Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model

Effective SARS-CoV-2 antiviral activity of hyperbranched polylysine nanopolymers

The coronavirus pandemic (COVID-19) had spread rapidly since December 2019, when it was first identified in Wuhan, China. As of April 2021, more than 130 million cases have been confirmed, with more than 3 million deaths, making it one of the deadliest pandemics in history. Different approaches must be put in place to confront a new pandemic: community-based behaviours (i.e., isolation and social distancing), antiviral treatments, and vaccines. Although behaviour-based actions have produced significant benefits and several efficacious vaccines are now available, there is still an urgent need for treatment options. Remdesivir represents the first antiviral drug approved by the Food and Drug Administration for COVID-19 but has several limitations in terms of safety and treatment benefits. There is still a strong request for other effective, safe, and broad-spectrum antiviral systems in light of future emergent coronaviruses. Here, we describe a polymeric nanomaterial derived from l-lysine, with an antiviral activity against SARS-CoV-2 associated with a good safety profile in vitro. Nanoparticles of hyperbranched polylysine, synthesized by l-lysine's thermal polymerization catalyzed by boric acid, effectively inhibit the SARS-CoV-2 replication. The virucidal activity is associated with the charge and dimension of the nanomaterial, favouring the electrostatic interaction with the viral surface being only slightly larger than the virions' dimensions. Low-cost production and easiness of synthesis strongly support the further development of such innovative nanomaterials as a tool for potential treatments of COVID-19 and, in general, as broad-spectrum antivirals. This journal i

The Dietary Intake of Polyphenols Is Associated with a Lower Risk of Severe Lumbar Spinal Stenosis: A Case-Control Analysis from the PREFACE Study

Polyphenols are naturally occurring compounds endowed with antioxidant and anti-inflammatory properties. We sought to examine the association of dietary polyphenols with the risk of severe lumbar spinal stenosis (LSS), a condition possibly characterized by a high inflammatory component. A case-control study included 156 patients with LSS and indication to surgery and 312 controls, matched (1:2) for sex, age (±6 months), and physical activity. The polyphenol intake was calculated by matching food consumption data from a 188-item food frequency questionnaire with the Phenol-Explorer database regarding the polyphenol content of each reported food. In a multivariable-adjusted logistic regression analysis including lifestyles, sociodemographic factors, and the Mediterranean Diet Score, a 1-standard deviation (SD) increase in dietary polyphenols intake was associated with lower odds of LSS (Odds ratio [OR] = 0.65; 95% CI: 0.47–0.89). Analyses of different polyphenol classes showed that a per 1-SD in the consumption of flavonoids and stilbenes was related to lower LSS risk (OR = 0.57; 95% CI: 0.42–0.78; OR = 0.40; 95% CI: 0.27–0.61, respectively). Further adjustment for the total dietary antioxidant capacity did not modify the strength of these associations. A diet rich in polyphenols is independently associated with a lower risk of severe LSS, possibly through mechanisms that include the anti-inflammatory potential of these bioactive compounds

Silencing Nfix rescues muscular dystrophy by delaying muscle regeneration

Muscular dystrophies are severe disorders due to mutations in structural genes, and are characterized by skeletal muscle wasting, compromised patient mobility, and respiratory functions. Although previous works suggested enhancing regeneration and muscle mass as therapeutic strategies, these led to no long-term benefits in humans. Mice lacking the transcription factor Nfix have delayed regeneration and a shift toward an oxidative fiber type. Here, we show that ablating or silencing the transcription factor Nfix ameliorates pathology in several forms of muscular dystrophy. Silencing Nfix in postnatal dystrophic mice, when the first signs of the disease already occurred, rescues the pathology and, conversely, Nfix overexpression in dystrophic muscles increases regeneration and markedly exacerbates the pathology. We therefore offer a proof of principle for a novel therapeutic approach for muscular dystrophies based on delaying muscle regeneration

What Is Italian Antispeciesism? An Overview of Recent Tendencies in Animal Advocacy

This chapter offers an overview of the different agents currently operating in Italy as part of the animal liberation movement. It analyses the impact on this social reality by books and essays published or translated in Italian in the last 20 years in the field of Animal Ethics. From the reception of Peter Singer and Tom Regan\u2019s ideas mediated by the work of Paola Cavalieri, Italian philosophers have shaped the narratives and the rhetoric of animal advocates and liberationists. On the other side, activists\u2019 debates on the best strategies to adopt involved intellectuals and enriched their production on Animal Liberation. Groups with an intersectional approach have paid particular attention to theoretical implications and political consequences of their acts, developing radical, non-anthropocentric forms of antispeciesism

Structure and Luminescence Properties of Eu3+-Doped Cubic Mesoporous Silica Thin Films

Eu3+ ions-doped cubic mesoporous silica thin films with a thickness of about 205 nm were prepared on silicon and glass substrates using triblock copolymer as a structure-directing agent using sol–gel spin-coating and calcination processes. X-ray diffraction and transmission electron microscopy analysis show that the mesoporous silica thin films have a highly ordered body-centered cubic mesoporous structure. High Eu3+ ion loading and high temperature calcination do not destroy the ordered cubic mesoporous structure of the mesoporous silica thin films. Photoluminescence spectra show two characteristic emission peaks corresponding to the transitions of5D0-7F1 and 5D0-7F2 of Eu3+ ions located in low symmetry sites in mesoporous silica thin films. With the Eu/Si molar ratio increasing to 3.41%, the luminescence intensity of the Eu3+ ions-doped mesoporous silica thin films increases linearly with increasing Eu3+ concentration

Preparation of TiO2 Anatase Nanocrystals by TiCl4 Hydrolysis with Additive H2SO4

A new methodology was developed to synthesize uniform titania anatase nanocrystals by the hydrolysis of titanium chloride in sulfuric acid aqueous solutions at 0–90°C. The samples were characterized by Raman spectroscopy, UV-visible spectroscopy, transmission electron microscopy (TEM), electron diffraction (ED), and an Energy dispersive X-ray spectroscopy (EDS). The effects of the reaction temperature, mole ratio of SO42− to Ti4+, and the calcinations temperature on the particle size and crystal phase were investigated. Depending on the acidity, the hydrolysis temperature, and the calcination temperature, rhombic anatase nanocrystals sizes in the range of 10 nm to 50 nm were obtained. In the additive of sulfuric acid, Raman spectra and electron diffraction confirmed that the nanoparticles are composed of anatase TiO2. No other titania phases, such as rutile or brookite, were detected

Thermal and Optical Characterization of Undoped and Neodymium-Doped Y3ScAl4O12 Ceramics

Y3–3xNd3xSc1Al4O12 (x = 0, 0.01, and 0.02) ceramics were fabricated by sintering at high temperature under vacuum. Unit cell parameter refinement and chemical analysis have been performed. The morphological characterization shows micrograins with no visible defects. The thermal analysis of these ceramics is presented, by measuring the specific heat in the temperature range from 300 to 500 K. Their values at room temperature are in the range 0.81–0.90 J g1–K–1. The thermal conductivity has been determined by two methods: by the experimental measurement of the thermal diffusivity by the photopyroelectric method, and by spectroscopy, evaluating the thermal load. The thermal conductivities are in the range 9.7–6.5 W K–1 m–1 in the temperature interval from 300 to 500 K. The thermooptic coefficients were measured at 632 nm by the dark mode method using a prism coupler, and the obtained values are in the range 12.8–13.3 × 10–6 K–1. The nonlinear refractive index values at 795 nm have been evaluated to calibrate the nonlinear optical response of these materials.This work is supported by the Spanish Government under projects MAT2011-29255-C02-01-02, MAT2013-47395-C4-4-R, and the Catalan Government under project 2014SGR1358. It was also funded by the European Commission under the Seventh Framework Programme, project Cleanspace, FP7-SPACE-2010-1-GA No. 263044