Estimating sliding drop width via side-view features using recurrent neural networks.

High speed side-view videos of sliding drops enable researchers to investigate drop dynamics and surface properties. However, understanding the physics of sliding requires knowledge of the drop width. A front-view perspective of the drop is necessary.

Extracellular membrane vesicles derived from Komagataeibacter oboediens exposed on the International Space Station fuse with artificial eukaryotic membranes in contrast to vesicles of reference bacterium.

Membranous Extracellular Vesicles (EVs) of Gram-negative bacteria are a secretion and delivery system that can disseminate bacterial products and interact with hosts and the environment. EVs of nonpathogenic bacteria deliver their contents by endocytosis into eukaryotic cells, however, no evidence exists for a fusion delivery mechanism. Here, we describe the fusion of exposed to space/Mars-like stressors simulated on the International Space Station vesicles (E-EVs) from Komagataeibacter oboediens to different types of model planar membranes in comparison with the EVs of the ground-based reference strain.

Determining glass transition in all-atom acrylic polymeric melt simulations using machine learning.

The functionality of many polymeric materials depends on their glass transition temperatures (Tg). In computer simulations, Tg is often calculated from the gradual change in macroscopic properties. Precise determination of this change depends on the fitting protocols.

Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes.

The chromatin in eukaryotic cells plays a fundamental role in all processes during a cell's life cycle. This nucleoprotein is normally tightly packed but needs to be unpacked for expression and division. The linker histones are critical for such packaging processes and while most experimental and simulation works recognize their crucial importance, the focus is nearly always set on the nucleosome as the basic chromatin building block.

Data-Driven Identification and Analysis of the Glass Transition in Polymer Melts.

Understanding the nature of glass transition, as well as the precise estimation of the glass transition temperature for polymeric materials, remains open questions in both experimental and theoretical polymer sciences. We propose a data-driven approach, which utilizes the high-resolution details accessible through the molecular dynamics simulation and considers the structural information on individual chains. It clearly identifies the glass transition temperature of polymer melts of weakly semiflexible chains.

Fast conformational clustering of extensive molecular dynamics simulation data.

We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach, we combine two dimensionality reduction algorithms (cc_analysis and encodermap) with a density-based spatial clustering algorithm (hierarchical density-based spatial clustering of applications with noise). The proposed scheme benefits from the strengths of the three algorithms while avoiding most of the drawbacks of the individual methods.

Generating a conformational landscape of ubiquitin chains at atomistic resolution by back-mapping based sampling.

Ubiquitin chains are flexible multidomain proteins that have important biological functions in cellular signalling. Computational studies with all-atom molecular dynamics simulations of the conformational spaces of polyubiquitins can be challenging due to the system size and a multitude of long-lived meta-stable states. Coarse graining is an efficient approach to overcome this problem-at the cost of losing high-resolution details.

Deep Learning to Analyze Sliding Drops.

State-of-the-art contact angle measurements usually involve image analysis of sessile drops. The drops are symmetric and images can be taken at high resolution. The analysis of videos of drops sliding down a tilted plate is hampered due to the low resolution of the cutout area where the drop is visible.

The Space-Exposed Kombucha Microbial Community Member Showed Only Minor Changes in Its Genome After Reactivation on Earth.

is the dominant taxon and cellulose-producing bacteria in the Kombucha Microbial Community (KMC). This is the first study to isolate the genome from a reactivated space-exposed KMC sample and comprehensively characterize it. The space-exposed genome was compared with the Earth-based reference genome to understand the genome stability of under extraterrestrial conditions during a long time.

Guanidine-II aptamer conformations and ligand binding modes through the lens of molecular simulation.

Regulation of gene expression via riboswitches is a widespread mechanism in bacteria. Here, we investigate ligand binding of a member of the guanidine sensing riboswitch family, the guanidine-II riboswitch (Gd-II). It consists of two stem-loops forming a dimer upon ligand binding.

Bacterial Cellulose Retains Robustness but Its Synthesis Declines After Exposure to a Mars-like Environment Simulated Outside the International Space Station.

Cellulose is a widespread macromolecule in terrestrial environments and a major architectural component of microbial biofilm. Therefore, cellulose might be considered a biosignature that indicates the presence of microbial life. We present, for the first time, characteristics of bacterial cellulose after long-term spaceflight and exposure to simuled Mars-like stressors.

Shotgun metagenomic analysis of kombucha mutualistic community exposed to Mars-like environment outside the International Space Station.

Kombucha is a multispecies microbial ecosystem mainly composed of acetic acid bacteria and osmophilic acid-tolerant yeasts, which is used to produce a probiotic drink. Furthermore, Kombucha Mutualistic Community (KMC) has been recently proposed to be used during long space missions as both a living functional fermented product to improve astronauts' health and an efficient source of bacterial nanocellulose. In this study, we compared KMC structure and functions before and after samples were exposed to the space/Mars-like environment outside the International Space Station in order to investigate the changes related to their re-adaptation to Earth-like conditions by shotgun metagenomics, using both diversity and functional analyses of Community Ecology and Complex Networks approach.

Fitness of Outer Membrane Vesicles From Is Altered Under the Impact of Simulated Mars-like Stressors Outside the International Space Station.

Outer membrane vesicles (OMVs), produced by nonpathogenic Gram-negative bacteria, have potentially useful biotechnological applications in extraterrestrial extreme environments. However, their biological effects under the impact of various stressors have to be elucidated for safety reasons. In the spaceflight experiment, model biofilm kombucha microbial community (KMC) samples, in which was a dominant community-member, were exposed under simulated Martian factors (i.

Back-mapping based sampling: Coarse grained free energy landscapes as a guideline for atomistic exploration.

One ongoing topic of research in MD simulations is how to enable sampling to chemically and biologically relevant time scales. We address this question by introducing a back-mapping based sampling (BMBS) that combines multiple aspects of different sampling techniques. BMBS uses coarse grained (CG) free energy surfaces (FESs) and dimensionality reduction to initiate new atomistic simulations.

Multimicrobial Kombucha Culture Tolerates Mars-Like Conditions Simulated on Low-Earth Orbit.

A kombucha multimicrobial culture (KMC) was exposed to simulated Mars-like conditions in low-Earth orbit (LEO). The study was part of the Biology and Mars Experiment (BIOMEX), which was accommodated in the European Space Agency's EXPOSE-R2 facility, outside the International Space Station. The aim of the study was to investigate the capability of a KMC microecosystem to survive simulated Mars-like conditions in LEO.

Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers.

Covalent modification of proteins by ubiquitin or ubiquitin chains is one of the most prevalent post-translational modifications in eukaryotes. Different types of ubiquitin chains are assumed to selectively signal respectively modified proteins for different fates. In support of this hypothesis, structural studies have shown that the eight possible ubiquitin dimers adopt different conformations.

Efficient Sampling and Characterization of Free Energy Landscapes of Ion-Peptide Systems.

Proteins that influence nucleation, growth, or polymorph selection during biomineralization processes are often rich in glutamic- or aspartic acid. Here, the interactions between carboxylate side chains and ions lead to an interplay of peptide conformations and ion structuring in solution. Molecular dynamics simulations are an ideal tool to mechanistically investigate these processes.

Molecular mechanism of synergy between the antimicrobial peptides PGLa and magainin 2.

PGLa and magainin 2 (MAG2) are amphiphilic α-helical membranolytic peptides from frog skin with known synergistic antimicrobial activity. By systematically mutating residues in the two peptides it was possible to identify the ones crucial for the synergy, as monitored by biological assays, fluorescence vesicle leakage, and solid-state N-NMR. Electrostatic interactions between anionic groups in MAG2 and cationic residues in PGLa enhance synergy but are not necessary for the synergistic effect.

Kombucha Multimicrobial Community under Simulated Spaceflight and Martian Conditions.

Kombucha microbial community (KMC) produces a cellulose-based biopolymer of industrial importance and a probiotic beverage. KMC-derived cellulose-based pellicle film is known as a highly adaptive microbial macrocolony-a stratified community of prokaryotes and eukaryotes. In the framework of the multipurpose international astrobiological project "BIOlogy and Mars Experiment (BIOMEX)," which aims to study the vitality of prokaryotic and eukaryotic organisms and the stability of selected biomarkers in low Earth orbit and in a Mars-like environment, a cellulose polymer structural integrity will be assessed as a biomarker and biotechnological nanomaterial.

Using Dimensionality Reduction to Systematically Expand Conformational Sampling of Intrinsically Disordered Peptides.

One of the approaches to improve our ability to characterize biologically important processes and to map out an underlying free energy landscape is to direct MD simulations to explore molecular conformational phase space faster. Intrinsically disordered systems with shallow free energy landscapes of a huge number of metastable minima pose a particular challenge in this regard. Both characterization of the often ill-defined conformational states as well as the assessment of the degree of convergence of phase space exploration are problematic.

Production of recombinant human apoptosis signal-regulating kinase 1 (ASK1) in Escherichia coli.

Apoptosis signal-regulating kinase 1 (ASK1) is a mediator of the MAPK signaling cascade, which regulates different cellular processes including apoptosis, cell survival, and differentiation. The increased activity of ASK1 is associated with a number of human diseases and this protein kinase is considered as promising therapeutic target. In the present study, the kinase domain of human ASK1 was expressed in Escherichia coli (E.

Homo- and heteromeric interaction strengths of the synergistic antimicrobial peptides PGLa and magainin 2 in membranes.

PGLa and magainin 2 (MAG2) are amphiphilic α-helical frog peptides with synergistic antimicrobial activity. In vesicle leakage assays we observed the strongest synergy for equimolar mixtures of PGLa and MAG2. This result was consistent with solid-state (15)N-NMR data on the helix alignment in model membranes.

The First Space-Related Study of a Kombucha Multimicrobial Cellulose-Forming Community: Preparatory Laboratory Experiments.

Biofilm-forming microbial communities are known as the most robust assemblages that can survive in harsh environments. Biofilm-associated microorganisms display greatly increased resistance to physical and chemical adverse conditions, and they are expected to be the first form of life on Earth or anywhere else. Biological molecules synthesized by biofilm -protected microbiomes may serve as markers of the nucleoprotein life.

Design and synthesis of novel protein kinase CK2 inhibitors on the base of 4-aminothieno[2,3-d]pyrimidines.

An extension of our previous research work has resulted in a number of new ATP-competitive CK2 inhibitors that have been identified among 4-aminothieno[2,3-d]pyrimidine derivatives. The most active compounds obtained in the course of the research are 3-(5-p-tolyl-thieno[2,3-d]pyrimidin-4-ylamino)-benzoic acid, 5e (NHTP23, IC50 = 0.01 μM), 3-(5-phenyl-thieno[2,3-d]pyrimidin-4-ylamino)-benzoic acid, 5g (NHTP25, IC50 = 0.

Metabarcoding of the kombucha microbial community grown in different microenvironments.

Introducing of the DNA metabarcoding analysis of probiotic microbial communities allowed getting insight into their functioning and establishing a better control on safety and efficacy of the probiotic communities. In this work the kombucha poly-microbial probiotic community was analysed to study its flexibility under different growth conditions. Environmental DNA sequencing revealed a complex and flexible composition of the kombucha microbial culture (KMC) constituting more bacterial and fungal organisms in addition to those found by cultural method.