How to evaluate the environmental safety of microbial plant protection products: A proposal

Plant protection products with active micro-organisms are allegedly less hazardous to the environment and wildlife than synthetic chemical pesticides. Nevertheless, they need a proper pre-marketing environmental safety evaluation because of their potential toxicity and pathogenicity. Scientific and technical guidance on such a safety evaluation for regulatory purposes is scarce. Therefore, a risk decision tree is proposed to provide such guidance and to discern the acceptable from the unacceptable environmental risks. The decision tree is based on the risk criteria of the European Union. It takes integrally into account the characterisation, identification and efficacy and also emission, exposure, environmental effects and, finally, the environmental risk assessment. Case by case expert judgement remains necessary in view of limited knowledge of microbial ecology, limited experience with regulatory test protocols and taxonomic difficulties in relation to the indigenousness of active micro-organisms. The decision tree offers regulatory guidance on the environmental safety evaluation of microbial plant protection products.     

Glycanogenomics: a qPCR-approach to investigate biological glycan function

As an indirect approach towards glycan structures, qRT-PCR analyses using the ΔΔC_T method were performed to investigate changes in expression levels of heparan sulfate-synthesising enzymes of stimulated and unstimulated HMVECs. We chose NDSTs as early enzymes initiating sulfation and 3OSTs which act late generating specific binding sites. Major changes in expression patterns were found for the NDST3 and 3OST1 isoforms. Both enzymes were down-regulated 7- and 6-fold, respectively, following TNF-α stimulation, and 3.5- and 7.6-fold following LPS-stimulation suggesting a common restructuring process of HS in inflammation leading to a less diverse sulfation pattern. Immunostaining of TNF-α-stimulated cells using a phage display-derived antibody specific for 3-O-sulfation and unsulfated regions of HS resulted in significant fluorescence changes between unstimulated and stimulated.     

How bacteria can block xenophagy: an insight from Salmonella

ABSTRACT

Xenophagy, a unique type of selective macroautophagy/autophagy, targets invading pathogens as part of the host immune response. In order to survive within the host, bacteria have established various self-defense mechanisms. In a recent paper from Feng Shao’s lab, the Salmonella effector protein SopF has been demonstrated to block xenophagy by interrupting the vacuolar type H⁺-translocating (v-) ATPase-ATG16L1 axis, which is important for antibacterial autophagy initiation. SopF can specifically ADP-ribosylate Gln124 on ATP6V0C, a v-ATPase component, thus influencing recruitment of ATG16L1 onto the bacteria-containing vacuole within the host cytosol.

Abbreviations: ATG: autophagy-related; S. Typhimurium: Salmonella enterica serovar Typhimurium; T3SS: type III secretion system     

How eukaryotic algae can adapt to the Spain's Rio Tinto: a neo-Darwinian proposal for rapid adaptation to an extremely hostile ecosystem

Microalgae contributed 60% of the total biomass in the extremely hostile (pH 2 and metal-rich waters) environment of Rio Tinto (which is used as a model for the astrobiology of Mars). These algae are closely related to nonextreme lineages, suggesting that adaptation to Rio Tinto water (RTW) must occur rapidly. Fitness from both the microalga Dictyosphaerium chlorelloides and the cyanobacterium Microcystis aeruginosa was inhibited when they were cultured in RTW. After further incubation for several weeks, D. chlorelloides survived, as a result of the growth of a variant that was resistant to RTW, but RTW-resistant cells did not appear in M. aeruginosa. A Luria-Delbrück fluctuation test revealed that D. chlorelloides RTW-resistant cells arose randomly by rare spontaneous mutations before the RTW exposure (1.38 x 10(-6) mutants per cell division). The mutants with a diminished fitness are maintained in nonextreme waters as the result of a balance between new RTW-resistant cells arising by mutation and RTW-resistant mutants eliminated by natural selection (equilibrium at c. 15 RTW-resistant per 10(7) wild-type cells). Rapid adaptation of eukaryotic algae to RTW could be the result of selection of RTW-resistant mutants occurring spontaneously in nonextreme populations that arrived fortuitously at the river in the past, or in the present continuously.     

Synchrotron protein footprinting: a technique to investigate protein-protein interactions.

Traditional approaches for macromolecular structure elucidation, including NMR, crystallography and cryo-EM have made significant progress in defining the structures of protein-protein complexes. A substantial number of macromolecular structures, however, have not been examined with atomic detail due to sample size and heterogeneity, or resolution limitations of the technique; therefore, the general applicability of each method is greatly reduced. Synchrotron footprinting attempts to bridge the gap in these methods by monitoring changes in accessible surface areas of discrete macromolecular moieties. As evidenced by our previous studies on RNA folding and DNA-protein interactions, the three-dimensional structure is probed by examining the reactions of these moieties with hydroxyl radicals generated by synchrotron X-rays. Here we report the application of synchrotron footprinting to the investigation of protein- protein interactions, as the novel technique has been utilized to successfully map the contact sites of gelsolin segment-1 in the gelsolin segment 1/actin complex. Footprinting results demonstrate that phenylalanine 104, located on the actin binding helix of gelsolin segment 1, is protected from hydroxyl radical modification in the presence of actin. This change in reactivity results from the specific protection of gelsolin segment-1, consistent with the substantial decrease in solvent accessibility of F104 upon actin binding, as calculated from the crystal structural of the gelsolin segment 1/actin complex. The results presented here establish synchrotron footprinting as a broadly applicable method to probe structural features of macromolecular complexes that are not amenable to conventional approaches.     

How to grow your cable bacteria: Establishment of a stable single-strain culture in sediment and proposal of Candidatus Electronema aureum GS

Cable bacteria are multicellular filamentous bacteria within the Desulfobulbaceae that couple the oxidation of sulfide to the reduction of oxygen over centimeter distances via long distance electron transport (LDET). So far, none of the freshwater or marine cable bacteria species have been isolated into pure culture. Here we describe a method for establishing a stable single-strain cable bacterium culture in partially sterilized sediment. By repeated transfers of a single cable bacterium filament from freshwater pond sediment into autoclaved sediment, we obtained strain GS, identified by its 16S rRNA gene as a member of Ca. Electronema. This strain was further propagated by transferring sediment clumps, and has now been stable within its semi-natural microbial community for several years. Its metagenome-assembled genome was 93% complete, had a size of 2.76 Mbp, and a DNA G + C content of 52%. Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) suggest the affiliation of strain GS to Ca. Electronema as a novel species. Cell size, number of outer ridges, and detection of LDET in the GS culture are likewise consistent with Ca. Electronema. Based on these combined features, we therefore describe strain GS as a new cable bacterium species of the candidate genus Electronema, for which we propose the name Candidatus Electronema aureum sp.nov. Although not a pure culture, this stable single-strain culture will be useful for physiological and omics-based studies; similar approaches with single-cell or single-filament transfers into natural medium may also aid the characterization of other difficult-to-culture microbes.     

Toward a recovery time: forest herbs insight related to anthropogenic acidification

Atmospheric deposition is a global concern contributing to soil acidification and biodiversity changes in forest ecosystems. Although acidifying deposition has decreased in the last decades in Europe, few evidence of ecosystem recovery from acidification has been reported until now. The objective of this study was to reconstruct spatiotemporal changes in soil pH across the entire French forest territory over the last 100‐year period through herb species assemblages. Data were collected from floristic databases resulting in a total of 120 216 plots covering French forests and spanning from 1910 to 2010. To define acidity figures, pH values were inferred from herb assemblages for each plot of the prediction dataset based on a weighted averaging partial least squares (WA‐PLS) model (R² = 0.80, SD = 0.59 for the validation dataset). Spatiotemporal trends of mean pH changes were obtained by comparing plots with respect to the period (mean year of the period = 1933, 1966, 1984, 1997, 2007) and substrate (acidic and nonacidic forest areas). Bioindicated pH highlighted a decrease in soil pH in both acidic and nonacidic forest areas. The sharpest and most significant pH decrease occurred before 1984 in acidic areas, reaching 0.34 pH units. Subsequently, no significant changes were observed, with a tendency toward stabilization. By contrast, the pH decrease reached 0.19 pH units in nonacidic areas, only reaching significance between 1984 and 1997. Thereafter, we observed a slight and significant pH increase. Spatially, pH trends revealed a regionalized character of acidification regarding the substrate, which could not be related to the extent of deposition modeled by the European Monitoring and Evaluation Programme. Both temporal and spatial trends highlight the lagged responses of nonacidic areas compared with acidic areas. Hence, floristic reconstructed pH trends demonstrate a gradual cessation and recovery from acidification of French forests after a period of intense atmospheric pollution.     

Liposome-entrapped tyrosinase: a tool to investigate the regulation of the Raper-Mason pathway

The effect of the entrapment of mushroom tyrosinase (EC 1.14.18.1) within liposomes on the enzyme activity and Km vs. L-3,4-dihydroxyphenylalanine is reported in the present work; the effect of cholesterol insertion within liposome membranes on the enzyme activity has also been studied. The oxidation rates of various monophenols and diphenols by free and liposome-integrated mushroom tyrosinase were measured and the oxidation latencies vs. different substrates investigated. The different substrates are apparently oxidized according to the properties of the substituents as electron donors or acceptors; the Km values vs. L-3,4-dihydroxyphenylalanine calculated on measuring O2 consumption are higher than those calculated on measuring the dopachrome production rates. It is interesting that natural substrates of tyrosinase are oxidized according to a negative catalysis by the liposome-entrapped enzyme; this point is discussed in relation to the well known cytotoxicity of some intermediates of the Raper-Mason pathway.     

Nucleic acid solvation: from outside to insight

Nucleic acids are polyanionic molecules that were historically considered to be solely surrounded by a shell of water molecules and a neutralizing cloud of monovalent and divalent cations. In this respect, recent experimental and theoretical reports demonstrate that water molecules within complex nucleic acid structures can display very long residency times, and assist drug binding and catalytic reactions. Finally, anions can also bind to these polyanionic systems. Many of these recent insights are provided by state-of-the-art molecular dynamics simulations of nucleic acid systems, which will be described together with relevant methodological issues.     

How to build a biofilm: a fungal perspective

Biofilms are differentiated masses of microbes that form on surfaces and are surrounded by an extracellular matrix. Fungal biofilms, especially those of the pathogen Candida albicans, are a cause of infections associated with medical devices. Such infections are particularly serious because biofilm cells are relatively resistant to many common antifungal agents. Several in vitro models have been used to elucidate the developmental stages and processes required for C. albicans biofilm formation, and recent studies have begun to define biofilm genetic control. It is clear that cell-substrate and cell-cell interactions, hyphal differentiation and extracellular matrix production are key steps in biofilm development. Drug resistance is acquired early in biofilm formation, and appears to be governed by different mechanisms in early and late biofilms. Quorum sensing might be an important factor in dispersal of biofilm cells. The past two years have seen the emergence of several genomic strategies to uncover global events in biofilm formation and directed studies to understand more specific events, such as hyphal formation, in the biofilm setting.