The phylogenetics of eight species of the Peromyscus truei and P. boylii species groups from 15 populations were analyzed based on mitochondrial DNA sequence differentiation, using 13 hexanucleotide specific restriction enzymes. P. difficilis, P. nasutus, and P. attwateri were found to be members of the same clade. P. leucopus was not found to be closely related to any of the species of the boylii or truei species groups. Phylogenetic interpretations for the remaining species differed based on Wagner and Dollo parsimony analyses. P. true appears to be most closely related to P. gratus based on Wagner parsimony and the phenetic analysis, while the relationship of P. gratus to other species could not be resolved based on Dollo parsimony.

The geomorphological impact of small fossorial mammals (adapted to digging and living underground), such as rodents can be significant, and both their direct and indirect effects may contribute to landscape formation. This thesis is based on empirical field studies of two burrowing rodent species in sub-polar environments, namely invasive House mice (Mus musculus) on sub-Antarctic Marion Island and Norwegian lemmings (Lemmus lemmus) in sub-Arctic Abisko. The spatial distribution, sediment displacements, impact on vegetation and microclimatic effects of the rodents are documented. Invasive mice and rats, introduced on sub-Antarctic Islands during the 19th century, lack natural enemies and are shown to have a significant direct and indirect geomorphic impact by direct sediment displacement, vegetation removal by burrowing, grazing and trampling and thereby exposing the sediments for rain, wind and frost processes.  The geomorphic impacts of lemmings are comparatively more limited as they rely on natural hollows and snow cover for protection and do not burrow to the same extent as other fossorial rodents in cold regions. Lemmings are thus suggested to have little impact on landform integrity, but can affect vegetation composition. A comparison of the findings from this study with published data on seven other rodent species and other physical mass transfer mechanisms in sub-polar and alpine environments suggests that fossorial rodents are a significant and sometimes dominant geomorphic force in sub-polar and alpine environments. The geomorphic work by ground squirrels, ice rats, plateau pikas and zokors is shown to be in the same order of magnitude as solifluction and rock falls. In alpine and periglacial environments these rodents are considered to act as key-stone species and ecosystem engineers through the creation of landforms by  dislocation and of soil and other impacts on soil properties, vegetation and ecosystem function

Dans ce travail de recherche doctorale, l’IRM des poumons à temps d'écho courts dite UTE (Ultra-short EchoTime) a été utilisée pour détecter le signal RMN du tissu pulmonaire afin de caractériser et étudier des modèlesexpérimentaux de maladies pulmonaires chez les rongeurs (rats et souris). En particulier, la technique radialeUTE a été appliquée pour détecter des biomarqueurs dans des modèles de broncho-pneumopathie chroniqueobstructive (BPCO) induite expérimentalement chez les rongeurs. La détection du signal RMN en provenancedu parenchyme pulmonaire a fourni de précieux indicateurs de la maladie associés à l'élargissement des alvéolespulmonaires et aux processus inflammatoires. De plus, la simplicité de mise en oeuvre de cette technique(absence de synchronisation cardiaque et pulmonaire) permet de réduire les temps d’acquisition et apparait bienadaptée aux études longitudinales. La mesure répétée du centre de l’espace-k à chaque temps de répétition de laséquence a été utilisée pour développer une méthode de post-synchronisation reposant sur la détection desmouvements cardio-respiratoires, et permettant de produire des images sans artefacts de mouvement. / In this work, ultra-short echo time (UTE) MR imaging of the lungs is presented as a way of detecting pulmonaryMRI signal, thus providing an opportunity to develop new imaging tools for the investigation of experimentalmodels of lung diseases in rodents. The UTE imaging technique (TE=450 μs) was implemented on a 4.7 Tscanner and applied to detect indicators of Chronic Obstructive Pulmonary Disease (COPD) inducedexperimentally in rodents. The improved signal detection from the lung parenchyma provided valuable markersof disease associated with airspace enlargement and inflammation. When used to investigate of inflammationspecificity, this technique had advantages when delineating regions of early cellular infiltration into the site ofinflammation. In the case of edematous signal quantification, the UTE technique was explored to improve thereliability of the volumetric measurements. This technique was demonstrated to be of use when easy protocolimplementation (relatively high throughput and low-cost experiments) and longitudinal studies (limitedinterference with physiopathology) are of concern. The repetitive probing of the k-space center with a temporalresolution of the sequence's repetition time achieved with this technique was used to develop a self-gatingmethod which relies on the tracking of cardio-respiratory motions, yielding images free from motion artifacts.

Dans cette thèse l’expression du récepteur CB1 dans l’hippocampe de souris mutantes ré-exprimant spécifiquement le gène spécifiquement dans certains types cellulaires du cerveau tels que : les neurones glutamatergiques du télencéphale dorsal, et les neurones GABAergiques a été analysé. De plus, dans le but de connaître la distribution anatomique exacte des récepteurs CB1 astrogliaux par rapport aux synapses excitatrices et inhibitrices, j’ai étudié l’expression des récepteurs CB1 dans les astrocytes de souris exprimant le récepteur CB1 seulement dans les astrocytes et une souris mutante ciblée pour exprimer la protéine cytoplasmique hrGFP diffusible dans les cellules astrogliales, ce qui permet une meilleure détection des prolongements astrocytaires. Les conclusions de ce travail de thèse sont les suivantes : la distance la plus commune entre le récepteur CB1 astroglial et la synapse la plus proche est de 400 à 800 nm. La majorité des synapses entourées par des astrocytes immunopositifs pour le récepteur CB1 dans l’hippocampe, est de nature excitatrice. Les souris mutantes ré-exprimant le récepteur CB1 caractérisées dans ce travail de thèse montrent : 1) l’expression du récepteur CB1 dans différents types cellulaires, 2) la réexpression est limitée à une population neuronale particulière ou aux astrocytes, 3) les niveaux endogènes de récepteurs CB1 sont maintenus dans les différents types cellulaires ré-exprimant le récepteur CB1. De façon générale, ces résultats nous montrent que les souris mutantes ré-exprimant le récepteur CB1 sont d’excellents outils pour l’étude fonctionnelle et translationnelle sur le rôle de ce récepteur dans le cerveau sain ou pathologique. / The Cannabinoid Type I receptor protein (CB1) expression in the hippocampus of rescue mice modified to express the gene exclusively in specific brain cell types: such as dorsal telencephalic glutamatergic neurons, or GABAergic neurons have been analyzed. Furthermore, aiming at knowing the exact anatomical distribution of the astroglial CB1 receptors with respect to the excitatory and inhibitory synapses, the CB1 receptor expression in astrocytes of mouse expressing CB1 receptor only in astrocytes and mutant mouse expressing the protein hrGFP into astrocytes (that allows for better detection of the astrocytic processes) have been also investigated. The results showed that the majority of the hippocampal synapses surrounded by CB1 receptor immunopositive astrocytes in the 400-800 nm range are of excitatory nature. Moreover, the CB1 receptor rescue mutant mice characterized in this Doctoral Thesis have proven 1) to express CB1 receptors in specific brain cell types; 2) the re-expression is limited to the particular brain cell populations; 3) the endogenous levels of CB1 receptors are maintained in the brain cell types re-expressing the receptor. Which makes this mutant mice excellent tools for functional and translational investigations on the role of the CB1 receptors in the normal and diseased brain.

Human activities are increasing the size, frequency and severity of disturbance across earth’s ecosystems including deserts. Exotic annual grasses have altered fire regimes by increasing the size, frequency, and severity of fires in these systems. Invertebrates make up a large proportion of ecosystem diversity, provide a wide range of ecosystem functions, and are good indicators of ecosystem function and resilience. Ants are particularly good indicators of ecosystem stability. The ability of rodents to modify plant community structure post-fire, could result in rodent communities having important indirect effects on invertebrate communities. In chapter 1 we report changes in ant forager abundance and diversity with fire and rodent treatments over a three year period in the Great Basin. We found that while rodents had significant effects on the plant community in burned plots, this did not affect the ant community. Fire, however played a significant role in determining ant species richness and Shannon’s diversity index. Ant richness and diversity were reduced in burned areas compared to unburned areas. Total ant forager abundance was unaffected by fire, however, the abundance of the most common ant species, Pogonomyrmex occidentalis, increased in burned areas. The overall abundance of the other species was reduced in burned areas. We saw increases in the densities of P. occidentalis mounds in burned areas, but the average size of those discs decreased. The total area occupied by P. occidentalis mounds remained equal between burned and unburned plots. In chapter 2 we compare the abundances of different groups of invertebrates, as well as the abundances and diversity of the ant communities, between fire and rodent treatments. We then compared how those responses differed between sites in the Great Basin and Mojave deserts. In this study, we found that the abundances of most invertebrate groups remained unaffected by fire and rodent treatments. In the Great Basin, however, the abundance of flying-foragers was reduced in burned areas. At both locations, ant species richness and Shannon’s diversity were reduced in burned areas. Species richness and Shannon’s diversity were negatively correlated with invasive plant cover at both sites, and invasive plant cover was positively correlated with fire. The loss of diversity can spell losses in important ecosystem functions, and invasive grass fire cycles threaten to make these losses permanent.

Globally emphasis has been given to identify emerging and re-emerging pathogens. Rapid urban expansion creates a problem which is two-fold. Firstly, increasing slum living conditions due to inadequate rate of infrastructure development results in an increased reliance on natural resources, including the capture and consumption of surrounding wildlife to subsist, thereby facilitating the transfer of emergent zoonotic pathogens. Secondly, through activities such as pollution or alien species introductions, the rapid transformation of once pristine environments, alters natural systems, potentially exposing these environments to new bacterial pathogens. Therefore, the main aim of this study was to assess overlooked bacterial species harboured by four host species (Bathyergus suillus, Georychus capensis, Cryptomys hottentotus hottentotus and Fukomys damarensis) belonging to the subterranean rodent family Bathyergidae, which inhabit an environment well-suited for an array of bacterial species, and which varied in their exposure to human settlements. Bacterial prevalence and diversity was initially evaluated using broad-range PCR techniques in combination with nucleotide sequencing. This revealed high levels of bacterial prevalence (82.91%) and mixed infections (22.60%) in bathyergid species. Two bacterial groups, the Bacillus cereus complex (a group of soil-dwelling bacterial strains with pathogenic potential with an overall prevalence of 8.55%) and haemotropic Mycoplasma strains (vector-borne bacterial strains of zoonotic potential with an overall prevalence of 1.28%) were subsequently selected for further genetic analysis with genus and species-specific PCRs. Bacillus molecular screening and phylogenetic analyses was achieved by targeting four gene regions with seven published primer assays and two novel PCR assays. This enabled identification of two B. cereus complex strains in bathyergid lungs and revealed an overall B. cereus complex prevalence of 17.95% for the 234 bathyergid lung samples screened. Bacillus genome prevalence was significantly higher in B. suillus individuals (45.35%), sampled in a peri-urban environment, compared to the other bathyergid species sampled from pristine habitats (ranging from 0% - 4.44%). Anthropogenic activities in the area where B. suillus was sampled could, at least partially, attribute to the perceived difference between urban and naturally sampled bathyergid species, highlighting the role of B. suillus to act as both a reservoir of potentially zoonotic pathogens and as a sentinel for anthropogenic soiling. Mycoplasma molecular screening using three different PCR assays, all targeting the 16S rRNA gene region, confirmed an overall haemotropic Mycoplasma prevalence of 24.13% in the 286 bathyergid organs (lung, spleen and liver) screened. A significantly higher prevalence and diversity of haemotropic Mycoplasma strains was found in B. suillus lungs (41.86%) compared to its naturally occurring relatives (ranging from 0%-36%). Phylogenetic analyses identified six novel haemotropic Mycoplasma strains, all grouping within a discrete monophyletic cluster, sister to Mycoplasma coccoides, and comprising two well-supported sub-clusters. The human introduction of commensal rodents harbouring Mycoplasma strains transferred through cosmopolitan arthropod vectors to indigenous bathyergids, likely underlies the higher prevalence in urban areas, although other biotic and abiotic factors affecting ectoparasite load also merit consideration. The data generated by the current study indicate the need to identify largely overlooked and potentially zoonotic bacterial pathogens in subterranean mammals and emphasises the importance of monitoring anthropogenically-introduced, opportunistic pathogens and the threats they pose to vulnerable communities and co-occurring, free-living animal species / Dissertation (MSc)--University of Pretoria, 2017. / Airports Company of South Africa (ACSA) / National Research Foundation (NRF) / Zoology and Entomology / MSc / Unrestricted

In deserts, global environmental changes, plant community structure, and soil water availability form a complex relationship characterized by direct and indirect relationships and feedbacks. Plant community structure is affected by the establishment and spread of invasive grasses, which form a positive feedback with wildfire. Plant community structure is also controlled by top-down trophic interactions by small-mammals and climate change, which alters the timing and amount of soil water. In deserts, soil water availability mediates the effects of global environmental changes and trophic interactions on plant community structure because it is the limiting resource for plant growth. In order to predict future changes in plant community structure, it is critical to understand how climate change, increased wildfire frequency and trophic interactions affect the establishment of invasive grasses and soil water after disturbance. Chapter 1. The objective was to understand the interactive effects of projected changes in climate, secondary wildfire, and rodent-exclusion on plant community structure. Mixed models revealed that all three factors interacted to magnify the establishment of the invasive annual grass B. tectorum in our post-fire experimental plots. In addition, structural equation models revealed that B. tectorum density was negatively correlated with the density of invasive annual forbs the following year, suggesting that B. tectorum competitively excludes other plant species. Chapter 2. The first specific aim was to understand the interactive effects of rodent-exclusion and secondary wildfire on the timing and amount of soil water availability. The second specific aim was to understand how invasive annual grass density controls soil water availability throughout the spring. Bayesian models revealed that rodent-exclusion and secondary wildfire affected soil water availability during specific windows of time throughout both experimental years. The most robust trend occurred in May of both experimental years, when rodent-exclusion, secondary fire plots had significantly less soil water availability than rodent-exclusion, single fire plots. Bayesian models also revealed there was little correlation between invasive grass density and soil water availability throughout the growing season.

MENVSC / Department of Ecology and Resource Management

Memory serves an integral function in every aspect of human life. Losing that function can be adevastating consequence of disease, dementia, and trauma. In order to develop treatments or prophylactics for memory disorders we must identify the neural basis of memory. Animal research has made prominent strides studying the neural correlates of memory by examining the more easily observable and manipulable neural correlates of spatial context, since the brain regions necessary for declarative memory intersect profoundly with those needed for spatial navigation. My research has two main goals. My first two studies, in Chapters 2 and 3, translate animal research relating the neural correlates of space to memory processes, and go beyond animal work to explore how internal features of experience such as goal states influence these conjunctive representations of space and memory. In Chapter 4, I expand my scope to examine how another internal feature, emotional context, affects the same brain regions on a network level to influence memory representations in the human brain. To perform these studies I recorded directly from the human brain in epilepsy patients performing a variety of memory tasks. First, I measured single-neuron activity as subjects navigated a virtual environment, encountering various objects at unique locations. As subjects moved through the environments, they were instructed to recall the locations of specific objects they encountered—I identified neurons in the human entorhinal cortex, called “memory-trace cells”, which selectively activated near the object-location that people were instructed to retrieve from memory. This is the first evidence that neurons in the brain can be tuned to the spatial context of an event for memory, and demonstrated a direct link between memory retrieval and the spatial tuning properties of neurons. For my second study, I examined whether spatially-tuned neurons in the MTL discharge at intervals organized by theta (2–10 Hz) oscillations (which represent network level brain-activity). I identified a particular pattern that is prominent in rodents, called “phase precession”, during which spatially-tuned neurons spike slightly faster than the network oscillation, and which is theorized to hold great value throughout the brain for learning and memory. In addition to discovering this pattern for spatial sequences, I discovered that phase precession was also present during more abstract features of experience, like the specific goal a person was seeking. These findings suggest that principles of network-level brain activity for organizing spatial navigation may extend to humans, and to broader forms of cognition and memory. Finally, I examined the role of the amygdala in memory encoding during a verbal episodic memory task, finding that the emotional context of a word influenced the probability of its subsequent recall. By measuring the prevalence and coordination of brain oscillations in the amygdala-hippocampal circuit, I found that gamma oscillations (30–120 Hz) increased in both regions as a function of word arousal and encoding success, and connectivity within the amygdala-hippocampal circuit also showed significant theta-gamma coupling as a function of memory and high arousal. Furthermore, direct 50 Hz stimulation impaired memory for high arousal words. These findings suggest a causal relationship between gamma oscillations in the amygdala-hippocampal circuit for memory as a function of emotional context during encoding. My work generalizes important neuronal principles from animal studies to humans (such as spatially-tuned neurons and phase precession), but also extends those findings more deeply to memory, and to internal/subjective aspects of memory that are difficult to directly measure in animals. Overall this work represents an important step towards understanding how the human brain enables declarative memory.

This dissertation explores the differential effects of fires and rodent communities on native and invasive desert plant communities. Chapter one examines the impacts of fire and repeat fires on fuel loads in two different Utah desert sites, one in the cool Great Basin Desert and one in the hyper-arid Mojave Desert, over the course of four years. We found that both desert sites responded with varying intensities to a single burn, but the effects of a reburn were not as pronounced. We also found that our Great Basin Desert site had a stronger response to fire than our Mojave Desert site, producing a higher plant fuel loads that could potentially exacerbate the changing fire regimes. These data can be used to help map the effects that climate change may have on fuel loads and the fire potential of these deserts. Chapter two uses a full factorial experimental design to compare the effects of rodent herbivory and fire on native versus invasive seedlings at our Mojave Desert field site. We found that rodent herbivory has a more negative impact on the survival of native seedlings than invasive seedlings. This could be because the invasives are grasses that tend to tolerate herbivory better than the native shrubs and forbs. Chapter three again uses a full factorial experimental design to assess the impacts of rodents and fire on the fate of native and invasive seeds at our field site in the Mojave Desert. We found that rodents removed seeds, and they did show preferences for some species of seed over others, but these preferences were not different between native and invasive seeds or seed mass. We propose that the preferences may be influenced by other seed traits such as water content, handling time or physical and chemical defenses. As with the seedlings in chapter two, fire did not have any impact on rodent seed preferences. These data highlight the importance of considering rodent effects on seeds used in restoration effects following wildfires.