Constraint-based models of metabolism seldom incorporate capacity constraints on intracellular fluxes due to the lack of experimental data. This can sometimes lead to inaccurate growth phenotype predictions. Meanwhile, other forms of data such as fitness profiling data from growth competition experiments have been demonstrated to contain valuable information for elucidating key aspects of the underlying metabolic network. Hence, the optimal capacity constraint identification (OCCI) algorithm is developed to reconcile constraint-based models of metabolism with fitness profiling data by identifying a set of flux capacity constraints that optimally fits a wide array of strains. OCCI is able to identify capacity constraints with considerable accuracy by matching 1,155 in silico-generated growth rates using a simplified model of Escherichia coli central carbon metabolism. Capacity constraints identified using experimental fitness profiles with OCCI generated novel hypotheses, while integrating thermodynamics-based metabolic flux analysis allowed prediction of metabolite concentrations.

<p>Understanding the mechanisms that underlie the formation of, and innovation in biochemical pathways is an important goal in evolutionary biology. The following work addresses the problem of biochemical pathway evolution in two ways. In the first chapter, I combine genetic manipulations and population genetic analyses to investigate the whether flux control in the aliphatic glucosinolate pathway of <italic> Arabidopsis thaliana</italic> drives evolutionary rate heterogeneity. My results indicate that the first enzyme in the pathway, CYP79F1, has majority flux control and is the only one to show convincing evidence for positive selection. The second chapter builds on the first by asking whether flux control is stable under a variety of environmental conditions. I find that flux control remains with CYP79F1, in all my environmental treatments. In the final chapter, I address the evolution of one enzyme in this pathway from <italic>Boechera stricta</italic> that is responsible for a gain-in-function polymorphism that results in increased fitness in nature. With molecular phylogenetic analysis, site-directed mutagenesis, structural biology and enzymatic assays, I determine what residues are under selection and test their functional effects. I find that just two mutations in this enzyme are responsible for the change in function, and discuss their position within the enzyme. Strikingly, the enzyme with majority flux control in <italic>A. thaliana</italic> is homologous to the enzyme responsible for the novel function in <italic>Boechera</italic>. Together these results suggest that selection may predictably exploit the same small subset of genes to optimize biochemical pathway output and for evolutionary innovation.</p> / Dissertation

<p>Quantifying carbon fluxes and pools of forest ecosystems is an active research area in global climate study, particularly in the currently and projected increasing atmospheric carbon dioxide concentration environment. Forest carbon dynamics are closely linked to the water cycle through plant stomata which are regulated by environmental conditions associated with atmospheric and soil humidity, air temperature and light. Thus, it is imperative to study both carbon and water fluxes of a forest ecosystem to be able to assess the impact of environmental changes, including those resulting from climate change, on global carbon and hydrologic cycles. However, challenges hampering such global study lie in the spatial heterogeneity of and the temporal variability of fluxes in forests around the globe. Moreover, continuous, long-term monitoring and measurements of fluxes are not feasible at global forest scale. Therefore, the need to quantify carbon and water fluxes and to identify key variables controlling them at multiple stands and time scales is growing. Such analyses will benefit the upscaling of stand-level observations to large- or global-scale modelling approaches. </p><p>I performed a series of studies investigating carbon and water fluxes in pine forests of various site characteristics, conditions and latitudinal locations. The common techniques used in these studies largely involved sap flux sensors to measure tree-level water flow which is scaled up to stand-level transpiration and a process-based model which calculates canopy light absorption and carbon assimilation constrained by the sap-flux beased canopy stomatal conductance (called Canopy Conductance Constrained Carbon Assimilation or 4C-A model). I collected and analyzed sap flux data from pine forests of two major species: Pinus taeda in temperate (36 °N) and Pinus sylvestris in boreal (64 °N) climatic zones. These forests were of different stage-related canopy leaf area and some were under treatments for elevated atmospheric CO2 concentration or fertilization. </p><p>I found that (Chapter 2) the 17-year long free-air CO2 enrichment (FACE) had little effect on canopy transpiration of a mixed forest with the dominant P. taeda and other broadleaved species as the understory in North Carolina, USA (Duke FACE). The result was due to the compensation of elevated [CO2]-induced increase of canopy leaf area for the reduction of mean canopy stomatal conductance. My next theoretical study (Chapter 3), comparing P. taeda (native at 36 °N in North Carolina), P. sylvestris (native at 64 °N in norther Sweden) and Pinus contorta (native at 58 °N in British Columbia, Canada) canopies, revealed that the interaction between crown architecture and solar elevation associated with site latitude of pine canopies affected the distribution and total amount of canopy light absorption and potentially photosynthesis such that the latitudinally prescribed needle organization of a pine canopy is optimal for light interception and survival in its native location. Then, I quantified and analyzed water fluxes in four pine forests: one composed of P. taeda in North Carolina and three containing P. sylvestris in northern Sweden (Chapter 4). The latter forests consisted of various stage-related canopy leaf area and nutrient status. Combining my estimates with other published results from forests of various types and latitudinal locations, I derived an approach to estimate daily canopy transpiration during the growing season based on a few environmental variables including atmospheric and soil humidity and canopy leaf area. Moreover, based on a water budget analysis, I discovered that the intra-annual variation of precipitation in a forest has a small effect on evapotranspiration and primarily affecting outflow; however, variation of precipitation across latitudes proportionally influences anuual evapotranspiration and outflow. Furthermore, the hydrologic analyses implied the `disequilibrium' of forest water cycling during the growing season when forests may use less and more water in dry and wet regions, respectively, than the incoming precipitation. Nevertherless, at annual timescale, most forests became in `equilibrium' by using similar proportion of incoming precipitation. Finally, (Chapter 5) I estimated and analyzed the temporal and spatial variabilities of carbon fluxes of the same four forests measured in Chapter 4 using the 4C-A computational approach and analyzed their resource-use efficiencies. I concluded that, based on my results and others as available, despite the differences in species clumping and latitudes which influence growing season length and solar elevation, the gross primary productivity can be conservatively linearly related to the canopy light absorption. However, based on previous findings from a global study, different allocation of the acquired carbon to the above- and belowground is regulated by soil nutrient status. </p><p>Overall, the findings in this dissertation offer new insights into the impacts of environmental changes on carbon and water dynamics in forests across multiple sites and temporal scales which will be useful for larger-scale analyses such as those pertaining to global climate projection.</p> / Dissertation

Rainforests are of great importance to global carbon cycling, but the importance of deforestation and change in land use is poorly understood due to a lack of studies quantifying the difference in carbon fluxes between original rainforest and agricultural land. Furthermore, the aquatic outgassing of neotropical systems have been proven to have greater impact on global carbon cycling than previously anticipated (Richey et al 2002).In this study we investigated the aquatic concentration and daily diffusive gas flux of CO2 and CH4 from 4 pristine sites and 4 impacted sites, respectively, in 4 streams running along a gradient of anthropological impaction in the Atlantic Rainforest, Brazil. Statistically significant differences between pristine and impacted sites were found in all streams for both CO2 and CH4. On average, the impacted sites were found to be emitting almost three times as much C into the atmosphere as the pristine sites, mainly owing to CO2 emissions (14172±5226 mg C m-2 d-1). Exploring an area of the neotropical carbon cycle that is not yet fully understood, the study draws attention to the significant difference in aquatic outgassing from rivers observed at different impaction levels and highlights the need for further field studies.

<p>Methane is an important greenhouse gas, and an ideal target for greenhouse gas emissions reductions. Unlike carbon dioxide, methane has a relatively short atmospheric lifetime, so reductions in methane emissions could have large and immediate impacts on anthropogenic radiative forcing. A more detailed understanding of the global methane budget could help guide effective emissions reductions efforts.</p><p>Humans have greatly altered the methane budget. Anthropogenic methane sources are approximately equal in flux to natural sources, and the current atmospheric methane concentration is ~2.5 times pre-industrial levels. The advent of hydraulic fracturing and resulting increase in unconventional natural gas extraction have introduced new uncertainties in the methane budget. At the same time, the next few decades could be a crucial period for controlling greenhouse gas emissions to avoid irreversible and catastrophic changes in global climate. Natural gas could provide lower-carbon fossil energy, but the climate benefits of this fuel source are highly dependent on the associated methane emissions. In this context of increasing uncertainty and growing necessity, quantifying the impact of natural gas extraction and use on the methane budget is an essential step in making informed decisions about energy.</p><p>In the work presented here, I track methane in the environment to address several areas of uncertainty in our present understanding of the methane budget. I apply the tools of methane analysis in a variety of environments, from rural groundwater supplies to an urban atmosphere, and at a range of scales, from individual point sources to regional flux. I first show that carbon isotopes of methane and co-occurrence of ethane are useful techniques for differentiating a range of methane sources. In so doing, I also show that leaks from natural gas infrastructure are a major source of methane in my study area, Boston, MA. I then build on this work by applying the same methane carbon isotope and ethane signatures to partition methane flux for the Boston metro region. I find that 88% of the methane enhancement in the atmosphere above Boston is due to pipeline natural gas. </p><p>In the final portion of this thesis and the two appendices, I move from the distribution side of the natural gas production chain to extraction, specifically addressing the potential impacts from hydraulic fracturing in my home state of North Carolina. I combine the methane source identification techniques of the previous sections with additional geochemical analyses to document the pre-drilling water quality in the Deep River Triassic Basin, an area which could be drilled for natural gas in the future. This data set is unique in that North Carolina has no pre-existing commercial oil and gas extraction, unlike other states where unconventional gas extraction is currently taking place. This research is, to my knowledge, the first to examine the hydrogeology of the Deep River Basin, in addition to providing an important background data set that could be used to track changes in water quality accompanying hydraulic fracturing in the region in the future.</p> / Dissertation

No description available.

Wireless sensing applications have extended into power transmission line monitoring applications. Minimal power consumption of sensor electronics have enabled kinetic energy harvesting systems to provides a means of self sustainability in the form of parasitic energy harvesting from power transmission lines. With this goal in mind, a miniature piezoelectric bimorph cantilever harvester has been developed using a magnetic tip mass which interacts with the oscillating magnetic flux surrounding power transmission wires. The focus of this thesis is develop an analytical model which can be used to optimize the amount of piezoelectric material to support sensory electronics. Special emphasis has also been placed on magnet orientation and geometry to ensure optimal magnetic flux interaction between input and output mechanisms. A single prototype harvester is designed with an arbitrary piezoelectric material length and experimentally validated at different conductor wire currents. The analytical model shows excellent agreement in frequency prediction for the prototype tested. Two damping techniques are used to experimentally extract modal damping ratios to predict peak mechanical and electrical responses at resonance frequencies. The miniature prototype design is less than 30 mm in length with only 10 mm piezoelectric material to produce a total volume of 154 10^-12 cm^3. The power output is measured at 174.1 W of power when positioned over top a 10 AWG copper conductor a distance of 6 mm with approximately 16 Amps of current passing though the conductor.

Studies have shown that including perennial forages in cropping rotations can increase soil carbon (C) and lower nitrous oxide (N2O) emissions when compared to continuous annual cropping. Research is needed to evaluate the inclusion of a perennial forage in an annual crop rotation on net carbon dioxide (CO2) and N2O fluxes, natural and agronomic drivers of seasonal greenhouse gases (GHGs), and the possibility of using forages as a C sequestration-CO2 mitigation tool. A long-term field experiment site to determine GHG budgets for Red River Valley cropping systems in Manitoba, Canada was used. The site consisted of four plots with the same annual rotation management history. A perennial legume, alfalfa, was grown in 2008 and 2009 on two plots and spring wheat and industrial oilseed-rapeseed grown on the other two plots in 2008 and 2009, respectively. Nitrous oxide and CO2 fluxes were measured continuously using the flux gradient micrometeorological method. For the net study period, the perennial phase sequestered twice the atmospheric CO2 (2070 kg C ha-1) compared to the annual crops. The annual rotation emitted 3.5 times more N2O than the perennial legume phase. When accounting for harvest C removals and considering GHGs in CO2-equivalent (eq.), the perennial legume phase was a net sink of 5440 kg CO2-eq. ha-1 and the annual rotation was a net source of 4500 kg CO2-eq. ha-1 for the two year study period. Information gathered will help bridge missing data gaps in national emission trends and enhance development of Canadian GHG mitigation models.

Sequestering atmospheric carbon in soil is an attractive option for mitigation of rising atmospheric carbon dioxide concentrations through agriculture. Perennial crops are more likely to gain carbon while annual crops are more likely to lose carbon. A pair of eddy covariance towers were set up near Winnipeg Manitoba, Canada to measure carbon flux over adjacent fertilized long-term perennial grass hay fields with high soil organic carbon. In 2009 the forage stand of one field (Treatment) was sprayed with herbicide, cut and bailed; following which cattle manure was applied and the land was tilled. The forage stand in the other field (Control) continued to be cut and bailed. Differences between net ecosystem productivity of the fields were mainly due to gross primary productivity; ecosystem respiration was similar for both fields. When biomass removals and manure applications are included in the carbon balance, the Treatment conversion lost 149 g C m^(-2) and whereas the Control sequestered 96 g C m^(-2), for a net loss of 245 g C m^(-2) over the June to December period (210 days). This suggests that perennial grass converted for annual cropping can lose more carbon than perennial grasses can sequester in a season.

主催：JST/CREST，Vrije University, ALTERRA, IBPC