Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics

We report a methodology to calculate the free energy of a shape transformation in a lipid membrane directly from a molecular dynamics simulation. The bilayer need not be homogeneous or symmetric and can be atomically detailed or coarse grained. The method is based on a collective variable that quantifies the similarity between the membrane and a set of predefined density distributions. Enhanced sampling of this “Multi-Map” variable re-shapes the bilayer and permits the derivation of the corresponding potential of mean force. Calculated energies thus reflect the dynamic interplay of atoms and molecules, rather than postulated effects. Evaluation of deformations of different shape, amplitude, and range demonstrates that the macroscopic bending modulus assumed by the Helfrich–Canham model is increasingly unsuitable below the 100-Å scale. In this range of major biological significance, direct free-energy calculations reveal a much greater plasticity. We also quantify the stiffening effect of cholesterol on bilayers of different composition and compare with experiments. Lastly, we illustrate how this approach facilitates analysis of other solvent reorganization processes, such as hydrophobic hydration. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.     

Amino Acid Modified RNA Bases as Building Blocks of an Early Earth RNA-Peptide World

Fossils of extinct species allow us to reconstruct the process of Darwinian evolution that led to the species diversity we see on Earth today. The origin of the first functional molecules able to undergo molecular evolution and thus eventually able to create life, are largely unknown. The most prominent idea in the field posits that biology was preceded by an era of molecular evolution, in which RNA molecules encoded information and catalysed their own replication. This RNA world concept stands against other hypotheses, that argue for example that life may have begun with catalytic peptides and primitive metabolic cycles. The question whether RNA or peptides were first is addressed by the RNA-peptide world concept, which postulates a parallel existence of both molecular species. A plausible experimental model of how such an RNA-peptide world may have looked like, however, is absent. Here we report the synthesis and physicochemical evaluation of amino acid containing adenosine bases, which are closely related to molecules that are found today in the anticodon stem-loop of tRNAs from all three kingdoms of life. We show that these adenosines lose their base pairing properties, which allow them to equip RNA with amino acids independent of the sequence context. As such we may consider them to be living molecular fossils of an extinct molecular RNA-peptide world.     

Mycotoxins in spices and culinary herbs from Italy and Tunisia

Abstract

Spices and aromatic herbs can be contaminated with mycotoxins, since of their preharvest, postharvest, and storage conditions. In this study, 112 samples of different spices and aromatic herbs were evaluated for their mycotoxins content by HPLC-MS/MS in order to highlight their possible risk linked with human use. The results showed that mycotoxins were occasionally detected only in samples of coriander, laurel, mint, rosemary, and verbena. In both geographical origins a different contamination was detected. Among the investigated mycotoxins, AFB2, AFG1, AFG2, T2 and HT2 were detected, whereas none of the samples contained AFB1 and FB1. The co-occurrence of two toxins were observed for some samples of rosemary and verbena. This study indicates that it is essential minimize the toxins in agriculture, industry, and food-product manufacturing for the consumer health protection.     

Therapeutic Potential of Highly Selective A3 Adenosine Receptor Ligands in the Central and Peripheral Nervous System

Ligands of the G_i protein-coupled adenosine A₃ receptor (A₃R) are receiving increasing interest as attractive therapeutic tools for the treatment of a number of pathological conditions of the central and peripheral nervous systems (CNS and PNS, respectively). Their safe pharmacological profiles emerging from clinical trials on different pathologies (e.g., rheumatoid arthritis, psoriasis and fatty liver diseases) confer a realistic translational potential to these compounds, thus encouraging the investigation of highly selective agonists and antagonists of A₃R. The present review summarizes information on the effect of latest-generation A₃R ligands, not yet available in commerce, obtained by using different in vitro and in vivo models of various PNS- or CNS-related disorders. This review places particular focus on brain ischemia insults and colitis, where the prototypical A₃R agonist, Cl-IB-MECA, and antagonist, MRS1523, have been used in research studies as reference compounds to explore the effects of latest-generation ligands on this receptor. The advantages and weaknesses of these compounds in terms of therapeutic potential are discussed.     

Anion-Responsive Fluorescent Supramolecular Gels

Three novel bis-urea fluorescent low-molecular-weight gelators (LMWGs) based on the tetraethyl diphenylmethane spacer—namely, L1, L2, and L3, bearing indole, dansyl, and quinoline units as fluorogenic fragments, respectively, are able to form gel in different solvents. L2 and L3 gel in apolar solvents such as chlorobenzene and nitrobenzene. Gelator L1 is able to gel in the polar solvent mixture DMSO/H₂O (H₂O 15% v/v). This allowed the study of gel formation in the presence of anions as a third component. An interesting anion-dependent gel formation was observed with fluoride and benzoate inhibiting the gelation process and H₂PO₄⁻, thus causing a delay of 24 h in the gel formation. The interaction of L1 with the anions in solution was clarified by ¹H-NMR titrations and the differences in the cooperativity of the two types of NH H-bond donor groups (one indole NH and two urea NHs) on L1 when binding BzO⁻ or H₂PO₄⁻ were taken into account to explain the inhibition of the gelation in the presence of BzO⁻. DFT calculations corroborate this hypothesis and, more importantly, demonstrate considering a trimeric model of the L1 gel that BzO⁻ favours its disruption into monomers inhibiting the gel formation.     

Characterization of the Phytochemical Composition and Bioactivities of Anacyclus maroccanus Ball. and Anacyclus radiatus Loisel Aerial Parts: Preliminary Evidence for the Possible Development of Moroccan Plants

In the present study, the phytochemical composition and bioactivities of A. maroccanus (AM) and A. radiatus (AR), two ecotypes collected in the Demnate road and Essaouira regions, respectively, were studied to highlight a pharmacological interest and to enable possible pharmaceutical development. To this end, methanolic and ethyl acetate extracts were prepared for each ecotype by fractionation; next, their phytochemical composition was evaluated by spectrophotometric and chromatographic analysis. Moreover, in line with the available evidence for Anacyclus spp. and their traditional use, a screening of bioactivities, including antioxidant, hypoglycemic, antiglycative, chelating, and antibacterial activities, was performed. The extracts were characterized by high amounts of polyphenols, tannins, and flavonoids, especially in the methanolic extracts; these samples were also enriched in carotenoids despite a lower chlorophyll content. Chlorogenic acid and rutin were the major identified compounds. The extracts also showed interesting hypoglycemic, antiglycative, and antibacterial properties, although with differences in efficacy and potency. Present results provide more scientific basis to the ethnopharmacological uses of Anacyclus spp. and suggest a further interest in AM and AR ecotypes as natural sources of bioactive compounds and/or phytocomplexes for possible pharmaceutical and nutraceutical developments.     

Stars in five-dimensional Kaluza–Klein gravity

In the five-dimensional Kaluza–Klein (KK) theory there is a well known class of static and electromagnetic-free KK-equations characterized by a naked singularity behavior, namely the Generalized Schwarzschild solution (GSS). We present here a set of interior solutions of five-dimensional KK-equations. These equations have been numerically integrated to match the GSS in the vacuum. The solutions are candidates to describe the possible interior perfect fluid source of the exterior GSS metric and thus they can be models for stars for static, neutral astrophysical objects in the ordinary (four-dimensional) spacetime.     

Organic contamination in clams,Venerupis aurea laeta and Cerastoderma edule glaucum,from Sicily (Italy)

Two species of edible clams Venerupis aurea laeta and Cerastoderma edule glaucum from Ganzirri Lake (Sicily, Italy) were investigated to determine OCP and PCB residues by GC-MS. Thirty-five samples were examined for two years in order to perform: a) their actual contamination; b) the daily dietary exposure of seafood consumers to the pollutants in question. In all the clams analysed in this study, PCB and OCP (4,4′-DDE) residues are always below the limits fixed by law. It seems that there is some seasonality of concentrations observed. In fact the more high concentrations of residues are detected in the hot months, for both species and years. Given the consumption of clams and the values obtained in this study for the two species analysed, it is possible estimate that the average daily dietary intake of NDL-PCB and of 4,4′-DDE for adults is really low.     

Flexible conducting polymer transistors with supercapacitor function

Planar organic electrochemical transistors (OECTs) using PEDOT:PSS as the channel material and nanostructured carbon (nsC) as the gate electrode material and poly(sodium 4‐styrenesulfonate (PSSNa) gel as the electrolyte were fabricated on flexible polyethylene terephthalate (Mylar^®) substrates. The nsC was deposited at room‐temperature by supersonic cluster beam deposition (SCBD). Interestingly, the OECT acts as a hybrid supercapacitor (to give a device that we indicate as transcap). The energy storage ability of transcaps has been studied with two cell configurations: one featuring PEDOT:PSS as the positive electrode and nsC as the negative electrode and another configuration with reversed electrode polarity. Potentiostatic charge/discharge studies show that both supercapacitors show good performance in terms of voltage retention, in particular, when PEDOT:PSS is used as the positive electrode. Galvanostatic charge–discharge characteristics show typical symmetric triangular shape, indicating a nearly ideal capacitive behavior with a high columbic efficiency (close to 100%). © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 96–103