Thesis (Ph.D.)--George Mason University, 2008. / Vita: p. 180. Thesis director: Thomas C. Wood. Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Environmental Science and Public Policy. Title from PDF t.p. (viewed Mar. 17, 2009). Includes bibliographical references (p. 156-179). Also issued in print.

Thesis (M.S. in Psych.)--School of Psychology, Georgia Institute of Technology, 2004. Directed by Terry Maple. / Includes bibliographical references (leaves 58-69).

Previously, the exact phylogenetic relationship between the giant panda (Ailuropoda melanoleuca) and the red panda (Ailurus fulgens) has been unclear, but with the advent of molecular sequencing technologies, these two animals are now known to be distantly related. Although taxonomically distinct, these two panda species have several things in common, primarily their almost exclusively bamboo diet, but also their similar physical adaptations to their diet and their sympatry in some locations. What was unknown was if their similarities also extended to their gastrointestinal tract (GIT) microbiota. Using next-generation 16S rRNA parallel sequencing technologies, we uncovered several factors that impact bacterial communities of the pandas and also found that the two panda species harbor distinct microbial communities. In general, the Firmicutes and the Proteobacteria dominate both pandas’ gut microbiomes, with lesser contributions by the Actinobacteria and the Bacteroidetes. However, for the red panda, sex, age, and season significantly alter GIT microbiota. For giant pandas, we found that bacterial communities differed significantly between their normal fecal samples and mucus excretions. Together, these data display the plasticity of their bacterial communities, with several factors shaping GIT microbiota. As both species are highly threatened, understanding the relationship between the panda and their gut microbiome has given insight into the overall health of these uniquely herbivorous carnivores.

Giant pandas are unique animals because of their digestive system is similar to carnivores but they have in fact adapted to a plant diet with bamboo as their main food source. According to fossils records, giant pandas were omnivorous approximately 7 million years ago, becoming almost vegetarian after 4.6 to 5 million years of evolution. However, their genome and anatomical structure do not favor bamboo digestion. For more than a decade, researchers have been questioning the underlying mechanism of their ability to digest bamboo. In 2010, the genome of giant panda was completed, which confirmed that their genome had no gene encoding for cellulolytic enzymes. Thus, the gut microbiota of giant panda, which has been hypothesized to play a key role in bamboo digestion, has garnered unprecedented attention. Researchers are also interested in the giant panda’s gut microbes due to their potential application in biomass conversion. In Chapters 2 and 3 of this thesis, the microbial catalog of the giant panda’s gut microbiota was characterized, showing possible age-related microbial dysbiosis. Moreover, the microbiota, both bacterial and fungal was highly individualized because very few operational taxonomic units were shared among the four pandas in this study. Novel homoacetogens were also identified in the giant panda using functional gene clone-library sequencing. Using metagenomic sequencing, I uncovered the first evidence of human and animal related viruses in the giant panda’s gut. In addition to the community structure, I also determined the metabolic pathways of the microbiome. From KEGG annotation, a metabolic pathway for both cellulose and hemicellulose metabolism was identified. Comparative metagenomic analysis indicated that the giant panda’s gut microbiome was taxonomically and functionally distinct from those in mammals. In Chapters 4 and 5, a total of 97 species of bacteria were isolated and identified using biochemical assays. Four of these bacteria showed powerful cellulolytic and hemicellulolytic activities on solid media. The gram-positive bacteria (HKUOP_BS) and the gram-negative bacteria (HKUOP_A14) were found to be rod shaped, facultative anaerobes that had the ability to powerfully hydrolyze both cellulose and hemicellulose using intracellular and extracellular enzymes respectively. In Chapter 6, I determined the complete genome of a cellulolytic bacterium, Klebsiella oxytoca HKUOPL1, from giant panda and further described the annotated virulence, drug resistant, functional and potential horizontal transferring genes. The phylogenomic tree indicated that K. oxytoca HKUOPL1 closely resembled the K. oxytoca KCTC 1686 strain commonly used in 2,3-butanediol production. In captive giant pandas, a mucous excretion episode usually occurs with mild to severe colic. To understand the host-microbial interactions during this episode, bacterial communities were compared between mucous excreta and normal feces. The shifts in community abundance (especially flooding of Clostridia) may be associated with the mucous excretion episode. This study provides a better understanding of the microbial community structure and function in the giant panda’s gut. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

We have performed calculations in order to evaluate the vacuum conditions for the twohadron physics experiments WASA and PANDA. WASA is an ongoing experiment whereasPANDA is an experiment under construction. There is an interest in improving the vacuumconditions for these experiments in order to reduce background interactions. The experimentswere modelled as longitudinal conductance limited vacuum systems in the molecular flowregime and the calculations were performed with VAKLOOP. The approach was to fit amodel of WASA to measurement data and then extend this model to PANDA in order tomake predictions. The model of WASA was successful in the sense that it reproduced themeasurement data within the measurement uncertainty. The model of PANDA showed somediscrepancies in comparison with calculations from the Target Technical Design Report ofPANDA, but an overall similar pressure profile is obtained. Finally, we have considered a wayof improving the conditions at PANDA by including extra pumping capacity in the system,concluding that lowering the pressure at the interaction point for PANDA is challenging. Anoutlook for further modelling is to make a more detailed comparison between our model andthe one from the Target Technical Design Report.

Preservation of giant pandas, Ailuropoda melanoleuca, is a worldwide concern. This study was designed to examine dietary and reproductive challenges associated with panda management. Phytoestrogens are natural plant compounds that mimic estrogen and often negatively impact mammalian reproduction. Phytoestrogens in bamboo, the panda’s primary food source, is unknown. Here, estrogen radioimmuno- and receptor-binding assays revealed estrogenic activity in three species of Phyllostachys bamboo. These results present indirect evidence of phytoestrogenic mimics in bamboo, but their relevance is still unknown. Studies were also conducted to observe panda reproductive behaviors in an attempt to augment the use of an artificial vagina (AV) for semen collection. A preliminary study confirmed the panda could differentiate between estrus urine and a water ‘control.’ However, when estrus urine was placed on the AV as an attractant, the subject didn’t approach the AV. Further investigation of dietary challenges and reproductive alternatives are needed to substantiate these findings.

This thesis is based and developed on the ambiguous and open conception, iconic species, which reveals the relationship between human society and non-human species that goes be- yond its biological status. From the case of the giant panda, I attempt to deconstruct the shap- ing process of an iconic species from multiple perspectives, which includes how a specific cultural context, or a specific historical period contributes to the shaping process and how the government and the public diverge or even clash around the shaping process. Then, I introduce my fieldwork where I through observing both giant pandas and red pandas in the exhibition centres called panda bases to analyse the encountering an iconic species in reality and their different influences on public awareness of the wildlife conservation. I also attempt to explore the various representative forms of an iconic species such as the Tibetan antelope ranging from the mascot to the film and follow the changes of its symbolic meanings in different forms. In conclusion, the thesis is aimed to reflect the hybrid features of the iconic species and pro- vide in-depth interpretation of the endless interactions between the human beings and other species.

This report concerns a detection module used for a pellet tracking system. Spheres of frozen hydrogen known as pellets can be used as internal targets in hadron physics experiments. Pellets are created some distance above the accelerator beam and directed in a pellet beam pipe to intersect the accelerator beam. To determine the position of a pellet in the interaction region in the case of an interaction, the pellets need to be tracked. This is done using tracking sections along the pellet beam pipe with measurement levels containing lasers illuminating the pellets and cameras, detecting the light. The pellet position in the interaction region can be reconstructed with an accuracy of 0.1 mm. To reach this accuracy there are high demands on the alignment of the cameras and lasers. Alignment by a pellet beam pipe is generally difficult so a solution enabling alignment elsewhere is desired. Therefore a detection module consisting of a plate with cameras and lasers mounted to it has been constructed. These cameras and lasers can be aligned in an alignment bench setup before being transported to a pellet beam pipe. The alignment of the cameras and lasers on the detection module must be maintained under certain conditions e.g. transportation, temperature changes, exposure to vibrations. This report covers investigations regarding the mechanical stability of the detection module under these conditions. Different alignment bench targets are investigated. The effects of the optics of the cameras and lasers and the functionality of the detection module are investigated.

The PANDA experiment is one of the main pillars of the Facility for Antiproton and Ion Research (FAIR), currently under construction in Darmstadt, Germany. PANDA will be a fixed target experiment designed for the study of non-perturbative phenomena of the strong interaction. Strange hyperon production is governed by m(s)  ~ 100 MeV, which corresponds to the confinement domain. Thus, hyperons are suitable probes in this energy region. This work is a simulation study focused on the feasibility of studying the production of Σ0-bar and Λ hyperons in the pbar p -> Σ0-bar Λ reaction with the PANDA detector. A 10^4 events sample simulated at p(beam) = 1.771 GeV/c is used to perform a single-tag (inclusive) and a double-tag (exclusive) event selection. From the former, it is concluded that the single-tag method does not provide with the clean signal required for spin observables extraction. In contrast, exclusive event selection provides with a signal reasonably clean from combinatorial background and completely clean from generic hadronic background events. A signal (Σ0-bar Λ) reconstruction efficiency of ε = 5.3 ± 0.2 % is obtained for exclusive event selection. The corresponding signal to background ratio is S/B(Total) ~ 6 and the significance value is ~ 21. In addition, an exclusive event selection is performed on a 10^4 events sample simulated at p_(beam) = 6 GeV/c. Almost all the generic hadronic background events are removed by the applied selection criteria. At this beam momentum, the obtained signal efficiency is ε = 6.1 ± 0.3%, the signal to total background ratio is S/B(Total) ~ 4 and the significance is ~22. Both efficiencies are smaller compared to a previous simulation study on this channel, but are large enough to enable a study of the exclusive production of the pbar p -> Σ0-bar Λ reaction at PANDA. The difference between the results of this thesis work and the previous work is attributed to the more realistic implementation of the signal production mechanism, as well as the detector and reconstruction algorithms.

The objective of this study was to develop near infrared reflectance spectroscopy (NIRS) calibration equations from bamboo and fecal samples to predict diet composition and the physiological status of giant pandas. Discrimination between branch, culm, and leaf parts of bamboo resulted in an Rsquare (R2) of 0.88. The calibration equation for discriminating between 4 species of bamboo had an R2 of 0.47. Calibration equations were created for all bamboo species combined to determine the ability of NIRS to predict the nutrient constituents of CP, NDF, ADF, DM, and OM. No R2 was lower than 0.96, with the exception of DM at 0.63, which was consistently difficult to accurately predict due to variation in factors relating to difference in location of lab work (humidity, shipping, methods, etc.). Giant panda diets vary between seasons from eating primarily leaf to eating almost only culm. When bamboo part samples were compared between March and October, all resulting R2s were above 0.80. The sensitivity analyses for leaf and culm samples within diet season produced inconclusive results, but sensitivity analyses for fecal samples yielded an ability to more greatly discriminate between months that were further apart. For giant panda physiological status calibrations, fecal samples were collected from the Memphis Zoo, Smithsonian's National Zoo, Zoo Atlanta, and San Diego Zoo from 2006 to 2007. One-hundred fecal spectra were used to develop discriminant equations with which to predict between adults and juveniles. The resulting calibration was 100% correct for both age classes. Predictions between 252 male and female fecal spectra were 89% correct for females and 90% correct for males. A small number of samples (N= 60) were used to create a discriminant equation to differentiate between pregnant and non pregnant females. The exercise resulted in an R2 of 0.68 and a prediction of 100% for both pregnant and not-pregnant. It has been determined through these studies that NIRS has the potential to determine nutrient composition of bamboo and giant panda fecals, but increased sampling and equation development is needed before these calibrations are applicable in a captive or wild giant panda setting.