The biosynthesis of DMSP by phytoplankton and algae has wide ranging impact on marine organisms. Release of DMSP and uptake by marine bacteria leads to the eventual catabolism of this osmolyte. Enzymatic breakdown of DMSP leads to acrylate and volatile DMS production, which is fluxed into the atmosphere. When DMS enters the atmosphere it undergoes oxidation, acting as nucleation sites for water. The nucleation of water, and the subsequent cloud formation increases the albedo and reflects solar radiation. Global climate has therefore been hypothesized to be dependent upon DMSP breakdown to DMS. The enzymatic production of acrylate is also of interest for industrial applications. Only six enzymes are known to act as a DMSP-lyase, causing the production of DMS. These enzymes are still being discovered, and until recently there was very limited analysis of the biochemical requirements for catalysis. The work presented here investigates these requirements and the structural properties that permit the elimination reaction yielding DMS.

Cupins are a large superfamily of enzymatic and non-enzymatic members that contain a conserved β-barrel domain, or double-stranded β-helix (DSBH) fold. The cupin superfamily is one of the most functionally diverse groups of proteins known to exist. The vast majority of cupins contain a mononuclear metal binding site at the core of the DSBH fold capable of binding different metal ions. One of the largest cupin subfamilies is known as the Fe(II)/α-ketoglutarate (αKG)-dependent dioxygenases. Prolyl 4-hydroxylases (P4Hs) belong to the group of Fe(II)/αKG-dependent dioxygenases and catalyze the formation of 4R-hydroxyproline (Hyp) from various proline-containing substrates. The formation of Hyp is an important post-translational modification to many different proteins involved in essential biochemical pathways. Abnormalities in these pathways can lead to diseases such as cancer, fibrosis, respiratory issues, scurvy, and stroke. An Fe(II)/αKG-dependent prolyl hydroxylase from Bacillus anthracis (BaP4H) was investigated to understand its substrate recognition ability and catalytic properties. Novel crystal structures were solved that revealed conformational changes upon substrate binding and key interactions of various ligands in the active site for different catalytic steps. Although the majority of cupin family enzymes catalyze a reaction using iron as an essential cofactor, other metal cofactors can allow the diverse biological transformations carried out by this group of enzymes. A class of enzymes known as dimethylsulfoniopropionate (DMSP) lyases uses different metal ions to catalyze the formation of acrylate and dimethylsulfide (DMS) from DMSP. DMSP is one of the most prevalent and significant molecules to the life and biogeochemistry of the oceans. The products DMS and acrylate are environmentally significant and industrially valuable. DMSP is predominantly catabolized by marine bacteria and can serve different functions. One of the most abundant bacteria in the ocean, Pelagibacter, was determined to contain a DMSP lyase DddK. The DddK catalyzed DMSP lyase activity in the presence of different metal ions has shown that it catalytically prefers Ni(II) compared to other transition metal ions examined. Spectroscopic, site-directed mutagenesis, and crystallographic studies illustrate central residues responsible for metal ion binding and possible roles in transition state stabilization. A greater mechanistic understanding of DMSP lyases will lead to more impactful information about global environmental climate regulation.

During magnetically disturbed periods, the spatially and temporally structured electron precipitation in the auroral zone creates a significant population of thermal secondary ions. Acceleration mechanisms exist that are capable of energizing the thermal population to suprathermal energies (1 eV to 1 keV). Suprathermal ions escape into the magnetosphere and undergo "bounce" motion along magnetic field lines. These ions are bound to the magnetic flux tubes, which undergo ExB convective drift within the magnetosphere. Magnetospheric convection transports flux tubes of bouncing suprathermal ions through the auroral zone and the subauroral polarization stream (SAPS) regions. Precipitating suprathermal ions enhance ionospheric plasma density structure and constitute a possible source for the enhanced echo occurrence observed by ground-based radars in the SAPS region. Satellite energy spectrometer data often show multiple bands of suprathermal particles with enhanced number and energy flux, and with an energy increase with increasing latitude. The present work examines the hypothesis that these signatures are the result of thermal secondary ions that have been accelerated out of the auroral ionosphere over the short time scales characterizing bursts of intense auroral electron precipitation. The analysis of three events of energy-dispersed ion signatures was facilitated by three-dimensional ion tracing software developed for this thesis. The short-lived acceleration hypothesis can account for the energy-dispersed ion signatures if there exist inter-hemispheric field aligned potentials of the order of 100 V. If the source of the ions is within the auroral zone, the suprathermal ions observed in the SAPS region are most likely to be O+ ions. The long bounce period of O+ (compared to H+) allows convection to transport O+ auroral ions equatorward through a convection reversal, into the SAPS region during a single half-bounce.

During magnetically disturbed periods, the spatially and temporally structured electron precipitation in the auroral zone creates a significant population of thermal secondary ions. Acceleration mechanisms exist that are capable of energizing the thermal population to suprathermal energies (1 eV to 1 keV). Suprathermal ions escape into the magnetosphere and undergo "bounce" motion along magnetic field lines. These ions are bound to the magnetic flux tubes, which undergo ExB convective drift within the magnetosphere. Magnetospheric convection transports flux tubes of bouncing suprathermal ions through the auroral zone and the subauroral polarization stream (SAPS) regions. Precipitating suprathermal ions enhance ionospheric plasma density structure and constitute a possible source for the enhanced echo occurrence observed by ground-based radars in the SAPS region. Satellite energy spectrometer data often show multiple bands of suprathermal particles with enhanced number and energy flux, and with an energy increase with increasing latitude. The present work examines the hypothesis that these signatures are the result of thermal secondary ions that have been accelerated out of the auroral ionosphere over the short time scales characterizing bursts of intense auroral electron precipitation. The analysis of three events of energy-dispersed ion signatures was facilitated by three-dimensional ion tracing software developed for this thesis. The short-lived acceleration hypothesis can account for the energy-dispersed ion signatures if there exist inter-hemispheric field aligned potentials of the order of 100 V. If the source of the ions is within the auroral zone, the suprathermal ions observed in the SAPS region are most likely to be O+ ions. The long bounce period of O+ (compared to H+) allows convection to transport O+ auroral ions equatorward through a convection reversal, into the SAPS region during a single half-bounce.

Le Dimethylsulfoniopropionate (DMSP) est une molécule à fort impact écologique couramment produite par le phytoplancton marin, mais très rarement chez les plantes à fleurs: seulement chez quelques genres (dont Spartina chez les Poacées). Bien que les étapes enzymatiques impliquées dans la voie de biosynthèse du DMSP soient connues chez les spartines, son origine ainsi que les gènes impliqués restent encore à découvrir chez les plantes. Cette étude s’est fixée pour objectif de contribuer à élucider les mécanismes à l’origine de cette fonction chez les spartines. Cette question a été appréhendée à travers différentes approches : biochimique, métabolomique, transcriptomique, génomique comparative et phylogénétique. Les résultats ont montré que la capacité à synthétiser le DMSP a une origine unique au sein du genre Spartina et se serait mise en place il y a 3-10 millions d’années. Cette capacité est intervenue chez l’ancêtre d’un des deux principaux clades (hexaploïde) de spartines, puis a été héritée chez toutes les espèces dérivant de ce clade (hexaploïdes à dodécaploïdes). Les espèces de l’autre clade (tétraploïde) et leurs descendants (quel que soit leur niveau de ploïdie) n’accumulent pas de DMSP. En utilisant les génomes séquencés des espèces de Poacées ainsi que les ressources génomiques et transcriptomiques disponibles chez les spartines, les gènes candidats intervenant dans les 4 étapes de la voie de biosynthèse proposée dans la littérature ont été explorés. L’identification des gènes intervenant dans les deux étapes intermédiaires, supposées spécifiques de la capacité de synthèse du DMSP représente un véritable défi dans la mesure où seules des activités enzymatiques putatives ont été proposées à ce jour (sans connaissance des enzymes spécifiques ni de leur séquence protéique). Nous avons pu identifier une série de gènes candidats pour chacune des deux fonctions concernées (décarboxylase et amine oxydase), comparer leur niveau de transcription entre les espèces DMSP+ et DMSP-, et prédire leur localisation cellulaire. De plus, des analyses d’activités enzymatiques ont permis de formuler de nouvelles hypothèses et pistes de recherches sur l’émergence de cette nouvelle voie de biosynthèse chez les spartines. / Dimethylsulfoniopropionate (DMSP) is an ecologically important molecule produced by most marine phytoplankton species, but very rarely by flowering plants: only in a few genera (including Spartina in Poaceae). Despite the different enzymatic steps involved in DMSP biosynthesis are well known, the origin of the function and the genes encoding the different enzymes are yet to be discovered. To explore the evolutionary mechanisms involved in the DMSP accumulation in Spartina, we used various approaches, including biochemical analyses, metabolomics, transcriptomics, comparative genomics and phylogenetics. Notably, we demonstrate that the ability to synthesize DMSP evolved once in the Spartina genus, sometimes 3-10 million years ago. This functional innovation occurred following the emergence of the hexaploid clade, and was inherited by all Spartina species deriving from this hexaploid ancestor. Spartina species belonging to the tetraploid clade and their deriving species do not accumulate DMSP (whatever their ploidy level). Using Poaceae sequenced genomes as well as Spartina genomic and transcriptomic resources obtained in our laboratory, candidate genes involved in the four different enzymatic steps of the DMSP biosynthesis pathway were searched. Identifying genes involved in the intermediate (2nd and 3rd) steps that are specific to this pathway was particularly challenging as only putative enzymatic activities have been proposed so far (corresponding protein sequences and genes are unknown). A set of candidate genes potentially involved in these two steps (with decarboxylase and amine oxydase activities) were identified and their transcription levels were compared among DMSP producing (DMSP+) and non-producing (DMSP-) Spartina species. Their putative cellular localization was also predicted. Moreover, enzymatic activity assays open new hypotheses and research perspectives regarding this enigmatic biosynthesis pathway in Spartina.

This thesis deals with the problem of light pollution. In the theoretical part it brings description of the types of light pollution, effects on organisms, information about remote sensing and characteristics of satellites which are used to map light pollution. Time composition images from DMSP satellites (F10-F18) are processed in the practical part. Changes in light intensity for the period 1992 to 2013 are described using these images. During visual assessment the most noticeable changes were obvious when comparing 1992 and 2013, when significant growth of light pollution was especially visible around cities. Statistical evaluation showed increasing values in the categories which contain higher DN (digital number) value. This increase also represents a shift to a higher light intensity level. The results suggest that light pollution in the Czech Republic tends to grow.

The boundaries of the cities are not immutable, they can be changed. With the development of the economies and societies, the population and pollution of cities are increasing. Some urban areas are expanding with more population or other dynamics of urbanization, while other urban areas are reducing with the changing of the dynamics. Therefore, detecting urban areas or delineating the boundaries of the cities is one of the most important steps for urban studies, which is closely related to human settlements and human activities. Remote sensing data (RS) is widely used to monitor and detect land use and land cover on the surface of the earth. But the extraction of urban areas from the ordinary RS data is not easy work. The Operational Linescan System (OLS) is the sensors of the Defense Meteorological Satellite Program (DMSP). The nighttime lights from the DMSP/OLS provide worldwide remotely sensed data to analyze long-term light emissions which are closely related to human activities. But the nighttime lights imagery data contains inherent errors. Therefore, the approaches to calibrate the data and extract the urban areas from the data are complicated. The long-term objective of this thesis is to delineate the boundaries of the natural cities of the continental United States of America (USA) from 1992 to 2010 of nightlight imagery data with all the different satellites. In this thesis, the coefficients for the intercalibration of the nightlight imagery data have been calculated based on the method developed by Elvidge, et al. (2009), but the coefficients are new and available. The approach used to determine the most appropriate threshold value is very important to eliminate the possible data error. The method to offset this possible error and delineate the boundaries of the cities from nightlight imagery data is the head/tail breaks classification, which is proposed by Jiang (2012b). The head/tail breaks classification is also useful for finding the ht-index of the extracted natural cities which is developed by Jiang and Yin (2013). The ht-index is an indicator of the underlying hierarchy of the data. The results of this study can be divided into two categories. In the first, the achieved coefficients for the intercalibration of nightlight images of the continental USA are shown in a table, and the achieved data of the urban areas are stored in a data archive. In the second, the different threshold values of the uncalibrated images and the individual threshold value of the calibrated images are shown in tables, and the results of the head/tail breaks classification and power law test are also drawn. The results show that the acquired natural cities obey the power law distribution. And the results also confirm that the head/tail breaks classification is available for finding a suitable threshold value for the nightlight imagery data. Key words: cities’ boundaries; DMSP/OLS; head/tail breaks classification; nighttime lights; power law; urban areas

Coccolithophores are single-celled marine phytoplankton, which produce intricate calcium carbonate platelets or ‘coccoliths’. Emiliania huxleyi is the most abundant and widespread coccolithophore, and is one of the most productive calcifying species on earth, playing a key role in global carbon, carbonate and sulphur cycles. Despite much research into coccolithophore biology, the underlying function of their coccoliths is still unknown. The main aim of the research reported in this thesis was to examine the impact of calcification on metabolism in coccolithophores. Calcification is a significant global process, so it is important to discover what effect it has on the metabolism of cells. The major metabolites each have different costs and benefits to the cell, which will vary depending on the habitat and environmental conditions the cell is in. By comparing the metabolite profiles of different strains, including calcifying, non-calcifying, haploid and diploid cells, differences in metabolite composition and potential patterns related to cell type were investigated. Low molecular weight (LMW) metabolites were characterised using a combination of metabolomic techniques. In agreement with previous research, dimethylsulphoniopropionate (DMSP) was the most abundant compound, followed by mannitol and glycine betaine (GBT). Less abundant sugars, polyols and amino acids were also identified. Environmental factors were manipulated to investigate how the principal metabolites were affected by salinity, different light intensities and nutrient (phosphate and nitrate) limitation. The data revealed a striking difference between haploid and diploid cells of the same strain, with the haploid containing lower concentrations of most of the major metabolites. Thus it is proposed that haploid cells have a different osmoregulatory strategy from the diploid cells. A negative correlation was found between DMSP and mannitol, suggesting that mannitol has a dual function, not only as a major storage compound but also as a principal compatible solute. Untargeted metabolite profiling is becoming a popular tool to investigate phenotypes and varying environmental conditions. LC-ESI-QTOF-MS/MS analyses of a wide range of metabolites showed that it is an effective method to identify differences and similarities between E. huxleyi strains grown in different conditions. Strain and growth phase appear to be the more important factors in differentiating metabolite profiles. Surprisingly there were no obvious metabolite profiling differences between calcifying and non-calcifying cells. Untargeted analysis can, however, be used to identify the compounds that did display differences, and which may be important biomarkers, so warrant further investigation. A range of metabolite profiling techniques highlighted important differences between strains, which will hopefully lead onto further research into the metabolome of E. huxleyi, and the unravelling of important metabolic pathways. There has been little research into the LMW metabolites of E. huxleyi, and especially comparisons between strains. Thus the use of metabolomics is a novel way to investigate the difference between cell types and the possible functions of calcification.

This thesis has two focuses. The major focus is an investigation of the nature of high-velocity ~2 km/s)ionospheric flows occasionally detected by the King Salmon SuperDARN radar at relatively low magnetic latitudes of 65^0. The second focus is a validation work on the quality of SuperDARN convection measurements. As an alternative convection-monitoring instrument, an ion drift meter onboard the DMSP satellite was chosen for comparison with SuperDARN. This study includes a broad range of velocities of up to ~1.5 km/s. Consideration of very large velocities is fundamentally important for successful research on the major topic of the thesis.<p>The validation work is performed first. Two approaches are undertaken. The first approach considers data at the raw level. SuperDARN F region line-of-sight velocities are directly compared with DMSP cross-track ion drifts in approximately the same directions. More than 200 satellite passes over the fields of view of five Northern Hemisphere and four Southern Hemisphere radars are considered. It is shown that all radars exhibit overall consistency with DMSP measurements and a linear fit line to the data has a slope of 0.8 with a tendency for SuperDARN velocities to be smaller. Radar echo range effects and the role of spatial inhomogeneity and temporal variations of the convection pattern are investigated. SuperDARN convection maps were generated for select events for which SuperDARN l-o-s data agree almost ideally with DMSP measurements.<p>Convection maps were obtained using all Northern Hemisphere SuperDARN radars. The full convection vectors were found to be in reasonable agreement with the DMSP ion drifts, although a small deterioration (~10%) was noticed. The overall agreement between SuperDARN and DMSP measurements implies SuperDARN observations are reliable for velocity magnitudes of up to ~1.5 km/s, and SuperDARN radars are suitable instruments for studying extremely fast ionospheric flows. These results also imply that radar measurements can be merged with DMSP measurements into a common data set to provide more reliable convection maps.<p>For the main focus of the thesis, a statistical investigation of the King Salmon radar echoes was performed to determine typical echo characteristics and compare them with data from other SuperDARN radars. It is shown that King Salmon regularly observes high-velocity echoes in the dusk sector at ~21:00 MLT and ~65^0 MLat. Individual events are presented with line-of-sight velocities (observed with the L-shell aligned beams) as high as 2 km/s. Statistically, the enhanced flows are the largest and cover the greatest area in the winter and are the smallest and cover the least area in the summer. Similar fast flows were discovered in the Unwin radar data (in the Southern Hemisphere, lowest magnetic latitude ~57^0) that became available near the completion time of this thesis. It is also shown that statistically, the Stokkseyri radar, which observes in the auroral zone and has a similar azimuthal orientation as King Salmon, does not observe similar high-velocity echoes. Geophysical conditions for the onset of high-velocity King Salmon flows in several individual events are then investigated. It is shown that fast flows are excited in close association with substorm progression near the King Salmon field of view. By comparing SuperDARN data with optical images obtained from the IMAGE satellite and particle data from the DMSP satellites it is shown that velocity enhancement begins at substorm onset and peaks 20-50 minutes later over a range of latitudes including the auroral and sub-auroral regions. During the substorm recovery phase, as bright aurora shifts poleward, exceptionally fast flows can be excited at the equatorial edge of the electron auroral oval and these flows can be classified as sub-auroral polarization stream (SAPS) flows. Variability of SAPS flows and their relationship to auroral oval processes are discussed. Finally, several suggestions for further research are presented.

This thesis has two focuses. The major focus is an investigation of the nature of high-velocity ~2 km/s)ionospheric flows occasionally detected by the King Salmon SuperDARN radar at relatively low magnetic latitudes of 65^0. The second focus is a validation work on the quality of SuperDARN convection measurements. As an alternative convection-monitoring instrument, an ion drift meter onboard the DMSP satellite was chosen for comparison with SuperDARN. This study includes a broad range of velocities of up to ~1.5 km/s. Consideration of very large velocities is fundamentally important for successful research on the major topic of the thesis.<p>The validation work is performed first. Two approaches are undertaken. The first approach considers data at the raw level. SuperDARN F region line-of-sight velocities are directly compared with DMSP cross-track ion drifts in approximately the same directions. More than 200 satellite passes over the fields of view of five Northern Hemisphere and four Southern Hemisphere radars are considered. It is shown that all radars exhibit overall consistency with DMSP measurements and a linear fit line to the data has a slope of 0.8 with a tendency for SuperDARN velocities to be smaller. Radar echo range effects and the role of spatial inhomogeneity and temporal variations of the convection pattern are investigated. SuperDARN convection maps were generated for select events for which SuperDARN l-o-s data agree almost ideally with DMSP measurements.<p>Convection maps were obtained using all Northern Hemisphere SuperDARN radars. The full convection vectors were found to be in reasonable agreement with the DMSP ion drifts, although a small deterioration (~10%) was noticed. The overall agreement between SuperDARN and DMSP measurements implies SuperDARN observations are reliable for velocity magnitudes of up to ~1.5 km/s, and SuperDARN radars are suitable instruments for studying extremely fast ionospheric flows. These results also imply that radar measurements can be merged with DMSP measurements into a common data set to provide more reliable convection maps.<p>For the main focus of the thesis, a statistical investigation of the King Salmon radar echoes was performed to determine typical echo characteristics and compare them with data from other SuperDARN radars. It is shown that King Salmon regularly observes high-velocity echoes in the dusk sector at ~21:00 MLT and ~65^0 MLat. Individual events are presented with line-of-sight velocities (observed with the L-shell aligned beams) as high as 2 km/s. Statistically, the enhanced flows are the largest and cover the greatest area in the winter and are the smallest and cover the least area in the summer. Similar fast flows were discovered in the Unwin radar data (in the Southern Hemisphere, lowest magnetic latitude ~57^0) that became available near the completion time of this thesis. It is also shown that statistically, the Stokkseyri radar, which observes in the auroral zone and has a similar azimuthal orientation as King Salmon, does not observe similar high-velocity echoes. Geophysical conditions for the onset of high-velocity King Salmon flows in several individual events are then investigated. It is shown that fast flows are excited in close association with substorm progression near the King Salmon field of view. By comparing SuperDARN data with optical images obtained from the IMAGE satellite and particle data from the DMSP satellites it is shown that velocity enhancement begins at substorm onset and peaks 20-50 minutes later over a range of latitudes including the auroral and sub-auroral regions. During the substorm recovery phase, as bright aurora shifts poleward, exceptionally fast flows can be excited at the equatorial edge of the electron auroral oval and these flows can be classified as sub-auroral polarization stream (SAPS) flows. Variability of SAPS flows and their relationship to auroral oval processes are discussed. Finally, several suggestions for further research are presented.