Folding mechanisms steer the amyloid fibril formation propensity of highly homologous proteins

Significant advances in the understanding of the molecular determinants of fibrillogenesis can be expected from comparative studies of the aggregation propensities of proteins with highly homologous structures but different folding pathways. Here, we fully characterize, by means of stopped-flow, T-jump, CD and DSC experiments, the unfolding mechanisms of three highly homologous proteins, zinc binding Ros87 and Ml153-149 and zinc-lacking Ml452-151. The results indicate that the three proteins significantly differ in terms of stability and (un)folding mechanisms. Particularly, Ros87 and Ml153-149 appear to be much more stable to guanidine denaturation and are characterized by folding mechanisms including the presence of an intermediate. On the other hand, metal lacking Ml452-151 folds according to a classic two-state model. Successively, we have monitored the capabilities of Ros87, Ml452-151 and Ml153-149 to form amyloid fibrils under native conditions. Particularly, we show, by CD, fluorescence, DLS, TEM and SEM experiments, that after 168 hours, amyloid formation of Ros87 has started, while Ml153-149 has formed only amorphous aggregates and Ml452-151 is still monomeric in solution. This study shows how metal binding can influence protein folding pathways and thereby control conformational accessibility to aggregation-prone states, which in turn changes aggregation kinetics, shedding light on the role of metal ions in the development of protein deposition diseases

A Novel Generalized Semi-Analytical Approach for Flood Control Reservoir Design

Flood control reservoir design requires estimating the total storable water volume or the maximum allowable discharge. This study proposes a novel Generalized Semi-Analytical Approach (GS-AA) to identify the maximum outlet discharge a flood control reservoir can handle for a specific return period. The approach exploits the analytical expression of Flow Duration Reduction (FDR) curves and combines them with an optimization algorithm to find the critical hydrograph and, thus, the hydrograph providing the maximum outlet discharge from the reservoir. The approach models the runoff process of the basin upstream of the reservoir, allowing users to choose any runoff model (RM). The proposed approach shows faster computational times than a fully numerical procedure, enabling potential users to explore and compare multiple reservoir configurations easily. Moreover, this approach addresses flow data limitation issues that prevent FDR curve derivation by correlating them to Intensity Duration Frequency curve parameters, expanding the potential applicability of the procedure in ungauged basins. Finally, results demonstrated the functionality of the procedure regardless of the chosen RM, offering widespread flexibility for users. The proposed GS-AA is a robust and adaptable tool for design and verification purposes to improve flood management strategies

The actin-myosin regulatory MRCK kinases: regulation, biological functions and associations with human cancer

The contractile actin-myosin cytoskeleton provides much of the force required for numerous cellular activities such as motility, adhesion, cytokinesis and changes in morphology. Key elements that respond to various signal pathways are the myosin II regulatory light chains (MLC), which participate in actin-myosin contraction by modulating the ATPase activity and consequent contractile force generation mediated by myosin heavy chain heads. Considerable effort has focussed on the role of MLC kinases, and yet the contributions of the myotonic dystrophy-related Cdc42-binding kinases (MRCK) proteins in MLC phosphorylation and cytoskeleton regulation have not been well characterized. In contrast to the closely related ROCK1 and ROCK2 kinases that are regulated by the RhoA and RhoC GTPases, there is relatively little information about the CDC42-regulated MRCKα, MRCKβ and MRCKγ members of the AGC (PKA, PKG and PKC) kinase family. As well as differences in upstream activation pathways, MRCK and ROCK kinases apparently differ in the way that they spatially regulate MLC phosphorylation, which ultimately affects their influence on the organization and dynamics of the actin-myosin cytoskeleton. In this review, we will summarize the MRCK protein structures, expression patterns, small molecule inhibitors, biological functions and associations with human diseases such as cancer

Experimental and numerical investigations of a river embankment model under transient seepage conditions

The evaluation of riverbank stability often represents an underrated problem in engineering practice, but is also a topical geotechnical research issue. In fact, it is certainly true that soil water content and pore water pressure distributions in the riverbank materials vary with time, due to the changeable effects of hydrometric and climatic boundary conditions, strongly influencing the bank stability conditions. Nonetheless, the assessment of hydraulic and mechanical behavior of embankments are currently performed under the simplified hypothesis of steady\u2010state seepage, generally neglecting the unsaturated soil related issues. In this paper, a comprehensive procedure for properly defining the key aspects of the problem is presented and, in particular, the soil characterization in partially saturated conditions of a suitably compacted mixture of sand and finer material, typical of flood embankments of the main river Po tributaries (Italy), is reported. The laboratory results have then been considered for modelling the embankment performance under transient seepage and following a set of possible hydrometric peaks. The outcome of the present contribution may provide meaningful geotechnical insights, for practitioners and researchers, in the flood risk assessment of river embankments

Protective Intestinal Effects of Pituitary Adenylate Cyclase Activating Polypeptide

Pituitary adenylate cyclase activating polypeptide (PACAP) is an endogenous neuropeptide widely distributed throughout the body, including the gastrointestinal tract. Several effects have been described in human and animal intestines. Among others, PACAP infl uences secretion of intestinal glands, blood fl ow, and smooth muscle contraction. PACAP is a well-known cytoprotective peptide with strong anti-apoptotic, anti-infl ammatory, and antioxidant effects. The present review gives an overview of the intestinal protective actions of this neuropeptide. Exogenous PACAP treatment was protective in a rat model of small bowel autotransplantation. Radioimmunoassay (RIA) analysis of the intestinal tissue showed that endogenous PACAP levels gradually decreased with longer-lasting ischemic periods, prevented by PACAP addition. PACAP counteracted deleterious effects of ischemia on oxidative stress markers and cytokines. Another series of experiments investigated the role of endogenous PACAP in intestines in PACAP knockout (KO) mice. Warm ischemia–reperfusion injury and cold preservation models showed that the lack of PACAP caused a higher vulnerability against ischemic periods. Changes were more severe in PACAP KO mice at all examined time points. This fi nding was supported by increased levels of oxidative stress markers and decreased expression of antioxidant molecules. PACAP was proven to be protective not only in ischemic but also in infl ammatory bowel diseases. A recent study showed that PACAP treatment prolonged survival of Toxoplasma gondii infected mice suffering from acute ileitis and was able to reduce the ileal expression of proinfl ammatory cytokines. We completed the present review with recent clinical results obtained in patients suffering from infl ammatory bowel diseases. It was found that PACAP levels were altered depending on the activity, type of the disease, and antibiotic therapy, suggesting its probable role in infl ammatory events of the intestine

Insights into the Hydromechanical Behavior of a River Embankment through Physical and Numerical Modeling

In the framework of a climate change scenario and growing land urbanization, a reliable assessment of river embankment safety conditions represents a key aspect to enhance the resilience of these critical infrastructures and support the development of design guidelines and flood risk reduction strategies. This paper aims at contributing to a deeper understanding of the effect of hydraulic loadings on the hydromechanical behavior of unsaturated river embankments through physical and numerical modeling. To fulfill this scope, two centrifuge tests were conducted on a small-scale physical model, representative for the tributary bank systems of the main river in Italy, the Po River. The model embankment featured a trapezoidal-shaped cross section and was made of a compacted silty sand mixture, overlying a homogeneous clayey silt foundation layer. A comprehensive laboratory investigation was carried out to estimate the geotechnical properties of both materials and the main outcomes are herein presented. To monitor the model response to the imposed hydraulic boundary conditions, the middle section of the embankment was extensively instrumented with miniaturized tensiometers, pore pressure transducers, and displacement sensors. Subsequently, a coupled flow-deformation finite-element (FE) model was set up to replicate the two centrifuge tests. Once validated, the numerical model was adopted to study the performance of an embankment under realistic flood scenarios as its hydraulic characteristics varied. The development of this numerical model made it possible to create a predictive tool for the assessment of the hydromechanical behavior of existing river embankments

The Thioredoxin-Regulated α-Amylase 3 of Arabidopsis thaliana Is a Target of S-Glutathionylation

Reactive oxygen species (ROS) are produced in cells as normal cellular metabolic by-products. ROS concentration is normally low, but it increases under stress conditions. To stand ROS exposure, organisms evolved series of responsive mechanisms. One such mechanism is protein S-glutathionylation. S-glutathionylation is a post-translational modification typically occurring in response to oxidative stress, in which a glutathione reacts with cysteinyl residues, protecting them from overoxidation. α-Amylases are glucan hydrolases that cleave α-1,4-glucosidic bonds in starch. The Arabidopsis genome contains three genes encoding α-amylases. The sole chloroplastic member, AtAMY3, is involved in osmotic stress response and stomatal opening and is redox-regulated by thioredoxins. Here we show that AtAMY3 activity was sensitive to ROS, such as H2O2. Treatments with H2O2 inhibited enzyme activity and part of the inhibition was irreversible. However, in the presence of glutathione this irreversible inhibition was prevented through S-glutathionylation. The activity of oxidized AtAMY3 was completely restored by simultaneous reduction by both glutaredoxin (specific for the removal of glutathione-mixed disulfide) and thioredoxin (specific for the reduction of protein disulfide), supporting a possible liaison between both redox modifications. By comparing free cysteine residues between reduced and GSSG-treated AtAMY3 and performing oxidation experiments of Cys-to-Ser variants of AtAMY3 using biotin-conjugated GSSG, we could demonstrate that at least three distinct cysteinyl residues can be oxidized/glutathionylated, among those the two previously identified catalytic cysteines, Cys499 and Cys587. Measuring the pKa values of the catalytic cysteines by alkylation at different pHs and enzyme activity measurement (pKa1 = 5.70 ± 0.28; pKa2 = 7.83 ± 0.12) showed the tendency of one of the two catalytic cysteines to deprotonation, even at physiological pHs, supporting its propensity to undergo redox post-translational modifications. Taking into account previous and present findings, a functional model for redox regulation of AtAMY3 is proposed

Aqueous phase reforming of the residual waters derived from lignin-rich hydrothermal liquefaction: investigation of representative organic compounds and actual biorefinery streams

Secondary streams in biorefineries need to be valorized to improve the economic and environmental sustainability of the plants. Representative model compounds of the water fraction from the hydrothermal liquefaction (HTL) of biomass were subjected to aqueous phase reforming (APR) to produce hydrogen. Carboxylic and bicarboxylic acids, hydroxyacids, alcohols, cycloketones and aromatics were identified as model compounds and tested for APR. The tests were performed with a Pt/C catalyst and the influence of the carbon concentration (0.3–1.8 wt. C%) was investigated. Typically, the increase of the concentration negatively affected the conversion of the feed toward gaseous products, without influencing the selectivity toward hydrogen production. A synthetic ternary mixture (glycolic acid, acetic acid, lactic acid) was subjected to APR to evaluate any differences in performance compared to the tests with single compounds. Indeed, glycolic acid reacted faster in the mixture than in the corresponding single compound test, while acetic acid remained almost unconverted. The influence of the reaction time, temperature and carbon concentration was also evaluated. Finally, residual water resulting from the HTL of a lignin-rich stream originating from an industrial-scale lignocellulosic ethanol process was tested for the first time, after a thorough characterization. In this framework, the stability of the catalyst was studied and found to be correlated to the presence of aromatics in the aqueous feedstock. For this reason, the influence of an extraction procedure for the selective removal of these compounds was explored, leading to an improvement in the APR performance