Arginine methylation expands the regulatory mechanisms and extends the genomic landscape under E2F control.

E2F is a family of master transcription regulators involved in mediating diverse cell fates. Here, we show that residue-specific arginine methylation (meR) by PRMT5 enables E2F1 to regulate many genes at the level of alternative RNA splicing, rather than through its classical transcription-based mechanism. The p100/TSN tudor domain protein reads the meR mark on chromatin-bound E2F1, allowing snRNA components of the splicing machinery to assemble with E2F1.

Spatiotemporal structure of cell fate decisions in murine neural crest.

Neural crest cells are embryonic progenitors that generate numerous cell types in vertebrates. With single-cell analysis, we show that mouse trunk neural crest cells become biased toward neuronal lineages when they delaminate from the neural tube, whereas cranial neural crest cells acquire ectomesenchyme potential dependent on activation of the transcription factor The choices that neural crest cells make to become sensory, glial, autonomic, or mesenchymal cells can be formalized as a series of sequential binary decisions. Each branch of the decision tree involves initial coactivation of bipotential properties followed by gradual shifts toward commitment.

Geochemical (soil) and phylogenetic (plant taxa) factors affecting accumulation of macro- and trace elements in three natural plant species.

A field study was carried out to estimate the variations in the concentrations of macro- and trace elements in the rhizosphere soil and in roots and leaves of three widely distributed plant species-couch grass, plantain, and yarrow collected simultaneously from two sites characterized by different soil parameters. Main attention was paid to environmental (soil characteristics) and phylogenetic (plant species) factors that can influence on the concentrations of different elements in the plants and in soils. Both the factors cannot be considered as independent, although their contribution to the plant elemental composition may be different.

Helminth-Related Tuftsin-Phosphorylcholine Compound and its Interplay with Autoimmune Diseases.

The hygiene theory represents one of the environmental facets that modulate the risk for developing autoimmune diseases. There is a reverse correlation between the presence of helminthes and flares of autoimmune diseases, which explains the rise in incidence of certain autoimmune diseases in developed countries. The protective properties of certain helminthes are attributed to their secretory compounds which immunomodulate the host immune network in order to survive.

Acquisition of L2 morphology by adult language learners.

Learning a new language requires the acquisition of morphological units that enable the fluent use of words in different grammatical contexts. While accumulating research has elucidated the neural processing of native morphology, much less is known about how second-language (L2) learners acquire and process morphology in their L2. To address this question, we presented native speakers as well as beginning and advanced learners of Finnish with spoken (1) derived words, (2) inflected words, (3) novel derivations (novel combinations of existing stem + suffix), and (4) pseudo-suffixed words (existing stem + pseudo-suffix) in a passive listening EEG experiment.

Helminth-Based Product and the Microbiome of Mice with Lupus.

The hygiene hypothesis claims that the lack of exposure to microorganisms in developed countries correlates with a rise in the incidence of autoimmune diseases. It was also found that helminths are able to modulate the immune response in hosts in order to survive. Consequently, several successful trials using helminths as a treatment for autoimmune patients have been reported.

Retromer in Synaptic Function and Pathology.

The retromer complex mediates export of select transmembrane proteins from endosomes to the trans-Golgi network (TGN) or to the plasma membrane. Dysfunction of retromer has been linked with slowly progressing neurodegenerative disorders, including Alzheimer's and Parkinson's disease (AD and PD). As these disorders affect synapses it is of key importance to clarify the function of retromer-dependent protein trafficking pathways in pre- and postsynaptic compartments.

Regression algorithm for calculating second-dimension retention indices in comprehensive two-dimensional gas chromatography.

Gas chromatography-mass spectrometry (GC-MS) is one of the most accurate, well developed, and reliable analytical tools for the analysis of volatile and semivolatile compounds. The GC-MS data have been extensively improved by enhancing the separation capacity via comprehensive two-dimensional gas chromatography (GC × GC). The reliability of the identification of the analytes in GC × GC-MS can be notably improved by applying the second-dimension retention index (I) as additional analytical parameter along with the commonly used first dimension retention index (I) and mass spectrum.

The effect of human leukocyte Antigens-DRB1 alleles on development of different tuberculosis forms in children.

Background: Nowadays, there is no doubt that the development of infectious process is determined not only by individual features of a human, but also by features of infection agent. It is commonly known that ability to form an adequate immune response is based on immunogenetic peculiarities of macroorganism.

Methods: The immunogenetic study was performed in 228 children from 1 to 15 years old with different manifestations of tuberculosis (TB).

The Effects of Chronic Amitriptyline on Zebrafish Behavior and Monoamine Neurochemistry.

Amitriptyline is a commonly used tricyclic antidepressant (TCA) inhibiting serotonin and norepinephrine reuptake. The exact CNS action of TCAs remains poorly understood, necessitating new screening approaches and novel model organisms. Zebrafish (Danio rerio) are rapidly emerging as a promising tool for pharmacological research of antidepressants, including amitriptyline.

Potential of wheat (Triticum aestivum L.) and pea (Pisum sativum) for remediation of soils contaminated with bromides and PAHs.

The aim of the research was to study a removal of polycyclic aromatic hydrocarbons (PAHs) and phytoextraction of bromine (Br) from contaminated soils. The experiments using pea and wheat seedlings as potential candidates for soil remediation were performed. The soil for the experiments was collected from a site slightly contaminated by some PAHs.

Ancestry inference of 96 population samples using microhaplotypes.

Microhaplotypes have become a new type of forensic marker with a great ability to identify and deconvolute mixtures because massively parallel sequencing (MPS) allows the alleles (haplotypes) of the multi-SNP loci to be determined directly for an individual. As originally defined, a microhaplotype locus is a short segment of DNA with two or more SNPs defining three or more haplotypes. The length is short enough, less than about 300 bp, that the read length of current MPS technology can produce a phase-known sequence of each chromosome of an individual.

Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads.

Transforming error-prone immunosequencing datasets into Ab repertoires is a fundamental problem in immunogenomics, and a prerequisite for studies of immune responses. Although various repertoire reconstruction algorithms were released in the last 3 y, it remains unclear how to benchmark them and how to assess the accuracy of the reconstructed repertoires. We describe an accurate IgReC algorithm for constructing Ab repertoires from high-throughput immunosequencing datasets and a new framework for assessing the quality of reconstructed repertoires.

Atrial time and voltage dispersion are both needed to predict new-onset atrial fibrillation in ischemic stroke patients.

Background: Atrial fibrillation (AF) is a known risk factor for ischemic stroke. Electrocardiographic predictors of AF in population studies such as the Framingham Heart Study, as well as in hypertensive patients have demonstrated a predictive value of the P-wave duration for development of AF. QRS vector magnitude has had a predictive value in ventricular arrhythmia development.

Non-permanent atrial fibrillation and oral anticoagulant therapy are related to survival during 10years after first-ever ischemic stroke.

Background: Atrial fibrillation (AF) detection in ischemic stroke patients triggers initiation of oral anticoagulant therapy (OAC). However, little is known regarding whether the persistency of AF affects long-term prognosis after ischemic stroke. We aimed to assess the impact of AF types and OAC on the outcome during a 10-year follow-up (FU) after first-ever ischemic stroke.

Vascular depression consensus report - a critical update.

Background: Vascular depression is regarded as a subtype of late-life depression characterized by a distinct clinical presentation and an association with cerebrovascular damage. Although the term is commonly used in research settings, widely accepted diagnostic criteria are lacking and vascular depression is absent from formal psychiatric manuals such as the Diagnostic and Statistical Manual of Mental Disorders, 5 edition - a fact that limits its use in clinical settings. Magnetic resonance imaging (MRI) techniques, showing a variety of cerebrovascular lesions, including extensive white matter hyperintensities, subcortical microvascular lesions, lacunes, and microinfarcts, in patients with late life depression, led to the introduction of the term "MRI-defined vascular depression".

Directed percolation process in the presence of velocity fluctuations: Effect of compressibility and finite correlation time.

The direct bond percolation process (Gribov process) is studied in the presence of random velocity fluctuations generated by the Gaussian self-similar ensemble with finite correlation time. We employ the renormalization group in order to analyze a combined effect of the compressibility and finite correlation time on the long-time behavior of the phase transition between an active and an absorbing state. The renormalization procedure is performed to the one-loop order.

Superfluid phase transition with activated velocity fluctuations: Renormalization group approach.

A quantum field model that incorporates Bose-condensed systems near their phase transition into a superfluid phase and velocity fluctuations is proposed. The stochastic Navier-Stokes equation is used for a generation of the velocity fluctuations. As such this model generalizes model F of critical dynamics.

Response of wheat and pea seedlings on increase of bromine concentration in the growth medium.

Biogeochemical cycles of bromine (Br) and its quantitative requirements for different plant species are still studied poorly. There is a need to examine Br pathways in plants and evaluate the factors important for Br accumulation in a plant. In the present work, the effects of different Br compounds on an uptake of Br by two plant species (wheat and pea) that tolerate Br differently (pea is more sensitive to Br compared with wheat) have been studied.

Predictors of new onset atrial fibrillation during 10-year follow-up after first-ever ischemic stroke.

Background: Paroxysmal atrial fibrillation (AF) may be underdiagnosed in ischemic stroke patients but may be pivotal for initiation of oral anticoagulation therapy. We assessed clinical and ECG predictors of new-onset AF during 10-year follow-up (FU) in ischemic stroke patients.

Methods: The study sample comprised of 227 first-ever ischemic stroke patients without AF (median age 73, interquartile range 25%-75% 63-80years, 92 female) and 1:1 age- and gender-matched controls without stroke and AF enrolled in the Lund Stroke Register from March 2001 to February 2002.

Coulomb-driven energy boost of heavy ions for laser-plasma acceleration.

An unprecedented increase of kinetic energy of laser accelerated heavy ions is demonstrated. Ultrathin gold foils have been irradiated by an ultrashort laser pulse at a peak intensity of 8×10^{19}  W/  cm^{2}. Highly charged gold ions with kinetic energies up to >200  MeV and a bandwidth limited energy distribution have been reached by using 1.

SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations.

Background: Adaptive alleles may rise in frequency as a consequence of positive selection, creating a pattern of decreased variation in the neighboring loci, known as a selective sweep. When the region containing this pattern is compared to another population with no history of selection, a rise in variance of allele frequencies between populations is observed. One challenge presented by large genome-wide datasets is the ability to differentiate between patterns that are remnants of natural selection from those expected to arise at random and/or as a consequence of selectively neutral demographic forces acting in the population.

Calcium signaling and meiotic exit at fertilization in Xenopus egg.

Calcium is a universal messenger that mediates egg activation at fertilization in all sexually reproducing species studied. However, signaling pathways leading to calcium generation and the mechanisms of calcium-induced exit from meiotic arrest vary substantially among species. Here, we review the pathways of calcium signaling and the mechanisms of meiotic exit at fertilization in the eggs of the established developmental model, African clawed frog, Xenopus laevis.

Ragout-a reference-assisted assembly tool for bacterial genomes.

Summary: Bacterial genomes are simpler than mammalian ones, and yet assembling the former from the data currently generated by high-throughput short-read sequencing machines still results in hundreds of contigs. To improve assembly quality, recent studies have utilized longer Pacific Biosciences (PacBio) reads or jumping libraries to connect contigs into larger scaffolds or help assemblers resolve ambiguities in repetitive regions of the genome. However, their popularity in contemporary genomic research is still limited by high cost and error rates.

ITPA (inosine triphosphate pyrophosphatase): from surveillance of nucleotide pools to human disease and pharmacogenetics.

Cellular nucleotide pools are often contaminated by base analog nucleotides which interfere with a plethora of biological reactions, from DNA and RNA synthesis to cellular signaling. An evolutionarily conserved inosine triphosphate pyrophosphatase (ITPA) removes the non-canonical purine (d)NTPs inosine triphosphate and xanthosine triphosphate by hydrolyzing them into their monophosphate form and pyrophosphate. Mutations in the ITPA orthologs in model organisms lead to genetic instability and, in mice, to severe developmental anomalies.