Analysis of patchclamp recordings: model-free multiscale methods and software.

Analysis of patchclamp recordings is often a challenging issue. We give practical guidance how such recordings can be analyzed using the model-free multiscale idealization methodology JSMURF, JULES, and HILDE. We provide an operational manual how to use the accompanying software available as an R-package and as a graphical user interface.

Effects of intranasal guanosine administration on brain function in a rat model of ischemic stroke.

Ischemic stroke is a major cause of morbidity and mortality worldwide and only few affected patients are able to receive treatment, especially in developing countries. Detailed pathophysiology of brain ischemia has been extensively studied in order to discover new treatments with a broad therapeutic window and that are accessible to patients worldwide. The nucleoside guanosine (Guo) has been shown to have neuroprotective effects in animal models of brain diseases, including ischemic stroke.

Doxycycline Interferes With Tau Aggregation and Reduces Its Neuronal Toxicity.

Tauopathies are neurodegenerative disorders with increasing incidence and still without cure. The extensive time required for development and approval of novel therapeutics highlights the need for testing and repurposing known safe molecules. Since doxycycline impacts α-synuclein aggregation and toxicity, herein we tested its effect on tau.

Extending the applicability of P3D for structure determination of small molecules.

The application of anisotropic nuclear magnetic resonance (NMR) parameters for the correct structural assignment of small molecules requires the use of partially ordered media. Previously we demonstrated that the use of P3D simulations using poly(-benzyl-L-glutamate) (PBLG) as an alignment medium allows for the determination of the correct diastereomer from extremely sparse NMR data. Through the analysis of the structural characteristics of small molecules in different alignment media, here we show that when steric or electrostatic factors dominate the alignment, P3D-PBLG retains its diastereomer discrimination power.

Synapsin Is Required for Dense Core Vesicle Capture and cAMP-Dependent Neuropeptide Release.

Release of neuropeptides from dense core vesicles (DCVs) is essential for neuromodulation. Compared with the release of small neurotransmitters, much less is known about the mechanisms and proteins contributing to neuropeptide release. By optogenetics, behavioral analysis, electrophysiology, electron microscopy, and live imaging, we show that synapsin SNN-1 is required for cAMP-dependent neuropeptide release in hermaphrodite cholinergic motor neurons.

Cytotoxicity and Membrane Permeability of Double-Chained 1,3-Dialkylimidazolium Cations in Ionic Liquids.

We have evaluated ionic liquids based on double-chained 1-alkyl-3-octylimidazolium cations ([CCIM], = 2, 4, 6, 8, 10, 12) for their cytotoxicity toward various cell lines. The toxicity of ionic liquids was correlated to their ability to partition into and permeabilize phosphocholine (POPC)- or phosphoglycerol (POPG)-based large unilamellar vesicles. Membrane partitioning of ionic liquids was assessed using the ζ-potential measurements, and membrane permeability was determined using fluorescence-based dye leakage assays.

Diagnostic value of diffusion-weighted STEAM-MRI in ischemic stroke.

Introduction: Diffusion-weighted imaging in stimulated echo acquisition mode (STEAM-DWI) is an interesting alternative with less susceptibility artifacts compared to the most commonly used diffusion-weighted echo-planar imaging (EPI-DWI). Sensitivity and specificity of a novel STEAM-DWI, described by Merrem et al. 2017 [1], were assessed in patients with ischemic stroke.

Molecular Profiling Reveals Involvement of ESCO2 in Intermediate Progenitor Cell Maintenance in the Developing Mouse Cortex.

Intermediate progenitor cells (IPCs) are neocortical neuronal precursors. Although IPCs play crucial roles in corticogenesis, their molecular features remain largely unknown. In this study, we aimed to characterize the molecular profile of IPCs.

SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts.

Summary: SpacePHARER (CRISPR Spacer Phage-Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage-host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein level, optimizing its scores for matching very short sequences, and combining evidence from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes.

Multiple haplotype reconstruction from allele frequency data.

Because haplotype information is of widespread interest in biomedical applications, effort has been put into their reconstruction. Here, we propose an efficient method, called haploSep, that is able to accurately infer major haplotypes and their frequencies just from multiple samples of allele frequency data. Even the accuracy of experimentally obtained allele frequencies can be improved by re-estimating them from our reconstructed haplotypes.

Selected tools to visualize membrane interactions.

In the past decade, we developed various fluorescence-based methods for monitoring membrane fusion, membrane docking, distances between membranes, and membrane curvature. These tools were mainly developed using liposomes as model systems, which allows for the dissection of specific interactions mediated by, for example, fusion proteins. Here, we provide an overview of these methods, including two-photon fluorescence cross-correlation spectroscopy and intramembrane Förster energy transfer, with asymmetric labelling of inner and outer membrane leaflets and the calibrated use of transmembrane energy transfer to determine membrane distances below 10 nm.

Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics.

Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian dynamics simulations can be carried out with the approximation of rigid body solutes moving through a continuum solvent. This allows the precomputation of interaction potential grids for the solutes, thereby allowing the computationally efficient calculation of forces.

Choice of fluorophore affects dynamic DNA nanostructures.

The ability to dynamically remodel DNA origami structures or functional nanodevices is highly desired in the field of DNA nanotechnology. Concomitantly, the use of fluorophores to track and validate the dynamics of such DNA-based architectures is commonplace and often unavoidable. It is therefore crucial to be aware of the side effects of popular fluorophores, which are often exchanged without considering the potential impact on the system.

Structure, gating and interactions of the voltage-dependent anion channel.

The voltage-dependent anion channel (VDAC) is one of the most highly abundant proteins found in the outer mitochondrial membrane, and was one of the earliest discovered. Here we review progress in understanding VDAC function with a focus on its structure, discussing various models proposed for voltage gating as well as potential drug targets to modulate the channel's function. In addition, we explore the sensitivity of VDAC structure to variations in the membrane environment, comparing DMPC-only, DMPC with cholesterol, and near-native lipid compositions, and use magic-angle spinning NMR spectroscopy to locate cholesterol on the outside of the β-barrel.

Inelastic Scattering of H Atoms from Surfaces.

We have developed an instrument that uses photolysis of hydrogen halides to produce nearly monoenergetic hydrogen atom beams and Rydberg atom tagging to obtain accurate angle-resolved time-of-flight distributions of atoms scattered from surfaces. The surfaces are prepared under strict ultrahigh vacuum conditions. Data from these experiments can provide excellent benchmarks for theory, from which it is possible to obtain an atomic scale understanding of the underlying dynamical processes governing H atom adsorption.

Enhancing the biocompatibility of rhodamine fluorescent probes by a neighbouring group effect.

Fluorescence microscopy is an essential tool for understanding dynamic processes in living cells and organisms. However, many fluorescent probes for labelling cellular structures suffer from unspecific interactions and low cell permeability. Herein, we demonstrate that the neighbouring group effect which results from positioning an amide group next to a carboxyl group in the benzene ring of rhodamines dramatically increases cell permeability of the rhodamine-based probes through stabilizing a fluorophore in a hydrophobic spirolactone state.

Synapsin Condensates Recruit alpha-Synuclein.

Neurotransmission relies on the tight spatial and temporal regulation of the synaptic vesicle (SV) cycle. Nerve terminals contain hundreds of SVs that form tight clusters. These clusters represent a distinct liquid phase in which one component of the phase are SVs and the other synapsin 1, a highly abundant synaptic protein.

FEZ1 Forms Complexes with CRMP1 and DCC to Regulate Axon and Dendrite Development.

Elaboration of neuronal processes is an early step in neuronal development. Guidance cues must work closely with intracellular trafficking pathways to direct expanding axons and dendrites to their target neurons during the formation of neuronal networks. However, how such coordination is achieved remains incompletely understood.

Evidence for additive and synergistic action of mammalian enhancers during cell fate determination.

Enhancer activity drives cell differentiation and cell fate determination, but it remains unclear how enhancers cooperate during these processes. Here we investigate enhancer cooperation during transdifferentiation of human leukemia B-cells to macrophages. Putative enhancers are established by binding of the pioneer factor C/EBPα followed by chromatin opening and enhancer RNA (eRNA) synthesis from H3K4-monomethylated regions.

Design of magnetic hybrid nanostructured lipid carriers containing 1,8-cineole as delivery systems for anticancer drugs: Physicochemical and cytotoxic studies.

The development of versatile carriers to deliver chemotherapeutic agents to specific targets with establishing drug release kinetics and minimum undesirable side effects is becoming a promising relevant tool in the medical field. Magnetic hybrid nanostructured lipid carriers (NLC) were prepared by incorporation of 1,8-cineole (CN, a monoterpene with antiproliferative properties) and maghemite nanoparticles (MNPs) into a hybrid matrix composed of myristyl myristate coated with chitosan. Hybrid NLC characterized by DLS and TEM confirmed the presence of positively charged spherical nanoparticles of around 250 nm diameter and +10.

One Plus One Makes Three: Triangular Coupling of Correlated Amino Acid Mutations.

Correlated mutations have played a pivotal role in the recent success in protein fold prediction. Understanding nonadditive effects of mutations is crucial for altering protein structure, as mutations of multiple residues may change protein stability or binding affinity in a manner unforeseen by the investigation of single mutants. While the couplings between amino acids can be inferred from homologous protein sequences, the physical mechanisms underlying these correlations remain elusive.

Translation error clusters induced by aminoglycoside antibiotics.

Aminoglycoside antibiotics target the ribosome and induce mistranslation, yet which translation errors induce bacterial cell death is unclear. The analysis of cellular proteins by quantitative mass spectrometry shows that bactericidal aminoglycosides induce not only single translation errors, but also clusters of errors in full-length proteins in vivo with as many as four amino acid substitutions in a row. The downstream errors in a cluster are up to 10,000-fold more frequent than the first error and independent of the intracellular aminoglycoside concentration.

Frequency comb referenced spectroscopy of A-X 0-0 transitions in SH.

We report absolute transition frequencies for the allowed transitions from the XΠ, v = 0, J″ = 3/2 rovibronic ground state of SH to the AΣ, v = 0 vibronic state. The frequencies have been determined with an uncertainty of less than 1 MHz, representing a more than 1000-fold improvement over previous measurements. Spectral traces are measured by scanning a frequency comb stabilized continuous-wave spectroscopy laser over the molecular transitions and detecting laser-induced fluorescence from SH molecules in a highly collimated molecular beam.