BAP1 enhances Polycomb repression by counteracting widespread H2AK119ub1 deposition and chromatin condensation.

BAP1 is mutated or deleted in many cancer types, including mesothelioma, uveal melanoma, and cholangiocarcinoma. It is the catalytic subunit of the PR-DUB complex, which removes PRC1-mediated H2AK119ub1, essential for maintaining transcriptional repression. However, the precise relationship between BAP1 and Polycombs remains elusive. Using embryonic stem cells, we show that BAP1 restricts H2AK119ub1 deposition to Polycomb target sites. This increases the stability of Polycomb with their targets and prevents diffuse accumulation of H2AK119ub1 and H3K27me3. Loss of BAP1 results in a broad increase in H2AK119ub1 levels that is primarily dependent on PCGF3/5-PRC1 complexes. This titrates PRC2 away from its targets and stimulates H3K27me3 accumulation across the genome, leading to a general chromatin compaction. This provides evidence for a unifying model that resolves the apparent contradiction between BAP1 catalytic activity and its role in vivo, uncovering molecular vulnerabilities that could be useful for BAP1-related pathologies.

Multiscale Approach for Tuning Communication among Chemical Oscillators Confined in Biomimetic Microcompartments.

ConspectusInspired by the biological world, new cross-border disciplines and technologies have emerged. Relevant examples include systems chemistry, which offers a bottom-up approach toward chemical complexity, and bio/chemical information and communication technology (bio/chemical ICT), which explores the conditions for propagating signals among individual microreactors separated by selectively permeable membranes. To fabricate specific arrays of microreactors, microfluidics has been demonstrated as an excellent method. In particular, droplet-based microfluidics is a powerful tool for encapsulating biological entities and chemical reagents in artificial microenvironments, mostly water-in-oil microdroplets. In these systems, the interfaces are liquid-liquid, and their physicochemical properties are key factors for tuning the coupling between molecular diffusion. Simple and double emulsions, where aqueous domains are in equilibrium with oil domains through boundary layers of amphiphilic molecules, are organized assemblies with high interfacial-area-to-volume ratios. These membranes can be engineered to obtain different surface charges, single- or multilayer stacking, and a variable degree of defects in molecular packing. Emulsions find application in many fields, including the food industry, pharmaceutics, and cosmetics. Furthermore, micro- and nanoemulsions can be used to model the propagation of chemical species through long distances, which is not only vital for cell signaling but also significant in molecular computing. Here we present in-depth research on the faceted world of solutions confined in restricted environments. In particular, we focused on the multiscale aspects of structure and dynamics from molecular to micro and macro levels. The Belousov-Zhabotinsky chemical reaction, known for its robustness and well-documented oscillatory behavior, was selected to represent a generic signal emitter/receiver confined within microenvironments separated by liquid-liquid interfaces. In this pulse generator, the temporal and spatial progressions are governed by periodic fluctuations in the concentration of chemical species, which act as activatory or inhibitory messengers over long distances. When organized into "colonies" or arrays, these micro-oscillators exhibit emergent dynamical behaviors at the population level. These behaviors can be finely tuned by manipulating the geometrical distribution of the oscillators and the properties of the interfaces at the nanoscale. By carefully selecting the membrane composition, it is possible to drive the system toward either in-phase, antiphase, or mixed synchronization regimes among individual oscillators, depending on messenger molecules. This relatively simple lab-scale model replicates some of the communication strategies commonly found in biological systems, particularly those based on the passive diffusion of chemical and electrical signals. It can help shed light on fundamental life processes and inspire new implementations in molecular computing and smart materials.

Radiographic evaluation of marginal bone levels around implants supporting splinted fixed bridges: A retrospective study on 412 implants.

OBJECTIVES: The effect of the implant position within the prosthesis on bone remodeling is scarcely documented so far. Thus, the aim of the present study was to investigate whether central implants may suffer higher peri-implant marginal bone levels (MBL) compared to laterals in case of fixed splinted bridges supported by ≥ three implants. MATERIALS AND METHODS: Partially edentulous subjects rehabilitated with at least one fixed bridge supported by ≥ three dental implants were enrolled. MBL was assessed radiographically by means of intraoral radiographs acquired with phosphor plates and imported in a dedicated software. MBL was calculated as the distance between the implant platform level and the most coronal visible bone-to-implant contact. A three-level linear mixed effects model was used for investigating the fixed effect of patient-, prosthesis-, and implant-level variables on the MBL. RESULTS: Overall, 90 patients rehabilitated with 130 splinted fixed bridges supported by 412 implants were included. The median follow-up was 136 months. The mean peri-implant MBL resulted statistically significantly higher at central implants if compared to lateral implants (p < .01). The estimated MBL averages for central and external implants were 1.68 and 1.18 mm, respectively. The prosthesis-level variables suggested that a cement-retained bridge was prone to a significant 0.82 mm higher MBL than a screw-retained one. Implant surface showed an association with MBL changes, although less pronounced than implant retention. CONCLUSIONS: In case of ≥3 adjacent implants supporting splinted bridges, central implants were more predisposed to MBL compared to laterals. At the prosthesis level, implants supporting cement-retained bridges were statistically more susceptible to MBL compared to screw-retained ones. Surface characteristics can also influence MBL stability at the implant level.

Bioprospecting for plant resilience to climate change: mycorrhizal symbionts of European and American beachgrass (Ammophila arenaria and Ammophila breviligulata) from maritime sand dunes.

Climate change and global warming have contributed to increase terrestrial drought, causing negative impacts on agricultural production. Drought stress may be addressed using novel agronomic practices and beneficial soil microorganisms, such as arbuscular mycorrhizal fungi (AMF), able to enhance plant use efficiency of soil resources and water and increase plant antioxidant defence systems. Specific traits functional to plant resilience improvement in dry conditions could have developed in AMF growing in association with xerophytic plants in maritime sand dunes, a drought-stressed and low-fertility environment. The most studied of such plants are European beachgrass (Ammophila arenaria Link), native to Europe and the Mediterranean basin, and American beachgrass (Ammophila breviligulata Fern.), found in North America. Given the critical role of AMF for the survival of these beachgrasses, knowledge of the composition of AMF communities colonizing their roots and rhizospheres and their distribution worldwide is fundamental for the location and isolation of native AMF as potential candidates to be tested for promoting crop growth and resilience under climate change. This review provides quantitative and qualitative data on the occurrence of AMF communities of A. arenaria and A. breviligulata growing in European, Mediterranean basin and North American maritime sand dunes, as detected by morphological studies, trap culture isolation and molecular methods, and reports on their symbiotic performance. Moreover, the review indicates the dominant AMF species associated with the two Ammophila species and the common species to be further studied to assess possible specific traits increasing their host plants resilience toward drought stress under climate change.

Effect of in vitro simulated digestion on the anti-Helicobacter Pylori activity of different Propolis extracts.

Helicobacter pylori (HP) is among the most common pathogens causing infection in humans worldwide. Oxidative stress and gastric inflammation are involved in the progression of HP-related gastric diseases, and they can be targeted by integrating conventional antibiotic treatment with polyphenol-enriched natural products. In this work, we characterised three different propolis extracts and evaluated their stability under in vitro simulated gastric digestion, compared to their main constituents alone. The extract with the highest stability to digestion (namely, the dark propolis extract, DPE) showed a minimum bactericidal concentration (MBC) lower than 1 mg/mL on HP strains with different virulence factors. Finally, since urease is one of the virulence factors contributing to the establishment of a microenvironment that promotes HP infection, we evaluated the possible inhibition of this enzyme by using molecular docking simulations and in vitro colorimetric assay, showing that galangin and pinocembrin may be involved in this activity.

The Lyotropic Nature of Halates: An Experimental Study.

Unlike halides, where the kosmotropicity decreases from fluoride to iodide, the kosmotropic nature of halates apparently increases from chlorate to iodate, in spite of the lowering in the static ionic polarizability. In this paper, we present an experimental study that confirms the results of previous simulations. The lyotropic nature of aqueous solutions of sodium halates, i.e., NaClO3, NaBrO3, and NaIO3, is investigated through density, conductivity, viscosity, and refractive index measurements as a function of temperature and salt concentration. From the experimental data, we evaluate the activity coefficients and the salt polarizability and assess the anions' nature in terms of kosmotropicity/chaotropicity. The results clearly indicate that iodate behaves as a kosmotrope, while chlorate is a chaotrope, and bromate shows an intermediate nature. This experimental study confirms that, in the case of halates XO3-, the kosmotropic-chaotropic ranking reverses with respect to halides. We also discuss and revisit the role of the anion's polarizability in the interpretation of Hofmeister phenomena.

Green Solvents for Eco-Friendly Synthesis of Dimethindene: A Forward-Looking Approach.

Dimethindene is a selective histamine H1 antagonist and is commercially available as a racemate. Upon analyzing the synthetic pathways currently available for the industrial preparation of dimethindene, we set up a sustainable approach for the synthesis of this drug, switching from petroleum-based volatile organic compounds (VOCs) to eco-friendly solvents, such as 2-methyltetrahydrofuran (2-MeTHF) and cyclopentyl methyl ether (CPME) belonging to classes 3 and 2, respectively. Beyond decreasing the environmental impact of the synthesis (E-factor: 24.1-54.9 with VOCs; 12.2-22.1 with 2-MeTHF or CPME), this switch also improved the overall yield of the process (from 10% with VOCs to 21-22% with 2-MeTHF or CPME) and remarkably simplified the manual operations, working under milder conditions. Typical metrics applied at the first and second pass, according to the CHEM21 metrics toolkit, were also calculated for the whole synthetic procedure of dimethindene, and the results were compared with those of the classical procedure.

Shape changes and budding of giant vesicles induced by an internal chemical trigger: an interplay between osmosis and pH change.

Shape transformation and budding of phospholipid/fatty acid giant hybrid vesicles can be induced by an internal chemical stimulus (pH change) when coupled with an osmotic shock. In particular, an autocatalytic enzymatic reaction set (urea-urease system), confined in the lumen of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/oleic acid (HOA) vesicles, can force the budding of the hosting vesicle, when properly fed by a trans-membrane substrate infusion. Herein, we elucidate the budding mechanism by simulating the shape changes of a vesicle during the enzymatic reaction. The area-difference-elasticity (ADE) theory is thus implemented to minimize the surface elastic energy and obtain the equilibrium shape at different values of the reduced volume and different values of the reduced preferred area difference (Δa0). Simulations, together with control experiments, unambiguously show that to obtain an effective vesicle shape transformation, the osmotic stress and the pH change in the lumen of the vesicle must act in synergy at the same timescale. Osmotic pressure induces a vesicle deflation (volume loss), while the pH change affects the preferred area difference between the outer and the inner membrane leaflets.

Synchronization scenarios induced by delayed communication in arrays of diffusively coupled autonomous chemical oscillators.

We study the impact of delayed feedbacks in the collective synchronization of ensembles of identical and autonomous micro-oscillators. To this aim, we consider linear arrays of Belousov-Zhabotinsky (BZ) oscillators confined in micro-compartmentalised systems, where the delayed feedback mimics natural lags that can arise due to the confinement properties and mechanisms driving the inter-oscillator communication. The micro-oscillator array is modeled as a set of Oregonator-like kinetics coupled via mass exchange of the chemical messengers. Changes in the synchronization patterns are explored by varying the delayed feedback introduced in the messenger species Br2. A direct transition from anti-phase to in-phase synchronization and back to the initial anti-phase scheme is observed by progressively increasing the time delay from zero to the value T0, which is the oscillation period characterising the system without any delayed coupling. The route from anti- to in-phase oscillations (and back) consists of regimes where windows of in-phase oscillations are periodically broken by anti-phase beats. Similarities between these phase transition dynamics and synchronization scenarios characterising the coordination of oscillatory limb movements are finally discussed.

Fungal pathogen uses sex pheromone receptor for chemotropic sensing of host plant signals.

For more than a century, fungal pathogens and symbionts have been known to orient hyphal growth towards chemical stimuli from the host plant. However, the nature of the plant signals as well as the mechanisms underlying the chemotropic response have remained elusive. Here we show that directed growth of the soil-inhabiting plant pathogen Fusarium oxysporum towards the roots of the host tomato (Solanum lycopersicum) is triggered by the catalytic activity of secreted class III peroxidases, a family of haem-containing enzymes present in all land plants. The chemotropic response requires conserved elements of the fungal cell integrity mitogen-activated protein kinase (MAPK) cascade and the seven-pass transmembrane protein Ste2, a functional homologue of the Saccharomyces cerevisiae sex pheromone α receptor. We further show that directed hyphal growth of F. oxysporum towards nutrient sources such as sugars and amino acids is governed by a functionally distinct MAPK cascade. These results reveal a potentially conserved chemotropic mechanism in root-colonizing fungi, and suggest a new function for the fungal pheromone-sensing machinery in locating plant hosts in a complex environment such as the soil.

Metal-Promoted Heterocyclization: A Heterosynthetic Approach to Face a Pandemic Crisis.

The outbreak of SARS-CoV-2 has drastically changed our everyday life and the life of scientists from all over the world. In the last year, the scientific community has faced this worldwide threat using any tool available in order to find an effective response. The recent formulation, production, and ongoing administration of vaccines represent a starting point in the battle against SARS-CoV-2, but they cannot be the only aid available. In this regard, the use of drugs capable to mitigate and fight the virus is a crucial aspect of the pharmacological strategy. Among the plethora of approved drugs, a consistent element is a heterocyclic framework inside its skeleton. Heterocycles have played a pivotal role for decades in the pharmaceutical industry due to their high bioactivity derived from anticancer, antiviral, and anti-inflammatory capabilities. In this context, the development of new performing and sustainable synthetic strategies to obtain heterocyclic molecules has become a key focus of scientists. In this review, we present the recent trends in metal-promoted heterocyclization, and we focus our attention on the construction of heterocycles associated with the skeleton of drugs targeting SARS-CoV-2 coronavirus.

Fast Approximations of Activation Functions in Deep Neural Networks when using Posit Arithmetic.

With increasing real-time constraints being put on the use of Deep Neural Networks (DNNs) by real-time scenarios, there is the need to review information representation. A very challenging path is to employ an encoding that allows a fast processing and hardware-friendly representation of information. Among the proposed alternatives to the IEEE 754 standard regarding floating point representation of real numbers, the recently introduced Posit format has been theoretically proven to be really promising in satisfying the mentioned requirements. However, with the absence of proper hardware support for this novel type, this evaluation can be conducted only through a software emulation. While waiting for the widespread availability of the Posit Processing Units (the equivalent of the Floating Point Unit (FPU)), we can already exploit the Posit representation and the currently available Arithmetic-Logic Unit (ALU) to speed up DNNs by manipulating the low-level bit string representations of Posits. As a first step, in this paper, we present new arithmetic properties of the Posit number system with a focus on the configuration with 0 exponent bits. In particular, we propose a new class of Posit operators called L1 operators, which consists of fast and approximated versions of existing arithmetic operations or functions (e.g., hyperbolic tangent (TANH) and extended linear unit (ELU)) only using integer arithmetic. These operators introduce very interesting properties and results: (i) faster evaluation than the exact counterpart with a negligible accuracy degradation; (ii) an efficient ALU emulation of a number of Posits operations; and (iii) the possibility to vectorize operations in Posits, using existing ALU vectorized operations (such as the scalable vector extension of ARM CPUs or advanced vector extensions on Intel CPUs). As a second step, we test the proposed activation function on Posit-based DNNs, showing how 16-bit down to 10-bit Posits represent an exact replacement for 32-bit floats while 8-bit Posits could be an interesting alternative to 32-bit floats since their performances are a bit lower but their high speed and low storage properties are very appealing (leading to a lower bandwidth demand and more cache-friendly code). Finally, we point out how small Posits (i.e., up to 14 bits long) are very interesting while PPUs become widespread, since Posit operations can be tabulated in a very efficient way (see details in the text).

A Flavone-Based Solvatochromic Probe with A Low Expected Perturbation Impact on the Membrane Physical State.

The study of the cell membrane is an ambitious and arduous objective since its physical state is regulated by a series of processes that guarantee its regular functionality. Among the different methods of analysis, fluorescence spectroscopy is a technique of election, non-invasive, and easy to use. Besides, molecular dynamics analysis (MD) on model membranes provides useful information on the possibility of using a new probe, following its positioning in the membrane, and evaluating the possible perturbation of the double layer. In this work, we report the rational design and the synthesis of a new fluorescent solvatochromic probe and its characterization in model membranes. The probe consists of a fluorescent aromatic nucleus of a 3-hydroxyflavone moiety, provided with a saturated chain of 18 carbon atoms and a zwitterionic head so to facilitate the anchoring to the polar heads of the lipid bilayer and avoid the complete internalization. It was possible to study the behavior of the probe in GUV model membranes by MD analysis and fluorescence microscopy, demonstrating that the new probe can efficiently be incorporated in the lipid bilayer, and give a color response, thanks to is solvatochromic properties. Moreover, MD simulation of the probe in the membrane supports the hypothesis of a reduced perturbation of the membrane physical state.

The alternative sigma factor SigF is a key player in the control of secretion mechanisms in Synechocystis sp. PCC 6803.

Cyanobacterial alternative sigma factors are crucial players in environmental adaptation processes, which may involve bacterial responses related to maintenance of cell envelope and control of secretion pathways. Here, we show that the Group 3 alternative sigma factor F (SigF) plays a pleiotropic role in Synechocystis sp. PCC 6803 physiology, with a major impact on growth and secretion mechanisms, such as the production of extracellular polysaccharides, vesiculation and protein secretion. Although ΔsigF growth was significantly impaired, the production of released polysaccharides (RPS) increased threefold to fourfold compared with the wild-type. ΔsigF exhibits also impairment in formation of outer-membrane vesicles (OMVs) and pili, as well as several other cell envelope alterations. Similarly, the exoproteome composition of ΔsigF differs from the wild-type both in amount and type of proteins identified. Quantitative proteomics (iTRAQ) and an in silico analysis of SigF binding motifs revealed possible targets/pathways under SigF control. Besides changes in protein levels involved in secretion mechanisms, our results indicated that photosynthesis, central carbon metabolism and protein folding/degradation mechanisms are altered in ΔsigF. Overall, this work provided new evidences about the role of SigF on Synechocystis physiology and associates this regulatory element with classical and non-classical secretion pathways.

Multivariate statistical analysis of chemical and electrochemical oscillators for an accurate frequency selection.

The effect of experimental parameters on the frequency of chemical oscillators has been systematically studied since the first observations of clock reactions. The approach is mainly based on univariate changes in one specific parameter while others are kept constant. The frequency is then monitored and the effect of each parameter is discussed separately. This type of analysis, however, does not take into account the multiple interactions among the controllable parameters and the synergic responses on the oscillation frequency. We have carried out a multivariate statistical analysis of chemical (BZ-ferroin catalyzed reaction) and electrochemical (Cu/Cu2O cathodic deposition) oscillators and identified the contributions of the experimental parameters on frequency variations. The BZ reaction presented a strong dependence on the initial concentration of sodium bromate and temperature, resulting in a frequency increase. The concentration of malonic acid, the organic substrate, affects the system but with lower intensity compared with the combination of sodium bromate and temperature. On the other hand, the Cu/Cu2O electrochemical oscillator was shown to be less sensitive to changes in the temperature. The applied current density and pH were the two parameters which most perturbed the system. Interestingly, the frequency behaved nonmonotonically with a quadratic dependence. The multivariate analysis of both oscillators exhibited significant differences - while the homogenous oscillator displayed a linear dependence with the factors, the heterogeneous one revealed a more complex dependence with quadratic terms. Our results may contribute, for instance, in the synthesis of self-organized materials in which an accurate frequency selection is required and, depending on its value, different physicochemical properties are obtained.

Catalyst-Free Synthesis of Polysubstituted 5-Acylamino-1,3-Thiazoles via Hantzsch Cyclization of α-Chloroglycinates.

A catalyst-free heterocyclization reaction of α-chloroglycinates with thiobenzamides or thioureas leading to 2,4-disubstituted-5-acylamino-1,3-thiazoles has been developed. The methodology provides straightforward access to valuable building blocks for pharmaceutically relevant compounds.

Lipid-Stabilized Water-Oil Interfaces Studied by Microfocusing Small-Angle X-ray Scattering.

Water-in-oil (w/o) simple emulsions are dispersed microconfined systems that find applications in many areas of advanced materials and biotechnology, such as the food industry, drug delivery, and cosmetics, to name but a few. In these systems, the structural and chemical properties of the boundary layer at the w/o interface are of paramount importance in determining functionality and stability. Recently, microfluidic methods have emerged as a valuable tool for fabricating monodisperse emulsion droplets. Because of the intrinsic flexibility of microfluidics, different interfaces can be obtained, and general principles governing their stability are needed to guide the experimental approach. Herein, we investigate the structural characteristics of the region encompassing the liquid/liquid (L/L) interface of w/o emulsions generated by a microfluidic device in the presence of phospholipid 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and other intercalating amphiphiles (dopants) using microfocused small-angle X-rays scattering (µ-SAXS). We show that phospholipids provide a stable and versatile boundary film of ∼100 µm whose basic units are swollen and uncorrelated DMPC bilayers. The internal arrangement of this interfacial film can be tuned by adding molecules with a different packing parameter, such as cholesterol, which is able to increase the stiffness of the lipid membranes and trigger interbilayer correlation.

Control of chemical chaos through medium viscosity in a batch ferroin-catalysed Belousov-Zhabotinsky reaction.

In this paper we show that the active interplay of nonlinear kinetics and transport phenomena in a chemical oscillator can be exploited to induce and control chaos. To this aim we use as a model system the ferroin-catalysed Belousov-Zhabotinsky (BZ) oscillating reaction, which is known to evolve to characteristic chaotic transient dynamics when carried out under batch and unstirred conditions. In particular, chemical chaos was found to appear and disappear by following a Ruelle-Takens-Newhouse (RTN) scenario. Here we use medium viscosity as a bifurcation parameter to tune the reaction-diffusion-convection (RDC) interplay and force the reaction in a specific sequence of dynamical regimes: either (i) periodic → quasi-periodic → chaotic or (ii) periodic → quasi-periodic or (iii) only periodic. The medium viscosity can be set by adding different amounts of surfactant (sodium dodecyl sulphate), known to have a little impact on the reaction mechanism, above its critical micelle concentration. Experimental results are supported by means of numerical simulations of a RDC model, which combines self-sustained oscillations to the related chemically-induced buoyancy convection.

Hydrogen production under salt stress conditions by a freshwater Rhodopseudomonas palustris strain.

Hydrogen represents a possible alternative energy carrier to face the growing request for energy and the shortage of fossil fuels. Photofermentation for the production of H2 constitutes a promising way for integrating the production of energy with waste treatments. Many wastes are characterized by high salinity, and polluted seawater can as well be considered as a substrate. Moreover, the application of seawater for bacterial culturing is considered cost-effective. The aims of this study were to assess the capability of the metabolically versatile freshwater Rhodopseudomonas palustris 42OL of producing hydrogen on salt-containing substrates and to investigate its salt stress response strategy, never described before. R. palustris 42OL was able to produce hydrogen in media containing up to 3 % added salt concentration and to grow in media containing up to 4.5 % salinity without the addition of exogenous osmoprotectants. While the hydrogen production performances in absence of sea salts were higher than in their presence, there was no significant difference in performances between 1 and 2 % of added sea salts. Nitrogenase expression levels indicated that the enzyme was not directly inhibited during salt stress, but a regulation of its expression may have occurred in response to salt concentration increase. During cell growth and hydrogen production in the presence of salts, trehalose was accumulated as a compatible solute; it protected the enzymatic functionality against salt stress, thus allowing hydrogen production. The possibility of producing hydrogen on salt-containing substrates widens the range of wastes that can be efficiently used in production processes.