Systematic and quantitative view of the antiviral arsenal of prokaryotes.

Bacteria and archaea have developed multiple antiviral mechanisms, and genomic evidence indicates that several of these antiviral systems co-occur in the same strain. Here, we introduce DefenseFinder, a tool that automatically detects known antiviral systems in prokaryotic genomes. We use DefenseFinder to analyse 21000 fully sequenced prokaryotic genomes, and find that antiviral strategies vary drastically between phyla, species and strains. Variations in composition of antiviral systems correlate with genome size, viral threat, and lifestyle traits. DefenseFinder will facilitate large-scale genomic analysis of antiviral defense systems and the study of host-virus interactions in prokaryotes.

Native Vineyard Non-Saccharomyces Yeasts Used for Biological Control of Botrytis cinerea in Stored Table Grape.

Postharvest spoilage fungi, such as Botrytis cinerea, are considered the main cause of losses of fresh fruit quality and vegetables during storage, distribution, and consumption. The current control strategy is the use of SO2 generator pads whose application is now largely under observation. A high quantity of SO2 can be deleterious for fresh fruits and vegetables and it is not allowed in organic agriculture. For this reason, great attention has been recently focused on identifying Biological Control Agents (BCA) to implement biological approaches devoid of chemicals. In this direction, we carried out our study in isolating five different non-Saccharomyces yeast strains from local vineyards in the South of Italy as possible BCA. We performed both in vitro and in vivo assays in semi-commercial conditions on detached grape berries stored at 0 °C, simulating the temperature normally used during cold storage, and obtained relevant results. We isolated three M. pulcherrima strains and one L. thermotolerans strain able to largely antagonize the development of the B. cinerea, at both in vitro and in vivo conditions. In particular, we detected the ability of the three isolates of M. pulcherrima strains Ale4, N20/006, and Pr7 and the L. thermotolerans strain N10 to completely inhibit (100% in reduction) the mycelial growth of B. cinerea by producing fungistatic compounds. We found, using an extracellular lytic enzymes activity assay, that such activity could be related to lipid hydrolyzation, ß-1,3-glucanase and pectinase activity, and pectinase and protease activity, depending on the yeasts used. Results from our in vitro assays allowed us to hypothesize for M. pulcherrima strains Ale4 and N20/006 a possible combination of both the production of soluble metabolites and volatile organic compounds to antagonize against B. cinerea growth. Moreover, in semi-commercial conditions, the M. pulcherrima strain N20/006 and L. thermotolerans strain N10 showed relevant antagonistic effect also at low concentrations (with a significantly reduction of 'slip skin' incidence of 86.4% and 72.7%, respectively), thus highlighting a peculiar property to use in commercial development for organic agriculture and the handling process.

Structural properties of ultra-small thorium and uranium dioxide nanoparticles embedded in a covalent organic framework.

We report the structural properties of ultra-small ThO2 and UO2 nanoparticles (NPs), which were synthesized without strong binding surface ligands by employing a covalent organic framework (COF-5) as an inert template. The resultant NPs were used to observe how structural properties are affected by decreasing grain size within bulk actinide oxides, which has implications for understanding the behavior of nuclear fuel materials. Through a comprehensive characterization strategy, we gain insight regarding how structure at the NP surface differs from the interior. Characterization using electron microscopy and small-angle X-ray scattering indicates that growth of the ThO2 and UO2 NPs was confined by the pores of the COF template, resulting in sub-3 nm particles. X-ray absorption fine structure spectroscopy results indicate that the NPs are best described as ThO2 and UO2 materials with unpassivated surfaces. The surface layers of these particles compensate for high surface energy by exhibiting a broader distribution of Th-O and U-O bond distances despite retaining average bond lengths that are characteristic of bulk ThO2 and UO2. The combined synthesis and physical characterization efforts provide a detailed picture of actinide oxide structure at the nanoscale, which remains highly underexplored compared to transition metal counterparts.

The sensitivity of yeasts and yeasts-like fungi to copper and sulfur could explain lower yeast biodiversity in organic vineyards.

Although differences in yeast biodiversity have often been found between vineyards subjected to organic protection or conventional protection, little is known about the effect of copper and sulfur fungicides (the only fungicides allowed in organic farming) on yeast populations. The sensitivity to copper and sulfur of 158 yeast isolates of seven different species (Aureobasidium pullulans, Hanseniaspora guilliermondii, H. uvarum, Metschnikowia sp., Pichia membranifaciens, Saccharomyces cerevisiae and Starmerella bacillaris) was evaluated. The species A. pullulans and St. bacillaris appeared to be more resistant to copper than the other species tested. The species A. pullulans, H. guilliermondii and Metschnikowia sp. had the highest sulfur resistance. Thus, only isolates of the species A. pullulans exhibited high resistance to both antifungal agents. These results may explain the lower diversity of yeasts present on berries and the strong dominance of the species A. pullulans for vineyards protected by copper or sulfur-based fungicides compared to other vineyards reported by several studies.

Chemical and Morphological Inhomogeneity of Aluminum Metal and Oxides from Soft X-ray Spectromicroscopy.

Oxygen and aluminum K-edge X-ray absorption spectroscopy (XAS), imaging from a scanning transmission X-ray microscope (STXM), and first-principles calculations were used to probe the composition and morphology of bulk aluminum metal, α- and γ-Al2O3, and several types of aluminum nanoparticles. The imaging results agreed with earlier transmission electron microscopy studies that showed a 2 to 5 nm thick layer of Al2O3 on all the Al surfaces. Spectral interpretations were guided by examination of the calculated transition energies, which agreed well with the spectroscopic measurements. Features observed in the experimental O and Al K-edge XAS were used to determine the chemical structure and phase of the Al2O3 on the aluminum surfaces. For unprotected 18 and 100 nm Al nanoparticles, this analysis revealed an oxide layer that was similar to γ-Al2O3 and comprised of both tetrahedral and octahedral Al coordination sites. For oleic acid-protected Al nanoparticles, only tetrahedral Al oxide coordination sites were observed. The results were correlated to trends in the reactivity of the different materials, which suggests that the structures of different Al2O3 layers have an important role in the accessibility of the underlying Al metal toward further oxidation. Combined, the Al K-edge XAS and STXM results provided detailed chemical information that was not obtained from powder X-ray diffraction or imaging from a transmission electron microscope.

U(III)-CN versus U(IV)-NC coordination in tris(silylamide) complexes.

Treatment of the metallacycle [UN*2(N,C)] [N* = N(SiMe3)2; N,C = CH2SiMe2N(SiMe3)] with [HNEt3][BPh4], [HNEt3]Cl, and [pyH][OTf] (OTf = OSO2CF3) gave the cationic compound [UN*3][BPh4] (1) and the neutral complexes [UN*3X] [X = Cl (3), OTf (4)], respectively. The dinuclear complex [{UN*(µ-N,C)(µ-OTf)}2] (5) and its tetrahydrofuran (THF) adduct [{UN*(N,C)(THF)(µ-OTf)}2] (6) were obtained by thermal decomposition of 4. The successive addition of NEt4CN or KCN to 1 led to the formation of the cyanido-bridged dinuclear compound [(UN*3)2(µ-CN)][BPh4] (7) and the mononuclear mono- and bis(cyanide) complexes [UN*3(CN)] (2) and [M][UN*3(CN)2] [M = NEt4 (8), K(THF)4 (9)], while crystals of [K(18-crown-6)][UN*3(CN)2] (10) were obtained by the oxidation of [K(18-crown-6)][UN*3(CN)] with pyridine N-oxide. The THF adduct of 1, [UN*3(THF)][BPh4], and complexes 2-7, 9 and 10 were characterized by their X-ray crystal structure. In contrast to their U(III) analogues [NMe4][UN*3(CN)] and [K(18-crown-6)]2[UN*3(CN)2] in which the CN anions are coordinated to the metal center via the C atom, complexes 2 and 9 exhibit the isocyanide U-NC coordination mode of the cyanide ligand. This U(III)/U(IV) differentiation has been analyzed using density functional theory calculations. The observed preferential coordinations are well explained considering the electronic structures of the different species and metal-ligand bonding energies. A comparison of the different quantum descriptors, i.e., bond orders, NPA/QTAIM data, and energy decomposition analysis, has allowed highlighting of the subtle balance between covalent, ionic, and steric factors that govern the U-CN/NC bonding.

U-CN versus Ce-NC coordination in trivalent complexes derived from M[N(SiMe3)2]3 (M = Ce, U).

Reactions of [MN*3] (M = Ce, U; N* = N(SiMe3)2) and NR4CN (R = Me, Et, or (n)Bu) or KCN in the presence of 18-crown-6 afforded the series of cyanido-bridged dinuclear compounds [NEt4][(MN*3)2(µ-CN)] (M = Ce, 2a, and U, 2b), [K(18-crown-6)(THF)2][(CeN*3)2(µ-CN)] (2'a), and [K(18-crown-6)][(UN*3)2(µ-CN)] (2'b), and the mononuclear mono-, bis-, and tris(cyanide) complexes [NEt4][MN*3(CN)] (M = Ce, 1a(Et), and U, 1b(Et)), [NMe4][MN*3(CN)] (M = Ce, 1a(Me), and U, 1b(Me)), [K(18-crown-6)][MN*3(CN)] (M = Ce, 1'a, and U, 1'b), [N(n)Bu4]2[MN*3(CN)2] (M = Ce, 3a, and U, 3b), [K(18-crown-6)]2[MN*3(CN)2] (M = Ce, 3'a, and U, 3'b), and [N(n)Bu4]2[MN*2(CN)3] (M = Ce, 4a, and U, 4b). The mono- and bis(cyanide) complexes were found to be in equilibrium. The formation constant of 3'b (K3'b) from 1'b at 10 °C in THF is equal to 5(1) × 10(-3), and -ΔH3'b = 104(2) kJ mol(-1) and -ΔS3'b = 330(5) J mol(-1) K(-1). The bis(cyanide) compound 3a or 3b was slowly transformed in solution into an equimolar mixture of the mono- and tris(cyanide) derivatives with elimination of N(n)Bu4N*. The crystal structures of 1a(Me), 1b(Me), 1'a·toluene, 1'b·toluene, 2'a, 2'b, 3a, 3'a, 3'b, 3'a·2benzene, 3'b·2benzene, 4a·0.5THF, and 4b·Et2O were determined. Crystals of the bis(cyanide) uranium complexes 3'b and 3'b·2benzene are isomorphous with those of the cerium counterparts 3'a and 3'a·2benzene, but they are not isostructural since the data revealed distinct coordination modes of the CN group, through the C or N atom to the U or Ce metal center, respectively. This differentiation has been analyzed using density functional theory calculations. The observed preferential coordination of the cyanide and isocyanide ions toward uranium or cerium in the bis(cyanide) complexes is corroborated by the consideration of the binding energies of these groups to the metals and by the comparison of DFT optimized geometries with the crystal structures. The better affinity of the cyanide ligand toward U(III) over Ce(III) metal center is related to the better energy matching between the 6d/5f uranium orbitals and the cyanide ligand ones, leading to a non-negligible covalent character of the bonding.

A versatile methodology for the regioselective C8-metalation of purine bases.

Purine nucleobases are excellent ligands for metal ions, forming normally coordinative Werner-type bonds by utilizing the N donor atoms of the nucleobase skeleton. Here we show that purines such as 8-chlorocaffeine and 8-bromo-9-methyladenine react with [Pt(PPh3)4] under oxidative addition of the C(8)-halogen bond to the metal center. The resulting Pt(II) complexes feature a C(8)-bound ylidene ligand. Protonation of the ylidene at the N(7/9)-atom yields complexes bearing a protic N-heterocyclic carbene ligand derived from the purine base with an NMe,NH-substitution pattern.

Bent thorocene complexes with the cyanide, azide and hydride ligands.

Reaction of the linear thorocene with NC(-), N3(-) and H(-) led to the bent derivatives [(Cot)2Th(X)](-) (X = CN, N3) and the bimetallic [{(Cot)2Th}2(µ-H)](-), whereas only [(Cot)2U(CN)](-) could be formed from (Cot)2U.