Examining the fundamental structure and processes of living cells at the nanoscale poses a unique analytical challenge, as cells are dynamic, chemically diverse, and fragile. A case in point is the ...cell membrane, which is too small to be seen directly with optical microscopy and provides little observational contrast for other methods. As a consequence, nanoscale characterization of the membrane has been performed ex vivo or in the presence of exogenous labels used to enhance contrast and impart specificity. Here, we introduce an isotopic labeling strategy in the gram-positive bacterium Bacillus subtilis to investigate the nanoscale structure and organization of its plasma membrane in vivo. Through genetic and chemical manipulation of the organism, we labeled the cell and its membrane independently with specific amounts of hydrogen (H) and deuterium (D). These isotopes have different neutron scattering properties without altering the chemical composition of the cells. From neutron scattering spectra, we confirmed that the B. subtilis cell membrane is lamellar and determined that its average hydrophobic thickness is 24.3 ± 0.9 Ångstroms (Å). Furthermore, by creating neutron contrast within the plane of the membrane using a mixture of H- and D-fatty acids, we detected lateral features smaller than 40 nm that are consistent with the notion of lipid rafts. These experiments-performed under biologically relevant conditions-answer long-standing questions in membrane biology and illustrate a fundamentally new approach for systematic in vivo investigations of cell membrane structure.
Continued miniaturization of microelectronics has led to increased energy and interface density within those electronics. With each new interface, a new thermal resistor is created, preventing heat ...from efficiently escaping the device. This is such a problem that Kapitza resistance or thermal boundary resistance is now the dominant cause of thermal resistance in most microelectronics. Thermal boundary resistance has been studied extensively. However, thermal boundary resistance remains poorly understood. In this review, the existing literature is critically looked at, focusing on molecular dynamic simulations of the Si/Ge interface, which has become the de facto standard against which most other methods and systems are compared. As such, the volume of literature available on this system is considerably larger than any other, and the depth of analysis that can be performed is far greater. A research strategy for the field is presented to maximize progress in controlling Kapitza resistance. It is proposed that benchmark systems need to be found so that calculations can be properly verified, and that the size effects on Kapitza resistance need to be fully characterized. Finally, strong evidence is presented that first‐principles calculations offer the best chances for meaningful future progress, preferably with anharmonic contributions intact.
Studies on factors of low birth weight in Malawi have neglected the flexible approach of using smooth functions for some covariates in models. Such flexible approach reveals detailed relationship of ...covariates with the response. The study aimed at investigating risk factors of low birth weight in Malawi by assuming a flexible approach for continuous covariates and geographical random effect. A Bayesian geo-additive model for birth weight in kilograms and size of the child at birth (less than average or average and higher) with district as a spatial effect using the 2010 Malawi demographic and health survey data was adopted. A Gaussian model for birth weight in kilograms and a binary logistic model for the binary outcome (size of child at birth) were fitted. Continuous covariates were modelled by the penalized (p) splines and spatial effects were smoothed by the two dimensional p-spline. The study found that child birth order, mother weight and height are significant predictors of birth weight. Secondary education for mother, birth order categories 2-3 and 4-5, wealth index of richer family and mother height were significant predictors of child size at birth. The area associated with low birth weight was Chitipa and areas with increased risk to less than average size at birth were Chitipa and Mchinji. The study found support for the flexible modelling of some covariates that clearly have nonlinear influences. Nevertheless there is no strong support for inclusion of geographical spatial analysis. The spatial patterns though point to the influence of omitted variables with some spatial structure or possibly epidemiological processes that account for this spatial structure and the maps generated could be used for targeting development efforts at a glance.
Properties of Polyvinylpyrrolidone in a Deep Eutectic Solvent Sapir, Liel; Stanley, Christopher B; Harries, Daniel
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
05/2016, Letnik:
120, Številka:
19
Journal Article
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Deep eutectic solvents (DES) are mixtures of two or more components with high melting temperatures, which form a liquid at room temperature. These DES hold great promise as green solvents for ...chemical processes, as they are inexpensive and environmentally friendly. Specifically, they present a unique solvating environment to polymers that is different from water. Here, we use small angle neutron scattering to study the polymer properties of the common, water-soluble, polyvinylpyrrolidone (PVP) in the prominent DES formed by a 1:2 molar mixture of choline chloride and urea. We find that the polymer adopts a slightly different structure in DES than in water, so that at higher concentrations the polymer favors a more expanded conformation compared to the same concentration in water. Yet, the osmotic pressure of PVP solutions in DES is very similar to that in water, indicating that both solvents are of comparable quality and that the DES components interact favorably with PVP. The osmotic pressure measurements within this novel class of promising solvents should be of value toward future technological applications as well as for osmotic stress experiments in nonaqueous environments.
Nucleophosmin (NPM1) is an abundant, oligomeric protein in the granular component of the nucleolus with roles in ribosome biogenesis. Pentameric NPM1 undergoes liquid-liquid phase separation (LLPS) ...via heterotypic interactions with nucleolar components, including ribosomal RNA (rRNA) and proteins which display multivalent arginine-rich linear motifs (R-motifs), and is integral to the liquid-like nucleolar matrix. Here we show that NPM1 can also undergo LLPS via homotypic interactions between its polyampholytic intrinsically disordered regions, a mechanism that opposes LLPS via heterotypic interactions. Using a combination of biophysical techniques, including confocal microscopy, SAXS, analytical ultracentrifugation, and single-molecule fluorescence, we describe how conformational changes within NPM1 control valency and switching between the different LLPS mechanisms. We propose that this newly discovered interplay between multiple LLPS mechanisms may influence the direction of vectorial pre-ribosomal particle assembly within, and exit from the nucleolus as part of the ribosome biogenesis process.
Repeat expansion in the C9orf72 gene is the most common cause of the neurodegenerative disorder amyotrophic lateral sclerosis (C9-ALS) and is linked to the unconventional translation of five ...dipeptide-repeat polypeptides (DPRs). The two enriched in arginine, poly(GR) and poly(PR), infiltrate liquid-like nucleoli, co-localize with the nucleolar protein nucleophosmin (NPM1), and alter the phase separation behavior of NPM1 in vitro. Here, we show that poly(PR) DPRs bind tightly to a long acidic tract within the intrinsically disordered region of NPM1, altering its phase separation with nucleolar partners to the extreme of forming large, soluble complexes that cause droplet dissolution in vitro. In cells, poly(PR) DPRs disperse NPM1 from nucleoli and entrap rRNA in static condensates in a DPR-length-dependent manner. We propose that R-rich DPR toxicity involves disrupting the role of phase separation by NPM1 in organizing ribosomal proteins and RNAs within the nucleolus.
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•R-rich DPRs sequester NPM1 into large, soluble phase-separation-inhibited complexes•NPM1 sequestration dissolves droplets in vitro and delocalizes nucleolar NPM1 in cells•poly(PR) entraps rRNA in static puncta in vitro and in nucleoli•poly(PR) interactions disrupt nucleolar organization in a length-dependent manner
ALS-associated dipeptide repeats (R-rich DPRs) alter NPM1 phase separation, leading to NPM1 sequestration and driving droplet dissolution in vitro and NPM1 delocalization from nucleoli. Further, poly(PR) DPRs entrap rRNA within static puncta in vitro and in nucleoli. We propose that disruption of nucleolar liquid-phase homeostasis contributes to arginine-rich DPR toxicity.
Although everything seemed clear about the Ag-Sb-S compounds belonging to one of the more deeply studied experimental systems, nature allowed us to discover a new polymorph of Ag3SbS3, which could ...represent a compound for assessing new technological potentialities. The new mineral species pyradoketosite, Ag3SbS3 (IMA 2019-132), was discovered in the pyrite + baryte + iron oxide ore deposit of the Monte Arsiccio mine, Apuan Alps, Tuscany, Italy. It occurs as brittle orange acicular crystals, up to 200 µm in length and 25 µm in thickness, with adamantine luster. Under reflected light, pyradoketosite is slightly bluish-gray, with abundant orange internal reflections. Bireflectance is weak, and anisotropism was not observed, being masked by abundant internal reflections. Minimum and maximum reflectance data for the wavelengths recommended by the Commission on Ore Mineralogy Rmin/Rmax (%) (λ, nm) are 32.8/32.9 (470), 30.2/30.7 (546), 29.0/29.6 (589), and 27.5/28.4 (650). Electron microprobe analysis gave (mean of 6 spot analyses, in wt%): Ag 59.81, Sb 22.63, S 17.78, total 100.22. On the basis of (Ag+Sb) = 4 atoms per formula unit, the empirical formula of pyradoketosite is Ag2.996(11)Sb1.004(11)S2.996(15). Pyradoketosite is monoclinic, space group P21/n, with a = 13.7510(15), b = 6.9350(6), c = 19.555(2) Å, β = 94.807(4)°, V = 1858.3(3) Å3, Z = 12. The crystal structure was solved and refined to R1 = 0.063 on the basis of 2682 unique reflections with Fo > 4σ(Fo) and 191 refined parameters. The structure of pyradoketosite can be described as formed by the alternation of {101} layers: an Sb-rich layer, Sb3AgS3, and two distinct Ag8S6 layers. This layered organization allows identifying structural relationships with the wittichenite-skinnerite pair. Pyradoketosite is associated with pyrargyrite, tetrahedrite-(Hg), valentinite, and probable pyrostilpnite in baryte + dolomite + quartz veins embedded in metadolostone. Its name derives from the old Greek words "πυρ" (fire) and "αδOκητοχ" (unforeseen), because of the unexpected occurrence of this third polymorph of the compound Ag3SbS3.
Objective- Inflammation-driven endothelial dysfunction initiates and contributes to the progression of atherosclerosis, and MPO (myeloperoxidase) has been implicated as a potential culprit. On ...release by circulating phagocytes, MPO is thought to contribute to endothelial dysfunction by limiting NO bioavailability via formation of reactive oxidants including hypochlorous acid. However, it remains largely untested whether specific pharmacological inhibition of MPO attenuates endothelial dysfunction. We, therefore, tested the ability of a mechanism-based MPO inhibitor, AZM198, to inhibit endothelial dysfunction in models of vascular inflammation. Approach and Results- Three models of inflammation were used: femoral cuff, the tandem stenosis model of plaque rupture in Apoe
mice, and C57BL/6J mice fed a high-fat, high-carbohydrate diet as a model of insulin resistance. Endothelial dysfunction was observed in all 3 models, and oral administration of AZM198 significantly improved endothelial function in the femoral cuff and tandem stenosis models only. Improvement in endothelial function was associated with decreased arterial MPO activity, determined by the in vivo conversion of hydroethidine to 2-chloroethidium, without affecting circulating inflammatory cytokines or arterial MPO content. Mechanistic studies in Mpo
mice confirmed the contribution of MPO to endothelial dysfunction and revealed oxidation of sGC (soluble guanylyl cyclase) as the underlying cause of the observed limited NO bioavailability. Conclusions- Pharmacological inhibition of MPO is a potential strategy to limit endothelial dysfunction in vascular inflammation. Visual Overview- An online visual overview is available for this article.
The nucleolus is a membrane-less organelle formed through liquid-liquid phase separation of its components from the surrounding nucleoplasm. Here, we show that nucleophosmin (NPM1) integrates within ...the nucleolus via a multi-modal mechanism involving multivalent interactions with proteins containing arginine-rich linear motifs (R-motifs) and ribosomal RNA (rRNA). Importantly, these R-motifs are found in canonical nucleolar localization signals. Based on a novel combination of biophysical approaches, we propose a model for the molecular organization within liquid-like droplets formed by the N-terminal domain of NPM1 and R-motif peptides, thus providing insights into the structural organization of the nucleolus. We identify multivalency of acidic tracts and folded nucleic acid binding domains, mediated by N-terminal domain oligomerization, as structural features required for phase separation of NPM1 with other nucleolar components in vitro and for localization within mammalian nucleoli. We propose that one mechanism of nucleolar localization involves phase separation of proteins within the nucleolus.
Conformational malleability allows intrinsically disordered proteins (IDPs) to respond agilely to their environments, such as nonspecifically interacting with in vivo bystander macromolecules (or ...crowders). Previous studies have emphasized conformational compaction of IDPs due to steric repulsion by macromolecular crowders, but effects of soft attraction are largely unexplored. Here we studied the conformational ensembles of the IDP FlgM in both polymer and protein crowders by small-angle neutron scattering. As crowder concentrations increased, the mean radius of gyration of FlgM first decreased but then exhibited an uptick. Ensemble optimization modeling indicated that FlgM conformations under protein crowding segregated into two distinct populations, one compacted and one extended. Coarse-grained simulations showed that compacted conformers fit into an interstitial void and occasionally bind to a surrounding crowder, whereas extended conformers snake through interstitial crevices and bind multiple crowders simultaneously. Crowder-induced conformational segregation may facilitate various cellular functions of IDPs.
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