Dissertations / Theses on the topic 'Terrestrial and marine systems'

Much of current ecological theory stems from experimental studies. These studies have often been conducted in closed systems, at spatial scales that are much smaller than the systems of interest. It is known that the outcome of these experiments may be seriously affected by artefacts associated with the caging procedures, as well as by the actual difference in spatial scale between experimental and target system. Yet, quantitative methods for estimating and removing artefacts of enclosure and for extrapolating experimental results to the scales of natural systems are largely lacking.

The aim of this thesis was to confront some of the problems encountered when scaling from experiments to nature in studies on predator-prey systems, with focus on effects of changes in spatial heterogeneity. Specifically, I examined mechanisms that may cause consumption rate estimates to depend on the size of the experimental arena. I also studied methods for scaling up these process rate estimates to natural predator-prey systems. The studies were performed on invertebrate predator-prey systems found in the northern Baltic Sea. Initially, a descriptive study of small-scale distribution patterns was performed, in order to get background information on how the behaviour of the organisms was manifested in the spatial structure of the community. Experimental studies of two predator-prey systems exposed an artefact that may be widespread in experiments aiming at quantifying biotic interactions. It is caused by predator and prey aggregating along the walls of the experimental containers. This behaviour affects the encounter rate between predator and prey, thereby causing consumption rates to be scale-dependent. Opposing the common belief that larger arenas always produce less biased results, this scale effect may instead be reduced by decreasing arena size. An alternative method for estimating the magnitude of, and subsequently removing, the artefact caused by aggregation along the arena wall was presented.

Once unbiased estimates of process functions have been derived, the next step is to scale up the functions to natural systems. This extrapolation entails a considerable increase in spatial heterogeneity, which may have important implications for the dynamics of the system. Moment approximation provides a method of taking the heterogeneity of natural populations into account in the extrapolation process. In the last study of the thesis, the concepts of moment approximation and how to estimate relevant heterogeneity were explained, and it was shown how the method may be used for adding space as a component to a dynamic predator-prey model. It was concluded that moment approximation provides a simple and useful technique for dealing with effects of spatial variation, and that a major benefit of the method is that it provides a way of visualising how heterogeneity affects ecological processes.

This thesis is a summary of enclosure and microcosm experiments that aimed to study the impact of allochtonous subsidies on food web dynamics in a heterogeneous food web. In the enclosure studies, a three trophic level littoral food web was used. The food web consisted of two growth forms of primary producers: phytoplankton and periphyton and their associated herbivores: scraping and filtering herbivores. The predator used, YOY perch, affects both pathways in the food web. Manipulation of the openness for the different trophic levels showed that the inflow of phytoplankton and cross-habitat foraging by the herbivore level reinforced the compensatory response between the two growth forms of primary producers

In the microcosm experiment, the response of an herbivore food web and a microbial community to inflow of resources and food web configuration was studied, using a model food web. The model food web consisted of two forms of primary producers, i.e. phytoplankton and periphyton, and two herbivores, i.e. Daphnia pulex feeding on phytoplankton, and Chydorus sphaericus feeding on both periphyton and phytoplankton. Three different food web configurations, all having the phytoplankton and periphyton, but either one of the herbivores, or both, were set up. The flow regimes consisted of an open treatment receiving a constant supply of phytoplankton, and a closed treatment with an initial resource pool. The effect of the inflow of phytoplankton was affected by the food web configuration. In the presence of D. pulex, the inflow of phytoplankton was made accessible to periphyton, and indirectly to C. sphaericus, which increased to such high densities that D. pulex was negatively affected. The inflow of phytoplankton had an indirect negative effect on the microbial community, since the biomass of herbivores increased, which imposed a higher grazing pressure on all parts of the microbial community.

Coral reefs are one of the most diverse ecosystems on the planet due partially to the habitat structure provided by corals. Corals are long lived organisms that can live for hundreds of years and as a result growth of many species is very slow. As a result of this, recovery of corals from disease outbreaks is very slow and difficult and therefore the ecosystem is deteriorating rapidly. Due to this increase in disease and its detrimental effect on coral reefs, it has become imperative to study how corals respond to disease outbreaks. The response of the coral to pathogens is believed to be controlled by the innate immune system. However, the immune pathways and components of these pathways used by cnidarians to combat pathogens are still rudimentary. This work showed that C3 and heat shock protein 70 are components of the coral immune system that positively respond to disease occurrence. As disease out breaks become more frequent, the question has arisen as to whether cnidarians have homologs to of the adaptive immune system that allow them to respond more rapidly to subsequent encounters with the same bacterium. In the cnidarian model system Exaiptasia pallida, immune priming occurs up to one month after the initial sub lethal exposure to the pathogen. This transient form of priming could be the result of host energy allocation in place of establishing long term immune priming which could be too energetically costly. Cnidarians may only activate priming during summer months, when ocean temperatures and bacterial load are high. Specificity of immune priming in E. pallida requires further investigation with more bacterial pathogens. In this dissertation, one bacterial strain shows specificity while the other does not. Furthermore, the priming response involves many pathways which include pathogen recognition, inflammation, and activation of NF-κB. The discovery of immune priming in a sea anemone shows that this phenomenon evolved earlier in the tree of life than previously thought. Additionally, identification of priming in E. pallida is suggestive of its presence in corals which would allow for potential vaccinations of vulnerable corals.

The development of human societies rests on functioning ecosystems. This thesis builds on integrated theories of linked social-ecological systems and complex adaptive systems to increase the understanding of how to strengthen the capacity of ecosystems to generate services that sustain human well-being. In this work, I analyze such capacity in human-dominated production ecosystems in Tanzania and Madagascar, and how this capacity is related to local management practices. Resilience of social-ecological systems refers to the capacity to buffer change, to re-organize following disruption, and for adaptation and learning. In Papers I and II, qualitative interview methods are used for mapping and analyses of management practices in the agroecosystem of the Mbulu highlands, Northern Tanzania. Practices such as soil and water conservation, maintenance of habitats for pollinators and predators of pests, intercropping, and landscape diversification, act to buffer food production in a variable environment and sustain underlying ecological processes. The practices are embedded in a decentralized but nested system of institutions, such as communal land rights and social networks, that can buffer for localized disturbances such as temporary droughts. Paper II compares these findings with practices in a farming system in Sweden, and suggests that similar mechanisms for dealing with uncertainty and change can exist in spite of different biophysical conditions. In Papers III and IV, interviews are combined with GIS tools and vegetation sampling to study characteristics and dynamics of the dry forests of Androy, southern Madagascar. Paper III reports on a previously underestimated capacity of the dry forest of southern Madagascar to regenerate, showing areas of regeneration roughly equal areas of degenerated forest (18 700 ha). The pattern of forest regeneration, degradation, and stable cover during the period 1986-2000 was related to the enforcement of customary property rights (Paper III). Paper IV reports on a network of locally protected forest patches in Androy that is embedded in a landscape managed for agricultural or livestock production and contributes to the generation of ecosystem services and ecosystem resilience at a landscape scale. Forest protection is secured by local taboos that provide a well-functioning and legitimate sanctioning system related to religious beliefs. In Paper V, two spatial modeling tools are used to assess the generation of two services, crop pollination and seed dispersal, by the protected forest patches in southern Androy. The functioning of these services is dependent on the spatial configuration of protected patches in the fragmented landscape and can be highly vulnerable to even small changes in landscape forest cover. In conclusion, many of the identified practices are found to make ecological sense in the context of complex systems and contribute to the resilience of social-ecological systems. The thesis illustrates that the capacity of human-dominated production ecosystems to sustain a flow of desired ecosystem services is strongly associated with local management practices and the governance system that they are embedded in, and that, contrary to what is often assumed, local management can and does add resilience for desired ecosystem services. These findings have substantial policy implications, as insufficient recognition of the dynamics of social-ecological interactions is likely to lead to failure of schemes for human development and biodiversity conservation.

This thesis describes the isolation and structure elucidation of ten novel secondary metabolites from one fungus (Pycnoporus cinnabarinus), four lichens (Chrysothrix xanthina, Candelaria concolor, Ramalina glaucescens and Xanthoria parietina), three algae (Plocamium mertensii, Laurencia filiformis and Laurencia elata), two plants (Haemodorum simplex and Dianella callicarpa) and one sponge (Dactylospongia sp). The structures of these isolated compounds were elucidated by a combination of spectroscopic and chemical methods. This thesis also reports two new crystal structures, the identification of two new methylsilylated derivatives as well as the isolation of thirty seven previously reported compounds in which the complete structural assignment by one and two dimensional nuclear magnetic resonance spectroscopy (NMR) has been carried out on known compounds with incomplete or no NMR spectroscopic data. Furthermore, detailed spectroscopic analyses resulted in the re assignment of 1H and 13C chemical shifts for several previously isolated natural products. The biological screening (antimicrobial, antiviral and antitumor assays) of crude extracts and isolated natural products has also been presented. The application of chemical profiling techniques including GCxGC and high pressure liquid chromatography-nuclear magnetic resonance (HPLC-NMR) were utilised to assist with the natural product dereplication process (chemical profiling), monitor chemical degradations in situ and to identify the presence of new natural products and artefacts. In total, fifteen separate terrestrial and marine organisms were investigated.

The widely accepted hypothetical model for polyether biosynthesis involves a polyene intermediate that undergoes an oxidative cyclisation via the corresponding polyepoxide. Recently, a triene shunt metabolite from monensin-producing Streptomyces cinnamonensis lent great support to this model. Sequencing of the gene cluster also supported this model. However, the role of two novel genes, monBI and monBII, was unclear. Deletion of these genes resulted in the production of a number of apparent monensin analogues, whilst abolishing monensin production itself. By isolating and characterising novel epimers of monensin, from one of these mutants, a role of the monB genes in the cyclisation of the final monensin intermediate is proposed. Acid-catalysed cyclisation of surmised cyclisation intermediates from this mutant served to confirm this proposal. An approach to trapping a triepoxide intermediate analogue that is unable to spontaneously cyclise was then explored. The preliminary results suggest that such an approach might lead to the isolation and characterisation of such a triepoxide. The closest marine relatives of the terrestrial polyethers are the ladder polyethers, such as brevetoxin and ciguatoxin. By extrapolating the polyepoxide model to all known marine ladder polyethers, a simple biosynthetic model is proposed, based on the development and justification of the “stereochemical uniformity rule”. Interestingly, application of this model and rule to the largest known ladder polyether, maitotoxin, reveals a stereochemical discrepancy at one of the ring junctions. It is thus suggested that this new rule may have uncovered an error in the established structure of this molecule, as well as being a potentially useful rule in the assignment of new ladder polyether ladder structures.

The work reported in this thesis applies a new isotope tracer, stable strontium isotopes (δ^88/86Sr), to address questions concerning changes in global climate that occur in response to continental weathering processes, and to constrain the modern marine geochemical Sr cycle. Stable Sr isotopes are a relatively new geochemical proxy, and as such their behavior needs to be understood in differing forms of marine calcium carbonate, the archives from which records of past stable Sr variability in the oceans can be constructed. Foraminifera, coccoliths and corals (both aragonite and high Mg calcite) acquire δ^88/86Sr values lighter than that of modern day seawater, (approximately 0.11, 0.05, 0.2 and 0.19 ‰ lighter than seawater at ~25°C respectively) providing a measureable offset which can be used to constrain the modern Sr outputs from the ocean and provide a better understanding of the modern Sr cycle. Using foraminifera as a sedimentary archive the first marine δ^88/86Sr record of seawater over the last two glacial cycles has been constructed, and used to investigate changing carbonate input and output over this 145 kyr period. Modelling of the large excursion of δ^88/86Sr to heavier values during Marine Isotope Stage (MIS) 3, reveals that this is more likely to be due to local changes in seawater or post-depositional alteration, rather then whole ocean changes. In the terrestrial environment δδ88/86^Sr has been measured in the dissolved load of rivers from the Himalaya. It is found that, in general, rivers draining carbonate catchments possess lighter isotopic δ^88/86Sr values than those from rivers draining silicates. Covariations of either δ88/86Sr vs. δ30Si or δ^88/86Sr vs. 1/[Sr] can be used to distinguish between rivers draining different catchment areas.

The investigation of the chromosomal variation in populations of the land snail Cepaea nemoralis (L.) marine snail Nucella lapillus (L.) is presented. The first study (Part 1) concerns the investigation of the karyotype of C. nemoralis in populations from a region of the Berkshire Downs (U.K.)in which there are marked area effects for both the visible and allozymic characters. The present investigation has shown that there are inter-populational differences in chromosome structure. The differences fall within the range found previously in several widespread populations in the British Isles, Northern Europe and America. There are no immediately obvious variations in chromosome structure associated with observable environmental variables. There are, however, marked non-random associations of karyomorphs within some of the "area effect populations". The implications of the distribution of the karyotypic variations between the populations are discussed. The second study (Part 11) concerns the identification of the chromosome pairs involved in the numerical (Robertsonian) and structural (inversion) polymorphisms of Nucella lapillus and the investigation of the two types of polymorphism in populations of low chromosome number. A new classification of the karyotype into five main groups A to E has been made. The chromosome pairs thought to contribute to the numerical polymorphism occur in groups A, B and C and the two inversion polymorphisms occur in groups A and C. The distribution of the two types of chromosomal polymorphism at Rottingdean, Sussex (U.K.) suggest that the inversion polymorphism from group C, and the numerical polymorphism, also from group C, occur independently of each other. The differences in the distribution of the two polymorphisms in the Rottingdean area and the differences in the distribution of the chromosome pairs involved in the numerical polymorphism in different populations are discussed.

This thesis presents an investigation into the chemistry of 6 substituted 5, 6-dihydro-a-pyrone compounds. A comprehensive review of these compounds was published in 1989 and the subsequent literature is covered in an updated review presented below. Eight 6-substituted 5,6-dihydro-a-pyrone metabolites from three different South African plant species Cryptocarya latijolia, Syncolostemon densiflorus, and Syncolostemon argenteus have been the subject of structural and stereochemical investigations. The absolute stereochemistry of the known compound "triacetate" from C. latijolia has been established as 6R-[2R,4S,6S-(triacetyloxy)heptylJ-5,6-dihydro-2H-pyran-2-one (74) using CD and acetonide formation with subsequent application of the modified Moshers method. The absolute stereochemistry of the related metabolite "diacetate", also from C. latijolia, has been assigned as 6R-[2S,4S-diacetyloxypentylJ-5,6-dihydro-2H-pyran-2-one (76). In addition, the outstanding stereochemistry at C-5' in syndenolide, from S. densiflorus, followed from conversion to its diacetonide and subsequent NMR analysis. Syndenolide is therefore 6R-[5S-(acetoxy)-IR,2R,3S-(trihydroxy)-heptylJ-5,6- dihydro-2H -pyran-2-one. The genus Syncolostemon has proved to be a rich source of a-pyrone compounds and the chemistry of S. argenteus, not investigated previously, was examined as part of an ongoing search for new 5,6-dihydro-a-pyrones. The study yielded five new a-pyrone natural products, synargentolide A-E. The structure of synargentolide A (82) has been assigned as 6R[4R,5R,6S-triacetyloxy-lE-heptenylJ-5,6-dihydro-2H-pyran-2-one using CD and NMR techniques. The structures of synargentolide B (87), C (92) and E (94) also followed from a detailed NMR analysis and the stereochemistry tentatively assigned based on CD and NMR data. Synargentolide D (93) was thermally unstable, and a paucity of material prevented stereochemical investigations, however the structure was determined from initial NMR analysis. The marine molluscs of the genus Siphonaria have only become the subject of chemical studies in the last fifteen years. These molluscs characteristically produce polypropionate type natural products. A review of Siphonarian polypropionate metabolites containing a pyrone functionality is presented. Examination of an endemic South African species Siphonaria serrata yielded one novel polypropionate metabolite containing a ),-pyrone functionality, siserrone A (131). The structure of this compound was unambiguously established using standard NMR experiments. The relative stereochemisty of the hemi-ketal moiety was assigned from a careful analysis of the ROESY NMR spectrum and the stereochemisty of the acyclic portion determined from a comparison of the 13C and 'H NMR data of a degradation product with the corresponding data of a synthetic compound. It was also established that the modified Moshers method could not be used to determine the absolute stereochemistry of the secondary hydroxy I substituent at C-11. The absolute stereochemistry of 131 was thus assigned in accordance with the proven stereochemistry of Siphonarian metabolites.

The Peruvian coast is one the best examples of cross-ecosystem food web exchanges, in which resources from one of the richest marine ecosystems subsidize consumers in one of the driest deserts on Earth. Marine subsidies are resources that originate in the marine ecosystem, and that contribute to increase the density of consumers in the recipient ecosystem. I examined the effects of marine subsidies on animal populations in the Peruvian coastal desert. I combined several approaches to study the linkages between marine resources and terrestrial consumers, such as surveying the spatial distribution and estimating the relative abundance of terrestrial consumers, studying the diet of geckos and lizards through stomach content analyses, and examining the desert food web with carbon and nitrogen stable isotope analyses. I found that the distribution and diet of desert consumers were tightly coupled to the availability of marine subsidies. I revealed linkages along two pathways of nutrient fluxes: tidal action that washes ashore macroalgae and cadavers of marine organisms, and animal transport in places where pinnipeds and seabirds congregate for reproduction. In the first pathway, intertidal algivivores made marine resources available to terrestrial consumers by moving between the intertidal and supratidal zone. The relative contribution of terrestrial and algal carbon sources varied among terrestrial consumers, because scorpions assimilated a lower proportion of energy from macroalgae than did geckos and solifuges. In the second pathway, I found that pinniped colonies influenced the diet of desert consumers, and contributed to support large populations of lizards and geckos. By combining field observations, and stomach and stable isotope analyses, I constructed a simplified food web for a large sea lion colony, showing the number of trophic levels that originate from pinniped-derived nutrients. My study demonstrates the enormous importance of marine resources for the diet of desert consumers. The near absence of rainfall along the Peruvian coast promotes an extreme dependence of terrestrial consumers on marine resources, and causes permanent food web effects that are affected by temporal variability in marine productivity, rather then temporal patterns of desert plant growth.

The Antarctic Peninsula (AP) is one of the fastest-warming regions on Earth. To assess whether this warming is part of the natural variability in the climate system, palaeoclimate archives are used to document the character of past climate changes and constrain predictions for the future. This investigation integrates a suite of radiocarbon dated marine sediment records from the continental shelf of the AP to provide a critical assessment of the distribution, timing, magnitude and forcing of Holocene climatic events. Sedimentary logs, diatom assemblages, stable isotopes and pigments were used as proxies to reconstruct AP ice sheet retreat, fluctuations in sea ice extent, changes in water mass circulation and ice shelf collapse events. This has revealed the spatial and temporal heterogeneity of climate events through the Holocene. The marine environment of the western AP (WAP) experienced deglaciation onset of the Mid Holocene climatic optimum and climatic deterioration into the Late Holocene considerably earlier than the marine environment of the eastern AP (EAP) and AP terrestrial records. These differences suggest that the climate of the WAP has been more closely connected with the SE Pacific, through coupled ocean-atmosphere interactions (such as the position of Southern Westerlies and El Nino Southern Oscillation frequency), whereas the EAP displayed a closer affinity with AP terrestrial records and the cryospheric influences of the Weddell Sea. This investigation has emphasised the complexity of the climate system of the AP on a range of spatial and temporal scales and highlighted that no single record can adequately represent regional palaeoclimate records must be developed from the oceans and continents and then interpreted as an assemblage.

NF-kB has become a major target in drug discovery.  The oceans cover 70% of our planet and form a habitat with unique environmental properties in which organisms producing chemically unique and biomedically powerful secondary metabolites thrive.  Here, the NF-kB inhibitory potential and the mechanism of action of natural products isolated from over two hundred Fijian and Scottish marine organisms and from the Fijian plant kava (Piper methysticum) are investigated.  The study reveals that 9% of crude extracts from marine organisms strongly inhibit the activation of NF-kB.  The NF-kB inhibitory potential is equally distributed throughout the tested phyla.  The kava-derivatives kavain and flavokavains A and B, as well as the isomalabaricanes stellettin A and B, two naphthopyrones, two cembranoids, the depsipeptide jasplakinolide, and the carotenoid astaxanthin isolated from Fijian marine organisms completely inhibit NF-kB activation at concentrations of less than 200 µg/mL.  The tested compounds mainly target the binding of NF-kB to DNA and processes upstream of the degradation of the cytoplasmic inhibitor of NF-kB, IkB, which, under basal conditions, prevents the activation of NF-kB by masking NF-kB’s nuclear localization site.  Altogether, the results of the present study give a first insight into NF-kB-inhibitory mechanisms triggered by marine natural products and by ethnobotanically used kava derivatives.  Together with the outcome of a still ongoing metabolomic analysis of the distribution of NF-kB inhibitors amongst Fijian marine natural products, the results of the present study will, most certainly, lead to a rapid and sustainable yield of unique and highly potent anti-cancer and anti-inflammatory substances in the near future.

This project investigated the fundamental principles of the Theory of Island Biogeography. How biodiversity is influenced by habitat age, size, isolation and quality was studied in two little-known ecosystems; pumice-rafted marine communities that travel through the Pacific Ocean and strand on shorelines, and Queensland's critically endangered Melaleuca irbyana forests. This research found that while habitat age, size and isolation were important for species richness; habitat quality, defined by resource availability and climate, was more influential for predicting biodiversity levels. Small pumice stones and small remnant forests can provide the conditions species need to prosper. Therefore, small and isolated habitats are also important to conserve.

The concept of building a space based telescope capable of directly imaging extra-solar planetary systems has been in existence for more than a decade. While the basic ideas of how such an instrument might work have already been discussed in the literature, specific details of the design have not been addressed that will enable a telescope of this class to be functionally realized. A straw man configuration of the instrument is examined here for its ability to acquire data of sufficient informational content and quality to produce images and spectra of distant planetary systems and to find what technical problems arise from analyzing the interferograms it delivers. Computer programs that simulate the signals expected to be produced by a structurally connected instrument (SCI) version of Terrestrial Planet Finder (TPF) and reconstruct images from those signals will be presented along with programs that extract planetary parameters. An abbreviated radiometric performance analysis will also be provided that will assist astronomers in designing an appropriate mission.

Sensory systems form the first point of contact between animals and their surroundings. The study of sensory systems is both a rich and diverse anatomical and behavioural field, and a potentially invaluable tool in evolutionary biology. This thesis examines four systems in three molluscan classes and ophiuroid echinoderms, addressing novel or poorly-understood systems and examining evolutionary trends by assessing the anatomy of more familiar structures in a phylogenetic context. The primary study system is a novel discovery reported herein throughout the chiton order Lepidopleurida, named the Schwabe organ. By combining detailed anatomical study, electrophysiology and behavioural experiments, 1 demonstrated that the Schwabe organ mediates light-avoidance behaviour and likely shares developmental origins with the chiton larval eye. A similar integrative approach was applied to a putative ‘visual* system in the ophiuroid Ophiocoma wendtii. Anatomical and behavioural results indicated that animals may use an extensive network of dermal photoreceptors for image formation, however this system differs substantially from the established model. The two final chapters focus on sensory and nervous systems in evolution. A re-description of scaphopod neuroanatomy in Rhabdus rectius demonstrates the potential power of a neurocladistic approach in solving deep phylogenetic questions, highlighting important similarities with cephalopod neural architecture and prompting the re-assignment of the major body axes in adult scaphopods. Finally, a study of eye reduction and eye loss in deep sea solariellid gastropods found surprising morphological diversity and differential progression between independent eye reductions, even within genera. This thesis makes several important contributions to our knowledge of four sensory systems and their evolution across two major invertebrate phyla: the Schwabe organ, extra-ocular photoreception in 0. wendtii, the Steiner organ and gastropod eyes. Overall, it also demonstrates the powerful nature of cross-disciplinary projects as well as the versatile role of sensory biology in broader evolutionary studies.

Natural products offer an unparalleled resource for the discovery and development of chemical tools to be used by humans. The terrestrial and marine environments contain unique niches where organisms chemically adapt to produce compounds that have proven useful medicinally and beyond. In the following chapters, several classes of novel natural products from terrestrial fungi and marine sponges will be presented. In some cases, synthetic methodology, biological activity and enzymatic target identification will also be presented. Chapters 2 and 3 highlight ramariolides A–D (2.18–2.21) and dhilirolides A–N (3.9–3.22), two new fungal derived compound classes isolated from terrestrial sources. The structure elucidation of these compounds will be presented alongside their biological activities as antimycobacterial and insecticidal agents, respectively. Chapter 4 contains the structure elucidation of three new members of the xestoquinone family of compounds, xestolactone A (4.19), xestosaprol O (4.20), and xestosaprol P (4.21) along with their potent inhibitory effect on human indolamine 2, 3-dioxygenase (hIDO). A new method for synthetic access to derivatives of these compounds is demonstrated in Chapter 5 along with a brief structure activity relationship (SAR) study. Lastly, Chapter 6 discusses latonduine A (6.9), a sponge-derived alkaloid, which has shown promise as a lead structure for the correction of cystic fibrosis (CF). Probes derived from latonduine A (6.9) have led to identification of poly (ADP-ribose) polymerase (PARP) as the enzymatic target. Methodology for the probes’ construction and SAR studies resulting in simplified synthetic analogues of latonduine will be presented.
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Wastewater containing ammonia is a product of oil refineries, coal gasification plants, slaughterhouses, dairy plants, distilleries, fertilizer plants and pharmaceutical operations; ammonia is also found in municipal wastewater. The ammonia is toxic to living organisms and it is desirable that it be removed. The foremost aim of this research was to use biologically activated ion exchange materials for ammonia removal from wastewater. In the past sand, plastic media and activated carbon as well as some ion exchange materials, e.g., clinoptilolite, have been used like a solid surface for bacteria growth. In this work some other materials were used for a combined biological and ion exchange process. The materials used were mordenite and Macronet MN 500 for terrestrial water, and modified zeolites for selective uptake of ammonia from marine waters. Clinoptilolite was used for comparison, as an ion exchanger which previously has been biologically activated. The ammonia adsorption characteristics of the materials in saline and non-saline synthetic wastewater were determined and compared with literature data. The data was fitted using Langmuir and Freundlich isotherms. The effect of the individual presence of potassium, calcium and magnesium ion upon ammonium ion uptake onto each material was also investigated. Bench scale ion-exchange stirred cell experiments were conducted to assess the uptake kinetics of ammonium ion. Process parameters include: initial ammonia concentration, the agitation rate, material particle size and mass of the material. The suitability of the ion exchange materials as a support for the growth of nitrifying bacteria was determined by observing the nitrification process in the flasks containing different materials, for the fresh and saline media. The ion exchangers were tested in continuous columns initially without bacterial growth and later with. To overcome the problem of low oxygen levels in the column and to avoid over aeration of the system, a novel design of columns was introduced, where aeration through the column was achieved by the air permeable silicon tubing. The synthetic material MN 500 exhibited the highest uptake capacity but the natural zeolites had the highest preference for ammonium ions in the presence of interfering cations. The ion exchange materials removed ammonia from saline water. A product of zeolitic nature, ZZ, exhibited the highest uptake capacity for ammonia removal from saline water. Natural zeolites were shown to be better media for bacterial growth in non-saline water. MN 500 exhibited better ammonia removal performance for the combined process in sea water compared to modified zeolite, ZZ. Both the clinoptilolite and mordenite used in non-saline medium, exhibited higher uptake capacity during the column experiments than for batch experiments. By introducing bacteria into the column, the uptake capacity was increased from the value of 0.15 to the value of 0.22meq/g for clinoptilolite. The improvement for the biologically active mordenite was from the value of 0.30meq/g without bacteria to the value of 0.4 meq/g with bacteria. The aeration of 2.88dm³/h, achieved by the tubing, provided better condition for the nitrification within the column, compared to the commonly used tank pre-aeration at the rate of 180dm³/h. The biologically active ion exchange column was not efficient in removing ammonia from saline water. High salt concentrations and slower nitrification in saline medium interfered the process significantly. It could be concluded that biologically active ion exchange is acceptable method for ammonia removal from non-saline wastewater. The possible way to improve the efficiency of the process in saline water would be to apply it in wastewaters in with nitrifying bacteria are already established. Mordenite proved to be more adequate for biological activation compared to commonly used clinoptilolite, which indicates that more ion exchange materials should be tested for combined process. The new aeration system within the columns proved to be more efficient compared to the commonly used tank pre-aeration.

Thesis (Ph. D.)--Florida State University, 2009.
Advisor: William T. Cooper III, Florida State University, College of Arts and Sciences, Dept. of Chemistry and Biochemistry. Title and description from dissertation home page (viewed Nov. 8, 2009). Document formatted into pages; contains xviii, 119 pages. Includes bibliographical references.

Despite an increased global interest in harmful algal bloom (HAB) species and eutrophication, the relationship between nutrient sources and changes in species composition or toxicity remains unclear. Stable isotopes are routinely used to identify and track nitrogen (N) sources to water bodies, as sources can be differentiated based on stable isotope values. While literature is available describing N fractionation by diatoms and coccolithophores, data are greatly lacking regarding isotope fractionation by dinoflagellates. Here we investigate the fractionation of nitrogen isotopes by saxitoxin-producing Alexandrium fundyense, to validate the use of the δ15N of particulate organic matter and identify the nitrogen source fueling a dinoflagellate bloom and its toxicity. The effects of N chemical form on isotope fractionation, toxin content, and toxicity, were investigated using isolates in single-N and mixed-N experiments. Growth on NO3-, NH4+, or urea, resulted in isotope fractionation of 2.761.48‰, 29.019.32‰, or 0.340.19‰, respectively, with the lowest cellular toxicity and toxin quotas reported during urea utilization. Toxin composition and growth rates, however, remained constant across all N treatments, showing no effects of NO3-, NH4+, or urea utilization. Alexandrium fundyense was then preconditioned to either NO3-, NH4+, or urea, and abruptly inoculated into mixed-N medium containing all three chemical forms. All treatments initially utilized NH4+ and urea upon inoculation into mixed medium, suggesting no effect of preconditioning. Cells only began utilizing NO3- after NH4+ decreased below 2-4 M in the medium. During the inhibition of NO3- uptake by NH4+ utilization, the cellular δ15N was at its lowest (-5‰), and through the course of the experiment, the δ15N continuously changed to mimic the isotope value of the most recent N source(s) being utilized. When utilizing multiple sources, the isotope signature of the cells fell between the signal of the two N sources. Together this suggests that in NO3- and urea rich environments, the 15NPOM would reliably look like the source or sources of nitrogen utilized, but that caution should be taken in NH4+ rich environments where the large value could lead to misinterpretation of the signal. Nutrients are only one factor influencing bloom dynamics, but information about the relative importance of natural or anthropogenic nutrients in the development and toxicity of bloom events is necessary to predict future shifts in phytoplankton species composition, density, and toxicity.

[EN] Multiple-Input Multiple-Output (MIMO) technology in Digital Terrestrial Television (DTT) networks has the potential to increase the spectral efficiency and improve network coverage to cope with the competition of limited spectrum use (e.g., assignment of digital dividend and spectrum demands of mobile broadband), the appearance of new high data rate services (e.g., ultra-high definition TV - UHDTV), and the ubiquity of the content (e.g., fixed, portable, and mobile). It is widely recognised that MIMO can provide multiple benefits such as additional receive power due to array gain, higher resilience against signal outages due to spatial diversity, and higher data rates due to the spatial multiplexing gain of the MIMO channel. These benefits can be achieved without additional transmit power nor additional bandwidth, but normally come at the expense of a higher system complexity at the transmitter and receiver ends. The final system performance gains due to the use of MIMO directly depend on physical characteristics of the propagation environment such as spatial correlation, antenna orientation, and/or power imbalances experienced at the transmit aerials. Additionally, due to complexity constraints and finite-precision arithmetic at the receivers, it is crucial for the overall system performance to carefully design specific signal processing algorithms. This dissertation focuses on transmit and received signal processing for DTT systems using MIMO-BICM (Bit-Interleaved Coded Modulation) without feedback channel to the transmitter from the receiver terminals. At the transmitter side, this thesis presents investigations on MIMO precoding in DTT systems to overcome system degradations due to different channel conditions. At the receiver side, the focus is given on design and evaluation of practical MIMO-BICM receivers based on quantized information and its impact in both the in-chip memory size and system performance. These investigations are carried within the standardization process of DVB-NGH (Digital Video Broadcasting - Next Generation Handheld) the handheld evolution of DVB-T2 (Terrestrial - Second Generation), and ATSC 3.0 (Advanced Television Systems Committee - Third Generation), which incorporate MIMO-BICM as key technology to overcome the Shannon limit of single antenna communications. Nonetheless, this dissertation employs a generic approach in the design, analysis and evaluations, hence, the results and ideas can be applied to other wireless broadcast communication systems using MIMO-BICM.
[ES] La tecnología de múltiples entradas y múltiples salidas (MIMO) en redes de Televisión Digital Terrestre (TDT) tiene el potencial de incrementar la eficiencia espectral y mejorar la cobertura de red para afrontar las demandas de uso del escaso espectro electromagnético (e.g., designación del dividendo digital y la demanda de espectro por parte de las redes de comunicaciones móviles), la aparición de nuevos contenidos de alta tasa de datos (e.g., ultra-high definition TV - UHDTV) y la ubicuidad del contenido (e.g., fijo, portable y móvil). Es ampliamente reconocido que MIMO puede proporcionar múltiples beneficios como: potencia recibida adicional gracias a las ganancias de array, mayor robustez contra desvanecimientos de la señal gracias a la diversidad espacial y mayores tasas de transmisión gracias a la ganancia por multiplexado del canal MIMO. Estos beneficios se pueden conseguir sin incrementar la potencia transmitida ni el ancho de banda, pero normalmente se obtienen a expensas de una mayor complejidad del sistema tanto en el transmisor como en el receptor. Las ganancias de rendimiento finales debido al uso de MIMO dependen directamente de las características físicas del entorno de propagación como: la correlación entre los canales espaciales, la orientación de las antenas y/o los desbalances de potencia sufridos en las antenas transmisoras. Adicionalmente, debido a restricciones en la complejidad y aritmética de precisión finita en los receptores, es fundamental para el rendimiento global del sistema un diseño cuidadoso de algoritmos específicos de procesado de señal. Esta tesis doctoral se centra en el procesado de señal, tanto en el transmisor como en el receptor, para sistemas TDT que implementan MIMO-BICM (Bit-Interleaved Coded Modulation) sin canal de retorno hacia el transmisor desde los receptores. En el transmisor esta tesis presenta investigaciones en precoding MIMO en sistemas TDT para superar las degradaciones del sistema debidas a diferentes condiciones del canal. En el receptor se presta especial atención al diseño y evaluación de receptores prácticos MIMO-BICM basados en información cuantificada y a su impacto tanto en la memoria del chip como en el rendimiento del sistema. Estas investigaciones se llevan a cabo en el contexto de estandarización de DVB-NGH (Digital Video Broadcasting - Next Generation Handheld), la evolución portátil de DVB-T2 (Second Generation Terrestrial), y ATSC 3.0 (Advanced Television Systems Commitee - Third Generation) que incorporan MIMO-BICM como clave tecnológica para superar el límite de Shannon para comunicaciones con una única antena. No obstante, esta tesis doctoral emplea un método genérico tanto para el diseño, análisis y evaluación, por lo que los resultados e ideas pueden ser aplicados a otros sistemas de comunicación inalámbricos que empleen MIMO-BICM.
[CAT] La tecnologia de múltiples entrades i múltiples eixides (MIMO) en xarxes de Televisió Digital Terrestre (TDT) té el potencial d'incrementar l'eficiència espectral i millorar la cobertura de xarxa per a afrontar les demandes d'ús de l'escàs espectre electromagnètic (e.g., designació del dividend digital i la demanda d'espectre per part de les xarxes de comunicacions mòbils), l'aparició de nous continguts d'alta taxa de dades (e.g., ultra-high deffinition TV - UHDTV) i la ubiqüitat del contingut (e.g., fix, portàtil i mòbil). És àmpliament reconegut que MIMO pot proporcionar múltiples beneficis com: potència rebuda addicional gràcies als guanys de array, major robustesa contra esvaïments del senyal gràcies a la diversitat espacial i majors taxes de transmissió gràcies al guany per multiplexat del canal MIMO. Aquests beneficis es poden aconseguir sense incrementar la potència transmesa ni l'ample de banda, però normalment s'obtenen a costa d'una major complexitat del sistema tant en el transmissor com en el receptor. Els guanys de rendiment finals a causa de l'ús de MIMO depenen directament de les característiques físiques de l'entorn de propagació com: la correlació entre els canals espacials, l'orientació de les antenes, i/o els desequilibris de potència patits en les antenes transmissores. Addicionalment, a causa de restriccions en la complexitat i aritmètica de precisió finita en els receptors, és fonamental per al rendiment global del sistema un disseny acurat d'algorismes específics de processament de senyal. Aquesta tesi doctoral se centra en el processament de senyal tant en el transmissor com en el receptor per a sistemes TDT que implementen MIMO-BICM (Bit-Interleaved Coded Modulation) sense canal de tornada cap al transmissor des dels receptors. En el transmissor aquesta tesi presenta recerques en precoding MIMO en sistemes TDT per a superar les degradacions del sistema degudes a diferents condicions del canal. En el receptor es presta especial atenció al disseny i avaluació de receptors pràctics MIMO-BICM basats en informació quantificada i al seu impacte tant en la memòria del xip com en el rendiment del sistema. Aquestes recerques es duen a terme en el context d'estandardització de DVB-NGH (Digital Video Broadcasting - Next Generation Handheld), l'evolució portàtil de DVB-T2 (Second Generation Terrestrial), i ATSC 3.0 (Advanced Television Systems Commitee - Third Generation) que incorporen MIMO-BICM com a clau tecnològica per a superar el límit de Shannon per a comunicacions amb una única antena. No obstant açò, aquesta tesi doctoral empra un mètode genèric tant per al disseny, anàlisi i avaluació, per la qual cosa els resultats i idees poden ser aplicats a altres sistemes de comunicació sense fils que empren MIMO-BICM.
Vargas Paredero, DE. (2016). Transmit and Receive Signal Processing for MIMO Terrestrial Broadcast Systems [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/66081
TESIS
Premiado

Nowadays, the digital terrestrial television (DTT) market is characterized by the high capacity needed for high definition TV services. There is a need for an efficient use of the broadcast spectrum, which requires new technologies to guarantee increased capacities. Non-Uniform Constellations (NUC) arise as one of the most innovative techniques to approach those requirements. NUCs reduce the gap between uniform Gray-labelled Quadrature Amplitude Modulation (QAM) constellations and the theoretical unconstrained Shannon limit. With these constellations, symbols are optimized in both in-phase (I) and quadrature (Q) components by means of signal geometrical shaping, considering a certain signal-to-noise ratio (SNR) and channel model. There are two types of NUC, one-dimensional and two-dimensional NUCs (1D-NUC and 2D-NUC, respectively). 1D-NUCs maintain the squared shape from QAM, but relaxing the distribution between constellation symbols in a single component, with non-uniform distance between them. These constellations provide better SNR performance than QAM, without any demapping complexity increase. 2D-NUCs also relax the square shape constraint, allowing to optimize the symbol positions in both dimensions, thus achieving higher capacity gains and lower SNR requirements. However, the use of 2D-NUCs implies a higher demapping complexity, since a 2D-demapper is needed, i.e. I and Q components cannot be separated. In this dissertation, NUCs are analyzed from both transmit and receive point of views, using either single-input single-output (SISO) or multiple-input multiple-output (MIMO) antenna configurations. In SISO transmissions, 1D-NUCs and 2D-NUCs are optimized for a wide range of SNRs and different constellation orders. The optimization of rotated 2D-NUCs is also investigated. Even though the demapping complexity is not increased, the SNR gain of these constellations is not significant. The highest rotation gain is obtained for low-order constellations and high SNRs. However, with multi-RF techniques, the SNR gain is drastically increased, since I and Q components are transmitted in different RF channels. In this thesis, multi-RF gains of NUCs with and without rotation are provided for some representative scenarios. At the receiver, two different implementation bottlenecks are explored. First, the demapping complexity of all considered constellations is analyzed. Afterwards, two complexity reduction algorithms for 2D-NUCs are proposed. Both algorithms drastically reduce the number of distances to compute. Moreover, both are finally combined in a single demapper. Quantization of NUCs is also explored in this dissertation, since LLR values and I/Q components are modified when using these constellations, compared to traditional QAM constellations. A new algorithm that is based on the optimization of the quantizer levels for a particular constellation is proposed. The use of NUCs in multi-antenna communications is also investigated. It includes the optimization in one or two antennas, the use of power imbalance, the cross-polar discrimination (XPD) between receive antennas, or the use of different demappers. Assuming different values for the parameters evaluated, new Multi-Antenna Non-Uniform Constellations (MA-NUC) are obtained by means of a particularized re-optimization process, specific for MIMO. At the receiver, an extended demapping complexity analysis is performed, where it is shown that the use of 2D-NUCs in MIMO extremely increases the demapping complexity. As an alternative, an efficient solution for 2D-NUCs and MIMO systems based on Soft-Fixed Sphere Decoding (SFSD) is proposed. The main drawback is that SFSD demappers do not work with 2D-NUCs, since they perform a Successive Interference Cancellation (SIC) step that needs to be performed in separated I and Q components. The proposed method quantifies the closest symbol using Voronoi regions and allows SFSD demappers to work.
Hoy en día, el mercado de la televisión digital terrestre (TDT) está caracterizado por la alta capacidad requerida para transmitir servicios de televisión de alta definición y el espectro disponible. Es necesario por tanto un uso eficiente del espectro radioeléctrico, el cual requiere nuevas tecnologías para garantizar mayores capacidades. Las constelaciones no-uniformes (NUC) emergen como una de las técnicas más innovadoras para abordar tales requerimientos. Las NUC reducen el espacio existente entre las constelaciones uniformes QAM y el límite teórico de Shannon. Con estas constelaciones, los símbolos se optimizan en ambas componentes fase (I) y cuadratura (Q) mediante técnicas geométricas de modelado de la señal, considerando un nivel señal a ruido (SNR) concreto y un modelo de canal específico. Hay dos tipos de NUC, unidimensionales y bidimensionales (1D-NUC y 2D-NUC, respectivamente). Las 1D-NUC mantienen la forma cuadrada de las QAM, pero permiten cambiar la distribución entre los símbolos en una componente concreta, teniendo una distancia no uniforme entre ellos. Estas constelaciones proporcionan un mejor rendimiento SNR que QAM, sin ningún incremento en la complejidad en el demapper. Las 2D-NUC también permiten cambiar la forma cuadrada de la constelación, permitiendo optimizar los símbolos en ambas dimensiones y por tanto obteniendo mayores ganancias en capacidad y menores requerimientos en SNR. Sin embargo, el uso de 2D-NUCs implica una mayor complejidad en el receptor. En esta tesis se analizan las NUC desde el punto de vista tanto de transmisión como de recepción, utilizando bien configuraciones con una antena (SISO) o con múltiples antenas (MIMO). En transmisiones SISO, se han optimizado 1D-NUCs para un rango amplio de distintas SNR y varios órdenes de constelación. También se ha investigado la optimización de 2D-NUCs rotadas. Aunque la complejidad no aumenta, la ganancia SNR de estas constelaciones no es significativa. La mayor ganancia por rotación se obtiene para bajos órdenes de constelación y altas SNR. Sin embargo, utilizando técnicas multi-RF, la ganancia aumenta drásticamente puesto que las componentes I y Q se transmiten en distintos canales RF. En esta tesis, se han estudiado varias ganancias multi-RF representativas de las NUC, con o sin rotación. En el receptor, se han identificado dos cuellos de botella diferentes en la implementación. Primero, se ha analizado la complejidad en el receptor para todas las constelaciones consideradas y, posteriormente, se proponen dos algoritmos para reducir la complejidad con 2D-NUCs. Además, los dos pueden combinarse en un único demapper. También se ha explorado la cuantización de estas constelaciones, ya que tanto los valores LLR como las componentes I/Q se ven modificados, comparando con constelaciones QAM tradicionales. Además, se ha propuesto un algoritmo que se basa en la optimización para diferentes niveles de cuantización, para una NUC concreta. Igualmente, se ha investigado en detalle el uso de NUCs en MIMO. Se ha incluido la optimización en una sola o en dos antenas, el uso de un desbalance de potencia, factores de discriminación entre antenas receptoras (XPD), o el uso de distintos demappers. Asumiendo distintos valores, se han obtenido nuevas constelaciones multi-antena (MA-NUC) gracias a un nuevo proceso de re-optimización específico para MIMO. En el receptor, se ha extendido el análisis de complejidad en el demapper, la cual se incrementa enormemente con el uso de 2D-NUCs y sistemas MIMO. Como alternativa, se propone una solución basada en el algoritmo Soft-Fixed Sphere Decoding (SFSD). El principal problema es que estos demappers no funcionan con 2D-NUCs, puesto que necesitan de un paso adicional en el que las componentes I y Q necesitan separarse. El método propuesto cuantifica el símbolo más cercano utilizando las regiones de Voronoi, permitiendo el uso de este tipo de receptor.
Actualment, el mercat de la televisió digital terrestre (TDT) està caracteritzat per l'alta capacitat requerida per a transmetre servicis de televisió d'alta definició i l'espectre disponible. És necessari per tant un ús eficient de l'espectre radioelèctric, el qual requereix noves tecnologies per a garantir majors capacitats i millors servicis. Les constel·lacions no-uniformes (NUC) emergeixen com una de les tècniques més innovadores en els sistemes de televisió de següent generació per a abordar tals requeriments. Les NUC redueixen l'espai existent entre les constel·lacions uniformes QAM i el límit teòric de Shannon. Amb estes constel·lacions, els símbols s'optimitzen en ambdós components fase (I) i quadratura (Q) per mitjà de tècniques geomètriques de modelatge del senyal, considerant un nivell senyal a soroll (SNR) concret i un model de canal específic. Hi ha dos tipus de NUC, unidimensionals i bidimensionals (1D-NUC i 2D-NUC, respectivament). 1D-NUCs mantenen la forma quadrada de les QAM, però permet canviar la distribució entre els símbols en una component concreta, tenint una distància no uniforme entre ells. Estes constel·lacions proporcionen un millor rendiment SNR que QAM, sense cap increment en la complexitat al demapper. 2D-NUC també canvien la forma quadrada de la constel·lació, permetent optimitzar els símbols en ambdós dimensions i per tant obtenint majors guanys en capacitat i menors requeriments en SNR. No obstant això, l'ús de 2D-NUCs implica una major complexitat en el receptor, ja que es necessita un demapper 2D, on les components I i Q no poden ser separades. En esta tesi s'analitzen les NUC des del punt de vista tant de transmissió com de recepció, utilitzant bé configuracions amb una antena (SISO) o amb múltiples antenes (MIMO). En transmissions SISO, s'han optimitzat 1D-NUCs, per a un rang ampli de distintes SNR i diferents ordes de constel·lació. També s'ha investigat l'optimització de 2D-NUCs rotades. Encara que la complexitat no augmenta, el guany SNR d'estes constel·lacions no és significativa. El major guany per rotació s'obté per a baixos ordes de constel·lació i altes SNR. No obstant això, utilitzant tècniques multi-RF, el guany augmenta dràsticament ja que les components I i Q es transmeten en distints canals RF. En esta tesi, s'ha estudiat el guany multi-RF de les NUC, amb o sense rotació. En el receptor, s'han identificat dos colls de botella diferents en la implementació. Primer, s'ha analitzat la complexitat en el receptor per a totes les constel·lacions considerades i, posteriorment, es proposen dos algoritmes per a reduir la complexitat amb 2D-NUCs. Ambdós algoritmes redueixen dràsticament el nombre de distàncies. A més, els dos poden combinar-se en un únic demapper. També s'ha explorat la quantització d'estes constel·lacions, ja que tant els valors LLR com les components I/Q es veuen modificats, comparant amb constel·lacions QAM tradicionals. A més, s'ha proposat un algoritme que es basa en l'optimització per a diferents nivells de quantització, per a una NUC concreta. Igualment, s'ha investigat en detall l'ús de NUCs en MIMO. S'ha inclòs l'optimització en una sola o en dos antenes, l'ús d'un desbalanç de potència, factors de discriminació entre antenes receptores (XPD), o l'ús de distints demappers. Assumint distints valors, s'han obtingut noves constel·lacions multi-antena (MA-NUC) gràcies a un nou procés de re-optimització específic per a MIMO. En el receptor, s'ha modificat l'anàlisi de complexitat al demapper, la qual s'incrementa enormement amb l'ús de 2D-NUCs i sistemes MIMO. Com a alternativa, es proposa una solució basada en l'algoritme Soft-Fixed Sphere Decoding (SFSD) . El principal problema és que estos demappers no funcionen amb 2D-NUCs, ja que necessiten d'un pas addicional en què les components I i Q necessiten separar-se. El mètode proposat quantifica el símbol més pròxim utilitzan
Fuentes Muela, M. (2017). Non-Uniform Constellations for Next-Generation Digital Terrestrial Broadcast Systems [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/84743
TESIS

The Nanoarchaeota are an enigmatic lineage of Archaea found in deep-sea hydrothermal vents and geothermal springs across the globe. These small (~100-400 nm) hyperthermophiles live ectosymbiotically with diverse hosts from the Crenarchaeota. Despite their broad distribution in high-temperature environments, very few Nanoarchaeota have been successfully isolated in co-culture with their hosts and nanoarchaeote genomes are poorly represented in public databases. However, the Nanoarchaeota provide unique insights into the structure and function of symbiosis in the archaeal domain. This study describes novel nanoarchaeotes from multiple geothermal habitats, using a combination of direct cultivation techniques and genomic analysis. A new nanoarchaeote from a New Zealand hot spring, Candidatus Nanoclepta minutus, was isolated in co-culture with its host. Like other terrestrial Nanoarchaeota, Cand. Ncl. minutus harbors genes for gluconeogenesis and archaeal flagella. Zestosphaera tikiterensis, the New Zealand host, was also isolated in pure culture and characterized. Phylogenetic analysis showed that both Cand. Ncl. minutus and Z. tikiterensis are new genera in the Nanoarchaeota and Crenarchaeota, respectively. Metagenome-assembled genomes (MAGs) from the Nanoarchaeota were also recovered from deep-sea hydrothermal vent sites. These MAGs capture a wide range of diversity in the Nanoarchaeota, representing three new species and two novel genera. Key nanoarchaeotal features were identified in the MAGs, including marker genes for archaeal flagella, gluconeogenesis and CRISPR-Cas regions. These studies greatly contribute to our understanding of nanoarchaeotal ecophysiology and provide key insights into the coding potential and diversity of Nanoarchaeota and their hosts.

The thesis presents tools and architecture regarding design of marine MSs in OSVs. It enlightens important aspects regarding the design based on a research study, and proposes a design methodology consisting of tools and architecture. From the research studies in chapter 2 it becomes clear that the most common propulsion system today for platform supply vessels (PSV) is the diesel-electric (DEL) propulsion system. Other concepts such as; dual fuel engines, Voith Schneider Propellers (VSP), hybrid systems, fuel cell power, wind power, nuclear power, and jet propulsion exist today but is not yet considered typical solutions. The research study in chapter 5, regarding current status on tools and architecture, shows that it exist very few dedicated and sophisticated tools and methodologies regarding early-design of MSs onboard OSVs. However, exceptions such as the software package GES, developed by TNO in Holland, were found and it is considered the most promising tool yet based on this study. GES share the same design philosophy as the proposed tool in chapter 8, which is regarding the MS as an energy system where power flow through components is modeled with respect to the bond graph theory. By utilizing the bond graph theory, unified interfacing is introduced. This approach is applicable in any energy domain and the variables describing the energy or power are kept in a general form; effort and flow. The proposed methodology, in chapter 7, presents structure and methods regarding the design process such as; concurrent engineering, hierarchical MS breakdown structure, component library scheme, and model documentation framework. The thesis presents, in chapter 8, a MS mock-up with a hierarchical system structure and unified interfacing between components. The mock-up is flexible in terms of sub-system or component reconfigurations and it allows for energy domain-independent performance analysis which is exemplified in chapter 8.5 and 8.6. The MS mock-up is considered far from complete in terms of user-friendliness, sub-system description, and component description, but it portraits trend lines regarding performance which are similar to what one may find by analyzing real MSs, which is considered the goal for developing this mock-up. The presented mock-up and methodologies are meant to exemplify how one can approach this challenge.

A computer model was constructed that allowed two vessels involved in a possible collision situation to take collision avoidance action following the "International Regulations for Preventing Collisions at Sea". The mariners’ actions were modelled by the concepts of the domain and the RDRR (Range to Domain/Range-rate). The domain was used to determine if a vessel was threatening and the RDRR to determine the time at which a vessel should give-way to a threatening target. Each vessel in the simulation had four domains corresponding to the type of encounter in which the vessel was involved. Values for the time at which a vessel manoeuvres and the domain radii were determined from an analysis of high quality cine films of the radar at H.M. Coastguard at St. Margaret's Bay, Dover. Information was also taken from simulator exercises set up on the Polytechnic radar simulator. The two ship encounter was then developed to become the multi-ship encounter and eventually was able to model over 400 vessels over a two day period through a computer representation of the Dover Strait. A further development included a computer graphical representation of a radar simulator running in real-time, and which allowed a mariner to navigate one of the vessels using computer control. A validation of the computer model was undertaken by comparing the simulated results with those observed from the cine films. Following the validation several examples of the computer model being used as a decision support system were included.

Thesis: Ph. D., Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 169-190).
Terrestrial organic carbon (OC) erosion, remineralization, transport through river networks, and burial in marine sediments is a major pathway of the global carbon cycle. However, our ability to constrain these processes and fluxes is largely limited by (i) analytical capability and (ii) temporal sampling resolution. To address issue (i), here I discuss methodological advancements and data analysis techniques for the Ramped PyrOx serial oxidation isotope method developed at WHOI. Ramped-temperature pyrolysis/oxidation coupled with the stable carbon (¹²C, ¹³C) and radiocarbon (¹⁴C) analysis of evolved CO₂ is a promising tool for understanding and separating complex OC mixtures. To quantitatively investigate distributions of OC source, reservoir age, and chemical structure contained within a single sample, I developed a kinetic model linking RPO-derived activation energy, ¹³C composition, and radiocarbon content. This tool provides a novel method to fundamentally address the unknown relationship between OC remineralization rates and chemical structure in various environmental settings. To address issue (ii), I additionally present results from time-series sample sets collected on two end-member systems: the Congo River (Central Africa) and the LiWu River (Taiwan). For the Congo River, bulk and plant-wax-lipid ¹³C compositions indicate that a majority of particulate OC is consistently derived from downstream, C₃-dominated rainforest ecosystems. Furthermore, bulk radiocarbon content and microbial lipid molecular distributions are strongly correlated with discharge, suggesting that pre-aged, swamp-forest-derived soils are preferentially exported when northern hemisphere discharge is highest. Combined, these results provide insight into the relationship between hydrological processes and fluvial carbon export. Lastly, I examined the processes controlling carbon source and flux in a set of soils and time-series fluvial sediments from the LiWu River catchment located in Taiwan. A comparison between bedrock and soil OC content reveals that soils can contain significantly less carbon than the underlying bedrock, suggesting that this material is remineralized to CO₂ prior to soil formation. Both the presence of bacterial lipids and a shift toward lower activation energy of ¹⁴C-free OC contained in soil saprolite layers indicate that this process is microbially mediated and that microbial respiration of rock-derived OC likely represents a larger geochemical flux than previously thought. The results presented in this thesis therefore provide novel insight into the role of rivers in the global carbon cycle as well as their response to environmental perturbations.
by Jordon Dennis Hemingway
Ph. D.

Thesis (M.S.)--Joint Program in Oceanography and Oceanographic Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), June 1996.
"May 1996."
Includes bibliographical references (leaves 66-68).
This thesis details two years of research conducted with the guidance and support of three advisors: Dr. J. K. Whelan, Dr. J. S. Seewald and Dr. T. I. Eglinton. Each of the three chapters represents a different, self-contained research project. All of the projects are related to the organic geochemistry of marine sediments, however, this is a fairly encompassing area of study. Chapters 1 and 2 stem from the same experimental study -- the use of hydrous-pyrolysis to investigate mechanisms leading to the production of petroleum-related products during kerogen maturation. Chapter 3, on the other hand, utilizes a recently developed technique of isolating and AMS-14C dating individual compounds from complex sedimentary organic mixtures. The samples used in each investigation came from all over the world. The first two chapters utilize ancient marine sediment samples obtained from an outcrop in California (Chpts. 1 and 2) and from a well in Alabama (Chpt. 2). In contrast, recent marine sediment samples were obtained from the Arabian and Black Seas for the third chapter. Several preparative and analytical methods are common to all three studies. Nevertheless, each employ techniques totally unique from one another and from previous investigations. In Chapter 1, for example, X-ray absorption spectroscopy (XANES) is used to determine the speciation of organic sulfur present in kerogen, bitumen, and bulk sediment samples. While Chapter 3 represents the first study in which the "4C ages of individual, known hydrocarbon biomarkers are determined after isolation by Preparative Capillary Gas Chromatography (PCGC). The insights gained by these investigations are discussed in detail in the following chapters. The common thread between the three chapters is that the source of organic matter, the rate at which it is delivered to marine sediments and the depositional environment, all set the stage for kerogen formation and eventual petroleum generation.
by Bryan C. Benitez-Nelson.
M.S.

Phytoplankton account for at least half of all primary production in estuarine waters and are at the center of biogeochemical cycles and material budgets. Environmental managers use water column chlorophyll-a (chl-a) concentrations as a basic water quality indictor, as the problems of eutrophication and hypoxia are intrinsically linked to excessive phytoplankton growth. Evidence suggests that the distribution and frequency of harmful algal blooms may be increasing worldwide. For the most part, phytoplankton communities follow a standard seasonal pattern, with specific groups dominating the assemblage during the time of year when environmental conditions correspond to their requisites for growth. However, climate change will result in incremental but consistent shifts in some environmental factors known to affect phytoplankton production and biomass accumulation. Mean surface temperatures in North American mid-Atlantic coastal and estuarine regions are steadily rising, and the frequency and severity of drought and storm events are projected to fluctuate, potentially increasing the severity of extreme weather events. Anthropogenically-induced nutrient loading, especially from non-point sources, is one of the largest consistent contributors to coastal marine eutrophication. The consequences of changes in these environmental factors to estuarine ecosystems and phytoplankton community dynamics are unclear. Because different phytoplankton groups respond to environmental changes in distinctive ways, some classes thrive during periods of environmental stability and others at times of temporary or sustained disturbance. to predict how phytoplankton and therefore water quality might respond to changes in climate and land use, we built mathematical phytoplankton kinetics sub-models that differentiate phytoplankton groups using taxonomic classes with well-defined functional characteristics. Then we integrated them into a reduced-complexity estuarine ecosystem model. The sub-models were designed to simulate daily biomass of diatoms, dinoflagellates, cyanobacteria, and raphidophytes in the New River Estuary, NC. We calibrated and validated the model using data collected from 2007 – 2012 through the Aquatic Estuarine monitoring module of the Defense Coastal/Estuarine Research Program. The model was a relatively good predictor of total chl-a and primary production, and a fair predictor of group dynamics. The model was employed in heuristic simulations of changes in temperature, nutrient loading, and freshwater delivery to predict their effects on overall phytoplankton biomass, productivity, and community composition. Increases in temperature had a modest effect on mean daily simulated phytoplankton production and chl-a, but considerably decreased the relative abundance of diatoms and simultaneously increased the relative abundance of cyanobacteria. The seasonal phenology of phytoplankton abundance also shifted in response to increased temperatures: chl-a concentrations were larger in the winter and spring and smaller in the summer and fall. The model was most sensitive to changes in the watershed nutrient load. Nutrient influx had a dramatic effect on the temporal and spatial extent of phytoplankton blooms. The relative abundance of dinoflagellates and raphidophytes increased in response to elevated nutrient loading, regardless of whether load was increased directly as in nutrient simulations or indirectly as in freshwater simulations. Initially, greater freshwater discharge increased total chl-a, productivity, and the frequency of phytoplankton blooms. However, these relationships leveled off or were reversed as flow continued to increase due to greater rates of flushing and light attenuation. Results demonstrated how models like this can be important tools for both heuristic understanding and environmental management. A benefit of this model is how easy it is to update to other estuarine systems through the re-parameterization of the phytoplankton groups.

Southeast Florida’s continual urban expansion will potentially increase anthropogenic pollution in adjacent coastal marine systems. Furthermore, increased nutrient loads could have detrimental effects on the already threatened Florida Reef Tract. The present study uses a stable isotopic approach to determine the sources and the impact of nutrients on the Florida Reef Tract. δ13C and δ15N analysis of macroalgae, sponges, and sediment were analyzed in order to determine nutrient inputs in this region. While δ13C data did not display any significant trends spatially, δ15N values of the majority of biota exhibited a strong East to West gradient with more enriched values close to shore. Relative enrichment in δ15N values were measured for sediments sampled along the Florida Reef Tract in comparison to a pristine Marquesas Keys sediment core. The δ15N data also implies that shoreline anthropogenic nutrients have more nutrient loading implications on reefs than major point sources.

Terrestrial organic matter (TOM) constitutes an important source of energy in many aquatic environments (streams, lakes, wetlands). This is the first study to examine the role of TOM in food webs of the rocky intertidal zone. We compared the consumption of red alder leaves (Alnus rubra) to common marine sources of drifting detritus along the southern Oregon coast (Nereocystis luetkeana, Phyllospadix spp., and Fucus gardneri). We used short term (hours to days) and long term (months) feeding experiments to compare the rate of consumption among each plant species during the Spring and Fall of 2014 and 2015. In addition, we quantified the amount of TOM in beach wrack and in the drift of two streams that flowed directly to the rocky intertidal zone. We also measured the food quality of each plant species (C:N and polyphenolic concentrations). On average, the two small streams in this study transported 1,113.6 kg AFDM/m3 of TOM per day during Fall leaf abscission to the rocky intertidal zone. Also, the biomass of terrestrial leaves in beach wrack varied from negligible (2.1 g AFDM) to the dominant source of detritus (60.7 g AFDM) depending on if it was the dominant riparian plant growing along the edges of the shore. Consistent with previous research, N. luetkeana was a high quality food (C:N = 15:1; polyphenolics = 418 mg/ml), whereas F. gardneri (C:N = 22:1; polyphenolics = 8098 mg/ml) was more recalcitrant. Phyllospadix spp. was puzzling because it had low concentrations of polyphenolics (800 mg/ml) but was not consumed. Alnus rubra had a high concentration of structural compounds (C:N = 33:1) and intermediate levels of polyphenolics (3,415 mg/ml after leaching). Both short term and long term experiments showed that the rates of consumption of Spring-shed, green leaves and freshly fallen brown leaves of A. rubra were intermediate between N. luetkeana and the less palatable marine species (F. gardneri and Phyllospadix spp.). Thus, A. rubra was eaten by common intertidal consumers and may constitute an important source of energy between brief inputs of more nutritious marine resources (e.g. N. luetkeana).

This doctoral thesis presents new ideas and research results on control of marine electric power system.

The main motivation for this work is the development of a control system, power management system (PMS) capable to improve the system robustness to blackout, handle major power system faults, minimize the operational cost and keep the power system machinery components under minimal stress in all operational conditions.

Today, the electric marine power system tends to have more system functionality implemented in integrated automation systems. The present state of the art type of tools and methods for analyzing marine power systems do only to a limited extent utilize the increased knowledge available within each of the mechanical and electrical engineering disciplines.

As the propulsion system is typically consisted of the largest consumers on the vessel, important interactions exists between the PMS and vessel propulsion system. These are interacted through the dynamic positioning (DP) controller, thrust allocation algorithm, local thruster controllers, generators' local frequency and voltage controllers. The PMS interacts with the propulsion system through the following main functions: available power static load control, load rate limiting control and blackout prevention control (i.e. fast load reduction). These functions serve to prevent the blackout and to ensure that the vessel will always have enough power.

The PMS interacts with other control systems in order to prevent a blackout and to minimize operational costs. The possibilities to maximize the performance of the vessel, increase the robustness to faults and decrease a component wear-out rate are mainly addressed locally for the individual control systems. The solutions are mainly implicative (for e.g. local thruster control, or DP thrust allocation), and attention has not been given on the interaction between these systems, the power system and PMS. Some of the questions that may arise regarding the system interactions, are as follows: how the PMS functionality may affect a local thruster control, how the local thruster control may affect the power system performance, how some consumers may affect the power system performance in normal operations and thus affect other consumers, how the power system operation may affect the susceptibility to faults and blackout, how various operating and weather conditions may affect the power system performance and thus propulsion performance though the PMS power limiting control, how propulsion performance may affect the overall vessel performance, which kind of faults can be avoided if the control system is re-structured, how to minimize the operational costs and to deal with the conflicting goals. This PhD thesis aims to provide answers to such questions.

The main contributions of this PhD thesis are:

− A new observer-based fast load reduction system for the blackout prevention control has been proposed. When compared to the existing fast load reduction systems, the proposed controller gives much faster blackout detection rate, high reliability in the detection and faster and more precise load reduction (within 150 miliseconds).

− New advanced energy management control strategies for reductions in the operational costs and improved fuel economy of the vessel.

− Load limiting controllers for the reduction of thruster wear-out rate. These controllers are based on the probability of torque loss, real-time torque loss and the thruster shaft

accelerations. The controllers provide means of redistributing thrust from load fluctuating thrusters to less load fluctuating ones, and may operate independently of the thrust allocation system. Another solution is also proposed where the load limiting controller based on thrust losses is an integrated part of DP thrust allocation algorithm.

− A new concept of totally integrated thrust allocation system, local thruster control and power system. These systems are integrated through PMS functionality which is contained within each thruster PLC, thereby distributed among individual controllers, and independent of the communications and dedicated controllers.

− Observer-based inertial controller and direct torque-loss controller (soft anti-spin controller) with particular attention to the control of machine wear-out rate. These controller contribute to general shaft speed control of electrical thrusters, generators and main propulsion prime movers.

The proposed controllers, estimators and concepts are demonstrated through time-domain simulations performed in MATLAB/SIMULINK. The selected data are typical for the required applications and may differ slightly for the presented cases.

Mathematical models for an All Electric Ship component library is developed in this thesis. The main motivation for writing this thesis is to develop a model library that gives the opportunity to simulate both existing and new machinery systems without having to remodel the entire system each time. The model library should support the process of modeling and reuse, and also emphasize openness to brace the modeler during the development and refinement phase. The bond graph approach is good when it comes to physical modeling of systems, it is a good tool for combining different energy domains and it may help understanding the system. In addition, bond graph is a powerful method to find dependencies between different components. By using causal analysis any problems in the model, e.g. algebraic constrains or dependent system variables will be detected, and necessary remodeling may be performed to handle such problems. The bond graph approach is therefore used when developing the component library. The component library consists of selected power producers like diesel and gas engines, fuel cell and synchronous generator, and power consumers like asynchronous motor with voltage source converter and generic load used for hotel and auxiliary loads. The library also consist of a ship model, propeller and environmental loads. Most of the components have been verified using test measurements from manufacturer and full scale measurements from a supply vessel operating in the North Sea. The main contributions of the thesis are: • Development of a flexible component library used for modeling and simulation of existing and new marine power plants. • Component models are verified using test measurements performed by manufacturer and full-scale measurements from a supply-vessel. • Simulation of selected cases of combined power plants during extreme dynamic loads are conducted. • Development of a hybrid causality generator model for increased flexibility when simulating combined power plants. The library components are developed using 20Sim. 20Sim is also used for time domain simulation of the power plant test cases.

The thesis deals with systems consisting of marine cables and subsea units. Such systems have wide applications in offshore subsea operations. After a general introduction, the thesis sets out to analyse both the static and dynamic behaviours of the system under various environmental and operational conditions. It endeavours to pursue a fundamental approach in order to reveal the basic characteristics of the system, in addition to developing numerical algorithms for predicting performance. The analysis of behaviour of marine cables consists of the following parts: Statics A semi-analytic approach is developed to predict the equilibrium configurations of marine cables. One-dimensional dynamics Using a coordinate transformation, the method can predict the unsteady dynamic behaviour of systems where the length of cable varies. Two-dimensional dynamics The methodology adopted in the one-dimension analysis is extended to a more general case. Three-dimensional dynamics An alternative approach based upon a lumped mass model is developed. Mathematical analysis reveals many interesting characteristics of the model. By applying modern control theory, a novel heave compensation mechanism is developed for marine systems of cables and subsea units. This mechanism involves an actively controlled winch system. A framework of optimal stochastic control is outlined for integrating all the elements of surface supported subsea operations. The thesis presents a variety of numerical examples in domenstrating the validity of the approaches adopted, along with discussions. Further developments are also recommended.

CIVINS
Approved for public release, distribution unlimited
This project utilized both shore-based and shipboard commercial marine radar technology to collect wave statistics. In the first application a shore-based system was installed at Yaquina Bay in Newport, Oregon in order to collect real-time wave information. This information was collected under the auspices of the Northwest Association of Networked Ocean Observing Systems (NANOOS) and will be used in ongoing studies on wave-current interaction. In the second application, a shipboard radar system was utilized to develop processing procedures and algorithms for collecting offshore wave data. These shipboard collections were in support of the environmental baseline study of the Reedsport Wave Energy Site, funded by the Oregon Wave Energy Trust (OWET).