Mining the Wheat Grain Proteome

Bread wheat is the most widely cultivated crop worldwide, used in the production of food products and a feed source for animals. Selection tools that can be applied early in the breeding cycle are needed to accelerate genetic gain for increased wheat production while maintaining or improving grain quality if demand from human population growth is to be fulfilled. Proteomics screening assays of wheat flour can assist breeders to select the best performing breeding lines and discard the worst lines. In this study, we optimised a robust LC–MS shotgun quantitative proteomics method to screen thousands of wheat genotypes. Using 6 cultivars and 4 replicates, we tested 3 resuspension ratios (50, 25, and 17 µL/mg), 2 extraction buffers (with urea or guanidine-hydrochloride), 3 sets of proteases (chymotrypsin, Glu-C, and trypsin/Lys-C), and multiple LC settings. Protein identifications by LC–MS/MS were used to select the best parameters. A total 8738 wheat proteins were identified. The best method was validated on an independent set of 96 cultivars and peptides quantities were normalised using sample weights, an internal standard, and quality controls. Data mining tools found particularly useful to explore the flour proteome are presented (UniProt Retrieve/ID mapping tool, KEGG, AgriGO, REVIGO, and Pathway Tools).     

Analysis of Integrin αIIb Subunit Dynamics Reveals Long-Range Effects of Missense Mutations on Calf Domains

Integrin α_IIbβ₃, a glycoprotein complex expressed at the platelet surface, is involved in platelet aggregation and contributes to primary haemostasis. Several integrin α_IIbβ₃ polymorphisms prevent the aggregation that causes haemorrhagic syndromes, such as Glanzmann thrombasthenia (GT). Access to 3D structure allows understanding the structural effects of polymorphisms related to GT. In a previous analysis using Molecular Dynamics (MD) simulations of α_IIb Calf-1 domain structure, it was observed that GT associated with single amino acid variation affects distant loops, but not the mutated position. In this study, experiments are extended to Calf-1, Thigh, and Calf-2 domains. Two loops in Calf-2 are unstructured and therefore are modelled expertly using biophysical restraints. Surprisingly, MD revealed the presence of rigid zones in these loops. Detailed analysis with structural alphabet, the Proteins Blocks (PBs), allowed observing local changes in highly flexible regions. The variant P741R located at C-terminal of Calf-1 revealed that the Calf-2 presence did not affect the results obtained with isolated Calf-1 domain. Simulations for Calf-1 + Calf-2, and Thigh + Calf-1 variant systems are designed to comprehend the impact of five single amino acid variations in these domains. Distant conformational changes are observed, thus highlighting the potential role of allostery in the structural basis of GT.     

Cell-Based Chemical Safety Assessment and Therapeutic Discovery Using Array-Based Sensors

Synthetic chemicals are widely used in food, agriculture, and medicine, making chemical safety assessments necessary for environmental exposure. In addition, the rapid determination of chemical drug efficacy and safety is a key step in therapeutic discoveries. Cell-based screening methods are non-invasive as compared with animal studies. Cellular phenotypic changes can also provide more sensitive indicators of chemical effects than conventional cell viability. Array-based cell sensors can be engineered to maximize sensitivity to changes in cell phenotypes, lowering the threshold for detecting cellular responses under external stimuli. Overall, array-based sensing can provide a robust strategy for both cell-based chemical risk assessments and therapeutics discovery.     

Al2O3-ZrO2 Finely Structured Multilayer Architectures from Suspension Plasma Spraying

Suspension plasma spraying (SPS) is an alternative to conventional atmospheric plasma spraying (APS) aiming at manufacturing thinner layers (i.e., 10-100 μm) due to the specific size of the feedstock particles, from a few tens of nanometers to a few micrometers. The staking of lamellae and particles, which present a diameter ranging from 0.1 to 2.0 μm and an average thickness from 20 to 300 nm, permits to manufacture finely structured layers. Moreover, it appears as a versatile process able to manufacture different coating architectures according to the operating parameters (suspension properties, injection configuration, plasma properties, spray distance, torch scan velocity, scanning step, etc.). However, the different parameters controlling the properties of the coating, and their interdependences, are not yet fully identified. Thus, the aim of this paper is, on the one hand, to better understand the influence of operating parameters on the coating manufacturing mechanisms (in particular, the plasma gas mixture effect) and, on the other hand, to produce Al₂O₃-ZrO₂ finely structured layers with large varieties of architectures. For this purpose, a simple theoretical model was used to describe the plasma torch operating conditions at the nozzle exit, based on experimental data (mass enthalpy, arc current intensity, thermophysical properties of plasma forming gases, etc.) and the influences of the spray parameters were determined by mean of the study of sizes and shapes of spray beads. The results enabled then to reach a better understanding of involved phenomena and their interactions on the final coating architectures permitting to manufacture several types of microstructures.     

Determination of Glyphosate and Its Metabolite AMPA (Aminomethylphosphonic Acid) in Cereals After Derivatization by Isotope Dilution and UPLC-MS/MS”

A straightforward analytical method has been developed for the determination of glyphosate and aminomethylphosphonic acid (AMPA), its major metabolite in cereals. This method entails a rapid extraction and derivatization with 9-fluorenylmethyl chloroformate followed by separation with a conventional reversed-phase rapid chromatography used in daily routine analysis and detection by electrospray ionization tandem mass spectrometry. To overcome matrix effects and compensate for any analyte losses during sample treatment, an isotopic dilution approach was used. Since 2010, the monitoring of cereals for the widely used herbicide glyphosate is obligatory to all European Union (EU)-member states, laid down in Commission Regulation (EC) No. 1213/2008. Hence, there is definitively a need for a reliable and easy-to-handle analytical method for monitoring of this compound. The proposed method can be run without having to make time-consuming changes on the equipment used for daily routine analysis. The analytical performance of the method was evaluated according to SANCO/10684/2009 criteria and demonstrated that this method is rugged and cost-effective, therefore suitable for monitoring purposes as well as legislative enforcements within the EU. The apparent recoveries of both analytes were between 97% and 113% with relative standard deviations less than 20%. The limits of quantification of glyphosate and AMPA were 0.02 mg/kg in cereal matrices. Finally, the accuracy of the method was assessed by analyzing a proficiency test material which was available from a previous round (EUPT-C4).     

Lessons from the organization of a proficiency testing program in food microbiology by interlaboratory comparison: analytical methods in use, impact of methods on bacterial counts and measurement uncertainty of bacterial counts

The proficiency testing program in food microbiology RAEMA (Réseau d'Analyses et d'Echanges en Microbiologie des Aliments), created in 1988, currently includes 450 participating laboratories. This interlaboratory comparison establishes proficiency in detection of Salmonella and Listeria monocytogenes, as well as enumeration of aerobic micro-organisms, Enterobacteriaceae, coliforms, beta-glucuronidase-positive Escherichia coli, anaerobic sulfito-reducing bacteria, Clostridium perfringens, coagulase-positive staphylococci, and L. monocytogenes. Twice a year, five units samples are sent to participants to assess their precision and trueness for enumeration and detection of micro-organisms. Most of participating laboratories use standard or validated alternative methods, they were 50-70% in 1994 and, for 5 years, they are 95%. An increasing use of alternative methods was also observed. This phenomenon is all the more significant as standard methods are laborious and time consuming; thus, 50% of the laboratories use alternative methods for the detection of Salmonella and L. monocytogenes. More and more laboratories use ready-to-use media and although the percentage is variable according to the microflora, we can consider that, today, 50-60% of the laboratories participating to the proficiency program only use ready-to-use media. The internal quality assurance programs lead also to an increasing use of media quality controls. The impact of analytical methods on bacterial counts was assessed by grouping together the results obtained by participating laboratories during the 10 last testing schemes from 1999 to 2003. The identified significant factors influencing enumeration results are variable from one microflora to another. Some of them significantly influence many microflora: the plating method (spiral plating or not) is influential for aerobic micro-organisms, Enterobacteriaceae, coliforms, and staphylococci, the type of culture medium and the medium manufacturer is influential for aerobic micro-organisms, Enterobacteriaceae, coliforms, E. coli, anaerobic sulfito-reducing bacteria, staphylococci, and L. monocytogenes. Others are specific of some micro-organisms: the resuscitation broth for L. monocytogenes, the mode of medium preparation for staphylococci and the incubation temperature for C. perfringens. These effects lead generally to small differences of about 0.1 log10 cfu g(-1), except for the enumeration of anaerobic sulfito-reducing bacteria, where the difference reaches 0.7 log10 cfu g(-1). These results, although difficult to extrapolate to all actual situations, which associate numerous food constituents and physiological states of bacteria to detect or numerate, allow nevertheless the quantification of interlaboratory variations linked to the methods in use. The analysis of bacterial counts obtained by the laboratories participating to the RAEMA proficiency testing program allowed also to validate a formula to calculate the repeatability of bacterial counts and to estimate the between-laboratory uncertainties for the majority of micro-organisms enumerated in food microbiology. The repeatability uncertainty is only indirectly affected by the method in use but depends essentially on the number of counted colonies. On the other hand, the between-laboratory uncertainty varies with the enumeration method in use, this variability is relatively small for the enumerations calling for methods without colony confirmation, i.e. for the enumeration of aerobic micro-organisms, Enterobacteriaceae, 'total' and thermotolerant coliforms, beta-glucuronidase-positive E. coli and coagulase-positive staphylococci with the technique using the rabbit-plasma fibrinogen agar. For these methods, the average between-laboratory standard deviation is 0.17 log10 cfu g(-1). The between-laboratory uncertainty is, on the contrary, larger for more complex techniques. For the enumeration of coagulase-positive staphylococci with the Baird-Parker agar, the between-laboratory standard deviation is equal to 0.23 log10 cfu g(-1), it is equal to 0.28 log10 cfu g(-1) for the enumeration of L. monocytogenes, to 0.34 log10 cfu g(-1) for the enumeration of C. perfringens, and to 0.47 log10 cfu g(-1) for the enumeration of anaerobic sulfito-reducing bacteria.     

Disrupting the methionine biosynthetic pathway in Candida guilliermondii: characterization of the MET2 gene as counter‐selectable marker

Candida guilliermondii (teleomorph Meyerozyma guilliermondii) is an ascomycetous species belonging to the fungal CTG clade. This yeast remains actively studied as a result of its moderate clinical importance and most of all for its potential uses in biotechnology. The aim of the present study was to establish a convenient transformation system for C. guilliermondii by developing both a methionine auxotroph recipient strain and a functional MET gene as selection marker. We first disrupted the MET2 and MET15 genes encoding homoserine‐O‐acetyltransferase and O‐acetylserine O‐acetylhomoserine sulphydrylase, respectively. The met2 mutant was shown to be a methionine auxotroph in contrast to met15 which was not. Interestingly, met2 and met15 mutants formed brown colonies when cultured on lead‐containing medium, contrary to the wild‐type strain, which develop as white colonies on this medium. The MET2 wild‐type allele was successfully used to transfer a yellow fluorescent protein (YFP) gene‐expressing vector into the met2 recipient strain. In addition, we showed that the loss of the MET2‐containing YFP‐expressing plasmid can be easily observed on lead‐containing medium. The MET2 wild‐type allele, flanked by two short repeated sequences, was then used to disrupt the LYS2 gene (encoding the α‐aminoadipate reductase) in the C. guilliermondii met2 recipient strain. The resulting lys2 mutants displayed, as expected, auxotrophy for lysine. Unfortunately, all our attempts to pop‐out the MET2 marker (following the recombination of the bordering repeat sequences) from a target lys2 locus were unsuccessful using white/brown colony colour screening. Nevertheless, this MET2 transformation/disruption system represents a new versatile genetic tool for C. guilliermondii. Copyright © 2014 John Wiley & Sons, Ltd.     

Modeling bread baking with focus on overall deformation and local porosity evolution

A two dimensional model of bread baking was developed including, for the first time, the dependence of dough viscosity on both temperature and moisture content, the carbon dioxide dissolved from liquid water together with gas generation from yeast at the beginning of baking and the shrinkage due to dough drying. Particular attention was paid to experimental validation of both overall and local variables such as local temperature, overall mass loss, and local moisture content, overall CO₂ released into the oven, and overall deformation and local expansion or shrinkage. Sensitivity studies on generation of carbon dioxide, gravity, and shrinkage are presented to discuss their influences on bread geometry, porosity (reflecting the alveolar structure) and gas pressure. © 2016 American Institute of Chemical Engineers AIChE J, 62: 3847–3863, 2016     

The Influence of Blend Ratio on the Morphology,Mechanical, Thermal,and Rheological Properties of PP/LDPE Blends

This paper reports on how the blend ratio and morphology influence the mechanical, thermal, thermomechanical, and rheological properties of poly(propylene) (PP)/low density polyethylene (LDPE) blends. The blend morphology is composed of the major matrix phase and the minor phase, with subinclusions of the major matrix existing within the minor phase. Blends containing low amounts (<20 wt%) of either phase exhibit partial miscibility but the phases are immiscible at higher contents. Partial miscibility of the blends is revealed by scanning electron microscopy studies showing fibril‐like structures and confirmed by rheology. The tensile modulus of the blends decreases with increasing amounts of LDPE, but low LDPE contents exhibit positive deviation from the mixing rule of mixture due to partial compatibility. The crystallinity of PP is affected less than that of LDPE in the blends. Thermomechanical and rheological properties of neat polymers are significantly influenced by blending. The blend ratio and morphology influence impact strength and elongation at break, and the result demonstrates that the 80/20 PP/LDPE blend offers a balance among the mechanical and material properties that are essential for flexible packaging applications.

     

Novel Tacrine‐Grafted Ugi Adducts as Multipotent Anti‐Alzheimer Drugs: A Synthetic Renewal in Tacrine–Ferulic Acid Hybrids

Herein we describe the design, multicomponent synthesis, and biological, molecular modeling and ADMET studies, as well as in vitro PAMPA‐blood–brain barrier (BBB) analysis of new tacrine–ferulic acid hybrids (TFAHs). We identified (E)‐3‐(hydroxy‐3‐methoxyphenyl)‐N‐{8[(7‐methoxy‐1,2,3,4‐tetrahydroacridin‐9‐yl)amino]octyl}‐N‐[2‐(naphthalen‐2‐ylamino)2‐oxoethyl]acrylamide (TFAH 10 n ) as a particularly interesting multipotent compound that shows moderate and completely selective inhibition of human butyrylcholinesterase (IC₅₀=68.2 nM ), strong antioxidant activity (4.29 equiv trolox in an oxygen radical absorbance capacity (ORAC) assay), and good β‐amyloid (Aβ) anti‐aggregation properties (65.6 % at 1:1 ratio); moreover, it is able to permeate central nervous system (CNS) tissues, as determined by PAMPA‐BBB assay. Notably, even when tested at very high concentrations, TFAH 10 n easily surpasses the other TFAHs in hepatotoxicity profiling (59.4 % cell viability at 1000 μM ), affording good neuroprotection against toxic insults such as Aβ_1–40, Aβ_1–42, H₂O₂, and oligomycin A/rotenone on SH‐SY5Y cells, at 1 μM . The results reported herein support the development of new multipotent TFAH derivatives as potential drugs for the treatment of Alzheimer′s disease.