The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis

An in-depth analysis of first-wave SARS-CoV-2 genome is required to identify various mutations that significantly affect viral fitness. In the present study, we performed a comprehensive in silico mutational analysis of 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), and spike (S) proteins with the aim of gaining important insights into first-wave virus mutations and their functional and structural impact on SARS-CoV-2 proteins. Our integrated analysis gathered 6000 SARS-CoV-2 sequences and identified 92 mutations in S, 37 in RdRp, and 11 in 3CLpro regions. The impact of these mutations was also investigated using various in silico approaches. Among these, 32 mutations in S, 15 in RdRp, and 3 in 3CLpro proteins were found to be deleterious in nature and could alter the structural and functional behavior of the encoded proteins. The D614G mutation in spike and the P323Lmutation in RdRp are the globally dominant variants with a high frequency. Most of the identified mutations were also found in the binding moiety of the viral proteins which determine their critical involvement in host–pathogen interactions and may represent drug targets. Furthermore, potential CD4+ and CD8+ T cell epitopes were predicted, and their overlap with genetic variations was explored. This study also highlights several hot spots in which HLA and drug selective pressure overlap. The findings of the current study may allow a better understanding of COVID-19 diagnostics, vaccines, and therapeutics.

Quantifying the differential functional behavior between the medial and lateral meniscus after posterior meniscus root tears

Meniscus tears of the knee are among the most common orthopedic knee injury. Specifically, tears of the posterior root can result in abnormal meniscal extrusion leading to decreased function and progressive osteoarthritis. Despite contemporary surgical treatments of posterior meniscus root tears, there is a low rate of healing and an incidence of residual meniscus extrusion approaching 30%, illustrating an inability to recapitulate native meniscus function. Here, we characterized the differential functional behavior of the medial and lateral meniscus during axial compression load and dynamic knee motion using a cadaveric model. We hypothesized essential differences in extrusion between the medial and lateral meniscus in response to axial compression and knee range of motion. We found no differences in the amount of meniscus extrusion between the medial and lateral meniscus with a competent posterior root (0.338mm vs. 0.235mm; p-value = 0.181). However, posterior root detachment resulted in a consistently increased meniscus extrusion for the medial meniscus compared to the lateral meniscus (2.233mm vs. 0.4705mm; p-value < 0.0001). Moreover, detachment of the posterior root of the medial meniscus resulted in an increase in extrusion at all angles of knee flexion and was most pronounced (4.00mm ± 1.26mm) at 30-degrees of knee flexion. In contrast, the maximum mean extrusion of the lateral meniscus was 1.65mm ± 0.97mm, occurring in full extension. Furthermore, only the medial meniscus extruded during dynamic knee flexion after posterior root detachment. Given the differential functional behaviors between the medial and lateral meniscus, these findings suggest that posterior root repair requires reducing overall meniscus extrusion and recapitulating the native functional responses specific to each meniscus.

Microbiome Associated with the Mycangia of Female and Male Adults of the Ambrosia Beetle Platypus cylindrus Fab. (Coleoptera: Curculionidae)

The ambrosia beetle Platypus cylindrus Fab. (Coleoptera: Curculionidae) is a major cork oak pest in Portugal. Female and male beetles have different roles in host tree colonization and are both equipped with prothoracic mycangia for fungal transportation. Despite a known beneficial role of bacteria in ambrosia beetles, information on bacterial composition associated with prothoracic mycangia structures is scarce. Bacterial community from mycangia of P. cylindrus male and female beetles collected from cork oak galleries was investigated by means of 16S metagenomics. Mycangia anatomical structure was also explored with histological techniques and X-ray computed microtomography to highlight evidence supporting biological sexual dimorphism. A bacterial community with highly diverse bacterial taxa with low abundances at the genus level was revealed. Lactobacillales, Leptotrichia, Neisseria, Rothia, and Sphingomonadaceae were significantly more abundant in males, while Acinetobacter, Chitinophagaceae, Enterobacteriaceae, Erwiniaceae, Microbacteriaceae, and Pseudoclavibacter were more abundant in females. Additionally, a core bacteriome of five genera was shared by both sexes. Histological examination revealed visible connections linking external and internal tissues in females, but none in males. Overall, these results provide the first insights into sexual differentiation for bacteria in a Platypodinae beetle species, identifying key patterns of bacteria distribution in the context of beetle ecology and functional behavior.

FDM Layering Deposition Effects on Mechanical Response of TPU Lattice Structures

Nowadays, fused deposition modeling additive technology is becoming more and more popular in parts manufacturing due to its ability to reproduce complex geometries with many different thermoplastic materials, such as the TPU. On the other hand, objects obtained through this technology are mainly used for prototyping activities. For this reason, analyzing the functional behavior of FDM parts is still a topic of great interest. Many studies are conducted to broaden the spectrum of materials used to ensure an ever-increasing use of FDM in various production scenarios. In this study, the effects of several phenomena that influence the mechanical properties of printed lattice structures additively obtained by FDM are evaluated. Three different configurations of lattice structures with designs developed from unit cells were analyzed both experimentally and numerically. As the main result of the study, several parameters of the FDM process and their correlation were identified as possible detrimental factors of the mechanical properties by about 50% of the same parts used as isotropic cell solids. The best parameter configurations in terms of mechanical response were then highlighted by numerical analysis.

Mechanistic Insights of Drug Resistance in Staphylococcus Aureus with Special Reference to Newer Antibiotics

Staphylococcus aureus is the most ubiquitous microorganism in both environment as well as animals and exists as commensal and pathogenic bacterium. In past few years it has been emerged as a superbug causing serious burden on healthcare system. This bacterium has been found to be the most resistant one toward most of the antibiotics due to its rapid structural and genetic modifications. This chapter will shed light on various types of molecular mechanisms responsible for resistance of Staphylococcus aureus showcasing how it has been emerged as a superbug. Moreover, the recent approaches which include exploring of different drug targets keeping in view the structural and functional behavior of the Staphylococcus aureus has also been discussed.

Hemicentin-1 is an essential extracellular matrix component of the dermal–epidermal and myotendinous junctions

The extracellular matrix architecture is composed of supramolecular fibrillar networks that define tissue specific cellular microenvironments. Hemicentins (Hmcn1 and Hmcn2) are ancient and very large members (> 600 kDa) of the fibulin family, whose short members are known to guide proper morphology and functional behavior of specialized cell types predominantly in elastic tissues. However, the tissue distribution and function of Hemicentins within the cellular microenvironment of connective tissues has remained largely unknown. Performing in situ hybridization and immunofluorescence analyses, we found that mouse Hmcn1 and Hmcn2 show a complementary distribution throughout different tissues and developmental stages. In postnatal dermal–epidermal junctions (DEJ) and myotendinous junctions (MTJ), Hmcn1 is primarily produced by mesenchymal cells (fibroblasts, tenocytes), Hmcn2 by cells of epithelial origin (keratinocytes, myocytes). Hmcn1−/− mice are viable and show no overt phenotypes in tissue tensile strength and locomotion tests. However, transmission electron microscopy revealed ultrastructural basement membrane (BM) alterations at the DEJ and MTJ of Hmcn1−/− mice, pointing to a thus far unknown role of Hmcn1 for BM and connective tissue boundary integrity.