Effects of the Temperature and the pH on the Main Protease of SARS-CoV-2: A Molecular Dynamics Simulation Study

The novel coronavirus, recognized as COVID-19, is the cause of an infection outbreak in December 2019. The effect of temperature and pH changes on the main protease of SARS-CoV-2 were investigated using all-atom molecular dynamics simulation. The obtained results from the root mean square deviation (RMSD) and root mean square fluctuations (RMSF) analyses showed that at a constant temperature of 25℃ and pH=5, the conformational change of the main protease is more significant than that of pH=6 and 7. Also, by increasing temperature from 25℃ to 55℃ at constant pH=7, a remarkable change in protein structure was observed. The radial probability of water molecules around the main protease was decreased by increasing temperature and decreasing pH. The weakening of the binding energy between the main protease and water molecules due to the increasing temperature and decreasing pH has reduced the number of hydrogen bonds between the main protease and water molecules. Finding conditions that alter the conformation of the main protease could be fundamental because this change could affect the virus’s functionality and its ability to impose illness.

A large-scale genome-based survey of acidophilic Bacteria suggests that genome streamlining is an adaption for life at low pH

Genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. Although this hypothesis has been explored in several cases of low nutrient (oligotrophic) and high temperature environments, little work has been carried out on microorganisms from low pH environments and what has been reported is inconclusive. In this study, we performed a large-scale comparative genomics investigation of more than 260 bacterial high-quality genome sequences of acidophiles, together with genomes of their closest phylogenetic relatives that live at circum-neutral pH. A statistically supported correlation is reported between reduction of genome size and decreasing pH that we demonstrate is due to gene loss and reduced gene sizes. This trend is independent from other genome size constraints such as temperature and G+C content. Genome streamlining in the evolution of acidophilic Bacteria is thus supported by our results. Analyses of predicted COG categories and subcellular location predictions indicate that acidophiles have a lower representation of genes encoding extra-cellular proteins, signal transduction mechanisms and proteins with unknown function, but are enriched in inner membrane proteins, chaperones, basic metabolism, and core cellular functions. Contrary to other reports for genome streamlining, there was no significant change in paralog frequencies across pH. However, a detailed analysis of COG categories revealed a higher proportion of genes in acidophiles in the following categories: 'Replication and repair', 'Amino acid transport' and 'Intracellular trafficking'. This study brings increasing clarity regarding genomic adaptations of acidophiles to life at low pH while putting elements such as the reduction of average gene size under the spotlight of streamlining theory.

Assessment and Application of Modified Cationic Polyvinyl Alcohol Emulsifiers in Bitumen Emulsions

In this work, a series of emulsifiers were prepared by changing the molar ratio of polyvinyl alcohol (PVA) to the long chain quaternary ammonium salt (A0). The emulsifiers were characterised by FTIR and 1HNMR. The stability of the emulsions was checked and evaluated by determining the phase separation and by UV-Vis spectrophotometry. The emulsion stability increased with increasing emulsifier concentration, which was mainly due to the reduced droplet size and increased viscosity of the emulsions. Stability was also dependent on pH. At pH values between 5 to 3, stability was increased, but at further decreasing pH values, the emulsion became unstable or the emulsion separated. This could be mainly because the excess of positive ions compresses the double electron layer. The experimental results showed that PVA as a macromolecular matrix material has a great application potential for the emulsification process.

The role of changing pH on olfactory success of predator–prey interactions in green shore crabs, Carcinus maenas

Arguably climate change is one of the biggest challenges faced by many organisms. One of the more significant of these is the decreasing pH level of the ocean, a consequence of the increasing amount of atmospheric CO2 being absorbed. With the current open ocean pH level of 8.15 projected to fall to just over 7.6 in 2100, the impacts could be devastating for marine species reliant upon olfaction to survive. Here, we show that Carcinus maenas (shore crab) can detect and respond to the presence of odour cues from predatory species with no significant change between both current and projected pH conditions. In contrast, C. maenas ability to detect and respond to prey cues is altered in the projected climate change conditions, with a delayed response being observed at pH 7.6. A difference can be seen between males and females, with males detecting prey cues faster than females in reduced pH, suggesting the potential for males to be better acclimated to future climate change conditions. The change in ocean chemistry is postulated to have a fundamental impact on chemical communication systems in aquatic species. Here, we show such negative impacts of altered pH on feeding responses in Carcinus maenas, a typically robust keystone intertidal species and confirm that not all behaviours are affected equally with potentially significant implications for such functional traits and species interactions.

Efficient treatment of esophageal nutrition bezoars: dissolution outmatches removal—the Zurich approach

Enteral feed bezoars are difficult to treat and can lead to serious adverse events. There is no standardized treatment approach and various strategies have been suggested. We herein describe three cases of successful dissolutions of feed bezoars consisting of Promote® Fibre Plus with sodium bicarbonate 8.4% in critically ill patients. To provide the rationale for this approach, the effect of sodium bicarbonate 8.4% on enteral feed concretions was studied in vitro. First, Promote® Fibres Plus was incubated with hydrochloric acid with gradually decreasing pH values to establish a pH at which the solution solidifies. The resulting enteral feed concretion was exposed to sodium bicarbonate 8.4% and Coca Cola®. All patients were successfully treated with sodium bicarbonate 8.4% without the need of lengthy or repeat endoscopies. In vitro, Promote® Fibres Plus solidifies when acidified below a pH of 4.6. The resulting enteral feed concretions dissolved when exposed to sodium bicarbonate 8.4%. Incubation with Coca Cola® had no effect. We provide evidence that enteral feed bezoars consisting of Promote® Fibres Plus can be efficiently and safely treated with sodium bicarbonate 8.4% offering a new approach for daily patient care.

Whole cell microalgal-cyanobacterial array biosensor for monitoring Cd, Cr and Zn in aquatic systems

Bioavailable content of metals in aquatic systems has become critical in assessing the toxic effect of metals accumulating in the environment. Considering the need for rapid measurements, an optical microalgal-cyanobacterial array biosensor was developed using two strains of microalgae, Mesotaenium sp. and a strain of cyanobacteria Synechococcus sp. to detect Cd2+, Cr6+ and Zn2+ in aquatic systems. Microalgal and cyanobacterial cells were immobilized in a 96-well microplate using sol-gel method using silica. Optimum operational conditions for the biosensor array such as exposure time, storage stability, pH, and multiple metal effect were tested. A 10 min exposure time yielded optimum fluorescence values. Metal toxicity increased with decreasing pH, resulting in low relative fluorescence (%) and decreased with increasing pH, resulting in higher relative fluorescence (%). The optimum storage time for biosensor strains were 4 weeks for microalgal cultures and 8 weeks for cyanobacterial culture, at 4 °C storage temperature. The metal mixtures showed less effect on the inhibition of relative fluorescence (%) of microalgal/cyanobacterial cultures, displaying an antagonistic behavior among the metals tested. As a single unit, this photosynthetic array biosensor will be a valuable tool in detecting multi-metals in aquatic systems.

Limnological changes and chironomid-inferred summer air temperature from the Late Pleniglacial to the Early Holocene in the East Carpathians

Here we provide the first chironomid record and associated summer air-temperature (TVII) reconstruction between ca. 16,800–9100 cal yr BP from Lake Saint Anne (SZA), situated in the Eastern Carpathians. SZA was formed by the youngest volcanic eruption of Ciomadul volcano at ca. 29,600 cal yr BP. Our main goals in this study are to test whether warming after Heinrich event 1 (H1; ca. 16,200 cal yr BP) had similar amplitude to the late glacial warming, while Younger Dryas (YD) summers remained relatively warm in this region of Europe. We found the most remarkable chironomid assemblage change with a TVII increase of ~3.5–3.8°C at ca. 16,350 cal yr BP at SZA, followed by another slight TVII increase of ~0.8–1.0°C at ca. 14,450 cal yr BP. Only very minor temperature variations were recorded between 14,450 cal yr BP and 11,700 cal yr BP, with an unexpected TVII decrease in the Early Holocene. Variations in water depth together with increasing analogue problems and paludification from ca. 14,200 cal yr BP onwards may have influenced the reliability of our paleotemperature record obtained from SZA. In addition, Sphagnum-indicated decreasing pH, and hence decreasing nutrient level, likely overrode the effect of summer air-temperature changes during the Early Holocene, and this may explain the bias in the chironomid-inferred summer air-temperature reconstruction in the Early Holocene section.

The impacts of past, present and future ocean chemistry on predatory planktonic snails

The atlantid heteropods represent the only predatory, aragonite shelled zooplankton. Atlantid shell production is likely to be sensitive to ocean acidification (OA), and yet we know little about their mechanisms of calcification, or their response to changing ocean chemistry. Here, we present the first study into calcification and gene expression effects of short-term OA exposure on juvenile atlantids across three pH scenarios: mid-1960s, ambient and 2050 conditions. Calcification and gene expression indicate a distinct response to each treatment. Shell extension and shell volume were reduced from the mid-1960s to ambient conditions, suggesting that calcification is already limited in today's South Atlantic. However, shell extension increased from ambient to 2050 conditions. Genes involved in protein synthesis were consistently upregulated, whereas genes involved in organismal development were downregulated with decreasing pH. Biomineralization genes were upregulated in the mid-1960s and 2050 conditions, suggesting that any deviation from ambient carbonate chemistry causes stress, resulting in rapid shell growth. We conclude that atlantid calcification is likely to be negatively affected by future OA. However, we also found that plentiful food increased shell extension and shell thickness, and so synergistic factors are likely to impact the resilience of atlantids in an acidifying ocean.

Physical mechanisms driving the reversible aggregation of Staphylococcus aureus and response to antimicrobials

Formation of non-sessile, auto-aggregated cells of Staphylococcus aureus contributes to surface colonization and biofilm formation, hence play a major role in the early establishment of infection and in tolerance to antimicrobials. Understanding the mechanism of aggregation and the impact of aggregation on the activity of antimicrobials is crucial in achieving a better control of this important pathogen. Previously linked to biological phenomena, physical interactions leading to S. aureus cellular aggregation and its protective features against antimicrobials remain unraveled. Herein, in-vitro experiments coupled with XDLVO simulations reveal that suspensions of S. aureus cells exhibit rapid, reversible aggregation (> 70%) in part controlled by the interplay between cellular hydrophobicity, surface potential and extracellular proteins. Changing pH and salt concentration in the extracellular media modulated the cellular surface potential but not the hydrophobicity which remained consistent despite these variations. A decrease in net cellular negative surface potential achieved by decreasing pH or increasing salt concentrations, caused attractive forces such as the hydrophobic and cell–protein interactions to prevail, favoring immediate aggregation. The aggregation significantly increased the tolerance of S. aureus cells to quaternary ammonium compounds (QAC). The well-dispersed cell population was completely inactivated within 30 s whereas its aggregated counterpart required more than 10 min.