Open source platform for the execution and analysis of mechanical refolding experiments

Abstract Motivation: Single-molecule force spectroscopy has facilitated the experimental investigation of biomolecular force-coupled kinetics, from which the kinetics at zero force can be extrapolated via explicit theoretical models. The atomic force microscope (AFM) in particular is routinely used to study protein unfolding kinetics, but only rarely protein folding kinetics. The discrepancy arises because mechanical protein refolding studies are more technically challenging. Results: We developed software that can drive and analyse mechanical refolding experiments when used with the commercial AFM setup 'Picoforce AFM', Bruker (previously Digital Instruments). We expect the software to be easily adaptable to other AFM setups. We also developed an improved method for the statistical characterization of protein folding kinetics, and implemented it into an AFM-independent software module. Availability: Software and documentation are available at http://code.google.com/p/refolding under Apache License 2.0. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Polymorph Separation by Ordered Patterning

We herein address the problem of polymorph selection by introducing a general and straightforward concept based on their ordering. We demonstrated the concept by the ordered patterning of four compounds capable of forming different polymorphs when deposited on technologically relevant surfaces. Our approach exploits the fact that, when the growth of a crystalline material is confined within sufficiently small cavities, only one of the possible polymorphs is generated. We verify our method by utilizing several model compounds to fabricate micrometric "logic patterns" in which each of the printed pixels is easily identifiable as comprising only one polymorph and can be individually accessed for further operations

Comparison of separation methods for immunomodulatory extracellular vesicles from helminths

Helminths survive within their host by secreting immunomodulatory compounds, which hold therapeutic potential for inflammatory conditions. Helminth-derived extracellular vesicles (EVs) are one such component proposed to possess immunomodulatory activities. Due to the recent discovery of helminth EVs, standardised protocols for EV separation are lacking. Excretory/secretory products of the porcine helminth, Ascaris suum, were used to compare three EV separation methods: Size exclusion chromatography (SEC), ultracentrifugation (UC) and a combination of the two. Their performance was evaluated by EV yield, sample purity and the ability of EVs to suppress lipopolysaccharide (LPS)-induced inflammation in vitro. We found that all three separation methods successfully separated helminth EVs with a similar EV yield. Functional studies showed that EVs from all three methods reduced LPS-induced levels of tumour necrosis factor (TNF-α) in a dose-dependent manner. Overall, the three separation methods showed similar performance, however, the combination of UC+SEC presented with slightly higher purity than either method alone

Conformational equilibria in monomeric alpha-synuclein at the single molecule level

Natively unstructured proteins defy the classical "one sequence-one structure" paradigm of protein science. Monomers of these proteins in pathological conditions can aggregate in the cell, a process that underlies socially relevant neurodegenerative diseases such as Alzheimer and Parkinson. A full comprehension of the formation and structure of the so-called misfolded intermediates from which the aggregated states ensue is still lacking. We characterized the folding and the conformational diversity of alpha-synuclein (aSyn), a natively unstructured protein involved in Parkinson disease, by mechanically stretching single molecules of this protein and recording their mechanical properties. These experiments permitted us to directly observe directly and quantify three main classes of conformations that, under in vitro physiological conditions, exist simultaneously in the aSyn sample, including disordered and "beta-like" structures. We found that this class of "beta-like" structures is directly related to aSyn aggregation. In fact, their relative abundance increases drastically in three different conditions known to promote the formation of aSyn fibrils: the presence of Cu2+, the occurrence of the pathogenic A30P mutation, and high ionic strength. We expect that a critical concentration of aSyn with a "beta-like" structure must be reached to trigger fibril formation. This critical concentration is therefore controlled by a chemical equilibrium. Novel pharmacological strategies can now be tailored to act upstream, before the aggregation process ensues, by targeting this equilibrium. To this end, Single Molecule Force Spectroscopy can be an effective tool to tailor and test new pharmacological agents.Comment: 37 pages, 9 figures (including supplementary material

Beyond the 2D Field‐Effect Charge Transport Paradigm in Molecular Thin‐Film Transistors

Organic field-effect transistors (OFETs) are considered almost purely interfacial devices with charge current mainly confined in the first two semiconducting layers in contact with the dielectric with no active role of the film thickness exceeding six to eight monolayers (MLs). By a combined electronic, morphological, structural, and theoretical investigation, it is demonstrated that the charge mobility and source–drain current in 2,20-(2,20-bithiophene-5,50-diyl)bis(5-butyl-5H-thieno[2,3-c]pyrrole-4,6)-dione (NT4N) organic transistors directly correlate with the out-of-plane domain size and crystallite orientation in the vertical direction, well beyond the dielectric interfacial layers. Polycrystalline films with thickness as high as 75 nm (≈30 MLs) and 3D molecular architecture provide the best electrical and optoelectronic OFET characteristics, highlighting that the molecular orientational order in the bulk of the film is the key-enabling factor for optimum device performance. X-ray scattering analysis and multiscale simulations reveal the functional correlation between the thickness-dependent molecular packing, electron mobility, and vertical charge distribution. These results call for a broader view of the fundamental mechanisms that govern field-effect charge transport in OFETs beyond the interfacial 2D paradigm and demonstrate the unexpected role of the out-of-plane domain size and crystallite orientation in polycrystalline films to achieve optimum electronic and optoelectronic properties in organic transistors

Graphene oxide doped polysulfone membrane adsorbers for the removal of organic contaminants from water

This work explored polysulfone (PS) – graphene oxide (GO) based porous membranes (PS-GO) as adsorber of seven selected organic contaminants of emerging concern (EOCs) including pharmaceuticals, personal care products, a dye and a surfactant from water. PS-GO was prepared by phase inversion method starting from a PS and GO mixture (5% w/w of GO). The porous PS-GO membranes showed asymmetric and highly porous micrometer sized pores on membrane top (diameter ≈20 μm) and bottom (diameter ≈2–5 μm) surfaces and tens of microns length finger like pores in the section. Nanomechanical mapping reveals patches of a stiffer material with Young modules comprised in the range 15–25 GPa, not present in PS pure membranes that are compatible with the presence of GO flakes on the membrane surfaces. PS-GO was immersed in EOCs spiked tap water and the adsorbance efficiency at different contact times and pH evaluated by HPLC analysis. Ofloxacin (OFLOX), benzophenone-3 (BP-3), rhodamine b (Rh), diclofenac (DCF) and triton X-100 (TRX) were removed with efficiency higher than 90% after 4 h treatments. Regeneration of PS-GO and reuse possibilities were demonstrated by washing with ethanol. The adsorption efficiencies toward OFLOX, Rh, DCF and carbamazepine (CBZ) were significantly higher than those of pure PS membrane. Moreover, PS-GO outperformed a commercial granular activated carbon (GAC) at low contact times and compared well at longer contact time for OFLOX, Rh, BP-3 and TRX suggesting the suitability of the newly introduced material for drinking water treatment

Epitaxial multilayers of alkanes on two-dimensional black phosphorus as passivating and electrically insulating nanostructures

© The Royal Society of Chemistry. Mechanically exfoliated two-dimensional (2D) black phosphorus (bP) is epitaxially terminated by monolayers and multilayers of tetracosane, a linear alkane, to form a weakly interacting van der Waals heterostructure. Atomic force microscopy (AFM) and computational modelling show that epitaxial domains of alkane chains are ordered in parallel lamellae along the principal crystalline axis of bP, and this order is extended over a few layers above the interface. Epitaxial alkane multilayers delay the oxidation of 2D bP in air by 18 hours, in comparison to 1 hour for bare 2D bP, and act as an electrical insulator, as demonstrated using electrostatic force microscopy. The presented heterostructure is a technologically relevant insulator-semiconductor model system that can open the way to the use of 2D bP in micro-and nanoelectronic, optoelectronic and photonic applications

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

© 2024 The Authors. Journal of Extracellular Vesicles, published by Wiley Periodicals, LLC on behalf of the International Society for Extracellular Vesicles. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY), https://creativecommons.org/licenses/by/4.0/Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly.Peer reviewe