Mass Spectrometric and Bio-Computational Binding Strength Analysis of Multiply Charged RNAse S Gas-Phase Complexes Obtained by Electrospray Ionization from Varying In-Solution Equilibrium Conditions

We investigated the influence of a solvent’s composition on the stability of desorbed and multiply charged RNAse S ions by analyzing the non-covalent complex’s gas-phase dissociation processes. RNAse S was dissolved in electrospray ionization-compatible buffers with either increasing organic co-solvent content or different pHs. The direct transition of all the ions and the evaporation of the solvent from all the in-solution components of RNAse S under the respective in-solution conditions by electrospray ionization was followed by a collision-induced dissociation of the surviving non-covalent RNAse S complex ions. Both types of changes of solvent conditions yielded in mass spectrometrically observable differences of the in-solution complexation equilibria. Through quantitative analysis of the dissociation products, i.e., from normalized ion abundances of RNAse S, S-protein, and S-peptide, the apparent kinetic and apparent thermodynamic gas-phase complex properties were deduced. From the experimental data, it is concluded that the stability of RNAse S in the gas phase is independent of its in-solution equilibrium but is sensitive to the complexes’ gas-phase charge states. Bio-computational in-silico studies showed that after desolvation and ionization by electrospray, the remaining binding forces kept the S-peptide and S-protein together in the gas phase predominantly by polar interactions, which indirectly stabilized the in-bulk solution predominating non-polar intermolecular interactions. As polar interactions are sensitive to in-solution protonation, bio-computational results provide an explanation of quantitative experimental data with single amino acid residue resolution.     

Opposing Roles of GSK3α and GSK3β Phosphorylation in Platelet Function and Thrombosis

One of the mechanisms by which PI3 kinase can regulate platelet function is through phosphorylation of downstream substrates, including glycogen synthase kinase-3 (GSK3)α and GSK3β. Platelet activation results in the phosphorylation of an N-terminal serine residue in GSK3α (Ser21) and GSK3β (Ser9), which competitively inhibits substrate phosphorylation. However, the role of phosphorylation of these paralogs is still largely unknown. Here, we employed GSK3α/β phosphorylation-resistant mouse models to explore the role of this inhibitory phosphorylation in regulating platelet activation. Expression of phosphorylation-resistant GSK3α/β reduced thrombin-mediated platelet aggregation, integrin α_IIbβ₃ activation, and α-granule secretion, whereas platelet responses to the GPVI agonist collagen-related peptide (CRP-XL) were significantly enhanced. GSK3 single knock-in lines revealed that this divergence is due to differential roles of GSK3α and GSK3β phosphorylation in regulating platelet function. Expression of phosphorylation-resistant GSK3α resulted in enhanced GPVI-mediated platelet activation, whereas expression of phosphorylation-resistant GSK3β resulted in a reduction in PAR-mediated platelet activation and impaired in vitro thrombus formation under flow. Interestingly, the latter was normalised in double GSK3α/β KI mice, indicating that GSK3α KI can compensate for the impairment in thrombosis caused by GSK3β KI. In conclusion, our data indicate that GSK3α and GSK3β have differential roles in regulating platelet function.     

A neural net-based model for decision making in marketing

The creation of models able to explain the relationship among sales and the different stimuli that reach the consumer, including publicity, is a very important topic in market research. Interrelations are loosely defined from a quantitative point of view, and studies are usually made at a macroeconomic or aggregate level. This paper presents a microscopic or individual-based model that represents explicitly every consumer, introduces ads as positive or negative reinforcers of consumer behaviour, and sales as results of individual decisions. Several experiments have been run on populations of these individuals or agents, and results checked against what is obvious or well known in reality. These experiments prove that the qualitative behaviour of the model closely resembles reality. Next step is to try to obtain quantitative results out of the model, and put it into an easy-to-use program.     

Solution decomposition of zinc dialkyl dithiophosphate and its effect on antiwear and thermal film formation studied by X-ray absorption spectroscopy

A detailed study was undertaken to investigate the effect of ZDDP oil solution chemistry changes due to thermal decomposition, on antiwear and thermal film chemistries, film thickness and wear. P and S K- and L-edge X-ray absorption near edge structure (XANES) spectroscopies were used to characterize film chemistry, and 31-P NMR spectroscopy was used to monitor the ZDDP oil solution chemistry. P L-edge XANES results of antiwear films prepared from ZDDP oil solutions preheated at 150°C for various lengths of time, showed a decrease in polyphosphate chain length as ZDDP thermal solution decomposition progressed. Film thickness and wear increased with increasing ZDDP oil solution preheating time (decomposition). Antiwear films formed from ZDDP oil solutions preheated at a higher temperature (200°C) for 1 and 3 h, yielded thinner films and showed catastrophic wear. 31-P NMR spectra showed that no oil soluble P containing species were left in solution after heating at 200°C for 1 h and yet the 200°C, 6 h antiwear film was found to be as thick as that generated from previously unheated solution. Wear was comparable to that obtained by using base oil alone. These films were found to be of short chain polyphosphate structure. ZDDP oil solution chemistry was also shown to have an effect on the chemistry of thermally generated films. Film chemistry changed with ZDDP oil solution heating time. A linkage isomer of ZDDP is proposed as an important precursor for film formation after analysis and comparison of an oil insoluble ZDDP decomposition product with the thermal and antiwear film chemistries. As with the related antiwear films, thermal film thickness was also shown to increase dramatically when ZDDP decomposition in solution increased. An overall mechanism for film formation, taking into account the ZDDP linkage isomer and the deposition of colloidal polyphosphate material, is proposed.     

Implementation of commonsense reasoning in organic reaction prediction system CSB

The internal structure of the CSB module for the computer-assisted prediction of chemical reactions is discussed. In particular, the implementation of the commonsense algorithm is presented, whose main task is to control the course of the computer reactions simulation, allowing to direct the generation towards real, satisfactory solutions.     

Establishment of a Rapid Detection System for ISG20-Dependent SARS-CoV-2 Subreplicon RNA Degradation Induced by Interferon-α

Inhaled nebulized interferon (IFN)-α and IFN-β have been shown to be effective in the management of coronavirus disease 2019 (COVID-19). We aimed to construct a virus-free rapid detection system for high-throughput screening of IFN-like compounds that induce viral RNA degradation and suppress the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We prepared a SARS-CoV-2 subreplicon RNA expression vector which contained the SARS-CoV-2 5′-UTR, the partial sequence of ORF1a, luciferase, nucleocapsid, ORF10, and 3′-UTR under the control of the cytomegalovirus promoter. The expression vector was transfected into Calu-3 cells and treated with IFN-α and the IFNAR2 agonist CDM-3008 (RO8191) for 3 days. SARS-CoV-2 subreplicon RNA degradation was subsequently evaluated based on luciferase levels. IFN-α and CDM-3008 suppressed SARS-CoV-2 subreplicon RNA in a dose-dependent manner, with IC50 values of 193 IU/mL and 2.54 μM, respectively. HeLa cells stably expressing SARS-CoV-2 subreplicon RNA were prepared and treated with the IFN-α and pan-JAK inhibitor Pyridone 6 or siRNA-targeting ISG20. IFN-α activity was canceled with Pyridone 6. The knockdown of ISG20 partially canceled IFN-α activity. Collectively, we constructed a virus-free rapid detection system to measure SARS-CoV-2 RNA suppression. Our data suggest that the SARS-CoV-2 subreplicon RNA was degraded by IFN-α-induced ISG20 exonuclease activity.     

Drinking water treatment options for taste and odor control

The effectiveness of drinking water treatment options for eliminating seasonal taste and odor events caused by phytoplankton blooms in the source water were evaluated. Dissolved air flotation (DAF), conventional gravity sedimentation (CGS), ozonation and granulated activated carbon (GAC) filtration processes were studied in pilot plant-scale experiments. Clarification by DAF consistently produced water with lower turbidity and particle counts (NP > 2.0 μm/ml) than CGS. Mean particle counts detected in water following DAF and CGS treatment were 3600 and 7500 particles/ml, respectively. The absolute abundance of phytoplankton in the source water was the single most important factor influencing DAF and CGS removal efficiency. Removal efficiencies for both processes were poorer at low source water biomass (near 250 μg/l) than at higher biomass concentrations (1750 μg/l). For the eight phytoplankton taxa present in the source water, DAF and CGS removal ranged from 29–85% and 21–49%, respectively. With the exception of the total nanoplankton for which removal by both processes was comparable, all other taxa were removed more efficiently by DAF than CGS. Flavor profile analysis (FPA) indicated that DAF alone could not completely mitigate the strong fishy, musty odors associated with some phytoplankton blooms. Ozone altered the fishy odor to an undesirable “plastic-like” odor. Only filtration through GAC/sand filters removed all odors. Removal of soluble constituents such as color and total organic carbon (TOC) by DAF and CGS were comparable for most of the year. During phytoplankton blooms, however, TOC removal by DAF was significantly greater than by CGS. TOC and color removal were substantially greater through GAC than through anthracite filters. A combination of DAF clarification and GAC filtration was the most effective treatment combination for removal of particulates, color and taste and odor compounds.     

Rosmarinic Acid and Sodium Citrate Have a Synergistic Bacteriostatic Effect against Vibrio Species by Inhibiting Iron Uptake

Background: New strategies are needed to combat multidrug-resistant bacteria. The restriction of iron uptake by bacteria is a promising way to inhibit their growth. We aimed to suppress the growth of Vibrio bacterial species by inhibiting their ferric ion-binding protein (FbpA) using food components. Methods: Twenty spices were selected for the screening of FbpA inhibitors. The candidate was applied to antibacterial tests, and the mechanism was further studied. Results: An active compound, rosmarinic acid (RA), was screened out. RA binds competitively and more tightly than Fe³⁺ to VmFbpA, the FbpA from V. metschnikovii, with apparent K_D values of 8 μM vs. 17 μM. Moreover, RA can inhibit the growth of V. metschnikovii to one-third of the control at 1000 μM. Interestingly, sodium citrate (SC) enhances the growth inhibition effect of RA, although SC only does not inhibit the growth. The combination of RA/SC completely inhibits the growth of not only V. metschnikovii at 100/100 μM but also the vibriosis-causative pathogens V. vulnificus and V. parahaemolyticus, at 100/100 and 1000/100 μM, respectively. However, RA/SC does not affect the growth of Escherichia coli. Conclusions: RA/SC is a potential bacteriostatic agent against Vibrio species while causing little damage to indigenous gastrointestinal bacteria.