The common concept in this thesis was to adapt and develop quantitative mass spectrometric assays focusing on reagents originating from the Human Protein Atlas project to quantify proteins in human cell lines, tissues and blood. The work is based around stable isotope labeled protein fragment standards that each represent a small part of a human protein-coding gene. This thesis shows how they can be used in various formats to describe the protein landscape and be used to standardize mass spectrometry experiments. The first part of the thesis describes the use of antibodies in combination with heavy stable isotope labeled antigens to establish a semi-automated protocol for protein quantification of complex samples with fast analysis time  (Paper~I). Paper II introduces a semi-automated cloning protocol that can be used to selectively clone variants of recombinant proteins, and highlights the automation process that is necessary for large-scale proteomics endeavors. This paper also describes the technology that was used to clone all protein standards that are used in all of the included papers.                       The second part of the thesis includes papers that focus on the generation and application of antibody-free targeted mass spectrometry methods. Here, absolute protein copy numbers were determined across human cell lines and tissues (Paper III) and the protein data was correlated against transcriptomics data. Proteins were quantified to validate antibodies in a novel method that evaluates antibodies based on differential protein expression across multiple cell lines (Paper IV). Finally, a large-scale study was performed to generate targeted proteomics assays (Paper V) based on protein fragments. Here, assay coordinates were mapped for more than 10,000 human protein-coding genes and a subset of peptides was thereafter used to determine absolute protein levels of 49 proteins in human serum.                       In conclusion, this thesis describes the development of methods for protein quantification by targeted mass spectrometry and the use of recombinant protein fragment standards as the common denominator. / <p>QC 20161013</p>

Bottlenose dolphins (Tursiops truncatus) kept in zoos and dolphinarias rarely get an outlet for their echolocation abilities as their pool environment is often quite barren. Not much research has been carried out on enrichments promoting echolocation for dolphins in human care. In the present study a setup with live fish was compared to a setup with air-filled floats (providing strong sonar targets, similar to the swim bladders of large fish) and a control setup. A PCL (porpoise click logger) was used to record the echolocation click trains produced by the dolphins and aimed at the three setups. Behavioural data was also collected from video footage. Both the PCL data and all the behavioural observations indicated that the fish setup was more interesting than the float and the control setup, for the dolphins to echolocate towards. However, there were some contradictions with some parameters, where the floats and control seemed to be more interesting. This was probably due to the location of the PCL hydrophone in relation to the floats and fish, and not because the dolphins had a real bigger interest in these setups. To increase the possibility for dolphins to perform more echolocation in human care and increase their welfare, live fish can be recommended as echolocation enrichment.

No description available.

O objetivo deste trabalho foi quantificar as concentrações de heat shock protein (HSP) 27 e 70 no músculo Longissimus thoracis bovino e avaliar o perfil proteico das amostras no decorrer do processo de maturação, bem como, a relação com as características de qualidade da carne. Foram utilizados 191 animais ½ Simental Sul Africano x ½ Nelore (½ S x ½ N), castrados e terminados em confinamento. Para qualidade da carne mensurou-se os valores de pH, cor (L*, a* e b*), perda de água por cocção (PAC) e força de cisalhamento (FC) em dois tempos de maturação (um e 14 dias). Para a quantificação de HSP 27 e 70 foram selecionadas 40 amostras em função dos valores de FC, e separadas em dois grupos (mais e menos macia) com 20 amostras cada, dentro de cada tempo de maturação (48h e 14 dias). Para realização da análise proteômica foram selecionados três animais de cada grupo e tempo de maturação. A concentração de HSP 27 apresentou diferença significativa (P &lt; 0,05) entre os tempos de maturação dentro dos dois grupos estudados. Já para a HSP 70 verificou-se diferença significativa (P &lt; 0,05) apenas para as amostras do grupo mais macia. A análise de correlação mostrou que as HSP 27 e 70 não interferiram nas características de qualidade da carne. A análise proteômica identificou seis proteínas diferencialmente abundantes (P &lt; 0,05) e o enriquecimento funcional demonstrou que essas proteínas estão relacionadas com processos biológicos e componentes celulares. A desmina e a glicerol-3-fosfato desidrogenase demonstraram correlação com a FC e coloração da carne, respectivamente. Os resultados indicam que as HSP 27 e 70 não podem ser apontadas como biomarcadores eficientes para qualidade de carne em animais ½ S x ½ N. Já a glicerol-3-fosfato desidrogenase demonstrou forte potencial em predizer a estabilidade da cor da carne. Desmina pode ser apontada como um importante biomarcador candidato associado à maciez da carne em animais ½ S x ½ N. / The aim of this work was to quantify the concentrations of heat shock protein (HSP) 27 and 70 in Longissimus thoracis muscle and evaluate the protein profile of the samples during the aging process and its relationship with meat quality characteristics. A total of 191 steers ½ Simmental South African x ½ Nellore (½ S x ½ N) feedlot-finished, were used in this work. For meat quality, pH values, color values (L *, a * and b *), cooking loss (CL) and shear force (SF) were measured in two aging times (one and 14 days). For quantification of HSP 27 and 70, 40 samples were selected according to the SF values and separated into two groups (more and less tender) with 20 samples each, according to the aging time (one and 14 days). To perform the proteomic analysis were selected three animals from each group and aging time. The concentration of HSP 27 showed a significant difference (P &lt; 0.05) between aging times within both groups. As for the HSP 70, there was a significant difference (P &lt; 0.05) for the tenderness samples. Correlation analysis showed that the HSP 27 and 70 didn\'t affect the meat quality traits. The proteomic analysis identified six proteins differentially expressed (P &lt; 0.05) and functional enrichment analysis demonstrated that these proteins are associated with biological processes and cellular components. Desmin and glycerol-3-phosphate dehydrogenase showed correlation with meat traits of SF and color, respectively. The results indicate that HSP 27 and 70 could not be identified as effective biomarkers for meat quality in ½ S x ½ N. However, glycerol-3-phosphate dehydrogenase showed a strong potential in predicting meat color stability. Desmin can be shown as a candidate biomarker associated with meat tenderness in ½ S x ½ N.

Cognitive processes include biases, such as cognitive judgment bias. Cognitive judgment bias influences how the surrounding is interpreted, and this can differ between individuals. However, thus far no formal framework exists to understand how cognitive judgment bias works. Here I investigated how environmental factors and personality influence cognitive judgment bias in Gallus gallus chicks. First I investigated how two environmental factors affected the cognitive judgment bias of laying hen chicks. Chicks were exposed to stress and/or environmental enrichment, and tested in a cognitive judgment bias test before and after collective unpredictable stressors were presented. The results showed that chicks living in enriched environments were faster to reach all cues after the collective stressors than chicks living in non-enriched environments. Individual differences are often observed in animals, even when raised under identical conditions; therefore I also investigated if variation in personality influence cognitive judgment bias. Red junglefowl chicks were thereby raised in equal environments and exposed to personality assays in addition to a cognitive judgment bias test. I demonstrated that less nervous chicks were more optimistic towards ambiguous and negative cues than more nervous chicks. Also previous studies have found indications of connections between cognitive bias and environment or personality. I conclude that environmental enrichment can buffer the influence of stress on cognitive judgment bias and that personality has a small influence on interpretations of stimuli. In the future, experiments in this field should focus on exploring more aspects on how cognitive biases occurs to improve our understanding of cognitive processes.

Much of the history of management and motivation theory is rooted in the desire to understand the factors that contribute to having a satisfied workforce. Job satisfaction is the most widely studied construct in the history of industrial/organizational psychology. The job characteristics model (JCM) holds that if jobs are enriched with high levels of specific job characteristics (i.e., task significance, task variety, task identity, autonomy and feedback), employees will report higher levels of job satisfaction. While this claim enjoys wide support in studies conducted in traditional, hierarchically based organizational environments, few studies have tested the JCM in team based organizational designs. This study also evaluated possible moderating influences of growth need strength (GNS; the need for personal growth and development within the job environment) and emotional reactivity (a measure of frustration with perceived obstacles in the work environment). It was hypothesized that employees with higher levels of GNS would respond more positively (via higher job satisfaction ratings) to enriched jobs than would employees with lower levels of GNS. Alternatively, it was hypothesized that employees with lower levels of emotional reactivity would respond more positively (via higher job satisfaction ratings) to enriched jobs than would employees with higher levels of emotional reactivity. Results indicated that four job characteristics (task significance, task variety, task identity and feedback) served as significant positive predictors of job satisfaction, while GNS moderated the relationships between task significance and task variety with job satisfaction in a way that supported the research hypothesis. Emotional reactivity was not found to moderate any of the relationships between individual job characteristics and job satisfaction. Overall, results support the relevance of the JCM to team based organizations, providing support for the assertion that the relationship between enriched jobs and higher levels of job satisfaction persists across professional work contexts, as well as the partial moderating influence of GNS.

No description available.

Cílem práce je vytvoření přehledu o existujících přístupech pro předzpracování dopravních dat se zaměřením na objevování sémantických trajektorií a návrh a vývoj rámce, který integruje dopravní data z GPS senzorů se sémantikou. Problém analýzy nezpracovaných trajektorií spočíva v tom, že není natolik vyčerpávající, jako analýza trajektorií, které obsahují smysluplný kontext. Po nastudování různých přístupů a algoritmů sleduje návrh a vývoj rámce, který objevuje semantická místa pomocí schlukovací metody záložené na hustotě, aplikované na body zastavení v trajektoriích. Návrh a implementace rámce byl zhodnotěn na veřejně přístupných datových souborech obsahujících nezpracované GPS záznamy.

Background: In the context of demographic changes and age-related diseases, there is a need to focus on the health of older people. Eating disabilities, such as difficulties to use cutlery, caused by various diseases (Parkinson's disease, consequences of a stroke) are becoming more frequent and solutions must be put in place. Objective: The purpose of this study is to create recipes of Fingerfoods for older adults over 65 years old with eating disabilities. These recipes should be prepared at home and rich in protein and energy. Design: A creative design was used to create products, and several variations were created from a basic recipe. The differences between the variations of a recipe are the ingredients that can be substituted or changed in quantity. Materials and Methods: Concerning the physical analysis, texture measurements, viscosity, and colorimetry were performed. The sensory evaluation was a hedonic test to measure the appreciation of the panel according to several criteria: appearance, smell, taste, texture, and overall appreciation. Results: The samples, according to the type of product, were measured for their hardness, their adhesiveness, their viscosity, and their colour. Results also show the appreciation of each sample, the comparisons of the appreciations, the ideas for improvement of the participants, and correlations between different data sets. Discussion: Results have been analysed and used to select the suitable recipes at each phase of the study. The milkshake was preferred when vanilla whey protein was added. The cheese balls were preferred with more chicken and less cheese. Soy flour was appreciated equally or more than wheat flour in the fish cakes and the salty muffins while chickpea flour was the least liked. In the set of recipes proposed for sensory evaluation, the most protein-rich ones were the most appreciated. Conclusion: In the end, four recipes have been selected based on the physical analysis, the sensory evaluation, and the nutritional content. The expected amount of protein was achieved for all products / <p>ISBN: 978-91-87973-61-1</p>

Analýza a interpretace variací DNA je důležité pro zkoumání genetického pozadí dědičnosti, nemocí a jiných fenotypových rysů. Tato práce stručně úvadí oblasti molekulární biologie a základních principů genetiky, popisuje metody pro anotační analýzy genetických variací, genomové asociační studie a metody pro analýzy obohacení s jejich implementací. V rámci této práce jsme představili nový webový nástroj Varanto, který může být použit k anotaci, vizualizaci a analýze genetických variací. Může být použit k analýze obohacení anotací pomocí hypergeometrického testu pro danou množinu variací. Varanto obsahuje uživatelské webové rozhraní vyvinuté pomocí frameworku Shiny jazyka R. Výkon a funkcionalita nástroje jsou testovány a demonstrovány podle výkonových benchmarků a na základě analýzy a interpretace dat z dříve publikovaných genomových asociačních studií.