CyVerse: Cyberinfrastructure for open science.

CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 124,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in three countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and open-source software.

Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads.

MOTIVATION: The Oxford Nanopore technology has a great potential for the analysis of methylated motifs in genomes, including whole-genome methylome profiling. However, we found that there are no methylation motifs detection algorithms, which would be sensitive enough and return deterministic results. Thus, the MEME suit does not extract all Helicobacter pylori methylation sites de novo even using the iterative approach implemented in the most up-to-date methylation analysis tool Nanodisco. RESULTS: We present Snapper, a new highly sensitive approach, to extract methylation motif sequences based on a greedy motif selection algorithm. Snapper does not require manual control during the enrichment process and has enrichment sensitivity higher than MEME coupled with Tombo or Nanodisco instruments that was demonstrated on H.pylori strain J99 studied earlier by the PacBio technology and on four external datasets representing different bacterial species. We used Snapper to characterize the total methylome of a new H.pylori strain A45. At least four methylation sites that have not been described for H.pylori earlier were revealed. We experimentally confirmed the presence of a new CCAG-specific methyltransferase and inferred a gene encoding a new CCAAK-specific methyltransferase. AVAILABILITY AND IMPLEMENTATION: Snapper is implemented using Python and is freely available as a pip package named "snapper-ont." Also, Snapper and the demo dataset are available in Zenodo (10.5281/zenodo.10117651).

G-Quadruplexes as Sensors of Intracellular Na+/K+ Ratio: Potential Role in Regulation of Transcription and Translation.

Data on the structure of G-quadruplexes, noncanonical nucleic acid forms, supporting an idea of their potential participation in regulation of gene expression in response to the change in intracellular Na+i/K+i ratio are considered in the review. Structural variety of G-quadruplexes, role of monovalent cations in formation of this structure, and thermodynamic stability of G-quadruplexes are described. Data on the methods of their identification in the cells and biological functions of these structures are presented. Analysis of information about specific interactions of G-quadruplexes with some proteins was conducted, and their potential participation in the development of some pathological conditions, in particular, cancer and neurodegenerative diseases, is considered. Special attention is given to the plausible role of G-quadruplexes as sensors of intracellular Na+i/K+i ratio, because alteration of this parameter affects folding of G-quadruplexes changing their stability and, thereby, organization of the regulatory elements of nucleic acids. The data presented in the conclusion section demonstrate significant change in the expression of some early response genes under certain physiological conditions of cells and tissues depending on the intracellular Na+i/K+i ratio.

Bayesian compositional regression with microbiome features via variational inference.

The microbiome plays a key role in the health of the human body. Interest often lies in finding features of the microbiome, alongside other covariates, which are associated with a phenotype of interest. One important property of microbiome data, which is often overlooked, is its compositionality as it can only provide information about the relative abundance of its constituting components. Typically, these proportions vary by several orders of magnitude in datasets of high dimensions. To address these challenges we develop a Bayesian hierarchical linear log-contrast model which is estimated by mean field Monte-Carlo co-ordinate ascent variational inference (CAVI-MC) and easily scales to high dimensional data. We use novel priors which account for the large differences in scale and constrained parameter space associated with the compositional covariates. A reversible jump Monte Carlo Markov chain guided by the data through univariate approximations of the variational posterior probability of inclusion, with proposal parameters informed by approximating variational densities via auxiliary parameters, is used to estimate intractable marginal expectations. We demonstrate that our proposed Bayesian method performs favourably against existing frequentist state of the art compositional data analysis methods. We then apply the CAVI-MC to the analysis of real data exploring the relationship of the gut microbiome to body mass index.

Casimir Self-Interaction Energy Density of Quantum Electrodynamic Fields.

Quantum electrodynamic fields possess fluctuations corresponding to transient particle-antiparticle dipoles, which can be characterized by a nonvanishing polarizability density. Here, we extend a recently proposed quantum scaling law to describe the volumetric and radial polarizability density of a quantum field corresponding to electrons and positrons and derive the Casimir self-interaction energy (SIE) density of the field, E[over ¯]_{SIE}, in terms of the fine-structure constant. The proposed model obeys the cosmological equation of state w=-1 and the magnitude of the calculated E[over ¯]_{SIE} lies in between the two recent measurements of the cosmological constant Λ obtained by the Planck Mission and the Hubble Space Telescope.

Pharmacological Modulation of Excitotoxicity through the Combined Use of NMDA Receptor Inhibition and Group III mGlu Activation Reduces TMT-Induced Neurodegeneration in the Rat Hippocampus.

We studied the neuroprotective properties of the non-competitive NMDA receptor antagonist memantine, in combination with a positive allosteric modulator of metabotropic glutamate receptors of Group III, VU 0422288. The treatment was started 48 h after the injection of neurotoxic agent trimethyltin (TMT) at 7.5 mg/kg. Three weeks after TMT injection, functional and morphological changes in a rat hippocampus were evaluated, including the expression level of genes characterizing glutamate transmission and neuroinflammation, animal behavior, and hippocampal cell morphology. Significant neuronal cell death occurred in the CA3 and CA4 regions, and to a lesser extent, in the CA1 and CA2 regions. The death of neurons in the CA1 field was significantly reduced in animals with a combined use of memantine and VU 0422288. In the hippocampus of these animals, the level of expression of genes characterizing glutamatergic synaptic transmission (Grin2b, Gria1, EAAT2) did not differ from the level in control animals, as well as the expression of genes characterizing neuroinflammation (IL1b, TGF beta 1, Aif1, and GFAP). However, the expression of genes characterizing neuroinflammation was markedly increased in the hippocampus of animals treated with memantine or VU 0422288 alone after TMT. The results of immunohistochemical studies confirmed a significant activation of microglia in the hippocampus three weeks after TMT injection. In contrast to the hilus, microglia in the CA1 region had an increase in rod-like cells. Moreover, in the CA1 field of the hippocampus of the animals of the MEM + VU group, the amount of such microglia was close to the control. Thus, the short-term modulation of glutamatergic synaptic transmission by memantine and subsequent activation of Group III mGluR significantly affected the dynamics of neurodegeneration in the hippocampus.

Four-Dimensional Scaling of Dipole Polarizability in Quantum Systems.

Polarizability is a key response property of physical and chemical systems, which has an impact on intermolecular interactions, spectroscopic observables, and vacuum polarization. The calculation of polarizability for quantum systems involves an infinite sum over all excited (bound and continuum) states, concealing the physical interpretation of polarization mechanisms and complicating the derivation of efficient response models. Approximate expressions for the dipole polarizability, α, rely on different scaling laws α∝R^{3}, R^{4}, or R^{7}, for various definitions of the system radius R. Here, we consider a range of single-particle quantum systems of varying spatial dimensionality and having qualitatively different spectra, demonstrating that their polarizability follows a universal four-dimensional scaling law α=C(4µq^{2}/ℏ^{2})L^{4}, where µ and q are the (effective) particle mass and charge, C is a dimensionless excitation-energy ratio, and the characteristic length L is defined via the L^{2} norm of the position operator. This unified formula is also applicable to many-particle systems, as shown by accurately predicting the dipole polarizability of 36 atoms, 1641 small organic molecules, and Bloch electrons in periodic systems.

Modeling Spin-Crossover Dynamics.

In this article, we review nonadiabatic molecular dynamics (NAMD) methods for modeling spin-crossover transitions. First, we discuss different representations of electronic states employed in the grid-based and direct NAMD simulations. The nature of interstate couplings in different representations is highlighted, with the main focus on nonadiabatic and spin-orbit couplings. Second, we describe three NAMD methods that have been used to simulate spin-crossover dynamics, including trajectory surface hopping, ab initio multiple spawning, and multiconfiguration time-dependent Hartree. Some aspects of employing different electronic structure methods to obtain information about potential energy surfaces and interstate couplings for NAMD simulations are also discussed. Third, representative applications of NAMD to spin crossovers in molecular systems of different sizes and complexities are highlighted. Finally, we pose several fundamental questions related to spin-dependent processes. These questions should be possible to address with future methodological developments in NAMD.

AcdR protein is an activator of transcription of 1-aminocyclopropane-1-carboxylate deaminase in Methylobacterium radiotolerans JCM 2831.

It has been previously shown that a number of plant associated methylotrophic bacteria contain an enzyme aminocyclopropane carboxylate (ACC) deaminase (AcdS) hydrolyzing ACC, the immediate precursor of ethylene in plants. The genome of the epiphytic methylotroph Methylobacterium radiotolerans JCM2831 contains an open reading frame encoding a protein homologous to transcriptional regulatory protein AcdR of the Lrp (leucine-responsive regulatory protein) family. The acdR gene of M. radiotolerans was heterologously expressed in Escherichia coli and purified. The results of gel retardation experiments have shown that AcdR specifically binds the DNA fragment containing the promoter-operator region of the acdS gene. ACC decreased electrophoretic mobility of the AcdR-DNA complex whereas leucine had no effect on the complex mobility. The mutant strains of M. radiotolerans obtained by insertion of a tetracycline cassette in the acdS or acdR gene lost the ACC-deaminase activity but the strains with complementation of the mutation recovered this function. The acdS- mutant but not acdR- strain expressed the xylE reporter gene under the control of acdS promoter region thus resulting in a catechol 2,3-dioxygenase activity. This suggested that AcdR in vivo functions as activator of transcription of the acdS gene. The results obtained in this study showed that in phytosymbiotic methylotroph Methylobacterium radiotolerans AcdR mediates activation of the acdS gene transcription in the presence of an inducer ACC or 2-aminoisobutyrate and the excess of the regulatory protein assists in transcription initiation even in the absence of the inducer. The model of regulation of acdS transcription in M. radiotolerans was proposed.

Increased Extracellular Sodium Concentration as a Factor Regulating Gene Expression in Endothelium.

Hyperosmotic stimulation of endothelial cells often leads to its dysfunction accompanied, among other things, by proinflammatory response. The mechanisms of this phenomenon are not fully understood. It may arise due to increase in the plasma Na+ concentration, due to increase in the extracellular osmolarity, increase in the intracellular Na+i/K+i ratio, and/or change in the cell stiffness. In the present study we investigated the effects of short-term increase in osmolarity of extracellular medium on the mRNA content of some genes important for endothelial function (including Na+i/K+i-sensitive ones) and the equivalent elasticity constant of human umbilical vein endothelial cells membranes. Hyperosmotic stimulation of these cells with NaCl but not mannitol resulted in accumulation of Na+ ions inside the cells despite the Na,K-ATPase activation, and was also accompanied by the decrease in their equivalent elasticity constant. The amount of IL1α mRNA decreased with increasing osmolarity of the extracellular medium, whereas the amount of ATF3, PAR2, and PTGS2 mRNAs increased only in response to the increasing NaCl concentration. At the same time, under the conditions of our experiments, we did not detect changes in the expression of the osmoprotective transcription factor NFAT5. The obtained data indicate that the increase of extracellular Na+ concentration in the physiological range is an independent factor that affects intracellular Na+i/K+i ratio and regulates expression of some genes (in particular, ATF3, PAR2, PTGS2) in endothelial cells.

The Improvement of Functional State of Brain Mitochondria with Astaxanthin in Rats after Heart Failure.

The relationship between neurological damage and cardiovascular disease is often observed. This type of damage is both a cause and an effect of cardiovascular disease. Mitochondria are the key organelles of the cell and are primarily subject to oxidative stress. Mitochondrial dysfunctions are involved in the etiology of various diseases. A decrease in the efficiency of the heart muscle can lead to impaired blood flow and decreased oxygen supply to the brain. Astaxanthin (AST), a marine-derived xanthophyll carotenoid, has multiple functions and its effects have been shown in both experimental and clinical studies. We investigated the effects of AST on the functional state of brain mitochondria in rats after heart failure. Isoproterenol (ISO) was used to cause heart failure. In the present study, we found that ISO impaired the functional state of rat brain mitochondria (RBM), while the administration of AST resulted in an improvement in mitochondrial efficiency. The respiratory control index (RCI) in RBM decreased with the use of ISO, while AST administration led to an increase in this parameter. Ca2+ retention capacity (CRC) decreased in RBM isolated from rat brain after ISO injection, and AST enhanced CRC in RBM after heart failure. The study of changes in the content of regulatory proteins such as adenine nucleotide translocase 1 and 2 (ANT1/2), voltage dependent anion channel (VDAC), and cyclophilin D (CyP-D) of mitochondrial permeability transition pore (mPTP) showed that ISO reduced their level, while AST restored the content of these proteins almost to the control value. In general, AST improves the functional state of mitochondria and can be considered as a prophylactic drug in various therapeutic approaches.

Isolation and Characterization of Homologically Expressed Methanol Dehydrogenase from Methylorubrum extorquens AM1 for the Development of Bioelectrocatalytical Systems.

(Ca2+)-dependent pyrroloquinolinequinone (PQQ)-dependent methanol dehydrogenase (MDH) (EC: 1.1.2.7) is one of the key enzymes of primary C1-compound metabolism in methylotrophy. PQQ-MDH is a promising catalyst for electrochemical biosensors and biofuel cells. However, the large-scale use of PQQ-MDH in bioelectrocatalysis is not possible due to the low yield of the native enzyme. Homologously overexpressed MDH was obtained from methylotrophic bacterium Methylorubrum extorquens AM1 by cloning the gene of only one subunit, mxaF. The His-tagged enzyme was easily purified by immobilized metal ion affinity chromatography (36% yield). A multimeric form (α6ß6) of recombinant PQQ-MDH possessing enzymatic activity (0.54 U/mg) and high stability was demonstrated for the first time. pH-optimum of the purified protein was about 9-10; the enzyme was activated by ammonium ions. It had the highest affinity toward methanol (KM = 0.36 mM). The recombinant MDH was used for the fabrication of an amperometric biosensor. Its linear range for methanol concentrations was 0.002-0.1 mM, the detection limit was 0.7 µM. The properties of the invented biosensor are competitive to the analogs, meaning that this enzyme is a promising catalyst for industrial methanol biosensors. The developed simplified technology for PQQ-MDH production opens up new opportunities for the development of bioelectrocatalytic systems.

Genome Complexity Browser: Visualization and quantification of genome variability.

Comparative genomics studies may be used to acquire new knowledge regarding genome architecture, which defines the rules for combining sets of genes in the genome of living organisms. Hundreds of thousands of prokaryotic genomes have been sequenced and assembled. However, computational tools capable of simultaneously comparing large numbers of genomes are lacking. We developed the Genome Complexity Browser, a tool that allows the visualization of gene contexts, in a graph-based format, and the quantification of variability for different segments of a genome. The graph-based visualization allows the inspection of changes in gene contents and neighborhoods across hundreds of genomes, simultaneously, which may facilitate the identification of conserved and variable segments of operons or the estimation of the overall variability associated with a particular genome locus. We introduced a measure called complexity, to quantify genome variability. Intraspecies and interspecies comparisons revealed that regions with high complexity values tended to be located in areas that are conserved across different strains and species.

Ab initio molecular dynamics on quantum computers.

Ab initio molecular dynamics (AIMD) is a valuable technique for studying molecules and materials at finite temperatures where the nuclei evolve on potential energy surfaces obtained from accurate electronic structure calculations. In this work, we present an approach to running AIMD simulations on noisy intermediate-scale quantum (NISQ)-era quantum computers. The electronic energies are calculated on a quantum computer using the variational quantum eigensolver (VQE) method. Algorithms for computation of analytical gradients entirely on a quantum computer require quantum fault-tolerant hardware, which is beyond NISQ-era. Therefore, we compute the energy gradients numerically using finite differences, the Hellmann-Feynman theorem, and a correlated sampling technique. This method only requires additional classical calculations of electron integrals for each degree of freedom without any additional computations on a quantum computer beyond the initial VQE run. As a proof of concept, AIMD simulations are demonstrated for the H2 molecule on IBM quantum devices. In addition, we demonstrate the validity of the method for larger molecules using full configuration interaction wave functions. As quantum hardware and noise mitigation techniques continue to improve, the method can be utilized for studying larger molecular systems.

Synaptic input as a directional cue for migrating interneuron precursors.

During CNS development, interneuron precursors have to migrate extensively before they integrate in specific microcircuits. Known regulators of neuronal motility include classical neurotransmitters, yet the mechanisms that assure interneuron dispersal and interneuron/projection neuron matching during histogenesis remain largely elusive. We combined time-lapse video microscopy and electrophysiological analysis of the nascent cerebellum of transgenic Pax2-EGFP mice to address this issue. We found that cerebellar interneuronal precursors regularly show spontaneous postsynaptic currents, indicative of synaptic innervation, well before settling in the molecular layer. In keeping with the sensitivity of these cells to neurotransmitters, ablation of synaptic communication by blocking vesicular release in acute slices of developing cerebella slows migration. Significantly, abrogation of exocytosis primarily impedes the directional persistence of migratory interneuronal precursors. These results establish an unprecedented function of the early synaptic innervation of migrating neuronal precursors and demonstrate a role for synapses in the regulation of migration and pathfinding.

Elevation of Intracellular Na+ Contributes to Expression of Early Response Genes Triggered by Endothelial Cell Shrinkage.

BACKGROUND/AIMS: Prolonged hyperosmotic shrinkage evokes expression of osmoprotective genes via nuclear factor NFAT5-mediated pathway and activates Na+ influx via hypertonicity-induced cation channels (HICC). In human umbilical vein endothelial cells (HUVEC) elevation of intracellular sodium concentration ([Na+]i) triggers transcription of dozens of early response genes (ERG). This study examined the role of monovalent cations in the expression of Na+i-sensitive ERGs in iso- and hyperosmotically shrunken HUVEC. METHODS: Cell volume was measured by 3D reconstruction of cell shape and as 14C-urea available space. Intracellular Na+ and K+ content was measured by flame atomic absorption spectrometry. ERG transcription was estimated by RT-PCR. RESULTS: Elevation of medium osmolality by 150 mM mannitol or cell transfer from hypo- to isosmotic medium decreased cell volume by 40-50%. Hyperosmotic medium increased [Na+]i by 2-fold whereas isosmotic shrinkage had no impact on this parameter. Hyperosmotic but not isosmotic shrinkage increased up-to 5-fold the content of EGR1, FOS, ATF3, ZFP36 and JUN mRNAs. Expression of these ERGs triggered by hyperosmotic shrinkage and Na+,K+-ATPase inhibition by 0.1 µM ouabain exhibited positive correlation (R2=0.9383, p=0.0005). Isosmotic substitution of NaCl by N-methyl-D-glucamine abolished an increment of [Na+]i and ERG expression triggered by mannitol addition. CONCLUSION: Augmented expression of ERGs in hyperosmotically shrunken HUVEC is mediated by elevation of [Na+]i.

Long-term impact of fecal transplantation in healthy volunteers.

BACKGROUND: Fecal microbiota transplantation (FMT) has been recently approved by FDA for the treatment of refractory recurrent clostridial colitis (rCDI). Success of FTM in treatment of rCDI led to a number of studies investigating the effectiveness of its application in the other gastrointestinal diseases. However, in the majority of studies the effects of FMT were evaluated on the patients with initially altered microbiota. The aim of our study was to estimate effects of FMT on the gut microbiota composition in healthy volunteers and to monitor its long-term outcomes. RESULTS: We have performed a combined analysis of three healthy volunteers before and after capsule FMT by evaluating their general condition, adverse clinical effects, changes of basic laboratory parameters, and several immune markers. Intestinal microbiota samples were evaluated by 16S rRNA gene and shotgun sequencing. The data analysis demonstrated profound shift towards the donor microbiota taxonomic composition in all volunteers. Following FMT, all the volunteers exhibited gut colonization with donor gut bacteria and persistence of this effect for almost ∼1 year of observation. Transient changes of immune parameters were consistent with suppression of T-cell cytotoxicity. FMT was well tolerated with mild gastrointestinal adverse events, however, one volunteer developed a systemic inflammatory response syndrome. CONCLUSIONS: The FMT leads to significant long-term changes of the gut microbiota in healthy volunteers with the shift towards donor microbiota composition and represents a relatively safe procedure to the recipients without long-term adverse events.

A discontinuous basis enables numerically exact solution of the Schrödinger equation around conical intersections in the adiabatic representation.

Solving the vibrational Schrödinger equation in the neighborhood of conical intersections in the adiabatic representation is a challenge. At the intersection point, first- and second-derivative nonadiabatic coupling matrix elements become singular, with the singularity in the second-derivative coupling (diagonal Born-Oppenheimer correction) being non-integrable. These singularities result from discontinuities in the vibronic functions associated with the individual adiabatic states, and our group has recently argued that these divergent matrix elements cancel when discontinuous adiabatic vibronic functions sum to a continuous total nonadiabatic wave function. Here we describe the realization of this concept: a novel scheme for the numerically exact solution of the Schrödinger equation in the adiabatic representation. Our approach is based on a basis containing functions that are discontinuous at the intersection point. We demonstrate that the individual adiabatic nuclear wave functions are themselves discontinuous at the intersection point. This proves that discontinuous basis functions are essential to any tractable method that solves the Schrödinger equation around conical intersections in the adiabatic representation with high numerical precision. We establish that our method provides numerically exact results by comparison to reference calculations performed in the diabatic representation. In addition, we quantify the energetic error associated with constraining the density to be zero at the intersection point, a natural approximation. Prospects for extending the present treatment of a two-dimensional model to systems of higher dimensionality are discussed.

Quantum-Mechanical Relation between Atomic Dipole Polarizability and the van der Waals Radius.

The atomic dipole polarizability α and the van der Waals (vdW) radius R_{vdW} are two key quantities to describe vdW interactions between atoms in molecules and materials. Until now, they have been determined independently and separately from each other. Here, we derive the quantum-mechanical relation R_{vdW}=const×α^{1/7}, which is markedly different from the common assumption R_{vdW}∝α^{1/3} based on a classical picture of hard-sphere atoms. As shown for 72 chemical elements between hydrogen and uranium, the obtained formula can be used as a unified definition of the vdW radius solely in terms of the atomic polarizability. For vdW-bonded heteronuclear dimers consisting of atoms A and B, the combination rule α=(α_{A}+α_{B})/2 provides a remarkably accurate way to calculate their equilibrium interatomic distance. The revealed scaling law allows us to reduce the empiricism and improve the accuracy of interatomic vdW potentials, at the same time suggesting the existence of a nontrivial relation between length and volume in quantum systems.

Dynamic Behavior of RNA Nanoparticles Analyzed by AFM on a Mica/Air Interface.

RNA is an attractive biopolymer for engineering self-assembling materials suitable for biomedical applications. Previously, programmable hexameric RNA rings were developed for the controlled delivery of up to six different functionalities. To increase the potential for functionalization with little impact on nanoparticle topology, we introduce gaps into the double-stranded regions of the RNA rings. Molecular dynamic simulations are used to assess the dynamic behavior and the changes in the flexibility of novel designs. The changes suggested by simulations, however, cannot be clearly confirmed by the conventional techniques such as nondenaturing polyacrylamide gel electrophoresis (native-PAGE) and dynamic light scattering (DLS). Also, an in vitro analysis in primary cultures of human peripheral blood mononuclear cells does not reveal any discrepancy in the immunological recognition of new assemblies. To address these deficiencies, we introduce a computer-assisted quantification strategy. This strategy is based on an algorithmic atomic force microscopy (AFM)-resolved deformation analysis of the RNA nanoparticles studied on a mica/air interface. We validate this computational method by manual image analysis and fitting it to the simulation-predicted results. The presented nanoparticle modification strategy and subsequent AFM-based analysis are anticipated to provide a broad spectrum approach for the future development of nucleic acid-based nanotechnology.