Chez les plantes, le RET (Root Extracellular Trap) est une structure cellulo-moléculaire jouant un rôle central dans la défense racinaire face aux stress abiotiques et biotiques. De nombreuses similitudes de composition ont été observées entre le RET et le NET (Neutrophil Extracellular Trap) du système immunitaire des mammifères, connu pour capturer et tuer certains microorganismes bactériens et fongiques. Le RET est composé de cellules frontières et de leurs sécrétions (composés de haut et de bas poids moléculaire) comprenant des polysaccharides de la paroi cellulaire, des protéoglycannes et des métabolites secondaires. Il contient également des protéines antimicrobiennes et de l'ADN extracellulaire, tout comme le NET. Dans le cadre de mon projet de thèse, nous avons caractérisé la composition moléculaire et la structuration de cette entité de défense chez deux légumineuses, le soja (Glycine max (Merr) L.) et le pois (Pisum sativum L.), par des approches d’imagerie cellulaire photonique et électronique. Nous avons également étudié l’impact du RET du soja sur des pathogènes telluriques, à savoir Phytophthora parasitica et Aphanomyces euteiches. Nous avons ainsi pu mettre en évidence la présence de différents morphotypes de cellules frontières et de mucilage au sein du RET de soja et de pois. Pour la première fois, nous avons montré la présence d’hétéromannanes, de xyloglucane et de cellulose dans le RET, formant une ossature stabilisant le mucilage et reliant les cellules frontières entre elles. Ces polysaccharides structuraux semblent être essentiels à l’intégrité structurale et fonctionnelle du RET. Enfin, nos résultats ont montré que le RET de soja était impliqué dans la défense précoce de la racine contre P. parasitica. Cette étude apporte de nouvelles connaissances relatives à la composition moléculaire et la structure du RET, nous amenant ainsi à comparer le RET à d’autres modèles que le NET des mammifères, tels que les biofilms bactériens et les mucilages de graines. En effet, de nombreuses similitudes existent entre ces différents complexes en termes de composition et de fonctionnement, qui méritent d’être explorer plus en détail dans l’avenir. / In higher plants, the RET (Root Extracellular Trap) is a complex made up of border cells and secretions, released by root tips and believed to play a central role in biotic and abiotic stress tolerance. This structure is quite similar to the Neutrophil Extracellular Trap (NET) known as one of the first lines of defense in mammals, able to trap and kill microbial pathogens. RET secretions consist of high and low-molecular weight compounds including cell wall polysaccharides, proteoglycans and secondary metabolites. They also contain a variety of anti-microbial proteins and extracellular DNA much like the NET. During my thesis work, we investigated the release and morphology of root border cells in soybean (Glycine max (Merr) L.) using light and scanning electron microscopy. The molecular composition of the mucilage was also investigated using immunocytochemistry, anti-cell wall glycan antibodies and confocal microscopy. Immunocytochemistry was also applied to pea (Pisum sativum L.) border cells and secretions to examine the occurrence of specific polysaccharides. We also studied the impact of soybean RET on the soilborne pathogens, Phytophthora parasitica and Aphanomyces euteiches. Our findings showed that root tips of soybean released three border cell morphotypes all of which secreted substantial amounts of mucilage. Immunocytochemical data showed that mucilage was enriched in pectin and the two hemicellulosic polysaccharides xyloglucan and heteromannan. Mucilage also contained cellulose, histone and extracellular DNA. Interestingly, the structural polysaccharides formed a fibrous network surrounding the cells and holding them together, supporting their role in maintaining mucilage architecture and integrity. In addition, we found that xyloglucan and cellulose were also secreted into the mucilage of pea, connecting border cells together. Finally, our findings revealed that RET prevented P. parasitica zoospores from colonizing soybean root tip, by stopping their penetration and inducing their death. Overall the study revealed novel insights into the composition, structure and function of plant RETs. Currently, the RET is much less studied than its mammal counterpart, the NET, but structural and functional similarities exist between these two traps. Interestingly, similarities do also exist between the RET and other important biological complexes, including bacterial biofilms and seed mucilage, that deserve to be further investigated and compared in the context of immunity.

Introduction Recently in our laboratory we needed a reliable and relatively simple source of aqueous solutions of [11C]CO2. We examined various methods of trapping [11C]CO2 gas both in solution and on ion exchange resins, followed by elution into aqueous phase. We favor simple methods that have high trapping and elution efficiencies and produce a highly concentrated solution. Furthermore, we desired methods that would minimize the use of hazardous reagents and materials with respect to both handling and disposal. We also considered the formulation of the final solution in terms of chemical compatibility with contacted materials, working with the assumption that dilute bicarbonate or carbonate solutions will have little reactivity with many materials. In a phantom, compatibility with materials (i.e. plastics, glues, metals, etc.) is important (1-4), while in (bio)geochemical studies – where transport of carbon is important – the chemical form of the radiolabelled molecule is important, but compatibility must be determined on a case-by-case basis (5-7). Small medical cyclotrons can easily produce carbon-11 as gaseous [11C]CO2, and various methods are utilized to incorporate carbon-11 into solution, often with unfavorable resource requirements, costs, or chemical properties. Commonly [11C]CO2 gas is bubbled through a strong base, forming the carbonate anion; but neutralizing a strong base (as to avoid special handling or disposal requirements) requires a large volume of diluent or buffer; or a very precise addition of acid – which if done improperly – may lead to an acidic pH and subsequent loss of [11C]CO2 from solution (8,9). Alternatively, [11C]CO2 (or [11C]CH4) can be converted to [11C]CH3I at high-yield, but requires specialized, expensive radio-synthesis equipment (10-12). [11C]CH3I can then be trapped in DMSO (albeit providing a volatile and hazardous solution) or used as a synthon en route to water soluble compounds such as [11C]choline (13). Finally, leftover radiolabelled radiopharmaceuticals from a carbon-11 imaging experiment could be used, but chemical compatibility (i.e. lipophilicity) of the radiolabelled compound may be of concern. Carbon dioxide gas will dissolve with a solubility of 1.5 g/L at STP (9) and slowly react with water to generate carbonic acid (H2CO3), a weak acid. Passing [11C]CO2 through a base-activated ion exchange cartridge, the [11C]CO2 reacts with hydroxide ions to form [11C]carbonate which is bound to the resin due to its higher selectivity for carbonate than hydroxide (14). Elution with excess bicarbonate displaces [11C]carbonate and neutralizes any remaining hydroxide, providing a 11C aqueous solution that is mildly basic, chemically non-hazardous, and very concentrated. Material and Methods [11C]CO2 gas trapping efficiency was evaluated for solutions and base-activated ion exchange resins. The gas was delivered either rapidly in a high-flow bolus directly from the cyclotron target or slowly in a low-flow helium stream during heating of a carbosieves column. Elution efficiency of ion exchange cartridges were evaluated for both fraction of trapped activity eluted and volume of solution needed for elution. [11C]CO2 was produced via the 14N(p,α)11C reaction on a CTI RDS111 – 11 MeV cyclotron at the Lawrence Berkeley National Laboratory’s Bio-medical Isotope Facility. The 7 mL target is pressurized to 315 psi with 1% O2/N2 gas, equating to 150 mL gas at STP. For direct-from-target trapping experiments, the target was decompressed and routed to the cartridge via 50 feet of 0.020” I.D. tubing until the target falls to atmospheric pressure (~55 seconds) providing an inhomogeneous flow – a short rapid burst of flow followed by a longer low-flow bleed. For helium-eluted experiments, the [11C]CO2 was unloaded from the cyclotron target and trapped on a room-temperature carbosieves column (15). Target gases were subsequently flushed from the column for 30 seconds with helium at 50 mL/min. After heating the column to 125 °C without gas flow, [11C]CO2 was eluted off the column in helium at 15 mL/min. [11C]CO2/He was bubbled through 9 aqueous and 2 organic solutions to test for trapping efficiency in a slow, steady helium stream at 15 mL/min (sodium hydroxide (0.96M, 0.096M, 0.0096M), sodium bicarbonate (1.14M, 0.57M, 0.057M), sodium carbonate (2.0M, 1.0M, 0.10M), ethanol, and DMSO (2mL ea.). An Ascarite-filled cartridge was attached to trap any untrapped [11C]CO2. Measures of radioactivity were made using a Capintec CRC-15R dose calibrator. Trapping efficiency for solutions is calculated as the fraction of radioactivity captured in solution relative to the sum of the solution and the Ascarite trap. Three different commercially available, ion ex-change cartridges were evaluated for trapping and elution efficiencies. FIGURE 1 shows a photo-graphic comparison of the physical size and shapes of the cartridges as well as a X-ray computed tomography (CT) cross sectional view of the internal ion exchange resin volume and dead volume of the cartridges. All cartridges were activated with 1 mL of 1 N aqueous NaOH followed by passing 10 mL deionized water then 10 mL of air through the cartridge. In both direct-from-target (n = 4) and helium-stream experiments (n = 3 or 4), cartridges were connected to [11C]CO2 delivery lines via Luer connections. The gas exiting the cartridge passed through an empty 3 mL crimp-top vial as a liquid trap en route to an Ascarite trap on the vent needle as described above. Trapping efficiency for cartridges is calculated as the fraction of radioactivity captured on the cartridge relative to the sum of the cartridge, the empty vial, and the Ascarite trap. Cartridges were eluted with 0.5 mL of saturated sodium bicarbonate solution (1.14 M @ 20°C) followed by 9.5 mL water and 10 mL air. Elution efficiency is calculated as the fraction of radioactivity eluted in 10 mL relative to the sum of the spent cartridge following elution and the 10 mL eluate (Equation 5). The pH of the eluate was measured using 0-14 pH test strips. Results and Conclusion The trapping of [11C]CO2 in all solutions was less than 70% of the total radioactivity with the exception of the 0.96 M and 0.096 M NaOH. With a higher concentration of base driving equilibrium towards carbonate stability, it could be expected that the most basic solution had the best trapping efficiency, but this attribute also means it is least desirable solution to work with from a hazardous material or chemical compatibility perspective. When [11C]CO2 was delivered in a helium stream, all three cartridges performed at near 100% efficiency, as shown in FIGURE 4. With higher flow, direct-from-target delivery, the cartridges trapped [11C]CO2 with a wider range of efficiencies: ICOH (99 ± 1 %), ORTG (90 ± 2 %), and QMA (79 ± 4 %). Elution resulted in > 99 % release of carbon-11 activity for both QMA and ORTG cartridges, but only 39 ± 3 % release from the ICOH cartridge. Elution efficiency of the trapped radioactivity (Equation 5) was independent of the method of [11C]CO2 delivery. Across all cartridges and delivery methods, the eluate was at about pH = 10. We recommend that the ORTG cartridge be used for trapping of [11C]CO2 gas with elution by > 300 µL of saturated bicarbonate solution. This recommendation is based on the better trapping for ORTG cartridges compared to the QMA cartridges in the direct-from-target [11C]CO2 delivery method and the smaller volume needed for elution of all trapped carbon. This method excels based on its simplicity, adaptability to automation, low-cost ($5/cartridge), and observations that a single ORTG cartridge suffers no loss of performance after multiple uses. A potential disadvantage to this method is that it involves using a carbon-containing eluent, which means that this method cannot be used for imaging experiments that require high specific activity. However, considering the eluate is a mildly basic aqueous solution, we expect that it will be compatible with a wide variety of materials and experimental applications.

No description available.

This thesis presents how deep learning can be utilized for detecting humans ina wildlife setting using image classification. Two different solutions have beenimplemented where both of them use a camera-equipped microprocessor to cap-ture the images. In one of the solutions, the deep learning model is run on themicroprocessor itself, which requires the size of the model to be as small as pos-sible. The other solution sends images from the microprocessor to a more pow-erful computer where a larger object detection model is run. Both solutions areevaluated using standard image classification metrics and compared against eachother. To adapt the models to the wildlife environment,transfer learningis usedwith training data from a similar setting that has been manually collected andannotated. The thesis describes a complete system’s implementation and results,including data transfer, parallel computing, and hardware setup. One of the contributions of this thesis is an algorithm that improves the classifi-cation performance on images where a human is far away from the camera. Thealgorithm detects motion in the images and extracts only the area where thereis movement. This is specifically important on the microprocessor, where theclassification model is too simple to handle those cases. By only applying theclassification model to this area, the task is more simple, resulting in better per-formance. In conclusion, when integrating this algorithm, a model running onthe microprocessor gives sufficient results to run as a camera trap for humans.However, test results show that this implementation is still quite underperform-ing compared to a model that is run on a more powerful computer.

La géophagie désigne l’ingestion volontaire de terre et est répandue à travers le règne animal, l’Homme inclus. Cette large distribution souligne la longue histoire évolutive du comportement et suggère que la terre ingérée confèrerait des bénéfices adaptatifs aux consommateurs. L’Homme possède une longue histoire de la géophagie. Depuis deux dizaines d’années, la géophagie chez les primates non-humains connaît un intérêt scientifique croissant. Elle a été observée chez 27% des espèces de primates reconnues actuellement. Deux hypothèses majeures expliqueraient la géophagie chez les primates :la supplémentation et la protection. Dans le premier cas, la terre ingérée procurerait des éléments essentiels que l’individu ne trouve pas dans d’autres ressources. Dans le second cas, la terre consommée protègerait son tractus gastro-intestinal contre les endoparasites et/ou contre les effets néfastes des composés secondaires contenus dans les items végétaux ingérés. Toutefois, le manque de recherches multidisciplinaires ne facilite pas la compréhension du comportement et de son rôle chez les primates. Cette thèse s’intéresse à la géophagie chez le singe laineux à queue jaune (Lagothrix flavicauda), espèce pour laquelle ce comportement n’avait pas encore été décrit. C’est un des plus grands et un des plus rares primates néo-tropicaux. Ce primate peu étudié est endémique du Pérou et en Danger Critique d’extinction. Il est arboricole et principalement frugivore. Un groupe de singes habitués à la présence de chercheurs a été suivi au site d’étude de La Esperanza, afin de dresser les premières caractéristiques de la géophagie (Chap. 4) :i) toutes les classes d’individus (âge/sexe) consomment de la terre ii) en de rares et brefs événements (15 ± 9 secondes), iii) principalement pendant la saison sèche. Les singes semblent développer des stratégies pour gérer les risques de prédation liés à la terrestrialité qu’implique la géophagie :ils sélectionnent les sites de géophagie selon des paramètres qui pourraient promouvoir leur sécurité ;ils sont plus vigilants ;ils consomment souvent de la terre ex situ, sur une haute branche. La géophagie nécessite donc acquisition de connaissances particulières et nos observations mettent en évidence que l’apprentissage débute très tôt dans la vie de l’individu, la mère jouant un rôle crucial dans le processus de transmission du comportement. Ce travail s’est aussi focalisé sur l’échantillonnage et l’analyse de la composition des terres consommées et contrôles (Chap. 5) :la terre ingérée contient plus d’argile et moins d’éléments essentiels (e.g. Ca, Mg, K, Fe), supportant davantage l’hypothèse de protection, l’argile étant connue pour ses propriétés d’adsorption et d’évacuation des toxines. Enfin, les patterns temporels de la consommation de la terre et des items végétaux ont montré que la géophagie est directement associée à l’augmentation de la consommation de feuilles pendant la saison sèche (Chap. 6). Nos résultats suggèrent que ces primates ingèrent de la terre pour se protéger des composés secondaires pouvant être plus abondants dans les feuilles en saison sèche. Cette étude souligne que des données comportementales détaillées ainsi que des recherches comprenant plusieurs axes d’investigation sont essentielles pour comprendre la façon dont les individus acquièrent les connaissances liées à une pratique si rare. / Geophagy, i.e. the deliberate ingestion of earth, is largely described across the animal kingdom, including in human and non-human primates. Its widespread distribution highlights its long evolutionary history and its widely hypothesized selective benefits. Humans have a long history of geophagy. Since two decades, scientific interest in non-human primate geophagy is growing. The behavior has been described in 27% of the known primate species. In non-human primates, two major adaptive hypotheses are proposed to explain geophagy. The supplementation one argues that earth provides micronutrients individuals cannot find in their diet. The protection one argues that earth protects the gastrointestinal tract from secondary plant compounds and/or parasites. However, multidisciplinary research is lacking to fully understand the geophagy behavior in primates.I studied the geophagy behavior in the yellow-tailed woolly monkey (Lagothrix flavicauda), for which there was no earth consumption data. This monkey is one of the largest and rarest neotropical primates but remains little studied. Yellow-tailed woolly monkeys are Critically Endangered and endemic to northern Peru. They are arboreal and have a primarily frugivorous diet. Their simple gastro-intestinal tract makes digestion of cell walls and secondary plant compounds difficult.One habituated group of yellow-tailed woolly monkeys was studied at La Esperanza study site, allowing to provide the first descriptions of (Chap. 4) i) individuals of all age/sex classes consumed earth ii) in rare and very brief events (15 ± 9 seconds), and iii) mainly occurring during dry seasons. We also examined how these arboreal primates deal with the higher predation pressure linked to this terrestrial behavior: yellow-tailed wooly monkeys selected sites according to some parameters that may ensure their safety; they showed increased vigilance; and they often consumed earth ex situ, on a branch. Geophagy therefore requires the acquisition of specific knowledge and our observations show that learning begins very early in the individual's life, the mother playing a crucial role in the behavior transmission process. This research also focused on sampling and analyzing the composition of consumed and control earths (Chap. 5): earth consumed was richer in clay and poorer in micronutrients (e.g. Ca, Mg, K, Fe), better supporting the protection hypothesis, as clay is known to adsorb and evacuate toxins. Finally, temporal patterns of earth and vegetal items consumptions was also examined and showed geophagy was directly associated with the increased leaf consumption during the dry season (Chap. 6) and, through a geophagy day, earth and leaves consumption were synchronized. This study suggests that these primates eat earth to protect themselves against gastro-intestinal disorders caused by an increased ingestion of secondary compounds that might be more abundant in leaves and during the dry season. It also underlines that detailed behavioral data and multiple axed research are necessary to understand how a rare practice implying specific knowledge and aptitudes emerge in the behavioral repertoire of an individual. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Use of Melatonin Derivatives as Spin Traps for Hydroxyl Radicals: A Computational Studies. Aaron Teye Caesar and Dr. Scott Jeffery Kirkby, Department of Chemistry, College of Arts and Sciences, East Tennessee State University, Johnson City, TN. Free radicals, especially reactive oxygen species, have been implicated in several deleterious processes which result in degenerative and cardiovascular diseases. Melatonin (N-acetyl-5-methoxytryptamin, MLT) is a naturally occurring antioxidant which has shown some potential for use as a spin trap. Spin traps react with short lived radicals such as hydroxy (.OH) or superoxide (O2-) to produce more stable products called spin adducts which may be characterized by electron paramagnetic resonance spectroscopy. This work examines whether MLT derivatives show improved spin adduct stability which may enhance their spin trapping characteristics. Electronic structure calculations of MLT, selected derivatives and 2-OH radical products were performed at the HF/6-31G(d), cc-pVDZ and DFT/B3LYP/6-31G(d) and cc-pVDZ levels of theory using NWChem. The stabilization energy was calculated using; ∆Estabilization = Espin adduct – (Espin trap + Ehydroxy radical). In units of hartrees, the results of 2-OHMLT, 2-OHMLT-Me and 2-OHMLT-CN are -0.43738, -1.60054, -1.60380 for HF/6-31G(d); -1.46071, -1.44788 and -1.46173 for DFT/6-31G(d) respectively. Also, HF/cc-pVDZ and DFTB3LYP/cc-pVDZ respectively gave -1.61268, -1.60233, -1.61409 and -1.44929, -0.26318, -1.45521.

One way of realizing a quantum computer is to use an ion trap. The research group Trapped Ion Quantum Technologies at Stockholm university were operating an ion trap with strontium ions. To increase the coherence time they installed a magnetic field shielding. Therefore the experimental setup had to be partially rebuilt. A new 405 nm laser was installed in order to speed up the ionization step of neutral strontium atoms. The characterization of the laser was performed and it showed that the laser could be operated at the required wavelength. The wavelength was characterized with respect to temperature and power. A scan of the 422 nm Doppler cooling laser was also performed and it showed that the Doppler cooling worked as intended. Lastly, Rabi oscillations were performed to see if coherent manipulation of the ion's quantum state worked as intended. This experiment was also successful but it showed some differences between having the magnetic shielding door open or closed which should be investigated further.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第18570号 / 工博第3931号 / 新制||工||1604(附属図書館) / 31470 / 京都大学大学院工学研究科都市社会工学専攻 / (主査)教授 松岡 俊文, 教授 小池 克明, 准教授 岸田 潔 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20048号 / 理博第4233号 / 新制||理||1609(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 中川 尚史, 教授 沼田 英治, 教授 中務 真人 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

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