Predicting proteinase specificities from free energy calculations

The role of the primary binding residue (P1) in complexes between three different subtilases (subtilisin Carlsberg, thermitase and proteinase K) and their canonical protein inhibitor eglin c have been studied by free energy calculations. Based on the crystal structures of eglin c in complex with subtilisin Carlsberg and thermitase, and a homology model of the eglin c-proteinase K complex, a total of 57 mutants have been constructed and docked into their host proteins. The binding free energy was then calculated using molecular dynamics (MD) simulations combined with the linear interaction energy (LIE) method for all complexes differing only in the nature of the amino acid at the P1 position. LIE calculations for 19 different complexes for each subtilase were thus carried out excluding proline. The effects of substitutions at the P1 position on the binding free energies are found to be very large, and positively charged residues (Arg, Lys and His) are particularly deleterious for all three enzymes. The charged variants of the acidic side chains are found to bind more favorably as compared to their protonated states in all three subtilases. Furthermore, hydrophobic amino acids are accommodated most favorably at the S1-site in all three enzymes. Comparison of the three series of binding free energies shows only minor differences in the 19 computed relative binding free energies among these subtilases. This is further reflected in the correlation coefficient between the 23 relative binding free energies obtained, including the possible protonation states of ionizable side chains, but excluding the P1 Pro, for subtilisin Carlsberg versus thermitase (0.95), subtilisin versus proteinase K (0.94) and thermitase versus proteinase K (0.96).     

27-GHz bandwidth high-speed monolithic integrated optoelectronicphotoreceiver consisting of a waveguide fed photodiode and anInAlAs/InGaAs-HFET traveling wave amplifier

A monolithic integrated photoreceiver for 1.55-μm wavelength has been designed for operation in a 20-Gb/s synchronous digital hierarchy system (SDH/SONET), based on a new integration concept. The optoelectronic integrated circuit (OEIC) receiver combines a waveguide-integrated PIN-photodiode and a traveling wave amplifier in coplanar waveguide layout with four InAlAs/InGaAs/InP-HFETs (0.7-μm gate length). The receiver demonstrates a bandwidth of 27 GHz with a low frequency transimpedance of 40 dBΩ. This is, to our knowledge, the highest bandwidth ever reported for a monolithic integrated photoreceiver on InP. Furthermore, a receiver sensitivity of -12 dBm in the fiber (20 Gb/s, BER=10^-9) and an overall optical input dynamic range of 27 dB is achieved. Optical time domain multiplex (TDM) system experiments of the receiver packaged in a module show an excellently shaped eye pattern for 20 Gb/s and an overall sensitivity of -30.5 dBm (BER=10^-9) [including erbium doped fiber amplifiers (EDFA)]     

Studies on the mashing conditions of teff (Eragrostis tef) malt as a raw material for lactic acid‐fermented gluten‐free beverage

Formation of extracts and fermentable sugars during mashing can be limited by incomplete starch gelatinisation. The aim of this research was to develop mashing programme for 100% teff malt as a potential raw material for gluten‐free lactic acid‐fermented beverage. Isothermal mashing at temperatures ranging between 60 and 84 °C was conducted, and the highest extract (85%) was observed for the wort samples produced at temperatures higher than 76 °C. Sixty‐minute rest at 71 °C resulted in higher fermentable sugars than other tested conversion rest temperatures. Inclusion of lower mashing‐in temperature in the mashing programme also substantially improved the concentrations of free amino nitrogen (128 mg L^?1) and fermentable sugar (58 g L^?1) in the final wort. Therefore, 30‐min rest at 40 °C followed by 60‐min rest at 71 °C and 10‐min rest at 78 °C was found to be a suitable mashing programme for teff malt.     

The effect of diet changes and food loss reduction in reducing the water footprint of an average American

ABSTRACT

We analyzed the consumptive water reduction of diet shifting along with food waste reductions in the case of the United States. We find that a dietary shift to healthy diet will not always lead to reduced water footprint. Dietary shifts to vegan and vegetarian diets provide larger reduction in the consumptive water footprint. Reducing food loss and waste produced the largest potential water footprint reduction in our analysis of the US food system. Our findings suggest that a combination of measures that include dietary shift, reducing caloric intake, and reducing food waste result in a significant decline in water footprint.     

Investigation of Chlorpyrifos and Its Transformation Products in Fruits and Spices by Combining Electrochemistry and Liquid Chromatography Coupled to Tandem Mass Spectrometry

The identification of transformation products (TPs) of pesticides in food is a crucial task difficult to tackle, due to the lack of standards. In this work, we present a novel methodology to synthesize five main TP standards of the insecticide chlorpyrifos (CPF) and to investigate their occurrence in selected fruits and spices. TPs were electrochemically (EC) synthesized using a boron-doped diamond electrode (BDD) and identified by EC coupled online to mass spectrometry, LC-MS/MS, and high-resolution mass spectrometry. CPF and its TPs were analyzed in the food samples by LC-MS/MS on multiple reaction monitoring (MRM) after dispersive solid-phase extraction. A good recovery of 83–103% for CPF and 65–85% for TPs was obtained. Matrix effects, which cause signal suppression, ranged between 81 to 95% for all targeted analytes. The limit of detection and quantification for CPF were 1.6–1.9 and 4.9–5.7 μg/kg, respectively. Among investigated samples, CPF was determined in fresh lemon (104 μg/kg), fenugreek seed (40 μg/kg), and black pepper (31 μg/kg). CPF content in all samples was lower than the EU maximum residue level (MRL). The most frequently detected TPs were diethylthiophosphate and diethylphosphate. Other TPs, CPF oxon and trichloropyridinol, were also detected. Hence, EC is a versatile tool to synthesize TP standards which enables the determination of contaminants and residues in foodstuffs even if no commercial standards are available.     

Part III: the influence of serial repitching of Saccharomyces pastorianus on the production dynamics of some important aroma compounds during the fermentation of barley and gluten‐free buckwheat and quinoa wort

The present paper is the last report of a comprehensive study regarding the influence of the serial repitching of Saccharomyces pastorianus TUM 34/70 on the composition of a barley, buckwheat or quinoa fermentation medium. In particular, it focuses on the production dynamics of important volatile compounds typically associated with the aroma of beer. Samples were taken every 24 h after 11 serial repitchings of a single starter culture, analysed for the particular aroma compound content by distillation followed by gas chromatography with flame ionization detection. The term ‘serial repitching factor’ is used for the first time to support the visual evaluation of the influence of serial repitching. Results showed that the levels of methanol in the quinoa wort fermentation were only slightly higher than in barley and in practical terms independent of successive fermentation. The behaviour of acetaldehyde in quinoa was similar to that in barley. However, there was a final 2‐fold lower production of some important aroma compounds compared with barley and buckwheat and for this reason quinoa cannot be recommended as a gluten‐free substitute to produce a bottom‐fermented beer. Regarding the buckwheat wort fermentation, a 2‐ to 3‐times lower final acetaldehyde content than in barley is desirable, whereas a relatively high methanol content is not desirable. Barley and buckwheat showed comparable sum concentrations and similar overall profiles of some important aroma compounds. From this perspective, buckwheat appears to be a promising substitute for barley as a brewing raw material. The overall conclusions of our comprehensive study (Parts I–III) are that buckwheat shows adequate brewing properties to substitute for barley in the commercial preparation of a bottom‐fermented gluten‐free beer‐like beverage, and yeast can be repitched at least 11 times. In contrast, quinoa in practical terms shows no substitutional potential for barley in beer; however, it has many nutritious advantages, thus the commercial preparation of a unique, bottom‐fermented gluten‐free ‘non‐beer‐like’ beverage – where the yeast could be repitched six times at most – appears feasible. Copyright © 2015 The Institute of Brewing & Distilling     

Part II: the influence of the serial repitching of Saccharomyces pastorianus on the uptake dynamics of amino acids during the fermentation of barley and gluten‐free buckwheat and quinoa wort

The present paper is part of a comprehensive study regarding the influence of the serial repitching of Saccharomyces pastorianus TUM 34/70 on the composition of the barley, buckwheat and quinoa fermentation medium. In particular, it focuses on the uptake dynamics of amino acids during 11 successive fermentations. Samples were taken every 20 h after pitching, analysed for the particular amino acid content and statistically evaluated. The term ‘completion time’ (t₉₅), here defined as the percentage attenuation time necessary for ~95% of the total assimilation, has been introduced. In addition, ‘the serial repitching factor’ is used for the first time to support the visual evaluation of the influence of serial repitching. Amino acids that were essentially affected by serial repitching were glutamine, arginine, alanine and tryptophan in barley, aspartate, glutamate and tryptophan in buckwheat, and all in the quinoa wort fermentation. As opposed to buckwheat and quinoa, in barley the amino acids behaved more or less independently from each other, which for buckwheat and quinoa indicates a more general systemic change in the yeast. From the amino acids point of view, buckwheat can be fully regarded as a suitable gluten‐free substitute for barley beer since the amino acid assimilation was very consistent and hardly influenced by the serial repitching, especially regarding the final amino acid assimilation. In the case of quinoa, the assimilation of all amino acids became significantly affected after the sixth fermentation and quinoa is probably unsuitable for the production of beer‐like beverages. Results suggest no substitutional potential of quinoa for barley beer, but if a nutrient‐rich beverage of choice from quinoa malt is intended to be prepared, it seems that the serial repitching is limited to six fermentations at most. Copyright © 2015 The Institute of Brewing & Distilling     

Simplified Method for Sizing Laterals with Two or More Diameters

The economic design of microirrigation and sprinkler laterals requires the use of a combination of diameters of different lengths. The present practice is to solve the basic hydraulic equations using a trial-and-error method for a given allowable head loss. This requires an iterative process that consumes time and limits the accuracy of the solution. Herein is presented a direct analytical approach that gives an exact solution. The method is compared with the trial-and-error approach and found to give the same result.     

Study of single-cell massive MIMO systems with channel aging and prediction

Wireless Networks - In this paper we consider a single-cell massive multiple-input-multiple-output scenario, where the number of base station (BS) antennas is larger than the number of single...