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Prostate cancer is consistently the most frequently diagnosed cancer in American males as well as the second leading cause of cancer-related mortality. This underscores the dire need to understand the healthy prostate and how it can transform into a diseased state. Therefore, I have sought to investigate the heterogeneity and ontogeny of the mouse and human prostate. To do this, I employed single-cell RNA-sequencing, electron microscopy, immunofluorescence, and immunohistochemical analyses to identify specific cell populations, as well as lineage tracing, organoid culture, and tissue recombination assays to assess the function and origin of these populations. I discovered a profound level of heterogeneity uniquely within the luminal epithelial compartment of the prostate, including several novel populations. These luminal populations differ in distribution between mouse prostate lobes and along the proximal-distal axis within each lobe. These populations demonstrated significant differences in progenitor behavior in both organoid culture and tissue recombination assays, as shown by their differential abilities to proliferate, generate patterned structures, and differentiate into distinct cell types. Comparisons of the mouse prostate cell populations to cells from several benign human prostate samples showed that there is also luminal heterogeneity in the human prostate, and that several mouse populations have substantial gene expression overlap with human prostate populations. The observed luminal heterogeneity as well as the functional differences were consistent across several different published studies of the mouse prostate, and cross-species transcriptional similarities between populations were maintained across additional human samples, indicating that these findings are robust. My findings suggest that the luminal compartment of the mouse prostate contains distinct populations of cells that may act as reserve progenitors, and that their distribution across the prostate lobes could be functional. Additionally, if these populations can be cells of origin for prostate cancer, then their differences in progenitor behavior could contribute to the heterogeneity observed in prostate cancer prognosis and treatment response, which could have substantial clinical implications for patients.

The Roanoke logperch (Percina rex) is a federally endangered large darter that occurs only within the Roanoke and Chowan drainages of Virginia. This dissertation examines multi-scale habitat use patterns by logperch in three river systems in Virginia, including comparisons among rivers and life stages. The first study in this dissertation compares microhabitat use patterns of logperch among the Roanoke, Pigg, and Nottoway rivers. My objectives are to: 1) compare available microhabitat and microhabitat use by logperch among these rivers; and 2) examine the transfer of habitat models among rivers. Habitat availability in the three rivers indicates that the Nottoway River is least impacted by human activity, while the Pigg River is most impacted. The Roanoke and Pigg rivers are found within the same region of Virginia and share many habitat characteristics. Logperch consistently use silt free, loosely embedded gravel in all rivers and can occupy a variety of depths and velocities to accommodate substrate requirements. Microhabitat models transfer better between the similar Pigg and Roanoke rivers. The second study in this dissertation compares micro- and meso-habitat use patterns by Roanoke logperch in the Roanoke and Nottoway rivers. My objectives are to: 1) compare micro- and meso-habitat use patterns of logperch in the Roanoke and Nottoway rivers; and 2) examine transfer of habitat models at both scales. An increase in scale from micro- to meso- habitat did not improve model transfer. Habitat selectivity and transfer was strongest at the microhabitat scale. Logperch appear to be microhabitat substrate specialists and mesohabitat generalists. The final study in this dissertation examines ontogenetic patterns of habitat use by Roanoke logperch in the Roanoke and Nottoway rivers. My goals are to: 1) examine habitat use by three age classes of logperch and 2) compare ontogenetic patterns of habitat use between the Roanoke and Nottoway rivers. In the Roanoke River, adult and subadult logperch primarily used run and riffle habitat, often over gravel substrate. Subadults were found in lower water velocities and more embedded microhabitats than adults. Young-of-year logperch were found in shallow, stagnant backwaters and secondary channels. In the Nottoway River, both adult and subadult logperch were found over sand and gravel in deep, low velocity pools and runs. Subadults were observed in slightly more silted, lower velocity habitat. Younger age classes of logperch appear to be more vulnerable to sedimentation caused by human activity. Evidence in this dissertation strongly indicates that logperch have strict substrate requirements and the distribution of habitat types and pathways of dispersal will be critical for completion of the logperch life cycle. A watershed-level conservation approach that addresses sediment loading and preserves ecological processes that provide ephemeral, seasonal, and persistent types of habitat required over logperch ontogeny will be most effective for management geared towards the recovery of this endangered species. / Ph. D.

During preliminary research on cobia (Rachycentron canadum, L.) it became increasingly clear that more in-depth information was required to provide enabling techniques for the cobia aquaculture industry to develop more rapidly. A unifying theme in many of the more important issues facing cobia aquaculture is nutrition. This led to nutritional investigations with larval and juvenile fish highlighting the impacts of dietary ingredients on animal performance. Indeed, nutrition can be viewed as a central lever of action through which many aspects of the physiology and the environmental (water) quality of the animal can be controlled. The first project focused on studying the larval development of cobia, a fish species highly suitable for aquaculture for which the industry is nascent. I described the time-course of development of external sensory organs, gut morphology and relevant digestive enzymes under controlled conditions using electron microscopy, histology and spectrophotometric assays. The developmental sequence of larval cobia could be separated in two phases, with a transition period between 12 and 14 days post hatch (dph). This transition is characterized by the formation of the intestinal loop, the establishment of basic cranial neuromast configuration, leading to the initiation of the onset of pancreatic enzymes and the increase of growth rate. In addition, the effects of dietary taurine supplementation and incorporation of mannan oligosaccharides (MOS) into live feeds on cobia larvae development was examined. Fish fed supplementary MOS did not grow faster but displayed higher microvilli length and density. In addition, MOS-fed fish were more resistant to salinity stress. The dietary supplementation of taurine resulted in a dramatic increase in survival, growth and development rates, and enzymatic activities. The second project aimed at refining cobia juvenile nutrition, assessing fish meal and fish oil replacements. Novel sources, including soy protein and oil, were investigated with and without amino acid and MOS supplementations, yielding promising results. Indeed, both fish meal and fish oil were replaced completely and successfully in feeds for juvenile cobia. In addition, novel ingredients (e.g. marine algae meals and soy protein concentrate) were identified to effectively achieve such replacement. The third and last project dealt with nutrient-gene interactions, specifically centering attention on immunostimulants for which the underlying mechanisms of action remain poorly characterized. Here, dietary MOS, nucleotides and selenomethionine (Se-met) were offered to zebrafish whose transcriptome was analyzed by microarray. The immune system, humoral or cellular, innate or adaptive, exhibited different patterns of response according to the immunostimulating nutrient used. In addition, various genes involved in cell cycle and cytokinesis were concomitantly expressed. An intriguing observation related to the insulinomimetic effect of Se-met. In other words, Se-met impacted pathways normally regulated by insulin, such as the MAPK and PI3K pathways. Some Insulin-like Growth Factors (IGF) and IGF bindgin proteins were up-regulated. Additional research is however necessary prior to advocating for the use of these additives, in order to further investigate their respective pros and cons. / Ph. D.

Hypoxia refers to any condition in which the water is less than fully saturated with oxygen. Although it is generally accepted that adults are more tolerant of hypoxic conditions than larval stages, there is little information to support this assumption. To determine whether reduced concentrations of dissolved oxygen (DO) affect fishes differently during various early life stages, I examined the responses of two species of fish (fathead minnows (Pimephales promelas) and rainbow trout (Oncorhynchus mykiss)) exposed to low dissolved oxygen concentrations at different ages during the first 100 days post-hatch. The changes in oxygen requirements and respiratory patterns that occur during ontogeny and exposure to hypoxia were observed. The results of this study suggest that the early larval stages appear to be at least as tolerant of short-term exposure to low dissolved oxygen concentrations as the older, more developed stages. Fathead minnows underwent a gradual transition from being metabolic conformers to regulators during development. Hemoglobin appeared to be playing a larger role in oxygen supply in the early post-hatch trout than in the minnows. Fathead minnow larvae produced relatively low concentrations of lactate upon exposure to hypoxia. Conversely, rainbow trout larvae exhibited significant increases in lactate concentration under similar conditions. This implies that there is a threshold oxygen concentration below which trout larvae utilize anaerobic metabolism to provide additional energy. Lactate dehydrogenase activity increased as the rainbow trout larvae aged, suggesting that they develop an anaerobic capacity which could be used to provide additional energy during hypoxia. The minnows did not exhibit this increase in activity. The ability of larval fishes to detect and avoid hypoxic conditions was also examined. The overall trends suggest that throughout this period of development, both fish species gradually leave an area as the dissolved oxygen concentration decline. Both species appeared to leave the hypoxic areas with deliberate motions, indicating that a directed sensor system allowed them to detect oxygen gradients. The results suggest that a combination of physiological, biochemical, and behavioral mechanisms may allow fishes to cope with hypoxia. / Ph. D.

Theoretical models of sexual selection assume that female mating preferences are fixed and variation found between individuals resulting solely from allelic variation at specific loci coding for sexual preferences. For the last decade, an increasing number of studies have demonstrated that individual phenotypic variation in preferences was common across a wide range of taxa and induced by the environmental context and the females’ condition. Further, developmental stages of life are crucial in the formation of behaviours in general and have proven to be determinant to learn sexual preferences in some species that dispense care for their young. However, very little studies have analysed how the early social and physical environments shape female mate choice in species that lack parental care. In this thesis, I used guppies (Poecilia reticulata), firstly, to investigate the influence of various aspects of the social environment provided by males during two ontogenetic phases. Secondly, I explored whether learned preferences in a foraging context during development could be transferred into a mating context. Considering the early social environment, I explored three distinctive features potentially displayed by males and that females might experience while growing. Females were reared with different values of a sexual trait not genetically preferred in the population (orange colour) and different values of a trait for which they had innate predisposition (total colour area). In both cases, females were exposed to the different treatments for the whole developmental period or for its later phase. My results indicated that females changed their sexual behaviours in response to both type of traits experienced, reversing sometimes their genetic preferences. Moreover, the timing of exposure seemed to be a key factor in the acquisition of preferences as females exposed only to the later part of development with different values of total colour didn’t rely anymore on colour patterns to discriminate among males. In a third body of experiment, I examined whether the overall phenotypic variance exhibited by males during whole development, independently of the values of a specific sexual cue, mediated female’s behaviours. In a context of high variance, female became choosier relatively to those experiencing less variance. As a response, males switched mating tactics and attempted more forced copulations. In its final part, my thesis searched for a link that might have arisen, owing to developmental conditions, between preferences using the same sensory modality in two behavioural contexts. Maturing females were given food that was associated to a certain colour and subsequently tested for both their coloured preference in a foraging and a sexual context. Although no foraging preference for the corresponding colour was detected, females that experienced a yellow stimulus preferred yellower males compared to females with other experiences. Taken together these results suggest that developmental conditions and especially the social environment play a pivotal role in the process of mate choice. Under some circumstances, learned mate preferences override genetically-based preferences highlighting the importance of non-genetic mechanisms. Accordingly, it is urgent to integrate in the study of sexual selection and reproductive isolation this dimension. In guppies, for instance, the effect of early social life might contribute to the maintenance of colour pattern polymorphism found in males.