Aquarius/SAC-D is a joint mission by National Aeronautics and Space Administration (NASA) and the Comision Nacional de Actividades Espaciales (CONAE), Argentine Space Agency. The satellite was launched in June 2011 and the prime remote sensing instrument is also named Aquarius (AQ). The main objective of this science program is to provide Sea Surface Salinity (SSS) maps of the global oceans every 7 days for understanding the Earth’s hydrologic cycle and for assessing long-term global climate change. The Aquarius instrument was built jointly by NASA’s Goddard Space Flight Center and the Jet Propulsion Laboratory. It is an active/passive L-band remote sensor that measures ocean brightness temperature (Tb) and radar backscatter, and these quantities are used to infer sea surface salinity. Other environmental parameters (e.g., sea surface temperature, wind speed and rain) also affect the microwave emitted radiance or brightness temperature. The SSS geophysical retrieval algorithm considers all these environmental parameters and makes the Tb corrections before retrieving SSS. Instantaneous rainfall can cause increase roughness that raises the ocean surface Tb. Further short term rain accumulation can produce a fresh water lens that floats on the ocean surface and dilutes the surface salinity. iv This thesis presents results of a study to develop an oceanic rain accumulation (RA) product that may be valuable to remote sensing engineers and algorithm developers and Aquarius scientists. The use of this RA product, along with in situ ocean salinity measurements from buoys, may be used to mitigate the effects of rain on the SSS retrieval

Microwave radiometers are highly sensitive receivers capable of measuring low levels of natural blackbody microwave emissions. Remote sensing by satellite microwave radiometers flying on low-earth, polar orbiting, satellites can infer a variety of terrestrial and atmospheric geophysical parameters for scientific and operational applications, such as weather and climate prediction. The objective of this thesis is to provide realistic simulated ocean brightness temperatures for the 3-channel Microwave Radiometer (MWR), which will be launched in May 2010 on the joint NASA/CONAE Aquarius/SAC-D Mission. These data will be used for pre-launch geophysical retrieval algorithms development and validation testing. Analyses are performed to evaluate the proposed MWR measurement geometry and verify the requirements for spatial/temporal sampling. Finally, a preliminary study is performed for the post-launch inter-satellite radiometric calibration using the WindSat polarimetric radiometer on the Coriolis satellite.

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<p>Teleosts take up metals by two major pathways: gills and/or gut. Past research is heavily focused on branchial uptake despite evidence that the gastro-intestinal tract (GIT) is the dominant route in some natural environments. To address this information gap, my thesis characterizes uptake mechanisms of Cd and Ca along the GIT of <em>Oncorhynchus mykiss</em>. Toxic effects of Cd, protective effects of Ca against Cd uptake, and Cd distribution within fish after ingestion are also explored.</p> <p>Four-week dietary Cd exposure affected growth and Ca regulation, while causing toxicity at the subcellular level. Elevated Ca in diets protected against accumulation and altered subcellular handling of Cd. Pre-exposure to different diets changed unidirectional uptake and binding rates of Cd and Ca, although they remained highly correlated. Binding rates of Cd to mucus can predict absorption rates of Cd<strong>.</strong></p> <p>A variety of <em>in vitro </em>and <em>in vivo </em>experiments on four distinct GIT segments (stomach, anterior-, mid-, and posterior- intestine) were undertaken to determine specific mechanisms of Cd and Ca uptake in freshwater trout. Cd transport was unaffected by solvent drag, but was stretch- and temperature- sensitive. Strong evidence for a common pathway for Ca and Cd transport was obtained. Cd also appeared to be taken up in part by zinc (ZIP-like) transporters and the divalent metal transporter DMT1. Ca uptake along the GIT appeared to be carrier-mediated, time- and concentration- dependent, but was not affected by solvent drag, or by Na concentration. Mucosal Cd did not inhibit Ca uptake. Ca, but not Cd, uptake rates were much lower in sea water-acclimated trout. Seawater and freshwater fish accumulated similar whole body Cd concentrations when fed contaminated diets for three weeks, but the majority of Cd in seawater trout remained in the posterior intestine tissue, while freshwater trout had higher internal burdens.</p> <p>This thesis advances the knowledge of metal uptake along the GIT of trout.</p> / Doctor of Science (PhD)

Average global ocean temperatures and the frequency and intensity of marine heat waves have been increasing over the last century. Temperature plays a critical role in defining the geographical range of the majority of marine species. Some species may respond to ocean warming trends by shifting their latitudinal and depth ranges, while others may be able to cope with changes in temperature through phenotypic plasticity and local adaptations. If a species is unable to shift its distribution or has limited thermal plasticity, it may face severe population declines or local extinction. Therefore, describing thermal tolerance limits is a useful tool for predicting how a given species will respond to ocean warming. Due to its commercial importance, sablefish (Anoplopoma fimbria) is a fish species of particular interest in British Columbia. Sablefish are semi-demersal and spawn along the continental slopes of the Pacific coast from California to Alaska. Their various life history stages occupy different depth strata and thus experience substantially different environments with respect to temperature (as well as salinity, oxygen, etc.). Adult sablefish spawn at depths that exceed 300 m and embryos sink to depths of ~1,000 m after fertilization. Embryos hatch into yolk-sac larvae until they become mobile at the post-yolk-sac larvae stage. The latter migrate to near-surface waters (<3 m) at which temperatures are approximately 12-15°C in the late spring. Heart rate is a temperature-dependent performance measure and has been used to gain insight into the thermal tolerance of many adult fishes. However, few studies have used this approach with the early life stages of fishes such as embryos and yolk-sac larvae (YSL). The purpose of this study was to assess whether sablefish embryos and YSL have the potential for cardiac acclimation by examining changes in their thermal tolerance limits when incubated at temperatures outside of what they experience in a natural setting (~5°C). Cardiac performance was assessed during an acute temperature challenge from 2.0° to 12.0°C in increments of 1.0°C (at a rate of 1°C 40 min-1) for individuals incubated at 3.0°C, 5.0°C (control), and 7.0°C. Embryos were video recorded at each 1.0°C increment and videos were viewed at a later date to determine heart rate at each temperature. This study attempted to use temperature breakpoint analysis, commonly used in studies of adults, on these early life stages to assess cardiac performance. It was hypothesized that sablefish embryos and yolk-sac larvae incubated at warmer temperatures would have a higher thermal tolerance than sablefish embryos and YSL incubated at colder temperatures, as seen in other fish species. There was some degree of thermal compensation of cardiac function with temperature in sablefish embryos and YSL as mean heart rate increased with incubation temperature throughout acute warming. YSL had consistently higher mean heart rate values at any given temperature of the acute temperature challenge when compared to embryos incubated at the same temperature. TAR is the temperature at which the heart first becomes arrhythmic is considered a sub-lethal index because the organism is expected to experience cardiac collapse soon after. TAR was reached for 100% of embryos incubated at 3.0°C at an average temperature of 8.6 ± 1.0°C. In contrast, only 18% and 33% of embryos incubated at 5.0° and 7.0°C exhibited arrhythmia (mean TAR were 9.0 ± 3.0 and 8.5± 1.5°C, respectively). The lower thermal limit for embryos incubated at 7.0°C was likely near 1.0°C, which was determined during preliminary testing. Neither the upper or lower limits were reached for YSL during the acute temperature challenge. No mortalities were observed during any acute temperature challenges. Overall percent mortality throughout the entirety of the experiment could not be determined due to limitations in the experimental setup and reduced staff working on this project due to COVID-19 safety protocols. This study is also the first to investigate whether transporting sablefish embryos from a hatchery to a research facility at different stages of development had an effect on their cardiac performance during acute warming. Embryos were transported in a cooler from the sablefish hatchery on Salt Spring Island to UVic via ferry and vehicular transport. Time of transportation did not significantly change the temperature at which heart rate reaches its maximum or TAR. There was also consistent overlap in mean heart rate ± standard error at each temperature of the acute temperature challenge between these two groups. Therefore, there appears to be no indication that transportation affected the heart rate response of sablefish embryos when incubated at the same temperature. However, future studies may want to confirm this by identifying and comparing other breakpoint temperatures that characterize physiological performance. Determining whether transportation has effects on cardiac performance may be of interest to other researchers who need to transport fish embryos from the field to the laboratory. Heart rate measurements during an acute temperature challenge of sablefish embryos and yolk-sac larvae (YSL) incubated at various temperatures provided initial insight to their overall success in a warming climate. Currently, it is projected that waters at depths of 1,000 m will warm on average by less than a degree by the end of the 21st century. The results of this study suggest that the early life stages of sablefish may not be exposed to critical temperatures in the near future, but future impacts on overall physiological decline remain unknown. The novel data presented here lay the groundwork for future researchers to continue to characterize the thermal tolerances of the early life stages of sablefish, and the likely response of this important species to ocean warming. / Graduate

The small intestine and yolk sac (YS) are important organs for nutrient absorption and innate immunity in chickens during the post-hatch or prehatch periods. These organs share a similar structure of epithelial cell-lined villi with tight junctions between adjacent cells. Probiotics have been reported to improve chicken growth performance and gut health including promotion of intestinal morphology. However, there are few studies that show the effect of probiotics on ontogeny of intestinal epithelial cells and antimicrobial peptides, or intestinal integrity in young healthy chicks. Heat stress during incubation was shown to increase mortality and decrease hatchability of chicks, while no studies have investigated the effect of heat stress on the integrity of the YS, which might be related to hatching performance. There were four studies conducted in this research: 1) a comparison of the effect of two probiotics on the ontogeny of small intestinal epithelial cells in young chicks; 2) the effect of two probiotics on mRNA abundance of tight junction proteins in the small intestine of young chicks; 3) the effect of high incubation temperature on mRNA abundance of tight junction proteins in the YS of broiler embryos; and 4) comparison of avian defense peptide mRNA abundance in the YS of broilers and layers. In study 1, Probiotics transiently decreased body weight gain (BWG) from day 2 to day 4, but did not affect body weight (BW) from day 2 to day 8, and small intestinal weight and intestinal morphology from day 2 to day 6. Probiotics did not affect marker gene expression of intestinal stem cells (Olfm4) and goblet cells (Muc2) in all small intestinal segments, but did increase expression of a marker gene of proliferating cells (Ki67), and decreased an antimicrobial peptide (liver-enriched antimicrobial peptide 2, LEAP2) in the jejunum at day 4. Probiotic 1 decreased PepT1, a marker of enterocytes in the duodenum at day 4. These results suggest that probiotics did not improve growth performance and intestinal morphology in young healthy chicks, but temporarily promoted intestinal epithelial cell proliferation and decreased LEAP2 antimicrobial peptide expression in the jejunum. In situ hybridization (ISH) showed that Ki67+ proliferating cells were mainly located in the crypt region and the blood vessels of villi. In study 2, Probiotic supplementation to newly hatched chicks for less than one week did not affect mRNA abundance of the tight junction proteins in the small intestine. Occludin (OCLN) mRNA, which was detected by ISH to be expressed in intestinal epithelial cells in both the villus and crypt regions, was greater in the duodenum of female chicks than males. In study 3, high incubation temperature starting from embryonic day 12 (E12) affected mRNA abundance of the tight junction proteins in the YS, including increased zonula occluden 1 (ZO1) at E13, increased junctional adhesion molecule A (JAMA) and heat shock protein 90 (HSP90) at E17, but decreased tight junction protein JAMA at E19 and OCLN at day of hatch (DOH). These results showed that the YS tight junction proteins were increased by short term heat exposure but decreased by long term heat exposure. In study 4, the expression of avian β defensin 10 (AvBD10), CATHs and toll-like receptors in the YS was examined. Toll-like receptors were highly expressed in the YS at early incubation stages (E7), while CATHs showed a peak expression from E9 to E13, which was similar to the expression pattern of AvBD10. CATHs and AvBD10 mRNA temporal expression patterns were similar in broilers and layers, while their expression levels were different. Layers, especially brown layers, had greater mRNA abundance for antimicrobial peptides such as AvBD10, CATH1, and CATH2 in the YS. These results demonstrate that the antimicrobial peptide temporal expression patterns in the YS are not affected by breed, but their expression levels are affected by breed. In summary, the small intestine and the YS are essential for nutrient uptake, innate immunity, and maintenance of integrity. The ontogeny of intestinal epithelial cells, such as proliferating cells can be modulated by probiotic supplementation. Similar to the small intestine, the YS can also express tight junction proteins, which can be affected by high incubation temperature. Antimicrobial peptide expression in the intestine of healthy young chicks is also transiently decreased by probiotic supplements. Avian defensin and cathelicidin expression patterns in the YS were not affected by breed. / Doctor of Philosophy / The small intestine and yolk sac are important organs for nutrient absorption in hatched chicks or embryonic chicks. These organs also serve as a barrier to prevent pathogens from entering the blood circulation. Intestinal epithelial cells along the villi renew rapidly by proliferation and differentiation. In this research, probiotics which are also known as direct fed microbials temporarily increased expression of the proliferating cell marker Ki67 in the jejunum of healthy young chicks, which suggests that probiotics promote intestinal epithelial cell proliferation. However, probiotics transiently decreased expression of an antimicrobial peptide, which may reduce immune protection in the gut. The yolk sac can also express tight junction proteins. The expression of tight junction proteins was affected by elevated incubation temperature in broiler embryos, which might be related to low hatchability of eggs exposed to heat stress. Avian defense peptides and pathogen recognition receptors were expressed in the YS, which implied that the yolk sac contained an innate immune function. The expression pattern of avian defense peptides was affected by breed (broilers and layers), while the expression level of avian defense peptides was greater in layers than broilers. In summary, the small intestine and the yolk sac are multifunctional organs. Their cell composition, structural integrity, and secretion of antimicrobial peptides can be affected by environmental factors, such as probiotic supplementation or high incubation temperature.

The incubation period is crucial for development and overall quality of a chick. The selection for fast growing broilers has allowed the birds to reach market weight at a faster rate making the incubation period a larger portion of a broiler's life. A faster growth rate can lead to the release of more metabolic heat inside of the egg toward the second half of incubation because the embryo shifts to a homeothermic state. More heat being released into the incubator can cause the incubation temperature to rise if the incubator is not electronically regulated or cannot be ventilated properly due to malfunction. A high incubation temperature can impact the hatchability, growth, and development of the chick. This thesis provides a more in-depth analysis of the effects of high incubation temperature (37.5°C versus 39.5°C) on the developing small intestine and yolk sac, which provide the chick with nutrients posthatch and during embryogenesis. Studying these organs and mechanisms occurring during this time could potentially indicate why chicks from eggs subjected to a higher incubation temperature are not developing and growing properly. Chicks from eggs incubated at a higher temperature had lower body weights, lower hatchability and lower villus height in the duodenum, jejunum, and ileum. There were also differences seen in the depth of the crypt, which is the site for stem cells. Chicks from eggs incubated at a higher temperature had a lower crypt depth in the duodenum and jejunum. There was no difference in the expression of the intestinal stem cell marker olfactomedin 4 (Olfm4) and mucin 2, which is secreted by goblet cells and forms mucus. In the yolk sac, heat shock proteins (HSP) 70 and 90 were elevated at embryonic day 15, and HSP90 still remained elevated at embryonic day 17. Chicks from eggs incubated at a higher temperature showed greater expression of peptide transporter 1 and avian beta-defensin 10 mRNA at embryonic day 13. Even though small intestinal morphology was impacted early posthatch and expression of genes in the yolk sac were elevated at embryonic day 13, there does not seem to be a long-lasting effect on the development of the small intestine or the yolk sac. It is still important to study the impact of the incubation environment to understand the development and growth of the chicks and how different incubation factors can impact the overall hatchability and health of the chick. / Master of Science / The incubation period is crucial for development and overall quality of a chick. The selection for fast growing broilers has allowed the birds to reach market weight at a faster rate making the incubation period a larger portion of a broiler’s life. A faster growth rate can lead to the release of more metabolic heat inside of the egg toward the second half of incubation because the embryo shifts to a homeothermic state. More heat being released into the incubator can cause the incubation temperature to rise if the incubator is not electronically regulated or cannot be ventilated properly due to malfunction. A high incubation temperature can impact the hatchability, growth, and development of the chick. This thesis provides a more in-depth analysis of the effects of high incubation temperature (37.5°C versus 39.5°C) on the developing small intestine and yolk sac, which provide the chick with nutrients posthatch and during embryogenesis. Studying these organs and mechanisms occurring during this time could potentially indicate why chicks from eggs subjected to a higher incubation temperature are not developing and growing properly. Chicks from eggs incubated at a higher temperature had lower body weights, lower hatchability and lower villus height in the duodenum, jejunum, and ileum. There were also differences seen in the depth of the crypt, which is the site for stem cells. Chicks from eggs incubated at a higher temperature had a lower crypt depth in the duodenum and jejunum. There was no difference in the expression of the intestinal stem cell marker olfactomedin 4 (Olfm4) and mucin 2, which is secreted by goblet cells and forms mucus. In the yolk sac, heat shock proteins (HSP) 70 and 90 were elevated at embryonic day 15, and HSP90 still remained elevated at embryonic day 17. Chicks from eggs incubated at a higher temperature showed greater expression of peptide transporter 1 and avian beta-defensin 10 mRNA at embryonic day 13. Even though small intestinal morphology was impacted early posthatch and expression of genes in the yolk sac were elevated at embryonic day 13, there does not seem to be a long-lasting effect on the development of the small intestine or the yolk sac. It is still important to study the impact of the incubation environment to understand the development and growth of the chicks and how different incubation factors can impact the overall hatchability and health of the chick.

Each mitotic chromosome is constituted by two sister chromatids whose correct segregation to the daughter cells is ensured by amphitelic attachment, in which the two sister kinetochores (KTs) are attached to microtubules (MTs) from opposite mitotic spindle poles. KT mis-attachments can occur in early mitosis and cause chromosome mis-segregation and aneuploidy if not corrected. These mis-attachments include monotelic (one attached and one unattached sister KT), syntelic (both sister KTs attached to the same spindle pole), and merotelic (a single KT attached to MTs from opposite spindle poles) attachments. A biochemical pathway named the Spindle Assembly Checkpoint (SAC) is responsible for delaying anaphase onset to allow correction of KT mis-attachments. SAC activation is believed to occur due to KT localization of certain SAC proteins and/or lack of tension, but only monotelic attachment has been proven to activate the SAC. To determine if and how other KT mis-attachments may activate the SAC, we studied how molecular composition and structure of the KT changes in response to different types of attachments. Our data suggest that monotelic attachment is the only type of attachment that can induce a SAC response thanks to the accumulation of the SAC protein Mad2 at the KT. Our data also indicate that structural changes of the KT, measured as intra- or inter-KT stretching, do not directly induce a SAC response. Instead, our findings suggest decreased KT stretching, especially in inter-KT stretching of syntelic chromosomes, may play a key role in bringing MCAK and other KT substrates closer to Aurora B kinase for rapid and efficient correction of KT mis-attachments. / Master of Science

Solvation-thermodynamics models based on computational quantum mechanics, such as the conductor-like screening model (COSMO), provide a good alternative to traditional group-contribution methods for predicting thermodynamic phase behavior. Two COSMO-based thermodynamic models are COSMO-RS (real solvents) and COSMO-SAC (segment activity coefficient). The main molecule-specific input for these models is the sigma profile, or the probability distribution of a molecular surface segment having a specific charge density. Generating the sigma profiles represents the most time-consuming and computationally expensive aspect of using COSMO-based methods. A growing number of scientists and engineers are interested in the COSMO-based thermodynamic models, but are intimidated by the complexity of generating the sigma profiles. This thesis presents the first free, open-literature database of 1,513 self-consistent sigma profiles, together with two validation examples. The offer of these profiles will enable interested scientists and engineers to use the quantum-mechanics-based, COSMO methods without having to do quantum mechanics. This thesis summarizes the application experiences reported up to October 2004 to guide the use of the COSMO-based methods. Finally, this thesis also provides a FORTRAN program and a procedure to generate additional sigma profiles consistent with those presented here, as well as a FORTRAN program to generate binary phase-equilibrium predictions using the COSMO-SAC model. / Master of Science