Cognitive functions of birds based on abstract visual stimuli

Spatial orientation of pigeons on a small scale was intensivelly studied in experiments using various types of arenas or mazes. In these experiments pigeons usually searched for food hidden in the goal area and they based their orientation on available landmarks. The development of new technologies allowed to test spatial cognition of pigeons also in virtual tasks, based exclusively on a schematic representation of an arena or maze on a touch screen. In experiments of this type pigeon marks the goal by pecking and it is rewarded by food from a feeder, located near the monitor. Study presented in this diploma thesis was based on combination of both types of spatial tasks. The information crucial for locating the goal was presented to pigeons on a computer screen in form of graphic stimuli, whereas the goal itself was formed by one of the 4 holes in corners of a transparent rectangular desk, standing in front of the monitor. Experiment with similar design was not yet published in the study of spatial cognition of pigeons. Two types of abstract graphic stimuli were tested. The first stimuli provided a spatial information about the location of a goal and had a form of small rectangular frame with a white spot in one of its corners. The frame represented the space of the response desk and the white spot...Prostorová orientace holubů na malé škále byla intenzivně studována v pokusech, využívajících různých typů arén či bludišť. V těchto experimentech holubi většinou hledali potravu ukrytou v cílovém místě a orientovali se podle poskytnutých orientačních bodů. Rozvoj nových technologií umožnil testovat prostorovou kognici holubů také ve virtuálních úlohách, založených pouze na schematickém znázornění arény nebo bludiště na dotykové obrazovce. V experimentech tohoto typu holub označuje cíl klovnutím a je odměněn potravou z krmítka, umístěného v blízkosti monitoru. Studie, prezentovaná v této diplomové práci, byla založena na kombinaci obou typů prostorových úloh. Klíčová informace pro nalezení cíle byla holubům promítána na monitoru počítače v podobě grafického stimulu, avšak cílem samotným byl jeden ze 4 otvorů v rozích průhledné obdélníkové desky, umístěné před monitorem. Experiment s podobným návrhem ve studiu prostorové kognice holubů dosud nebyl publikován. Testovány byly dva typy abstraktních grafických stimulů. První z nich poskytoval prostorovou informaci o umístění cíle a měl podobu malého obdélníkového rámečku s bílým bodem vždy v jednom z svých rohů. Rámeček představoval prostor odpověďové desky, bílý bod pak pozici cílového otvoru. Druhý stimul neobsahoval implicitní prostorovou informaci o...Department of ZoologyKatedra zoologieFaculty of SciencePřírodovědecká fakult

Molekulární mechanismy funkce Wip1 fosfatázy v buněčné odpovědi na poškození DNA

Lidské buňky jsou neustále vystaveny různým faktorům, které způsobují poškození DNA a aktivují odpověď na poškození DNA (DDR). V závislosti na závažnosti poškození DNA může DDR napomáhat dočasnému zastavení cyklu buněk (kontrolní bod buněčného cyklu, "checkpoint"), trvalému zastavení růstu (senescence) nebo programované buněčné smrti (apoptóze). Signál DDR je regulován kaskádou post-translačních modifikací, kde klíčovými mediátory jsou fosfoproteinové kinázy ATM, ATR a DNA-PK. Fosfatáza Wip1 (kódovaná genem PPM1D) hraje důležitou roli v ukončení DDR fosforylací mnoha cílů těchto kináz. V této práci jsme zkoumali funkce PPM1D nezávislé na kontrolních bodech buněčného cyklu v buňkách a popsali jsme několik nových substrátů. Zjistili jsme, že PPM1D interaguje se shelterinovým komplexem a nachází se na telomerách. PPM1D desfosforyluje shelterinový protein TRF2 na S410. Fosforylace TRF2 na S410 zvyšovala jeho interakci s TIN2, což nepřímo zvyšovalo množství TPP1 na telomerách. Buňky s overexpresí PPM1D měly zvýšený počet telomerických fúzí. Tato zjištění mohou být velmi důležitá pro některé typy rakoviny, zvláště ty, které vykazují vysoké hladiny PPM1D nebo obsahují mutace v C-konci PPM1D. Pro ověření publikovaných, a detekci možných nových, substrátů PPM1D jsme vyvinuli novou metodu, využívající...Human cells are constantly exposed to diverse factors causing DNA lesions, which activate the DNA damage response (DDR). Depending on the severity of DNA damage, DDR can promote temporary cell cycle arrest (checkpoint), permanent growth arrest (senescence) or programmed cell death (apoptosis). DDR signalling is regulated by a cascade of post- translational modifications, where key mediators are represented by protein kinases ATM, ATR and DNA-PK. Wip1 phosphatase (encoded by PPM1D gene) plays an important role in DDR termination by dephosphorylation of many targets of these kinases. In this thesis, we investigated checkpoint-independent functions of PPM1D in cells and described several new substrates. We discovered, that PPM1D interacts with the shelterin complex and localizes at telomeres. PPM1D dephosphorylates the shelterin component TRF2 at S410. TRF2 S410 phosphorylation enhanced TRF2 interaction with TIN2, indirectly also increasing recruitment of TPP1 to telomeres. Importantly, cells over expressing PPM1D showed increased number of telomeric fusions. These findings might be very relevant for some cancer types, in particular those expressing high levels of PPM1D or carrying C-terminally truncated mutations in PPM1D. To validate the published substrates and to detect possible new targets of...Katedra genetiky a mikrobiologieDepartment of Genetics and MicrobiologyPřírodovědecká fakultaFaculty of Scienc

Transcription profiles of mitochondrial genes correlate with mitochondrial DNA haplotypes in a natural population of Silene vulgaris

<p>Abstract</p> <p>Background</p> <p>Although rapid changes in copy number and gene order are common within plant mitochondrial genomes, associated patterns of gene transcription are underinvestigated. Previous studies have shown that the gynodioecious plant species <it>Silene vulgaris </it>exhibits high mitochondrial diversity and occasional paternal inheritance of mitochondrial markers. Here we address whether variation in DNA molecular markers is correlated with variation in transcription of mitochondrial genes in <it>S. vulgaris </it>collected from natural populations.</p> <p>Results</p> <p>We analyzed RFLP variation in two mitochondrial genes, <it>cox1 </it>and <it>atp1</it>, in offspring of ten plants from a natural population of <it>S. vulgaris </it>in Central Europe. We also investigated transcription profiles of the <it>atp1 </it>and <it>cox1 </it>genes. Most DNA haplotypes and transcription profiles were maternally inherited; for these, transcription profiles were associated with specific mitochondrial DNA haplotypes. One individual exhibited a pattern consistent with paternal inheritance of mitochondrial DNA; this individual exhibited a transcription profile suggestive of paternal but inconsistent with maternal inheritance. We found no associations between gender and transcript profiles.</p> <p>Conclusions</p> <p>Specific transcription profiles of mitochondrial genes were associated with specific mitochondrial DNA haplotypes in a natural population of a gynodioecious species <it>S. vulgaris</it>.</p> <p>Our findings suggest the potential for a causal association between rearrangements in the plant mt genome and transcription product variation.</p

High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora

Includes bibliographical references.Background: Species within the angiosperm genus Silene contain the largest mitochondrial genomes ever identified. The enormity of these genomes (up to 11 Mb in size) appears to be the result of increased non-coding DNA, which represents >99 % of the genome content. These genomes are also fragmented into dozens of circular-mapping chromosomes, some of which contain no identifiable genes, raising questions about if and how these "empty" chromosomes are maintained by selection. To assess the possibility that they contain novel and unannotated functional elements, we have performed RNA-seq to analyze the mitochondrial transcriptome of Silene noctiflora. Results: We identified regions of high transcript abundance in almost every chromosome in the mitochondrial genome including those that lack any annotated genes. In some cases, these transcribed regions exhibited higher expression levels than some core mitochondrial protein-coding genes. We also identified RNA editing sites throughout the genome, including 97 sites that were outside of protein-coding gene sequences and found in pseudogenes, introns, UTRs, and transcribed intergenic regions. Unlike in protein-coding sequences, however, most of these RNA editing sites were only edited at intermediate frequencies. Finally, analysis of mitochondrial small RNAs indicated that most were likely degradation products from longer transcripts, but we did identify candidates for functional small RNAs that mapped to intergenic regions and were not associated with longer RNA transcripts. Conclusions: Our findings demonstrate transcriptional activity in many localized regions within the extensive intergenic sequence content in the S. noctiflora mitochondrial genome, supporting the possibility that the genome contains previously unidentified functional elements. However, transcription by itself is not proof of functional importance, and we discuss evidence that some of the observed transcription and post-transcriptional modifications are non-adaptive. Therefore, further investigations are required to determine whether any of the identified transcribed regions have played a functional role in the proliferation and maintenance of the enormous non-coding regions in Silene mitochondrial genomes.Published with support from the Colorado State University Libraries Open Access Research and Scholarship Fund

Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia

<p>Abstract</p> <p>Background</p> <p>Mitochondrial gene loss and functional transfer to the nucleus is an ongoing process in many lineages of plants, resulting in substantial variation across species in mitochondrial gene content. The Caryophyllaceae represents one lineage that has experienced a particularly high rate of mitochondrial gene loss relative to other angiosperms.</p> <p>Results</p> <p>In this study, we report the first complete mitochondrial genome sequence from a member of this family, <it>Silene latifolia</it>. The genome can be mapped as a 253,413 bp circle, but its structure is complicated by a large repeated region that is present in 6 copies. Active recombination among these copies produces a suite of alternative genome configurations that appear to be at or near "recombinational equilibrium". The genome contains the fewest genes of any angiosperm mitochondrial genome sequenced to date, with intact copies of only 25 of the 41 protein genes inferred to be present in the common ancestor of angiosperms. As observed more broadly in angiosperms, ribosomal proteins have been especially prone to gene loss in the <it>S. latifolia </it>lineage. The genome has also experienced a major reduction in tRNA gene content, including loss of functional tRNAs of both native and chloroplast origin. Even assuming expanded wobble-pairing rules, the mitochondrial genome can support translation of only 17 of the 61 sense codons, which code for only 9 of the 20 amino acids. In addition, genes encoding 18S and, especially, 5S rRNA exhibit exceptional sequence divergence relative to other plants. Divergence in one region of 18S rRNA appears to be the result of a gene conversion event, in which recombination with a homologous gene of chloroplast origin led to the complete replacement of a helix in this ribosomal RNA.</p> <p>Conclusions</p> <p>These findings suggest a markedly expanded role for nuclear gene products in the translation of mitochondrial genes in <it>S. latifolia </it>and raise the possibility of altered selective constraints operating on the mitochondrial translational apparatus in this lineage.</p

Intraspecific Inversions Pose a Challenge for the trnH-psbA Plant DNA Barcode

BACKGROUND: The chloroplast trnH-psbA spacer region has been proposed as a prime candidate for use in DNA barcoding of plants because of its high substitution rate. However, frequent inversions associated with palindromic sequences within this region have been found in multiple lineages of Angiosperms and may complicate its use as a barcode, especially if they occur within species. METHODOLOGY/PRINCIPAL FINDINGS: Here, we evaluate the implications of intraspecific inversions in the trnH-psbA region for DNA barcoding efforts. We report polymorphic inversions within six species of Gentianaceae, all narrowly circumscribed morphologically: Gentiana algida, Gentiana fremontii, Gentianopsis crinita, Gentianopsis thermalis, Gentianopsis macrantha and Frasera speciosa. We analyze these sequences together with those from 15 other species of Gentianaceae and show that typical simple methods of sequence alignment can lead to misassignment of conspecifics and incorrect assessment of relationships. CONCLUSIONS/SIGNIFICANCE: Frequent inversions in the trnH-psbA region, if not recognized and aligned appropriately, may lead to large overestimates of the number of substitution events separating closely related lineages and to uniting more distantly related taxa that share the same form of the inversion. Thus, alignment of the trnH-psbA spacer region will need careful attention if it is used as a marker for DNA barcoding

On the genome constitution and evolution of intermediate wheatgrass (Thinopyrum intermedium: Poaceae, Triticeae)

<p>Abstract</p> <p>Background</p> <p>The wheat tribe Triticeae (Poaceae) is a diverse group of grasses representing a textbook example of reticulate evolution. Apart from globally important grain crops, there are also wild grasses which are of great practical value. Allohexaploid intermediate wheatgrass, <it>Thinopyrum intermedium </it>(2n = 6x = 42), possesses many desirable agronomic traits that make it an invaluable source of genetic material useful in wheat improvement. Although the identification of its genomic components has been the object of considerable investigation, the complete genomic constitution and its potential variability are still being unravelled. To identify the genomic constitution of this allohexaploid, four accessions of intermediate wheatgrass from its native area were analysed by sequencing of chloroplast <it>trn</it>L-F and partial nuclear GBSSI, and genomic <it>in situ </it>hybridization.</p> <p>Results</p> <p>The results confirmed the allopolyploid origin of <it>Thinopyrum intermedium </it>and revealed new aspects in its genomic composition. Genomic heterogeneity suggests a more complex origin of the species than would be expected if it originated through allohexaploidy alone. While <it>Pseudoroegneria </it>is the most probable maternal parent of the accessions analysed, nuclear GBSSI sequences suggested the contribution of distinct lineages corresponding to the following present-day genera: <it>Pseudoroegneria</it>, <it>Dasypyrum</it>, <it>Taeniatherum</it>, <it>Aegilops </it>and <it>Thinopyrum</it>. Two subgenomes of the hexaploid have most probably been contributed by <it>Pseudoroegneria </it>and <it>Dasypyrum</it>, but the identity of the third subgenome remains unresolved satisfactorily. Possibly it is of hybridogenous origin, with contributions from <it>Thinopyrum </it>and <it>Aegilops</it>. Surprising diversity of GBSSI copies corresponding to a <it>Dasypyrum</it>-like progenitor indicates either multiple contributions from different sources close to <it>Dasypyrum </it>and maintenance of divergent copies or the presence of divergent paralogs, or a combination of both. <it>Taeniatherum</it>-like GBSSI copies are most probably pseudogenic, and the mode of their acquisition by <it>Th. intermedium </it>remains unclear.</p> <p>Conclusions</p> <p>Hybridization has played a key role in the evolution of the Triticeae. Transfer of genetic material via extensive interspecific hybridization and/or introgression could have enriched the species' gene pools significantly. We have shown that the genomic heterogeneity of intermediate wheatgrass is higher than has been previously assumed, which is of particular concern to wheat breeders, who frequently use it as a source of desirable traits in wheat improvement.</p

First aid education on university

Projekt "Zachraň život na ZČU" umožnil realizaci kurzů první pomoci pro studenty, akademické pracovníky a další zaměstnance univerzity. Kurzy byly sestaveny po domluvě s odborným garantem a na realizaci dvouhodinových kurzů se podíleli studenti oboru Zdravotnický záchranář Západočeské univerzity v Plzni. Hlavním cílem této bakalářské práce je zjistit, jestli koncept realizace kurzů je funkční a do dalších let ho můžeme ponechat anebo jestli zavést organizační změny v rámci časové dotace a tematických okruhů. Jako dílčí cíle bylo stanoveno zjistit, jaké jsou znalosti první pomoci u účastníků kurzů před a po absolvování kurzu, porovnat znalosti akademických pracovníků a studentů a popsat postup pořádání kurzů. Zájem o kurzy první pomoci na Západočeské univerzitě v Plzni stále trvá a podaří-li se nám sepsat postup, jakým způsobem kurzy pořádat, nemusely by nutně skončit poté, co hlavní řešitelka projektu ukončí studium.ObhájenoThe project "Zachraň život na ZČU" has enabled the implementation of first aid courses for students, academics and other workers at University of West Bohemia. The courses were prepared after consultation with a guarantor. The courses were also realized by students of the paramedical rescue of the University of West Bohemia. The main aim of this bachelor thesis is to find out if the concept of implementation of courses is functional or if it's necessary to put any changes in organization of time or thematic areas. As a partial objective we determined to find out first-aid knowledge of course before and after the course to compare the knowledge of students and academic stuff and to describe course arrangement. The interest in first aid courses at the University of West Bohemia in Pilsen is still actual and if we describe the technique how to organize it well, the project won´t have to end after the initiator of this project has finished studying