Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes

Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images

Analysis of the stressors of high school students

Tato bakalářská práce se zabývá problematikou stresu středoškoláků. Práce je dělena na část teoretickou a praktickou. V teoretické části se autorka zabývá vymezením pojmu stres, jeho druhy a fázemi, jednotlivými stresory, náročnými životními situacemi jako je konflikt, frustrace, deprivace, technikami pomáhajícími vyrovnat se s náročnými životními situacemi, vývojovými specifiky středoškoláků, jejich nejčastějšími stresory, prevencí stresu a technikami ke zvládání stresu. V empirické části vymezuje autorka hlavní výzkumný cíl a pět dílčích cílů. Hlavním výzkumným cílem práce bylo zmapovat stresory působící na středoškoláky a to v jednotlivých věkových kategoriích, v závislosti na pohlaví a na různých typech škol. Výzkum byl prováděn formou smíšeného výzkumu, tedy kombinací kvalitativní a kvantitativní strategie. Respondenty výzkumného šetření byli studenti prvních a posledních ročníků Sportovní a podnikatelské střední školy a Střední průmyslové školy dopravní v Plzni studenti učebních oborů. Získaná data autorka interpretuje formou tabulek a grafů.ObhájenoThis bachelor thesis focuses on the stress of secondary school pupils. The paper is divided into a theoretical and practical part. The theoretical part deals with the definition of stress, its types and stages, various stressors, difficult life situations such as conflict, frustration, deprivation. Next, it presents techniques helping to cope with difficult life situations, lists the development specifics of secondary school students and their most common stressors. Lastly, it covers stress prevention and stress management. In the chapter methodology, the author defines a main research aim and five objectives. The main research aim was to map the stressors that can influence the pupils in various age categories depending on their sex and different types of schools. The research was conducted through combined research, which is a combination of qualitative and quantitative strategies. The respondents of the survey were first and final year students of Sports and Business Secondary School and of Secondary School of Transport in Pilsen - students of vocational courses. The data obtained are interpreted through tables and graphs

Burgundy and Central Bohemia - partnership of two EU regions

The bachelor thesis entitled {\clqq}Burgundy and Central Bohemia {--} partnership of two EU regions`` consists of seven chapters. The theoretical part describes briefly the regions of Burgundy and Central Bohemia, the Maison de Bourgogne and the origin of the partnership between these regions. The second part turns to cooperation at the level of microregions and towns and deals with four main areas of the cooperation between the regions - culture, education, economic cooperation and tourist trade. The possibilities of EU subsidies to this cooperation are also described. A summary in French is included

Coeliac Disease and Other Symptoms of Gluten Intolerance

Předkládaná bakalářská práce nese název "Celiakie a jiné nesnášenlivosti lepku". Je tvořena teoretickou a praktickou částí. Teoretická část obsahuje tři kapitoly, ve kterých je popsána problematika nesnášenlivosti lepku nejen z oblasti medicínské, ale i z oblasti psychosociální a ekonomické. Mimo jiné je zde popsána i propojenost nesnášenlivosti lepku a oboru Výchova ke zdraví. V rámci praktické části byl proveden kvantitativní výzkum formou dotazníkového šetření, kdy respondenty byli lidé s celiakií či jinou chorobou, při které musí být dodržována bezlepková dieta.Katedra psychologieObhájenoThe given bachelor thesis is called "Coeliac Disease and Other Intolerances to Gluten". It consists of a theoretical and a practical part. The theoretical part includes three chapters which describe the problem of gluten intolerance not only from medical but psychological and economic point of view, too. We also describe the connection between gluten intolerance and Health Education field. The practical part deals with quantitative research done by a questionnaire, respondents being people suffering with coeliac disease or other illnesses requiring glutenfree diet

Evaluation of Subsidies in Recovery of Landscape within the Operational Programme Environment

Public expenses are often evaluated in terms of their effectiveness. This is caused by the character of financial resources and by the fact that public activities are dependent on those resources. This paper addresses the evaluation of financial subsidies within the Operational Programme Environment 2007–2013. From the perspective of financial subsidies, the Operational Programme Environment was the second largest programme in the Czech Republic offering almost 4.92 billion EUR. Verifying the effectiveness of the management of these public funds is highly desirable, as the use of public funds is associated with a risk of over-exploitation. The main aim of the paper is to evaluate the supported projects and to offer new indicators. The assessment was based on the 3E survey. The results of the research confirmed that among the evaluated projects the desired outcomes are achieved at greater efficiency

The Cell-Wall β-d-Glucan in Leaves of Oat (Avena sativa L.) Affected by Fungal Pathogen Blumeria graminis f. sp. avenae

In addition to the structural and storage functions of the (1,3; 1,4)-β-d-glucans (β-d-glucan), the possible protective role of this polymer under biotic stresses is still debated. The aim of this study was to contribute to this hypothesis by analyzing the β-d-glucans content, expression of related cellulose synthase-like (Csl) Cs1F6, CslF9, CslF3 genes, content of chlorophylls, and β-1,3-glucanase content in oat (Avena sativa L.) leaves infected with the commonly occurring oat fungal pathogen, Blumeria graminis f. sp. avenae (B. graminis). Its presence influenced all measured parameters. The content of β-d-glucans in infected leaves decreased in all used varieties, compared to the non-infected plants, but not significantly. Oats reacted differently, with Aragon and Vaclav responding with overexpression, and Bay Yan 2, Ivory, and Racoon responding with the underexpression of these genes. Pathogens changed the relative ratios regarding the expression of CslF6, CslF9, and CslF3 genes from neutral to negative correlations. However, changes in the expression of these genes did not statistically significantly affect the content of β-d-glucans. A very slight indication of positive correlation, but statistically insignificant, was observed between the contents of β-d-glucans and chlorophylls. Some isoforms of β-1,3-glucanases accumulated to a several-times higher level in the infected leaves of all varieties. New isoforms of β-1,3-glucanases were also detected in infected leaves after fungal infection

Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes

Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images. Abbreviations: 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1.</p