The experiments described in this thesis employ local lentiviral knockdowns in brain areas of female zebra finches followed by behavioural assays consisting of preference and Go/Nogo tasks.... Show moreThe experiments described in this thesis employ local lentiviral knockdowns in brain areas of female zebra finches followed by behavioural assays consisting of preference and Go/Nogo tasks. Ultimately, the targeted brain areas are extracted for gene expression analyses.The findings suggest that localised reduction of FoxP1 expression in HVC or CMM of female zebra finches does not impair the establishment or maintenance of auditory memories of conspecific song nor the females’ ability to discriminate or categorise auditory stimuli based on spectral or sequential features. Females which received a knockdown of FoxP1 in HVC as adults requested fewer familiar and unfamiliar playbacks and had a lower preference for familiar song than their matched controls. This might suggest that FoxP1 contributes to motivational behaviours in female zebra finches.Gene expression analyses links FoxP1 to pathways that have previously also been associated with FOXP2 in mammals including retinoic acid signalling and the SLIT-ROBO signalling cascade. Altered energy metabolism in different brain areas might also contribute to the observed phenotypes.Ultimately, the results presented in this thesis suggest implications of the transcription factor FoxP1 beyond vocal motor learning which need to be investigated in future studies. Show less
One of the essential functions of microglia is to continuously sense changes in their environment and adapt to those changes. For this purpose, they use a set of genes termed the sensome. This... Show moreOne of the essential functions of microglia is to continuously sense changes in their environment and adapt to those changes. For this purpose, they use a set of genes termed the sensome. This sensome is comprised of the most abundantly expressed receptors on the surface of microglia. In this study, we updated previously identified mouse microglial sensome by incorporating an additional published RNAseq dataset into the data-analysis pipeline. We also identified members of the human microglial sensome using two independent human microglia RNAseq data sources. Using both the mouse and human microglia sensomes, we identified a key set of genes conserved between the mouse and human microglial sensomes as well as some differences between the species. We found a key set of 57 genes to be conserved in both mouse and human microglial sensomes. We define these genes as the "microglia core sensome". We then analyzed expression of genes in this core sensome in five different datasets from two neurodegenerative disease models at various stages of the diseases and found that, overall, changes in the level of expression of microglial sensome genes are specific to the disease or condition studied. Our results highlight the relevance of data generated in mice for understanding the biology of human microglia, but also stress the importance of species-specific gene sets for the investigation of diseases involving microglia. Defining this microglial specific core sensome may help identify pathological changes in microglia in humans and mouse models of human disease. Show less
This thesis provides an overview of DNA replication proteins that potentially may serve as targets for antimicrobials in drug-resistant pathogens and includes the in silico identification of the... Show moreThis thesis provides an overview of DNA replication proteins that potentially may serve as targets for antimicrobials in drug-resistant pathogens and includes the in silico identification of the replication proteins of C. difficile. Additionally, the mode of action and the current developmental status of the compounds directed at the core replication machinery and accessory replication proteins are discussed (Chapter 2). In chapter 3 we determined the complete genome sequence of our reference laboratory strain, C. difficile 630Δerm, and compared this sequence to the sequence of C. difficile 630. This revealed an unexpected transposition of the mobile genetic element CTn5. The genome sequence now offers an appropriate reference for all molecular work on this strain. Apart from the identification and characterization of gyrase and DNA polymerase in previous studies, no information on DNA replication proteins or the mechanism of replication was available. To address this hiatus, we sought out to identify core replication proteins and to experimentally validate the functional role of these proteins. The findings of this experimental work, with a focus on helicase and primase, are presented in chapter 4 and chapter 5, respectively. Show less
In this thesis I studied the functions of the zebrafish orthologs of the human TLR5 and TLR2 genes that were shown to be responsible for recognition of bacterial flagellin and a broad spectrum... Show moreIn this thesis I studied the functions of the zebrafish orthologs of the human TLR5 and TLR2 genes that were shown to be responsible for recognition of bacterial flagellin and a broad spectrum of bacterial cell wall components, respectively. One of the focal points of this thesis is the difference at the transcriptomic level of the downstream pathway of the TLR5 and TLR2 receptors and the roles of TLR signaling in host innate immune responses to infection by Mycobacterium marinum, a close relative to Mycobacterium tuberculosis and a natural pathogen of zebrafish. The new possibilities for analysis of transcriptomes using RNA deep sequencing make it highly attractive to analyze the responses of an entire test animal model at the system biology level. Furthermore, we used genetic knockdown and knockout tools to further analyze the function of TLR5 and TLR2 and downstream signaling partners in innate immunity, infectious disease and insulin resistance. Show less
In the last decade the study of the innate immune system has gained renewed scientific momentum as a result of the discovery of essential receptor families, such as the Toll-like receptor (TLR)... Show moreIn the last decade the study of the innate immune system has gained renewed scientific momentum as a result of the discovery of essential receptor families, such as the Toll-like receptor (TLR) family, that are required for pathogen recognition. These receptors detect specific molecular structures of microorganisms and in turn are able to trigger host immune responses. The work described in this thesis focuses on the use of the zebrafish embryo as a model to study the vertebrate immune system in order to gain new insights into the mechanisms of innate immune defence against bacterial infections and TLR signalling. Making use of a Salmonella infection model in combination with microarray technology and gene knock-down studies we were able to thoroughly characterize the embryonic host transcriptome response to a bacterial infection. Furthermore, we have demonstrated important functions for key signalling molecules in the innate immune response, including Tlr5, MyD88 and Traf6 and discovered new downstream targets of the TLR signalling pathway. The data presented here will enable in-depth functional follow-up studies that will provide new insights into the mechanisms of innate immune defence systems. This, in combination with future applications of zebrafish embryo infection models in high-throughput compound screens, holds much promise for the discovery of novel anti-microbial and anti-inflammatory drugs. Show less
