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Investigating the environmental conditions that drive mercury methylation in freshwater systemsKhairallah, Anthony January 2024 (has links)
Methylmercury (MeHg) is a hazardous neurotoxin that bioaccumulates throughout the food web, which is converted from inorganic mercury (Hg) by microorganisms in oxygen-deprived (hypoxic, or anoxic) conditions. Climate change challenges the ability to limit Hg methylation in the environment since increasing temperatures are predicted to increase the prevalence of hypoxic and anoxic conditions in water columns. My Master thesis project aimed to investigate the diversity, abundance, composition, and structure of Hg-methylating communities to tie together the influence of environmental conditions. To do so, I used bioinformatic tools to analyze a dataset containing freshwater environmental DNA sequences from a broad diversity of metagenomes. The dataset was collected in tandem with environmental metadata (e.g., oxygen) which was used to compare the abundance of one of the two Hg-methylating genes; hgcA. I found that the majority of hgcA genes came from metagenomes collected in hypoxic and anoxic water layers. Interestingly, certain metagenomes in hypoxic and anoxic water layers did not contain any hgcA genes and thus potentially no Hg methylators. Some hgcA genes were found in metagenomes from oxic water layers, which could be explained by settling particles originating from the sediment-water interface acting as oxygen deprived niches. These findings are crucial as they imply that the anticipated changes in freshwater oxygenation, resulting from climate change, will lead to increased niches for Hg-methylating microorganisms. Particularly, increasing algal blooms and persistent lake stratification leads to more deoxygenated water columns, which explains why MeHg can become an increasing hazard to animal and human well-being.
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Μελέτη της υδροδυναμικής, της τροφικότητας και της υποξίας ενός κλειστού Μεσογειακού κόλπου (Αμβρακικός)Κουντουρά, Κρυσταλλία 26 August 2014 (has links)
Αναφορές για την υποξία ή ακόμη και την ανοξία, υπήρχαν παγκοσμίως σε όλη τη διάρκεια των γεωλογικών ετών. Ωστόσο, η αρνητική τάση της συγκέντρωσης του οξυγόνου στις θάλασσες, που καταγράφεται μετά το 1950, σε συνδυασμό με τις αυξημένες διαστάσεις που λαμβάνει καθημερνά η υποξία, αλλά και τις δυσοίωνες προβλέψεις για ετήσια μελλοντική μείωση των συγκεντρώσεων του οξυγόνου, έχουν οδηγήσει στο χαρακτηρισμό της ως ένα παγκόσμιο πρόβλημα.
Ο συνδυασμός φυσικών και ανθρωπογενών διεργασιών, αλλά και οι αρνητικές επιδράσεις του ευτροφισμού, ως αποτέλεσμα της παροχής μεγάλων ποσοτήτων θρεπτικών αλάτων αζώτου και φωσφόρου, σχετίζονται άμεσα με την παγκόσμια αύξηση των υποξικών περιοχών. Ανάμεσα στα πιο επιρρεπή περιβάλλοντα στην εμφάνιση υποξικών/ανοξικών συνθηκών είναι οι ημί-κλειστοι κόλποι. Η επικράτηση ή ακόμη και η εκδήλωση υποξικών συνθηκών σε ένα τέτοιο περιβάλλον, εκτός από την αρνητική επίδραση που έχει στους οργανισμούς και τα ενδιαιτήματά τους, επηρεάζει άμεσα αφενός την τροφική αλυσίδα και αφετέρου τις βιογεωχημικές διεργασίες που λαμβάνουν χώρα στο εσωτερικό του.
Ο Αμβρακικός Κόλπος, αποτελεί ένα χαρακτηριστικό παράδειγμα ημί-κλειστου κόλπου, τύπου φιόρδ, στη Μεσόγειο, εφόσον το μοναδικό σημείο επικοινωνίας του με την ανοιχτή θάλασσα είναι ο στενός δίαυλος του Ακτίου. Παρά τη σημαντικότητα του συγκεκριμένου περιβάλλοντος, η εξέλιξη και η ανάπτυξη του ανθρώπινου παράγοντα, έχουν οδηγήσει το οικοσύστημα του κόλπου σε ιδιαίτερα οριακό σημείο, υποβαθμίζοντας συνεχώς την ποιότητα των υδάτων του.
Σκοπό της συγκεκριμένης διδακτορικής διατριβής, αποτέλεσε η παρακολούθηση, κατανόηση και ερμηνεία του τρόπου λειτουργίας ενός Μεσογειακού κλειστού κόλπου, συμπεριλαμβανομένης της υδροδυναμικής κυκλοφορίας και των φυσικοχημικών διεργασιών που λαμβάνουν χώρα στο εσωτερικό του, καθώς επίσης και η ανάδειξη της δυναμικής και του μηχανισμού δημιουργίας της υποξικής/ανοξικής ζώνης που χαρακτηρίζει ένα τέτοιο περιβάλλον.
Για την επίτευξη των προαναφερθέντων, πραγματοποιήθηκε συστηματική παρακολούθηση των φυσικοχημικών, ωκεανογραφικών και μετεωρολογικών χαρακτηριστικών του συστήματος του Αμβρακικού, μέσω μιας σειράς εποχιακών και διμηνιαίων δειγματοληψιών, συνολικής διάρκειας δύο ετών. Επιπρόσθετα, για τις ανάγκες της μελέτης της υδροδυναμικής κυκλοφορίας του κόλπου, προσομοιώθηκε η κυκλοφορία του, χρησιμοποιώντας ένα κατάλληλο τρισδιάστατο αριθμητικό ομοίωμα. Η βαθμονόμηση, η επαλήθευση και η προσομοίωση της υδροδυναμικής του Αμβρακικού, πραγματοποιήθηκε χρησιμοποιώντας δεδομένα, τα οποία και συλλέχθηκαν κατά τη διάρκεια των διετών δειγματοληψιών.
Η μόνιμη στρωμάτωση της υδάτινης στήλης του κόλπου, σε όλη τη διάρκεια του έτους, ως αποτέλεσμα της παροχής μεγάλων ποσοτήτων γλυκού νερού επιφανειακά, σε συνδυασμό με τον εμπλουτισμό της υδάτινης στήλης με θρεπτικά στοιχεία, είναι οι σημαντικότερες διεργασίες οι οποίες οδήγησαν στην περεταίρω υποβάθμιση του συστήματος τα τελευταία τριάντα χρόνια. Τα κύρια χαρακτηριστικά αυτής, είναι η επικράτηση πλέον υποξικών συνθηκών στο μεγαλύτερο τμήμα του κόλπου, καθώς επίσης και η εποχιακή εμφάνιση ανοξικών συνθηκών στο βαθύτερο στρώμα της υδάτινης στήλης.
Η δυναμική της υποξικής ζώνης, η οποία αναπτύσσεται στο εσωτερικό του κόλπου, εκφράζεται μέσω ενός ιδιαίτερα γνώριμου προτύπου κυρίως σε παρόμοια περιβάλλοντα (τύπου φιόρδ) των Σκανδιναβικών χωρών, ωστόσο, σπάνιου ή ακόμη και πρωτόγνωρου για τα Μεσογειακά δεδομένα. Η εισροή των υδάτων της ανοιχτής θάλασσας, η οποία λαμβάνει χώρα σαν ένα ρεύμα, πυκνού νερού κοντά στο πυθμένα, είναι η κύρια αιτία εμπλουτισμού των βαθύτερων στρωμάτων του κόλπου με οξυγόνο. Το γεγονός αυτό έχει ως αποτέλεσμα η υδάτινη στήλη να οξυγονώνεται από τα βαθύτερα προς τα ρηχότερα τμήματα αυτής και ένα στρώμα νερού υποξικών/ανοξικών συνθηκών να επιπλέει σε ενδιάμεσα βάθη.
Η προσομοίωση της ετήσιας υδροδυναμικής κυκλοφορίας του Αμβρακικού, ενός συστήματος με τόσο ιδιαίτερα μορφολογικά και υδρολογικά χαρακτηριστικά, βοήθησε στην κατανόηση και περιγραφή των υδροδυναμικών διεργασιών που λαμβάνουν χώρα ετησίως και ελέγχουν την οξυγόνωση του βαθύτερου τμήματος της υδάτινης στήλης. Ανάμεσα στις πιο σημαντικές συγκαταλέγονται η διαφορά πυκνότητας μεταξύ των υδάτων της ανοιχτής θάλασσας και του βαθύτερου τμήματος του Αμβρακικού, η οποία σε συνδυασμό με την έκταση του πυκνοκλινούς και την παροχή γλυκού νερού από του δύο ποταμούς που εκβάλλουν στο εσωτερικό, ελέγχουν το βάθος της εισροής και κατ’ επέκταση το βαθμό της οξυγόνωσης του βαθύτερου στρώματος του κόλπου.
Από την ολοκληρωμένη παρακολούθηση των χημικών χαρακτηριστικών της υδάτινης στήλης, την εκτίμηση της ποιότητας και της τροφικής κατάστασης των υδάτων του Αμβρακικού, προέκυψε στο συμπέρασμα ότι τελικά ο Αμβρακικός, είναι ένα μεσοτροφικό και εποχιακά ευτροφικό περιβάλλον. Ο ευτροφικός χαρακτήρας του κόλπου, χρονικά συνδέεται άμεσα με την περίοδο των μέγιστων παροχών των ποταμών, υποδεικνύοντας την καθοριστική συμβολή τους στην ποιότητα των υδάτων του κόλπου. / Hypoxic or even anoxic references existed globally throughout the geological age. However, the negative trend of the oxygen concentration is recorded after 1950. This, in combination with the increased dimensions that hypoxia is daily receiving and also ominous predictions for the future annual reduction of its concentrations, have led to the characterization as a global problem.
The combination of natural and anthropogenic processes and also the negative effects of eutrophication as a result of the enrichment with large amounts of nutrients, such as nitrogen and phosphorus, are directly related to the global increase of hypoxic areas. Among the most prone environments in appearance of hypoxic / anoxic conditions are semi-enclosed bays. The dominance or even the appearance of hypoxic conditions in such an environment, apart from the negative impact that it has on organisms and their habitats, directly affects both the food chain and also the biogeochemical processes that take place inside it.
Amvrakikos Gulf, is a characteristic example of semi-enclosed bay, fjord-type, in the Mediterranean Sea, as its only connection with the open sea is the narrow inlet of Aktio. Despite the importance of this environment, the evolution and development of human factors have led the ecosystem of the gulf in particular boundary point, degrading constantly the water quality.
The main purpose of this thesis, has been the monitoring, understanding and interpretation the mode of operation of a Mediterranean semi-enclosed bay, including hydrodynamic circulation and physicochemical processes that take place inside, as well as highlighting of dynamic and forming mechanism of hypoxic / anoxic zone which characterizes such an environment.
In order the above targets to be achieved, a systematic monitoring of physico-chemical, oceanographic and meteorological characteristics of Amvrakikos Gulf takes place, through a series of seasonal and bimonthly samplings, of two years duration. Additionally, for the purposes of the study of hydrodynamic circulation, an appropriate three-dimensional hydrodynamic model was used. The calibration and verification of the hydrodynamic model and the simulation of the hydrodynamic circulation takes place using data, which were collected during the two-year sampling.
The permanent stratification of the water column , throughout the year, as a result of the surface enrichment with large quantities of fresh water ,in combination with the water column' s enrichment with nutrients, are the most important processes which lead to further degradation of the system over the last thirty years. The main characteristics of this degradation are the dominance of hypoxic conditions in the greater part of the gulf, and the seasonal occurrence of anoxic conditions in the deepest layer of the water column.
The dynamics of the hypoxic zone, which grows inside the gulf, expressed through a very familiar pattern mainly in similar environments (fjord-type) of the Scandinavian countries, however, it is rare or even unprecedented for the Mediterranean area. The inflow of waters of the open sea, which occurs as a stream of dense water near the bottom, is the main reason of enrichment of the deepest layers of the bay with oxygen. This has resulted in the water column to be oxygenated from its deepest to the shallowest parts and a water layer with hypoxic / anoxic conditions to be floated at intermediate depths.
The simulation of the annual hydrodynamic circulation of Amvrakikos Gulf, a system with both morphological and hydrological characteristics, helped the understanding and description of hydrodynamic processes that take place annually and monitor the oxygenation of the deepest parts of the water column. Among the most important processes are included the density difference between the waters of the open sea and the deepest part of Amvrakikos Gulf, which combined with the extent of pycnocline and supply of fresh water from the two rivers that flow inside, control the depth of the input and consequently the degree of oxygenation of the deeper layer of the gulf.
The comprehensive monitoring of the chemical characteristics of the water column, the assess of the quality and trophic status of waters of Amvrakikos Gulf have shown that eventually Amvrakikos Gulf is a mesotrophic and seasonally eutrophic environment. The eutrophic character of the gulf, is directly related to the period of maximum discharges of rivers, indicating the vital contribution to the water quality of the bay.
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Bayesian Statistical Analysis in Coastal Eutrophication Models: Challenges and SolutionsNojavan Asghari, Farnaz January 2014 (has links)
<p>Estuaries interfacing with the land, atmosphere and open oceans can be influenced in a variety of ways by anthropogenic activities. Centuries of overexploitation, habitat transformation, and pollution have degraded estuarine ecological health. Key concerns of public and environmental managers of estuaries include water quality, particularly the enrichment of nutrients, increased chlorophyll a concentrations, increased hypoxia/anoxia, and increased Harmful Algal Blooms (HABs). One reason for the increased nitrogen loading over the past two decades is the proliferation of concentrated animal feeding operations (CAFOs) in coastal areas. This dissertation documents a study of estuarine eutrophication modeling, including modeling of major source of nitrogen in the watershed, the use of the Bayesian Networks (BNs) for modeling eutrophication dynamics in an estuary, a documentation of potential problems of using BNs, and a continuous BN model for addressing these problems.</p><p>Environmental models have emerged as great tools to transform data into useful information for managers and policy makers. Environmental models contain uncertainty due to natural ecosystems variability, current knowledge of environmental processes, modeling structure, computational restrictions, and problems with data/observations due to measurement error or missingness. Many methodologies capable of quantifying uncertainty have been developed in the scientic literature. Examples of such methods are BNs, which utilize conditional probability tables to describe the relationships among variables. This doctoral dissertation demonstrates how BNs, as probabilistic models, can be used to model eutrophication in estuarine ecosystems and to explore the effects of plausible future climatic and nutrient pollution management scenarios on water quality indicators. The results show interaction among various predictors and their impact on ecosystem health. The synergistic eftects between nutrient concentrations and climate variability caution future management actions.</p><p>BNs have several distinct strengths such as the ability to update knowledge based on Bayes' theorem, modularity, accommodation of various knowledge sources and data types, suitability to both data-rich and data-poor systems, and incorporation of uncertainty. Further, BNs' graphical representation facilitates communicating models and results with environmental managers and decision-makers. However, BNs have certain drawbacks as well. For example, they can only handle continuous variables under severe restrictions (1- Each continuous variable be assigned a (linear) conditional Normal distribution; 2- No discrete variable have continuous parents). The solution, thus far, to address this constraint has been discretizing variables. I designed an experiment to evaluate and compare the impact of common discretization methods on BNs. The results indicate that the choice of discretization method severely impacts the model results; however, I was unable to provide any criteria to select an optimal discretization method.</p><p>Finally, I propose a continuous variable Bayesian Network methodology and demonstrate its application for water quality modeling in estuarine ecosystems. The proposed method retains advantageous characteristics of BNs, while it avoids the drawbacks of discretization by specifying the relationships among the nodes using statistical and conditional probability models. The Bayesian nature of the proposed model enables prompt investigation of observed patterns, as new conditions unfold. The network structure presents the underlying ecological ecosystem processes and provides a basis for science communication. I demonstrate model development and temporal updating using the New River Estuary, NC data set and spatial updating using the Neuse River Estuary, NC data set.</p> / Dissertation
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Functions of GluN2D-containing NMDA receptors in dopamine neurons of the substantia nigra pars compactaMorris, Paul George January 2018 (has links)
Dopamine (DA) neurons of the substantia nigra pars compacta (SNc) have a key role in regulation of voluntary movement control. Their death is a hallmark of Parkinson’s disease, characterised by inhibited motor control, including muscle rigidity and tremor. Excitatory input to SNc-DA neurons is primarily from the subthalamic nucleus, and in PD these afferents display a higher frequency firing, as well as increased burst firing, which could cause increased excitatory activity in SNc-DA neurons. NMDA receptors (NMDARs) bind the excitatory neurotransmitter glutamate, and are essential for learning and memory. In SNc-DA neurons, NMDARs have a putative triheteromeric subunit arrangement of GluN1 plus GluN2B and/or GluN2D. Wild type (WT) mice, and those lacking the gene for GluN2D (Grin2D-null), were used to explore its role in various aspects of DA neuronal function and dysfunction using patch-clamp electrophysiology, viability assaying, and immunofluorescence. Pharmacological intervention using subunit-specific inhibitors ifenprodil and DQP-1105 on elicited NMDAR-EPSCs suggested a developmental shift from primarily GluN2B to GluN2B/D. Activity dependent regulation was assessed by high frequency burst stimulation of glutamatergic afferents: in comparison to controls, significant downregulation of NMDARs was observed in SNc-DA neurons, though no differences were observed based on genotype. This regulatory function may be a neuroprotective or homeostatic response. Ambient extracellular glutamate elicits tonic NMDAR activity in SNc-DA neurons, which may be important for maintaining basal levels of excitability: the role of GluN2D was assessed by recording the deflection in baseline current caused by application of competitive NMDAR antagonist D-AP5. There was a significantly larger NMDAR-mediated current in WT vs Grin2D-null mice, indicating that GluN2D has a role in binding ambient glutamate. Dysfunction of glutamate uptake could be a secondary pathophysiological occurrence in the SNc, leading to increased ambient glutamate: the effect of this was explored by application of the competitive glutamate transporter blocker TBOA. Here, the NMDAR-mediated portion of this current was significantly higher in WT mice in comparison to Grin2D-null. Interestingly, dose-response data obtained from bath application of NMDA showed significantly larger currents in Grin2D-null animals vs WT, but only at the top of the response curve (~1-10 mM), which may indicate a capability for larger conductance in Grin2D-null animals at high NMDAR saturation due to replacement of GluN2D with GluN2B. GluN2D may therefore be neuroprotective, by attenuating peak current flow in response to very high agonist concentrations. Lastly, GluN2D has been found to decrease NMDAR open probability under hypoxic conditions, potentially conferring resistance to hypoxia / ischemia related excitotoxicity. Therefore, low (15% O2 / 80% N2 / 5% CO2) vs high (95% O2 / 5% CO2) oxygen conditions were used along with immunofluorescent propidium iodide cell death assaying and immunofluorescent labeling for DA neurons in order to compare levels of DA neuronal death in the SNc based on oxygen status and genotype. Whilst there was a significant submaximal effect based on O2 status, genotype did not confer a practical resistance under these conditions. In summary, NMDARs have diverse roles in SNc-DA neurons which may both serve to maintain normal function and protect the cell against potentially pathological conditions.
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