Evaluation of SARS-CoV-2 entry, inflammation and new therapeutics in human lung tissue cells

The development of physiological models that reproduce SARS-CoV-2 infection in primary human cells will be instrumental to identify host-pathogen interactions and potential therapeutics. Here, using cell suspensions directly from primary human lung tissues (HLT), we have developed a rapid platform for the identification of viral targets and the expression of viral entry factors, as well as for the screening of viral entry inhibitors and anti-inflammatory compounds. The direct use of HLT cells, without long-term cell culture and in vitro differentiation approaches, preserves main immune and structural cell populations, including the most susceptible cell targets for SARS-CoV-2; alveolar type II (AT-II) cells, while maintaining the expression of proteins involved in viral infection, such as ACE2, TMPRSS2, CD147 and AXL. Further, antiviral testing of 39 drug candidates reveals a highly reproducible method, suitable for different SARS-CoV-2 variants, and provides the identification of new compounds missed by conventional systems, such as VeroE6. Using this method, we also show that interferons do not modulate ACE2 expression, and that stimulation of local inflammatory responses can be modulated by different compounds with antiviral activity. Overall, we present a relevant and rapid method for the study of SARS-CoV-2.

Dynamic structural cell responses in the thymus to acute injury, regeneration, and age

The thymus, the primary site of T cell development, is extremely sensitive to insult but also harbors tremendous capacity for repair. Using single cell sequencing of thymic structural cells, as well as functional and structural analyses, we revealed distinct regenerative programs by endothelial and mesenchymal subsets after injury that stimulated epithelial repair; the compartment primarily supporting T cell development. Thymic function not only declined over lifespan, contributing to immune aging, but the capacity of the thymus to regenerate after damage also declined in old mice. This could be attributed to an inability of the old microenvironment to induce reparative programs; leading to reduced ability to restore tissue structure and function. These findings provide a detailed framework for the response of structural cells to aging and acute damage, which could have considerable implications for our understanding of aging immunity and recovery from treatments such as chemotherapy and bone marrow transplant.

Candida albicans phosphate transport, facilitating nucleotide sugar biosynthesis, contributes to cell wall stability.

The Candida albicans high-affinity phosphate transporter Pho84 is required for normal Target of Rapamycin signaling, oxidative stress resistance and virulence of this fungal pathogen. It also contributes to C. albicans’ tolerance of two antifungal drug classes, polyenes and echinocandins. Echinocandins inhibit biosynthesis of a major cell wall component, beta-1,3-glucan. Cells lacking Pho84 were hypersensitive to other forms of cell wall stress beyond echinocandin exposure, while their cell wall integrity signaling response was weak. Metabolomics experiments showed that levels of phosphoric intermediates, including nucleotides like ATP and nucleotide sugars, were low in pho84 mutant compared to wild type cells recovering from phosphate starvation. Non-phosphoric precursors like nucleobases and nucleosides were elevated. Outer cell wall phosphomannan biosynthesis requires a nucleotide sugar,GDP-mannose. The nucleotide sugar UDP-glucose is the substrate of enzymes that synthesize two major structural cell wall polysaccharides, beta-1,3- and beta-1,6-glucan. Another nucleotide sugar, UDP-N-acetylglucosamine, is the substrate of chitin synthases which produce a stabilizing component of the intercellular septum and of lateral cell walls. Lack of Pho84 activity, and phosphate starvation, potentiated pharmacological or genetic perturbation of these enzymes. Our model is that low substrate concentrations of beta-D-glucan- and chitin synthases diminish enzymatic reaction rates and potentiate pharmacologic inhibitors to decrease the yield of their cell wall-stabilizing products. Phosphate import is not conserved between fungal and human cells, and humans do not synthesize beta-D-glucans or chitin. Hence inhibiting these processes simultaneously could yield potent antifungal effects with low toxicity to humans.

Finite element modeling of shape memory polyurethane foams for treatment of cerebral aneurysms

In this paper, a thermo-mechanical analysis of shape memory polyurethane foams (SMPUFs) with aiding of a finite element model (FEM) for treating cerebral aneurysms (CAs) is introduced. Since the deformation of foam cells is extremely difficult to observe experimentally due to their small size, a structural cell-assembly model is established in this work via finite element modeling to examine all-level deformation details. Representative volume elements of random equilateral Kelvin open-cell microstructures are adopted for the cell foam. Also, a user-defined material subroutine (UMAT) is developed based on a thermo-visco-elastic constitutive model for SMPUFs, and implemented in the ABAQUS software package. The model is able to capture thermo-mechanical responses of SMPUFs for a full shape memory thermodynamic cycle. One of the latest treatments of CAs is filling the inside of aneurysms with SMPUFs. The developed FEM is conducted on patient-specific basilar aneurysms treated by SMPUFs. Three sizes of foams are selected for the filling inside of the aneurysm and then governing boundary conditions and loadings are applied to the foams. The results of the distribution of stress and displacement in the absence and presence of the foam are compared. Due to the absence of similar results in the specialized literature, this paper is likely to fill a gap in the state of the art of this problem and provide pertinent results that are instrumental in the design of SMPUFs for treating CAs.

Seeing gene expression in cells: the future of structural biology

Although much is known about the machinery that executes fundamental processes of gene expression in cells, much also remains to be learned about how that machinery works. A recent paper by O’Reilly et al. reports a major step forward in the direct visualization of central dogma processes at submolecular resolution inside bacterial cells frozen in a native state. The essential methodologies involved are cross-linking mass spectrometry (CLMS) and cryo-electron tomography (cryo-ET). In-cell CLMS provides in vivo protein interaction maps. Cryo-ET allows visualization of macromolecular complexes in their native environment. These methods have been integrated by O’Reilly et al. to describe a dynamic assembly in situ between a transcribing RNA polymerase (RNAP) and a translating ribosome – a complex known as the expressome – in the model bacterium Mycoplasma pneumoniae 1 . With the application of improved data processing and classification capabilities, this approach has allowed unprecedented insights into the architecture of this molecular assembly line, confirming the existence of a physical link between RNAP and the ribosome and identifying the transcription factor NusA as the linking molecule, as well as making it possible to see the structural effects of drugs that inhibit either transcription or translation. The work provides a glimpse into the future of integrative structural cell biology and can serve as a roadmap for the study of other molecular machineries in their native context.

The Contribution of G-Layer Glucose in Salix Clones for Biofuels; Comparative Enzymatic and HPLC Analysis of Stem Cross-Sections

Background Interest on the use of short-rotation willow as a lignocellulose resource for liquid transport fuels has increased greatly over the last ten years. Investigations have shown the advantages and potential of using Salix spp. for such fuels but have also emphasized the wide variations existing in the compositional structure between different species and genotypes in addition to their effects on overall yield. The present work studied the importance of tension wood (TW) as a readily available source of glucose in two-year-old stems of four Salix clones (Tora, Björn, Jorr, Loden). Studies involved application of a novel approach whereby TW-glucose and residual sugars and lignin were quantified using stem cross-sections with results correlated with HPLC analyses of milled wood. Compositional analyses were made for four points along stems and glucose derived from enzyme saccharification of TW gelatinous (G) layers (G-glucose), structural cell wall glucose (CW-glucose) remaining after saccharification and total glucose (T-glucose) determined both theoretically and from HPLC analyses. Comparisons were also made between presence of other characteristic sugars as well as acid-soluble and -insoluble lignin. Results Initial studies showed good agreement between using stem serial sections and milled powder for determining total sugar and lignin. Therefore, sections were used throughout the work. HPLC determination of T-glucose in Salix clones varied between 47.1–52.8%, showing a trend for higher T-glucose with increasing height (Björn, Tora and Jorr). Using histochemical/microscopy and image analysis, Tora (24.2%) and Björn (28.2%) showed greater volumes of % TW than Jorr (15.5%) and Loden (14.0%). Total G-glucose with enzyme saccharification of TW G-layers varied between 3.7–14.7% increasing as the total TW volume increased. CW-glucose measured after enzyme saccharification showed mean values of 41.9–49.1%. Total lignin between and within clones showed small differences with mean variations of 22.4–22.8% before, and 22.4–24.3% after enzyme saccharification. Calculated theoretical and quantified values for CW-glucose at different heights for clones were similar with strong correlation: T-glucose = G-glucose + CW-glucose. Pearson´s correlation displayed a strong and positive correlation between T-glucose and G-glucose, % TW and stem height, and between G-glucose with % TW and stem height. Conclusions The use of stem cross-sections to estimate TW together with enzyme saccharification represents a viable approach for determining freely available G-glucose from TW allowing comparisons between Salix clones. Using stem sections provides for discrete morphological/compositional tissue comparisons between clones with results consistent with traditional wet chemical analysis approaches where entire stems are milled and analyzed. The four clones showed variable TW and presence of total % G-glucose in the order Björn > Tora > Jorr > Loden. Calculated in terms of 1 m3, Salix stems Tora and Björn would contain ca. 0.24 and 0.28 m3 of tension wood representing a significant amount of freely available glucose.

The Importance of Extraction Protocol on the Analysis of Novel Waste Sources of Lignocellulosic Biomass

As the utilization and consumption of lignocellulosic biomass increases, so too will the need for an adequate supply of feedstock. To meet these needs, novel waste feedstock materials will need to be utilized. Exploitation of these novel feedstocks will require information both on the effects of solvent extraction on the succeeding analysis of potential novel feedstocks and how accurate current methodologies are in determining the composition of novel lignocellulosic feedstocks, particularly the carbohydrate and lignin fractions. In this study, the effects of solvent extraction on novel feedstocks, including tree foliage, tree bark and spent mushroom compost, with 95% ethanol, water and both sequentially were examined. Chemical analyses were carried out to determine the moisture content, ash, extractives, post-hydrolysis sugars, Klason lignin (KL) and acid-soluble lignin (ASL) within the selected feedstocks. The result of extraction could be seen most strongly for Klason lignin, with a strong association between higher levels of Klason lignin levels and greater amounts of non-removed extractives (tree foliage and bark). Higher Klason lignin levels are reported to be due the condensation of non-removed extractives during hydrolysis, hence the lower Klason lignin determinations following extraction are more exact. In addition, total sugar determinations were lower following extractions. This is because of the solubility of non-cell-wall carbohydrates; thus, the determinations following extraction are more accurate representations of structural cell-wall polysaccharides such as cellulose. Such determinations will assist in determining the best way to utilize novel feedstocks such as those analyzed in this work.

The Influence of Oxidative Stress on Thyroid Diseases

Thyroid diseases, including neoplasms, autoimmune diseases and thyroid dysfunctions, are becoming a serious social problem with rapidly increasing prevalence. The latter is increasingly linked to oxidative stress. There are many methods for determining the biomarkers of oxidative stress, making it possible to evaluate the oxidative profile in patients with thyroid diseases compared to the healthy population. This opens up a new perspective for investigating the role of elevated parameters of oxidative stress and damage in people with thyroid diseases, especially of neoplastic nature. An imbalance between oxidants and antioxidants is observed at different stages and in different types of thyroid diseases. The organ, which is part of the endocrine system, uses free radicals (reactive oxygen species, ROS) to produce hormones. Thyroid cells release enzymes that catalyse ROS generation; therefore, a key role is played by the internal defence system and non-enzymatic antioxidants that counteract excess ROS not utilised to produce thyroid hormones, acting as a buffer to neutralise free radicals and ensure whole-body homeostasis. An excess of free radicals causes structural cell damage, undermining genomic stability. Looking at the negative effects of ROS accumulation, oxidative stress appears to be implicated in both the initiation and progression of carcinogenesis. The aim of this review is to investigate the oxidation background of thyroid diseases and to summarise the links between redox imbalance and thyroid dysfunction and disease.

An All-Solid-State Coaxial Structural Battery Using Sodium-Based Electrolyte

The transition to a sustainable society is paramount and requires the electrification of vehicles, the grid, industry, data banks, wearables, and IoT. Here, we show an all-solid-state structural battery where a Na+-based ferroelectric glass electrolyte is combined with metallic electrodes/current collectors (no traditional cathode present at fabrication) and thin-ply carbon-fiber laminates to obtain a coaxial multifunctional beam. This new concept aims to optimize the volume of any hollow beam-like structure by integrating an electrochemical system capable of both harvesting thermal and storing electrical energy while improving its mechanical performance. The coaxial cell is a coaxial cable where the dielectric is ferroelectric. The electrochemical results demonstrated the capability of performing three-minute charges to one-day discharges (70 cycles) and long-lasting discharges (>40 days at 1 mA) showing an energy density of 56.2 Wh.L−1 and specific energy of 38.0 Wh.kg−1, including the whole volume and weight of the structural cell. This is the highest specific energy among safe structural cells, while no Na+-based structural cells were found in the literature. The mechanical tests, instead, highlighted the coaxial cell capabilities to withstand severe inelastic deformation without compromising its functionalities, while increasing the flexural strength of the hosting structure. Moreover, the absence of alkali metals and liquid electrolytes together with its enhanced thermal properties makes this coaxial structural battery a valid and safe alternative as an energy reservoir for all the applications where traditional lithium-ion batteries are not suitable.

The Synthesis of Organoclays Based on Clay Minerals with Different Structural Expansion Capacities

An important goal in environmental research for industrial activity and sites is the investigation and development of effective adsorbents for chemical pollutants that are widespread, inexpensive, unharmful to the environment, and have the required adsorption selectivity. Organoclays are adsorption materials that can be obtained by modifying clays and clay minerals with various organic compounds through intercalation and surface grafting. Organoclays have important practical applications as adsorbents of a wide range of organic pollutants and some inorganic contaminants. The traditional raw materials for the synthesis of organoclays are phyllosilicates with the expanding structural cell of the smectite group, such as montmorillonite. Moreover, other phyllosilicates and inosilicates are used to synthesize organoclay to a limited extent. The purpose of this review was to analyze the possibility of using minerals of other groups with different abilities to expand the structure and structural charge for the adsorption of chemical environmental pollutants. The structural characteristics of various groups of phyllosilicates and chain minerals that affect their ability to modify organic surfactants and the adsorption properties of prepared organoclays were reviewed.