F4-Neuroprostane Effects on Human Sperm

Swim-up selected human sperm were incubated with 7 ng F4-neuroprostanes (F4-NeuroPs) for 2 and 4 h. Sperm motility and membrane mitochondrial potential (MMP) were evaluated. The percentage of reacted acrosome was assessed by pisum sativum agglutinin (PSA). Chromatin integrity was detected using the acridine orange (AO) assay and localization of the ryanodine receptor was performed by immunofluorescence analysis. Sperm progressive motility (p = 0.02) and the percentage of sperm showing a strong MMP signal (p = 0.012) significantly increased after 2 h F4-NeuroP incubation compared to control samples. The AO assay did not show differences in the percentage of sperm with dsDNA between treated or control samples. Meanwhile, a significantly higher number of sperm with reacted acrosomes was highlighted by PSA localization after 4 h F4-NeuroP incubation. Finally, using an anti-ryanodine antibody, the immunofluorescence signal was differentially distributed at 2 and 4 h: a strong signal was evident in the midpiece and postacrosomal sheath (70% of sperm) at 2 h, whereas a dotted one appeared at 4 h (53% of sperm). A defined concentration of F4-NeuroPs in seminal fluid may induce sperm capacitation via channel ions present in sperm cells, representing an aid during in vitro sperm preparation that may increase the positive outcome of assisted fertilization

Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code

In molecular dynamics simulations we can often increase the time step by imposing constraints on bond lengths and bond angles. This allows us to extend the length of the time interval and therefore the range of physical phenomena that we can afford to simulate. We examine the existing algorithms and software for solving nonlinear constraint equations in parallel and we explain why it is necessary to advance the state-of-the-art. We present ILVES-PC, a new algorithm for imposing bond constraints on proteins accurately and efficiently. It solves the same system of differential algebraic equations as the celebrated SHAKE algorithm, but ILVES-PC solves the nonlinear constraint equations using Newton’s method rather than the nonlinear Gauss-Seidel method. Moreover, ILVES-PC solves the necessary linear systems using a specialized linear solver that exploits the structure of the protein. ILVES-PC can rapidly solve constraint equations as accurately as the hardware will allow. The run-time of ILVES-PC is proportional to the number of constraints. We have integrated ILVES-PC into GROMACS and simulated proteins of different sizes. Compared with SHAKE, we have achieved speedups of up to 4.9× in single-threaded executions and up to 76× in shared-memory multi-threaded executions. Moreover, ILVES-PC is more accurate than P-LINCS algorithm. Our work is a proof-of-concept of the utility of software designed specifically for the simulation of polymers

Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase

Phenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded enzyme, decreasing or abolishing its catalytic activity, and leading to an elevated concentration of phenylalanine in the blood, which is neurotoxic. Several therapeutic approaches have been developed to treat the more severe manifestations of the disorder, but they are either not entirely effective or difficult to adhere to throughout life. In a search for novel pharmacological chaperones to treat PKU, a lead compound was discovered (compound IV) that exhibited promising in vitro and in vivo chaperoning activity on PAH. The structure of the PAH-IV complex has been reported. Here, using alchemical free energy calculations (AFEC) on the structure of the PAH-IV complex, we design a new generation of compound IV-analogues with a higher affinity for the enzyme. Seventeen novel analogues were synthesized, and thermal shift and isothermal titration calorimetry (ITC) assays were performed to experimentally evaluate their stabilizing effect and their affinity for the enzyme. Most of the new derivatives bind to PAH tighter than lead compound IV and induce a greater thermostabilization of the enzyme upon binding. Importantly, the correspondence between the calculated alchemical binding free energies and the experimentally determined ¿¿Gb values is excellent, which supports the use of AFEC to design pharmacological chaperones to treat PKU using the X-ray structure of their complexes with the target PAH enzyme. © 2022 by the authors. Licensee MDPI, Basel, Switzerland

Proba-3: ESA’s Small Satellites Precise Formation Flying Mission to Study the Sun’s Inner Corona as Never Before

This paper showcases ESA’s Proba-3 mission as a demonstration of how small satellites, in combination with formation flying technology, can achieve relevant scientific goals and perform scientific measurements not possible otherwise, all within a tight cost and programmatic context. The study of the Sun inner corona down to 1.1 solar radius can only be performed by creating in space artificial eclipses with a large distance between a Coronograph instrument and an occulting disk, much bigger than the size of any spacecraft that can fit within a launcher. Proba-3 will achieve these enhanced scientific observations by controlling two small satellites (~1.5 m cubes in the 200-300kg range) as a 150 m long ‘large virtually rigid structure’ by maintaining millimetre and arc second relative precision. In effect the paired satellites will fly as a giant virtual satellite creating an ‘externally occulted’ coronagraph, in which a satellite imager is shielded from glaring sunlight by an occulting disk on the other satellite, forming an artificial eclipse. Precise station keeping for Coronagraphy will be kept for 6 consecutive hours within each 20 hour orbit for a minimum total of 1000 hours of scientific observations over the 2 years of mission lifetime. This will be achieved autonomously, without relying on the ground for active control of the formation. In addition, Proba-3 will practically demonstrate formation flying technologies enabling other future science missions: station-keeping at different relative distances (from 25 m up to 250 m); approaching and separating in precise formation without losing millimetre precision; the capability to repoint the formation as a virtual rigid body away from the Sun and the combination of station keeping, resizing and re-targeting manoeuvres. Proba-3 is at full speed in the assembly, integration and verification phase, with the aim of launching Proba-3 in two years’ time. The paper describes the overall Proba-3 mission concept and detailed design, the different challenges that were overcome in spacecraft design, formation flying metrology and control, and the need to implement novel verification and operation approaches to achieve the world’s first precise formation flying mission

MS-based targeted profiling of oxylipins in COVID-19: A new insight into inflammation regulation

The key role of inflammation in COVID-19 induced many authors to study the cytokine storm, whereas the role of other inflammatory mediators such as oxylipins is still poorly understood. IMPRECOVID was a monocentric retrospective observational pilot study with COVID-19 related pneumonia patients (n = 52) admitted to Pisa University Hospital between March and April 2020. Our MS-based analytical platform permitted the simultaneous determination of sixty plasma oxylipins in a single run at ppt levels for a comprehensive characterisation of the inflammatory cascade in COVID-19 patients. The datasets containing oxylipin and cytokine plasma levels were analysed by principal component analysis (PCA), computation of Fisher's canonical variable, and a multivariate receiver operating characteristic (ROC) curve. Differently from cytokines, the panel of oxylipins clearly differentiated samples collected in COVID-19 wards (n = 43) and Intensive Care Units (ICUs) (n = 27), as shown by the PCA and the multivariate ROC curve with a resulting AUC equal to 0.92. ICU patients showed lower (down to two orders of magnitude) plasma concentrations of anti-inflammatory and pro-resolving lipid mediators, suggesting an impaired inflammation response as part of a prolonged and unsolvable pro-inflammatory status. In conclusion, our targeted oxylipidomics platform helped shedding new light in this field. Targeting the lipid mediator class switching is extremely important for a timely picture of a patient's ability to respond to the viral attack. A prediction model exploiting selected lipid mediators as biomarkers seems to have good chances to classify patients at risk of severe COVID-19

Statement of Foliar Fertilization Impact on Yield, Composition, and Oxidative Biomarkers in Rice

In rice crops, fertilization is a naturalized practice, although inefficient, that could be improved by applying foliar fertilization. Phytoprostanes (PhytoPs) and phytofurans (PhytoFs) are products of α-linolenic acid peroxidation, useful as biomarkers of oxidative degradation in higher plants. The objective was to determine the effect of the foliar fertilization on the concentration of PhytoPs and PhytoFs and its relationships with modifications of yield and quality of rice productions. It was described that the concentration of biomarkers of stress decreased with the application of foliar fertilization, being the response significantly different depending the genotypes and compound monitored. Moreover, fertilization did not modify significantly the parameters of yield (961.2 g m−2), 1000 whole-grain (21.2 g), and protein content (10.7% dry matter). Therefore, this is the first work that describes the effect of fertilization on PhytoPs and PhytoFs in rice genotypes and reinforces the capacity of these compounds as biomarkers to monitor specific abiotic stress, in this case, represented by nutritional stress.Facultad de Ciencias Agrarias y Forestale

Selective targeting of human and animal pathogens of the helicobacter genus by flavodoxin inhibitors: Efficacy, synergy, resistance and mechanistic studies

Antimicrobial resistant (AMR) bacteria constitute a global health concern. Helicobacter py-lori is a Gram-negative bacterium that infects about half of the human population and is a major cause of peptic ulcer disease and gastric cancer. Increasing resistance to triple and quadruple H. pylori eradication therapies poses great challenges and urges the development of novel, ideally narrow spectrum, antimicrobials targeting H. pylori. Here, we describe the antimicrobial spectrum of a family of nitrobenzoxadiazol-based antimicrobials initially discovered as inhibitors of flavodoxin: an essential H. pylori protein. Two groups of inhibitors are described. One group is formed by nar-row-spectrum compounds, highly specific for H. pylori, but ineffective against enterohepatic Helico-bacter species and other Gram-negative or Gram-positive bacteria. The second group includes ex-tended-spectrum antimicrobials additionally targeting Gram-positive bacteria, the Gram-negative Campylobacter jejuni, and most Helicobacter species, but not affecting other Gram-negative pathogens. To identify the binding site of the inhibitors in the flavodoxin structure, several H. pylori-flavodoxin variants have been engineered and tested using isothermal titration calorimetry. An initial study of the inhibitors capacity to generate resistances and of their synergism with antimicrobials commonly used in H. pylori eradication therapies is described. The narrow-spectrum inhibitors, which are ex-pected to affect the microbiota less dramatically than current antimicrobial drugs, offer an oppor-tunity to develop new and specific H. pylori eradication combinations to deal with AMR in H. pylori. On the other hand, the extended-spectrum inhibitors constitute a new family of promising antimi-crobials, with a potential use against AMR Gram-positive bacterial pathogens. © 2021 by the authors. Licensee MDPI, Basel, Switzerland