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Much research is being conducted into the causes of human cancer. A number of human autosomal recessive diseases such as Xeroderma Pigmentosum are characterized at least in part by a defect or aberration in one or more forms of DNA repair and at the same time an elevated incidence of cancer. Also, carcinogens cause mutations in DNA and the greater the carcinogenicity, the greater the mutagenicity. As a result, much attention has been focused on DNA repair and its relationship to cancer incidence. The HCR of V antigen formation by UV-irradiated Adenovirus type 2 (Ad 2) was examined using apparently normal human fibroblasts, tumor cells (HeLa CCL2), and cells transformed by Ad 5 DNA (293, 293 N3S). A decrease in the HCR of V antigen formation was found for HeLa CCL2 cells as compared to apparently normal human fibroblasts, but not for the transformed cells. These results are discussed in terms of the characteristics of the cell types. Herpes simplex virus type I encodes a polymerase and thymidine kinase (tk) activity which are involved in viral DNA synthesis. Paa ᷇ 5, an HSV-1 mutant containing one or more mutations in the polymerase gene is an antimutator. If these are also involved in viral DNA repair, then the HSV-1 polymerase, tk activity, and mutant polymerases conferring altered mutation rates should provide excellent tools with which to probe cellular DNA repair processes and mutagenesis. The study of the HCR of plaque forming ability of HSV-1 KOS wild type (WT), Paa ᷇ 5 and PTK3B (lacking thymidine kinase activity ) using VERO cells revealed a decrease in the HCR of Paa ᷇ 5 and increase of surviving fractions of PTK3B with respect to that of HSV-1 KOS WT. Similar studies using apparently normal human fibroblasts, Xeroderma Pigmentosum and Cockayne Syndrome cells also implicated the HSV-1 polymerase in viral DNA repair. The results are discussed in terms of the function of the HSV-1 polymerase and the DNA repair abilities of XP and CS cells. / Thesis / Master of Science (MSc)

I used results from camera traps set for tigers (Panthera tigris) during 2001-2011 in the Hukaung Valley Wildlife Sanctuary of northern Myanmar to assess overall biodiversity of large mammal and bird species, and to identify differences in photo rates inside and outside of the most protected core area of the Sanctuary. A total of 403 camera stations were deployed during October-July in the dry seasons of 2001-2011, 260 inside the Core area and 143 Outside. From 10,750 trap-nights I obtained 2,077 independent photos of wildlife species and 699 of domestic animals and humans, including 35 species of wild mammals (19 carnivores, 4 primates, 1 elephant, 6 even-toed ungulates, 1 pangolin, and 4 rodents) and 16 species of wild birds. Of these, 1 is considered critically endangered, 7 are endangered, 11 are vulnerable, and 5 are nearly threatened. Some species that probably occur in the Sanctuary (e.g., arboreal or semi-aquatic mammals) were not photographed, likely because of camera placement. In total, 48 wild species were photographed in the Core area vs. only 33 at locations Outside of the core area. Generally, few photos of any domestic animal species were obtained inside 9 the Core area, and no photos insurgents were obtained there, but many more photos of poachers and villagers, but also park rangers, were obtained there. Increased patrol efforts may have helped maintain species presence in the Core area, but differences in photo rates between areas were likely mostly influenced by differences in elevation, slope, density of streams, trails, and roads, and perhaps vegetative cover type. Tiger abundance is most influenced naturally by prey availability and anthropogenically by poaching. In the Hukaung Valley Wildlife Sanctuary in northern Myanmar, a major conservation area established to protect tigers, tiger presence has declined. This study was conducted to assess habitat occupancy and distribution of principal tiger prey species in the Core part of the Sanctuary by surveying for sign on 1650.9 km partitioned into 554 sampling units during November 2007 and May 2008. Using standard occupancy model in the program PRESENCE (6.2), habitat occupancy and detection probabilities were predicted and the best candidate model for each species was selected using the Akaike information criterion (AIC). By incorporating 7 environmental and 4 social covariates, the predicted habitat occupancy rates were 0.76 (SE=0.196, naïve estimate = 0.5162) for gaur (Bos gaurus), 0.91 (SE=0.03, naïve estimate = 0.7762) for sambar (Rusa unicolor), 0.57 (SE = 0.003, naïve estimate = 0.3195) for wild pigs (Sus scrofa) and 0.89 (SE = 0.001, naïve estimate = 0.7996) for muntjac (Muntiacus muntjak). Overall, shorter Euclidean distances to ranger stations and trails, decreased stream density, and broadleaved evergreen/semi-deciduous forest and relatively rare rain-fed cropland habitat occurrence positively influenced prey habitat occupancy; conversely, shorter Euclidean distances to villages, roads, and streams, higher elevations, and occurrence of mixed broadleaved and needle-leaved forest habitat 10 negatively influenced occupancy. In addition, Euclidean distance to ranger stations, trails, and roads positively affections species detections, whereas shorter Euclidean distance to villages and streams, high elevations, and high precipitation negatively affected detections. Results indicate that all four prey species were relatively well-distributed through the Sanctuary Core area. However, comparisons with tiger and prey indices of abundance elsewhere suggest that prey density is low and would not likely support many tigers.

Forty-three radio-collared black bears (Ursus americanus) captured in northwestern Virginia were released in the Mt. Rogers National Recreation Area (MRA) in southwestern Virginia, and monitored from June 1990-March 1992. Survival was 0.23 over the 22 month study; male (0.12) and female (0.37) survival rates were not different (P = 0.16). Vehicle collisions caused most of the mortality (53%), but legal harvest outside of the study area (16%) and illegal kills in the study area (11%) also were important. Female bears failed to reproduce in the first winter following translocation, but during the second winter mean litter size was 2.75 (n = 4). A computer simulation of the female segment of the translocated population at the MRA predicted 45 females in the population in 1992, but only 29 females by 2002. The instantaneous rate of increase of the simulated population was -0.05 from 1993-2002. Mean distance translocated from capture to release was 297.7 km. Eleven bears remained in their release areas (i.e., moved <10 km from release), while 32 left their release areas. The mean distance moved from release to recovery/last location was 3.6 km for the former and 48.8 km for the latter. There was no difference (P > 0.05) in the probability of remaining in or leaving the study area for either sex. Bears recovered dead were more frequently outside the study area than in the study area (P < 0.01). For bears that left their release areas, the mean direction of travel from release to recovery/last location relative to the capture location (i.e., release to capture direction = 0°) was 31° and did not differ (P > 0.05) from the homeward direction. Despite some homeward orientation, no bears returned to their capture areas during this study. / Master of Science

Mule deer (<i>Odocoileus hemionus</i>) population dynamics, movements, and habitat use were studied on the Pinon Canyon Maneuver Site in southeastern Colorado during January 1983-December 1984. Thirty-eight adults and 28 fawns were radio collared, and 35 adults were color collared or ear tagged. Population estimates were 365 and 370 deer for 1983 and 1984, respectively. The sex ratio (yearling and adult) was 60 males: 100 females. Adult female pregnancy rate was 95%; the mean litter size for females over 1.5 years was 1.7 fawns. Annual fawn survival was 29% in 1983 and 22% in 1984. Coyote (<i>Canis Iatram</i>) predation was responsible for 76% of fawn mortality. Adult survival was 88% in 1983 and 87% in 1984; coyote predation accounted for 67%, and hunting for 33% of the annual adult mortality. The calculated annual rate of increase (λ) was 1.01, indicating a stable population. Seasonal home range size differed (p < 0.05) between males and females only in the fall. Females preferred pinyon-juniper woodland in all seasons, and shrub grassland in winter, summer and fall; proportional use of woodland/open grassland and shrub/open grassland edge was greater than proportional availability. Males preferred pinyon-juniper woodland and avoided open grassland in all seasons. Fawns preferred shrub grassland and shrub/open grassland edge; they avoided cholla/open grassland edge. Fawns selected bed sites with greater (P < 0.05) concealment cover at all 0.5 m intervals up to 2 m in height, and greater ground cover of trees, shrubs, and grasses (P < 0.01) than random sites. / Master of Science

In the 50+ years since the discovery of magnetic compass orientation by migratory songbirds, evidence for the use of magnetic cues has been obtained for a range of taxonomic groups, including several classes of vertebrate and invertebrate taxa. Surprisingly, however, the biophysical mechanisms and biological substrate that underlie magnetic sensing are still not fully understood. Moreover, while use of magnetic cues for compass orientation is intuitive, the functional significance of other forms of behavioral responses mediated by magnetic cues, such as spontaneous magnetic alignment, is less clear. The following research was carried out to investigate the mechanisms underlying magnetic orientation in vertebrates and invertebrates. This involved the modification of existing experimental systems to characterize responses to magnetic cues in laboratory animals (flies, mice) and the development of novel techniques for studying the role of magnetic cues in the spatial behavior of free-living animals (red foxes). Chapter II examines magnetic orientation in wild-type Drosophila melanogaster larvae. We show that three strains of larvae reared under non-directional ultraviolet (UV) light exhibit quadramodal spontaneous orientation along the anti-cardinal compass directions (i.e. northeast, southeast, southwest, northwest) when tested in a radially symmetrical environment under UV light. Double-blind experiments cancelling the horizontal component of the magnetic field confirmed that the response is dependent on magnetic cues rather non-magnetic features of the test environment. Furthermore, we argue that the larval quadramodal pattern of response is consistent with properties of magnetic compass orientation observed in previous studies of adult Drosophila and laboratory mice, both of which have been proposed to be mediated by a light-dependent magnetic compass mechanism. Chapter III explores the use of novel biologging techniques to collect behavioral and spatial data from free-roaming mammals. Specifically, a previous observational study of free- roaming red foxes found a 4-fold increase in the success of predatory 'mousing' attacks when foxes were facing ~north-northeast, consistent with magnetic alignment responses reported for a range of terrestrial animals. The authors propose that the magnetic field may be used to increase accuracy of mousing attacks. Using tri-axial accelerometer and magnetometer bio-loggers fitted to semi-domesticated red foxes, we created ']magnetic ethograms' from behavioral and magnetic machine learning algorithms 'trained'] to identify three discrete behaviors (i.e. foraging, trotting, and mousing-like jumps) from raw accelerometer signatures and to classify the magnetic headings of mousing-like jumps into 45° sectors from raw magnetometer data. The classifier's ability to accurately identify behaviors from a separate fox not used to train the algorithm suggests that these techniques can be used in future experiments to obtain reliable magnetic ethograms for free-roaming foxes. We also developed the first radio-frequency emitting collar that broadcasts in the low MHz frequency range shown to disrupt magnetic compass responses in a host of animals. The radio-frequency collars coupled with biologgers will provide a powerful tool to characterize magnetic alignment responses in predatory red foxes and can be adapted for use in studies of magnetic alignment and magnetic compass orientation in other free-roaming mammals. Chapter 3 discusses findings from a magnetic nest building assay involving male labratory mice. Mice trained to position nests in one of four directions relative to the magnetic field exhibited both learned magnetic compass responses and fixed magnetic nest positioning orientation consistent with northeast-southwest spontaneous magnetic alignment behavior previously reported for wild mice and bank voles. This is the first mammalian assay in which both learned magnetic compass orientation and spontaneous magnetic alignment were exhibited in the same species, and suggests that the use of magnetic cues in rodents may be more flexible that previously realized. / Ph. D. / A variety of animals have been shown to use the Earth’s magnetic field to help guide diverse spatial behaviors, however, the underlying sensory mechanisms mediating this sense remain elusive. Evidence for two distinct sensory mechanisms has come from behavioral studies involving a wide range of organisms, including migratory birds, newts, mole rats, mice, and several classes of invertebrates. The following research was carried out to determine the underlying sensory mechanisms mediating magnetic sensing in larval fruit flies. Properties consistent with a light-dependent, photoreceptor-based mechanism were found to underlie innate magnetic alignment behavior in larval flies, similar to the proposed compass mechanism thought to mediate compass responses in migratory birds and newts. A reanalysis of two previous studies of learned magnetic compass responses in adult fruit flies and laboratory mice show similar behaviors when compared to that of larval flies, suggesting a common underlying light-dependent magnetic mechanism across these groups. Furthermore, we provide evidence for learned magnetic compass responses in laboratory mice, where the orientation of individuals appears to be dependent on properties of the local environment (e.g. electromagnetic, temperature, humidity) in training and testing. These data suggest that the use of magnetic cues in mammals is context-dependent and more flexible than previously recognized. We have also developed new technologies for studies of magnetic orientation in free-roaming animals. Specifically, bio-logging devices containing triaxial accelerometer and magnetometer sensors where used to create ‘magnetic ethograms’, where the behavior and magnetic alignment of an animal can be reliably and accurately extracted from raw sensor data. We also discuss possible field experiments that can be performed to provide a specific test of the underlying sensory mechanism mediating magnetic behavior in free-roaming animals. This work will likely be of interest to a broad range of disciplines including sensory ecology, ethology, quantum chemistry, biophysics, wildlife management, and conservation.

Monitoring the distribution, abundance and demography of species is vital to ensure that conservation efforts are appropriate and effective. Monitoring enables evaluation of responses to natural or human disturbance, highlights the need for management interventions and enables these interventions to be assessed and refined. The methods used largely depend on the specific aim of monitoring and behaviour of the target species, as well as the time and spatial scale that monitoring is required to cover. The European pine marten (Martes martes) is one of few remaining mammalian predators native to the UK. Since persecution in the early 19th century resulted in their near extinction, pine martens have recovered part of their former range in Scotland. Their recent recovery and an overlap in territory with vulnerable prey species such as the capercaillie (Tetrao urogallus) make the collection of accurate baseline data and subsequent monitoring of population trends vital for conservation efforts. Faecal counts have traditionally been used to provide a relative measure of population density for pine marten. In most cases, absolute measures of population density require individual identification. Non-invasive genotyping can provide this information but the quality of DNA from these samples is often poor. Here, the process is refined for pine marten faeces (scats) and hair samples. DNA degradation increased significantly for scats exposed to rainfall, with the rate of DNA amplification success reduced by 38% over a 16 day period. Success rates for hair samples were higher when more hair follicles were included in the analysis. Population densities were estimated for three forests in Scotland using a robust combination of non-invasive genotyping of hair samples and spatially explicit capture recapture modelling. Population density estimates of 0.07 (95% CI 0.03 - 0.16) to 0.38 km-2 (95% CI 0.11 - 1.07) were obtained which are within the range of previous estimates for forests elsewhere in Scotland. The first attempt to quantify the relationship between traditional scat counts and home range size was then conducted; a significant negative correlation exists but only when population density is relatively low. Previous studies suggest that pine martens in Western Europe are less forest dependent than those in Eastern Europe. Results from this thesis support this, with populations at the highest density found at sites with intermediate forest cover. This tolerance of lower forest cover is also apparent in the diet. Despite a preference for Myodes voles in populations in Eastern Europe, those in Western Europe show a strong preference for Microtus voles as well as a higher level of frugivory. We assess the autumn diet of four populations in Scotland assess the effect of forest cover and sex on the diet. There was no evidence of differential consumption of Microtus voles or birds between the sexes. Our analysis shows that frugivory is influenced by forest fragmentation, with a 5-fold increase in the occurrence of fruit (from 2% to 10%) as forest cover increased from 4% to 47%. Diversionary feeding has been suggested as a management technique to reduce the depredation of capercaillie by pine martens. This thesis presents the first attempt to quantify the success and cost-efficacy of diversionary feeding for a range of problems (crop damage, threatened safety, livestock depredation) across 30 experimental trials. The strategy proved more effective when targeted towards food-limited populations, and when aiming to alleviate habitat damage or risks to human safety rather than depredation. A novel decision-making framework was developed to aid managers with the initial planning of the strategy and its subsequent implementation within an adaptive format. Further to this, the feasibility of using diversionary feeding with a view to reduce the depredation of capercaillie by pine martens was assessed. Questionnaire responses were collected from people who have provided food for pine martens throughout Scotland. A positive reaction to food was observed, with 58% of respondents reporting that initial visits occurred within one week of placement and 46% reporting that subsequent visits were received daily. These results suggest that diversionary feeding may be a viable option for pine marten management, although testing of its impact on capercaillie productivity would be required.