Role of temperature and Suwannee River natural organic matter on inactivation kinetics of rotavirus and bacteriophage MS2 by solar irradiation

Although the sunlight-mediated inactivation of viruses has been recognized as an important process that controls surface water quality, the mechanisms of virus inactivation by sunlight are not yet clearly understood. We investigated the synergistic role of temperature and Suwannee River natural organic matter (SRNOM), an exogenous sensitizer, for sunlight-mediated inactivation of porcine rotavirus and MS2 bacteriophage. Upon irradiation by a full spectrum of simulated sunlight in the absence of SRNOM and in the temperature range of 14-42 °C, high inactivation rate constants, k(obs), of MS2 (k(obs) ≤ 3.8 h(-1) or 1-log(10) over 0.6 h) and rotavirus (k(obs) ≤ 11.8 h(-1) or ～1-log(10) over 0.2 h) were measured. A weak temperature (14-42 °C) dependence of k(obs) values was observed for both viruses irradiated by the full sunlight spectrum. Under the same irradiation condition, the presence of SRNOM reduced the inactivation of both viruses due to attenuation of lower wavelengths of the simulated sunlight. For rotavirus and MS2 solutions irradiated by only UVA and visible light in the absence of SRNOM, inactivation kinetics were slow (k(obs) < 0.3 h(-1) or <1-log(10) unit reduction over 7 h) and temperature-independent for the range considered. Conversely, under UVA and visible light irradiation and in the presence of SRNOM, temperature-dependent inactivation of MS2 was observed. For rotavirus, the SRNOM-mediated exogenous inactivation was only important at temperatures >33 °C, with low rotavirus k(obs) values (k(obs) ≈ 0.2 h(-1); 1-log(10) unit reduction over 12 h) for the temperature range of 14-33 °C. These k(obs) values increased to 0.5 h(-1) at 43 °C and 1.5 h(-1) (1-log(10) reduction over 1.6 h) at 50 °C. While SRNOM-mediated exogenous inactivation of MS2 was triggered by singlet oxygen, the presence of hydrogen peroxide was important for rotavirus inactivation in the 40-50 °C range.     

A bacteriophage reagent for Salmonella: molecular studies on Felix 01

Felix 01 (F01) is a bacteriophage originally isolated by Felix and Callow which lyses almost all Salmonella strains and has been widely used as a diagnostic test for this genus. Molecular information about this phage is entirely lacking. In the present study, the DNA of the phage was found to be a double-stranded linear molecule of about 80 kb. 11.5 kb has been sequenced and in this region A + T content is 60%. There are relatively few restriction endonuclease cleavage sites in the native genome and clones show this is due to their absence rather than modification. A restriction map of the genome has been constructed. The ends of the molecule cannot be ligated although they contain 5' phosphates. At least 60% of the genome must encode proteins. In the sequenced portion, many open reading frames exist and these are tightly packed together. These have been examined for homology to published proteins but only 1 to 17 shows similarity to known proteins. F01 is therefore the prototype of a new phage family. On the basis of restriction sites, codon usage and the distribution of nonsense codons in the unused reading frames, a strong case can be made for natural selection that reacts to mRNA structure and function.     

Expert evaluation of traffic signs: conventional vs. alternative designs

Traffic sign comprehension is significantly affected by their compliance with ergonomics design principles. Despite the UN Convention, designs vary among countries. The goal of this study was to establish theoretical and methodological bases for evaluating the design of conventional and alternative signs. Thirty-one conventional signs and 1–3 alternatives for each conventional sign were evaluated for their compliance with three ergonomics guidelines for sign design: physical and conceptual compatibility, familiarity and standardisation. Twenty-seven human factors and ergonomics experts from 10 countries evaluated the signs relative to their compliance with the guidelines. Analysis of variance across alternatives revealed that for 19 of the 31 signs, an alternative design received a significantly higher rating in its ergonomics design than the conventional sign with the same meaning. We also found a very high correlation between the experts’ ratings and comprehension from previous studies. In conclusion, many countries use signs for which better alternative designs exist, and therefore UN Convention signs should be re-examined, and ergonomics experts evaluation can serve as a good surrogate for road users’ comprehension surveys.

Practitioner summary: This study presents theoretical and methodological bases for evaluating the design of UN Conventional and alternative traffic signs. Human factors and ergonomics experts evaluated 31 conventional and 68 alternative road signs, based on ergonomics principles for sign design. Results indicated the need to re-examine poorly designed UN Convention signs.     

On Boundary Condition Capturing for Multiphase Interfaces

This review paper begins with an overview of the boundary condition capturing approach to solving problems with interfaces. Although the authors’ original motivation was to extend the ghost fluid method from compressible to incompressible flow, the elliptic nature of incompressible flow quickly quenched the idea that ghost cells could be defined and used in the usual manner. Instead the boundary conditions had to be implicitly captured by the matrix formulation itself, leading to the novel approach. We first review the work on the variable coefficient Poisson equation, noting that the simplicity of the method allowed for an elegant convergence proof. Simplicity and robustness also allowed for a quick extension to three-dimensional two-phase incompressible flows including the effects of viscosity and surface tension, which is discussed subsequently. The method has enjoyed popularity in both computational physics and computer graphics, and we show some comparisons with the traditional delta function approach for the visual simulation of bubbles. Finally, we discuss extensions to problems where the velocity is discontinuous as well, as is the case for premixed flames, and show an example of multiple interacting liquids that includes all of the aforementioned phenomena.     

Nanopatterned electrically conductive films of semiconductor nanocrystals

We present the first semiconductor nanocrystal films of nanoscale dimensions that are electrically conductive and crack-free. These films make it possible to study the electrical properties intrinsic to the nanocrystals unimpeded by defects such as cracking and clustering that typically exist in larger-scale films. We find that the electrical conductivity of the nanoscale films is 180 times higher than that of drop-cast, microscopic films made of the same type of nanocrystal. Our technique for forming the nanoscale films is based on electron-beam lithography and a lift-off process. The patterns have dimensions as small as 30 nm and are positioned on a surface with 30 nm precision. The method is flexible in the choice of nanocrystal core-shell materials and ligands. We demonstrate patterns with PbS, PbSe, and CdSe cores and Zn(0.5)Cd(0.5)Se-Zn(0.5)Cd(0.5)S core-shell nanocrystals with a variety of ligands. We achieve unprecedented versatility in integrating semiconductor nanocrystal films into device structures both for studying the intrinsic electrical properties of the nanocrystals and for nanoscale optoelectronic applications.     

UV radiation induces genome-mediated, site-specific cleavage in viral proteins

Much research has been dedicated to understanding the molecular basis of UV damage to biomolecules, yet many questions remain regarding the specific pathways involved. Here we describe a genome-mediated mechanism that causes site-specific virus protein cleavage upon UV irradiation. Bacteriophage MS2 was disinfected with 254 nm UV, and protein damage was characterized with ESI- and MALDI-based FT-ICR, Orbitrap, and TOF mass spectroscopy. Top-down mass spectrometry of the products identified the backbone cleavage site as Cys46-Ser47 in the virus capsid protein, a location of viral genome-protein interaction. The presence of viral RNA was essential to inducing backbone cleavage. The similar bacteriophage GA did not exhibit site-specific protein cleavage. Based on the major protein fragments identified by accurate mass analysis, a cleavage mechanism is proposed by radical formation. The mechanism involves initial oxidation of the Cys46 side chain followed by hydrogen atom abstraction from Ser47 C(α). Computational protein QM/MM studies confirmed the initial steps of the radical mechanism. Collectively, this study describes a rare incidence of genome-induced protein cleavage without the addition of sensitizers.     

Secretome Analysis of Arabidopsis–Trichoderma atroviride Interaction Unveils New Roles for the Plant Glutamate:Glyoxylate Aminotransferase GGAT1 in Plant Growth Induced by the Fungus and Resistance against Botrytis cinerea

The establishment of plant–fungus mutualistic interaction requires bidirectional molecular crosstalk. Therefore, the analysis of the interacting organisms secretomes would help to understand how such relationships are established. Here, a gel-free shotgun proteomics approach was used to identify the secreted proteins of the plant Arabidopsis thaliana and the mutualistic fungus Trichoderma atroviride during their interaction. A total of 126 proteins of Arabidopsis and 1027 of T. atroviride were identified. Among them, 118 and 780 were differentially modulated, respectively. Bioinformatic analysis unveiled that both organisms’ secretomes were enriched with enzymes. In T. atroviride, glycosidases, aspartic endopeptidases, and dehydrogenases increased in response to Arabidopsis. Additionally, amidases, protein-serine/threonine kinases, and hydro-lyases showed decreased levels. Furthermore, peroxidases, cysteine endopeptidases, and enzymes related to the catabolism of secondary metabolites increased in the plant secretome. In contrast, pathogenesis-related proteins and protease inhibitors decreased in response to the fungus. Notably, the glutamate:glyoxylate aminotransferase GGAT1 was secreted by Arabidopsis during its interaction with T. atroviride. Our study showed that GGAT1 is partially required for plant growth stimulation and on the induction of the plant systemic resistance by T. atroviride. Additionally, GGAT1 seems to participate in the negative regulation of the plant systemic resistance against B. cinerea through a mechanism involving H₂O₂ production.     

Method of Calculation of Stability Constants of Fulvic Complexes on the Example of Copper

On the example of copper fulvate, it is discussed the method of calculation of stability constants of fulvic complexes. At pH = 8, the complex formation of copper（ll） ions with fulvic acids was studied by the solubility method. Fulvic acids were separated from the river Mtkvari by the adsorption-chromotographic method. The charcoal （BAU, Russia） was used as a sorbent. The suspension of copper（If） hydroxide was used as the solid phase, on which was added the increasing quantity of standard solution of fulvic acids. In diluted solutions, at pH = 8 the dominant form of copper（lI） is copper dihydroxo complex Cu（OH）^zO. It was established that in the Cu（OH）2 （solid）-Cu（OH）^20 （solution）-FA^2-H20 system, dominates copper dyhydroxo fulvate complex with the structure 1：1, [Cu（OH）2FA]^2. The average stability constant of copper dyhydroxo fulvate complex was calculated based on experimental data fl [Cu（OH）2FAJ^2 = 4.5× l0^5.