What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants.

Many problems of modern genetics and functional genomics require the assessment of functional effects of sequence variants, including gene expression changes. Machine learning is considered to be a promising approach for solving this task, but its practical applications remain a challenge due to the insufficient volume and diversity of training data. A promising source of valuable data is a saturation mutagenesis massively parallel reporter assay, which quantitatively measures changes in transcription activity caused by sequence variants.

Global distribution of earthworm diversity.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass.

Analysis of Biased Competition and Cooperation for Attention in the Cerebral Cortex.

A new approach to understanding the interaction between cortical areas is provided by a mathematical analysis of biased competition, which describes many interactions between cortical areas, including those involved in top-down attention. The analysis helps to elucidate the principles of operation of such cortical systems, and in particular the parameter values within which biased competition operates. The analytic results are supported by simulations that illustrate the operation of the system with parameters selected from the analysis.

Networks of random trees as a model of neuronal connectivity.

We provide an analysis of a randomly grown 2-d network which models the morphological growth of dendritic and axonal arbors. From the stochastic geometry of this model we derive a dynamic graph of potential synaptic connections. We estimate standard network parameters such as degree distribution, average shortest path length and clustering coefficient, considering all these parameters as functions of time.

After-effects of 10 Hz tACS over the prefrontal cortex on phonological word decisions.

Introduction: Previous work in the language domain has shown that 10 Hz rTMS of the left or right posterior inferior frontal gyrus (pIFG) in the prefrontal cortex impaired phonological decision-making, arguing for a causal contribution of the bilateral pIFG to phonological processing. However, the neurophysiological correlates of these effects are unclear. The present study addressed the question whether neural activity in the prefrontal cortex could be modulated by 10 Hz tACS and how this would affect phonological decisions.

Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes.

The structure and properties of diphenylalanine (FF) peptide nanotubes (PNT) based on phenylalanine were investigated by various molecular modeling methods. The main approach employed semi-empirical quantum-chemical methods (PM3 and AM1). Ab initio, density functional theory methods and molecular mechanical approaches were also used.

Thermodynamics of 3D diamond-like epitaxial (film) morphologies on 1D modulated substrate: Weak crystallization theory.

Being inspired by recent theoretical findings in block copolymer ordering, we present, within the simplest version of the Landau weak crystallization theory, a consistent treatment of the thin film thermodynamics. It is first shown that a proper design of the period of a 1D modulated substrate results in the formation of a 3D morphology whose symmetry is close to a cubic diamond one and differs from the latter due to a symmetry violation caused by the block copolymer-substrate interaction. The corresponding phase portraits are built.

Analytic theory of relativistic self-focusing for a Gaussian light beam entering a plasma: Renormalization-group approach.

Using the renormalization-group approach, we consider an analytic theory describing the formation of a self-focusing structure of a laser beam in a plasma with relativistic nonlinearity for a given radial intensity distribution at the entrance and derive approximate analytic solutions. We study three stationary self-focused waveguide propagation modes with respect to controlling laser-plasma parameters for a Gaussian radial intensity distribution at the plasma boundary. The proposed theory specifies the domains and their boundaries on the plane of the controlling parameters where (1) self-trapping, (2) self-focusing on the axis, and (3) tubular self-focusing solutions occur.

Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.

The integrative analysis of high-throughput reporter assays, machine learning, and profiles of epigenomic chromatin state in a broad array of cells and tissues has the potential to significantly improve our understanding of noncoding regulatory element function and its contribution to human disease. Here, we report results from the CAGI 5 regulation saturation challenge where participants were asked to predict the impact of nucleotide substitution at every base pair within five disease-associated human enhancers and nine disease-associated promoters. A library of mutations covering all bases was generated by saturation mutagenesis and altered activity was assessed in a massively parallel reporter assay (MPRA) in relevant cell lines.

The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in .

Inorganic polyphosphate (polyP) is crucial for adaptive reactions and stress response in microorganisms. A convenient model to study the role of polyP in yeast is the strain CRN/PPN1 that overexpresses polyphosphatase Ppn1 with stably decreased polyphosphate level. In this study, we combined the whole-transcriptome sequencing, fluorescence microscopy, and polyP quantification to characterize the CRN/PPN1 response to manganese and oxidative stresses.

Phase relations of theta oscillations in a computer model of the hippocampal CA1 field: Key role of Schaffer collaterals.

The hippocampal theta rhythm (4-12 Hz) is one of the most important electrophysiological processes in the hippocampus, it participates in cognitive hippocampal functions, such as navigation in space, novelty detection, and declarative memory. We use neural network modeling to study the mechanism of theta rhythm emergence in the CA1 microcircuitry. Our model of the CA1 field includes biophysical representation of major cell types related to the theta rhythm emergence: excitatory pyramidal cells and two types of inhibitory interneurons, PV+ basket cells and oriens lacunosum-moleculare (OLM) cells.

A Comparative Study of Intramolecular Mobility of Single Siloxane and Carbosilane Dendrimers via Molecular Dynamics Simulations.

A comparative analysis of intramolecular dynamics of four types of isolated dendrimers from the fourth to the seventh generations belonging to the siloxane and carbosilane families, differing in spacer length, core functionality, and the type of chemical bonds, has been performed via atomic molecular dynamics simulations. The average radial and angular positions of all Si branching atoms of various topological layers within the dendrimer interior, as well as their variations, have been calculated, and the distributions of the relaxation times of their radial and angular motions have been found. It has been shown that the dendrons of all the dendrimers elongate from the center and decrease in a solid angle with an increasing generation number.

Petawatt Laser Guiding and Electron Beam Acceleration to 8 GeV in a Laser-Heated Capillary Discharge Waveguide.

Guiding of relativistically intense laser pulses with peak power of 0.85 PW over 15 diffraction lengths was demonstrated by increasing the focusing strength of a capillary discharge waveguide using laser inverse bremsstrahlung heating. This allowed for the production of electron beams with quasimonoenergetic peaks up to 7.

Potential Markers of Autoimmune Diseases, Alleles rs115662534(T) and rs548231435(C), Disrupt the Binding of Transcription Factors STAT1 and EBF1 to the Regulatory Elements of Human CD40 Gene.

CD40 receptor is expressed on B lymphocytes and other professional antigen-presenting cells. The binding of CD40 to its ligand CD154 on the surface of T helper cells plays an important role in the activation of B lymphocytes required for production of antibodies, in particular, against autoantigens. Association of several single nucleotide polymorphisms (SNPs) located in the non-coding areas of human CD40 locus with the elevated risk of autoimmune diseases has been demonstrated.

svist4get: a simple visualization tool for genomic tracks from sequencing experiments.

Background: High-throughput sequencing often provides a foundation for experimental analyses in the life sciences. For many such methods, an intermediate layer of bioinformatics data analysis is the genomic signal track constructed by short read mapping to a particular genome assembly. There are many software tools to visualize genomic tracks in a web browser or with a stand-alone graphical user interface.

Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains.

TMA20 (MCT-1), TMA22 (DENR) and TMA64 (eIF2D) are eukaryotic translation factors involved in ribosome recycling and re-initiation. They operate with P-site bound tRNA in post-termination or (re-)initiation translation complexes, thus participating in the removal of 40S ribosomal subunit from mRNA stop codons after termination and controlling translation re-initiation on mRNAs with upstream open reading frames (uORFs), as well as initiation on some specific mRNAs. Here we report ribosomal profiling data of strains with individual deletions of , or both and genes.

An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana.

Background: Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. Some of them include samples treated by environmental or biotic stresses. However, most studies explore only limited set of organs and developmental stages (leaves or seedlings).

Comparative analysis of plastocyanin-cytochrome f complex formation in higher plants, green algae and cyanobacteria.

Mechanisms of the complex formation between plastocyanin and cytochrome f in higher plants (Spinacia oleracea and Brassica rapa), green microalgae Chlamydomonas reinhardtii and two species of cyanobacteria (Phormidium laminosum and Nostoc sp.) were investigated using combined Brownian and molecular dynamics simulations and hierarchical cluster analysis. In higher plants and green algae, electrostatic interactions force plastocyanin molecule close to the heme of cytochrome f.

CpG traffic lights are markers of regulatory regions in human genome.

Background: DNA methylation is involved in the regulation of gene expression. Although bisulfite-sequencing based methods profile DNA methylation at a single CpG resolution, methylation levels are usually averaged over genomic regions in the downstream bioinformatic analysis.

Results: We demonstrate that on the genome level a single CpG methylation can serve as a more accurate predictor of gene expression than an average promoter / gene body methylation.

Mask-based approach to phasing of single-particle diffraction data. II. Likelihood-based selection criteria.

A new type of mask-selection criterion is suggested for mask-based phasing. In this phasing approach, a large number of connected molecular masks are randomly generated. Structure-factor phases corresponding to a trial mask are accepted as an admissible solution of the phase problem if the mask satisfies some specified selection rules that are key to success.

Should the Treatment of Amyloidosis Be Personified? Molecular Mechanism of Amyloid Formation by Aβ Peptide and Its Fragments.

Aβ and Aβ peptides are believed to be associated with Alzheimer's disease. Aggregates (plaques) of Aβ fibrils are found in the brains of humans affected with this disease. The mechanism of formation of Aβ fibrils has not been studied completely, which hinders the development of a correct strategy for therapeutic prevention of this neurodegenerative disorder.

Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data.

Objectives: Mammalian genomics studies, especially those focusing on transcriptional regulation, require information on genomic locations of regulatory regions, particularly, transcription factor (TF) binding sites. There are plenty of published ChIP-Seq data on in vivo binding of transcription factors in different cell types and conditions. However, handling of thousands of separate data sets is often impractical and it is desirable to have a single global map of genomic regions potentially bound by a particular TF in any of studied cell types and conditions.

Structural characterization of geranylgeranyl pyrophosphate synthase GACE1337 from the hyperthermophilic archaeon Geoglobus acetivorans.

A novel type 1 geranylgeranyl pyrophosphate synthase GACE1337 has been identified within the genome of a newly identified hyperthermophilic archaeon Geoglobus acetivorans. The enzyme has been cloned and over-expressed in Escherichia coli. The recombinant enzyme has been biochemically and structurally characterized.

Search for Functional Flexible Regions in the G-protein Family: New Reading of the FoldUnfold Program.

Background: Unstructured regions in proteins can vary from several amino acid residues to a completely disordered sequence. Since such regions play an important role in the protein functioning, much attention is being paid to their prediction. Special different programs are available for this purpose; however, predictions obtained vary from protein to protein.