Literature search – Exploring in silico protein toxicity prediction methods to support the food and feed risk assessment

This report is the outcome of an EFSA procurement (NP/EFSA/GMO/2018/01) reviewing relevant scientific information on in silico prediction methods for protein toxicity, that could support the food and feed risk assessment. Several proteins are associated with adverse (toxic) effects in humans and animals, by a variety of mechanisms. These are produced by plants, animals and bacteria to prevail in hostile environments. In the present report, we present an integrated pipeline to perform a comprehensive literature and database search applied to proteins with toxic effects. \u201cToxin activity\u201d and \u201ctoxin-antitoxin system\u201d strings were used as inputs for this pipeline. UniProtKB was considered as the reference database, and only the UniProtKB curator-reviewed proteins were considered in the pipeline. Experimentally- determined structures and homology-based in silico 3D models were retrieved from protein structures repositories; family-, domain-, motif- and other molecular signature-related information was also obtained from specific databases which are part of the InterPro consortium. Protein aggregation associated with adverse effects was also investigated using different search strategies. This work can serve as the basis for further exploring novel risk assessment strategies for new proteins using in silico predictive methods

Harnack type estimates and Hölder continuity for non-negative solutions to certain sub-critically singular parabolic partial differential equations

A two-parameter family of Harnack type inequalities for non-negative solutions of a class of singular, quasilinear, homogeneous parabolic equations is established, and it is shown that such estimates imply the Hoelder continuity of solutions. These classes of singular equations include p-Laplacean type equation in the sub-critical range 1<p\le\frac2N/(N+1) and equations of the porous medium type in the sub-critical range 0<m\le(N-2)_+/N

Vitis vinifera - a chemotaxonomic approach: Pollen wall proteins

The electrophoretic pattern of the pollen wall proteins from clones of cv. Nebbiolo grown in different areas show a geographical clustering. Vermentino, Pigato and Favorita are found virtually identical both by morphological and biochemical criteria

Harnack's Estimates: Positivity and Local Behavior of Degenerate and Singular Parabolic Equations

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What if? Mouse proteomics after gene inactivation

The complex interactions among proteins and of proteins with small molecular weight protein ligands are overturned every time one of the components of the network is missing. For study purposes, animal models lacking one protein are obtained by experimental manipulation of the genome: in the knocking out approach, a gene is altered through the insertion of an artificial DNA sequence, which halts the transcription-translation sequence of events. In this review we have compiled the research papers that analyze the effects of knocking out individual genes on the proteomes of various tissues/organs throughout the body. We have gathered and organized all the available evidence and then compared the proteomic data in order to stress the context-specificity of the outcome every time two or more organs were investigated in the same KO mice. Finally, in a symmetrical approach to the above, we surveyed whether there is any obvious overlap among the effects of different KO on the same organ, marking affection of general pathways or lacking specificity of the gene targeting. Specific attention was put on the possible involvement of cellular stress markers

Vitis vinifera - a chemotaxonomic approach: Anthocyanins in the skin

The gaining of new knowledge about varietal differences in grapevines can be useful for the designing of genetic improvement programs. More and more, chemical methods complement ampelographic ones in the study of variability in grapevines. This work is aimed at the anthocyanin profiling of red-coloured grapes, of which ca. 120 cultivars were sampled; among these there were a high number of old Italian vines and 30 Vitis vinifera ssp. silvestris originating from different areas of Italy. Anthocyanins were HPLC separated and quantified with the aid of an inverse phase microbore column and a photodiode detector. Grapevines were numerically separated in groups using as indexes the percentage of the 5 monoglucosides present, the summations of: acetic esters; malvidin-3-monoglucoside-caffeoate plus all 5 p-coumaric esters; as well as a series of relations correlated to certain enzymatic activities necessary for the esterification of glucosides, hydroxylation and methylation in the biosynthesis of several anthocyanins. Data derived from the study of indexes of varietal enzymatic activity enable us to qualify differences between grapevines linked to the synthesis of anthocyanins. The stability of anthocyanic profiles within the same grape variety enables the use of this technique for taxonomic purposes. This research study discusses the use of this technique for classification and analysis of grape phylogenesis. An in-depth look into the relations between cultivated and wild varieties is given

S-Thiolation Targets Albumin in Heart Failure

Human serum albumin (HSA) is associated with several physiological functions, such as maintaining oncotic pressure and microvascular integrity, among others. It also represents the major and predominant antioxidant in plasma due to the presence of the Cys34 sulfhydryl group. In this study, we assessed qualitative and quantitative changes in HSA in patients with heart failure (HF) and their relationship with the severity of the disease. We detected by means of mass spectrometry a global decrease of the HSA content in the plasma of HF patients in respect to control subjects, a significant increase of thio-HSA with a concomitant decrease in the reduced form of albumin. Cysteine and, at a lesser extent, homocysteine represent the most abundant thiol bound to HSA. A strong inverse correlation was also observed between cysteine-HSA and peak VO2/kg, an index of oxygen consumption associated with HF severity. Moreover, in HL-1 cardiomyocytes incubated with H2O2, we showed a significant decrease of cell viability in cells treated with thio-HSA in respect to restored native-HSA. In conclusion, we found for the first time that S-thiolation of albumin is increased in the plasma of HF patients and induced changes in the structure and antioxidant function of HSA, likely contributing to HF progression