• MeSH
• kauzalita MeSH
• pravděpodobnost MeSH

• Konspekt
• Přírodní vědy. Matematické vědy
• NLK Obory
• přírodní vědy
• statistika, zdravotnická statistika

Nonequilibrium dynamics and non-neutral processes, such as trait-dependent dispersal, are often missing from quantitative island biogeography models despite their potential explanatory value. One of the most influential nonequilibrium models is the taxon cycle, but it has been difficult to test its validity as a general biogeographical framework. Here, we test predictions of the taxon cycle model using six expected phylogenetic patterns and a time-calibrated phylogeny of Indo-Pacific Odontomachus (Hymenoptera: Formicidae: Ponerinae), one of the ant genera that E.O. Wilson used when first proposing the hypothesis. We used model-based inference and a newly developed trait-dependent dispersal model to jointly estimate ancestral biogeography, ecology (habitat preferences for forest interiors, vs. "marginal" habitats, such as savannahs, shorelines, disturbed areas) and the linkage between ecology and dispersal rates. We found strong evidence that habitat shifts from forest interior to open and disturbed habitats increased macroevolutionary dispersal rate. In addition, lineages occupying open and disturbed habitats can give rise to both island endemics re-occupying only forest interiors and taxa that re-expand geographical ranges. The phylogenetic predictions outlined in this study can be used in future work to evaluate the relative weights of neutral (e.g., geographical distance and area) and non-neutral (e.g., trait-dependent dispersal) processes in historical biogeography and community ecology.

• MeSH
• ekosystém MeSH
• Formicidae klasifikace   genetika   MeSH
• fylogeneze * MeSH
• fylogeografie 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

BACKGROUND: All currently available methods of network/association inference from microarray gene expression measurements implicitly assume that such measurements represent the actual expression levels of different genes within each cell included in the biological sample under study. Contrary to this common belief, modern microarray technology produces signals aggregated over a random number of individual cells, a "nitty-gritty" aspect of such arrays, thereby causing a random effect that distorts the correlation structure of intra-cellular gene expression levels. RESULTS: This paper provides a theoretical consideration of the random effect of signal aggregation and its implications for correlation analysis and network inference. An attempt is made to quantitatively assess the magnitude of this effect from real data. Some preliminary ideas are offered to mitigate the consequences of random signal aggregation in the analysis of gene expression data. CONCLUSION: Resulting from the summation of expression intensities over a random number of individual cells, the observed signals may not adequately reflect the true dependence structure of intra-cellular gene expression levels needed as a source of information for network reconstruction. Whether the reported effect is extrime or not, the important point, is to reconize and incorporate such signal source for proper inference. The usefulness of inference on genetic regulatory structures from microarray data depends critically on the ability of investigators to overcome this obstacle in a scientifically sound way. REVIEWERS: This article was reviewed by Byung Soo KIM, Jeanne Kowalski and Geoff McLachlan.

• MeSH
• lidé MeSH
• modely genetické MeSH
• neparametrická statistika MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů metody   statistika a číselné údaje   MeSH
• stanovení celkové genové exprese metody   statistika a číselné údaje   MeSH
• výpočetní biologie metody   statistika a číselné údaje   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• práce podpořená grantem MeSH
• přehledy MeSH
• Research Support, N.I.H., Extramural MeSH

INTRODUCTION: Intracranial EEG (iEEG) data is a powerful way to map brain function, characterized by high temporal and spatial resolution, allowing the study of interactions among neuronal populations that orchestrate cognitive processing. However, the statistical inference and analysis of brain networks using iEEG data faces many challenges related to its sparse brain coverage, and its inhomogeneity across patients. METHODS: We review these challenges and develop a methodological pipeline for estimation of network structure not obtainable from any single patient, illustrated on the inference of the interaction among visual streams using a dataset of 27 human iEEG recordings from a visual experiment employing visual scene stimuli. 100 ms sliding window and multiple band-pass filtered signals are used to provide temporal and spectral resolution. For the connectivity analysis we showcase two connectivity measures reflecting different types of interaction between regions of interest (ROI): Phase Locking Value as a symmetric measure of synchrony, and Directed Transfer Function-asymmetric measure describing causal interaction. For each two channels, initial uncorrected significance testing at p < 0.05 for every time-frequency point is carried out by comparison of the data-derived connectivity to a baseline surrogate-based null distribution, providing a binary time-frequency connectivity map. For each ROI pair, a connectivity density map is obtained by averaging across all pairs of channels spanning them, effectively agglomerating data across relevant channels and subjects. Finally, the difference of the mean map value after and before the stimulation is compared to the same statistic in surrogate data to assess link significance. RESULTS: The analysis confirmed the function of the parieto-medial temporal pathway, mediating visuospatial information between dorsal and ventral visual streams during visual scene analysis. Moreover, we observed the anterior hippocampal connectivity with more posterior areas in the medial temporal lobe, and found the reciprocal information flow between early processing areas and medial place area. DISCUSSION: To summarize, we developed an approach for estimating network connectivity, dealing with the challenge of sparse individual coverage of intracranial EEG electrodes. Its application provided new insights into the interaction between the dorsal and ventral visual streams, one of the iconic dualities in human cognition.

• Publikační typ
• časopisecké články MeSH

By its very nature and philosophy, non-violence (and the practice or action of civil disobedience) amounts to violence. At its best, non-violence is the philosophy of using peaceful means, not force, to bring about political or social change. Civil disobedience implies the willful and deliberate violation of a certain law, civil rule and political authority in resistance to some real or perceived injustice. In other words, civil disobedience is the philosophical tradition that upholds non-violence as the sole route to resisting oppression and injustice. This implies psychological retaliation. But the question is, is the very idea of civil disobedience, as the practice of non-violence, not itself violent? In consideration of this, this article indicates the nature of civil disobedience, provides a typology of violence, and there-from argues that if violence implies violation (whether physical or psychological); that if nonviolence denounces violence; and that if civil disobedience is the praxis of non-violence, then by its very nature, theory and practice, non-violence/civil disobedience amounts to some form of violation or violence – the supposed evil that it is meant to cure.

• MeSH
• lidé MeSH
• násilí klasifikace   psychologie   MeSH
• násilnosti klasifikace   psychologie   MeSH
• občanské nepokoje klasifikace   psychologie   MeSH
• sociální problémy klasifikace   psychologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• přehledy MeSH

• MeSH
• anatomie srovnávací MeSH
• epitel ultrastruktura   MeSH
• fylogeneze MeSH
• mikroskopie elektronová rastrovací MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• srovnávací studie MeSH

• MeSH
• fylogeneze MeSH
• molekulární evoluce MeSH

• Konspekt
• Obecná botanika
• NLK Obory
• botanika
• NLK Publikační typ
• učebnice vysokých škol

Sequenced genomic data for carnivorous plants are scarce, especially regarding the mitogenomes (MTs) and further studies are crucial to obtain a better understanding of the topic. In this study, we sequenced and characterized the mitochondrial genome of the tuberous carnivorous plant Genlisea tuberosa, being the first of its genus to be sequenced. The genome comprises 729,765 bp, encoding 80 identified genes of which 36 are protein-coding, 40 tRNA, four rRNA genes, and three pseudogenes. An intronic region from the cox1 gene was identified that encodes an endonuclease enzyme that is present in the other sequenced species of Lentibulariaceae. Chloroplast genes (pseudogene and complete) inserted in the MT genome were identified, showing possible horizontal transfer between organelles. In addition, 50 pairs of long repeats from 94 to 274 bp are present, possibly playing an important role in the maintenance of the MT genome. Phylogenetic analysis carried out with 34 coding mitochondrial genes corroborated the positioning of the species listed here within the family. The molecular dynamism in the mitogenome (e.g. the loss or pseudogenization of genes, insertion of foreign genes, the long repeats as well as accumulated mutations) may be reflections of the carnivorous lifestyle where a significant part of cellular energy was shifted for the adaptation of leaves into traps molding the mitochondrial DNA. The sequence and annotation of G. tuberosa's MT will be useful for further studies and serve as a model for evolutionary and taxonomic clarifications of the group as well as improving our comprehension of MT evolution.

• MeSH
• fylogeneze MeSH
• genom mitochondriální * genetika   MeSH
• hluchavkotvaré * genetika   MeSH
• mitochondriální DNA MeSH
• mitochondriální geny MeSH
• RNA transferová genetika   MeSH
• Publikační typ
• časopisecké články MeSH

In most eukaryotes, centromere is determined by the presence of the centromere-specific histone variant CenH3. Two types of chromosome morphology are generally recognized with respect to centromere organization. Monocentric chromosomes possess a single CenH3-containing domain in primary constriction, whereas holocentric chromosomes lack the primary constriction and display dispersed distribution of CenH3. Recently, metapolycentric chromosomes have been reported in Pisum sativum, representing an intermediate type of centromere organization characterized by multiple CenH3-containing domains distributed across large parts of chromosomes that still form a single constriction. In this work, we show that this type of centromere is also found in other Pisum and closely related Lathyrus species, whereas Vicia and Lens genera, which belong to the same legume tribe Fabeae, possess only monocentric chromosomes. We observed extensive variability in the size of primary constriction and the arrangement of CenH3 domains both between and within individual Pisum and Lathyrus species, with no obvious correlation to genome or chromosome size. Search for CenH3 gene sequences revealed two paralogous variants, CenH3-1 and CenH3-2, which originated from a duplication event in the common ancestor of Fabeae species. The CenH3-1 gene was subsequently lost or silenced in the lineage leading to Vicia and Lens, whereas both genes are retained in Pisum and Lathyrus. Both of these genes appear to have evolved under purifying selection and produce functional CenH3 proteins which are fully colocalized. The findings described here provide the first evidence for a highly dynamic centromere structure within a group of closely related species, challenging previous concepts of centromere evolution.

• MeSH
• centromera genetika   MeSH
• chromatin metabolismus   MeSH
• chromozomy rostlin genetika   MeSH
• duplikace genu * MeSH
• Fabaceae cytologie   genetika   MeSH
• fylogeneze MeSH
• genetická variace MeSH
• metafáze genetika   MeSH
• molekulární evoluce MeSH
• molekulární sekvence - údaje MeSH
• rostlinné geny * MeSH
• rostlinné proteiny chemie   MeSH
• sekvence aminokyselin MeSH
• sekvence nukleotidů MeSH
• selekce (genetika) MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

We present a comprehensive characterization of the nucleoside N-ribohydrolase (NRH) family in two model plants, Physcomitrella patens (PpNRH) and maize (Zea mays; ZmNRH), using in vitro and in planta approaches. We identified two NRH subclasses in the plant kingdom; one preferentially targets the purine ribosides inosine and xanthosine, while the other is more active toward uridine and xanthosine. Both subclasses can hydrolyze plant hormones such as cytokinin ribosides. We also solved the crystal structures of two purine NRHs, PpNRH1 and ZmNRH3. Structural analyses, site-directed mutagenesis experiments, and phylogenetic studies were conducted to identify the residues responsible for the observed differences in substrate specificity between the NRH isoforms. The presence of a tyrosine at position 249 (PpNRH1 numbering) confers high hydrolase activity for purine ribosides, while an aspartate residue in this position confers high activity for uridine. Bud formation is delayed by knocking out single NRH genes in P. patens, and under conditions of nitrogen shortage, PpNRH1-deficient plants cannot salvage adenosine-bound nitrogen. All PpNRH knockout plants display elevated levels of certain purine and pyrimidine ribosides and cytokinins that reflect the substrate preferences of the knocked out enzymes. NRH enzymes thus have functions in cytokinin conversion and activation as well as in purine and pyrimidine metabolism.

• MeSH
• biokatalýza * účinky léků   MeSH
• cytokininy chemie   metabolismus   MeSH
• dusík farmakologie   MeSH
• fenotyp MeSH
• fylogeneze MeSH
• genový knockout MeSH
• hydrolýza účinky léků   MeSH
• kinetika MeSH
• krystalografie rentgenová MeSH
• kukuřice setá účinky léků   enzymologie   genetika   MeSH
• mechy účinky léků   enzymologie   genetika   růst a vývoj   MeSH
• molekulární modely MeSH
• molekulární sekvence - údaje MeSH
• mutageneze cílená MeSH
• mutantní proteiny chemie   metabolismus   MeSH
• N-glykosylhydrolasy chemie   genetika   metabolismus   MeSH
• pyrimidiny chemie   metabolismus   MeSH
• ribonukleosidy chemie   metabolismus   MeSH
• sekvence aminokyselin MeSH
• sekvenční seřazení MeSH
• substrátová specifita účinky léků   MeSH
• vazebná místa MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH