Using soil profiles of seeds and molecular markers as proxies for sawgrass and wet prairie slough vegetation in Shark Slough, Everglades National Park

We measured the abundance of Cladium jamaicense (Crantz) seeds and three biomarkers in freshwater marsh soils in Shark River Slough (SRS), Everglades National Park (ENP) to determine the degree to which these paleoecological proxies reflect spatial and temporal variation in vegetation. We found that C. jamaicense seeds and the biomarkers Paq, total lignin phenols (TLP) and kaurenes analyzed from surface soils were all significantly correlated with extant aboveground C. jamaicense biomass quantified along a vegetation gradient from a C. jamaicense to a wet prairie/slough (WPS) community. Our results also suggest that these individual proxies may reflect vegetation over different spatial scales: Paq and kaurenes correlated most strongly (R 2 = 0.88 and 0.99, respectively) with vegetation within 1 m of a soil sample, while seeds and TLP reflected vegetation 0–20 m upstream of soil samples. These differences in the spatial scale depicted by the different proxies may be complementary in understanding aspects of historic landscape patterning. Soil profiles of short (25 cm) cores showed that downcore variation in C. jamaicense seeds was highly correlated with two of the three biomarkers (Paq, R 2 = 0.84, p<0.005; TLP, R 2 = 0.97, p<0.0001), and all four of the proxies indicated a recent increase in C. jamaicense biomass at the site. Using a preliminary depth-to-age relationship based on matching charcoal peaks with available ENP fire records (1980-present) specific to our coring site, we found that peak-depths in C. jamaicense seed concentration appeared to correspond to recent minimum water levels (e.g., 1989 and 2001), and low seed abundance corresponded to high water levels (e.g., 1995), consistent with the known autecology of C. jamaicense. In summary, the combination of C. jamaicense seeds and biomarkers may be useful for paleoecological reconstruction of vegetation change and ultimately in guaging the success of ongoing efforts to restore historic hydrologic conditions in the South Florida Everglades.

Functional genomic and molecular analyses of transcripts related to glycerol synthesis and trafficking in rainbow smelt (Osmerus mordax) using cold temperature-induced models of glycerol production

The rainbow smelt (Osmerus mordax) is an anadromous teleost that produces type II antifreeze protein (AFP) and accumulates modest urea and high glycerol levels in plasma and tissues as adaptive cryoprotectant mechanisms in sub-zero temperatures. It is known that glyceroneogenesis occurs in liver via a branch in glycolysis and gluconeogenesis and is activated by low temperature; however, the precise mechanisms of glycerol synthesis and trafficking in smelt remain to be elucidated. The objective of this thesis was to provide further insight using functional genomic techniques [e.g. suppression subtractive hybridization (SSH) cDNA library construction, microarray analyses] and molecular analyses [e.g. cloning, quantitative reverse transcription - polymerase chain reaction (QPCR)]. Novel molecular mechanisms related to glyceroneogenesis were deciphered by comparing the transcript expression profiles of glycerol (cold temperature) and non-glycerol (warm temperature) accumulating hepatocytes (Chapter 2) and livers from intact smelt (Chapter 3). Briefly, glycerol synthesis can be initiated from both amino acids and carbohydrate; however carbohydrate appears to be the preferred source when it is readily available. In glycerol accumulating hepatocytes, levels of the hepatic glucose transporter (GLUT2) plummeted and transcript levels of a suite of genes (PEPCK, MDH2, AAT2, GDH and AQP9) associated with the mobilization of amino acids to fuel glycerol synthesis were all transiently higher. In contrast, in glycerol accumulating livers from intact smelt, glycerol synthesis was primarily fuelled by glycogen degradation with higher PGM and PFK (glycolysis) transcript levels. Whether initiated from amino acids or carbohydrate, there were common metabolic underpinnings. Increased PDK2 (an inhibitor of PDH) transcript levels would direct pyruvate derived from amino acids and / or DHAP derived from G6P to glycerol as opposed to oxidation via the citric acid cycle. Robust LIPL (triglyceride catabolism) transcript levels would provide free fatty acids that could be oxidized to fuel ATP synthesis. Increased cGPDH (glyceroneogenesis) transcript levels were not required for increased glycerol production, suggesting that regulation is more likely by post-translational modification. Finally, levels of a transcript potentially encoding glycerol-3-phosphatase, an enzyme not yet characterized in any vertebrate species, were transiently higher. These comparisons also led to the novel discoveries that increased G6Pase (glucose synthesis) and increased GS (glutamine synthesis) transcript levels were part of the low temperature response in smelt. Glucose may provide increased colligative protection against freezing; whereas glutamine could serve to store nitrogen released from amino acid catabolism in a non-toxic form and / or be used to synthesize urea via purine synthesis-uricolysis. Novel key aspects of cryoprotectant osmolyte (glycerol and urea) trafficking were elucidated by cloning and characterizing three aquaglyceroporin (GLP)-encoding genes from smelt at the gene and cDNA levels in Chapter 4. GLPs are integral membrane proteins that facilitate passive movement of water, glycerol and urea across cellular membranes. The highlight was the discovery that AQP10ba transcript levels always increase in posterior kidney only at low temperature. This AQP10b gene paralogue may have evolved to aid in the reabsorption of urea from the proximal tubule. This research has contributed significantly to a general understanding of the cold adaptation response in smelt, and more specifically to the development of a working scenario for the mechanisms involved in glycerol synthesis and trafficking in this species.

Developmental and molecular aberrations associated with deterioration of oocytes during FSH-receptor deficiency

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Ionic, cellular and molecular mechanisms underlying the QT prolongation and arrhythmias in diabetic cardiocomplications

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Genetic and Molecular Basis of Encapsulation and Capsule Diversity in Kingella kingae

Kingella kingae is a bacterial pathogen that is increasingly recognized as an etiology of septic arthritis, osteomyelitis, bacteremia, and endocarditis in young children. The pathogenesis of K. kingae disease starts with bacterial adherence to the respiratory epithelium of the posterior pharynx. Previous work has identified type IV pili and a trimeric autotransporter protein called Knh (Kingella NhhA homolog) as critical factors for adherence to human epithelial cells. Additional studies established that the presence of a polysaccharide capsule interferes with Knh-mediated adherence. Given the inhibitory role of capsule during adherence we sought to uncover the genes involved in capsule expression to understand how capsule is elaborated on the cell surface. Additionally, this work aimed to further characterize capsule diversity among K. kingae clinical isolates and to investigate the relationship between capsule type and site of isolation.

We first set out to identify the carbohydrates present in the K. kingae capsule present in the prototype strain 269-492. Glycosyl composition and NMR analysis of surface extractable polysaccharides demonstrated two distinct polysaccharides, one consisting of GalNAc and Kdo with the structure →3)-β-GalpNAc-(1→5)-β-Kdop-(2→ and the other containing galactose alone with the structure →5)-β-Galf-(1→.

To discern the two polysaccharides we disrupted the ctrA gene required for surface localization of the K. kingae polysaccharide capsule and observed a loss of GalNAc and Kdo but no effect on the presence of Gal in bacterial surface extracts. In contrast, deletion of the pamABCDE locus involved in production of a reported galactan exopolysaccharide eliminated Gal but had no effect on the presence of GalNAc and Kdo in surface extracts. These results established that K. kingae strain KK01 produces a polysaccharide capsule with the structure →3)-β-GalpNAc-(1→5)-β-Kdop-(2→ and a separate exopolysaccharide with the structure →5)-β-Galf-(1→.

Having established that K. kingae produces a capsule comprised of GalNAc and Kdo, we next set out to identify the genetic determinants of capsule through a transposon mutagenesis screen. In addition to the previously identified ctrABCD operon, lipA, lipB, and a putative glycosyltransferase termed csaA (capsule synthesis region A gene A) were found to be essential for the production of surface-localized capsule. The ctr operon, lipA, lipB, and csaA were found to be present at unlinked locations throughout the genome, which is atypical for gram-negative organisms that elaborate a capsule dependent on an ABC-type transporter for surface localization. Through examining capsule localization in the ctrA, lipA, lipB, and csaA mutant strains, we determined that the ctrABCD, lipA/lipB, and csaA gene products respectively function in capsule export, assembly, and synthesis, respectively. The GalNAc transferase and Kdo transferase domains found in CsaA further support its role in catalyzing the synthesis of the GalNAc-Kdo capsule in the K. kingae prototype strain.

To investigate the capsule diversity that exists in K. kingae we screened a panel of strains isolated from patients with invasive disease or healthy carriers for the csaA capsule synthesis locus. We discovered that Kingella kingae expresses one of 4 capsule synthesis loci (csa, csb, csc, or csd) associated with a capsule consisting of Kdo and GalNAc (type a), Kdo and GlcNAc (type b), Kdo and ribose (type c), and GlcNAc and galactose (type d), respectively. Cloning of the csa, csb, csc, or csd locus into the empty flanking gene region in a non-encapsulated mutant (creation of an isogenic capsule swap) was sufficient to produce either the type a, type b, or type c capsule, respectively, further supporting the role of these loci in expression of a specific polysaccharide linkage. Capsule type a and capsule type b accounted for 96% of invasive strains. Conversely, capsule type c and capsule type d were found disproportionately among carrier isolates, suggesting that capsule type is important in promoting invasion and dissemination.

In conclusion, we discovered that Kingella kingae expresses a polysaccharide capsule and an exopolysaccharide on its surface that require distinct genetic loci for surface localization. Further investigation into genetic determinants of encapsulation revealed the loci ctrABCD, lipA/lipB, and a putative glycosyltransferase are required for capsule expression, with the gene products having roles in capsule export, assembly, and synthesis, respectively. The putative glycosyltransferase CsaA was determined to be a bifunctional enzyme with both GalNAc-transferase and Kdo-transferase activity. Furthermore, we discovered a total of 4 capsule types expressed in clinical isolates of K. kingae, each with a distinct capsule synthesis locus. The variation in the proportion of capsule types found between invasive strains and carriage strains suggest that capsule type is important in promoting invasion and dissemination. Taken together, this work expands our knowledge of the capsule types expressed among K. kingae carrier and invasive isolates and provides insights into the common genetic determinants of capsule expression. These contributions may lead to selecting clinically relevant capsule types to develop into a capsule based vaccine to prevent K. kingae colonization.

Developmental and molecular aberrations associated with deterioration of oocytes during FSH-receptor deficiency

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Ionic, cellular and molecular mechanisms underlying the QT prolongation and arrhythmias in diabetic cardiocomplications

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Bulk and molecular proxies of sediment core GeoB6518-1

A 20 kyr long sediment sequence from the Congo deep sea fan (core GeoB 6518-1), one of the world's largest deep sea river fans, has been analysed for bulk and molecular proxies in order to reconstruct the marine, soil and plant organic carbon (OC) contributions to these sediments since the last glacial maximum. The bulk proxies applied, C/N ratio and d13Corg, ranged from 10 to 12.5 and from -24.5 to -21 per mill VPDB, respectively. As molecular proxies, concentrations of marine derived alkenones and terrestrial derived odd-numbered n-alkanes were used, which varied between 0.2 and 4 µg/g dry weight sediment. In addition, the branched vs. isoprenoid tetraether (BIT) index, a proxy for soil organic matter input, was used, which varied from 0.3 to 0.5 in this core. Application of binary mixing models, based on the different individual proxies, showed estimates for terrestrial OC input varying by up to 50% due to the heterogeneous nature of the OC. Application of a three end-member mixing model using the d13Corg content, the C/N ratio and the BIT index, enabled the distinction of soil and plant organic matter as separate contributors to the sedimentary OC pool. The results show that marine OC accounts for 20% to 40% of the total OC present in the deep sea fan sediments over the last 20 kyr and that soil OC accounts for about half (45% on average) of the OC present. This suggests that soil OC represents the majority of the terrestrial OC delivered to the fan sediments. Accumulation rates of the plant and soil OC fractions over the last 20 kyr varied by a factor of up to 5, and are strongly related to sediment accumulation rates. They showed an increase starting at ca. 17 kyr BP, a decline during the Younger Dryas, peak values during the early Holocene and lower values in the late Holocene. This pattern matches with reconstructions of past central African humidity and Congo River discharge from the same core and revealed that central African precipitation patterns exert a dominant control on terrestrial OC deposition in the Congo deep sea fan. Marine OC accumulation rates are only weakly related to sediment accumulation rates and vary only little over time compared to the terrigenous fractions. These variations are likely a result of enhanced preservation during times of higher sedimentation rates and of relative small fluctuations in primary production due to wind-driven upwelling.

Polymer Fluid Dynamics: Continuum and Molecular Appoaches

To solve problems in polymer fluid dynamics, one needs the equation of continuity, motion, and energy. The last two equations contain the stress tensor and the heat-flux vector for the material. There are two ways to formulate the stress tensor: (1) one can write a continuum expression for the stress tensor in terms of kinematic tensors, or (2) one can select a molecular model that represents the polymer molecule, and then develop an expression for the stress tensor from kinetic theory. The advantage of the kinetic theory approach is that one gets information about the relation between the molecular structure of the polymers and the rheological properties. In this review, we restrict the discussion primarily to the simplest stress tensor expressions or “constitutive equations” containing from two to four adjustable parameters, although we do indicate how these formulations may be extended to give more complicated expressions. We also explore how these simplest expressions are recovered as special cases of a more general framework, the Oldroyd 8-constant model. The virtue of studying the simplest models is that we can discover some general notions as to which types of empiricisms or which types of molecular models seem to be worth investigating further. We also explore equivalences between continuum and molecular approaches. We restrict the discussion to several types of simple flows, such as shearing flows and extensional flows. These are the flows that are of greatest importance in industrial operations. Furthermore, if these simple flows cannot be well described by continuum or molecular models, then it is not necessary to lavish time and energy to apply them to more complex flow problems.

The adaptive response of humans to exercise: Impact of exercise intensity, fibre-type specific responses and molecular patterns of response

In an attempt to improve the current understanding of the adaptive response to exercise in humans, this dissertation performed a series of studies designed to examine the impact of training intensity and mode on aerobic capacity and performance, fibre-type specific adaptations to training, and individual patterns of response across molecular, morphological and genetic factors. Project #1 determined that training intensity, session dose, baseline VO2max and total training volume do not influence the magnitude of change in VO2max by performing a meta-regression, and meta-analysis of 28 different studies. The intensity of training had no effect on the magnitude of increase in maximal oxygen uptake in young healthy participants, but similar adaptations were achieved with lower training doses following high intensity training. Project # 2 determined the acute molecular response, and training-induced adaptations in aerobic performance, aerobic capacity and muscle phenotype following high-intensity interval training (HIT) or endurance exercise (END). The acute molecular response (fibre recruitment and signal activation) and training-induced adaptations in aerobic capacity, aerobic performance, and muscle phenotype were similar following HIT and END. Project # 3 examined the impact of baseline muscle morphology and molecular characteristics on the training response, and if muscle adaptations are coordinated. The muscle phenotype of individuals who experience the largest improvements (high responders) were lower before training for some muscle characteristics and molecular adaptations were coordinated within individual participants. Project # 4 examined the impact of 2 different intensities of HIT on the expression of nuclear and mitochondrial encoded genes targeted by PGC-1α. A systematic upregulation of nuclear and mitochondrial encoded genes was not present in the early recovery period following acute HIT, but the expression of mitochondrial genes were coordinated at an individual level. Collectively, results from the current dissertation contribute to our understanding of the molecular mechanisms influencing skeletal muscle and whole-body adaptive responses to acute exercise and training in humans.

Energy levels and radiative rates for Cr-like Cu VI and Zn VII

Energy levels and radiative rates (. A-values) for transitions in Cr-like Cu VI and Zn VII are reported. These data are determined in the quasi-relativistic approach (QR), by employing a very large configuration interaction (CI) expansion which is highly important for these ions. No radiative rates are available in the literature to compare with our results, but our calculated energies are in close agreement with those compiled by NIST and other available theoretical data, for a majority of the levels. The A-values (and resultant lifetimes) are listed for all significantly contributing E1, E2 and M1 radiative transitions among the energetically lowest 322 levels of each ion.

Energy levels and radiative rates for transitions in Cr-like Co IV and Ni V

We report calculations of energy levels and radiative rates (A-values) for transitions in Cr-like Co IV and Ni V. The quasi-relativistic Hartree-Fock (QRHF) code is adopted for calculating the data although grasp (general-purpose relativistic atomic structure package) and flexible atomic code (fac) have also been employed for comparison purposes. No radiative rates are available in the literature to compare with our results, but our calculated energies are in close agreement with those compiled by NIST for a majority of the levels. However, there are discrepancies for a few levels of up to 3%. The A-values are listed for all significantly contributing E1, E2 and M1 transitions, and the corresponding lifetimes reported, although unfortunately no previous theoretical or experimental results exist to compare with our data.

Radiative rates for E1, E2, M1, and M2 transitions in S-like to F-like tungsten ions (W LIX to W LXVI)

Calculations of energy levels, radiative rates and lifetimes are reported for eight ions of tungsten, i.e. S-like (W LIX) to F-like (W LXVI). A large number of levels have been considered for each ion and extensive configuration interaction has been included among a range of configurations. For the calculations, the general-purpose relativistic atomic structure package (. grasp) has been adopted, and radiative rates (as well as oscillator strengths and line strengths) are listed for all E1, E2, M1, and M2 transitions of the ions. Comparisons have been made with earlier available experimental and theoretical energies, although these are limited to only a few levels for most ions. Therefore for additional accuracy assessments, particularly for energy levels, analogous calculations have been performed with the flexible atomic code (. fac).

Radiative rates for E1, E2, M1, and M2 transitions in Br-like ions with 43≤Z≤50

Energies and lifetimes are reported for the eight Br-like ions with 43≤Z≤50, namely Tc IX, Ru X, Rh XI, Pd XII, Ag XIII, Cd XIV, In XV, and Sn XVI. Results are listed for the lowest 375 levels, which mostly belong to the 4s²4p⁵, 4s²4p⁴4ℓ, 4s4p⁶,4s²4p⁴5ℓ, 4s²4p³4d², 4s4p⁵4ℓ, and 4s4p⁵5ℓ configurations. Extensive configuration interaction among 39 configurations (generating 3990 levels) has been considered and the general-purpose relativistic atomic structure package (grasp) has been adopted for the calculations. Radiative rates are listed for all E1, E2, M1, and M2 transitions involving the lowest 375 levels. Previous experimental and theoretical energies are available for only a few levels of three, namely Ru X, Rh XI and Pd XII. Differences with the measured energies are up to 4% but the present results are an improvement (by up to 0.3 Ryd) in comparison to other recently reported theoretical data. Similarly for radiative rates and lifetimes, prior results are limited to those involving only 31 levels of the 4s²4p⁵, 4s²4p⁴4d, and 4s4p⁶ configurations for the last four ions. Moreover, there are generally no discrepancies with our results, although the larger calculations reported here differ by up to two orders of magnitude for a few transitions.

Radiative rates for E1, E2, M1, and M2 transitions in F-like ions with 37≤Z≤53

Calculations of energy levels, radiative rates and lifetimes are reported for 17 F-like ions with 37≤Z≤53. For brevity, results are only presented among the lowest 113 levels of the 2s²2p⁵, 2s2p⁶, 2s²2p⁴3ℓ, 2s2p⁵3ℓ, and 2p⁶3ℓ configurations, although the calculations have been performed for up to 501 levels in each ion. The general-purpose relativistic atomic structure package (grasp) has been adopted for the calculations, and radiative rates (along with oscillator strengths and line strengths) are listed for all E1, E2, M1, and M2 transitions of the ions. Comparisons are made with earlier available experimental and theoretical energies, although these are limited to only a few levels for most ions. Therefore for additional accuracy assessments, particularly for energy levels, analogous calculations have been performed with the Flexible Atomic Code (fac), for up to 72 259 levels. Limited previous results are available for radiative rates for comparison purposes, and no large discrepancy is observed for any transition and/or ion.