Stability and deformation of biomolecular condensates under the action of shear flow.

Biomolecular condensates play a key role in cytoplasmic compartmentalization and cell functioning. Despite extensive research on the physico-chemical, thermodynamic, or crowding aspects of the formation and stabilization of the condensates, one less studied feature is the role of external perturbative fluid flow. In fact, in living cells, shear stress may arise from streaming or active transport processes. Here, we investigate how biomolecular condensates are deformed under different types of shear flows. We first model Couette flow perturbations via two-way coupling between the condensate dynamics and fluid flow by deploying Lattice Boltzmann Molecular Dynamics. We then show that a simplified approach where the shear flow acts as a static perturbation (one-way coupling) reproduces the main features of the condensate deformation and dynamics as a function of the shear rate. With this approach, which can be easily implemented in molecular dynamics simulations, we analyze the behavior of biomolecular condensates described through residue-based coarse-grained models, including intrinsically disordered proteins and protein/RNA mixtures. At lower shear rates, the fluid triggers the deformation of the condensate (spherical to oblated object), while at higher shear rates, it becomes extremely deformed (oblated or elongated object). At very high shear rates, the condensates are fragmented. We also compare how condensates of different sizes and composition respond to shear perturbation, and how their internal structure is altered by external flow. Finally, we consider the Poiseuille flow that realistically models the behavior in microfluidic devices in order to suggest potential experimental designs for investigating fluid perturbations in vitro.

Dynamics and Structures of Amyloid Aggregates under Fluid Flows.

In this work, we investigate how fluid flows impact the aggregation mechanisms of Aß40 proteins and Aß16-22 peptides and mechanically perturb their (pre)fibrillar aggregates. We exploit the OPEP coarse-grained model for proteins and the Lattice Boltzmann Molecular Dynamics technique. We show that beyond a critical shear rate, amyloid aggregation speeds up in Couette flow because of the shorter collisions times between aggregates, following a transition from diffusion limited to advection dominated dynamics. We also characterize the mechanical deformation of (pre)fibrillar states due to the fluid flows (Couette and Poiseuille), confirming the capability of (pre)fibrils to form pathological loop-like structures as detected in experiments. Our findings can be of relevance for microfluidic applications and for understanding aggregation in the interstitial brain space.

Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases.

In this work, we investigated the lactate dehydrogenase (LDH) from Selenomonas ruminantium (S. rum), an enzyme that differs at key amino acid positions from canonical allosteric LDHs. The wild type (Wt) of this enzyme recognises pyuvate as all LDHs. However, introducing a single point mutation in the active site loop (I85R) allows S. Rum LDH to recognize the oxaloacetate substrate as a typical malate dehydrogenase (MalDH), whilst maintaining homotropic activation as an LDH. We report the tertiary structure of the Wt and I85RLDH mutant. The Wt S. rum enzyme structure binds NADH and malonate, whilst also resembling the typical compact R-active state of canonical LDHs. The structure of the mutant with I85R was solved in the Apo State (without ligand), and shows no large conformational reorganization such as that observed with canonical allosteric LDHs in Apo state. This is due to a local structural feature typical of S. rum LDH that prevents large-scale conformational reorganization. The S. rum LDH was also studied using Molecular Dynamics simulations, probing specific local deformations of the active site that allow the S. rum LDH to sample the T-inactive state. We propose that, with respect to the LDH/MalDH superfamily, the S. rum enzyme possesses a specificstructural and dynamical way to ensure homotropic activation.

Six Sigma can significantly reduce costs of poor quality of the surgical instruments sterilization process and improve surgeon and operating room personnel satisfaction.

Operating room (OR) management is a complex multidimensional activity combining clinical and managerial aspects. This longitudinal observational study aimed to assess the impact of Six-Sigma methodology to optimize surgical instrument sterilization processes. The project was conducted at the operating theatre of our tertiary regional hospital during the period from July 2021 to December 2022. The project was based on the surgical instrument supply chain analysis. We applied the Six Sigma lean methodology by conducting workshops and practical exercises and by improving the surgical instrument process chain, as well as checking stakeholders' satisfaction. The primary outcome was the analysis of Sigma improvement. Through this supply chain passed 314,552 instruments in 2022 and 22 OR processes were regularly assessed. The initial Sigma value was 4.79 ± 1.02σ, and the final one was 5.04 ± 0.85σ (SMD 0.60, 95%CI 0.16-1.04, p = 0.010). The observed improvement was estimated in approximately $19,729 of cost savings. Regarding personnel satisfaction, 150 questionnaires were answered, and the overall score improved from 6.6 ± 2.2 pts to 7.0 ± 1.9 pts (p = 0.013). In our experience the application of the Lean Six Sigma methodology to the process of handling the surgical instruments from/to the OR was cost-effective, significantly decreased the costs of poor quality and increased internal stakeholder satisfaction.

Evolution of large Aß16-22 aggregates at atomic details and potential of mean force associated to peptide unbinding and fragmentation events.

Atomic characterization of large nonfibrillar aggregates of amyloid polypeptides cannot be determined by experimental means. Starting from ß-rich aggregates of Y and elongated topologies predicted by coarse-grained simulations and consisting of more than 100 Aß16-22 peptides, we performed atomistic molecular dynamics (MD), replica exchange with solute scaling (REST2), and umbrella sampling simulations using the CHARMM36m force field in explicit solvent. Here, we explored the dynamics within 3 µs, the free energy landscape, and the potential of mean force associated with either the unbinding of one single peptide in different configurations within the aggregate or fragmentation events of a large number of peptides. Within the time scale of MD and REST2, we find that the aggregates experience slow global conformational plasticity, and remain essentially random coil though we observe slow beta-strand structuring with a dominance of antiparallel beta-sheets over parallel beta-sheets. Enhanced REST2 simulation is able to capture fragmentation events, and the free energy of fragmentation of a large block of peptides is found to be similar to the free energy associated with fibril depolymerization by one chain for longer Aß sequences.

Elucidations on the Performance and Reversibility of Treatment with Hyaluronic Acid Based Dermal Fillers: In vivo and in vitro Approaches.

Purpose: The aim of this study was to investigate the performance and the reversibility of different classes of Hyaluronic Acid (HA) dermal fillers. We analysed 4 HA based fillers, belonging to 3 different chemical classes of products, commonly used in the field of wrinkles correction: linear HA 8 mg/mL (Viscoderm 0.8), thermically stabilized hybrid complexes of high and low molecular weight HA molecules at a concentration of 32 mg/mL and 45 mg/mL respectively (Profhilo and Profhilo Structura) and cross-linked HA 25 mg/mL (Aliaxin GP). Methods: The products were tested by a well-established animal model. The generated implants were analyzed through High-Frequency Ultrasound technology. Then, reversibility of the treatment was evaluated by enzymatic degradation kinetics studies, characterised by a combined approach of Carbazole assay and HP-SEC/TDA method. Results: Implants generated by linear HA 8 mg/mL remained detectable by ultrasound acquisition for 4 weeks, whereas those generated by injection of HA hybrid complex 32 mg/mL were detectable for 10 weeks. HA hybrid complex 45 mg/mL and cross-linked HA 25 mg/mL were detectable for 29 and at least 33 weeks, respectively. Enzymatic degradation kinetics studies demonstrated that the HA content in HA hybrid complex 45 mg/mL was almost completely depolymerized and homogeneous after 3 h of treatment. For cross-linked HA 25 mg/mL, 24 h of incubation are needed to obtain the same degree of depolymerization. Conclusion: The study confirmed the ability of the experimental model to predict the behaviour of HA based dermal fillers in vivo and showed the innovative aspects of HA hybrid complex 45 mg/mL, that combines the high-safety profile, in terms of reversibility of the treatment, of the linear HA-based products with the durability of a high degree cross-linked gels, paving the way to the chance to be used for a wide range of applications in the field of aesthetic medicine.

Protein Conformational Space at the Edge of Allostery: Turning a Nonallosteric Malate Dehydrogenase into an "Allosterized" Enzyme Using Evolution-Guided Punctual Mutations.

We unveil the intimate relationship between protein dynamics and allostery by following the trajectories of model proteins in their conformational and sequence spaces. Starting from a nonallosteric hyperthermophilic malate dehydrogenase, we have tracked the role of protein dynamics in the evolution of the allosteric capacity. Based on a large phylogenetic analysis of the malate (MalDH) and lactate dehydrogenase (LDH) superfamily, we identified two amino acid positions that could have had a major role for the emergence of allostery in LDHs, which we targeted for investigation by site-directed mutagenesis. Wild-type MalDH and the single and double mutants were tested with respect to their substrate recognition profiles. The double mutant displayed a sigmoid-shaped profile typical of homotropic activation in LDH. By using molecular dynamics simulations, we showed that the mutations induce a drastic change in the protein sampling of its conformational landscape, making transiently T-like (inactive) conformers, typical of allosteric LDHs, accessible. Our data fit well with the seminal key concept linking protein dynamics and evolvability. We showed that the selection of a new phenotype can be achieved by a few key dynamics-enhancing mutations causing the enrichment of low-populated conformational substates.

Biochemical, structural and dynamical studies reveal strong differences in the thermal-dependent allosteric behavior of two extremophilic lactate dehydrogenases.

In this work, we combined biochemical and structural investigations with molecular dynamics (MD) simulations to analyze the very different thermal-dependent allosteric behavior of two lactate dehydrogenases (LDH) from thermophilic bacteria. We found that the enzyme from Petrotoga mobilis (P. mob) necessitates an absolute requirement of the allosteric effector (fructose 1, 6-bisphosphate) to ensure functionality. In contrast, even without allosteric effector, the LDH from Thermus thermophilus (T. the) is functional when the temperature is raised. We report the crystal structure of P. mob LDH in the Apo state solved at 1.9 Å resolution. We used this structure and the one from T. the, obtained previously, as a starting point for MD simulations at various temperatures. We found clear differences between the thermal dynamics, which accounts for the behavior of the two enzymes. Our work demonstrates that, within an allosteric enzyme, some areas act as local gatekeepers of signal transmission, allowing the enzyme to populate either the T-inactive or the R-active states with different degrees of stringency.

Evaluation of Wound Healing Activity of Salvia haenkei Hydroalcoholic Aerial Part Extract on in vitro and in vivo Experimental Models.

PURPOSE: The aim of the present study was to evaluate the potential wound healing activity of the hydroalcoholic extract of Salvia haenkei on in vitro and in vivo experimental models. MATERIALS AND METHODS: Preliminary analytical characterization of the hydroalcoholic extract of Salvia haenkei was made by reversed-phase high performance liquid chromatography (RP-HPLC) that permitted identification of a qualitative fingerprint of the extract of aerial parts. The wound healing activity of the hydroalcoholic extract of Salvia haenkei was evaluated in vitro by the scratch assay on human dermal fibroblasts and human epidermal keratinocytes and in vivo by standardized mouse excisional splinting model. Real-time PCR (RT-PCR) experiments were performed to analyze gene expression levels of inflammatory markers. RESULTS: The scratch assay tests showed that the treatment with the hydroalcoholic extract of Salvia haenkei did not induce an increase in the fibroblasts migration rate with respect to the positive control. Instead, the hydroalcoholic extract of Salvia haenkei was effective in improving the wound closure rate on keratinocyte cell cultures with an almost total invasion of the scratch after 48 h of treatment; whereas the positive control, at the same time point, showed only a 67% reduction of the wound size. In vivo experiments showed that the groups treated with the extract of Salvia haenkei completely re-epithelized the wound in 2.7 days, a timing that was comparable with the action of the positive control that took only 2.1 days. Gene expression analysis showed that Salvia haenkei positively regulated the signaling pathway of the nuclear factor-κB (NF-κB) transcription factor. CONCLUSION: The results suggested that the hydroalcoholic extract of Salvia haenkei induced a clear wound healing effect.

A novel animal model for residence time evaluation of injectable hyaluronic acid-based fillers using high-frequency ultrasound-based approach.

BACKGROUND: Hyaluronic acid (HA)-based devices are among the most popular filler agents for skin rejuvenation. One of the principal goals is the improvement in residence time of HA-based products, to increase their performance and reduce frequency of the treatment. So, understanding fillers, behavior after subcutaneous injection is a fundamental aspect for discovery and optimization of new products. Current in vivo approaches to detect/quantify injected HA fillers are not always well optimized or easy to apply. OBJECTIVE: To develop more efficacious and noninvasive diagnostic tools to make a quantitative evaluation of the degradation of fillers in a small animal model. MATERIALS AND METHODS: We evaluated the residence time of different HA-based fillers, fluorescein-labeled and not, injected subcutaneously in mice. Volumes of fillers were monitored through high-frequency ultrasound (HF-US) method while fluorescence intensity through the well-established fluorescence living imaging method. To confirm the effectiveness of HF-US, obtained volumetric measurements were compared with fluorescence intensity values. RESULTS: Both the presented methods revealed the same degradation kinetics for the tested products. CONCLUSION: The two used methods are fully comparable and quantitatively accurate. The presented approach has been proved to be noninvasive, sensitive, and reproducible.

Sample-to-sample fluctuations of power spectrum of a random motion in a periodic Sinai model.

The Sinai model of a tracer diffusing in a quenched Brownian potential is a much-studied problem exhibiting a logarithmically slow anomalous diffusion due to the growth of energy barriers with the system size. However, if the potential is random but periodic, the regime of anomalous diffusion crosses over to one of normal diffusion once a tracer has diffused over a few periods of the system. Here we consider a system in which the potential is given by a Brownian bridge on a finite interval (0,L) and then periodically repeated over the whole real line and study the power spectrum S(f) of the diffusive process x(t) in such a potential. We show that for most of realizations of x(t) in a given realization of the potential, the low-frequency behavior is S(f)∼A/f^{2}, i.e., the same as for standard Brownian motion, and the amplitude A is a disorder-dependent random variable with a finite support. Focusing on the statistical properties of this random variable, we determine the moments of A of arbitrary, negative, or positive order k and demonstrate that they exhibit a multifractal dependence on k and a rather unusual dependence on the temperature and on the periodicity L, which are supported by atypical realizations of the periodic disorder. We finally show that the distribution of A has a log-normal left tail and exhibits an essential singularity close to the right edge of the support, which is related to the Lifshitz singularity. Our findings are based both on analytic results and on extensive numerical simulations of the process x(t).