Classification and Usage of Languages, Grammars and Machines

Tato bakalářská práce se zabývá teorií jazyků, gramatik a automatů. Ukázky použití konečných automatů v praxi na názorných příkladech a vytvoření programu, pro firmu Paradise Casino Admiral a.s. . Účelem tohoto programu je vyplnění evidence docházky na základě rozpisu služeb, který musí navrhnout manažerka pro svoje oddělení každý měsíc. Tento program by měl manažerce usnadnit a hlavně urychlit práci, kterou doposud vykonávala ručně.This bachelor thesis is focused on theory of languages, grammars and automats, on showing real examples of linale machine and on creating program for firm "Paradise Casino Admiral a.s.". Purpose of mentioned program is to ease and speed up the work of department manager by tracking of employee attendance from preset workshift schedule

How and why DNA barcodes underestimate the diversity of microbial eukaryotes

Background: Because many picoplanktonic eukaryotic species cannot currently be maintained in culture, direct sequencing of PCR-amplified 18S ribosomal gene DNA fragments from filtered sea-water has been successfully used to investigate the astounding diversity of these organisms. The recognition of many novel planktonic organisms is thus based solely on their 18S rDNA sequence. However, a species delimited by its 18S rDNA sequence might contain many cryptic species, which are highly differentiated in their protein coding sequences. Principal Findings: Here, we investigate the issue of species identification from one gene to the whole genome sequence. Using 52 whole genome DNA sequences, we estimated the global genetic divergence in protein coding genes between organisms from different lineages and compared this to their ribosomal gene sequence divergences. We show that this relationship between proteome divergence and 18S divergence is lineage dependant. Unicellular lineages have especially low 18S divergences relative to their protein sequence divergences, suggesting that 18S ribosomal genes are too conservative to assess planktonic eukaryotic diversity. We provide an explanation for this lineage dependency, which suggests that most species with large effective population sizes will show far less divergence in 18S than protein coding sequences. Conclusions: There is therefore a trade-off between using genes that are easy to amplify in all species, but which by their nature are highly conserved and underestimate the true number of species, and using genes that give a better description of the number of species, but which are more difficult to amplify. We have shown that this trade-off differs between unicellular and multicellular organisms as a likely consequence of differences in effective population sizes. We anticipate that biodiversity of microbial eukaryotic species is underestimated and that numerous ''cryptic species'' will become discernable with the future acquisition of genomic and metagenomic sequences

Organellar inheritance in the green lineage: insights from Ostreococcus tauri

Along the green lineage (Chlorophyta and Streptophyta), mitochondria and chloroplast are mainly uniparentally transmitted and their evolution is thus clonal. The mode of organellar inheritance in their ancestor is less certain. The inability to make clear phylogenetic inference is partly due to a lack of information for deep branching organisms in this lineage. Here, we investigate organellar evolution in the early branching green alga Ostreococcus tauri using population genomics data from the complete mitochondrial and chloroplast genomes. The haplotype structure is consistent with clonal evolution in mitochondria, while we find evidence for recombination in the chloroplast genome. The number of recombination events in the genealogy of the chloroplast suggests that recombination, and thus biparental inheritance, is not rare. Consistent with the evidence of recombination, we find that the ratio of the number of nonsynonymous to the synonymous polymorphisms per site is lower in chloroplast than in the mitochondria genome. We also find evidence for the segregation of two selfish genetic elements in the chloroplast. These results shed light on the role of recombination and the evolutionary history of organellar inheritance in the green lineage

Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling

Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic data for two natural picophytoplankton populations from the coastal upwelling waters off central Chile. About 60% of the reads of each sample could be mapped to the genome of Bathycoccus strain from the Mediterranean Sea (RCC1105), representing a total of 9 Mbp (sample T142) and 13 Mbp (sample T149) of non-redundant Bathycoccus genome sequences. WGA did not amplify all regions uniformly, resulting in unequal coverage along a given chromosome and between chromosomes. The identity at the DNA level between the metagenomes and the cultured genome was very high (96.3% identical bases for the three larger chromosomes over a 360 kbp alignment). At least two to three different genotypes seemed to be present in each natural sample based on read mapping to Bathycoccus RCC1105 genome

Principals' perceptions of virtual learning as part of the overall curricula in Illinois public high schools

Includes bibliographical references (pages [158]-166)This study electronically surveyed Illinois public high-school principals to determine what variables affected their schools' participation in virtual learning as part of their overall curricula. Data were collected by way of an online survey on the Internet. The study examined the relationship between Illinois public high-schools' participation in virtual learning and school enrollments, district financial constraints, and their geographic location. Likewise, the study examined the relationship between the principals' knowledge and attitudes toward technology and virtual learning. Finally, the overall goal of this study was to determine if principals perceived they were the primary reason that virtual learning had been implemented or will be implemented in Illinois public high schools. The study investigated five research questions. All research questions (1–5) were analyzed by using frequency tables. Crosstabs and Pearson's chi-square were used for research questions 2, 3, 4, and 5. The study found that most (66.4%) Illinois public high schools were participating in virtual learning or were planning to implement it within the next five years. Schools with large student enrollments were more likely to be participating in virtual learning than schools with small enrollments. Likewise, schools of urban areas were more likely to be participating in virtual learning than schools located in small rural areas of the state. Schools with districts that pose no financial constraints were more likely to be participating in virtual learning than schools with districts that posed many financial constraints. The study found that the more knowledgeable principals were about technology and virtual learning, the more apt their schools were participating in virtual learning. Finally, the study determined that the principals do not perceive themselves as the primary reason virtual learning has been or will be implemented into their schools' overall curricula.Ed.D. (Doctor of Education

Clues about the genetic basis of adaptation emerge from comparing the proteomes of two Ostreococcus ecotypes (Chlorophyta, Prasinophyceae).

International audienceWe compared the proteomes of two picoplanktonic Ostreococcus unicellular green algal ecotypes to analyze the genetic basis of their adaptation with their ecological niches. We first investigated the function of the species-specific genes using Gene Ontology databases and similarity searches. Although most species-specific genes had no known function, we identified several species-specific functions involved in various cellular processes, which could be critical for environmental adaptations. Additionally, we investigated the rate of evolution of orthologous genes and its distribution across chromosomes. We show that faster evolving genes encode significantly more membrane or excreted proteins, consistent with the notion that selection acts on cell surface modifications that is driven by selection for resistance to viruses and grazers, keystone actors of phytoplankton evolution. The relationship between GC content and chromosome length also suggests that both strains have experienced recombination since their divergence and that lack of recombination on the two outlier chromosomes could explain part of their peculiar genomic features, including higher rates of evolution

Evolution of Codon Usage In The Smallest Photosynthetic Eukaryotes And Their Giant Viruses

Prasinoviruses are among the largest viruses (>200 kbp) and encode several hundreds of protein coding genes, including most genes of the DNA replication machinery and several genes involved in transcription and translation, as well as tRNAs. They can infect and lyse small eukaryotic planktonic marine green algae, thereby affecting global algal population dynamics. Here we investigate the causes of codon usage bias in one prasinovirus, OtV5, and its host Ostreococcus tauri, during a viral infection using microarray expression data. We show that (i) codon usage bias in the host and in the viral genes increases with expression levels and (ii) optimal codons use those tRNAs encoded by the most abundant host tRNA genes, supporting the notion of translational optimization by natural selection. We find evidence that viral tRNA genes complement the host tRNA pool for those viral amino acids whose host tRNAs are in short supply. We further discuss the coevolution of Codon usage bias in hosts and prasinoviruses by comparing optimal codons in 3 evolutionary Diverged host--‐virus specific pairs whose complete genome sequences are known