STXMPy: a new software package for automated region of interest selection and statistical analysis of XANES data

<p>Abstract</p> <p>Background</p> <p>Soft X-ray spectromicroscopy based absorption near-edge structure analysis, is a spectroscopic technique useful for investigating sample composition at a nanoscale of resolution. While the technique holds great promise for analysis of biological samples, current methodologies are challenged by a lack of automatic analysis software e. g. for selection of regions of interest and statistical comparisons of sample variability.</p> <p>Results</p> <p>We have implemented a set of functions and scripts in Python to provide a semiautomatic treatment of data obtained using scanning transmission X-ray microscopy. The toolkit includes a novel line-by-line absorption conversion and data filtering automatically identifying image components with significant absorption. Results are provided to the user by direct graphical output to the screen and by output images and data files, including the average and standard deviation of the X-ray absorption spectrum. Using isolated mouse melanosomes as a sample biological tissue, application of STXMPy in analysis of biological tissues is illustrated.</p> <p>Conclusion</p> <p>The STXMPy package allows both interactive and automated batch processing of scanning transmission X-ray microscopic data. It is open source, cross platform, and offers rapid script development using the interpreted Python language.</p

Tenzidek önrendeződése fémfelületeken és hordozókon = Self-organization of surfactants on metal particles and supports

Adszorpciós mikrokalorimetriával jellemeztük tenzidek adszorpcióját (az adszorpciós réteg komplex szerkezetét) nemesfém nanorészecskéken, hidrofil és hidrofób katalizátor hordozókon. Új típusú kolloidkémiai módszereket dolgoztunk ki tenzidekkel stabilizált, méret- és morfológia-kontrollált nemesfém nanorészecskék előállítására réteges szerkezetű hordozók (montmorillonit; hidrotalcit) interlamelláris terében. A katalizátorokat szerkezetérzékeny vizsgálati módszerekkell jellemeztük (XRD, TEM, HR-TEM, IR-Raman és UV-vis spektroszkópia, titrációs- és áramlásos mikrokalorimetria). Az anyagok aktív és szelektív heterogén katalizátoroknak bizonyultak folyadékfázisú hidrogénezési reakciókban; alkinek alkénekké történő átalakításában. Hidrogénszorpciós méréseink szerint a Pd/H béta-hidrid képződés nem befolyásolja e reakciók kötésszelektivitását. Adszorpciós-folyadékkromatográfiás eljárást dolgoztunk ki hordozós átmenetifém katalizátorok diszperzitásának meghatározására. A tenzidek önrendeződésén alapuló ''in-situ'' módszert fejlesztettünk ki átmenetifém és átmenetifém ötvözet nanorészecskék előállítására MCM-41 hordozók mezopórusaiban. A katalizátorok nagy aktivitást és szelektivitást mutattak alkinek alkénekké történő hidrogénezési reakcióiban. | Measurements of the adsorption of surfactants on noble metal nanoparticles and hydrophilic and hydrophobic support materials have been performed by adsorption microcalorimetry. Surfactant-stabilized, size- and morphology-controlled noble metal nanoparticles have been synthesized and deposited in the interlamellar space of layer-structured materials (montmorillonite; hydrotalcite) by novel colloid chemical methods. The heterogeneous catalysts have been characterized by structure-sensitive instrumental methods (XRD, TEM, HR-TEM, IR-Raman and UV-vis spectroscopy, titration- and flow-microcalorimetry). These catalysts proved to be active and selective in the liquid-phase hydrogenations of alkynes to alkenes. Hydrogen sorption measurements indicated that bond-selectivity is not affected by Pd/H beta-hydride formation. A novel adsorption-liquid chromatographic method has been developed for the determination of the dispersion of supported noble metal catalysts. The self-organization of surfactants has been utilized for the ''in-situ'' generation of noble metal and alloyed noble metal nanoparticles in MCM-41 host matrices. These materials proved to be active and selective in the liquid-phase hydrogenations of aklynes to alkenes

Substrate engagement of integrins α5 β1 and αv β3 is necessary, but not sufficient, for high directional persistence in migration on fibronectin

The interplay between specific integrin-mediated matrix adhesion and directional persistence in cell migration is not well understood. Here, we characterized fibroblast adhesion and migration on the extracellular matrix glycoproteins fibronectin and vitronectin, focusing on the role of α5 β1 and αv β3 integrins. Fibroblasts manifested high directional persistence in migration on fibronectin-, but not vitronectin-coated substrates, in a ligand density-dependent manner. Fibronectin stimulated α5 β1-dependent organization of the actin cytoskeleton into oriented, ventral stress fibers, and assembly of dynamic, polarized protrusions, characterized as regions free of stress fibers and rich in nascent adhesions at their edge. Such protrusions correlated with persistent, local leading edge advancement, but were not sufficient, nor necessary for directional migration over longer times. Selective blocking of αv β3 or α5 β1 integrins using small molecule integrin antagonists reduced directional persistence on fibronectin, indicating integrin cooperativity in maintaining directionality. On the other hand, patterned substrates, designed to selectively engage either integrin, or their combination, were not sufficient to establish directional migration. Overall, our study demonstrates adhesive coating-dependent regulation of directional persistence in fibroblast migration and challenges the generality of the previously suggested role of β1 and β3 integrins in directional migration.Instituto de Investigaciones Fisicoquímicas Teóricas y AplicadasConsejo Nacional de Investigaciones Científicas y Técnica

Substrate engagement of integrins α5 β1 and αv β3 is necessary, but not sufficient, for high directional persistence in migration on fibronectin

The interplay between specific integrin-mediated matrix adhesion and directional persistence in cell migration is not well understood. Here, we characterized fibroblast adhesion and migration on the extracellular matrix glycoproteins fibronectin and vitronectin, focusing on the role of α5 β1 and αv β3 integrins. Fibroblasts manifested high directional persistence in migration on fibronectin-, but not vitronectin-coated substrates, in a ligand density-dependent manner. Fibronectin stimulated α5 β1-dependent organization of the actin cytoskeleton into oriented, ventral stress fibers, and assembly of dynamic, polarized protrusions, characterized as regions free of stress fibers and rich in nascent adhesions at their edge. Such protrusions correlated with persistent, local leading edge advancement, but were not sufficient, nor necessary for directional migration over longer times. Selective blocking of αv β3 or α5 β1 integrins using small molecule integrin antagonists reduced directional persistence on fibronectin, indicating integrin cooperativity in maintaining directionality. On the other hand, patterned substrates, designed to selectively engage either integrin, or their combination, were not sufficient to establish directional migration. Overall, our study demonstrates adhesive coating-dependent regulation of directional persistence in fibroblast migration and challenges the generality of the previously suggested role of β1 and β3 integrins in directional migration.Instituto de Investigaciones Fisicoquímicas Teóricas y AplicadasConsejo Nacional de Investigaciones Científicas y Técnica

Zwitterionic Dendrimersomes: A Closer Xenobiotic Mimic of Cell Membranes

Building functional mimics of cell membranes is an important task toward the development of synthetic cells. So far, lipid and amphiphilic block copolymers are the most widely used amphiphiles with the bilayers by the former lacking stability while membranes by the latter are typically characterized by very slow dynamics. Herein, we introduce a new type of Janus dendrimer containing a zwitterionic phosphocholine hydrophilic headgroup (JDPC ) and a 3,5-substituted dihydrobenzoate-based hydrophobic dendron. JDPC self-assembles in water into zwitterionic dendrimersomes (z-DSs) that faithfully recapitulate the cell membrane in thickness, flexibility, and fluidity, while being resilient to harsh conditions and displaying faster pore closing dynamics in the event of membrane rupture. This enables the fabrication of hybrid DSs with components of natural membranes, including pore-forming peptides, structure-directing lipids, and glycans to create raft-like domains or onion vesicles. Moreover, z-DSs can be used to create active synthetic cells with life-like features that mimic vesicle fusion and motility as well as environmental sensing. Despite their fully synthetic nature, z-DSs are minimal cell mimics that can integrate and interact with living matter with the programmability to imitate life-like features and beyond. This article is protected by copyright. All rights reserved.This article is protected by copyright. All rights reserved

Zwitterionic Dendrimersomes: A Closer Xenobiotic Mimic of Cell Membranes

Building functional mimics of cell membranes is an important task toward the development of synthetic cells. So far, lipid and amphiphilic block copolymers are the most widely used amphiphiles with the bilayers by the former lacking stability while membranes by the latter are typically characterized by very slow dynamics. Herein, a new type of Janus dendrimer containing a zwitterionic phosphocholine hydrophilic headgroup (JDPC) and a 3,5-substituted dihydrobenzoate-based hydrophobic dendron is introduced. JDPC self-assembles in water into zwitterionic dendrimersomes (z-DSs) that faithfully recapitulate the cell membrane in thickness, flexibility, and fluidity, while being resilient to harsh conditions and displaying faster pore closing dynamics in the event of membrane rupture. This enables the fabrication of hybrid DSs with components of natural membranes, including pore-forming peptides, structure-directing lipids, and glycans to create raft-like domains or onion vesicles. Moreover, z-DSs can be used to create active synthetic cells with life-like features that mimic vesicle fusion and motility as well as environmental sensing. Despite their fully synthetic nature, z-DSs are minimal cell mimics that can integrate and interact with living matter with the programmability to imitate life-like features and beyond

Unraveling the Mechanism and Kinetics of Binding of an LCI-eGFP-Polymer for Antifouling Coatings

The ability of proteins to adsorb irreversibly onto surfaces opens new possibilities to functionalize biological interfaces. Herein, the mechanism and kinetics of adsorption of protein-polymer macromolecules with the ability to equip surfaces with antifouling properties are investigated. These macromolecules consist of the liquid chromatography peak I peptide from which antifouling polymer brushes are grafted using single electron transfer-living radical polymerization. Surface plasmon resonance spectroscopy reveals an adsorption mechanism that follows a Langmuir-type of binding with a strong binding affinity to gold. X-ray reflectivity supports this by proving that the binding occurs exclusively by the peptide. However, the lateral organization at the surface is directed by the cylindrical eGFP. The antifouling functionality of the unimolecular coatings is confirmed by contact with blood plasma. All coatings reduce the fouling from blood plasma by 8894% with only minor effect of the degree of polymerization for the studied range (DP between 101 and 932). The excellent antifouling properties, combined with the ease of polymerization and the straightforward coating procedure make this a very promising antifouling concept for a multiplicity of applications