<p>The global carbon cycle is subject to intense research, where sources and sinks for greenhouse gases, carbon dioxide in particular, are estimated for various systems and biomes. Lakes have previously been neglected in carbon balance estimations, but have recently been recognized to be significant net sources of CO2.</p><p>This thesis estimates emission of carbon dioxide (CO2) from boreal lakes and factors regulating the CO2 saturation from field measurements of CO2 concentration along with a number of chemical, biological and physical parameters. Concentration of dissolved organic carbon (DOC) was found to be the most important factor for CO2 saturation in lake water, whereas climatic parameters such as precipitation, temperature and global radiation were less influential. All lakes were supersaturated with and, thus, sources of CO2. Sediment incubation experiments indicated that in-lake mineralization processes during summer stratification mainly occurred in the pelagial. Approximately 10% of the CO2 emitted from the lake surface was produced in epilimnetic sediments. </p><p>The mineralization of DOC and emission of CO2 from freshwaters was calculated on a catchment basis for almost 80,000 lakes and 21 major catchments in Sweden, together with rates of sedimentation in lakes and export of organic carbon to the sea. The total export of terrestrial organic carbon to freshwaters could thereby be estimated and consequently also the importance of lakes for the withdrawal of organic carbon export from terrestrial sources to the sea. Lakes removed 30-80% of imported terrestrial organic carbon, and mineralization and CO2 emission were much more important than sedimentation of carbon. The carbon loss was closely related to water retention time, where catchments with short residence times (<1 year) had low carbon retentions, whereas in catchments with long residence times (>3 years) a majority of the imported TOC was removed in the lake systems. </p><p>The Gulf of Bothnia was also studied in this thesis and found to be a net heterotrophic system, emitting large amounts of CO2 to the atmosphere on an annual basis. The rate of CO2 emission was depending on the balance between primary production and bacterial respiration, and the system was oscillating between being a source and a sink of CO2.</p>

Recent work has demonstrated that vast amounts of soil organic carbon (SOC) are redistributed and buried within Canadian croplands; however, the effects of redistribution on SOC dynamics and biological properties of the soil environment remain unknown. Because soil microorganisms are drivers of carbon (C) turnover in soil, the effects of such processes on microbial community dynamics are important in assessing the overall effects of redistribution and the stability of displaced C. This is particularly important in the face of future climate change scenarios and potential disturbances. The objectives of this study were to examine microbial community dynamics with depth and among landscape positions in an eroded landscape, and to assess C mineralization response between surface and subsurface soil layers in a depositional position. Microbial abundance was highly influenced by SOC redistribution. This was most evident in the buried backslope position where substantial soil and SOC deposition had occurred, creating a very thick A horizon (ca. 80 cm). Phospholipid fatty acid (PLFA) analysis revealed substantial concentrations of microbial biomass located at depth (30-60 cm), which was greater than PLFA concentration at the soil surface and correlated with SOC concentration. Community structure analysis demonstrated the strong influence of landscape position and depth in structuring microbial communities near the soil surface (0-20 cm). Communities in positions that were predominantly erosional were the most different from those in the depositional position, accounting for the largest amount of variation (60%) in the overall analysis. The existence of distinct microbial communities found in depositional material (0-25 cm) and within the buried A horizon (30-80 cm) in the buried backslope position indicate a strong influence of depth and redistribution in structuring microbial communities. The existence of significant viable biomass in the buried A horizon of the depositional position leads to question the persistence of highly concentrated, buried SOC over many decades. When soils from surface (0-5 and 20-25 cm) and subsurface (40-45 and 65-70 cm) depths were incubated in surface-like conditions, greater mineralization response in surface relative to subsurface soils, despite relatively similar SOC concentration, suggests that redistribution protects buried C from decomposition. Distinct microbial communities found at the onset and completion of the mineralization study between surface and subsurface soil layers may indicate the influence of microbial community structure on mineralization response. Depth was the largest source of variation in microbial community structure, and although a shift occurred after exposure to incubation conditions, the effect of depth remained the strongest influence. This work indicates that SOC redistribution strongly influences microbial abundance and community structure development, primarily driven by altered substrate gradients occurring with depth, and suggests that C is less susceptible to decomposition once buried in depositional positions.

Fracture healing requires a series of events including inflammatory response and callus formation, callus remodeling and bone healing. Fracture healing is a complex process, there are several overlapping phases , including inflammation , cartilage formation and bone remodeling, there are many internal or external factors could impact on fracture healing, leading to delayed bone healing or non healing. The global androgen receptor knockout (GARKO) mice has been know to reduce bone mass in endochondral bone and osteoblast mineralization, but the impact for callus formation in fracture healing is still unclear. The goals of study is to investigate the role of androgen and androgen receptor in wild-type (WT) mice and GARKO mice after fracture healing during callus formation and bone mineralization and bone remodeling. Therefore, long-term animal experiments observed by micro-computed tomography to study the roles of androgen and androgen receptor on the process and mechanisms of fracture healing is necessary. We applied in vivo micro-computer tomography (Micro-CT) to build up the three-dimensional model images at different time points for wild-type mice and GARKO mice after fracture healing and observe the bone healing process of micro-structure of the development of callus during fracture healing. The callus tissue morphology observed by histological staining to study the proportion and position of collagen, fibrous tissue and bone. The results show that the healing of WT mice is better than GARKO mice. GARKO mice develop smaller callus size and less bone volume and show delayed healing. In general, orchiectomy (ORX) decreases callus size in WT mice but not in GARKO mice. However, the healing rate of elderly GARKO mice is not obvious in comparison with young GARKO mice. Together, our study demonstrated that the androgen and androgen receptor regulate fracture healing and play an important role in bone repair and healing. Our mouse model may be used for the therapeutic drug screening of bone fractures caused by osteoporosis.

The Little Grand Wash normal fault near Green River, eastern Utah, hosts a series of naturally occurring CO₂ seeps in the form of active and extinct CO₂-charged springs distributed along the fault zone. I have studied the association of fault structure with CO₂-related alteration as an analogue for the long-term (1,000- to 10,000-year) effects of leakage through faults in CO₂ sequestration reservoirs. Structure and alteration in a portion of the Little Grand Wash fault zone were mapped at a 1:700 scale in order to determine the association of faulting with CO₂-related diagenesis. I combined structural and diagenetic mapping were combined with laboratory analyses of mineralogical, isotopic and textural changes in order to assess controls on the migration of CO₂ traveling up the fault and its effects on the fault itself. The fault zone is 200 m wide at its widest and contains 4-5 major subparallel fault segments that form multiple soft- and hard-linked relay ramps. The area includes a travertine deposit and related sandstone alteration: outcrop-visible coloration, porosity-occluding calcite cement and veins occasionally so abundant that they obliterate the rock fabric. Structural mapping shows that the travertine is located at an intersection of major fault segments constituting the hard link of a 450-meter-long relay ramp. Sandstone alteration is confirmed to be related to the CO₂ seep by mapping its distribution, which shows a decrease in concentration away from the travertine, and by the unique isotopic signature of calcite cement near the travertine. At distances greater than 25 m from the travertine intense alteration disappears, though scattered fault-subparallel veins and patchy, burial-related calcite cement remain. Intense alteration is limited to major fault overlaps and does not permeate the fault zone along its entire length, nor does it extend outside the zone. This indicates that rising CO₂-laden fluids do not flow uniformly through the entire fault zone, but that vertical flow is channeled at fault intersections. In thin section, porosity near the travertine has been extensively or completely occluded by calcite cement. Permeability in some conduit samples is less than 1 mD, three or four orders of magnitude lower than sandstone away from the travertine. In active CO₂ conduits, such reduction in porosity and permeability would occlude the preferred flow conduit and ultimately restrict upward flow of CO₂-charged water. X-ray diffraction detects small amounts of goethite and hematite and a decrease in chlorite-smectite in altered conduit sandstones. Calcite is abundant, but many authigenic minerals predicted by geochemical models of CO₂ influx into sandstone reservoirs are not observed, including kaolinite, aragonite, dolomite, siderite, ankerite or dawsonite. This difference between observed and predicted mineral occurrence likely results from differences in mineral kinetics between natural and laboratory systems. Prediction of leakage risk based on fault geometry improves the ability to assess the suitability of potential carbon sequestration reservoirs, many of which will be faulted. The point seep nature of leakage through a fault zone limits the amount of CO₂ that can escape over time and also enables targeted surface monitoring for CO₂ escape into the atmosphere--both critical for ensuring the effectiveness of injection projects and earning the trust necessary for carbon sequestration to gain public acceptance. The point seep nature of leakage also accelerates the rate at which conduits may seal through mineralization, since precipitation from a large volume of fluid is focused in a narrow conduit. The presence of multiple fossil and active seep locations along the Little Grand Wash fault, active at different times in the geologic past, indicates that cementation may be effective in sealing single conduits but that fault systems with complex geometry such as Little Grand Wash may continue to leak for a long period of time. / text

Agronomic practices, including tillage, crop rotation and N fertilization, have been developed to efficiently manage soil N dynamics and crop N nutrition. These practices can affect soil organic carbon (SOC) and soil total nitrogen (STN) sequestration, and consequently influence soil nitrogen mineralization (SNM) and crop N nutrition. However, little research has been systematically and simultaneously conducted to examine the effect of agronomic management on (1) SOC and STN stocks; (2) SNM; and (3) crop N nutrition. Burley tobacco (Nicotiana tobacum L.) is a N demanding crop and subject to inefficiency in N fertilization. Moreover, conservation tillage and rotation have been integrated into traditionally tillage intensive tobacco cropping systems. Thus, a tobacco tillage and rotation study was used to test how agronomic practices can affect N dynamics and crop N status in a series of sequential experiments. Firstly, different tobacco production systems were utilized to investigate the effects of tillage and rotation on soil aggregate stabilization and associated SOM sequestration. No-tillage and rotation management enhanced SOC and STN stocks, mainly by increasing the proportion of macroaggregates and SOC and STN concentrations. Secondly, a series of studies were conducted on SNM, including: (1) comparison of laboratory and in situ resin-core methods in estimating SNM; (2) evaluation of the influence of N fertilizer application on SNM; and (3) comparison of chemical indices for predicting SNM across management treatments over time. Laboratory method had different results relative to in situ method due to sample pretreatments. Fertilizer N application had a priming effect on SNM, but priming depended on both the N fertilizer rate and the background SOM level. The effect of rotation/tillage treatments on SNM was stable across years and SOC appeared to be the best indicator of SNM among other soil carbon and N estimates. Thirdly, a N fertilizer study for different tillage systems was conducted in 2012 and 2013. Crop parameters and plant available N (PAN) were collected to investigate the impact of tillage on tobacco production. Crop parameters showed that no-tillage can result in N deficiency in dry years. Similar PAN for both tillage methods suggested N deficiency in no-till tobacco was due to the crop’s lower N uptake capacity. In 2014, tobacco root analysis confirmed that no-tillage can result in less root exploration of the soil volume than conventional tillage.

The global carbon cycle is subject to intense research, where sources and sinks for greenhouse gases, carbon dioxide in particular, are estimated for various systems and biomes. Lakes have previously been neglected in carbon balance estimations, but have recently been recognized to be significant net sources of CO2. This thesis estimates emission of carbon dioxide (CO2) from boreal lakes and factors regulating the CO2 saturation from field measurements of CO2 concentration along with a number of chemical, biological and physical parameters. Concentration of dissolved organic carbon (DOC) was found to be the most important factor for CO2 saturation in lake water, whereas climatic parameters such as precipitation, temperature and global radiation were less influential. All lakes were supersaturated with and, thus, sources of CO2. Sediment incubation experiments indicated that in-lake mineralization processes during summer stratification mainly occurred in the pelagial. Approximately 10% of the CO2 emitted from the lake surface was produced in epilimnetic sediments. The mineralization of DOC and emission of CO2 from freshwaters was calculated on a catchment basis for almost 80,000 lakes and 21 major catchments in Sweden, together with rates of sedimentation in lakes and export of organic carbon to the sea. The total export of terrestrial organic carbon to freshwaters could thereby be estimated and consequently also the importance of lakes for the withdrawal of organic carbon export from terrestrial sources to the sea. Lakes removed 30-80% of imported terrestrial organic carbon, and mineralization and CO2 emission were much more important than sedimentation of carbon. The carbon loss was closely related to water retention time, where catchments with short residence times (&lt;1 year) had low carbon retentions, whereas in catchments with long residence times (&gt;3 years) a majority of the imported TOC was removed in the lake systems. The Gulf of Bothnia was also studied in this thesis and found to be a net heterotrophic system, emitting large amounts of CO2 to the atmosphere on an annual basis. The rate of CO2 emission was depending on the balance between primary production and bacterial respiration, and the system was oscillating between being a source and a sink of CO2.

The Beattie syenite is composed of a series of lenticular bodies of syenitic rocks, situated immediately north of the Porcupine-Destor fault zone in the town of Duparquet, approximately 32 km north of Rouyn-Noranda in the Abitibi Subprovince. The principal body is 3.3 km long and 470 m in width and is flanked by a series of smaller lenses to the south and northeast. The intrusion has been zircon dated at 2682±1Ma and 2682.9±1.1 Ma and hosted the major part of the Au-mineralization of the now defunct Beattie mine, which was an important producer of gold in the area from 1933 to 1956 (9.66 Mt at 4.88 g/t Au). A total of 5 petrographic units are defined here, on the basis of field relationships, macroscopic textures, petrology and mineralogy: 1- The porphyritic Beattie syenite unit is composed of 2% to 10% of tabular sub- to anhedral feldspar phenocrysts about 2 mm to 10 mm in size, set in a red feldspathic and aphanitic matrix. This unit can be strongly cataclastic with abundant hydrothermal minerals. 2- The equigranular magnetite-bearing syenite unit includes few feldspar phenocrysts, about 2 mm to 10 mm in a fine-grained matrix. It is characterized by unaltered titanite, epidote, hornblende porphyroblasts and is the only unit with actinolite replacing clinopyroxene. 3- The porphyritic Central Duparquet syenite unit contains between 2% - 25% of coarse equant euhedral feldspar phenocrysts, about 5 mm to 16 mm in size, in a red or sometimes grey aphanitic matrix. 4- The megaporphyritic syenite unit is composed of very coarse alkali feldspar phenocrysts, typically 1 cm to 6 cm across, in a red aphanitic matrix. The phenocrysts often form a glomeroporphyritic texture. 5- The lath syenite unit occurs as numerous ~m-width thin dykes, which cross-cut all other petrographic units. These dykes display a characteristic trachytic texture, as defined by the preferential alignment of alkali feldspar laths, which are typically 1 cm to 3 cm in a grey or red aphanitic matrix. Petrology and geochemistry investigations revealed that the syenite intruded into the older 2720-2718 Ma volcanic Deguisier Formation and the <2687±2 Ma sediments of the Porcupine Group. Detailed geochemical analysis revealed that the Deguisier Formation is composed of three units, forming a complete tholeiitic suite. The Deguisier Formation is proposed here to have been produced in a volcanic arc setting. Detailed petrological, mineralogical and geochemical studies indicate that, the syenite is part of the alkaline series and is metaluminous to peraluminous. The syenite intruded at shallow depths through a sequence of injections, yielding the five comagmatic units. The syenite and country rocks were then subjected to a series of hydrothermal alterations and brittle deformation events, combined with metamorphism to the greenschist facies. The Au-mineralization in this region is attributed to the hydrothermal alteration with brittle deformation.

The development of bioengineered cartilage for replacement of damaged articular cartilage has gained momentum in recent years. One such approach has been developed in the Kandel lab, whereby cartilage is formed by seeding primary articular chondrocytes on the top surface of a porous biodegradable calcium polyphosphate (CPP) bone substitute, permitting anchorage of the tissue within the pores of the substrate; however, the interfacial shear properties of the tissue-substrate interface of these biphasic constructs are 1 to 2 orders of magnitude lower than the native cartilage-subchondral bone interface. To overcome this limitation, a strategy was devised to generate a zone of calcified cartilage (ZCC), thereby mimicking the native architecture of the osteochondral junction; however, the ZCC was located slightly above the cartilage-CPP interface. Thus, it was hypothesized that polyphosphate released from the CPP substrate and accumulating in the tissue inhibits the formation of the ZCC at the tissue-substrate interface. Based on this information, a strategy was devised to generate biphasic constructs incorporating a properly located ZCC. This approach involved the application of a thin calcium phosphate film to the surfaces of porous CPP via a sol-gel procedure, thereby limiting the accumulation of polyphosphate in the cartilaginous tissue. This modification to the substrate surface did not negatively impact the quality of the in vitro-formed cartilage tissue or the ZCC. Interfacial shear testing of biphasic constructs demonstrated significantly improved interfacial shear properties in the presence of a properly located ZCC. These studies also led to the observation that chondrocytes produce endogenous polyphosphate and that its levels in deep zone cartilage appear inversely related to mineral deposition within the tissue. Using an in vitro model of cartilage calcification, it was demonstrated that polyphosphate levels are modulated in part by the inhibitory effects of fibroblast growth factor 18 on exopolyphosphatase activity in the tissue. Polyphosphate also appears to act in a feedback loop to control exopolyphosphatase activity. Interestingly, polyphosphate also exhibits positive effects on cartilage matrix accumulation. The potential implication of polyphosphate in the maintenance of articular cartilage homeostasis is intriguing and must be investigated further.

The development of bioengineered cartilage for replacement of damaged articular cartilage has gained momentum in recent years. One such approach has been developed in the Kandel lab, whereby cartilage is formed by seeding primary articular chondrocytes on the top surface of a porous biodegradable calcium polyphosphate (CPP) bone substitute, permitting anchorage of the tissue within the pores of the substrate; however, the interfacial shear properties of the tissue-substrate interface of these biphasic constructs are 1 to 2 orders of magnitude lower than the native cartilage-subchondral bone interface. To overcome this limitation, a strategy was devised to generate a zone of calcified cartilage (ZCC), thereby mimicking the native architecture of the osteochondral junction; however, the ZCC was located slightly above the cartilage-CPP interface. Thus, it was hypothesized that polyphosphate released from the CPP substrate and accumulating in the tissue inhibits the formation of the ZCC at the tissue-substrate interface. Based on this information, a strategy was devised to generate biphasic constructs incorporating a properly located ZCC. This approach involved the application of a thin calcium phosphate film to the surfaces of porous CPP via a sol-gel procedure, thereby limiting the accumulation of polyphosphate in the cartilaginous tissue. This modification to the substrate surface did not negatively impact the quality of the in vitro-formed cartilage tissue or the ZCC. Interfacial shear testing of biphasic constructs demonstrated significantly improved interfacial shear properties in the presence of a properly located ZCC. These studies also led to the observation that chondrocytes produce endogenous polyphosphate and that its levels in deep zone cartilage appear inversely related to mineral deposition within the tissue. Using an in vitro model of cartilage calcification, it was demonstrated that polyphosphate levels are modulated in part by the inhibitory effects of fibroblast growth factor 18 on exopolyphosphatase activity in the tissue. Polyphosphate also appears to act in a feedback loop to control exopolyphosphatase activity. Interestingly, polyphosphate also exhibits positive effects on cartilage matrix accumulation. The potential implication of polyphosphate in the maintenance of articular cartilage homeostasis is intriguing and must be investigated further.

Inland waters process large amounts of organic carbon, contributing to CO2 and CH4 emissions, as well as storing organic carbon (OC) over geological timescales. Recently, it has been shown that the magnitude of these processes is of global significance. It is therefore important to understand what regulates OC cycling in inland waters and how is that affected by climate change. This thesis investigates the constraints on microbial processing of sediment OC, as a key factor of the carbon cycling in boreal lakes. Sediment bacterial metabolism was primarily controlled by temperature but also regulated by OC quality/origin. Temperature sensitivity of sediment OC mineralization was similar in contrasting lakes and over long-term. Allochthonous OC had a strong constraining effect on sediment bacterial metabolism and biomass, with increasingly allochthonous sediments supporting decreasing bacterial metabolism and biomass. The bacterial biomass followed the same pattern as bacterial activity and was largely regulated by similar factors. The rapid turnover of bacterial biomass as well as the positive correlation between sediment mineralization and bacterial biomass suggest a limited effect of bacterial grazing. Regardless of the OC source, the sediment microbial community was more similar within season than within lakes. A comparison of data from numerous soils as well as sediments on the temperature response of OC mineralization showed higher temperature sensitivity of the sediment mineralization. Furthermore, the low rates of areal OC mineralization in sediments compared to soils suggest that lakes sediments are hotspots of OC sequestration. Increased sediment mineralization due to increase in temperature in epilimnetic sediments can significantly reduce OC burial in boreal lakes. An increase of temperature, as predicted for Northern latitudes, under different climate warming scenarios by the end of the twenty-first century, resulted in 4–27% decrease in lake sediment OC burial for the entire boreal zone.