We study the sl(3) web algebra via morphisms on foams. A pre-foam is a cobordism between two webs that contains singular arcs, which are sets of points whose neighborhoods are homeomorphic to the cross-product of the letter "Y'' and the unit interval. Pre-foams may have a distinguished point, and it can be moved around as long as it does not cross a singular arc. A foam is an isotopy class of pre-foams modulo a set of certain relations involving dots on the pre-foams. Composition in Foams is achieved by stacking pre-foams. We compute the cohomology ring of the sl(3) web algebra and apply a functor from the cohomology ring of the sl(3) web algebra to {\bf Foams}. Afterwards, we use this to study the $\mathfrak{sl}(3)$ web algebra via morphisms on foams.

The boundaries between freshwater and terrestrial ecosystems can be areas of important subsidy transfers. These subsidies, such as leaf litter inputs to streams or aquatic emerging insects into riparian zones, link food webs and provide benefits to consumers in the form of nutrients and energy. Subsidies from aquatic systems tend to have high levels of essential long chain polyunsaturated fatty acids (LC-PUFAs), such as eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) that are only produced by certain forms of aquatic algae. These LC-PUFAs are highly important in growth, development, and other metabolic functions across animal groups (Brett and Muller-Navarra 1997, Gladyshev et al. 2009).

Silks from araneoid spiders have become an active area of research for material scientists, biochemists, and molecular biologists. Mechanical properties of spider silk such as elasticity, tensile strength, and toughness make the manufacturing of silk for medical sutures, body armor, ropes and other synthetic material applications great possibilities. The difficulties of having a black widow spider farm to harvest silk, due to their cannibalistic nature, make recombinant expression of silk proteins a fundamental goal of spider silk research. In order to express silk fibers, cDNAs encoding the corresponding silk fiber products must first be isolated and identified. One of the first steps in gene identification relies on the identification of the proteins in the silk fibers. No previous study has demonstrated the molecular constituents of gumfooted lines. In the course of this research, the core fibroins in the gumfooted lines were identified to be members of the Major Ampullate Spidroin family (MaSp), using mass spectrometry. This research was the first to identify the core fibroins of the gumfooted lines. Novel peptide fragments from solubilized gumfooted lines were acquired from manual de novo MSIMS sequencing after in-gel tryptic digestion. These peptide fragments showed post-translational modifications consistent with glycosylation, which aligns with the reported chemical properties of glue proteins. Novel peptide sequences were also acquired from the attachment discs as well as novel scanning electron microscopy images and reveal, for the first time, the physical attributes and molecular properties of threads attached to the surface of an immobilized structure. This study was the first to identify the molecular constituents of the attachment discs.

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Anthropogenic global change is altering food web dynamics. Global change comprises factors, like temperature, sound, light and more. In this dissertation, I evaluate how two factors, sound and temperature, alter prairie communities. In Chapter 1, I test if sound influences grasshopper respiration rate, thereby altering diet. Some sound frequencies increased grasshopper respiration rate while others decreased respiration rate. Frequencies that elevated respiration rate led to grasshoppers consuming more carbohydrate-rich foods compared to protein-rich foods. This diet change stems from a carbon deficit due to increased respiration rate and could act as a mechanism by which sound pollution indirectly alters plant communities. In Chapter 2, I test the hypothesis that sound can alter grasshopper movement. In response to sound-induced stress grasshoppers may alter their movement in one of two ways: in situ and displacement. I found no evidence that grasshoppers, nor non-Orthopteran insects alter their movement in the presence of sound. This chapter provides foundational methods to evaluate sound for applications in conservation and management. Further research will improve techniques for grassland or agricultural systems. Temperature is another driver of community change. What is less understood is how warming influences predator-pollinator relationships. In Chapter 3, I ask if warming alters a spider that consumes pollinators in a prairie system. My results indicate that pollinators benefit when spiders are not on the flower. Warming shifts spiders down the plant, thus positively impacting pollinator-plant interactions. In addition, warming may benefit plants two-fold if spiders shift their diet to herbivores. This requires additional research, but it is evident that warming generates a positive indirect effect on plants. These chapters contribute to a growing understanding of how global change is restructuring ecosystems. While global change may alter population dynamics or lead to evolutionary change over longer time scales, behavioral responses happen rapidly and can drive ecological dynamics in the short term. My dissertation demonstrates that sound and temperature alter animal behavior that cascades to lower trophic levels. Thus, in addition to demonstrating the indirect effects of global change, these experiments contribute to growing literature on the importance of top-down control in shaping ecosystems.

Spider silk is known for its extraordinary material properties, being both very strong and extensible. Even though the fibers outperform many synthetic and natural materials, it is impractical to collect industrial amounts of silk from spiders due to their cannibalistic and venomous nature; they cannot be farmed like the commercial silk worm Bombyx mori. Thus, scientists have turned to molecular and engineering techniques to replicate the spider's silk and spinning apparatus. In the current literature there is no detailed protocol on the production of consistent synthetic fibers. To accomplish this, the fibroins and natural spinning apparatus were taken apart and analyzed in order to develop a protocol that biomimics the spider's system. The laboratory procedure, using the natural process as an example, was simplified to: protein production, purification, concentration, fiber spinning, and lastly post spin draw. Large quantities of truncated MaSp I spidroin (spider fibroin) was purified from E. coli and successfully spun into fibers using customized spinning, spooling, and stretching apparatuses. The final fiber products displayed mechanical properties that were comparable to other reported synthetic fibers, but more importantly also displayed low experimental variability between samples. The protocol developed in this study can be further used to characterize other spidroins and silk proteins, and can be further advanced to produce even better fibers with enhanced properties.

Forested streams are closely linked to terrestrial catchments which affects their biogeochemical cycling and carbon inputs. Catchment disturbances alter stream water quality and food webs, including changes in productivity. Such changes in stream conditions can potentially alter consumers’ reliance on autochthonous (in-stream) or allochthonous (terrestrial) sources and mercury bioaccumulation. A recent outbreak of the spruce budworm (SBW) that feeds on spruce and fir trees has provided the unique opportunity to examine stream food web responses across watersheds experiencing a range of defoliation in the Gaspé Peninsula, Québec. This project compares streams in twelve watersheds which were selectively sprayed to control SBW and create a gradient in defoliation. Food web samples (food sources, invertebrates, fish) were analyzed for stable isotopes of carbon and nitrogen in 2019 and 2020 to characterize food web structure, and algal productivity was measured in 2019. Hierarchical partitioning models were used throughout the study to compare the contributions of various local and landscape conditions to stream responses. Models indicated that watershed defoliation contributed to increasing autochthonous production, although some invertebrates were more allochthonous in heavily defoliated watersheds, and brook diets were unaffected by defoliation. Next, food web samples were analyzed for methylmercury (food sources, invertebrates) or total mercury (fish) and trophic magnification slopes were determined for each stream food web. Mercury levels in carnivorous invertebrates and brook trout were driven by dissolved organic carbon (DOC), but not consumer autochthony or watershed defoliation. Additionally, rates of trophic magnification were not related to defoliation severity or DOC. This study found that defoliation contributed to increasing autochthonous production and invertebrate consumer allochthony. However, this disturbance did not increase consumer mercury levels or biomagnification in stream food webs. These findings suggest that intervention to reduce defoliation would mitigate algal responses and dietary shifts, but not mercury cycling as it is influenced by DOC levels in the streams of this region. / Thesis / Master of Science (MSc) / A recent spruce budworm outbreak is causing widespread defoliation of spruce and fir trees, but the impacts to stream environments, including primary production, its consumption, and contaminant levels, are largely unknown. Streams are sensitive to conditions in the surrounding terrestrial environment, as such changes can affect the diets of stream invertebrates and fish and are also linked to increased contaminant levels in aquatic organisms. Specifically, mercury is a metal that is transferred through diet and can reach toxic levels in fish. This study found that defoliation is contributing to increased algal production in streams in the Gaspé Peninsula, Québec. However, some stream invertebrates consumed more terrestrial material in streams that had heavier defoliation. Furthermore, defoliation and algal diets did not increase levels of mercury in aquatic organisms, but this contaminant was affected by increasing concentrations of dissolved organic carbon in the streams. These findings suggest that forest defoliation can alter organisms’ diets but not mercury levels.

Examining how ecological processes are influenced by spatial variation can provide valuable insights into how communities are formed and how they may change in dynamic landscapes. In this thesis I address three objectives surrounding the spatial and temporal variation in species’ recruitment and predation, the influence of habitat isolation on consumer-resource relationships, and the influence of habitat fragmentation on a multi-trophic system. I used marine invertebrates, specifically crustaceans, bivalves, and sessile species as a model system. First, I address the spatial and temporal variation in local and regional processes in a multispecies assemblage of marine sessile invertebrates. Using diverse communities of marine sessile invertebrates as a model system I tested the hypothesis that spatial and temporal variation in recruitment and predation would shape local communities, and that both recruitment and predation would have significant effects on the abundance and structure of adult communities. I found that both recruitment and predation vary through time and space leading to the emergence of regional community divergence. I also address how habitat isolation interacts with top-down and bottom-up processes in seagrass ecosystems. Spatial structure of the habitat may mediate top-down and bottom-up controls of species abundances through decreased habitat connectivity and increased habitat isolation. I manipulated top down and bottom up processes by excluding mesograzers, adding resources, or altering both factors in isolated and contiguous patches of artificial seagrass. I then measured epiphyte recruitment, epiphyte abundances, and macroalgae abundance. I paired this with epiphyte sampling from isolated natural seagrass patches. I found that habitat isolation significantly decreased the abundance of epiphytes settling on seagrass blades due to dispersal limitation for epiphytic invertebrates. I found that consumers had strong effects on epiphyte biomass in continuous habitats, but not isolated habitats. Resource additions increased macroalgae cover and epiphyte biomass only in isolated habitats. The results suggest that isolated habitats may be nutrient limited and that top-down effects are stronger in continuous habitats, while bottom-up effects may dominate in isolated habitats. In my third objective, I address how habitat fragmentation may alter marine food webs. I examined whether predation rates, prey, and predator behavior differed between continuous and fragmented seagrass habitat in a multi-trophic context at two sites in Barnegat Bay, NJ. I hypothesized that blue crab predation rates and foraging would decrease in fragmented seascapes, due to a reduction in adult blue crab densities, increasing survival rates of juvenile blue crabs and hard clams. I expected hard clams to exhibit weaker predator avoidance behavior in fragmented habitats because of decreased predation. I found that species’ responses to fragmentation were different based on trophic level. Clams experienced higher predation and burrowed deeper in continuous habitats at both sites. Densities of blue crabs, the primary predator of hard clams, were higher in continuous habitats at both sites. Predation on juvenile blue crabs was significantly higher in fragmented seagrass at one site. Our results suggest that in fragmented seascapes, the impact of fragmentation on higher trophic level predators may drive predation rates and prey responses across the seascape, which may lead to trophic cascades in fragmented habitats. / Biology

Les systèmes dits Sensor Webs sont des middlewares informatiques assurant la communication entre les capteurs et les applications. En tant que véritables médiateurs, la popularité de ces systèmes n’a cessé de grandir depuis l’apparition des tout premiers capteurs. Plus récemment, l’émergence de nouveaux paradigmes tels que l’Internet des Objets (IoT) a complètement révolutionné les systèmes basés sur les capteurs en général. Parmi eux, les Sensor Webs ne dérogent pas à cette règle et doivent désormais répondre à de nouveaux défis, notamment en termes d’intégration, de Qualité des Observations (QoO) et d’adaptation système. Dans ce travail de recherche, nous proposons une nouvelle génération de Sensor Webs capables d’adapter la QoO distribuée de manière autonomique et de manière spécifique à chaque application (QASWS). Premièrement, nous introduisons un framework générique destiné aux chercheurs et développeurs souhaitant concevoir leur propre solution QASWS. Dans un deuxième temps, nous instancions ce framework et proposons un prototype de plateforme d’intégration pour l’évaluation de la QoO à la demande (iQAS). Après avoir évalué ses performances, nous présentons trois cas d’utilisation pour la plateforme iQAS. Finalement, nous concluons cette étude en imaginant l’apport de certains paradigmes transverses vis-à-vis de la QoO dans un futur proche. / Sensor Web systems are computer middlewares that aim at bridging the gap between sensors and applications. As true mediators, the popularity of such systems has steadily grown since the appearance of the very first sensors. More recently, the emergence of new paradigms such as the Internet of Things (IoT) has completely revolutionized the sensing research field. As a consequence, Sensor Webs should now cope with new challenges pertaining to integration, Quality of Observation (QoO) and system adaptation. In this research work, we propose a novel generation of Sensor Webs able to adapt the delivered QoO in an autonomic and application-specific manner (QASWS). First, we introduce a generic framework intended for researchers and developers who want to conceive their own QASWS solution. Then, we instantiate this framework and propose a prototype of an integration platform for QoO assessment as a service (iQAS). After evaluating its performances, we present three use cases for the iQAS platform. Finally, we conclude this work by foreseeing the benefits of some transverse paradigms with regard to QoO in the near future.