Protocol for observing microtubules and microtubule ends in both fixed and live primary microglia cells.

Microtubule dynamics and orientation have crucial roles in many vital cellular processes. However, functional live imaging of microtubules and/or microtubule ends in primary microglia can be challenging. Here, we present a protocol for observing microtubules and microtubule ends in both fixed and live primary microglia cells. We describe steps for microglia culture and in vitro stimulation, SiR-tubulin labeling, lentivirus preparation, live imaging, immunostaining, and image acquisition. We also provide procedures for SiR-tubulin, EB3-EGFP, and EB1 analyses. For complete details on the use and execution of this protocol, please refer to Rosito et al. (2023).1.

Microglia reactivity entails microtubule remodeling from acentrosomal to centrosomal arrays.

Microglia reactivity entails a large-scale remodeling of cellular geometry, but the behavior of the microtubule cytoskeleton during these changes remains unexplored. Here we show that activated microglia provide an example of microtubule reorganization from a non-centrosomal array of parallel and stable microtubules to a radial array of more dynamic microtubules. While in the homeostatic state, microglia nucleate microtubules at Golgi outposts, and activating signaling induces recruitment of nucleating material nearby the centrosome, a process inhibited by microtubule stabilization. Our results demonstrate that a hallmark of microglia reactivity is a striking remodeling of the microtubule cytoskeleton and suggest that while pericentrosomal microtubule nucleation may serve as a distinct marker of microglia activation, inhibition of microtubule dynamics may provide a different strategy to reduce microglia reactivity in inflammatory disease.

Spatial coherence of light inside three-dimensional media.

Speckle is maybe the most fundamental interference effect of light in disordered media, giving rise to fascinating physical phenomena and cutting edge applications. While speckle formed outside a sample is easily measured and analysed, true bulk speckle, as formed inside random media, is difficult to investigate directly due to the obvious issue of physical access. Furthermore, its proper theoretical description poses enormous challenges. Here we report on the first direct measurements of spatially resolved intensity correlations of light inside a disordered medium, using embedded DNA strings decorated with emitters separated by a controlled nanometric distance. Our method provides in situ access to fundamental properties of bulk speckles as their size and polarization degrees of freedom, both of which are found to deviate significantly from theoretical predictions. The deviations are explained, by comparison with rigorous numerical calculations, in terms of correlations among polarization components and non-universal near-field contributions at the nanoscale.

Chemo-physical properties of asbestos bodies in human lung tissues studied at the nano-scale by non-invasive, label free x-ray imaging and spectroscopic techniques.

In the lungs, asbestos develops an Fe-rich coating (Asbestos Body, AB) that becomes the actual interface between the foreign fibers and the host organism. Conventional approaches to study ABs require an invasive sample preparation that can alter them. In this work, a novel combination of x-ray tomography and spectroscopy allowed studying unaltered lung tissue samples with chrysotile and crocidolite asbestos. The thickness and mass density maps of the ABs obtained by x-ray tomography were used to derive a truly quantitative elemental analysis from scanning x-ray fluorescence spectroscopy data. The average mass density of the ABs is compatible with that of highly loaded ferritin, or hemosiderin. The composition of all ABs analyzed was similar, with only minor differences in the relative elemental fractions. Silicon concentration decreased in the core-to-rim direction, indicating a possible partial dissolution of the inner fiber. The Fe content in the ABs was higher than that possibly contained in chrysotile and crocidolite. This finding opens two opposite scenarios, the first with Fe coming from the fiber bulk and concentrating on the surface as long as the fiber dissolves, the second where the Fe that takes part to the formation of the AB originates from the host organism Fe-pool.

Pressure-induced amorphization and existence of molecular and polymeric amorphous forms in dense SO2.

We report here the pressure-induced amorphization and reversible structural transformation between two amorphous forms of SO2: molecular amorphous and polymeric amorphous, with the transition found at 26 GPa over a broad temperature regime, 77 K to 300 K. The transformation was observed by both Raman spectroscopy and X-ray diffraction in a diamond anvil cell. The results were corroborated by ab initio molecular dynamics simulations, where both forward and reverse transitions were detected, opening a window to detailed analysis of the respective local structures. The high-pressure polymeric amorphous form was found to consist mainly of disordered polymeric chains made of three-coordinated sulfur atoms connected via oxygen atoms, with few residual intact molecules. This study provides an example of polyamorphism in a system consisting of simple molecules with multiple bonds.

Light controls stamen elongation via cryptochromes, phytochromes and COP1 through HY5 and HYH.

In Arabidopsis, stamen elongation, which ensures male fertility, is controlled by the auxin response factor ARF8, which regulates the expression of the auxin repressor IAA19. Here, we uncover a role for light in controlling stamen elongation. By an extensive genetic and molecular analysis we show that the repressor of light signaling COP1, through its targets HY5 and HYH, controls stamen elongation, and that HY5 - oppositely to ARF8 - directly represses the expression of IAA19 in stamens. In addition, we show that in closed flower buds, when light is shielded by sepals and petals, the blue light receptors CRY1/CRY2 repress stamen elongation. Coherently, at flower disclosure and in subsequent stages, stamen elongation is repressed by the red and far-red light receptors PHYA/PHYB. In conclusion, different light qualities - sequentially perceived by specific photoreceptors - and the downstream COP1-HY5/HYH module finely tune auxin-induced stamen elongation and thus male fertility.

Dimethyl Fumarate Reduces Microglia Functional Response to Tissue Damage and Favors Brain Iron Homeostasis.

Dimethyl fumarate (DMF) is the only available approved drug for first line treatment of multiple sclerosis (MS), a lethal condition impairing central nervous system (CNS). To date, however, little is known of its mechanisms of action. Only recently, it has been suggested that DMF exerts neuroprotective effects acting as an immunomodulator and that it may alter the activation state of microglia cells, crucial in MS pathogenesis. However, DMF effects on microglia functions are still not well determined. Here, we examine the effects of DMF treatment on microglia functional activities, as phenotype, morphology, processes motility and rearrangement, migration, ATP response and iron uptake in mouse primary microglia culture and acute hippocampal slices. We found that DMF treatment reduces microglia motility, downregulating functional response to ATP, increases ferritin uptake and pushes microglia towards an anti-inflammatory phenotype, thus reducing its proinflammatory reactivity in response to tissue damage. These results highlight the effects of this compound on microglia functions and provide new insights on the mechanism of action of DMF in MS treatment.

SMO-M2 mutation does not support cell-autonomous Hedgehog activity in cerebellar granule cell precursors.

Growth and patterning of the cerebellum is compromised if granule cell precursors do not properly expand and migrate. During embryonic and postnatal cerebellar development, the Hedgehog pathway tightly regulates granule cell progenitors to coordinate appropriate foliation and lobule formation. Indeed, granule cells impairment or defects in the Hedgehog signaling are associated with developmental, neurodegenerative and neoplastic disorders. So far, scant and inefficient cellular models have been available to study granule cell progenitors, in vitro. Here, we validated a new culture method to grow postnatal granule cell progenitors as hedgehog-dependent neurospheres with prolonged self-renewal and ability to differentiate into granule cells, under appropriate conditions. Taking advantage of this cellular model, we provide evidence that Ptch1-KO, but not the SMO-M2 mutation, supports constitutive and cell-autonomous activity of the hedgehog pathway.

Simple-to-Complex Transformation in Liquid Rubidium.

We investigated the atomic structure of liquid Rb along an isothermal path at 573 K, up to 23 GPa, by X-ray diffraction measurements. By raising the pressure, we observed a liquid-liquid transformation from a simple metallic liquid to a complex one. The transition occurs at 7.5 ± 1 GPa which is slightly above the first maximum of the T-P melting line. This transformation is traced back to the density-induced hybridization of highest electronic orbitals leading to the accumulation of valence electrons between Rb atoms and to the formation of interstitial atomic shells, a behavior that Rb shares with Cs and is likely to be common to all alkali metals.

Muscle Expression of SOD1G93A Triggers the Dismantlement of Neuromuscular Junction via PKC-Theta.

AIM: Neuromuscular junction (NMJ) represents the morphofunctional interface between muscle and nerve. Several chronic pathologies such as aging and neurodegenerative diseases, including muscular dystrophy and amyotrophic lateral sclerosis, display altered NMJ and functional denervation. However, the triggers and the molecular mechanisms underlying the dismantlement of NMJ remain unclear. RESULTS: Here we provide evidence that perturbation in redox signaling cascades, induced by muscle-specific accumulation of mutant SOD1G93A in transgenic MLC/SOD1G93A mice, is causally linked to morphological alterations of the neuromuscular presynaptic terminals, high turnover rate of acetylcholine receptor, and NMJ dismantlement. The analysis of potential molecular mechanisms that mediate the toxic activity of SOD1G93A revealed a causal link between protein kinase Cθ (PKCθ) activation and NMJ disintegration. INNOVATION: The study discloses the molecular mechanism that triggers functional denervation associated with the toxic activity of muscle SOD1G93A expression and suggests the possibility of developing a new strategy to counteract age- and pathology-associated denervation based on pharmacological inhibition of PKCθ activity. CONCLUSIONS: Collectively, these data indicate that muscle-specific accumulation of oxidative damage can affect neuromuscular communication and induce NMJ dismantlement through a PKCθ-dependent mechanism. Antioxid. Redox Signal. 28, 1105-1119.

Excimer based fluorescent pyrene-ferritin conjugate for protein oligomerization studies and imaging in living cells.

Ferritin self-assembly has been widely exploited for the synthesis of a variety of nanoparticles for drug-delivery and diagnostic applications. However, despite the crucial role of ferritin self-assembly mechanism for probes encapsulation, little is known about the principles behind the oligomerization mechanism. In the present work, the novel "humanized" chimeric Archaeal ferritin HumAfFt, displaying the transferrin receptor-1 (TfR1) recognition motif typical of human H homopolymer and the unique salt-triggered oligomerization properties of Archaeoglobus fulgidus ferritin (AfFt), was site-selectively labeled with N-(1-pyrenyl)maleimide on a topologically selected cysteine residue inside the protein cavity, next to the dimer interface. Pyrene characteristic fluorescence features were exploited to investigate the transition from a dimeric to a cage-like 24-meric state and to visualize the protein in vitro by two photon fluorescence microscopy. Indeed, pyrene fluorescence changes upon ferritin self-assembly allowed to establish, for the first time, the kinetic and thermodynamic details of the archaeal ferritins oligomerization mechanism. In particular, the magnesium induced oligomerization proved to be faster than the monovalent cation-triggered process, highly cooperative, complete at low MgCl2 concentrations, and reversed by treatment with EDTA. Moreover, pyrene intense excimer fluorescence was successfully visualized in vitro by two photon fluorescence microscopy as pyrene-labeled HumAfFt was actively uptaken into HeLa cells by human transferrin receptor TfR1 recognition, thus representing a unique nano-device building block for two photon fluorescence cell imaging.

Structure of Water in Zn2+ Aqueous Solutions from Ambient Conditions up to the Gigapascal Pressure Range: A XANES and Molecular Dynamics Study.

The structural modifications induced on a 0.5 M Zn2+ aqueous solution by increasing the pressure to 6.4 GPa were investigated using a combination of X-ray absorption near edge structure (XANES) spectroscopy and molecular dynamics (MD) simulations. The Zn K-edge XANES experimental spectra show two different trends depending on the pressure and temperature conditions of the system. On the one hand, when the pressure is increased to 1.0 GPa while keeping the temperature at 300 K, the highly structured nature of Zn2+ second hydration shell is preserved. On the other hand, when the Zn2+ aqueous solution is simultaneously pressurized and heated to follow the melting curve above 1.0 GPa, the Zn2+ second shell loses its high degree of structuring and becomes much more disordered and unstructured. These results are confirmed by the analysis of MD simulations of Zn2+ aqueous solutions under high pressure. By combining distance and angular distribution functions it is possible to highlight the loss of water structuring in the Zn2+ second coordination shell that takes place upon pressurization and heating. A progressive crowding of the Zn2+ second shell is observed with increasing pressure; the water structure becomes remarkably different from that found at ambient conditions, and for pressure values higher than 1.0 GPa the tetrahedral arrangements of water molecules is highly distorted. Moreover, MD simulations of Zn2+ aqueous solutions performed at 1.0 GPa and at increasing temperature values have shown that the loss of water structuring in the Zn2+ second coordination shell observed by simultaneously pressurizing and heating is due to a combined effect of pressure and temperature, both producing an increase of the Zn2+ second-shell disorder.

Switching off hydrogen-bond-driven excitation modes in liquid methanol.

Hydrogen bonding plays an essential role on intermolecular forces, and consequently on the thermodynamics of materials defined by this elusive bonding character. It determines the property of a vital liquid as water as well as many processes crucial for life. The longstanding controversy on the nature of the hydrogen bond (HB) can be settled by looking at the effect of a vanishing HB interaction on the microscopic properties of a given hydrogen-bonded fluid. This task suits the capabilities of computer simulations techniques, which allow to easily switch off HB interactions. We then use molecular dynamics to study the microscopic properties of methanol, a prototypical HB liquid. Fundamental aspects of the dynamics of methanol at room temperature were contextualised only very recently and its rich dynamics was found to have striking analogies with that of water. The lower temperature (200 K) considered in the present study led us to observe that the molecular centre-of-mass dynamics is dominated by four modes. Most importantly, the computational ability to switch on and off hydrogen bonds permitted us to identify which, among these modes, have a pure HB-origin. This clarifies the role of hydrogen bonds in liquid dynamics, disclosing new research opportunities and unexplored interpretation schemes.

The mutant p53-ID4 complex controls VEGFA isoforms by recruiting lncRNA MALAT1.

The abundant, nuclear-retained, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been associated with a poorly differentiated and aggressive phenotype of mammary carcinomas. This long non-coding RNA (lncRNA) localizes to nuclear speckles, where it interacts with a subset of splicing factors and modulates their activity. In this study, we demonstrate that oncogenic splicing factor SRSF1 bridges MALAT1 to mutant p53 and ID4 proteins in breast cancer cells. Mutant p53 and ID4 delocalize MALAT1 from nuclear speckles and favor its association with chromatin. This enables aberrant recruitment of MALAT1 on VEGFA pre-mRNA and modulation of VEGFA isoforms expression. Interestingly, VEGFA-dependent expression signatures associate with ID4 expression specifically in basal-like breast cancers carrying TP53 mutations. Our results highlight a key role for MALAT1 in control of VEGFA isoforms expression in breast cancer cells expressing gain-of-function mutant p53 and ID4 proteins.

The hydrogen-bond collective dynamics in liquid methanol.

The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HB dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature.

Dynamical crossover at the liquid-liquid transformation of a compressed molten alkali metal.

Density-driven phase transformations are a known phenomenon in liquids. Pressure-driven transitions from an open low-density to a higher-density close-packed structure were observed for a number of systems. Here, we show a less intuitive, inverse behavior. We investigated the electronic, atomic, and dynamic structures of liquid Rb along an isothermal line at 573 K, at 1.2-27.4 GPa, by means of ab initio molecular dynamics simulations and inelastic x-ray scattering experiments. The excellent agreement of the simulations with experimental data performed up to 6.6 GPa validates the overall approach. Above 12.5 GPa, the breakdown of the nearly-free-electron model drives a transition of the pure liquid metal towards a less metallic, denser liquid, whose first coordination shell is less compact. Our study unveils the interplay between electronic, structural, and dynamic degrees of freedom along this liquid-liquid phase transition. In view of its electronic nature, we believe that this behavior is general for the first group elements, thus shedding new light into the high-pressure properties of alkali metals.

K-edge XANES investigation of octakis(DMSO)lanthanoid(III) complexes in DMSO solution and solid iodides.

The potential of high energy XANES (X-ray absorption near edge structure) as a tool for the structural analysis of lanthanoid-containing systems has been explored. The K-edge XANES spectra of La(3+), Gd(3+), and Lu(3+) ions both in DMSO solution and solid octakis(DMSO)lanthanoid(III) iodides have been analysed. Although the K-edges of lanthanoids cover the energy range of 38 (La) to 65 (Lu) keV, the large widths of the core hole states do not appreciably reduce the potential structural information of the XANES data. We show that, for lanthanoid compounds, accurate structural parameters are obtained from the analysis of K-edge XANES signals if a deconvolution procedure is carried out. We found that in solid octakis(DMSO)lanthanoid(III) iodides the Ln(3+) ions are coordinated by eight DMSO ligands arranged in a quite symmetric fashion. In DMSO solution the Ln(3+) ions retain a regular eight-coordination structure and the coordination number does not change along the series. In contrast to when in water the second coordination shell has been found to provide a negligible contribution to the XANES spectra of Ln(3+) ions in DMSO solution.

Hydration properties of the Zn2+ ion in water at high pressure.

The structure and dynamics of water in ionic solutions at high pressure have been investigated using a combined approach based on extended X-ray absorption fine structure (EXAFS) spectroscopy and Molecular Dynamics (MD) simulations. Modification of the hydration properties of the Zn(2+) ion induced by a pressure increase from ambient condition up to ∼6.4 GPa has been revealed and accurately analyzed. With increasing pressure the first hydration shell of the Zn(2+) ion has been found to retain an octahedral symmetry with a shortening of the Zn-O distance up to 0.09 Šand an increased width associated with thermal motion, as compared to the ambient condition hydration complex. A very interesting picture of the dynamic behavior of the first hydration shell has emerged from the analysis of the simulations: up to 2.5 GPa no exchange events between first and second shell water molecules occurred, while above this pressure value several exchange events take place in the solution following an associative interchange mechanism. This result can be explained by the very high compression and packing of the solvent which force second shell water molecules to enter the Zn(2+) first hydration shell. MD simulations indicate a strong pressure effect also on the structure of the second coordination shell which is compressed and becomes more disordered and less structured with increasing pressure. The water mobility and the ion diffusion coefficient have been found to increase in the high density conditions, as a consequence of the rupture of the hydrogen bond network caused by pressure.

Atomic absorption background of Ba in EXAFS analysis of BaFe(12)O(19) nanoparticles.

The approximate barium X-ray atomic absorption in the energy region of L-edges is reconstructed from the absorption spectrum of an aqueous solution of BaCl(2). The result is corroborated by comparison with pure atomic absorption spectra of neighbour elements Xe and Cs. The application of the atomic absorption signal as a proper EXAFS background is demonstrated and discussed in the analysis of Ba hexaferrite nanoparticles with a very weak structural signal. The essential gain is found in the decrease of uncertainty intervals of structural parameters and their correlations. A simple analytical model of the absorption background for the practical EXAFS analysis is demonstrated.