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Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the FlyBi dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.

Abstract The role, magnitude, and molecular nature of trans-driven expression variation underlying the upregulation of detoxification genes in pesticide resistant arthropod populations has remained enigmatic. In this study, we performed expression quantitative trait locus (eQTL) mapping (n = 458) between a pesticide resistant and a susceptible strain of the generalist herbivore and crop pest Tetranychus urticae. We found that a single trans eQTL hotspot controlled large differences in the expression of a subset of genes in different detoxification gene families, as well as other genes associated with host plant use. As established by additional genetic approaches including RNAi gene knockdown, a duplicated gene with a nuclear hormone receptor HR96-related ligand-binding domain was identified as causal for the expression differences between strains. The presence of a large family of HR96-related genes in T. urticae may enable modular control of detoxification and host plant use genes, facilitating this species’ known and rapid evolution to diverse pesticides and host plants.

In the last decades, Chemical, Biological, Radiological and Nuclear (CBRN) threats have become serious risks prompting countries to prioritize preparedness for such incidents. As CBRN scenarios are very difficult and expensive to recreate in real life, computer simulation is particularly suited for assessing the effectiveness of contingency plans and identifying areas of improvement. These computer simulation exercises require realistic and dynamic victim profiles, which are unavailable in a civilian context. In this paper we present a set of civilian nerve agent injury profiles consisting of clinical parameters and their evolution, as well as the methodology used to create them. These injury profiles are based on military injury profiles and adapted to the civilian population, using sarin for the purpose of illustration. They include commonly measured parameters in the prehospital setting. We demonstrate that information found in military sources can easily be adjusted for a civilian population using a few simple assumptions and validated methods. This methodology can easily be expanded to other chemical warfare agents as well as different ways of exposure. The resulting injury profiles are generic so they can also be used in tabletop and live simulation exercises. Modeling and simulation, if used correctly and in conjunction with empirical data gathered from lessons learned, can assist in providing the evidence practices for effective and efficient response decisions and interventions, considering the contextual factors of the affected area and the specific disaster scenario.

Abstract Background Generalist herbivores such as the two-spotted spider mite Tetranychus urticae thrive on a wide variety of plants and can rapidly adapt to novel hosts. What traits enable polyphagous herbivores to cope with the diversity of secondary metabolites in their variable plant diet is unclear. Genome sequencing of T. urticae revealed the presence of 17 genes that code for secreted proteins with strong homology to “intradiol ring cleavage dioxygenases (DOGs)” from bacteria and fungi, and phylogenetic analyses show that they have been acquired by horizontal gene transfer from fungi. In bacteria and fungi, DOGs have been well characterized and cleave aromatic rings in catecholic compounds between adjacent hydroxyl groups. Such compounds are found in high amounts in solanaceous plants like tomato, where they protect against herbivory. To better understand the role of this gene family in spider mites, we used a multi-disciplinary approach to functionally characterize the various T. urticae DOG genes. Results We confirmed that DOG genes were present in the T. urticae genome and performed a phylogenetic reconstruction using transcriptomic and genomic data to advance our understanding of the evolutionary history of spider mite DOG genes. We found that DOG expression differed between mites from different plant hosts and was induced in response to jasmonic acid defense signaling. In consonance with a presumed role in detoxification, expression was localized in the mite’s gut region. Silencing selected DOGs expression by dsRNA injection reduced the mites’ survival rate on tomato, further supporting a role in mitigating the plant defense response. Recombinant purified DOGs displayed a broad substrate promiscuity, cleaving a surprisingly wide array of aromatic plant metabolites, greatly exceeding the metabolic capacity of previously characterized microbial DOGs. Conclusion Our findings suggest that the laterally acquired spider mite DOGs function as detoxification enzymes in the gut, disarming plant metabolites before they reach toxic levels. We provide experimental evidence to support the hypothesis that this proliferated gene family in T. urticae is causally linked to its ability to feed on an extremely wide range of host plants.

Abstract The phenylpropanoid cinnamic acid (CA) is a plant metabolite that can occur under a trans‐ or cis‐form. In contrast to the proven bioactivity of the cis‐form (c‐CA), the activity of trans‐CA (t‐CA) is still a matter of debate. We tested both compounds using a submerged rice coleoptile assay and demonstrated that they have opposite effects on cell elongation. Notably, in the tip of rice coleoptile t‐CA showed an inhibiting and c‐CA a stimulating activity. By combining transcriptomics and (untargeted) metabolomics with activity assays and genetic and pharmacological experiments, we aimed to explain the underlying mechanistic processes. We propose a model in which c‐CA treatment activates proton pumps and stimulates acidification of the apoplast, which in turn leads to the loosening of the cell wall, necessary for elongation. We hypothesize that c‐CA also inactivates auxin efflux transporters, which might cause a local auxin accumulation in the tip of the coleoptile. For t‐CA, the phenotype can partially be explained by a stimulation of cell wall polysaccharide feruloylation, leading to a more rigid cell wall. Metabolite profiling also demonstrated that salicylic acid (SA) derivatives are increased upon t‐CA treatment. As SA is a known antagonist of auxin, the shift in SA homeostasis provides an additional explanation of the observed t‐CA‐mediated restriction on cell growth.

This study provides a comprehensive comparison among the most common gluten-free (GF) brewing practices, with a focus on the impact of each treatment on physicochemical parameters and consumer acceptability of the final beer. In addition, the influence of a longer cold maturation on the natural reduction of the gluten content was investigated. Prolyl endopeptidase addition was found to be the most effective treatment in reducing gluten levels (−75.93%), followed by silica gel (−53.09%), longer cold maturation (−4.32%), and tannins (−1.85%). Nonetheless, none of the treated beer samples was gluten-free (gluten content > 20 ppm) due to the high nitrogen content of the original wort. The silica gel application treatment affected the physicochemical and sensory characteristics of the final beer the least. According to the difference from control test results, no significant difference in terms of overall liking, appearance, odor/aroma, or taste was observed between the silica gel-treated sample and control beer (p > 0.05). On the other hand, the application of enzymes and tannins significantly affected the appearance and the beer odor/aroma. Nevertheless, all beer samples received positive sensory acceptance scores.

The conversion of raw grains to malt is a pivotal step in the beer production process. By germination, the grains produce enzymes necessary for the conversion of starch into sugars during the mashing process, but also cell wall constituents are broken down which aids in wort filtration. Further, storage proteins are converted into soluble peptides and amino acids important for yeast nutrition during fermentation. However, the performance of the malting process and the quality of malt produced is also significantly influenced by the active microbial communities that naturally colonise the barley grains. These diverse microbial communities have the potential to produce extracellular enzymes, phytohormones, mycotoxins, and exopolysaccharides, and also compete with the grains for oxygen. While microbes can contribute positively to the break-down of cell wall β-glucans and arabinoxylans, they can also negatively impact the final malt quality by production of gushing precursors, compounds leading to premature yeast flocculation (PYF) and mycotoxins. This review provides an overview of the current knowledge on the different microbial communities interacting with the barley grain on the field and during malt production, their influence on the quality of produced malt, and the brewing process. Further, current strategies to control the proliferation of detrimental microbial species during malting are presented, including a summary on recent techniques to identify, quantify and functionally characterise the barley malting microbiome. [ABSTRACT FROM AUTHOR]

Mashing is a decisive brewing step, affecting wort quality. Critical mashing parameters include time, temperature, pH, mash density and oxygen uptake. While the pH-dependent biochemical changes during mashing have been researched, the oxidative processes remain unclear. This work explores the impact of pH conditions during mashing on the biochemical composition and oxidative properties of wort. In laboratory trials, mashing was conducted at different mashing-in pH (4.5, 5.0, 5.2, 5.4, 6.0). The sweet worts were analyzed for extract, fermentable sugars, limit dextrins, amino acids, soluble proteins, polyphenols, color, aldehydes, transition metals, reducing potential, and rate of radical formation. Differences were found in enzymatic activities (particularly proteolysis), color, aldehydes, transition metal ions, the rate of radical formation and the rate of oxygen consumption. Notably, when adjusting the pH at mashing-in, the obtained wort tends to gravitate toward the pH of the unadjusted wort, underscoring its buffering capacity. This was reflected by similar properties of the produced worts, indicating pH playing a lesser role during mashing compared to time/temperature. However, under extreme acidified conditions (pH 4.5 at mashing-in), the produced wort markedly deviates. An intriguing negative correlation between the reducing potential and the content of transition metal ions with the rate of radical formation is discussed. [ABSTRACT FROM AUTHOR]

Increasing popularity of sour beer urges the development of novel solutions for controlled fermentations both for fast acidification and consistency in product flavor and quality. One possible approach is the use of Saccharomyces cerevisiae in co-fermentation with Lactobacillus species, which produce lactic acid as a major end-product of carbohydrate catabolism. The ability of lactobacilli to ferment beer is determined by their capacity to sustain brewing-related stresses, including hop iso-α acids, low pH and ethanol. Here, we evaluated the tolerance of Lactobacillus brevis BSO464 and Lactobacillus buchneri CD034 to beer conditions and different fermentation strategies as well as their use in the brewing process in mixed fermentation with a brewer’s yeast, S. cerevisiae US-05. Results were compared with those obtained with a commercial Lactobacillus plantarum (WildBrewTM Sour Pitch), a strain commonly used for kettle souring. In pure cultures, the three strains showed varying susceptibility to stresses, with L. brevis being the most resistant and L. plantarum displaying the lowest stress tolerance. When in co-fermentation with S. cerevisiae, both L. plantarum and L. brevis were able to generate sour beer in as little as 21 days, and their presence positively influenced the composition of flavor-active compounds. Both sour beers were sensorially different from each other and from a reference beer fermented by S. cerevisiae alone. While the beer produced with L. plantarum had an increased intensity in fruity odor and dried fruit odor, the L. brevis beer had a higher total flavor intensity, acidic taste and astringency. Remarkably, the beer generated with L. brevis was perceived as comparable to a commercial sour beer in multiple sensory attributes. Taken together, this study demonstrates the feasibility of using L. brevis BSO464 and L. plantarum in co-fermentation with S. cerevisiae for controlled sour beer production with shortened production time.