En contexte équatorial, les sédiments intertidaux sont colonisés par un continuum écologique allant de vasières en cours de stabilisation à des sols colonisés par divers faciès de mangroves. Les fonctions microbiennes édaphiques de ces écosystèmes sont méconnues. Ces recherches ont donc eu pour objectif de définir les facteurs de contrôle et de variabilité spatio-temporelle des fonctions microbiennes des milieux estuariens et littoraux de Guyane française. Elles ont été conduites sur divers stades de colonisation biologique de ces habitats et à diverses échelles spatio-temporelles en tenant compte du rôle de l'instabilité hydro-sédimentaire et des variabilités induites par les saisons hydro-climatiques. Différents facteurs pouvant influencer les fonctions microbiennes ont été considérés : i) la qualité chimique (RMN solide du 13C) de la MOS en fonction de la composition des formations végétales et de leurs stades de développement ; ii) les caractéristiques physico-chimiques des sédiments et des eaux interstitielles en fonction de la localisation des divers faciès de mangroves. Les résultats ont mis en évidence l'importance des instabilités hydro-sédimentaires dans la mise en place et la structuration des fonctions microbiennes sédimentaires de Guyane. En outre, pour les différents modèles étudiés, les facteurs de structuration sont apparus variables. Néanmoins, la MO, en termes de quantité et de qualité, s'est révélée être un facteur prépondérant pour l'expression de ces fonctions des stades allant de la vasière nue à la jeune mangrove. En revanche, il est apparu plus difficile de discerner des facteurs structurants génériques pour les divers faciès de mangroves matures. / Under equatorial conditions, coastal sediments of intertidal mudflats form an ecological continuum, from bare mud being stabilized to soil settled by various mangrove facies. Edaphic microbial functions of terrestrial ecosystems are extensively documented; on the contrary, this is not the case with regards to sedimentary environment. This study had the main objective defining the drivers of the spatiotemporal variability of microbial functions (aerobic respiration, metabolic diversity, and enzyme activities) in coastal sediments of French Guiana. These researches were carried out according to biological colonization states (mudflats, pioneer and mature mangroves) and using various spatiotemporal scales considering the fundamental role of the hydro-sedimentary instability and potential variability due to hydro-climatic seasons. Different factors which can influence microbial functions were studied: i) the chemical quality (13C solid-state NMR) of OM with respect to vegetation presence and composition, and its development state; ii) the physicochemical characteristics of sediments and porewaters according to localization and topography of the different mangrove facies. Generally, results showed the importance of hydro-sedimentary instability for the establishment and structuring of microbial functions. Moreover, giving the different models, structuring factors were variables. However, OM, in terms of quantity and quality, was overriding for the expression of these functions and this was true for the evolution states from mudflat to young mangrove. By contrast, it appeared much more difficult discerning generalizable drivers for mature mangroves.

The respective kinetics of bacterial leucine aminopeptidase and [beta]-glucosidase activities were investigated to improve understanding of factors controlling activity and hydrolytic capacity in estuarine organic-poor sands. Depth distributions of enzyme activity and bulk organic matter content were determined in sediments of Aransas Bay and Copano Bay Texas, to investigate enzyme dynamics as related to the geochemical properties of the sediment. Vertical profiles of activity in sediment showed that the enzymes were more active at the surface and that the potential hydrolysis rate of leucine aminopeptidase was higher than that of [beta]-glucosidase. Vertical patterns of enzyme activity correlated (weakly) with variations in sediment organic matter (TOC, TN, and carbohydrates) content. Enrichments of sediment samples with monomeric organic compounds and inorganic nutrients did not affect leucine aminopeptidase and [beta]-glucosidase activities in short- and long-term incubations. Enzyme activity was independent of nutrient availability and suggested that microbial communities were not nutrient-limited. Time-course assays of bacterial hydrolysis of TOC, TN, and carbohydrates provided information about how substrate limitation may affect enzyme activity. Positive correlations between bulk TOC and TN content and enzyme activity indicated enzyme dependence on polymeric substrate content. Induction of enzyme activity after sediment enrichments with specific labile compounds confirmed the importance of available organic substrate to enzyme hydrolysis efficiency. A kinetic approach established the occurrence of enzyme inhibition and its effects on enzyme hydrolytic capacity. The addition of a specific-enzyme substrate to sediment samples modified enzyme parameters and indicated that a substrate-reversible type of inhibitor could reduce enzyme hydrolytic capacity. The addition of polyphenol, as a natural inhibitor of enzyme activity, to the sediment resulted in a concomitant reduction of leucine aminopeptidase activity and ammonium regeneration rate, and thus demonstrated a close coupling between enzyme activity and sediment ammonium regeneration. These research results demonstrate the dynamic nature of the hydrolytic enzymes, provide information about the mechanisms of induction and inhibition of activity, and demonstrate some implications of reducing the hydrolytic capacity to organic matter decomposition and nutrient regeneration rates. / text

Deuteration is the replacement of a hydrogen atom by deuterium atom in a molecule. The replacement begins at the most acidic hydrogen in the molecule. In ATP, the deshielded hydrogen is C8-H which is the first replaced during deuteration. During ATP deuteration some of the ATP is hydrolysed to ADP concurrently. Using kinetic analysis, it was confirmed that the ATP hydrolysis that occurs is 1st order in ATP concentration, while the hydrogen replacement is 2nd order. The ATP and its C8 deuterated analogue were tested against three enzymes shikimate kinase (SK), acetate kinase (AK) and glutamine synthetase (GS) to determine if a kinetic isotope effect (KIE) exists in these systems. With AK and GS, the KIED increased as the KIEH decreased, while with SK the KIED decreased as the KIEH increased as the concentration of the ATP or deuterated analogue increased. Deuteration of imidazole and purine compounds reduced the specific activity of AK or SK at low concentrations in an enzyme-catalysed reaction. From a library of imidazole-containing compounds that inhibited SK, three compounds were selected and their IC50 values were determined on the SK-catalysed reaction. These compounds show a differential potency and efficiency between their protonated and deuterated analogues when compared in a 1:1 mixture. Synthesized purines incorporating three different substituents at N-9 were tested against AK or SK for their ability to lower the specific activity of the enzymes used / Physics / M. Sc. (Physics)

No description available.

Ruminant animals consuming low N-diet have been reported to have increased urea reabsorption with the Nguni being categorized as N-recycling ruminant. The enzymes associated with N-cycling are hypothesized to contribute to survival of the Nguni in harsh conditions. Enzymes responsible for such a function needed to be characterized in order to determine their effect in the functioning of the Nguni as opposed to Hereford breed. Crude enzymes from both breeds were separated from most or some contaminants by sephadex G-25, DEAE sephacel, and different affinity column chromatography. CPS and GDH were successfully purified and characterized by LC-MS/MS and further analysed by ProteinPilot™, blasted and matched >95% with those of Bos Taurus. Comparison of characterized enzymes and those which failed to ionise such as ARG, GS and GA was done using kinetics and graphs annotating specific activities. Partial purification and characterization was in part achieved. / Life and Consumer Sciences / M. Sc. (Life Sciences)

<p>Coronaviruses (CoVs) are single-stranded, positive-sense RNA viruses in the Coronaviridae family. Within this family are four different genera, Alpha-, Beta-, Gamma-, and Deltacoronaviruses with human-infecting CoVs spanning the Alpha- and Beta-CoV genera. Most notably, Severe Acute Respiratory Syndrome Coronavirus-1 (SARS-CoV-1) and SARS-CoV-2 are Betacoronaviruses that spread worldwide in their outbreaks from 2002-2003 (SARS-CoV-1) and 2019-2020 (SARS-CoV-2). Human-infecting Alphacoronaviruses, NL63-CoV and 229E-CoV, have caused milder infections involving respiratory disease, gastroenteritis, and in more severe cases, death. Despite milder disease, Alphacoronaviruses are the cause of 15-30% of severe upper and lower respiratory tract infections each year. There have been recent efforts in the development of potent, small-molecule inhibitors to treat SARS-CoV-2 infection but there is an ongoing need to develop new and effective anti-coronavirus therapeutics to treat other human-infecting CoVs circulating society. Coronaviruses encode two essential proteases, the papain-like protease (PLP) and the 3C-like protease. PLPs are cysteine proteases located in non-structural protein 3 (nsp3). PLPs processes the viral polyprotein, releasing the first three nonstructural proteins encoded in the virus, and also are involved in evading the innate immune response through deubiquitinating (DUB) and deISGylating activity. </p> <p><br></p> <p>This study compares the substrate specificity and catalytic function of multiple human-infecting PLPs from both Alpha- and Beta-CoVs including NL63-CoV PLP2, 229E-CoV PLP2, Canine-CoV PLP2, FIPV-CoV PLP2, PEDV-CoV PLP2, SARS-CoV-1 PLpro, and SARS-CoV-2 PLpro. Interestingly, Alphacoronavirus PLP2s have a >400-fold greater catalytic efficiency for ubiquitin compared to Betacoronaviruses PLpro. This work also identifies a non-covalent scaffold of inhibitors that has pan-CoV inhibition; however, the IC50 values are >30-fold higher for NL63-CoV PLP2 than for SARS-CoV-1 PLpro. The X-ray structures of NL63 PLP2 and 229E PLP2 were determined to 2.1 Å and 1.8 Å, respectively, and provide structural information about the substrate and inhibitor binding region that could be the result in the differences in Alpha- and Betacoronavirus PLP function. Since PLP does not function as a single-domain in vivo, it is critical to understand the function of PLP when tethered to other domains of nsp3. This study also investigates nine different constructs of SARS-CoV-2 nsp3 with increasing domains, ranging from the single PLpro domain to Ubl1-Ydomain ΔTM1-TM2. Interestingly, the longer constructs of SARS-CoV-2 nsp3 show less catalytic efficiency for Ub-AMC and greater affinity for ISG15-AMC, with 8-fold lower Km values compared to PLpro alone. Lastly, each SARS-CoV-2 nsp3 construct was inhibited by a known PLpro inhibitor, GRL-0617, with reported IC50 values ranging from 0.91 μM to 1.9 μM. These data show that GRL-0617 still remains a lead compound to be optimized for cellular potency. </p> <p><br></p> <p>Overall, this dissertation advances the understanding of the kinetic and structural differences between Alphacoronavirus PLP2 and Betacoronavirus PLpro enzymes in the efforts of developing a pan-CoV inhibitor. Additionally, these data provide initial kinetic and biophysical characterization of PLpro within the larger context of nsp3 to elucidate the function of PLpro in its most native context during coronaviral infection.</p>

Introduktion och syfte: Kariesutveckling influeras av faktorer hos både värd och bakterier. Men när olika individer exponeras för samma nivåer av externa riskfaktorer, är en del individer mer mottagliga för karies jämfört med andra. En förklaring skulle kunna vara olika glykosylering av glykoprotein i saliven. I denna pilotstudie undersökte vi skillnaden i nivåer av monosackariderna sialinsyra, fukos och galaktos hos personer som aldrig haft karies och personer som har/har haft karies. Syftet var även att undersöka om plackenzym kan vara en modifierare av nämnda glykoprotein.Material och metod: Två grupper, med 10 individer i varje, inkluderades i studien. Ena gruppen hade DMFT = 0 och den andra DMFT ≥ 1. Saliv och plack samlades och innehållet av bundna monosackarider (sialinsyra, fukos och galaktos) samt glykosidaser (sialidas, β-fukosidas, β-galaktosidas, α-glukosidas och N-acetylglukosaminidas) analyserades med en fluorometer. Även salivflödet kalkylerades.Resultat: Innehållet av både sialinsyra och galaktos var signifikant högre i gruppen med DMFT = 0, medan innehållet av fukos inte skilde sig åt signifikant mellan grupperna. Ingen signifikant skillnad kunde ses mellan de två grupperna avseende enzymaktivitet och salivflöde.Konklusion: Högre nivåer av bunden sialinsyra och galaktos fanns hos gruppen med DMFT = 0. Resultaten indikerar att dessa monosackarider kan vara en möjlig markör för oral hälsa. Större longitudinella studier behövs för att verifiera sambandet. / Introduction and aim: Caries development is affected by factors within bacteria and host. But when different individuals are exposed to same levels of external risk factors, some individuals are still more susceptible to caries. One explanation could be different glycosylation of salivary glycoproteins. In this pilot study, we investigated the difference in levels of the monosaccharides sialic acid, fucose and galactose between individuals with or without previous caries experience. We also aimed to investigate if plaque glycosidases could be a modifier of these glycoproteins.Material and method: Two groups, with 10 subject in each, were included in this study. One group had DMFT = 0 and the other DMFT ≥ 1. Saliva and plaque were collected and content of bound monosaccharides (sialic acid, fucose and galactose) and glycosidases (sialidase, α-fucosidase, β-galactosidase, α-glucosidase and N-acetylglucosaminidase) were detected using absorbance and fluoroscens respectively. Salivary flow rate was also measured.Results: Content of both sialic acid and galactose were significantly higher in the group with DMFT = 0, while the content of fucose did not differ significantly between the groups. No significant differences could be seen between the two groups (DMFT = 0 and DMFT ≥ 1) regarding any of the investigated glycosidases and salivary flow rate. Conclusion: Higher levels of bound sialic acid and galactose were found in the group with DMFT = 0 and the results indicate that these monosaccharides could be a possible marker for oral health. Larger longitudinal studies are needed to verify this correlation.

La dihyrofolate réductase de type II R67 (DHFR R67) est une enzyme bactérienne encodée par un plasmide donc aisément transmissible. Elle catalyse la réaction de réduction du dihydrofolate (DHF) en tétrahydrofolate (THFA) essentiel pour la prolifération cellulaire. La DHFR R67 est une enzyme qui dépend du cofacteur NADPH. La DHFR R67 est différente, structurellement et génétiquement, de l’enzyme DHFR chromosomale présente chez tous les organismes et elle est résistante au triméthoprime (TMP) qui est largement utilisé dans les traitements antibactériens chez l’Homme. Aucun inhibiteur sélectif contre la DHFR R67 n’est actuellement répertorié. Le but de cette étude a été d’identifier des molécules qui pourront inhiber la DHFR R67 sélectivement, sans affecter la DHFR humaine (DHFRh). La vérification de la qualité des essais enzymatiques en conditions déterminées pour le criblage d’inhibiteurs sur plusieurs lectrices à plaques a identifié des appareils appropriés pour l’analyse. L’étude de l’activité enzymatique de la DHFR R67 et de la DHFRh en présence des solvants organiques et liquides ioniques (LIs), comme des co-solvants pour le criblage rationnel d’inhibiteurs, a montré que certains LIs peuvent servir de milieu alternatif pour les essais enzymatiques. Le criblage rationnel basé sur l’approche du design d’un inhibiteur à partir de petites molécules, a révélé des molécules primaires qui inhibent la DHFR R67 de façon faible, mais sélective. Le test des composés biologiquement actifs qui comprennent des petits fragments, a montré l’augmentation de l’affinité entre la DHFR R67 et les composés testés. Trois composés ont été déterminés comme des inhibiteurs sélectifs prometteurs pour la DHFR R67. / Type II R-plasmid encoded dihyrofolate reductase (DHFR), R67 DHFR is a bacterial enzyme that catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate (THFA) which is essential for cell proliferation. R67 DHFR is an enzyme that depends on the cofactor NADPH as the hydride donor. R67 DHFR is distinct, structurally and genetically, from E. coli chromosomal DHFR (DHFR Ec) and it provides drug resistance to the widely-administered antibiotic trimethoprim (TMP). No selective inhibitor against R67 DHFR exists currently. The goal of this study was to discover molecules that can selectively inhibit R67 DHFR, without affecting human DHFR (hDHFR). Verification of the quality of enzyme assays under defined conditions for inhibitor screening on plate readers found several appropriate instruments for analysis. The study of the enzymatic activity of R67 DHFR and hDHFR in the presence of organic solvents and ionic liquids (ILs), as co-solvents for rational screening of inhibitors, showed that ILs can provide alternative media for enzymatic assays. Rational screening based on the approach of fragment-based drug design, revealed primary molecules that inhibited DHFR R67 weakly, but selectively. The testing of more complex compounds with known biological activities gave ligands with increased affinity for R67 DHFR. Three compounds were identified as promising selective inhibitors for R67 DHFR.

Zweck der molekularen Bildgebung ist es, biologische Prozesse auf zellulärer und molekularer Ebene zu messen und zu charakterisieren, um so die Ursachen von Krankheiten und Veränderungen im Organismus zu diagnostizieren. Sie basiert auf dem Einsatz molekularer Bildgebungssonden, welche einen spezifischen biologischen Vorgang darstellen oder sich spezifisch in dem zu untersuchenden Gewebe anreichern oder aktiviert werden. Ziel dieser Arbeit war die Entwicklung und Analyse neuer Bildgebungssonden für die spezifische in-vivo-Bildgebung der Apoptose und von Enzymaktivitäten mittels Magnetresonanztomographie (MRT) auf der Grundlage sehr kleiner Eisenoxidnanopartikel (very small iron oxide particles, VSOP). VSOP sind superparamagnetisch und durch ihre negativ geladene Citrathülle elektrostatisch stabilisiert. Für die Apoptose-Bildgebung sollte durch Bindung des Proteins Annexin A5 (AnxA5) an die Citrathülle der VSOP eine zielgerichtete Sonde hergestellt werden (AnxA5-VSOP). Für die Bildgebung von Enzymaktivitäten sollte eine durch die Matrixmetalloproteinase-9 (MMP-9) aktivierbare Sonde hergestellt werden (Protease-spezifische Eisenoxidpartikel, PSOP). / The goal of molecular imaging is to characterize and measure biological processes at cellular and molecular levels for the purpose of diagnosing the cause of diseases and molecular abnormalities. Molecular imaging is based on the use of probes with a high affinity to the target tissue and / or which are specifically activated. The aim of this study was to develop and analyze new molecular imaging probes for the in vivo imaging of apoptosis and enzyme activity using magnetic resonance imaging (MRI), based on very small iron oxide particles (VSOP). VSOP are superparamagnetic and electrostatically stabilized due to their negatively charged citrate surface. For the imaging of apoptosis the protein annexin A5 (AnxA5) was coupled to the citrate surface (AnxA5-VSOP). For the imaging of enzyme activities an activatable imaging probe with a cleavage site for the matrix metalloproteinase 9 (MMP-9) was synthesized (protease-specific iron oxide particles, PSOP).

Im Rahmen der Studien zur Wirkung von Bleinitrat auf die Embryonalstadien des afrikanischen Welses Clarias gariepinus wurde zunächst der Einfluß der Besamung auf den Härtungsprozess des Chorions untersucht, um die Bedeutung des gehärteten Chorions als Schutzfunktion im Hinblick auf Schadstoffeinwirkung zu klären. Das Studium der Embryonalentwicklung war erforderlich, um das Ausmaß der Änderung der Normalentwicklung unter dem Einfluß von Bleinitrat bewerten zu können. Im Rahmen der toxikologischen Untersuchungen der Wirkung des Bleinitrats auf die Embryonalstadien wurden folgende biologische Marker (Biomarker) betrachtet: Änderungen in der Entwicklung und der Schlüpfrate, morphologische und histologische Änderungen, sowie biochemische Veränderungen (Änderungen von Stoffwechsel-Enzymaktivitäten) und molekulare Veränderungen (Erfassung von DNA-Schädigungen). Die Exposition der besamten Eier mit Bleinitrat führte zu einer Verlängerung der Inkubationszeit und zu starken Mißbildungen. Der Rückgang der Häufigkeiten der Mißbildungen mit der Zeit ließ die Annahme zu, daß die mißgebildeten Embryonen starben. Im Gegensatz zu den morphologischen Mißbildungen wurden histopathologische Effekte nur bei Embryonen gefunden, die den höchsten Dosierungen (300 µg/l und 500 µg/l Bleinitrat) ausgesetzt waren. Nach dem Schlupf war das Muster der Enzymaktivitäten nach Exposition mit Bleinitrat uneinheitlich; die Aktivität von G6PDH nahm zu, die von LDH nahm ab und die von PK zeigte unregelmäßige Fluktuationen. Die Embryonalstadien zeigten signifikante Dosis-abhängige Antworten über die Zeit, da das Ausmaß der DNA-Schädigungen signifikant mit den Bleinitrat Konzentrationen anstieg. Vor dem Schlupf konnten bei den Embryonen nach Bleinitrat Exposition keine Änderungen in den Enzymaktivitäten gefunden werden und nur geringe DNA-Schädigungen, d.h die toxischen Effekte waren sehr gering. Eine Erklärung könnte die schützende Wirkung der Eihülle gegenüber Schadstoffen sein. Die gewählten Biomarker stellen sensitive Detektionsmethoden für Bleinitrat dar. So könnten sie sich als sinnvolle Bioindikatoren für Ägypten erweisen, da dort zunehmend Umweltverschmutzung mit Blei und Bleiakkumulation in Lebensmitteln zu verzeichnen ist. / In order to study the embryo-toxic effects of lead nitrate of the African catfish Clarias gariepinus, we first had to study the effect of fertilization on the hardening process of the chorion to clarify the role of the hardened chorion on the protection of the embryo from the pollutants. Also we had to study the embryonic development of C. gariepinus for providing us with a model for comparison when normal patterns of development are altered due the exposure to lead nitrate. The present toxicological work focuses on lead toxicity in different developmental stages of C. gariepinus considering different biological markers (biomarkers) comprising changes in the development and hatching rate, morphological and histological changes, biochemical changes (alteration of metabolic enzymes activity) and molecular changes (monitoring of DNA damage). Exposure of fertilized eggs to lead nitrate prolonged the incubation period and caused severe morphological malformations. Since the frequencies of the morphological malformations decreased with time, we conclude a lethal impact and selected mortality of abnormal embryos. Unlike the morphological malformation, histopathological changes were only recorded in embryos exposed to the highest dosages (300 µg/l and 500 µg/l lead nitrate). In the post-hatching stages, the patterns of the enzymes activities after lead exposure varied, G6PDH increased, LDH decreased and PK showed fluctuations. Embryonic stages revealed significant dose-related DNA damage response over time, since the degree of DNA damage increased significantly with higher lead concentrations. No specific response in the activities of the selected enzymes and low DNA damage were recorded in the pre-hatching stage after exposure to the lead nitrate doses. This means the lead nitrate had a minute toxic effect on the pre-hatched embryos. We conclude that, low susceptibility in pre-hatching stages is most probably a consequence of the chorion, which seems to protect the embryos from a range of external pollutants. The selected biomarkers were sensitive detection methods for low-level toxicity of lead nitrate. Thus, these are useful tools for biomonitoring, urgently required in Egypt with regard to increasing environmental deposition of lead and bioaccumulation in human food recently observed.