Protein model refinement using structural fragment tessellation

A method is described for the refinement of rough protein models based on finding a selection of structural fragments that match the model. Unlike most fragment-based methods, these are not necessarily contiguous in the sequence and form a tiling (tessellation) that covers most of the structure. The residue positions of the fragments are then used as a target for the model atoms to generate a revised model which is used as the basis of a subsequent pattern definition and search. The method was shown to improve the recognition of the native fold in a series of decoys largely as a result of improved secondary structure representation.     

Disupersilylperoxo Radical Anion [tBu3SiOOSitBu3]⋅−: An Intermediate of Supersilanide Oxidation

In the oxidative process of the supersilanide anion [SitBu₃]^?, radical species are generated. The continuous wave (cw)‐EPR spectrum of the reaction solution of Na[SitBu₃] with O₂ revealed a signal, which could be characterized as disupersilylperoxo radical anion [tBu₃SiOOSitBu₃]^?? affected by sodium ions though ion‐pair formation. A mechanism is suggested for the oxidative process of supersilanide, which in a further step can be helpful in a better understanding of the oxidation process of isoelectronic phosphanes.     

Total and inorganic arsenic in dietary supplements based on herbs, other botanicals and algae—a possible contributor to inorganic arsenic exposure

The content of total and inorganic arsenic was determined in 16 dietary supplements based on herbs, other botanicals and algae purchased on the Danish market. The dietary supplements originated from various regions, including Asia, Europe and USA. The contents of total and inorganic arsenic was determined by inductively coupled plasma mass spectrometry (ICP-MS) and anion exchange HPLC-ICP-MS, respectively, were in the range of 0.58 to 5.0 mgkg^?1 and 0.03 to 3.2 mg?kg^?1, respectively, with a ratio between inorganic arsenic and total arsenic ranging between 5 and 100 %. Consumption of the recommended dose of the individual dietary supplement would lead to an exposure to inorganic arsenic within the range of 0.07 to 13 μg?day^?1. Such exposure from dietary supplements would in worst case constitute 62.4 % of the range of benchmark dose lower confidence limit values (BMDL₀₁ at 0.3 to 8 μg kg bw^?1 kg^?1 day^?1) put down by European Food Safety Authority (EFSA) in 2009, for cancers of the lung, skin and bladder, as well as skin lesions. Hence, the results demonstrate that consumption of certain dietary supplements could contribute significantly to the dietary exposure to inorganic arsenic at levels close to the toxicological limits established by EFSA.     

Simultaneous multi-residue pesticide analysis in soil samples with ultra-high-performance liquid chromatography–tandem mass spectrometry using QuEChERS and pressurised liquid extraction methods

To assess soil contamination, it is important to be able to measure different classes of pesticides simultaneously. For this reason we developed a sensitive ultra-high-performance liquid chromatography–tandem mass spectrometry method for the simultaneous analysis of 25 pesticides in soil samples. Multi-class pesticides (triazines, phenylureas, phenoxy acid pesticides etc.) were analysed using a single mass spectrometry method with a fast polarity switching option, allowing the analysis of 19 compounds in the positive ionisation mode and six compounds in the negative ionisation mode. Extraction of pesticides from soil samples was performed employing a pressurised liquid extraction (PLE) and a quick, easy, cheap, effective, rugged and safe (QuEChERS) procedure, recently developed for the extraction of multi-residue pesticides from food matrices. The extraction efficiency, performance and recoveries of these two procedures were evaluated and compared. In addition, we studied the effect of matrix on signal suppression or enhancement. Isotope-labelled internal standards (ILIS) were used to compensate the suppression or enhancement of signal intensities in the extracted samples. The method was validated using reference soil material (EUROSOIL 7) spiked with 50 μg/kg of each pesticide. The average recovery by PLE varied between 65.1% and 122.2% with RSDs of 1.7–23.4%. QuEChERS provided better recoveries for most of the pesticides, the extraction recovery ranging from 79.4% to 113.3% with RSDs of 1.0–12.2%. Limits of quantification for all target compounds were within a range of 0.1–2.9 µg/kg.     

An application of comonotonicity and convex ordering to present values with truncated stochastic interest rates

A subject often recurring in recent financial and actuarial research is the investigation of present value functions with stochastic interest rates. Only in the case of uncomplicated payment streams and rather basic interest rate models is an exact analytical result for the distribution function available. In the present contribution, we introduce the concept of truncated stochastic interest rates, useful to adapt general stochastic models to specific financial requirements, and we show how to obtain analytical results for bounds for the present value. We elaborate our method in extension for the Hull and White model and related models. We illustrate the accuracy of the approximations graphically, and we use the bounds to estimate the Value-at-Risk.     

Photoacoustic measurements of Lorentz broadening in CO2 between 25° C and 450° C

A variable temperature photoacoustic cell has been constructed and tested by studying the interplay of CO₂, H₂O, and NH₃ in synthetic smoke. Saturation effects for CO₂ and NH₃ have been modeled and compared with experiments, and results are obtained for the vibrational relaxation rate associated with NH₃-H₂O collisions. The cell has been used for studying the temperature dependence of self-broadening and N₂ broadening of CO₂ lines. The temperature dependence of the scattering rate is well described by a T ^–n law with n=0.77 in both cases. This result agrees with previous results obtained by tunable diode laser spectroscopy, but disagrees with results obtained by indirect methods.Supported by the Danish Science Research Council under grant no. 11-7777, and by FLS-airloq A/S     

Hydrolysis of lactose by β-glycosidase CelB from hyperthermophilic archaeon Pyrococcus furiosus

Applied Biochemistry and Biotechnology - Recombinant β-glycosidase CelB from the hyperthermophilic archaeon Pyrococcus furiosus was produced through expression of the plasmid-encoded gene in...     

Investigation of the GeO2-1,6-diaminohexane-water-pyridine-HF phase diagram leading to the discovery of two novel layered germanates with extra-large rings

The systematic exploration of the phase diagram of the GeO(2)-1,6-diaminohexane-water-pyridine-HF system has allowed the identification of specific roles of the HF, H(2)O contents, and HF/H(2)O ratio in the formation of Ge(7)X(19) (Ge(7)), Ge(9)X(25-26) (Ge(9)), and Ge(10)X(28) (Ge(10)) clusters (X = O, OH, F). This work has led to the discovery of two novel structures with extra-large 18-membered rings accommodating 1,6-diaminohexane (DAH): SU-63, |1.5H(2)DAH|[Ge(7)O(14)X(3)]·2H(2)O, a layered germanate constructed from Ge(7) clusters with the Kagome? topology, and SU-64, |11H(2)DAH|[Ge(9)O(18)X(4)][Ge(7)O(14)X(3)](6)·16H(2)O, a germanate built of two-dimensional slabs containing both Ge(7) and Ge(9) clusters (X = OH or F). We also put SU-64 in context with previously reported cluster germanate compounds with related topologies by means of a simple crystal deconstruction study.     

Nanogels with Selective Intracellular Reactivity for Intracellular Tracking and Delivery

A multimodal approach for hydrogel-based nanoparticles was developed to selectively allow molecular conjugated species to either be released inside the cell or remain connected to the polymer network. Using the intrinsic difference in reactivity between esters and amides, nanogels with an amide-conjugated dye could be tracked intracellularly localizing next to the nucleus, while ester-conjugation allowed for liberation of the molecular species from the hydrogel network inside the cell, enabling delivery throughout the cytoplasm. The release was a result of particle exposure to the intracellular environment. The conjugation approach and polymer network building rely on the same chemistry and provide a diverse range of possibilities to be used in nanomedicine and theranostic approaches.