Pyridinic-N Coordination Effect on the Adsorption and Activation of CO2 by Single Vacancy Iron-Doped Graphene.

Graphene doped with different transition metals has been recently proposed to adsorb CO2 and help reduce the greenhouse effect. Iron-doped graphene is one of the most promising candidates for this task, but there is still a lack of full understanding of the adsorption mechanism. In this work, we analyze the electronic structure, geometry, and charge redistribution during adsorption of CO2 molecules by single vacancy iron-doped graphene by DFT calculations using the general gradient approximation of Perdew, Burke, and Ernzernhof functional (PBE) and the van der Waals density functional (vdW). To understand the impact of the pyridinic-N coordination of the iron atom, we gradually replaced the neighboring carbon atoms by nitrogen atoms. The analysis indicates that chemisorption and physisorption occur when the molecule is adsorbed in the side-on and end-on orientation, respectively. Adsorption is stronger when pyridinic-N coordination increases, and the vdW functional describes the chemical interactions and adsorption energy differently in relation to PBE without significant structural changes. The development of the chemical interactions with the change of coordination in the system is further investigated in this work with crystal overlap Hamilton population (COHP) analysis.

Cloning and expression analysis of an endo-1,3-ß-D-glucosidase from Phytophthora cinnamomi.

Phytophthora is considered one of the most destructive genus for many agricultural plant species worldwide, with a strong environmental and economic impact. Phytophthora cinnamomi is a highly aggressive Phytophthora species associated with the forest decline and responsible for the ink disease in chestnut trees (Castanea sativa Miller), a culture which is extremely important in Europe. This pathogenicity occurs due to the action of several enzymes like the hydrolysis of 1,3-ß-glucans at specific sites by the enzyme endo-1,3-ß-D-glucosidase. The aim of this work to analyze the heterologous expression in two microorganisms, Escherichia coli and Pichia pastoris, of an endo-1,3-ß-D-glucosidase encoded by the gene ENDO1 (AM259651) from P. cinnamomi. Different plasmids were used to clone the gene on each organism and the real-time quantitative polymerase chain reaction was used to determine its level of expression. Homologous expression was also analyzed during growth in different carbon sources (glucose, cellulose, and sawdust) and time-course experiments were used for endo-1,3-ß-D-glucosidase production. The highest expression of the endo-1,3-ß-D-glucosidase gene occurred in glucose after 8 h of induction. In vivo infection of C. sativa by P. cinnamomi revealed an increase in endo-1,3-ß-D-glucosidase expression after 12 h. At 24 h its expression decreased and at 48 h there was again a slight increase in expression, and more experiments in order to further explain this fact are underway.

Levan-Capped Silver Nanoparticles for Bactericidal Formulations: Release and Activity Modelling.

An environmentally friendly technique was used to produce levan-capped silver nanoparticles of about 30 nm (with a loading of 30%) that showed bactericide effect, for E. coli and B. subtilis. That effect was mathematically studied with a dose-response model (lethal dose of 12.4 ppm and 6.8 ppm respectively). These silver nanoparticles were subsequently introduced in a gel to create a silver release system with bacteria inhibition activity. Silver release from the gel and its bactericidal activity was theoretically studied to develop a unique model that is able to predict accurately both silver release and lethal dose for any type of bacteria. This model will be useful for performing predictions for future silver in gel applications.

Clinical features and short-term outcomes of cancer patients with suspected and unsuspected pulmonary embolism: the EPIPHANY study.

The study aimed to identify predictors of overall 30-day mortality in cancer patients with pulmonary embolism including suspected pulmonary embolism (SPE) and unsuspected pulmonary embolism (UPE) events. Secondary outcomes included 30- and 90-day major bleeding and venous thromboembolism (VTE) recurrence.The study cohort included 1033 consecutive patients with pulmonary embolism from the multicentre observational ambispective EPIPHANY study (March 2006-October 2014). A subgroup of 497 patients prospectively assessed for the study were subclassified into three work-up scenarios (SPE, truly asymptomatic UPE and UPE with symptoms) to assess outcomes.The overall 30-day mortality rate was 14%. The following variables were associated with the overall 30-day mortality on multivariate analysis: VTE history, upper gastrointestinal cancers, metastatic disease, cancer progression, performance status, arterial hypotension <100 mmHg, heart rate >110 beats·min-1, basal oxygen saturation <90% and SPE (versus overall UPE).The overall 30-day mortality was significantly lower in patients with truly asymptomatic UPE events (3%) compared with those with UPE-S (20%) and SPE (21%) (p<0.0001). Thirty- and 90-day VTE recurrence and major bleeding rates were similar in all the groups.In conclusion, variables associated with the severity of cancer and pulmonary embolism were associated with short-term mortality. Our findings may help to develop pulmonary embolism risk-assessment models in this setting.

Transcriptomics as a tool to discover new antibacterial targets.

The emergence of antibiotic-resistant pathogens, multiple drug-resistance, and extremely drug-resistant strains demonstrates the need for improved strategies to discover new drug-based compounds. The development of transcriptomics, proteomics, and metabolomics has provided new tools for global studies of living organisms. However, the compendium of expression profiles produced by these methods has introduced new scientific challenges into antimicrobial research. In this review, we discuss the practical value of transcriptomic techniques as well as their difficulties and pitfalls. We advocate the construction of new databases of transcriptomic data, using standardized formats in addition to standardized models of bacterial and yeast similar to those used in systems biology. The inclusion of proteomic and metabolomic data is also essential, as the resulting networks can provide a landscape to rationally predict and exploit new drug targets and to understand drug synergies.

Null mutants of Candida albicans for cell-wall-related genes form fragile biofilms that display an almost identical extracellular matrix proteome.

By two-dimensional gel electrophoresis (2-DE) and mass spectrometry, we have characterized the polypeptide species present in extracts obtained by 60% ethanol treatment of whole mature (48 h) biofilms formed by a reference strain (CAI4-URA3) and four Candida albicans null mutants for cell-wall-related genes (ALG5, CSA1, MNN9 and PGA10) Null mutants form fragile biofilms that appeared partially split and weakly attached to the substratum contrary to those produced by the reference strain. An almost identical, electrophoretic profile consisting of about 276 spots was visualized in all extracts examined. Proteomic analysis led to the identification of 131 polypeptides, corresponding to 86 different protein species, being the rest isoforms-83 displayed negative hydropathic indexes and 82 lack signal peptide. The majority of proteins appeared at pI between 4 and 6, and molecular mass between 10 and 94 kDa. The proteins identified belonged to the following Gene Ontology categories: 21.9% unknown molecular function, 16.2% oxidoreductase activity, 13.3% hydrolase activity and 41.8% distributed between other different GO categories. Strong defects in biofilm formation appreciated in the cell-wall mutant strains could be attributed to defects in aggregation due to abnormal cell wall formation rather than to differences in the biofilm extracellular matrix composition.

The UmGcn5 gene encoding histone acetyltransferase from Ustilago maydis is involved in dimorphism and virulence.

We isolated a gene encoding a histone acetyltransferase from Ustilago maydis (DC.) Cda., which is orthologous to the Saccharomyces cerevisiae GCN5 gene. The gene was isolated from genomic clones identified by their specific hybridization to a gene fragment obtained by the polymerase chain reaction (PCR). This gene (Umgcn5; um05168) contains an open reading frame (ORF) of 1421bp that encodes a putative protein of 473 amino acids with a Mr. of 52.6kDa. The protein exhibits a high degree of homology with histone acetyltransferases from different organisms. Null a2b2 ΔUmgcn5 mutants were constructed by substitution of the region encoding the catalytic site with a hygromycin B resistance cassette. Null a1b1 ΔUmgcn5 mutants were isolated from genetic crosses of a2b2 ΔUmgcn5 and a1b1 wild-type strains in maize. Mutants displayed a slight reduction in growth rate under different conditions, and were more sensitive than the wild type to stress conditions, but more important, they grew as long mycelial cells, and formed fuzz-like colonies under all conditions where wild-type strains grew in the yeast-like morphology and formed smooth colonies. This phenotype was not reverted by cAMP addition. Mutants were not virulent to maize plants, and were unable to form teliospores. These phenotypic alterations of the mutants were reverted by their transformation with the wild-type gene.

Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset.

Animal studies have demonstrated the ability of pancreatic acinar cells to transform into pancreatic ductal adenocarcinoma (PDAC). However, the tumorigenic potential of human pancreatic acinar cells remains under debate. To address this gap in knowledge, we expand sorted human acinar cells as 3D organoids and genetically modify them through introduction of common PDAC mutations. The acinar organoids undergo dramatic transcriptional alterations but maintain a recognizable DNA methylation signature. The transcriptomes of acinar organoids are similar to those of disease-specific cell populations. Oncogenic KRAS alone do not transform acinar organoids. However, acinar organoids can form PDAC in vivo after acquiring the four most common driver mutations of this disease. Similarly, sorted ductal cells carrying these genetic mutations can also form PDAC, thus experimentally proving that PDACs can originate from both human acinar and ductal cells. RNA-seq analysis reveal the transcriptional shift from normal acinar cells towards PDACs with enhanced proliferation, metabolic rewiring, down-regulation of MHC molecules, and alterations in the coagulation and complement cascade. By comparing PDAC-like cells with normal pancreas and PDAC samples, we identify a group of genes with elevated expression during early transformation which represent potential early diagnostic biomarkers.

Human NKCC2 cation­Cl­ co-transporter complements lack of Vhc1 transporter in yeast vacuolar membranes.

Cation­chloride co-transporters serve to transport Cl­ and alkali metal cations. Whereas a large family of these exists in higher eukaryotes, yeasts only possess one cation­chloride co-transporter, Vhc1, localized to the vacuolar membrane. In this study, the human cation­chloride co-transporter NKCC2 complemented the phenotype of VHC1 deletion in Saccharomyces cerevisiae and its activity controlled the growth of salt-sensitive yeast cells in the presence of high KCl, NaCl and LiCl. A S. cerevisiae mutant lacking plasma-membrane alkali­metal cation exporters Nha1 and Ena1-5 and the vacuolar cation­chloride co-transporter Vhc1 is highly sensitive to increased concentrations of alkali­metal cations, and it proved to be a suitable model for characterizing the substrate specificity and transport activity of human wild-type and mutated cation­chloride co-transporters.

Green Biosynthesis of Tin Oxide Nanomaterials Mediated by Agro-Waste Cotton Boll Peel Extracts for the Remediation of Environmental Pollutant Dyes.

The sustainable synthesis of metal oxide materials provides an ecofriendly and more exciting approach in the domain of a clean environment. Besides, plant extracts to synthesize nanoparticles have been considered one of the more superior ecofriendly methods. This paper describes the biosynthetic preparation route of three different sizes of tetragonal structure SnO2 nanoparticles (SNPs) from the agro-waste cotton boll peel aqueous extract at 200, 500, and 800 °C for 3 h and represents a low-cost and alternative preparation method. The samples were characterized by X-ray diffraction, Fourier transform infrared spectrophotometry, ultraviolet-visible absorption spectroscopy, high-resolution transmission electron microscopy (HR-TEM), and energy-dispersive X-ray spectroscopy. Surface area and porosity size distribution were identified by nitrogen adsorption-desorption isotherms and Brunauer-Emmett-Teller analysis. The photocatalytic properties of the SNP samples were studied against methylene blue (MB) and methyl orange (MO), and the degradation was evaluated with three different size nanomaterials of 3.97, 8.48, and 13.43 nm. Photocatalytic activities were carried out under a multilamp (125 W Hg lamps) photoreactor. The smallest size sample exhibited the highest MB degradation efficiency within 30 min than the most significant size sample, which lasted 80 min. Similarly, in the case of MO, the smallest sample showed a more superior degradation efficiency with a shorter period (40 min) than the large-size samples (100 min). Therefore, our studies suggested that the developed SNP nanomaterials could be potential, promising photocatalysts against the degradation of industrial effluents.

Biogenic Photo-Catalyst TiO2 Nanoparticles for Remediation of Environment Pollutants.

This article reports a benign environmentally friendly fabrication method of titanium dioxide (TDO) nanoparticles (named TDO NPs3, TDO NPs5, and TDO NPs8) using aqueous extract of durva herb waste. This synthesis process avoids use of harmful substances and persistent chemicals throughout the order and enables us to control the size of the nanomaterials. Characterization of TDO nanoparticles was analyzed by ultraviolet-visible spectroscopy, X-ray diffraction, and Fourier transform infrared spectroscopy. The morphological nature of the TDO samples was inspected by transmission electron microscopy, which indicated that the TDO NPs3, TDO NPs5, and TDO NPs8 were spherical in shape, with average sizes of 5.14, 12.54, and 29.61 nm, respectively. The stability of TDO nanoparticles was assessed using thermogravimetric analysis and dynamic light scattering analysis. These samples could be used for degradation of polluting industrial textile dyes, such as methylene blue (MB) and rhodamine B (Rh-B). Remarkably, the TDO NPs3 sample (5.14 nm size) exhibits a noticeable degradation of the MB dye in a shorter time period (50 min) than the TDO NPs8 sample with a size of 29.61 nm (120 min). The TDO NPs3 sample was also tested for degradation of Rh-B dye, showing high degradation efficiency over a short period of time (60 min). In contrast, the TDO NPs8 sample showed degradation of the Rh-B dye in 120 min. The effect of the dye concentration and the catalyst dose to remove dye pollutants has also been investigated. The synthesized TDO NPs act as exceptional catalysts for the degradation of dyes, and they are promising materials for the degradation of industrial polluting dyes.

Ure2 is involved in nitrogen catabolite repression and salt tolerance via Ca2+ homeostasis and calcineurin activation in the yeast Hansenula polymorpha.

Disruption of HpURE2 resulted in a low expression of genes encoding nitrate-assimilatory proteins; sensitivity to Li(+), Na(+), and Cd(2+); no induction of ENA1; low levels of the GATA-type transcription factor Gat1; and low intracellular Ca(2+) levels. Gat1 levels were also very low in a Δcnb1 mutant lacking the regulatory subunit of calcineurin. The strain Δure2 was very sensitive to the calcineurin inhibitor FK506 and displayed several phenotypes reminiscent of Δcnb1. The reporter 4xCDRE-lacZ, containing calcineurin-dependent response elements in its promoter, revealed that calcineurin activation was reduced in HpΔure2. Expression of ScURE2 in Δure2 rescued nitrogen catabolite repression and Cd(2+) tolerance but not those phenotypes depending on calcineurin activation, such as salt tolerance and nitrate assimilation gene derepression. HpΔure2 showed an increased expression of the gene PMR1 encoding the Golgi Ca(2+)-ATPase, whereas that of PMC1 encoding the vacuolar Ca(2+)-ATPase remained unaltered. PMR1 up-regulation was abolished by deletion of the GATA-type transcription factor GAT2 in a HpΔure2 genetic background, and normal Ca(2+) levels were recovered. Moreover, overexpression of GAT2 or PMR1 yielded strains mimicking the phenotype of the HpΔure2. This suggests that the low Ca(2+) levels in the HpΔure2 mutant are due to the high levels of Pmr1 that replenish the Golgi Ca(2+) content, thus acting as a negative signal for Ca(2+) entry into the cell. We conclude that HpUre2 is involved in salt tolerance and also in nitrate assimilation gene derepression via Ca(2+) homeostasis regulation and calcineurin activation, which control the levels of Gat1.

Fungicidal monoclonal antibody C7 interferes with iron acquisition in Candida albicans.

We have developed a monoclonal antibody (MAb), C7, that reacts with the Als3p and enolase present in the Candida albicans cell wall and exerts three anti-Candida activities: candidacidal activity and inhibition of both adhesion and filamentation. To investigate the mode of action of MAb C7 on fungal viability, we examined changes in the genome-wide gene expression profile of C. albicans grown in the presence of a subinhibitory concentration of MAb C7 (12.5 µg/ml) by using microarrays. A total of 49 genes were found to be differentially expressed upon treatment with MAb C7. Of these, 28 were found to be upregulated and 21 were found to be downregulated. The categories of upregulated genes with the largest number of variations were those involved in iron uptake or related to iron homeostasis (42.86%), while the energy-related group accounted for 38.10% of the downregulated genes (8/21). Results were validated by real-time PCR. Since these effects resembled those found under iron-limited conditions, the activity of MAb C7 on C. albicans mutants with deletions in key genes implicated in the three iron acquisition systems described in this yeast was also assessed. Only mutants lacking the TPK1 gene and, to a lesser extent, the TPK2 gene were less sensitive to the candidacidal effect of MAb C7. FeCl(3) or hemin at concentrations of ≥ 7.8 µM reversed the candidacidal effect of MAb C7 on C. albicans in a concentration-dependent manner. The results presented in this study provide evidence that the candidacidal effect of MAb C7 is related to the blockage of the reductive iron uptake pathway of C. albicans.

The role of diclofenac sodium in the dimorphic transition in Candida albicans.

Diclofenac sodium is a non-steroidal anti-inflammatory drug that inhibits filamentation in Candida albicans. Here we examined the effect of diclofenac sodium on hypha formation in C. albicans. The C. albicans cells were treated with various concentrations of diclofenac sodium (50, 100, 200 and 500microg/ml) and incubated at 37 degrees C for 2h. The characteristics of hypha formation were then assessed microscopically in both liquid and solid media. The results indicated that the effect of diclofenac sodium was dependent on the concentration of this compound, and preincubation with 500microg/ml diclofenac sodium completely inhibited hypha formation in both liquid and solid media. RT-qPCR analysis of RNA extracted from C. albicans indicated that the levels of expression of agglutinin-like sequence 3 (ALS3), RAS1, EFG1 mRNA, which are regulated by the cAMP-EFG1 pathway in C. albicans and three hypha-specific genes (ALS1, ECE1 and HWP1), were decreased in diclofenac sodium treated cells compared to the levels in controls. Our results also demonstrated that diclofenac sodium possesses potent anti yeast-hypha transition activity in vitro and it could be useful in combined therapy with conventional antifungal agents in the management of treatment of Candida albicans infections.

Controlled electroplating and electromigration in nickel electrodes for nanogap formation.

We report the fabrication of nickel nanospaced electrodes by electroplating and electromigration for nanoelectronic devices. Using a conventional electrochemical cell, nanogaps can be obtained by controlling the plating time alone and after a careful optimization of electrodeposition parameters such as electrolyte bath, applied potential, cleaning, etc. During the process, the gap width decreases exponentially with time until the electrode gaps are completely bridged. Once the bridge is formed, the ex situ electromigration technique can reopen the nanogap. When the gap is ∼ 1 nm, tunneling current-voltage characterization shows asymmetry which can be corrected by an external magnetic field. This suggests that charge transfer in the nickel electrodes depends on the orientation of magnetic moments.

Latent and active tuberculosis infections in migrants and travellers: A retrospective analysis from the Spanish +REDIVI collaborative network.

BACKGROUND: Tuberculosis (TB) is the leading cause of infectious disease mortality worldwide. We analysed active and latent TB infections (LTBI) from the Spanish Network for the Study of Imported Infectious Diseases by Travellers and Immigrants (+REDIVI). METHODS: Observational, retrospective, multicentre study of TB and LTBI registered in the +REDIVI network from October 2009 to December 2016. RESULTS: Of 1008 cases of LTBI, 884 (87.7%) were immigrants; 93 (4.5%), immigrants visiting friends and relatives (VFR); 2 (0.9%), VFR-travellers; and 29 (1.1%), travellers. Absolute (N = 157 vs. N = 75) and relative (12.5% vs. 5.9%) frequency decreased over the study period (p = 0.003). Median time to diagnosis was 24.6 months (females 50.3 vs males 11.9; p < 0.001). Of 448 TB cases, 405 (90.4%) were in immigrants; 30 (6.7%), VFR-immigrants; 6 (1.3%), VFR-travellers; and 7 (1.6%), travellers. Median time to diagnosis was 62.5 months (females 86.6 vs males 70.1; p = 0.0075). There were 8 multidrug resistant TB cases and 1 extensively drug resistant case of TB, all in immigrants. CONCLUSION: TB was frequently diagnosed more than 5 years after arrival in Spain. Screening programmes for TB and LTBI in immigrants should be considered beyond this time point. Women showed a higher diagnostic delay for both latent and active TB.

Proteomic analysis reveals metabolic changes during yeast to hypha transition in Yarrowia lipolytica.

Fungal dimorphism is important for survival in different environments and has been related to virulence. The ascomycete Yarrowia lipolytica can grow as yeast, pseudomycelial or mycelial forms. We have used a Y. lipolytica parental strain and a Deltahoy1 mutant, which is unable to form hypha, to set up a model for dimorphism and to characterize in more depth the yeast to hypha transition by proteomic techniques. A two-dimensional gel electrophoresis (2-DE) based differential expression analysis of Y. lipolytica yeast and hyphal cells was performed, and 45 differentially expressed proteins were detected; nine with decreased expression in hyphal cells were identified. They corresponded to the S. cerevisiae homologues of Imd4p, Pdx3p, Cdc19, Sse1p, Sol3p, Sod2p, Xpt1p, Mdh1p and to the unknown protein YALIOB00924g. Remarkably, most of these proteins are involved in metabolic pathways, with four showing oxidoreductase activity. Furthermore, taking into account that this is the first report of 2-DE analysis of Y. lipolytica protein extracts, 35 more proteins from the 2D map of soluble yeast proteins, which were involved in metabolism, cell rescue, energy and protein synthesis, were identified.

Identification and characterization of a cell wall porin from Gordonia jacobaea.

Gordonia jacobaea is a bacterium belonging to the mycolata group characterized by its ability to produce carotenoids. Mycolic acids in the cell wall contribute to reducing the permeability of their envelopes requiring the presence of channel-forming proteins to allow the exchange of hydrophilic molecules with the surrounding medium. Identification and purification of the channel-forming proteins was accomplished by SDS-PAGE, Mass spectrometry and Mass peptide fingerprinting and the channel-forming activity was studied by reconstitution in lipid bilayers. Here, we describe for the first time the presence of a cell-wall protein from G. jacobaea with channel-forming activity. Our results suggest that this protein bears a low similarity to other hypothetical proteins from the genus Gordonia of uncharacterized functions. The channel has an average single-channel conductance of 800 pS in 1 M KCl, is moderately anion-selective, and does not show any voltage dependence for voltages between +100 and -100 mV. The channel characteristics suggest that this protein could be of relevance in the import and export of negatively charged molecules across the cell wall. This could contribute to design treatments for mycobacterial infections, as well as being of interest in biotechnology applications.

Prognostic value of computed tomography pulmonary angiography indices in patients with cancer-related pulmonary embolism: Data from a multicenter cohort study.

OBJECTIVE: To analyze the prognostic value of pulmonary artery obstruction versus right-ventricle (RV) dysfunction radiologic indices in cancer-related pulmonary embolism (PE). METHODS: We enrolled 303 consecutive patients with paraneoplastic PE, evaluated by computed tomography pulmonary angiography (CTPA) between 2013 and 2014. The primary outcome measure was serious complications at 15days. Multivariate analyses were conducted by using binary logistic and robust regressions. Radiological features such as the Qanadli index (QI) and RV dysfunction signs were analyzed with Spearman's partial rank correlations. RESULTS: RV diameter was the only radiological variable associated with an adverse outcome. Subjects with enlarged RV (diameter>45mm) had more 15-day complications (58% versus 40%, p=0.001). The QI correlated with the RV diameter (r=0.28, p<0.001), left ventricle diameter (r=-0.19, p<0.001), right ventricular-to-left ventricular diameter ratio (r=0.39, p<0.001), pulmonary artery diameter (r=0.22, p<0.001), and pulmonary artery/ascending aorta ratio (r=0.27, p<0.001). A QI≥50% was only associated with 15-day complications in subjects with enlarged RV, inverted intraventricular septum, or chronic cardiopulmonary diseases. The central or peripheral PE location did not affect the correlations among radiological variables and was not associated with clinical outcomes. CONCLUSIONS: Right ventricular dysfunction signs in CTPA are more useful than QI in predicting cancer-related PE outcome.