Efekt periferního zánětu na změny v genové expresi u pěvců a papoušků

(in Czech) Ptáci hrají významné role při udržování ekologické rovnováhy jako predátoři, roznašeči semen, cyklátoři živin a opylovači, což z nich činí nedílnou součást mnoha ekosystémů. Ptáci jsou často vlajkovými druhy a jsou tak důležití pro ochranu volně žijících živočichů obecně. Některé ptačí populace jsou globálně propojené v důsledku migrace, což je činí náchylnými k epidemiím infekcí. Ptáci také čelí různým existenčním hrozbám v náročných podmínkách prostředí, od pouští po studené hory. Aby se vyrovnali s těmito různorodými prostředími, potřebují nejen fyziologické adaptace, ale také velmi dobře vybavený imunitní systém optimalizovaný na patogeny běžné v prostředí, které obývají. Jak dobře imunitní systém hostitele reaguje na patogeny, určuje celkovou fitness a přežití jedince. Vhled do funkce ptačích imunitních systémů je velmi důležitý, protože ptáci jsou zásobárnou nesčetných patogenů. Byli primárním zdrojem několika velkých epidemií vedoucích k celosvětovým úmrtím lidí a zvířat (např. Covid 19, ptačí chřipka, virus západonilské horečky). Podobně jako všechny živé bytosti jsou ptačí hostitelé a patogeny vždy v neustálém adaptačním závodě ve zbrojení. Tato koevoluce hostitelů a jejich patogenů tvoří základ vývoje imunitního systému hostitele. Patogeny využívají různé mechanismy, aby se...(English) Birds have well-defined roles in maintaining the ecological balance as predators, seed dispersers, nutrient cyclers, and pollinators making them an integral part of many ecosystems. Birds are often the flag-ship species and are important for wildlife preservation. Some of the avian populations are very well connected across the globe through their annual migration, increasing risks of epidemics of infections. Birds also face different levels of existence encounters in challenging living conditions like deserts and cold mountains. To cope with these diverse environments not only need physiological adaptations, but also a very well-equipped immune system, optimised to challenges common to the environment they inhabit. How well a host immune system responds to pathogens determines the overall fitness of the organism and its survival. Insight into the avian immune system functions is of great significance as birds are reservoirs of innumerable pathogens. They have been the primary source of several major epidemics' onset leading to worldwide human and animal fatalities (e.g., COVID-19, Avian influenza, or West Nile virus outbreaks). Similar to all living beings, avian hosts and pathogens are always in a continuous adaptational arms race. This coevolution of hosts and their pathogens forms the...Katedra zoologieDepartment of ZoologyPřírodovědecká fakultaFaculty of Scienc

Bioinformatics solutions for confident identification and targeted quantification of proteins using tandem mass spectrometry

Proteins are the structural supports, signal messengers and molecular workhorses that underpin living processes in every cell. Understanding when and where proteins are expressed, and their structure and functions, is the realm of proteomics. Mass spectrometry (MS) is a powerful method for identifying and quantifying proteins, however, very large datasets are produced, so researchers rely on computational approaches to transform raw data into protein information. This project develops new bioinformatics solutions to support the next generation of proteomic MS research. Part I introduces the state of the art in proteomic bioinformatics in industry and academia. The business history and funding mechanisms are examined to fill a notable gap in management research literature, and to explain events at the sponsor, GlaxoSmithKline. It reveals that public funding of proteomic science has yet to come to fruition and exclusively high-tech niche bioinformatics businesses can succeed in the current climate. Next, a comprehensive review of repositories for proteomic MS is performed, to locate and compile a summary of sources of datasets for research activities in this project, and as a novel summary for the community. Part II addresses the issue of false positive protein identifications produced by automated analysis with a proteomics pipeline. The work shows that by selecting a suitable decoy database design, a statistically significant improvement in identification accuracy can be made. Part III describes development of computational resources for selecting multiple reaction monitoring (MRM) assays for quantifying proteins using MS. A tool for transition design, MRMaid (pronounced „mermaid‟), and database of pre-published transitions, MRMaid-DB, are developed, saving practitioners time and leveraging existing resources for superior transition selection. By improving the quality of identifications, and providing support for quantitative approaches, this project brings the field a small step closer to achieving the goal of systems biology.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Investigation of ancient proteins in archaeological material

Although several studies have positively identified dairy proteins from ancient dental calculus, other dietary protein identifications are exceedingly rare. The manuscripts included in this thesis include the identification of 20 different dietary proteins that could be taxonomically identified to the species level from 10 different species. One of our primary goals for this thesis was to evaluate any potential biases in our dietary protein recovery, and to gain a deeper understanding of the factors that influence dietary protein preservation within dental calculus. Although our sample sizes are small, we did find evidence of biases in the types of proteins we have recovered thus far. All proteins identified were potential allergens with IgE binding sites, low monomer molecular weight, resistance to changes in pH and temperature, and resistance to degradation through enzymatic proteolysis. The identified proteins primarily had functions in host defense or storage

The Bermuda Triangle : the pragmatics, policies, and principles for data sharing in the history of the Human Genome Project

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of the History of Biology 51 (2018): 693–805, doi:10.1007/s10739-018-9538-7.The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner’s proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology