Small-angle X-ray and neutron scattering are well-established, non-invasive experimental techniques to interrogate global structural properties of biological membrane mimicking systems under ...physiologically relevant conditions. Recent developments, both in bottom-up sample preparation techniques for increasingly complex model systems, and in data analysis techniques have opened the path toward addressing long standing issues of biological membrane remodelling processes. These efforts also include emerging quantitative scattering studies on live cells, thus enabling a bridging of molecular to cellular length scales. Here, we review recent progress in devising compositional models for joint small-angle X-ray and neutron scattering studies on diverse membrane mimics - with a specific focus on membrane structural coupling to amphiphatic peptides and integral proteins - and live
Escherichia coli
. In particular, we outline the present state-of-the-art in small-angle scattering methods applied to complex membrane systems, highlighting how increasing system complexity must be followed by an advance in compositional modelling and data-analysis tools.
We review compositional models for analyzing small-angle X-ray and neutron scattering data of complex membrane mimics and live cells.
The maintenance of synaptic changes resulting from long-term potentiation (LTP) is essential for brain function such as memory and learning. Different LTP phases have been associated with diverse ...molecular processes and pathways, and the molecular underpinnings of LTP on the short, as well as long time scales, are well established. However, the principles on the intermediate time scale of 1-6 hours that mediate the early phase of LTP (E-LTP) remain elusive. We hypothesize that the interplay between specific features of postsynaptic receptor trafficking is responsible for sustaining synaptic changes during this LTP phase. We test this hypothesis by formalizing a biophysical model that integrates several experimentally-motivated mechanisms. The model captures a wide range of experimental findings and predicts that synaptic changes are preserved for hours when the receptor dynamics are shaped by the interplay of structural changes of the spine in conjunction with increased trafficking from recycling endosomes and the cooperative binding of receptors. Furthermore, our model provides several predictions to verify our findings experimentally.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Recent research has identified higher prevalence of offending behavior in patients with comorbid schizophrenia spectrum disorder (SSD) and substance use disorder (SUD) compared to patients with SSD ...only and to the general population. However, findings on the subgroup of patients with SUD, SSD and offending behavior in forensic psychiatric care are scarce and inconsistent. The present study used machine learning to uncover more detailed characteristics of offender patients in forensic psychiatric care with comorbid SSD and SUD.
Using machine learning algorithms, 370 offender patients (91.6 % male, mean age of M = 34.1, SD = 10.2) and 558 variables were explored in order to build three models to differentiate between no substance use disorder, cannabis use disorder and any other substance use disorder. To counteract the risk of overfitting, the dataset was split, employing variable filtering, machine learning model building and selection embedded in a nested resampling approach on one subset. The best model was then selected and validated on the second data subset.
Distinguishing between SUD vs. no drug use disorder yielded models with an AUC of 70 and 78. Variables assignable to demographics, social disintegration, antisocial behavior and illness were identified as most influential for the distinction. The model comparing cannabis use disorder with other substance use disorders provided no significant differences.
From a clinical perspective, offender patients suffering from schizophrenia spectrum and comorbid substance use disorder seem particularly challenging to treat, but initial differences in psychopathology will dissipate over inpatient treatment. Our data suggest that offender patients may benefit from appropriate treatment that focuses on illicit drug abuse to reduce criminal behavior and improve social integration.
Transcription, translation, and turnover of transcripts and proteins are essential for cellular function. The contribution of those factors to protein levels is under debate, as transcript levels and ...cognate protein levels do not necessarily correlate due to regulation of translation and protein turnover. Here we propose neuronal polarity as a third factor that is particularly evident in the CNS, leading to considerable distances between somata and axon terminals. Consequently, transcript levels may negatively correlate with cognate protein levels in CNS regions, i.e., transcript and protein levels behave reciprocally. To test this hypothesis, we performed an integrative inter‐omics study and analyzed three interconnected rat auditory brainstem regions (cochlear nuclear complex, CN; superior olivary complex, SOC; inferior colliculus, IC) and the rest of the brain as a reference. We obtained transcript and protein sets in these regions of interest (ROIs) by DNA microarrays and label‐free mass spectrometry, and performed principal component and correlation analyses. We found 508 transcript|protein pairs and detected poor to moderate transcript|protein correlation in all ROIs, as evidenced by coefficients of determination from 0.34 to 0.54. We identified 57‐80 negatively correlating gene products in the ROIs and intensively analyzed four of them for which the correlation was poorest. Three cognate proteins (Slc6a11, Syngr1, Tppp) were synaptic and hence candidates for a negative correlation because of protein transport into axon terminals. Thus, we systematically analyzed the negatively correlating gene products. Gene ontology analyses revealed overrepresented transport/synapse‐related proteins, supporting our hypothesis. We present 30 synapse/transport‐related proteins with poor transcript|protein correlation. In conclusion, our analyses support that protein transport in polar cells is a third factor that influences the protein level and, thereby, the transcript|protein correlation.
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Many studies have addressed the disparity between transcript and protein levels. By contrast, only very few studies have analyzed negatively correlating gene products, i.e., the scenario where transcript and protein levels behave reciprocally. In our datasets of transcript and protein levels, we find evidence that cellular polarity, which is particularly evident in neuronal tissue, causes negatively correlating transcript|protein pairs and, hence, poor transcript|protein correlation. We conclude that, aside from transcriptional regulation and protein turnover, neuronal polarity is a third important factor determining transcript|protein correlation.
Open Science: This manuscript was awarded with the Open Materials and Open Data Badge (https://osf.io/ha28n/)
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A global analysis model has been developed for randomly oriented, fully hydrated, inverted hexagonal (HII) phases formed by many amphiphiles in aqueous solution, including membrane lipids. The model ...is based on a structure factor for hexagonally packed rods and a compositional model for the scattering length density, enabling also the analysis of positionally weakly correlated HII phases. Bayesian probability theory was used for optimization of the adjustable parameters, which allows parameter correlations to be retrieved in much more detail than standard analysis techniques and thereby enables a realistic error analysis. The model was applied to different phosphatidylethanolamines, including previously unreported HII data for diC14:0 and diC16:1 phosphatidylethanolamine. The extracted structural features include intrinsic lipid curvature, hydrocarbon chain length and area per lipid at the position of the neutral plane.
A global small‐angle scattering model for unoriented, fully hydrated, inverted hexagonal phases is provided. The model is evaluated using Bayesian probability theory to obtain reliable estimates for the structural parameters.
The inflammatory response after myocardial infarction (MI) is a precisely regulated process that greatly affects subsequent remodeling. Here, we show that basophil granulocytes infiltrated infarcted ...murine hearts, with a peak occurring between days 3 and 7. Antibody-mediated and genetic depletion of basophils deteriorated cardiac function and resulted in enhanced scar thinning after MI. Mechanistically, we found that basophil depletion was associated with a shift from reparative Ly6Clo macrophages toward increased numbers of inflammatory Ly6Chi monocytes in the infarcted myocardium. Restoration of basophils in basophil-deficient mice by adoptive transfer reversed this proinflammatory phenotype. Cellular alterations in the absence of basophils were accompanied by lower cardiac levels of IL-4 and IL-13, two major cytokines secreted by basophils. Mice with basophil-specific IL-4/IL-13 deficiency exhibited a similarly altered myeloid response with an increased fraction of Ly6Chi monocytes and aggravated cardiac function after MI. In contrast, IL-4 induction in basophils via administration of the glycoprotein IPSE/α-1 led to improved post-MI healing. These results in mice were corroborated by the finding that initially low counts of blood basophils in patients with acute MI were associated with a worse cardiac outcome after 1 year, characterized by a larger scar size. In conclusion, we show that basophils promoted tissue repair after MI by increasing cardiac IL-4 and IL-13 levels.
We studied the mechanical leaflet coupling of prototypic mammalian plasma membranes using neutron spin-echo spectroscopy. In particular, we examined a series of asymmetric phospholipid vesicles with ...phosphatidylcholine and sphingomyelin enriched in the outer leaflet and inner leaflets composed of phosphatidylethanolamine/phosphatidylserine mixtures. The bending rigidities of most asymmetric membranes were anomalously high, exceeding even those of symmetric membranes formed from their cognate leaflets. Only asymmetric vesicles with outer leaflets enriched in sphingolipid displayed bending rigidities in conformity with these symmetric controls. We performed complementary small-angle neutron and x-ray experiments on the same vesicles to examine possible links to structural coupling mechanisms, which would show up in corresponding changes in membrane thickness. In addition, we estimated differential stress between leaflets originating either from a mismatch of their lateral areas or spontaneous curvatures. However, no correlation with asymmetry-induced membrane stiffening was observed. To reconcile our findings, we speculate that an asymmetric distribution of charged or H-bond forming lipids may induce an intraleaflet coupling, which increases the weight of hard undulatory modes of membrane fluctuations and hence the overall membrane stiffness.
We developed a global X-ray data analysis method to determine the intrinsic curvatures of lipids hosted in inverted hexagonal phases. In particular, we combined compositional modelling with molecular ...shape-based arguments to account for non-linear mixing effects of guest-in-host lipids on intrinsic curvature. The technique was verified by all-atom molecular dynamics simulations and applied to sphingomyelin and a series of phosphatidylcholines and ceramides with differing composition of the hydrocarbon chains. We report positive lipid curvatures for sphingomyelin and all phosphatidylcholines with disaturated and monounsaturated hydrocarbons. Phosphatidylcholines with diunsaturated hydrocarbons in turn yielded intrinsic lipid curvatures with negative values. All ceramides, with chain lengths varying between C2:0 and C24:0, displayed significant negative lipid curvature values. Moreover, we report non-additive mixing for C2:0 ceramide and sphingomyelin. This suggests for sphingolipids that in addition to lipid headgroup and hydrocarbon chain volumes also lipid-specific interactions are important contributors to membrane curvature stress.
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•Molecular-shape-based theory for non-linear lipid curvature mixing•Global analysis of SAXS patterns of inverted hexagonal phases using compositional modelling and Bayesian probability theory•MD simulations of inverted hexagonal phases•Non-additive mixing of palmitoyl sphingomyelin and C2:0 ceramide
We studied the transleaflet coupling of compositionally asymmetric liposomes in the fluid phase. The vesicles were produced by cyclodextrin-mediated lipid exchange and contained dipalmitoyl ...phosphatidylcholine (DPPC) in the inner leaflet and different mixed-chain phosphatidylcholines (PCs) as well as milk sphingomyelin (MSM) in the outer leaflet. In order to jointly analyze the obtained small-angle neutron and X-ray scattering data, we adapted existing models of trans-bilayer structures to measure the overlap of the hydrocarbon chain termini by exploiting the contrast of the terminal methyl ends in X-ray scattering. In all studied systems, the bilayer-asymmetry has large effects on the lipid packing density. Fully saturated mixed-chain PCs interdigitate into the DPPC-containing leaflet and evoke disorder in one or both leaflets. The long saturated acyl chains of MSM penetrate even deeper into the opposing leaflet, which in turn has an ordering effect on the whole bilayer. These results are qualitatively understood in terms of a balance of entropic repulsion of fluctuating hydrocarbon chain termini and van der Waals forces, which is modulated by the interdigitation depth. Monounsaturated PCs in the outer leaflet also induce disorder in DPPC despite vestigial or even absent interdigitation. Instead, the transleaflet coupling appears to emerge here from a matching of the inner leaflet lipids to the larger lateral lipid area of the outer leaflet lipids.
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We report on the response of asymmetric lipid membranes composed of palmitoyl oleoyl phosphatidylethanolamine and palmitoyl oleoyl phosphatidylglycerol, to interactions with the frog peptides ...L18W-PGLa and magainin 2 (MG2a), as well as the lactoferricin derivative LF11-215. In particular we determined the peptide-induced lipid flip-flop, as well as membrane partitioning of L18W-PGLa and LF11-215, and vesicle dye-leakage induced by L18W-PGLa. The ability of L18W-PGLa and MG2a to translocate through the membrane appears to correlate with the observed lipid flip-flop, which occurred at the fastest rate for L18W-PGLa. The higher structural flexibility of LF11-215 in turn allows this peptide to insert into the bilayers without detectable changes of membrane asymmetry. The increased vulnerability of asymmetric membranes to L18W-PGLa in terms of permeability, appears to be a consequence of tension differences between the compositionally distinct leaflets, but not due to increased peptide partitioning.
We report on the response of asymmetric lipid membranes composed of palmitoyl oleoyl phosphatidylethanolamine and palmitoyl oleoyl phosphatidylglycerol, to interactions with the frog peptides L18W-PGLa and magainin 2 (MG2a), as well as the lactoferricin derivative LF11-215.
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