Parallel evolution provides powerful natural experiments for studying repeatability of evolution and genomic basis of adaptation. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested. We sampled foothill and alpine populations in all regions known to harbor the alpine ecotype and used SNP genotyping to test for repeated alpine colonization. Then, we combined field surveys and a common garden experiment to quantify phenotypic parallelism. Genetic clustering by region but not elevation and coalescent simulations demonstrated parallel origin of alpine ecotype in four mountain regions. Alpine populations exhibited parallelism in height and floral traits which persisted after two generations in cultivation. In contrast, leaf traits were distinctive only in certain region(s), reflecting a mixture of plasticity and genetically determined non-parallelism. We demonstrate varying degrees and causes of parallelism and non-parallelism across populations and traits within a plant species. Parallel divergence along a sharp elevation gradient makes A. arenosa a promising candidate for studying genomic basis of adaptation.

• Klíčová slova
• Arabidopsis, adaptation, alpine environments, convergence, parallel evolution, phenotypic parallelism,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. RESULTS: We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. CONCLUSIONS: The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.

• Klíčová slova
• Assembly, Metagenomics, NGS analysis, Parallel processing, Viral dark matter, Viromes, Virus, Visualization,
• MeSH
• genetická variace MeSH
• genomika metody   MeSH
• internet * MeSH
• lidé MeSH
• mikrobiota genetika   MeSH
• software * MeSH
• viry genetika   MeSH
• vysoce účinné nukleotidové sekvenování * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Recently, we reported an inhibitory effect of guanine substitutions on the conformational switch from antiparallel to parallel quadruplexes (G4) induced by dehydrating agents. As a possible cause, we proposed a difference in the sensitivity of parallel and antiparallel quadruplexes to the guanine substitutions in the resulting thermodynamic stability. Reports on the influence of guanine substitutions on the biophysical properties of intramolecular parallel quadruplexes are rare. Moreover, such reports are often complicated by the multimerisation tendencies of parallel quadruplexes. To address this incomplete knowledge, we employed circular dichroism spectroscopy (CD), both as stopped-flow-assisted fast kinetics measurements and end-point measurements, accompanied by thermodynamic analyses, based on UV absorption melting profiles, and electrophoretic methods. We showed that parallel quadruplexes are significantly more sensitive towards guanine substitutions than antiparallel ones. Furthermore, guanine-substituted variants, which in principle might correspond to native genomic sequences, distinctly differ in their biophysical properties, indicating that the four guanines in each tetrad of parallel quadruplexes are not equal. In addition, we were able to distinguish by CD an intramolecular G4 from intermolecular ones resulting from multimerisation mediated by terminal tetrad association, but not from intermolecular G4s formed due to inter-strand Hoogsteen hydrogen bond formation. In conclusion, our study indicates significant variability in parallel quadruplex structures, otherwise disregarded without detailed experimental analysis.

• Klíčová slova
• DNA secondary structure, circular dichroism, multimerisation, parallel guanine quadruplex, stopped-flow,
• MeSH
• cirkulární dichroismus MeSH
• DNA chemie   genetika   MeSH
• G-kvadruplexy MeSH
• guanin chemie   MeSH
• konformace nukleové kyseliny MeSH
• molekulární modely MeSH
• substituce aminokyselin * MeSH
• termodynamika MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA MeSH
• guanin MeSH

Computational design of new proteins is often performed by optimizing the amino acid sequence. This sequence is characterized by an energy (lower energy means better propensity to form the desired 3D structure) that is sampled and minimized. Here, we use the parallel tempering algorithm to accelerate this task. ESMfold was used to predict the structures of the sampled proteins and calculate energy. Starting from random amino acid sequences, each sequence was sampled using the Monte Carlo method at one of a series of temperatures, and these replicas were being exchanged by the parallel tempering method. A series of 100 or 200 residue proteins was designed to maximize confidence in structure prediction and globularity and minimize surface hydrophobic residues. We show that parallel tempering is a viable alternative to Monte Carlo sampling without replica exchanges and simulated annealing or related energy-based protein design methods, especially in the situation where a continuous flow of designed sequences is desired.

• Klíčová slova
• ESMfold, Monte Carlo, machine learning, parallel tempering, protein design, replica exchange,
• MeSH
• algoritmy * MeSH
• hydrofobní a hydrofilní interakce MeSH
• konformace proteinů MeSH
• metoda Monte Carlo MeSH
• molekulární modely MeSH
• proteinové inženýrství * metody   MeSH
• proteiny * chemie   genetika   MeSH
• sekvence aminokyselin MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteiny * MeSH

Functional and structural adjustments of plants in response to environmental factors, including those occurring in alpine habitats, can result in transient acclimation, plastic phenotypic adjustments and/or heritable adaptation. To unravel repeatedly selected traits with potential adaptive advantage, we studied parallel (ecotypic) and non-parallel (regional) differentiation in leaf traits in alpine and foothill ecotypes of Arabidopsis arenosa. Leaves of plants from eight alpine and eight foothill populations, representing three independent alpine colonization events in different mountain ranges, were investigated by microscopy techniques after reciprocal transplantation. Most traits clearly differed between the foothill and the alpine ecotype, with plastic adjustments to the local environment. In alpine populations, leaves were thicker, with altered proportions of palisade and spongy parenchyma, and had fewer trichomes, and chloroplasts contained large starch grains with less stacked grana thylakoids compared to foothill populations. Geographical origin had no impact on most traits except for trichome and stomatal density on abaxial leaf surfaces. The strong parallel, heritable ecotypic differentiation in various leaf traits and the absence of regional effects suggests that most of the observed leaf traits are adaptive. These trait shifts may reflect general trends in the adaptation of leaf anatomy associated with the colonization of alpine habitats.

• Klíčová slova
• adaptation, alpine environment, ecotype, leaf anatomy, parallel evolution,
• Publikační typ
• časopisecké články MeSH

Parallel adaptive radiations have arisen following the colonization of islands by lizards and lakes by fishes. In these classic examples, parallel adaptive radiation is a response to the ecological opportunities afforded by the colonization of novel ecosystems and similar adaptive landscapes that favour the evolution of similar suites of ecomorphs, despite independent evolutionary histories. Here, we demonstrate that parallel adaptive radiations of cichlid fishes arose in South American rivers. Speciation-assembled communities of pike cichlids (Crenicichla) have independently diversified into similar suites of novel ecomorphs in the Uruguay and Paraná Rivers, including crevice feeders, periphyton grazers and molluscivores. There were bursts in phenotypic evolution associated with the colonization of each river and the subsequent expansion of morphospace following the evolution of the ecomorphs. These riverine clades demonstrate that characteristics emblematic of textbook parallel adaptive radiations of island- and lake-dwelling assemblages are feasible evolutionary outcomes even in labile ecosystems such as rivers.

• Klíčová slova
• Crenicichla, cichlid, convergence, diversification, parallel evolution, species flock,
• MeSH
• biologická adaptace genetika   MeSH
• biologická evoluce * MeSH
• cichlidy anatomie a histologie   genetika   MeSH
• ekosystém MeSH
• fenotyp MeSH
• fylogeneze MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• jezera MeSH
• ostrovy MeSH
• řeky * MeSH
• sekvenování celého genomu MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Geografické názvy
• ostrovy MeSH
• Uruguay MeSH

Modelling the flow properties of rubber blends makes it possible to predict their rheological behaviour during the processing and production of rubber-based products. As the nonlinear nature of such complex processes complicates the creation of exact analytical models, it is appropriate to use artificial intelligence tools in this modelling. The present study was implemented to develop a highly efficient artificial neural network model, optimised using a novel training algorithm with fast parallel computing to predict the results of rheological tests of rubber blends performed under different conditions. A series of 120 real dynamic viscosity-time curves, acquired by a rubber process analyser for styrene-butadiene rubber blends with varying carbon black contents vulcanised at different temperatures, were analysed using a Generalised Regression Neural Network. The model was optimised by limiting the fitting error of the training dataset to a pre-specified value of less than 1%. All repeated calculations were made via parallel computing with multiple computer cores, which significantly reduces the total computation time. An excellent agreement between the predicted and measured generalisation data was found, with an error of less than 4.7%, confirming the high generalisation performance of the newly developed model.

• Klíčová slova
• curing process, generalised regression neural network, intelligent modelling, parallel computing, rubber blends,
• Publikační typ
• časopisecké články MeSH

Parallel evolution is common in nature and provides one of the most compelling examples of rapid environmental adaptation. In contrast to the recent burst of studies addressing genomic basis of parallel evolution, integrative studies linking genomic and phenotypic parallelism are scarce. Edaphic islands of toxic serpentine soils provide ideal systems for studying rapid parallel adaptation in plants, imposing strong, spatially replicated selection on recently diverged populations. We leveraged threefold independent serpentine adaptation of Arabidopsis arenosa and combined reciprocal transplants, ion uptake phenotyping, and available genome-wide polymorphisms to test if parallelism is manifested to a similar extent at both genomic and phenotypic levels. We found pervasive phenotypic parallelism in functional traits yet with varying magnitude of fitness differences that was congruent with neutral genetic differentiation between populations. Limited costs of serpentine adaptation suggest absence of soil-driven trade-offs. On the other hand, the genomic parallelism at the gene level was significant, although relatively minor. Therefore, the similarly modified phenotypes, for example, of ion uptake arose possibly by selection on different loci in similar functional pathways. In summary, we bring evidence for the important role of genetic redundancy in rapid adaptation involving traits with polygenic architecture.

• Klíčová slova
• Adaptation, Arabidopsis, genetic redundancy, natural selection, parallel evolution, reciprocal transplant,
• MeSH
• Arabidopsis * genetika   MeSH
• fenotyp MeSH
• fyziologická adaptace genetika   MeSH
• genomika MeSH
• půda MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• půda MeSH

• Klíčová slova
• Vie Scope®, difficult intubation, parallel technique,
• MeSH
• intratracheální intubace metody   MeSH
• laryngoskopie metody   MeSH
• laryngoskopy * MeSH
• lidé MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• dopisy MeSH
• komentáře MeSH

Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of ecological environments during domestication, it is yet to be determined whether they have a common genetic basis for flowering time. In this study, we show, through map-based cloning, that flowering time in sorghum is controlled by a major quantitative trait locus (QTL) Heading Date 1 (HD1), located on chromosome 10. The causal gene encodes the CONSTANS gene family which contains a CCT domain. A 5-bp deletion of a minor allele present in the coding sequence leads to a gene frameshift that delays flowering in sorghum. In contrast, in foxtail millet, association mapping of HD1 showed a common causal site with a splicing variant from "GT" to "AT" that was highly correlated with flowering time. In addition, the rice HD1 gene is known to harbor several causal variants controlling flowering time. These data indicate that the major flowering time QTL HD1 was under parallel domestication in sorghum, foxtail millet, and rice. The pattern of common mixed minor, or even rare, causal alleles in HD1 across different species may be representative of the genetic basis of the domestication syndrome. Furthermore, large DNA sequence analysis of HD1 revealed multiple origins for domesticated sorghum and a single origin for domesticated foxtail millet.

• Klíčová slova
• comparative mapping, flowering time, parallel domestication,
• MeSH
• DNA rostlinná genetika   MeSH
• genetická variace MeSH
• genetické lokusy MeSH
• jedlá semena genetika   MeSH
• klonování DNA MeSH
• mapování chromozomů MeSH
• molekulární sekvence - údaje MeSH
• párování bází genetika   MeSH
• rostlinné geny * MeSH
• rostlinné proteiny chemie   genetika   MeSH
• rýže (rod) genetika   MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza DNA MeSH
• sekvenční delece MeSH
• sekvenční seřazení MeSH
• selekce (genetika) MeSH
• Setaria (rostlina) genetika   MeSH
• Sorghum genetika   MeSH
• terciární struktura proteinů MeSH
• zemědělství * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH
• rostlinné proteiny MeSH