Shedding Light on Photosynthesis: The Impacts of Atmospheric Conditions and Plant Canopy Structure on Ecosystem Carbon Uptake.

The Earth’s climate is influenced by complex interactions of physical, chemical, and biological processes that link terrestrial ecosystems and the atmosphere. One of these interactions involves the use of light in photosynthesis, which allows plants to remove CO2 from the atmosphere and slow the unprecedented rate of climate change the Earth is experiencing. However, modeling future climate remains challenging, in part because of limited knowledge of mechanisms controlling the effects of light on gross ecosystem CO2 uptake (conceptually, photosynthetic activity integrated across all leaves in a plant canopy). Unlike previous studies, this dissertation uses data from atmospheric science, ecosystem ecology, and plant physiology to provide evidence for mechanistic links between physical, biophysical, and ecological controls on the effects of light on processes tied to gross ecosystem CO2 uptake—specifically, ecosystem gross primary production (GPP) and leaf photosynthesis. First, this dissertation empirically demonstrates that the dominant effect of clouds is to reduce total light above canopies. However, optically thin clouds increase scattered, diffuse light, which canopies use more efficiently than they use direct light. This offsets reductions in total light and results in no net change in GPP under thin clouds, while GPP decreases under optically thick clouds because both diffuse and direct light decrease. Second, ground-based measurements indicate that the rate of increase in GPP with diffuse light changes throughout the day. The magnitude of increase depends on how canopies interact with the angle of incoming light to biophysically alter the distribution of light within canopies and thus, the proportions of leaves contributing to GPP. Third, the distribution of species and light within one forest canopy leads to differences in some of the rate-limiting biochemical reactions in leaf photosynthesis. These field-based data indicate which assumptions representing canopies in Earth system models may not have support in situ, and could be contributing to errors in model estimates of future climate. Overall, this dissertation identifies mechanisms through which clouds and plant canopy structure alter land-atmosphere CO2 fluxes and subsequently, Earth’s climate. It also provides an important interdisciplinary framework for testing assumptions about the feedbacks that living organisms form with their environment.PhDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/133446/1/chengs_1.pd

Novel Applications and Refinements of Ultrasound Techniques in Perinatal and Infant Death Investigation

The decline in parental consent for perinatal autopsies has led to the development of less invasive autopsy techniques, primarily using imaging and in some cases acquiring tissue samples through laparoscopic techniques via small incisions. Whilst post-mortem MRI (PMMR) has been extensively tested, and shown to be a suitable modality for determining the cause of death/demise in the perinatal cohort, it is not widely available. This thesis explores the utility of a poorly explored, yet more accessible, cheaper, dynamic imaging modality widely used in ‘live’ paediatric imaging for the purposes of a less invasive autopsy – the perinatal post-mortem ultrasound (PMUS). I present a systematic review of the limited literature of PMUS diagnostic accuracy for perinatal death investigation encompassing 4 publications with 455 cases in total. This reveals an overall pooled whole body sensitivity rate of 73.3% [95% CI 59.9, 83.5] and specificity rate of 96.6% [95% CI 92.6, 98.4] . A comprehensive imaging protocol for whole body PMUS is also presented based on my own experience in scanning 272 perinatal deaths. An analysis in 130 of these cases with autopsy as a reference standard, showed that brain and abdominal diagnoses yielded the highest sensitivity rates (90.9% and 92.3% respectively), with spinal, cardiac and thoracic diagnoses yielding the lowest sensitivity rates (50%, 50% and 57.1% respectively). Imaging of the brain and heart however were the least likely to be of diagnostic quality (76.8% and 78.3% diagnostic cases respectively), particularly in macerated fetuses. In a subset of cases where PMUS and 1.5T PMMR were performed, there was no significant difference in whole body diagnostic accuracy rates (concordance rates for PMUS versus PMMR of 86.4% [95%CI 77.7, 92.0] versus 88.6% [95% CI 80.3, 93.7]), although PMMR yielded fewer non-diagnostic brain and cardiac examinations (2.9% and 2.9% non-diagnostic brain and cardiac PMMR cases versus 22.8% and 14.7% non-diagnostic PMUS cases). In the second part of my thesis, I describe the development of an ‘incisionless’ ultrasound guided biopsy method using a single entry site for the biopsy needle – the umbilical vein. This ‘INTACT’ biopsy method allowed for a ‘non-invasive’ autopsy with tissue sampling, with a biopsy success rate of 76.1% overall for all organs, with highest individual organ success rates >90% for heart and lungs. I conclude by discussing how best to incorporate PMUS into clinical practice and suggest areas for future researc

Competing complexity metrics and adults' production of complex sentences

The adequacy of 11 metrics for measuring linguistic complexity was evaluated by applying each metric to language samples obtained from 30 different adult speakers, aged 60-90 years. The analysis then determined how well each metric indexed age-group differences in complexity. In addition, individual differences in the complexity of adults' language were examined as a function of these complexity metrics using structural equation modeling techniques. In a follow-up study, judges listened to sentences in noise, rated their comprehensibility, and attempted to recall each sentence verbatim. Hierarchical multiple regression was used to evaluate the structural equation model, derived from the language samples, with respect to sentence comprehensibility and recall. While most of the metrics provided an adequate account of age-group and individual differences in complexity, the amount of embedding and the type of embedding proved to predict how easily sentences are understood and how accurately they are recalled

Cleaved end-face quality of microstructured polymer optical fibres

The cutting of a microstructured polymer optical fibre to form an optical end-face is studied. The effect of the temperature and speed of the cutting blade on the end-face is qualitatively assessed and it is found that for fibres at temperatures in the range 70–90 C, a blade at a similar temperature moving at a speed of less than 0.5 mm/s produces a good quality end-face. The nature of the damage caused by the cutting process was examined and found to vary with fibre temperature, blade quality and cut depth. Thermo-mechanical analysis showed that the drawn material was significantly more visco-elastic than the annealed raw material in the 70-90 C temperature range. The behaviour of the surface damage with cut depth was found to be consistent with the behaviour of a visco-elastic material

Metabolomic study of the LDL receptor null mouse fed a high-fat diet reveals profound perturbations in choline metabolism that are shared with ApoE null mice

Failure to express or expression of dysfunctional low-density lipoprotein receptors (LDLR) causes familial hypercholesterolemia in humans, a disease characterized by elevated blood cholesterol concentrations, xanthomas, and coronary heart disease, providing compelling evidence that high blood cholesterol concentrations cause atherosclerosis. In this study, we used 1H nuclear magnetic resonance spectroscopy to examine the metabolic profiles of plasma and urine from the LDLR knockout mice. Consistent with previous studies, these mice developed hypercholesterolemia and atherosclerosis when fed a high-fat/cholesterol/cholate-containing diet. In addition, multivariate statistical analysis of the metabolomic data highlighted significant differences in tricarboxylic acid cycle and fatty acid metabolism, as a result of high-fat/cholesterol diet feeding. Our metabolomic study also demonstrates that the effect of high-fat/cholesterol/cholate diet, LDLR gene deficiency, and the diet-genotype interaction caused a significant perturbation in choline metabolism, notably the choline oxidation pathway. Specifically, the loss in the LDLR caused a marked reduction in the urinary excretion of betaine and dimethylglycine, especially when the mice are fed a high-fat/cholesterol/cholate diet. Furthermore, as we demonstrate that these metabolic changes are comparable with those detected in ApoE knockout mice fed the same high-fat/cholesterol/cholate diet they may be useful for monitoring the onset of atherosclerosis across animal models

Flight Mechanics and Control of Escape Manoeuvres in Hummingbirds. I. Flight Kinematics

Hummingbirds are nature’s masters of aerobatic manoeuvres. Previous research shows that hummingbirds and insects converged evolutionarily upon similar aerodynamic mechanisms and kinematics in hovering. Herein, we use three-dimensional kinematic data to begin to test for similar convergence of kinematics used for escape flight and to explore the effects of body size upon manoeuvring. We studied four hummingbird species in North America including two large species (magnificent hummingbird, Eugenes fulgens, 7.8 g, and blue-throated hummingbird, Lampornis clemenciae, 8.0 g) and two smaller species (broad-billed hummingbird, Cynanthus latirostris, 3.4 g, and black-chinned hummingbirds Archilochus alexandri, 3.1 g). Starting from a steady hover, hummingbirds consistently manoeuvred away from perceived threats using a drastic escape response that featured body pitch and roll rotations coupled with a large linear acceleration. Hummingbirds changed their flapping frequency and wing trajectory in all three degrees of freedom on a stroke-by-stroke basis, likely causing rapid and significant alteration of the magnitude and direction of aerodynamic forces. Thus it appears that the flight control of hummingbirds does not obey the ‘helicopter model’ that is valid for similar escape manoeuvres in fruit flies. Except for broad-billed hummingbirds, the hummingbirds had faster reaction times than those reported for visual feedback control in insects. The two larger hummingbird species performed pitch rotations and global-yaw turns with considerably larger magnitude than the smaller species, but roll rates and cumulative roll angles were similar among the four species

Flight Mechanics and Control of Escape Manoeuvres in Hummingbirds. II. Aerodynamic Force Production, Flight Control and Performance Limitations

The superior manoeuvrability of hummingbirds emerges from complex interactions of specialized neural and physiological processes with the unique flight dynamics of flapping wings. Escape manoeuvring is an ecologically relevant, natural behaviour of hummingbirds, from which we can gain understanding into the functional limits of vertebrate locomotor capacity. Here, we extend our kinematic analysis of escape manoeuvres from a companion paper to assess two potential limiting factors of the manoeuvring performance of hummingbirds: (1) muscle mechanical power output and (2) delays in the neural sensing and control system. We focused on the magnificent hummingbird (Eugenes fulgens, 7.8 g) and the black-chinned hummingbird (Archilochus alexandri, 3.1 g), which represent large and small species, respectively. We first estimated the aerodynamic forces, moments and the mechanical power of escape manoeuvres using measured wing kinematics. Comparing active-manoeuvring and passive-damping aerodynamic moments, we found that pitch dynamics were lightly damped and dominated by the effect of inertia, while roll dynamics were highly damped. To achieve observed closed-loop performance, pitch manoeuvres required faster sensorimotor transduction, as hummingbirds can only tolerate half the delay allowed in roll manoeuvres. Accordingly, our results suggested that pitch control may require a more sophisticated control strategy, such as those based on prediction. For the magnificent hummingbird, we estimated that escape manoeuvres required muscle mass-specific power 4.5 times that during hovering. Therefore, in addition to the limitation imposed by sensorimotor delays, muscle power could also limit the performance of escape manoeuvres

Ornamental marine species culture in the coral triangle: seahorse demonstration project in the Spermonde Islands, Sulawesi, Indonesia.

Ornamental marine species ('OMS') provide valuable income for developing nations in the Indo-Pacific Coral Triangle, from which most of the specimens are exported. OMS culture can help diversify livelihoods in the region, in support of management and conservation efforts to reduce destructive fishing and collection practices that threaten coral reef and seagrass ecosystems. Adoption of OMS culture depends on demonstrating its success as a livelihood, yet few studies of OMS culture exist in the region. We present a case study of a land-based culture project for an endangered seahorse (Hippocampus barbouri) in the Spermonde Islands, Sulawesi, Indonesia. The business model demonstrated that culturing can increase family income by seven times. A Strengths Weaknesses Opportunities Threats (SWOT) analysis indicated good collaboration among diverse stakeholders and opportunities for culturing non-endangered species and for offshoot projects, but complicated permitting was an issue as were threats of market flooding and production declines. The OMS international market is strong, Indonesian exporters expressed great interest in cultured product, and Indonesia is the largest exporting country for H. barbouri. Yet, a comparison of Indonesia ornamental marine fish exports to fish abundance in a single local market indicated that OMS culture cannot replace fishing livelihoods. Nevertheless, seahorse and other OMS culture can play a role in management and conservation by supplementing and diversifying the fishing and collecting livelihoods in the developing nations that provide the majority of the global OMS