clusters
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- MeSH
- Betacoronavirus MeSH
- COVID-19 epidemiologie přenos prevence a kontrola MeSH
- epidemický výskyt choroby MeSH
- koronavirové infekce epidemiologie přenos prevence a kontrola MeSH
- trasování kontaktů MeSH
- Konspekt
- Veřejné zdraví a hygiena
- NLK Obory
- veřejné zdravotnictví
- infekční lékařství
- epidemiologie
- NLK Publikační typ
- publikace WHO
4 strany
- MeSH
- COVID-19 epidemiologie přenos prevence a kontrola MeSH
- epidemický výskyt choroby prevence a kontrola MeSH
- kontrola infekce metody organizace a řízení MeSH
- koronavirové infekce epidemiologie prevence a kontrola přenos MeSH
- Konspekt
- Veřejné zdraví a hygiena
- NLK Obory
- veřejné zdravotnictví
- epidemiologie
- infekční lékařství
- NLK Publikační typ
- publikace WHO
BACKGROUND: Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arabidopsis thaliana, 45S rRNA genes are found in two large ribosomal DNA (rDNA) clusters and little is known about the contribution of each to the overall transcription pattern in the species. RESULTS: By taking advantage of genome sequencing data from the 1001 Genomes Consortium, we characterize rRNA gene sequence variation within and among accessions. Notably, variation is not restricted to the pre-rRNA sequences removed during processing, but it is also present within the highly conserved ribosomal subunits. Through linkage mapping we assign these variants to a particular rDNA cluster unambiguously and use them as reporters of rDNA cluster-specific expression. We demonstrate that rDNA cluster-usage varies greatly among accessions and that rDNA cluster-specific expression and silencing is controlled via genetic interactions between entire rDNA cluster haplotypes (alleles). CONCLUSIONS: We show that rRNA gene cluster expression is controlled via complex epistatic and allelic interactions between rDNA haplotypes that apparently regulate the entire rRNA gene cluster. Furthermore, the sequence polymorphism we discovered implies that the pool of rRNA in a cell may be heterogeneous, which could have functional consequences.
BACKGROUND: Ubiquitin ligases (Ub-ligases) are essential intracellular enzymes responsible for the regulation of proteome homeostasis, signaling pathway crosstalk, cell differentiation and stress responses. Individual Ub-ligases exhibit their unique functions based on the nature of their substrates. They create a complex regulatory network with alternative and feedback pathways to maintain cell homeostasis, being thus important players in many physiological and pathological conditions. However, the functional classification of Ub-ligases needs to be revised and extended. METHODS: In the current study, we used a novel semantic biclustering technique for expression profiling of Ub-ligases and ubiquitination-related genes in the murine gastrointestinal tract (GIT). We accommodated a general framework of the algorithm for finding tissue-specific gene expression clusters in GIT. In order to test identified clusters in a biological system, we used a model of epithelial regeneration. For this purpose, a dextran sulfate sodium (DSS) mouse model, following with in situ hybridization, was used to expose genes with possible compensatory features. To determine cell-type specific distribution of Ub-ligases and ubiquitination-related genes, principal component analysis (PCA) and Uniform Manifold Approximation and Projection technique (UMAP) were used to analyze the Tabula Muris scRNA-seq data of murine colon followed by comparison with our clustering results. RESULTS: Our established clustering protocol, that incorporates the semantic biclustering algorithm, demonstrated the potential to reveal interesting expression patterns. In this manner, we statistically defined gene clusters consisting of the same genes involved in distinct regulatory pathways vs distinct genes playing roles in functionally similar signaling pathways. This allowed us to uncover the potentially redundant features of GIT-specific Ub-ligases and ubiquitination-related genes. Testing the statistically obtained results on the mouse model showed that genes clustered to the same ontology group simultaneously alter their expression pattern after induced epithelial damage, illustrating their complementary role during tissue regeneration. CONCLUSIONS: An optimized semantic clustering protocol demonstrates the potential to reveal a readable and unique pattern in the expression profiling of GIT-specific Ub-ligases, exposing ontologically relevant gene clusters with potentially redundant features. This extends our knowledge of ontological relationships among Ub-ligases and ubiquitination-related genes, providing an alternative and more functional gene classification. In a similar way, semantic cluster analysis could be used for studding of other enzyme families, tissues and systems.
- MeSH
- gastrointestinální trakt metabolismus MeSH
- lidé MeSH
- myši MeSH
- sémantika * MeSH
- shluková analýza MeSH
- ubikvitin genetika metabolismus MeSH
- ubikvitinligasy * genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Lots of brain diseases are recognized by EEG recording. EEG signal has a stochastic character, this stochastic nature makes the evaluation of EEG recording complicated. Therefore we use automatic classification methods for EEG processing. This methods help the expert to find significant or physiologically important segments in the EEG recording. The k-means algorithm is a frequently used method in practice for automatic classification. The main disadvantage of the k-means algorithm is the necessary determination of the number of clusters. So far there are many methods which try to determine optimal number of clusters for k-means algorithm. The aim of this study is to test functionality of the two most frequently used methods on EEG signals, concretely the elbow and the silhouette method. In this feasibility study we compared the results of both methods on simulated data and real EEG signal. We want to prove with the help of an expert the possibility to use these functions on real EEG signal. The results show that the silhouette method applied on EEG recordings is more time-consuming than the elbow method. Neither of the methods is able to correctly recognize the number of clusters in the EEG record by expert evaluation and therefore it is not applicable to the automatic classification of EEG based on k-means algorithm.
- MeSH
- algoritmy MeSH
- elektroencefalografie * metody MeSH
- lidé MeSH
- počítačová simulace MeSH
- počítačové zpracování signálu MeSH
- shluková analýza MeSH
- výzkum MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
We examined chromosomal distribution of major ribosomal DNAs (rDNAs), clustered in the nucleolar organizer regions (NORs), in 18 species of moths and butterflies using fluorescence in situ hybridization with a codling moth (Cydia pomonella) 18S rDNA probe. Most species showed one or two rDNA clusters in their haploid karyotype but exceptions with 4-11 clusters also occurred. Our results in a compilation with previous data revealed dynamic evolution of rDNA distribution in Lepidoptera except Noctuoidea, which showed a highly uniform rDNA pattern. In karyotypes with one NOR, interstitial location of rDNA prevailed, whereas two-NOR karyotypes showed mostly terminally located rDNA clusters. A possible origin of the single interstitial NOR by fusion between two NOR-chromosomes with terminal rDNA clusters lacks support in available data. In some species, spreading of rDNA to new, mostly terminal chromosome regions was found. The multiplication of rDNA clusters without alteration of chromosome numbers rules out chromosome fissions as a major mechanism of rDNA expansion. Based on rDNA dynamics in Lepidoptera and considering the role of ordered nuclear architecture in karyotype evolution, we propose ectopic recombination, i.e., homologous recombination between repetitive sequences of non-homologous chromosomes, as a primary motive force in rDNA repatterning.
- MeSH
- chromozomy genetika MeSH
- DNA genetika MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- genetická variace MeSH
- genom hmyzu MeSH
- hybridizace in situ fluorescenční MeSH
- karyotypizace MeSH
- molekulární evoluce MeSH
- motýli genetika MeSH
- můry genetika MeSH
- organizátor jadérka genetika MeSH
- rekombinace genetická MeSH
- repetitivní sekvence nukleových kyselin MeSH
- ribozomální DNA genetika MeSH
- RNA ribozomální 18S genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
