMAS) and satellite-transition magic angle spinning (STMAS) are two well-known techniques for obtaining high-resolution, or "isotropic", NMR spectra of quadrupolar nuclei. It has recently been shown that dynamics-driven modulation of the quadrupolar interaction on the microsecond timescale results in linewidths in isotropic STMAS spectra that are strongly broadened, while, in contrast, the isotropic MQMAS linewidths remain narrow. Here, we use this novel methodology in an 27Al (I = 5/2) NMR study of the calcined-dehydrated aluminophosphate AlPO-14 and two forms of as-synthesized AlPO-14, one prepared with isopropylamine (C3H7NH2) as the template molecule and one with piperidine (C5H10NH). For completeness, the 31P and 13C (both I = 1/2) MAS NMR spectra are also presented. A comparison of the 27Al MQMAS and STMAS NMR results show that, although calcined AlPO-14 appears to have a rigid framework structure, the extent of motion in the two as-synthesized forms is significant, with clear evidence for dynamics on the microsecond timescale in the immediate environments of all four Al sites in each material. Variable-temperature 27Al STMAS NMR studies of the two as-synthesized AlPO forms reveal the dynamics to be complex, with the motions of both the guest water molecules and organic template molecules shown to be contributing. The sensitivity of the STMAS NMR experiment to the presence of microsecond timescale dynamics is such that it seems likely that this methodology will prove useful in NMR studies of host-guest interactions in a wide variety of framework materials.     

Computer simulations of block copolymer tethered nanoparticle self-assembly

We perform molecular simulations to study the self-assembly of block copolymer tethered cubic nanoparticles. Minimal models of the tethered nanoscale building blocks (NBBs) are utilized to explore the structures arising from self-assembly. We demonstrate that attaching a rigid nanocube to a diblock copolymer affects the typical equilibrium morphologies exhibited by the pure copolymer. Lamellar and cylindrical phases are observed in both systems but not at the corresponding relative copolymer tether block fractions. The effect of nanoparticle geometry on phase behavior is investigated by comparing the self-assembled structures formed by the tethered NBBs with those of their linear ABC triblock copolymer counterparts. The tethered nanocubes exhibit the conventional triblock copolymer lamellar and cylindrical phases when the repulsive interactions between different blocks are symmetric. The rigid and bulky nature of the cube induces interfacial curvature in the tethered NBB phases compared to their linear ABC triblock copolymer counterparts. We compare our results with those structures obtained from ABC diblock copolymer tethered nanospheres to further elucidate the role of cubic nanoparticle geometry on self-assembly.     

Simultaneous determination of synthetic phosphodiesterase-5 inhibitors found in a dietary supplement and pre-mixed bulk powders for dietary supplements using high-performance liquid chromatography with diode array detection and liquid chromatography-electrospray ionization tandem mass spectrometry

A high-performance liquid chromatography-diode array detection (HPLC-DAD) method and a liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) method were developed to screen for the presence of synthetic phosphodiesterase-5 (PDE-5) inhibitors and their analogues, namely sildenafil, vardenafil, tadalafil, homosildenafil, acetildenafil and hydroxyhomosildenafil. The methods were applied to pre-market samples submitted to the Health Sciences Authority of Singapore (HSA) for testing. One sample was in the form of capsules while six other samples were pre-mixed bulk powder samples for dietary supplements to be repackaged or formulated into the final dosage forms (usually capsules). Identification of PDE-5 inhibitors and their analogues was achieved by comparing individual peak retention times, UV spectra and mass spectra with those of reference standards. The seven samples were found to contain at least one of the following compounds: sildenafil, vardenafil, hydroxyhomosildenafil, homosildenafil and acetildenafil. The five compounds were simultaneously determined by LC-ESI-MS/MS in multiple reactions monitoring (MRM) scan mode. The method has been validated for accuracy, precision, linearity and sensitivity.