Density functional theory studies of the adsorption of hydrogen sulfide on aluminum doped silicane

First principles total energy calculations have been performed to study the hydrogen sulfide (H₂S) adsorption on silicane, an unusual one monolayer of Si(111) surface hydrogenated on both sides. The H₂S adsorption may take place in dissociative or non-dissociative forms. Silicane has been considered as: (A) non-doped with a hydrogen vacancy, and doped in two main configurations; (B) with an aluminum replacing a hydrogen atom and (C-n; n?=?1, 2, 3) with an aluminum replacing a silicon atom at a lattice site. In addition, three supercells; 4x4, 3x3 and 2x2 have been explored for both non-doped and doped silicane. The non-dissociative adsorption takes place in geometries (A), (C-1), (C-2) and (C-3) while the dissociative in (B). Adsorption energies of the dissociative case are larger than those corresponding to the non-dissociated cases. In the dissociative adsorption, the molecule is fragmented in a HS structure and a H atom which are bonded to the aluminum to form a H-S-Al-H structure. The presence of the doping produces some electronic changes as the periodicity varies. Calculations of the total density of states (DOS) indicate that in most cases the energy gap decreases as the periodicity changes from 4x4 to 2x2. The features of the total DOS are explained in terms of the partial DOS. The reported charge density plots explain quite well the chemisorptions and physisorptions of the molecule on silicane in agreement with adsorption energies.     

The influence of cis‐acting P1 protein and translational elements on the expression of Potato virus Y helper‐component proteinase (HCPro) in heterologous systems and its suppression of silencing activity

In the Potyvirus genus, the P1 protein is the first N‐terminal product processed from the viral polyprotein, followed by the helper‐component proteinase (HCPro). In silencing suppression patch assays, we found that Potato virus Y (PVY) HCPro expressed from a P1‐HCPro sequence increased the accumulation of a reporter gene, whereas protein expressed from an HCPro sequence did not, even with P1 supplied in trans. This enhancing effect of P1 has been noted in other potyviruses, but has remained unexplained. We analysed the accumulation of PVY HCPro in infiltrated tissues and found that it was higher when expressed from P1‐HCPro than from HCPro sequences. Co‐expression of heterologous suppressors increased the steady‐state level of mRNA expressed from the HCPro sequence, but not that of protein. This suggests that, in the absence of P1 upstream, either HCPro acquires a conformation that affects negatively its activity or stability, or that its translation is reduced. To test these options, we purified HCPro expressed in the presence or absence of upstream P1, and found no difference in purification pattern and final soluble state. By contrast, alteration of the Kozak context in the HCPro mRNA sequence to favour translation increased partially suppressor accumulation and activity. Furthermore, protein activity was not lower than in protein expressed from P1‐HCPro sequences. Thus, a direct role for P1 on HCPro suppressor activity or stability, by influencing its conformation during translation, can be excluded. However, P1 could still have an indirect effect favouring HCPro accumulation. Our data highlight the relevance of cis‐acting translational elements in the heterologous expression of HCPro.     

Pepino mosaic virus triple gene block protein 1 (TGBp1) interacts with and increases tomato catalase 1 activity to enhance virus accumulation

Various plant factors are co‐opted by virus elements (RNA, proteins) and have been shown to act in pathways affecting virus accumulation and plant defence. Here, an interaction between Pepino mosaic virus (PepMV) triple gene block protein 1 (TGBp1; p26) and tomato catalase 1 (CAT1), a crucial enzyme in the decomposition of toxic hydrogen peroxide (H₂O₂), was identified using the yeast two‐hybrid assay, and confirmed via an in vitro pull‐down assay and bimolecular fluorescent complementation (BiFC) in planta. Each protein was independently localized within loci in the cytoplasm and nuclei, sites at which their interaction had been visualized by BiFC. Following PepMV inoculation, CAT mRNA and protein levels in leaves were unaltered at 0, 3 and 6 days (locally) and 8 days (systemically) post‐inoculation; however, leaf extracts from the last two time points contained increased CAT activity and lower H₂O₂ levels. Overexpression of PepMV p26 in vitro and in planta conferred the same effect, suggesting an additional involvement of TGBp1 in potexvirus pathogenesis. The accumulation of PepMV genomic and subgenomic RNAs and the expression of viral coat protein in noninoculated (systemic) leaves were reduced significantly in CAT‐silenced plants. It is postulated that, during PepMV infection, a p26–CAT1 interaction increases H₂O₂ scavenging, thus acting as a negative regulator of plant defence mechanisms to promote PepMV infections.     

Experimental design of a simple medium for the bioluminescence of Aliivibrio fischeri and mathematical modelling for growth estimation

Increasing numbers of studies are using Aliivibrio fischeri (A. fischeri), a marine bioluminescent bacterium as a model, however the culture medium used for its growth are complex and expensive. The objectives of this study were: (1) to evaluate the effect of yeast extract, tryptone, and NaCl to select a simple and inexpensive culture medium suitable for A. fischeri growth and bioluminescence induction; and (2) to compare the performance of mathematical models to predict the growth of A. fischeri. A fractional factorial design was performed to evaluate the effect of yeast extract, tryptone, and sodium chloride on the luminescence of A. fischeri. The result showed that sodium chloride is the most important factor, congruent with its inducer role in bioluminescence. The best medium for bioluminescence induction was selected through an optimization plot, this medium is inexpensive, and generates the same luminescence as commercial formulations. The estimation of A. fischeri growth at OD₆₀₀ measurement was statistically analyzed. All evaluated models fitted the data adequately (r²  > 0.96). The nonlinear models Gompertz, Richards and logistic provided a lower variation and a better fit of the growth estimation (r² >0.99), showing that these mathematical models can be used for the accurate growth prediction of A. fischeri.     

Molecular insights into human monoamine oxidase (MAO) inhibition by 1,4-naphthoquinone: evidences for menadione (vitamin K3) acting as a competitive and reversible inhibitor of MAO

Monoamine oxidase (MAO) catalyzes the oxidative deamination of biogenic and exogenous amines and its inhibitors have therapeutic value for several conditions including affective disorders, stroke, neurodegenerative diseases and aging. The discovery of 2,3,6-trimethyl-1,4-naphthoquinone (TMN) as a nonselective and reversible inhibitor of MAO, has suggested 1,4-naphthoquinone (1,4-NQ) as a potential scaffold for designing new MAO inhibitors. Combining molecular modeling tools and biochemical assays we evaluate the kinetic and molecular details of the inhibition of human MAO by 1,4-NQ, comparing it with TMN and menadione. Menadione (2-methyl-1,4-naphthoquinone) is a multitarget drug that acts as a precursor of vitamin K and an inducer of mitochondrial permeability transition. Herein we show that MAO-B was inhibited competitively by 1,4-NQ (K_i = 1.4 μM) whereas MAO-A was inhibited by non-competitive mechanism (K_i = 7.7 μM). Contrasting with TMN and 1,4-NQ, menadione exhibited a 60-fold selectivity for MAO-B (K_i = 0.4 μM) in comparison with MAO-A (K_i = 26 μM), which makes it as selective as rasagiline. Fluorescence and molecular modeling data indicated that these inhibitors interact with the flavin moiety at the active site of the enzyme. Additionally, docking studies suggest the phenyl side groups of Tyr407 and Tyr444 (for MAO-A) or Tyr398 and Tyr435 (for MAO-B) play an important role in the interaction of the enzyme with 1,4-NQ scaffold through forces of dispersion as verified for menadione, TMN and 1,4-NQ. Taken together, our findings reveal the molecular details of MAO inhibition by 1,4-NQ scaffold and show for the first time that menadione acts as a competitive and reversible inhibitor of human MAO.     

Molecular dynamics simulations of T-20 HIV fusion inhibitor interacting with model membranes

T-20 (also known as enfuvirtide) is a fusion inhibitor peptide known to have some effectiveness in the control of progression of HIV infection by inhibiting the fusion of the HIV envelope with the target cell membrane. Recent results indicate that T-20 is able to interact with membranes in the liquid disordered state but not with membranes in an ordered state, which could be linked to its effectiveness. A detailed molecular picture of the interaction of these molecules with membranes is still lacking. To this effect, extensive molecular dynamics simulations (100 ns) were carried out to investigate the interaction between T-20 and bilayers of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and POPC/cholesterol (1:1). Membrane properties such as area/lipid, density profiles, order parameters and membrane thickness were studied. It was observed that T-20 has the ability to interact to different extents with both model membranes in this study and that peptide interaction with the bilayer surface has a local effect on membrane structure. The formation of hydrogen bonding between certain peptide residues and the POPC phosphate group was observed. However, T-20 showed a more limited extent of interaction with model membranes when compared with other, more efficient, peptides (such as T-1249). This effect is most notable in POPC/Chol membranes in which interaction is especially weak, owing to less peptide residues acting as H bond donors to POPC and virtually no H bonds being formed between T-20 and cholesterol. This lower ability to interact with membranes is probably correlated with its smaller inhibitory efficiency.     

The Multiplicity of Infection of a Plant Virus Varies during Colonization of Its Eukaryotic Host

The multiplicity of infection (MOI), i.e., the number of virus genomes that infect a cell, is a key parameter in virus evolution, as it determines processes such as genetic exchange among genomes, selection intensity on viral genes, epistatic interactions, and the evolution of multipartite viruses. In fact, the MOI level is equivalent to the virus ploidy during genome expression. Nevertheless, there are few experimental estimates of MOI, particularly for viruses with eukaryotic hosts. Here we estimate the MOI of Tobacco mosaic virus (TMV) in its systemic host, Nicotiana benthamiana. The progress of infection of two TMV genotypes, differently tagged with the green or red fluorescent proteins GFP and RFP, was monitored by determining the number of leaf cell protoplasts that showed GFP, RFP, or GFP and RFP fluorescence at different times postinoculation. This approach allowed the quantitative analysis of the kinetics of infection and estimation of the generation time and the number of infection cycles required for leaf colonization. MOI levels were estimated from the frequency of cells infected by only TMV-GFP or TMV-RFP. The MOI was high, but it changed during the infection process, decreasing from an initial level of about 6 to a final one of 1 to 2, with most infection cycles occurring at the higher MOI levels. The decreasing MOI can be explained by mechanisms limiting superinfection and/or by genotype competition within double-infected cells, which was shown to occur in coinfected tobacco protoplasts. To our knowledge, this is the first estimate of MOI during virus colonization of a eukaryotic host.Virus evolution has been a very active area of research in the last few decades, as viruses are both important pathogens of humans, animals, and plants and good models to experimentally test hypotheses on parasite evolution or, more generally, central questions on evolutionary biology (11, 12, 21, 36). Considerable efforts have been devoted to modeling the evolution of viral populations. However, contrasting the theoretical models with reality may be hindered by limited experimental information on important parameters of the virus life cycle. The multiplicity of infection (MOI), i.e., the number of virus particles or genomes that may infect a cell, is a key parameter in many models of virus evolution (5, 6, 14, 15, 37, 38, 39, 52, 53, 57, 61) for which experimental estimates are scant.When a cell is coinfected by different viral genomes, competition may lead to decreased fitness of individual genotypes in comparison with their fitness in single infections (15, 31, 40). Thus, limiting coinfection may result in a selective advantage for viruses (58), which have developed mechanisms to prevent superinfection of previously infected cells (51, 60). On the other hand, infection of a cell by more than one virus genome is a prerequisite for two central phenomena in virus genetics to take place: recombination and complementation of defective mutants. Recombination between viral strains during replication in the same cell and complementation of defective mutants have been extensively documented for viruses infecting prokaryotes, animals, and plants (2, 25, 56), indicating that there must be some degree of coinfection and, hence, that the MOI must be higher than one in at least some infected cells. However, estimates of MOI in the natural hosts of viruses are surprisingly scarce in spite of this parameter''s relevance: values of about 2 to 3 have been reported for different DNA or RNA bacteriophages (26, 41, 51, 58), and a value of 4 to 5 was reported for Autographa californica nuclear polyhedrosis virus infecting larvae of the moth Tricoplusia ni (3), to our knowledge, the only estimate for a virus in its eukaryotic host. We are not aware of estimates reported for viruses infecting mammals or plants, although a MOI of about 3 can be inferred from the number of proviral copies of HIV in spleen cells of infected patients (29). This paucity of data may be due to the technical difficulty of directly measuring MOI, particularly within a eukaryotic host. Genetic approaches may provide valid alternatives for estimating MOI levels (3, 58), and here, the MOI of a plant virus is estimated through the analysis of the relative frequencies of two genotypes during the process of host colonization.Host colonization by plant-infecting viruses has been known for a long time to be a two-step phenomenon. First, colonization proceeds slowly from the initially infected cells to their neighbors by way of the cytoplasmic connections called plasmodesmata, a process known as cell-to-cell movement. After infection thus reaches the cells in the vasculature, the second step, known as long-distance or systemic movement, occurs as viruses move faster to distant organs through the vascular tissue, the phloem in most cases (59). As a result of these processes, the virus population within the infected plant may be strongly structured. Analyses of different viruses in different host plant species have shown that systemic movement causes population bottlenecks that may be severe (16, 28, 32, 34, 46), resulting in differences in the genetic composition of the virus subpopulations in different systemically infected organs. No analysis of population bottlenecks during cell-to-cell movement has been reported, but data indicate that the virus population within a leaf has a strong spatial structure with a separate distribution of different genotypes in different leaf areas. These reports derive from analyses of viruses that differ in genomic organization and gene expression strategies in different host plant species (9, 10, 23, 55); they indicate that a separate distribution of viral genotypes within the infected leaf is a general phenomenon and suggest limitation of coinfection. Data on the spatial exclusion of virus genotypes within the infected leaf are in apparent contradiction with the abundant evidence of recombination and complementation of defective mutants, which has been widely documented for plant viruses (19, 44, 50, 62). It should be pointed out that all reports on the spatial exclusion of virus genotypes in an infected leaf derive from microscopy observations, mostly at late times after infection of the tissue. No information is available on the kinetics of leaf colonization by viruses, and current data do not allow the estimation of MOI.In this report, we estimate the MOI of a plant RNA virus, Tobacco mosaic virus (TMV), in its systemic host, Nicotiana benthamiana. For this, we have reexamined the process of virus colonization by monitoring the progress of infection of two TMV genotypes in inoculated and in systemically infected leaves. The two TMV genotypes differed in the expression of fluorescent tags, either the green fluorescent protein (GFP) from Aequorea victoria (42, 43) or a red fluorescent protein (RFP) from Discosoma sp. (49). The expression of GFP and RFP allowed the precise quantification of the number of cells infected by either one or both TMV genotypes, and these data allowed the estimation of genotype frequencies and of MOI. The results show evidence of strong spatial structure of the virus population, with most cells being infected by either TMV-GFP or TMV-RFP alone and only a small fraction of cells being double infected. The kinetics of the single and double infections show that the MOI changes with time, decreasing as colonization progresses and therefore suggesting that exclusion mechanisms operate at later times after infection.     

Translocation of Tomato bushy stunt virus P19 protein into the nucleus by ALY proteins compromises its silencing suppressor activity

The P19 protein of Tomato bushy stunt virus is a potent suppressor of RNA silencing and, depending on the host species, is required for short- and long-distance virus movement and symptom production. P19 interacts with plant ALY proteins and relocalizes a subset of these proteins from the nucleus to the cytoplasm. Here we showed that coexpression by agroinfiltration in Nicotiana benthamiana of P19 and the subset of ALY proteins that are not relocalized from the nucleus interfered with the ability of P19 to suppress RNA silencing. We demonstrated that this interference correlates with the relocation of P19 from the cytoplasm into the nucleus, and by constructing and analyzing chimeric ALY genes, we showed that the C-terminal part of the central, RNA recognition motif of ALY is responsible for interaction with P19, relocalization or nonrelocalization of ALY, and inhibition of silencing suppression by P19. We studied the interaction of ALY and P19 by using the technique of bimolecular fluorescence complementation to show that these proteins associate physically in the nucleus but not detectably in the cytoplasm, and we present a model to explain the dynamics of this interaction.     

Risk of Hemorrhage during Needle-Based Ophthalmic Regional Anesthesia in Patients Taking Antithrombotics: A Systematic Review

Background

Patients undergoing ophthalmic surgery are usually elderly and, due to systemic disease, may be on long-term therapy, such as antithrombotic agents. Rates of hemorrhagic complications associated with invasive procedures may be increased by the use of anticoagulants and antiplatelet agents.

Objective

To compare the incidence of hemorrhagic complications in patients undergoing needle-based ophthalmic regional anesthesia between patients on antithrombotic therapy and those not on such therapy.

Methods

A systematic review was conducted by two independent reviewers based on searches of Cochrane, LILACS, PubMed, Scopus, Web of Science, and the “gray” literature (Google Scholar). The end search date was May 8, 2015, across all databases.

Results

Five studies met the eligibility criteria. In three studies, individual risk of bias was low, and in two of them, moderate. In all studies, no differences regarding mild to moderate incidence of hemorrhagic complications were found between patients using antithrombotics (aspirin, clopidogrel, and warfarin) and those not using them. Rates of severe hemorrhagic complication were very low (0.04%) in both groups, supporting the safety of needle blocks, even in patients using antithrombotics. High heterogeneity across studies prevented meta-analysis. Limitations to these results include low statistical power in three experimental studies and a large 95% confidence interval in the two retrospective cohorts.

Conclusion

In this review, none of the selected studies showed significant bleeding related to needle-based ophthalmic regional anesthesia in association with the use of aspirin, clopidogrel, or vitamin K inhibitors. Since the available data is not powerful enough to provide a reliable evaluation of the true effect of antithrombotics in this setting, new studies to address these limitations are necessary.