PRC2-EZH1 contributes to circadian gene expression by orchestrating chromatin states and RNA polymerase II complex stability.

Circadian rhythmicity of gene expression is a conserved feature of cell physiology. This involves fine-tuning between transcriptional and post-transcriptional mechanisms and strongly depends on the metabolic state of the cell. Together these processes guarantee an adaptive plasticity of tissue-specific genetic programs. However, it is unclear how the epigenome and RNA Pol II rhythmicity are integrated. Here we show that the PcG protein EZH1 has a gateway bridging function in postmitotic skeletal muscle cells. On the one hand, the circadian clock master regulator BMAL1 directly controls oscillatory behavior and periodic assembly of core components of the PRC2-EZH1 complex. On the other hand, EZH1 is essential for circadian gene expression at alternate Zeitgeber times, through stabilization of RNA Polymerase II preinitiation complexes, thereby controlling nascent transcription. Collectively, our data show that PRC2-EZH1 regulates circadian transcription both negatively and positively by modulating chromatin states and basal transcription complex stability.

LINE-1 RNA triggers matrix formation in bone cells via a PKR-mediated inflammatory response.

Transposable elements (TEs) are mobile genetic modules of viral derivation that have been co-opted to become modulators of mammalian gene expression. TEs are a major source of endogenous dsRNAs, signaling molecules able to coordinate inflammatory responses in various physiological processes. Here, we provide evidence for a positive involvement of TEs in inflammation-driven bone repair and mineralization. In newly fractured mice bone, we observed an early transient upregulation of repeats occurring concurrently with the initiation of the inflammatory stage. In human bone biopsies, analysis revealed a significant correlation between repeats expression, mechanical stress and bone mineral density. We investigated a potential link between LINE-1 (L1) expression and bone mineralization by delivering a synthetic L1 RNA to osteoporotic patient-derived mesenchymal stem cells and observed a dsRNA-triggered protein kinase (PKR)-mediated stress response that led to strongly increased mineralization. This response was associated with a strong and transient inflammation, accompanied by a global translation attenuation induced by eIF2α phosphorylation. We demonstrated that L1 transfection reshaped the secretory profile of osteoblasts, triggering a paracrine activity that stimulated the mineralization of recipient cells.

Anisotropic Mechanical Response of Bovine Pericardium Membrane Through Bulge Test and In-Situ Confocal-Laser Scanning.

In this work, we present a new experimental setup for the assessment of the anisotropic properties of Bovine Pericardium (BP) membranes. The chemically fixed BP samples have been subjected to a bulge test with in situ confocal laser scanning at increasing applied pressure. The high resolution topography provided by the confocal laser scanning has allowed to obtain a quantitative measure of the bulge displacement; after polynomial fitting, principal curvatures have been obtained and a degree of anisotropy (DA) has been defined as the normalized difference between the maximum and minimum principal curvatures. The experiments performed on the BP membranes have allowed us to obtain pressure-displacement data which clearly exhibit distinct principal curvatures indicating an anisotropic response. A comparison with curvatures data obtained on isotropic Nitrile Buthadiene Rubber (NBR) samples has confirmed the effectiveness of the experimental setup for this specific purpose. Numerical simulations of the bulge tests have been performed with the purpose of identifying a range of constitutive parameters which well describes the obtained range of DA on the BP membranes. The DA values have been partially validated with biaxial tests available in literature and with suitably performed uni-axial tensile tests.

New insights into the functional role of retrotransposon dynamics in mammalian somatic cells.

Retrotransposons are genetic elements present across all eukaryotic genomes. While their role in evolution is considered as a potentially beneficial natural source of genetic variation, their activity is classically considered detrimental due to their potentially harmful effects on genome stability. However, studies are increasingly shedding light on the regulatory function and beneficial role of somatic retroelement reactivation in non-pathological contexts. Here, we review recent findings unveiling the regulatory potential of retrotransposons, including their role in noncoding RNA transcription, as modulators of mammalian transcriptional and epigenome landscapes. We also discuss technical challenges in deciphering the multifaceted activity of retrotransposable elements, highlighting an unforeseen central role of this neglected portion of the genome both in early development and in adult life.

Transcriptomic and Network Analyses Reveal Immune Modulation by Endocannabinoids in Approach/Avoidance Traits.

Approach and avoidance (A/A) tendencies are stable behavioral traits in responding to rewarding and fearful stimuli. They represent the superordinate division of emotion, and individual differences in such traits are associated with disease susceptibility. The neural circuitry underlying A/A traits is retained to be the cortico-limbic pathway including the amygdala, the central hub for the emotional processing. Furthermore, A/A-specific individual differences are associated with the activity of the endocannabinoid system (ECS) and especially of CB1 receptors whose density and functionality in amygdala differ according to A/A traits. ECS markedly interacts with the immune system (IS). However, how the interplay between ECS and IS is associated with A/A individual differences is still ill-defined. To fill this gap, here we analyzed the interaction between the gene expression of ECS and immune system (IS) in relation to individual differences. To unveil the deep architecture of ECS-IS interaction, we performed cell-specific transcriptomics analysis. Differential gene expression profiling, functional enrichment, and protein-protein interaction network analyses were performed in amygdala pyramidal neurons of mice showing different A/A behavioral tendencies. Several altered pro-inflammatory pathways were identified as associated with individual differences in A/A traits, indicating the chronic activation of the adaptive immune response sustained by the interplay between endocannabinoids and the IS. Furthermore, results showed that the interaction between the two systems modulates synaptic plasticity and neuronal metabolism in individual difference-specific manner. Deepening our knowledge about ECS/IS interaction may provide useful targets for treatment and prevention of psychopathology associated with A/A traits.

Stiffness of Fluid and Gel Phase Lipid Nanovesicles: Weighting the Contributions of Membrane Bending Modulus and Luminal Pressurization.

The mechanical properties of biogenic membranous compartments are thought to be relevant in numerous biological processes; however, their quantitative measurement remains challenging for most of the already available force spectroscopy (FS)-based techniques. In particular, the debate on the mechanics of lipid nanovesicles and on the interpretation of their mechanical response to an applied force is still open. This is mostly due to the current lack of a unified model being able to describe the mechanical response of both gel and fluid phase lipid vesicles and to disentangle the contributions of membrane rigidity and luminal pressure. In this framework, we herein propose a simple model in which the interplay of membrane rigidity and luminal pressure to the overall vesicle stiffness is described as a series of springs; this approach allows estimating these two contributions for both gel and fluid phase liposomes. Atomic force microscopy-based FS, performed on both vesicles and supported lipid bilayers, is exploited for obtaining all the parameters involved in the model. Moreover, the use of coarse-grained full-scale molecular dynamics simulations allowed for better understanding of the differences in the mechanical responses of gel and fluid phase bilayers and supported the experimental findings. The results suggest that the pressure contribution is similar among all the probed vesicle types; however, it plays a dominant role in the mechanical response of lipid nanovesicles presenting a fluid phase membrane, while its contribution becomes comparable to the one of membrane rigidity in nanovesicles with a gel phase lipid membrane. The results presented herein offer a simple way to quantify two of the most important parameters in vesicle nanomechanics (membrane rigidity and internal pressurization), and as such represent a first step toward a currently unavailable, unified model for the mechanical response of gel and fluid phase lipid nanovesicles.

Green Biocompatible Method for the Synthesis of Collagen/Chitin Composites to Study Their Composition and Assembly Influence on Fibroblasts Growth.

A green biocompatible route for the deposition and simultaneous assembly, by pH increment, of collagen/chitin composites was proposed. Both assembled and unassembled samples with different collagen/chitin ratios were synthesized, maintaining the ß-chitin polymorph. The first set showed a microfibrous organization with compositional submicron homogeneity. The second set presented a nanohomogeneous composition based on collagen nanoaggregates and chitin nanofibrils. The sets were tested as scaffolds for fibroblast growth (NIH-3T3) to study the influence of composition and assembly. In the unassembled scaffolds, the positive influence of collagen on cell growth mostly worn out in 48 h, while the addition of chitin enhanced this effect for over 72 h. The assembled samples showed higher viability at 24 h but a less positive effect on viability along the time. This work highlighted critical aspects of the influence that composition and assembly has on fibroblast growth, a knowledge worth exploiting in scaffold design and preparation.

AFM-Based High-Throughput Nanomechanical Screening of Single Extracellular Vesicles.

The mechanical properties of extracellular vesicles (EVs) are known to influence their biological function, in terms of, e.g., cellular adhesion, endo/exocytosis, cellular uptake, and mechanosensing. EVs have a characteristic nanomechanical response which can be probed via force spectroscopy (FS) and exploited to single them out from nonvesicular contaminants or to discriminate between subtypes. However, measuring the nanomechanical characteristics of individual EVs via FS is a labor-intensive and time-consuming task, usually limiting this approach to specialists. Herein, we describe a simple atomic force microscopy based experimental procedure for the simultaneous nanomechanical and morphological analysis of several hundred individual nanosized EVs within the hour time scale, using basic AFM equipment and skills and only needing freely available software for data analysis. This procedure yields a "nanomechanical snapshot" of an EV sample which can be used to discriminate between subpopulations of vesicular and nonvesicular objects in the same sample and between populations of vesicles with similar sizes but different mechanical characteristics. We demonstrate the applicability of the proposed approach to EVs obtained from three very different sources (human colorectal carcinoma cell culture, raw bovine milk, and Ascaris suum nematode excretions), recovering size and stiffness distributions of individual vesicles in a sample. EV stiffness values measured with our high-throughput method are in very good quantitative accord with values obtained by FS techniques which measure EVs one at a time. We show how our procedure can detect EV samples contamination by nonvesicular aggregates and how it can quickly attest the presence of EVs even in samples for which no established assays and/or commercial kits are available (e.g., Ascaris EVs), thus making it a valuable tool for the rapid assessment of EV samples during the development of isolation/enrichment protocols by EV researchers. As a side observation, we show that all measured EVs have a strikingly similar stiffness, further reinforcing the hypothesis that their mechanical characteristics could have a functional role.

Gold nanoparticles interacting with synthetic lipid rafts: an AFM investigation.

Inorganic nanoparticles (NPs) represent promising examples of engineered nanomaterials, providing interesting biomedical solutions in several fields, like therapeutics and diagnostics. Despite the extensive number of investigations motivated by their remarkable potential for nanomedicinal applications, the interactions of NPs with biological interfaces are still poorly understood. The effect of NPs on living organisms is mediated by biological barriers, such as the cell plasma membrane, whose lateral heterogeneity is thought to play a prominent role in NPs adsorption and uptake pathways. In particular, biological membranes feature the presence of rafts, that is segregated lipid micro and/or nanodomains in the so-called liquid ordered phase (Lo ), immiscible with the surrounding liquid disordered phase (Ld ). Rafts are involved in various biological functions and act as sites for the selective adsorption of materials on the membrane. Indeed, the thickness mismatch present along their boundaries generates energetically favourable conditions for the adsorption of NPs. Despite its clear implications in NPs internalisation processes and cytotoxicity, a direct proof of the selective adsorption of NPs along the rafts' boundaries is still missing to date. Here we use multicomponent supported lipid bilayers (SLBs) as reliable synthetic models, reproducing the nanometric lateral heterogeneity of cell membranes. After being characterised by atomic force microscopy (AFM) and neutron reflectivity (NR), multidomain SLBs are challenged by prototypical inorganic nanoparticles, that is citrated gold nanoparticles (AuNPs), under simplified and highly controlled conditions. By exploiting AFM, we demonstrate that AuNPs preferentially target lipid phase boundaries as adsorption sites. The herein reported study consolidates and extends the fundamental knowledge on NPs-membrane interactions, which constitute a key aspect to consider when designing NPs-related biomedical applications. LAY DESCRIPTION: Inorganic nanoparticles (NPs) represent promising examples of engineered nanomaterials, offering interesting biomedical solutions in multiple fields like therapeutics and diagnostics. Despite being extensively investigated due to their remarkable potential for nanomedicinal applications, the interaction of NPs with biological systems is in several cases still poorly understood. The interaction of NPs with living organisms is mediated by biological barriers, such as the cell plasma membrane. Supported lipid bilayers (SLBs) represent suitable synthetic membrane models for studying the physicochemical properties of natural interfaces and their interaction with inorganic nanomaterials under simplified and controlled conditions. Recently, multicomponent SLBs were developed in order to mimic the lateral heterogeneity of most biological membranes. In particular, biological membranes feature the presence of rafts, that is segregated lipid micro and/or nanodomains, enriched in cholesterol, sphingomyelin, saturated glycerophospholipids and glycosphingolipids: these lipids segregate in the so-called liquid-ordered phase (Lo ), characterised by a high molecular packing degree, which promotes the phase separation from the surrounding liquid-crystalline (disordered, Ld ) phase, where the intermolecular mobility is increased. Rafts are thought to participate in the formation and targeting of nano-sized biogenic lipid vesicles and are also actively involved in multiple membrane processes. Indeed, Lo -Ld phase boundaries represent high energy areas, providing active sites for the preferential adsorption of external material. The selective adsorption of NPs along the phase boundaries of rafted membranes has been theorised and indirectly probed by different research groups; however, a direct proof of this phenomenon is still missing to date. We herein exploit atomic force microscopy (AFM) to directly visualise the preferential adsorption of gold nanoparticles (AuNPs) along the phase boundaries of multicomponent SLBs (previously characterised by neutron reflectivity), obtained from synthetic vesicles containing both an Ld and an Lo phase. The quantitative localisation and morphometry of AuNPs adsorbed on the SLB reveal important information on their interaction with the lipid matrix and directly prove the already theorised differential NPs-lipid interaction at the phase boundaries. The presented results could help the development of future NP-based applications, involving NPs adsorption on membranes with nanoscale phase segregations.

Stable and Biocompatible Monodispersion of C60 in Water by Peptides.

The lack of solubility in water and the formation of aggregates hamper many opportunities for technological exploitation of C60. Here, different peptides were designed and synthesized with the aim of monomolecular dispersion of C60 in water. Phenylalanines were used as recognizing moieties, able to interact with C60 through π-π stacking, while a varying number of glycines were used as spacers, to connect the two terminal phenylalanines. The best performance in the dispersion of C60 was obtained with the FGGGF peptidic nanotweezer at a pH of 12. A full characterization of this adduct was carried out. The peptides disperse C60 in water with high efficiency, and the solutions are stable for months both in pure water and in physiological environments. NMR measurements demonstrated the ability of the peptides to interact with C60. AFM measurements showed that C60 is monodispersed. Electrospray ionization mass spectrometry determined a stoichiometry of C60@(FGGGF)4. Molecular dynamics simulations showed that the peptides assemble around the C60 cage, like a candy in its paper wrapper, creating a supramolecular host able to accept C60 in the cavity. The peptide-wrapped C60 is fully biocompatible and the C60 "dark toxicity" is eliminated. C60@(FGGGF)4 shows visible light-induced reactive oxygen species (ROS) generation at physiological saline concentrations and reduction of the HeLa cell viability in response to visible light irradiation.

ß-Chitin Nanofibril Self-Assembly in Aqueous Environments.

Chitin is one of the most studied biopolymers but the understanding of how it assembles from molecules to microfibers is still limited. Organisms are able to assemble chitin with precise control over polymorphism, texture, and final morphology. The produced hierarchical structure leads to materials with outstanding mechanical properties. In this study, the self-assembly in aqueous solutions of ß-chitin nanofibrils, as far as possible similar to their native state, is investigated. These nanofibrils increase their tendency to self-assemble in fibers, up to millimetric length and ≈10 µm thickness, with the pH increasing from 3 to 8, forming loosely organized bundles as observed using cryo-transmission electron microscopy. The knowledge from this study contributes to the understanding of the self-assembly process that follows chitin once extruded from cells in living organisms. Moreover, it describes a model system which can be used to investigate how other biomolecules can affect the self-assembly of chitin nanofibrils.

Spatial confinement induces hairpins in nicked circular DNA.

In living cells, DNA is highly confined in space with the help of condensing agents, DNA binding proteins and high levels of supercoiling. Due to challenges associated with experimentally studying DNA under confinement, little is known about the impact of spatial confinement on the local structure of the DNA. Here, we have used well characterized slits of different sizes to collect high resolution atomic force microscopy images of confined circular DNA with the aim of assessing the impact of the spatial confinement on global and local conformational properties of DNA. Our findings, supported by numerical simulations, indicate that confinement imposes a large mechanical stress on the DNA as evidenced by a pronounced anisotropy and tangent-tangent correlation function with respect to non-constrained DNA. For the strongest confinement we observed nanometer sized hairpins and interwound structures associated with the nicked sites in the DNA sequence. Based on these findings, we propose that spatial DNA confinement in vivo can promote the formation of localized defects at mechanically weak sites that could be co-opted for biological regulatory functions.

Tuning Mechanical Properties of Pseudopeptide Supramolecular Hydrogels by Graphene Doping.

Supramolecular hydrogels, obtained from small organic molecules, may be advantageous over polymeric ones for several applications, because these materials have some peculiar properties that differentiate them from the traditional polymeric hydrogels, such as elasticity, thixotropy, self-healing propensity, and biocompatibility. We report here the preparation of strong supramolecular pseudopeptide-based hydrogels that owe their strength to the introduction of graphene in the gelling mixture. These materials proved to be strong, stable, thermoreversible and elastic. The concentration of the gelator, the degree of graphene doping, and the nature of the trigger are crucial to get hydrogels with the desired properties, where a high storage modulus coexists with a good thixotropic behavior. Finally, NIH-3T3 cells were used to evaluate the cell response to the presence of the most promising hydrogels. The hydrogels biocompatibility remains good, if a small degree of graphene doping is introduced.

The analysis of the different functions of starch-phosphorylating enzymes during the development of Arabidopsis thaliana plants discloses an unexpected role for the cytosolic isoform GWD2.

The genome of Arabidopsis thaliana encodes three glucan, water dikinases. Glucan, water dikinase 1 (GWD1; EC 2.7.9.4) and phosphoglucan, water dikinase (PWD; EC 2.7.9.5) are chloroplastic enzymes, while glucan, water dikinase 2 (GWD2) is cytosolic. Both GWDs and PWD catalyze the addition of phosphate groups to amylopectin chains at the surface of starch granules, changing its physicochemical properties. As a result, GWD1 and PWD have a positive effect on transitory starch degradation at night. Because of its cytosolic localization, GWD2 does not have the same effect. Single T-DNA mutants of either GWD1 or PWD or GWD2 have been analyzed during the entire life cycle of A. thaliana. We report that the three dikinases are all important for proper seed development. Seeds from gwd2 mutants are shrunken, with the epidermal cells of the seed coat irregularly shaped. Moreover, gwd2 seeds contain a lower lipid to protein ratio and are impaired in germination. Similar seed phenotypes were observed in pwd and gwd1 mutants, except for the normal morphology of epidermal cells in gwd1 seed coats. The gwd1, pwd and gwd2 mutants were also very similar in growth and flowering time when grown under continuous light and all three behaved differently from wild-type plants. Besides pinpointing a novel role of GWD2 and PWD in seed development, this analysis suggests that the phenotypic features of the dikinase mutants in A. thaliana cannot be explained solely in terms of defects in leaf starch degradation at night.

Self-organization of functional materials in confinement.

This Account aims to describe our experience in the use of patterning techniques for addressing the self-organization processes of materials into spatially confined regions on technologically relevant surfaces. Functional properties of materials depend on their chemical structure, their assembly, and spatial distribution at the solid state; the combination of these factors determines their properties and their technological applications. In fact, by controlling the assembly processes and the spatial distribution of the resulting structures, functional materials can be guided to technological and specific applications. We considered the principal self-organizing processes, such as crystallization, dewetting and phase segregation. Usually, these phenomena produce defective molecular films, compromising their use in many technological applications. This issue can be overcome by using patterning techniques, which induce molecules to self-organize into well-defined patterned structures, by means of spatial confinement. In particular, we focus our attention on the confinement effect achieved by stamp-assisted deposition for controlling size, density, and positions of material assemblies, giving them new chemical/physical functionalities. We review the methods and principles of the stamp-assisted spatial confinement and we discuss how they can be advantageously exploited to control crystalline order/orientation, dewetting phenomena, and spontaneous phase segregation. Moreover, we highlight how physical/chemical properties of soluble functional materials can be driven in constructive ways, by integrating them into operating technological devices.

Improvement of Topical Palmitoylethanolamide Anti-Inflammatory Activity by Pegylated Prodrugs.

A small library of polyethylene glycol esters of palmitoylethanolamide (PEA) was synthesized with the aim of improving the pharmacokinetic profile of the parent drug after topical administration. Synthesized prodrugs were studied for their skin accumulation, pharmacological activities, in vitro chemical stability, and in silico enzymatic hydrolysis. Prodrugs proved to be able to delay and prolong the pharmacological activity of PEA by modification of its skin accumulation profile. Pharmacokinetic improvements were particularly evident when specific structural requirements, such as flexibility and reduced molecular weight, were respected. Some of the synthesized prodrugs prolonged the pharmacological effects 5 days following topical administration, while a formulation composed by PEA and two pegylated prodrugs showed both rapid onset and long-lasting activity, suggesting the potential use of polyethylene glycol prodrugs of PEA as a suitable candidate for the treatment of skin inflammatory diseases.

Customizing properties of ß-chitin in squid pen (gladius) by chemical treatments.

The squid pen (gladius) from the Loligo vulgaris was used for preparation of ß-chitin materials characterized by different chemical, micro- and nano-structural properties that preserved, almost completely the macrostructural and the mechanical ones. The ß-chitin materials obtained by alkaline treatment showed porosity, wettability and swelling that are a function of the duration of the treatment. Microscopic, spectroscopic and synchrotron X-ray diffraction techniques showed that the chemical environment of the N-acetyl groups of the ß-chitin chains changes after the thermal alkaline treatment. As a consequence, the crystalline packing of the ß-chitin is modified, due to the intercalation of water molecules between ß-chitin sheets. Potential applications of these ß-chitin materials range from the nanotechnology to the regenerative medicine. The use of gladii, which are waste products of the fishing industry, has also important environmental implications.

Molecularly imprinted polymer coupled to UHPLC-MS/MS for the analysis of phomopsins in lupin samples.

The demand for plant-based protein sources in the food industry has significantly increased in recent years, leading to the introduction of legume-based products as meat substitutes. However, concerns regarding food quality have emerged, particularly related to the presence of mycotoxins. This study addresses the need for the sensitive detection of phomopsins (PHOs), a class of peptide-based toxins. A selective extraction method using molecularly imprinted polymer (MIP) coupled with ultra-high performance liquid chromatography and tandem mass spectrometry (UHPLC-MS/MS) was focused on the most toxic Phomopsin A (PHO-A). A rapid ultrasonochemical synthesis of MIP (5 min) was proposed and its performance was optimized in response to various factors, including the choice of dummy template and the selection of the monomer. The methacrylic acid-vinyl pyridine (MAA-VP) MIP exhibited high selectivity and affinity for PHO-A. The method was tested in lupin samples and the validation, according to SANTE/11312/2021 international guidelines, gave excellent recovery (80-90 %), low matrix effects, and high accuracy and precision. Real samples analysis confirmed the presence of PHO-A in artificially fungal inoculated lupins, with levels ranging from 0.377 to 0.576 mg kg-1. In order to identify further PHOs, a semi-untargeted approach using multiple reaction monitoring-information dependent acquisition-enhanced product ion (MRM-IDA-EPI) was developed. PHO-B, PHO-D, PHO-E and PHO-P, rarely previously reported in lupin matrix, were tentatively identified. This study accounts for the effectiveness of MIP-based extraction coupled with UHPLC-triple quadrupole with linear ionic trap-MS/MS (UHPLC-QqQ-LIT-MS/MS) for quantification of PHO-A and putative detection of other PHOs, offering a promising method for investigating this class of toxins in food.

Fingerprinting alkaloids for traceability: Semi-untargeted UHPLC-MS/MS approach in raw lupins as a case study.

Lupin seeds are recognized for their nutritional value and potential health benefits, but they contain also a significant amount of alkaloids, an anti-nutritive class of compounds, which vary significantly in composition within and between species due to environmental factors. In this study, we developed a predictive multi-experiment approach using ultra-high performance liquid chromatography coupled with triple quadrupole with linear ionic trap tandem mass spectrometry (UHPLC-QqQ-LIT-MS/MS) for comprehensive alkaloid profiling and geographical classification of Lupinus albus L. samples originating from four different Italian regions. Six targeted quinolizidine alkaloids were detected and 21 other alkaloids were putatively identified. Hierarchical Cluster Analysis (HCA) and partial least squares discriminant analysis (PLS-DA) were applied to explore the data structure and successfully classify samples according to their geographical origin. The data demonstrate the efficacy of the developed approach in providing valuable insights in alkaloid profiles of lupin seeds and their potential as markers for geographical traceability.