Coarse-Grained and Atomistic MD Simulations of RNA and DNA Folding

Although the main features of the protein folding problem are coming into clearer focus, the microscopic viewpoint of nucleic acid folding mechanisms is only just beginning to be addressed. Experiments, theory, and simulations are pointing to complex thermodynamic and kinetic mechanisms. As is the case for proteins, molecular dynamics (MD) simulations continue to be indispensable tools for providing a molecular basis for nucleic acid folding mechanisms. In this review, we provide an overview of biomolecular folding mechanisms focusing on nucleic acids. We outline the important interactions that are likely to be the main determinants of nucleic acid folding energy landscapes. We discuss recent MD simulation studies of empirical force field and Go-type MD simulations of RNA and DNA folding mechanisms to outline recent successes and the theoretical and computational challenges that lie ahead.     

Influence of the Pathogen <Emphasis Type="Italic">Candidatus</Emphasis> Liberibacter Solanacearum on Tomato Host Plant Volatiles and Psyllid Vector Settlement

Candidatus Liberibacter solanacearum (CLso) is an unculturable bacterium vectored by the tomato potato psyllid (TPP) Bactericera cockerelli and has been associated with Zebra chip disease in potato and with other economically relevant symptoms observed in solanaceous crops. By altering their host and vector’s biological system, pathogens are able to induce changes that benefit them by increasing their transmission rate. Understanding these changes can enable better targeting of mechanisms to control pathogen outbreaks. Here, we explored how the CLso infectious status affects the volatile organic compounds (VOCs) of the tomato plant, and whether the CLso infectious status of TPP influences host plant settlement. These chemical and behavioral changes can ultimately affect the rate of encounter between the host and the vector. Results from headspace volatile collection of tomato plants showed that CLso infected tomato plants emitted a qualitatively and quantitatively different blend of VOCs compared to sham-infected plants. By a factorial experiment, we showed that CLso negative (CLso-) TPP preferred to settle 70 % more often on infected tomato plants, while CLso positive (CLso+) TPP were found 68 % more often on sham-infected tomato plants. These results provide new evidence in favor of both host and vector manipulation by CLso.     

ICA1L Is Associated with Small Vessel Disease: A Proteome-Wide Association Study in Small Vessel Stroke and Intracerebral Haemorrhage

Small vessel strokes (SVS) and intracerebral haemorrhages (ICH) are acute outcomes of cerebral small vessel disease (SVD). Genetic studies combining both phenotypes have identified three loci associated with both traits. However, the genetic cis-regulation at the protein level associated with SVD has not been studied before. We performed a proteome-wide association study (PWAS) using FUSION to integrate a genome-wide association study (GWAS) and brain proteomic data to discover the common mechanisms regulating both SVS and ICH. Dorsolateral prefrontal cortex (dPFC) brain proteomes from the ROS/MAP study (N = 376 subjects and 1443 proteins) and the summary statistics for the SVS GWAS from the MEGASTROKE study (N = 237,511) and multi-trait analysis of GWAS (MTAG)-ICH–SVS from Chung et al. (N = 240,269) were selected. We performed PWAS and then a co-localization analysis with COLOC. The significant and nominal results were validated using a replication dPFC proteome (N = 152). The replicated results (q-value < 0.05) were further investigated for the causality relationship using summary data-based Mendelian randomization (SMR). One protein (ICA1L) was significantly associated with SVS (z-score = −4.42 and p-value = 9.6 × 10⁻⁶) and non-lobar ICH (z-score = −4.8 and p-value = 1.58 × 10⁻⁶) in the discovery PWAS, with a high co-localization posterior probability of 4. In the validation PWAS, ICA1L remained significantly associated with both traits. The SMR results for ICA1L indicated a causal association of protein expression levels in the brain with SVS (p-value = 3.66 × 10⁻⁵) and non-lobar ICH (p-value = 1.81 × 10⁻⁵). Our results show that the association of ICA1L with SVS and non-lobar ICH is conditioned by the cis-regulation of its protein levels in the brain.     

Entwicklungen von verschleiß-und korrosionsbeständigen Oberflächensystemen. Development of wear and corrosion resistant surface syatems

Develpoment of wear and corrosion resistant surface systems In this study two methods are described to realize wear and corrosion resistant surface systems: Plasma diffusion treatment (PDT) and Plasma assited CVD (PACVD). Plasma nitriding, Plasma nitrocarburizing and plasma boriding are used to treat different kinds of substrates. The advances of PACVD and the development of low temperature PACVD and industrial applications of these techniques are explained.     

Applications of computer difference spectroscopy in ion-exchange resins analysis

Infrared spectra demonstrate the use of computer difference spectroscopy and other dataprocessing routines to derive and enhance the difference spectra that relates the concentration of a resin to the concentration of other resins in the mixture. Therefore, a simple quantitative treatment accounting for the resin concentration has been determined. © 1995 John Wiley & Sons, Inc.     

Phase development and pore stability of yttria- and ytterbia-stabilized zirconia aerogels

High-porosity yttria- and ytterbia-stabilized zirconia aerogels offer the potential of extremely low thermal conductivity materials for high-temperature applications. Yttria- and ytterbia-doped zirconia aerogels were synthesized using a sol-gel approach over the dopant range of 0-20 atomic percent. Surface area, pore volume, and morphology of the as-dried aerogels and materials thermally exposed for short periods of time to temperatures up to 1200°C were characterized by nitrogen physisorption, scanning and transmission electron microscopy, and X-ray diffraction. The aerogels as supercritically dried all were X-ray amorphous. At a 5% dopant level, a tetragonal structure with a smaller monoclinic phase developed on thermal exposure. Mixed tetragonal and cubic phases or predominantly cubic materials were observed at higher dopant levels, depending on the dopant level, temperature and exposure time. The formation of crystalline phases was accompanied by loss of surface area and pore volume, although some mesoporous structure was maintained on short-term exposure to 1000°C. Incorporation of the smaller Yb atom into the lattice structure resulted in smaller lattice dimensions on crystallization than was seen with Y doping and favored a more highly equiaxed structure. Aerogels synthesized with 15% Y maintained the smallest particle size without evidence of sintering at 1100°C. Largest shrinkage and loss of pore volume occurred on crystallization from the amorphous phase, with further loss of pores at temperatures above 1000°C attributable to changes in lattice parameters.     

Nitrogen fixation and productivity of winter annual legume cover crops in Upper Midwest organic cropping systems

Nutrient Cycling in Agroecosystems - Legume cover crops can play a valuable role in maintaining and increasing soil quality and nitrogen availability, but are infrequently grown in the Upper...     

Characterization of Extra Virgin Olive Oil from Southern Brazil

Six olive oils extracted from the cultivars Arbequina, Arbosana, Coratina, Frantoio, Koroneiki, and Picual from 2017 and 2018 harvests, cultivated in Pinheiro Machado, Rio Grande do Sul, Brazil, are evaluated for standard oil composition parameters and bioactive constituents (pigments, tocopherols, and phenolic compounds). Multivariate principal component analysis (PCA) and univariate ANOVA and Fisher's LSD test are used to verify the effect of cultivar and harvest year on oil composition. Olive oil composition met extra virgin olive oil (EVOO) standard parameters and is influenced by both cultivar and harvest year. EVOO produced in 2018 has greater chlorophyll, caffeic acid, ligstroside aglycone, hydroxyoleuropein aglycone, syringic acid, and hydroxytyrosol acetate contents than the EVOOs from 2017. Linoleic acid, ferulic acid, ligstroside aglycone, and hydroxytyrosol acetate are the variables whose contents most contributed to the differentiation of oils by cultivar in both harvest years. Chemical characterization analyses allow for the differentiation of oil composition based on harvest year and cultivar. Metabolic quality data obtained here support the establishment of a local EVOO profile and the compounds that most contributed to treatment differentiation may serve as markers that can be utilized in determining origin, cultivar, and harvest year. Practical Applications: Olive production in Brazil is recent and is based on European cultivars which have not been bred for the local environmental conditions. Therefore, the measurement of olive oil metabolic quality will determine cultivar adaptability to local edaphoclimatic conditions as well as assist in the establishment of a standard of identity for the product and promote the development of its market. Olive oil produced in Southern Brazil shows high quality, and is especially rich in phenolic compounds. Although harvest year influences oil composition, oil from both harvests meet EVOO standards and cultivar specific metabolic markers are observed. This study provides the foundation for olive producers in Southern Brazil to seek authentication of the geographical origin of olive oil.     

Neighborhood sociodemographics and change in built infrastructure

While increasing evidence suggests an association between physical infrastructure in neighborhoods and health outcomes, relatively little research examines how neighborhoods change physically over time and how these physical improvements are spatially distributed across populations. This paper describes the change over 25 years (1985–2010) in bicycle lanes, off-road trails, bus transit service and parks, and spatial clusters of changes in these domains relative to neighborhood sociodemographics in four US cities that are diverse in terms of geography, size, and population. Across all four cities we identified increases in bicycle lanes, off-road trails, and bus transit service, with spatial clustering in these changes that related to neighborhood sociodemographics. Overall, we found evidence of positive changes in physical infrastructure commonly identified as supportive of physical activity. However, the patterning of infrastructure change by sociodemographic change encourages attention to the equity in infrastructure improvements across neighborhoods.     

Processing of Polymer-Derived Ceramic Composite Coatings on Steel

Polymer-derived ceramic composites are being investigated as environmental barrier coatings to protect stainless steel from oxidation and carburization. Coatings have been produced using poly(hydridomethylsiloxane) as a preceramic polymer and titanium disilicide as an expansion agent. Processing parameters have been optimized and a relationship has been derived to predict the final coating thickness based on slurry viscosity and dip coating withdrawal speed. Microstructural analysis reveals a composite coating of oxidized filler particles in a silica matrix. A diffusion layer is visible at the coating–steel interface, indicating good bonding. The optimized coatings are ∼18 μm thick, and have some residual porosity and a density of 2.56 g/cm³.