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Detection of subpopulation-specific neuronal membrane molecules using single-cell expression data
Zátko, Matěj ; Modrák, Martin (advisor) ; Kubovčiak, Jan (referee)
Single-cell RNA sequencing is a powerful technology that allows the investigation of gene expression at an unprecedented level. Insights into gene expression in individual cells can help biologists uncover cellular heterogeneity and identify previously unknown cell types. Here, we use single-cell RNA sequencing datasets that reveal subtypes of mouse neurons to find population-specific membrane proteins. These proteins could potentially serve as entry points for targeted drug distribution, allowing for drugs to act only on se- lected neuronal populations. We start by identifying five suitable single-cell mouse neuron datasets. Next, we present an overview and a comparison of currently available methods for differential gene expression analysis, an approach that involves quantifying variations in gene expression between groups and/or conditions, based on previous benchmarks. Lastly, we apply the Wilcoxon rank-sum test to selected datasets in order to identify population-specific membrane proteins. 1
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Effects of microbiota composition on emergence of depressions and behavioural disorders in animals
Bartková, Nikola ; Vinkler, Michal (advisor) ; Kubovčiak, Jan (referee)
The aim of this study is to summarize the current knowledge on the influence of gut microbiota composition on behavioural disorders in selected mammals and birds. Current research focuses on the influence of gut microbiota on the development of mental illnesses in humans and the potential therapeutic use of manipulating its composition. This paper briefly summarizes the main mechanisms of microbiota influence on the development of mental illnesses. The gut microbiota may also influence the development of behavioural disorders in animals. The literature suggests that changes in gut microbiota composition in humans with mental illnesses and animals with behavioural disorders share some similarities. In general, they are related mainly to a reduced abundance of selected genera of short-chain fatty acid producing bacteria and an increased abundance of gram-negative bacteria. The exceptions are destructive behavioural disorders in animals, which are associated with increased abundance of the Clostridia class and decreased abundance of the Lactobacillus genus. To prevent their development under stress, the thesis proposes the probiotic use of Lactobacillus rhamnosus. To manipulate the composition of the gut microbiota in the treatment of depressive disorders in humans, the administration of probiotics,...
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Interspecific variation of gastointestinal microbiota in passerine birds
Kubovčiak, Jan ; Kreisinger, Jakub (advisor) ; Vlčková, Klára (referee)
in English Vertebrates host complex microbial communities in their intestinal system. This gut microbiome (GM) comprises billions of bacterial cells closely interacting with a host's physiology. Despite contemporary progress in this field, present knowledge of vertebrate GM is based on studies carried out only on a limited set of host species, including humans, captive rodents and few economically important mammals and birds. On the contrary, knowledge of GM in wild living, non-mammalian species is still rather insufficient. Thus, this thesis aims to analyze GM in wild passerine populations and to investigate potential patterns in GM composition. Main objective is to provide evidence that GM composition is dependent on host species, and of co-divergence between GM composition variability and host phylogeny. Additional focus is devoted to diversity analysis among individual bacterial genera regarding their phylogeny. Using the Illumina MySeq platform, we sequenced amplicons of bacterial 16s rRNA gene obtained from fecal samples of 486 individuals representing 57 Czech Republic passerine species and 107 individuals representing 38 Cameroon Republic species. A modified approach was applied during data processing. In the first step, analyzed dataset was sorted by classifying sequences to respective...
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Research of vertebrate-microbiota relationship using germ-free organisms
Kubovčiak, Jan ; Kreisinger, Jakub (advisor) ; Hájková, Petra (referee)
Germ free (axenic) animals are individuals reared under specific conditions preventing their contact with surrounding microorganisms. Some of the features observed in these individuals vary from those observed in naturally colonized counterparts. These differences probably reflect the influence of presence of a complex intestinal microbial population in the intestine, which influences important physiological functions of the host body by various mechanisms. Thus, nature of these differences allows to study relationship of the host, vertebrate in this case and its microbiota, which evolved into a complicated system of interactions providing relatively stable coexistence. Germ free research of this relationship is focused on interactions between microbiota and host's immune system, metabolism, morphology of digestive tract and behavior. This thesis provides summary of research outcomes on previously mentioned topics. Powered by TCPDF (www.tcpdf.org)
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