Inferring adaptive codon preference to understand sources of selection shaping codon usage bias.

Alternative synonymous codons are often used at unequal frequencies. Classically, studies of such codon usage bias (CUB) attempted to separate the impact of neutral from selective forces by assuming that deviations from a predicted neutral equilibrium capture selection. However, GC-biased gene conversion (gBGC) can also cause deviation from a neutral null. Alternatively, selection has been inferred from CUB in highly expressed genes, but the accuracy of this approach has not been extensively tested, and gBGC can interfere with such extrapolations (e.g., if expression and gene conversion rates covary). It is therefore critical to examine deviations from a mutational null in a species with no gBGC. To achieve this goal, we implement such an analysis in the highly AT rich genome of Dictyostelium discoideum, where we find no evidence of gBGC. We infer neutral CUB under mutational equilibrium to quantify “adaptive codon preference,” a nontautologous genome wide quantitative measure of the relative selection strength driving CUB. We observe signatures of purifying selection consistent with selection favoring adaptive codon preference. Preferred codons are not GC rich, underscoring the independence from gBGC. Expression-associated “preference” largely matches adaptive codon preference but does not wholly capture the influence of selection shaping patterns across all genes, suggesting selective constraints associated specifically with high expression. We observe patterns consistent with effects on mRNA translation and stability shaping adaptive codon preference. Thus, our approach to quantifying adaptive codon preference provides a framework for inferring the sources of selection that shape CUB across different contexts within the genome

Variable-parameter NiTi ultrasonic spot welding with Cu interlayer

NiTi thin sheets were ultrasonic spot welded with a Cu interlayer, where different welding vibration amplitudes were applied to study the influence on the surface and interface microstructural characteristics, phase transformation behavior and mechanical response of the joints, which aimed to enhance the joint performance by proper optimization of the process parameters. An excellent bonding interface was achieved when an optimized vibration amplitude was applied, with a recrystallized microstructure formed in the Cu foil side near the bonding interface, which helped to improve the mechanical performance of the joints. Joints made with vibration amplitude of 55 mu m had an improved strength compared to the NiTi base material

Microstructure, phase transformation, electrochemistry, X-ray visibility and mechanical properties

Funding Information: Supporting for the Chinese Civil Aviation Administration (No. U1933129 ), Key Program of the Natural Science Foundation of Tianjin (No. 19JCZDJC39000 ). JPO acknowledges the Fundação para a Ciência e Tecnologia ( FCT ) for its support via the project UID/00667/2020 (UNIDEMI). JPO acknowledges funding by national funds from FCT - Fundação para a Ciência e a Tecnologia , I.P., in the scope of the projects LA/P/0037/2020 , UIDP/50025/2020 and UIDB/50025/2020 of the Associate Laboratory Institute of Nanostructures, Nanomodelling and Nanofabrication – i3N. Publisher Copyright: © 2022 The AuthorsWire and arc additive manufacturing (WAAM) technology was used for the fabrication of NiTiTa (2.5 at. % Ta) shape memory alloys (SMAs) for the first time, using commercialy available NiTi wire and Ta foil as the feedstock materials. The addition of Ta significantly increased the phase transformation temperatures, leading to a room-temperature microstructure composed of both B19′ martensite and B2 austenite, and (Ti,Ta)2Ni precipitates distributed at the grain boundaries. Compared with the WAAM fabricated NiTi counterpart, the corrosion potential (Ecorr) of the NiTiTa material increased from − 0.55 to − 0.44 V, while the corrosion current density (Icorr) decreased from 1.90 × 10−6 to 4.2 × 10−7 A/cm2. The X-ray brightness increased from 19.6 to 56.4 %. These results indicate that the addition of Ta can enhance the corrosion resistance and X-ray visibility of NiTiTa parts. Furthermore, the WAAM fabricated NiTiTa material was able to retain a stable superelastic response under 10 loading-unloading cycles, highlighting the great potential application value in the biomedical field. Our work provides an innovative method for additively manufacturing NiTi-based multi-component SMAs through WAAM.publishersversionpublishe

Microstructure and mechanical properties of dissimilar NiTi and 304 stainless steel joints produced by ultrasonic welding

(No. U1933129) (No. 18JCQNJC04100, No. 19JCZDJC39000 No. 19YFFCYS00090 UID/00667/2020Superelastic NiTi alloy and 304 stainless steel (304 SS) were joined with a Cu interlayer by ultrasonic spot welding (USW) using different welding energy inputs. The surface morphology, interfacial microstructure, mechanical properties, and fracture mechanisms of the dissimilar NiTi/304 SS USWed joints were studied. The results showed that the surface oxidation intensified with increasing ultrasonic welding energy due to mutual rubbing between tools and sheets. The weld interface microstructure exhibited voids or unbonded zones at low energy inputs, while an intimate contact was established at the joining interface when applying a higher energy input of 750 J. With increasing energy input to 750 J, the weld interface shows two interfaces due to the behavior of plastic flow of Cu interlayer. The lap-shear load of the joints first increased, achieving a maximum value of ∼690 N at an energy input of 750 J, and then decreased with further increase in welding energy. Interfacial failure was observed at NiTi/Cu interface at all energy inputs, and no intermetallic compounds were found on the fracture surfaces of both the NiTi/Cu and Cu/304 SS interfaces.publishersversionpublishe

Effect of adhesive system and application strategy on reduction of dentin permeability

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)This study evaluated the effect of adhesive systems and application strategies on dentin hydraulic conductance (HC). The buccal enamel was removed from bovine incisors to simulate laminate cavity preparations. After removing the roots and the coronal pulp, the buccal dentin was treated with EDTA solution (0.5 M) for 5 minutes, rinsed, ultrasonicated for 12 minutes and connected to a permeability device. HC of the specimens was measured at 10 psi (n = 5). Permeability was measured before and after bonding procedures using G-Bond (GB), Clearfil Tri-S Bond (CTS), Hybrid Coat (HY), Bond Force (BF), Adper Easy Bond (AEB) Silorane (SI), Clearfil SE Bond (CSE) and Adper Scotchbond Multi-Purpose (SMP) adhesives systems, which were applied following three strategies: 1) according to the manufacturers' instructions; 2) two coats of all-in-one self-etching adhesives (GB, CTS, HY, BF, AEB) or priming step plus two coats of bonding resin for the other systems (SI, CSE and SMP); and 3) a thin layer of a flowable composite applied over one coat of all-in-one self-etching adhesives or primed surface for SI, CSE and SMP adhesives. No significant difference was observed among the application modes concerning their ability to reduce HC. None of the adhesives showed complete sealing (100%) of the bovine tooth dentin. SI exhibited lower HC than SMP, however, they were not significantly different from the other systems. The results suggest that all systems tested result in an HC reduction of more than 90%. The wet bonding technique seemed to be more sensitive for dentin sealing.265397403Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)CNPq [303587/2007-5

In Vitro Evaluation of the Antiviral Potential of Guettarda angelica Against Animal Herpesviruses

Background: The number of antiviral studies using plant extracts has increased in the last decades, and the results have shown that plants are potential sources of compounds that are able to inhibit and/or decrease viral infections. The selection of these plants by ethnopharmacological criteria increases the probability of finding new substances with significant pharmacological and biological activities. Hence, Brazil has an advantage in this area due to its extensive biodiversity and ethnological diversity. Guettarda angelica is a plant from the Brazilian Caatinga region the roots of which are popularly used for various therapeutic purposes, including veterinary use. The aim of this work was to investigate the in vitro antiviral activity of extracts of plant parts from G. angelica against three animal herpesviruses: bovine (BoHV-1), suid (SuHV-1) and equine (EHV-1) herpesviruses type 1. Materials, Methods & Results: The extracts of roots, leaves and seeds of G. angelica were initially screened for in vitro antiviral activity against these herpesviruses using the virus yield reduction assay. The MDBK cells were used in assays with BoHV-1 and SuHV-1, and the Vero cells with EHV-1. For these assays, the cells previously treated with the extracts in non-cytotoxic concentrations were inoculated with logarithmic dilutions of each virus, The viral inhibitory activity of extracts was calculated by difference of virus titer between treated infected cells and non-treated infected cells. Only the aqueous extract from seeds (AEs) showed a significant antiviral activity (P < 0.01, ANOVA followed by Tukey test) against all herpesviruses leading continuous studies, Thus, the selectivity index (SI) of this extract was determined by MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] colorimetric assay by calculating the ratio CC(50)over IC50. The 50% cytotoxic concentration (CC50) was defined as the extract concentration that reduced the cell viability by 50% when compared to untreated controls; the 50% inhibitory concentration (IC50) was defined as the concentration of the extract that inhibited 50% of viral replication when compared to the virus control. The CC50 and IC50 obtained from nonlinear regression analysis of concentration-effect curves by the GraphPad Prism 5 Demo program and represented the means +/- standard deviation of three independent experiments. The CC5(0) for Vero cells was 400.60 +/- 0.20 mu g/mL, while the CC50 for MDBK cells was 920.50 +/- 0.19 mu g/mL. The IC50 values of the AEs on the BoHV-1, SuHV-1 and EHV-1 were 22.79 mu g/mL, 91.30 mu g/mL and 19.95 mu g/mL, respectively. The SI values of this extract for each virus obtained from these data were 40.39, 10.08 and 20.08 for BoHV-1, SuHV-1, and EHV-1, respectively. Discussion: To ensure the antiviral activity of a plant extract and consequently its future use as antiviral agent is crucial the obtainment of its selectivity index or safety index. It is guarantee of a true antiviral effect and not the result of cytotoxicity of the extract on cells, and that could be confused with an antiviral activity. Other important point are the extract IC50 values less than 100 mu g/mL. The results of the AEs of G. angelica are in accordance with these considerations indicating that the Go angelica seeds may be a potential source of antiviral compounds insurance and encouraging further investigation of them.40