Probing polyoxometalate-protein interactions using molecular dynamics simulations

The molecular interactions between the Ce(IV)-substituted Keggin anion [PW11O39Ce(OH2)4]3- (CeK) and hen egg white lysozyme (HEWL), was investigated by molecular dynamics (MD) simulations. We compared the analysis of CeK with the Ce(IV)-substituted Keggin dimer [(PW11O39)2Ce]10- (CeK2) and the Zr(IV)-substituted Lindqvist anion [W5O18Zr(OH2)(OH)]3- (ZrL) in order to understand how POM features such as the shape, the size, the charge or the type of incorporated metal ion influence the POM···protein interactions. Simulations revealed two regions of the protein, in which the CeK anion interacts strongly: the cationic sites formed by Arg21 on one hand and by Arg45 and Arg68 on the other. The two sites can be related with the observed selectivity in the hydrolytic cleavage of HEWL. The POMs chiefly interact with the side chains of the positively charged (arginines and lysines) and the polar uncharged (tyrosines, serines and aspargines) residues via electrostatic attraction and hydrogen bonding with the oxygens of the POM framework. The CeK anion shows higher protein affinity than the CeK2 and ZrL anions, because it is less hydrophilic and it has the right size and shape for stablishing interactions with several residues simultaneously. The larger and more negatively charged CeK2 anion has a high solvent-accessible surface, which is sub-optimal for the interaction, while the smaller ZrL anion is highly hydrophilic and it cannot interact simultaneously with several residues so efficiently

Thermoplastic cassava starch-chitosan bilayer films containing essential oils

[EN] Starch-chitosan bilayer films, containing or not essential oils in the casted chitosan layer were obtained by thermo-compression. Bilayer films exhibited a good interfacial adhesion and better mechanical resistance than starch monolayers, although they were less stretchable and less transparent. Starchchitosan films were effective at controlling the bacterial growth in pork meat, but the thermal treatment applied to obtain the bilayers reduced their antimicrobial properties as compared to chitosan monolayers. The addition of essential oils did not promote any antimicrobial action in chitosan mono and bilayer films applied to pork meat. The final amount of essential oils in the films was very limited probably due to the losses occurred during film processing method. Other strategies to incorporate the essential oils into chitosan-based films should be used to improve their final retention in the film matrix and their effective release into the coated food. (C) 2017 Elsevier Ltd. All rights reserved.The authors acknowledge the financial support provided by the Spanish Ministerio de Economia y Competividad (Projects AGL2013-42989-R and AGL2016-76699-R). Author Cristina Valencia-Sullca thanks the Peruvian Grant National Program (PRONABEC).Valencia-Sullca, CE.; Vargas, M.; Atarés Huerta, LM.; Chiralt, A. (2018). Thermoplastic cassava starch-chitosan bilayer films containing essential oils. Food Hydrocolloids. 75:107-115. https://doi.org/10.1016/j.foodhyd.2017.09.008S1071157

Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning

The new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes pathological pulmonary symptoms. Most efforts to develop vaccines and drugs against this virus target the spike glycoprotein, particularly its S1 subunit, which is recognised by angiotensin-converting enzyme 2. Here we use the in-house developed tool CaverDock to perform virtual screening against spike glycoprotein using a cryogenic electron microscopy structure (PDB-ID: 6VXX) and the representative structures of five most populated clusters from a previously published molecular dynamics simulation. The dataset of ligands was obtained from the ZINC database and consists of drugs approved for clinical use worldwide. Trajectories for the passage of individual drugs through the tunnel of the spike glycoprotein homotrimer, their binding energies within the tunnel, and the duration of their contacts with the trimer's three subunits were computed for the full dataset. Multivariate statistical methods were then used to establish structure-activity relationships and select top candidate for movement inhibition. This new protocol for the rapid screening of globally approved drugs (4359 ligands) in a multi-state protein structure (6 states) showed high robustness in the rate of finished calculations. The protocol is universal and can be applied to any target protein with an experimental tertiary structure containing protein tunnels or channels. The protocol will be implemented in the next version of CaverWeb (https://loschmidt.chemi.muni.cz/caverweb/) to make it accessible to the wider scientific community. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology

An Assessment of the Effectiveness of High Definition Cameras as Remote Monitoring Tools for Dolphin Ecology Studies.

Research involving marine mammals often requires costly field programs. This paper assessed whether the benefits of using cameras outweighs the implications of having personnel performing marine mammal detection in the field. The efficacy of video and still cameras to detect Indo-Pacific bottlenose dolphins (Tursiops aduncus) in the Fremantle Harbour (Western Australia) was evaluated, with consideration on how environmental conditions affect detectability. The cameras were set on a tower in the Fremantle Port channel and videos were perused at 1.75 times the normal speed. Images from the cameras were used to estimate position of dolphins at the water’s surface. Dolphin detections ranged from 5.6 m to 463.3 m for the video camera, and from 10.8 m to 347.8 m for the still camera. Detection range showed to be satisfactory when compared to distances at which dolphins would be detected by field observers. The relative effect of environmental conditions on detectability was considered by fitting a Generalised Estimation Equations (GEEs) model with Beaufort, level of glare and their interactions as predictors and a temporal auto-correlation structure. The best fit model indicated level of glare had an effect, with more intense periods of glare corresponding to lower occurrences of observed dolphins. However this effect was not large (-0.264) and the parameter estimate was associated with a large standard error (0.113).The limited field of view was the main restraint in that cameras can be only applied to detections of animals observed rather than counts of individuals. However, the use of cameras was effective for long term monitoring of occurrence of dolphins, outweighing the costs and reducing the health and safety risks to field personal. This study showed that cameras could be effectively implemented onshore for research such as studying changes in habitat use in response to development and construction activities

Outcome of children and adolescents with central nervous system tumors in phase I trials

Central nervous system (CNS) tumors are a leading cause of death in pediatric oncology. New drugs are desperately needed to improve survival. We evaluated the outcome of children and adolescents with CNS tumors participating in phase I trials within the Innovative Therapies for Children with Cancer (ITCC) consortium. Patients with solid tumors aged < 18 years at enrollment in their first dose-finding trial between 2000 and 2014 at eight ITCC centers were included retrospectively. Survival was evaluated using univariate/multivariate analyses. Overall, 114 patients were included (109 evaluable for efficacy). Median age was 10.2 years (range 1.0-17.9). Main diagnoses included: medulloblastoma/primitive neuroectodermal tumors (32.5%) and high-grade gliomas (23.7%). Complete/partial responses (CR/PR) were reported in 7.3% patients and stable disease (SD) in 23.9%. Performance status of 90-100%, school/work attendance, normal ALT/AST and CR/PR/SD correlated with better overall survival (OS) in the univariate analysis. No variables assessable at screening/enrollment were associated with OS in the multivariate analysis. Five patients (4.5%) were discontinued from study due to toxicity. No toxic deaths occurred. Median OS was 11.9 months with CR/PR, 14.5 months with SD and 3.7 months with progressive disease (p < 0.001). The enrollment of children and adolescents with CNS tumors in phase I trials is feasible, safe and offers potential benefit for the patients. Sustained disease stabilization has a promising role as a marker of anti-tumor activity in children with CNS tumors participating in phase I trials

Effects of crystallization and dopant concentration on the emission behavior of TiO2:Eu nanophosphors

Uniform, spherical-shaped TiO2:Eu nanoparticles with different doping concentrations have been synthesized through controlled hydrolysis of titanium tetrabutoxide under appropriate pH and temperature in the presence of EuCl3·6H2O. Through air annealing at 500°C for 2 h, the amorphous, as-grown nanoparticles could be converted to a pure anatase phase. The morphology, structural, and optical properties of the annealed nanostructures were studied using X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy [EDS], and UV-Visible diffuse reflectance spectroscopy techniques. Optoelectronic behaviors of the nanostructures were studied using micro-Raman and photoluminescence [PL] spectroscopies at room temperature. EDS results confirmed a systematic increase of Eu content in the as-prepared samples with the increase of nominal europium content in the reaction solution. With the increasing dopant concentration, crystallinity and crystallite size of the titania particles decreased gradually. Incorporation of europium in the titania particles induced a structural deformation and a blueshift of their absorption edge. While the room-temperature PL emission of the as-grown samples is dominated by the 5D0 - 7Fj transition of Eu+3 ions, the emission intensity reduced drastically after thermal annealing due to outwards segregation of dopant ions

Flavonoids in Kidney Health and Disease

This review summarizes the latest advances in knowledge on the effects of flavonoids on renal function in health and disease. Flavonoids have antihypertensive, antidiabetic, and antiinflammatory effects, among other therapeutic activities. Many of them also exert renoprotective actions that may be of interest in diseases such as glomerulonephritis, diabetic nephropathy, and chemically-induced kidney insufficiency. They affect several renal factors that promote diuresis and natriuresis, which may contribute to their well-known antihypertensive effect. Flavonoids prevent or attenuate the renal injury associated with arterial hypertension, both by decreasing blood pressure and by acting directly on the renal parenchyma. These outcomes derive from their interference with multiple signaling pathways known to produce renal injury and are independent of their blood pressure-lowering effects. Oral administration of flavonoids prevents or ameliorates adverse effects on the kidney of elevated fructose consumption, high fat diet, and types I and 2 diabetes. These compounds attenuate the hyperglycemia-disrupted renal endothelial barrier function, urinarymicroalbumin excretion, and glomerular hyperfiltration that results from a reduction of podocyte injury, a determinant factor for albuminuria in diabetic nephropathy. Several flavonoids have shown renal protective effects against many nephrotoxic agents that frequently cause acute kidney injury (AKI) or chronic kidney disease (CKD), such as LPS, gentamycin, alcohol, nicotine, lead or cadmium. Flavonoids also improve cisplatin- or methotrexate-induced renal damage, demonstrating important actions in chemotherapy, anticancer and renoprotective effects. A beneficial prophylactic effect of flavonoids has been also observed against AKI induced by surgical procedures such as ischemia/reperfusion (I/R) or cardiopulmonary bypass. In several murine models of CKD, impaired kidney function was significantly improved by the administration of flavonoids from different sources, alone or in combination with stem cells. In humans, cocoa flavanols were found to have vasculoprotective effects in patients on hemodialysis. Moreover, flavonoids develop antitumor activity against renal carcinoma cells with no toxic effects on normal cells, suggesting a potential therapeutic role in patients with renal carcinoma.This study was supported by grants from the Carlos III Health Institute of Spain, and the Red de Investigación Renal REDinREN number 5 012/0021. FEDER una manera de hacer Europa

21st Century drought-related fires counteract the decline of Amazon deforestation carbon emissions

Tropical carbon emissions are largely derived from direct forest clearing processes. Yet, emissions from drought-induced forest fires are, usually, not included in national-level carbon emission inventories. Here we examine Brazilian Amazon drought impacts on fire incidence and associated forest fire carbon emissions over the period 2003–2015. We show that despite a 76% decline in deforestation rates over the past 13 years, fire incidence increased by 36% during the 2015 drought compared to the preceding 12 years. The 2015 drought had the largest ever ratio of active fire counts to deforestation, with active fires occurring over an area of 799,293 km2. Gross emissions from forest fires (989 ± 504 Tg CO2 year−1) alone are more than half as great as those from old-growth forest deforestation during drought years. We conclude that carbon emission inventories intended for accounting and developing policies need to take account of substantial forest fire emissions not associated to the deforestation process