Natural History of a Satellite DNA Family: From the Ancestral Genome Component to Species-Specific Sequences, Concerted and Non-Concerted Evolution

Satellite DNA (satDNA) is the most variable fraction of the eukaryotic genome. Related species share a common ancestral satDNA library and changing of any library component in a particular lineage results in interspecific differences. Although the general developmental trend is clear, our knowledge of the origin and dynamics of satDNAs is still fragmentary. Here, we explore whole genome shotgun Illumina reads using the RepeatExplorer (RE) pipeline to infer satDNA family life stories in the genomes of Chenopodium species. The seven diploids studied represent separate lineages and provide an example of a species complex typical for angiosperms. Application of the RE pipeline allowed by similarity searches a determination of the satDNA family with a basic monomer of ~40 bp and to trace its transformation from the reconstructed ancestral to the species-specific sequences. As a result, three types of satDNA family evolutionary development were distinguished: (i) concerted evolution with mutation and recombination events; (ii) concerted evolution with a trend toward increased complexity and length of the satellite monomer; and (iii) non-concerted evolution, with low levels of homogenization and multidirectional trends. The third type is an example of entire repeatome transformation, thus producing a novel set of satDNA families, and genomes showing non-concerted evolution are proposed as a significant source for genomic diversity

The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the “library hypothesis”

Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome. Highly variable satDNA is involved in various genome functions, and a clear link between satellites and phenotypes exists in a wide range of organisms. However, little is known about the origin and temporal dynamics of satDNA. The "library hypothesis" indicates that the rapid evolutionary changes experienced by satDNAs are mostly quantitative. Although this hypothesis has received some confirmation, a number of its aspects are still controversial. A recently developed next-generation sequencing (NGS) method allows the determination of the satDNA landscape and could shed light on unresolved issues. Here, we explore low-coverage NGS data to infer satDNA evolution in the phylogenetic context of the diploid species of the Chenopodium album aggregate. The application of the Illumina read assembly algorithm in combination with Oxford Nanopore sequencing and fluorescent in situ hybridization allowed the estimation of eight satDNA families within the studied group, six of which were newly described. The obtained set of satDNA families of different origins can be divided into several categories, namely group-specific, lineage-specific and species-specific. In the process of evolution, satDNA families can be transmitted vertically and can be eliminated over time. Moreover, transposable element-derived satDNA families may appear repeatedly in the satellitome, creating an illusion of family conservation. Thus, the obtained data refute the "library hypothesis", rather than confirming it, and in our opinion, it is more appropriate to speak about "the library of the mechanisms of origin".Peer reviewe

The structural diversity of CACTA transposons in genomes of Chenopodium (Amaranthaceae, Caryophyllales) species: specific traits and comparison with the similar elements of Angiosperms

Background: CACTA transposable elements (TEs) comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) transposons. Over recent decades, CACTA elements were widely identified in species from the plant, fungi, and animal kingdoms, but sufficiently studied in the genomes of only a few model species although non-model genomes can bring additional and valuable information. It primarily concerned the genomes of species belonging to clades in the base of large taxonomic groups whose genomes, to a certain extent, can preserve relict and/or possesses specific traits. Thus, we sought to investigate the genomes of Chenopodium (Amaranthaceae, Caryophyllales) species to unravel the structural variability of CACTA elements. Caryophyllales is a separate branch of Angiosperms and until recently the diversity of CACTA elements in this clade was unknown. Results: Application of the short-read genome assembly algorithm followed by analysis of detected complete CACTA elements allowed for the determination of their structural diversity in the genomes of 22 Chenopodium album aggregate species. As a result: (i) the presence of two CACTA transposons subtypes coexisting in single genome; (ii) gaining of additional protein conserved domains within the coding sequence; (iii) the presence of captured gene fragments, including key genes for flower development; and (iv) presence of captured satDNA arrays were identified. Wide comparative database analysis revealed that identified events are scattered through Angiosperms in different proportions. Conclusions: Our study demonstrated that while preserving the basic element structure a wide range of coding and non-coding additions to CACTA transposons occur in genomes of C. album aggregate species. Ability to relocate additions inside genome in combination with proposed novel functional features of structurally-different CACTA elements can impact evolutionary trajectory of the host genome.Peer reviewe

Cryptic invasion suggested by a cytogeographic analysis of the halophytic Puccinellia distans complex (Poaceae) in Central Europe

Introduction: Despite the wealth of studies dealing with the invasions of alien plants, invasions of alien genotypes of native species (cryptic invasions) have been vastly neglected. The impact of cryptic invasions on the biodiversity of plant communities can, however, be significant. Inland saline habitats and halophytes (i.e., salt-tolerant plant species) are especially threatened by this phenomenon as they inhabit fragmented remnants of largely destroyed habitats, but at the same time some of these halophytic species are rapidly spreading along salt-treated roads. To study potential cryptic invasion of halophytes, the patterns of genome size and ploidy variation in the Puccinellia distans complex (Poaceae), the most rapidly spreading roadside halophyte in Central Europe, were investigated. Methods: DNA flow cytometry with confirmatory chromosome counts were employed to assess ploidy levels of 1414 individuals from 133 populations of the P. distans complex. In addition, climatic niche modelling was used to predict the distributions of selected cytotypes. Results: Eight groups differing in ploidy level and/or genome size were discovered, one diploid (2x; 2n = 14), two tetraploid (4xA, 4xB; 2n = 28), one pentaploid (5x; 2n = 35), three hexaploid (6xA, 6xB, 6xC; 2n = 42), and one heptaploid (7x; 2n = 49). The hexaploids (mostly the 6xC cytotype) were widespread through the study area, spreading intensively in both anthropogenic and natural habitats and probably hybridizing with the natural habitat dwelling tetraploids. In contrast, the non-hexaploid cytotypes rarely spread and were predominantly confined to natural habitats. Discussion: The extensive spread of the hexaploid cytotypes along roadsides has most likely facilitated their incursion into natural habitats. The colonization of new natural habitats by the hexaploids may pose a threat to the indigenous Puccinellia populations by compromising their genetic integrity and/or by outcompeting them

Funding and accounting of public benefit corporations in specific conditions of the People in Need

This thesis deals with non-governmental organizations, specifically focuses on public benefit corporation. The aim is familiar with the specifics of accounting and funding of non-profit organizations in conditions of specific public benefit corporation. First, is the work focused on general information about the non-profit sector, followed by information about non-governmental organizations and then there is dedicated the public benefit corporation. There are characterized the public benefit corporations by law. Include the ways of the funding and the accounting specifics differential non-profit organizations (public benefit corporation) from business entities. In the practical part the thesis is focused on specific public benefit corporation The People in Need and there are analyzed the methods of funding and cost, income and profit or loss in the years 2008, 2009, 2010

Communication Barriers of the Beginning Teacher

katedra: KFL; přílohy: 2 ilustrace, 10 tabulek, 1 dotazník, 21 grafů; rozsah: 101 s., 8 příl.The Diploma Thesis deals with communication barriers of the teachers in the 2nd grade of basic school in their proffesional beginnings. The main aim of the DT is to inform the teacher-beginner about potential difficulties during the communication with pupils and the aim is also to provide methodical recommendations for managing these difficulties. The chapters identify and subsequently explain the particular barriers. Simultaneously, the recommendation to prevent and avoid these barriers is offered to the reader. The conclusion pursues questionnaire survey {\clqq} The beginning Teacher``, that completes the questions with data collected from the teachers in the 2nd grade of basic schools. The results of the survey provide an overview of the most common teachers´ barriers in the locality of Liberec.Diplomová práce pojednává o komunikačních bariérách učitelů 2. stupně ZŠ v počátcích jejich profesní dráhy. Hlavním účelem práce je informovanost začínajícího pedagoga o možných nesnázích při komunikaci s žáky a metodická doporučení k úspěšnému zvládnutí těchto potíží. Kapitoly identifikují a následně vysvětlují jednotlivé bariéry. Zároveň je čtenáři nabídnuto doporučení k jejich předcházení a odstranění. Závěr práce je věnován dotazníkovému šetření {\clqq}Začínající učitel``, které danou problematiku doplňuje o data nasbíraná mezi učiteli 2.stupně ZŠ. Výsledky průzkumu poskytují přehled nejčastějších bariér učitelů v Libereckém kraji

Cycling in the Central Bohemia Region

The aim of this thesis Cycling in the Central Bohemia Region is to analyse the state of cycling in selected microregion, to analyse preconditions for further development of cycling and to assess the state of cyclepaths in the microregion. The emphasis is put on the development of cycling as an equivalent means of transport. The other aim is to identify the key problems of cycling and to propose own solutions, which would lead to elimination of problems, which have been found. This thesis also includes a detailed analysis of parking cycling infrastructure and proposals for adequate measures for its improvement

Evaluation of strategic changes in the Berlitz company

Předmětem diplomové práce je návrh komunikačního mixu společnosti a následné zhodnocení dopadu změn přístupu společnosti k vlastní firemní strategii. Pro tento účel byla vybrána jazyková škola Berlitz Schools of Languages, spol. s r.o. Práce obsahuje teoretické poznatky z oblasti marketingu, analýzu firmy a analýzu trhu. Cílem předkládané práce je navrhnout změny, které zvýší konkurenceschopnost firmy a zhodnotit přijaté změny v přístupu ke strategii.The subject of this bachelor's thesis is a proposal of marketing communication mix for the company followed by evaluation of the incidence of changes in company's approach in its own strategy. For this purpose has been chosen a language school Berlitz Schools of Languages, s.r.o. The thesis contains theory of marketing as well as the company analysis and the market analysis. The main objective is to propose changes that would intensify a competitive advantage of the company, and then to evaluate strategic changes that have been accepted.

Office personnel activities analysis

Cílem bakalářské práce je detailně prozkoumat a posoudit personální práci, klíčové personální činnosti a fungování personálního útvaru ve společnosti Pivovar, a.s. (fiktivní název), zjištěné skutečnosti porovnat s dostupnými teoretickými poznatky a případně navrhnout opatření na zlepšení personální práce ve sledované společnosti. Součástí práce je také úvaha nad vlivem národnosti členů vrcholných orgánů společnosti na fungování personálního útvaru a tvorbu personální strategie

Pedagogical evaluation of the training of runners from the 800 m category, older pupils

Title: Pedagogical evaluation training runners from the 800 m category, older pupils Written by: Bc. Michaela Jandová Thesis supervisor: PhDr. Aleš Kaplan, Ph.D. Objectives: : implementation of educational evaluation training process runner in the 800 m category, older pupils during the two annual training macrocycle, 2007/2008 and 2008/2009 Methodology: Content analysis of a training documentation of the selected runner, based on two annual training periods (2007/2008 and 2008/2009), focusing on the monitoring of selected general and special training indicators. Results: In the 2008/2009 season, the monitored runner improved his personal records on 800 m and 300 m tracks compared to the previous season. He has run more kilometers both in total and in individual training indicators. Several deficiencies can be seen among general training indicators, where it is evident that in the 2008/2009 season there was a lower number of days with training load and higher number of days when the runner was limited by sickness or other reasons. After analyzing selected training indicators and the graphic waves of training load among individual cycles within the two training periods, we have come to conclusion that the runner's performance on 800 m track was mostly impacted by the following special training..