Abundance, distribution and habitat preferences of the lizard species present on Motunau Island, off the Canterbury coast of New Zealand, were investigated. The aim of the study was to investigate the extent to which recent vegetation change on Motunau Island has effected the lizard community and what implications this has for the future management of the Island. Three species of lizard occur on Motunau Island; the common gecko (Hoplodactylus maculatus), common skink (Oligosoma nigriplantare polychroma) and spotted skink (O. lineoocellatum). Rabbits (Oryctolagus cuniculus) were present on the island from 1862 until their eradication in 1962. Since then, vegetation on the island has changed from being tussock-dominated to being dominated by exotic weeds. Data from lizard pitfall trap surveys carried out in 1967-75 by Tony Whitaker of the Department of Scientific and Industrial Research (DSIR) were compared with new pitfall trapping data to determine if changes in the lizard population had occurred in response to these vegetation changes. The abundance of O. n. polychroma and H. maculatus does not appear to change significantly. The distribution of these two species were significantly correlated but neither showed any preference for a particular type. The abundance of O. lineoocellatum was significantly greater in 1996/97 than in the earlier DSlR surveys. This could be a result of the vegetation becoming more open and more structurally complex since the early surveys. This would offer greater opportunities for O. lineoocellatum (which is strongly heliothermic) to thermoregulate and forage. O. lineoocellatum showed no consistent significant preference towards any habitat type, although they tended to be found more in 'margin' habitat. Research into pitfall trapping and the way lizard behaviour may influence pitfall trapping data needs to be undertaken as there is a possible trap bias in this study. Management of Motunau Island needs to ensure that a structurally complex environment is maintained to ensure high numbers of all three lizard species can continue to coexist.

The presence of ultraviolet patterns on body, as well as perception of ultraviolet spectrum by special photoreceptors, is part of sensory ecology of many animal species, including reptiles. Most current research discusses the importance of ultraviolet signs in coloration of diurnal species. The aim of our study was to find out what character have the reflective signs in ultraviolet spectrum in overall coloration of common leopard gecko (Eubplepharis macularius) through a digital photography. The reflective pattern is present in both adults and juveniles and passes as well as the rest of the coloration by significant ontogenetic changes. Another aim was to evaluate the role of ultraviolet reflecting signs in the biology of this crepuscular-nocturnal species. We expect that the pattern contributes to their antipredatory strategies during their first few months of life, and also a white reflecting surface is preserved in adulthood, especially on their tail, which is differently coloured than the rest of the body.

No description available.

The eyes of snakes and most geckos, as well as a number of other disparate squamate taxa, are shielded beneath a layer of transparent integument referred to as the “reptilian spectacle.” Derived from the embryonic fusion of palpebral tissues, the spectacle contains a number of specializations of the skin to benefit vision while still allowing it to function as the primary barrier to the environment. For example, in nearly all species that possess it, it is markedly thinned compared to the surrounding integument and its keratinized scale is optically transparent. While the spectacle may thus seem ideally adapted to vision in allowing the eyes to be always unoccluded, it does have a few drawbacks. One such drawback is its vascularity, the implications of which are still not fully understood, but are explored herein. As no recent synthesis exists of the body of knowledge on reptilian spectacles, the first chapter of this thesis consists of a review of spectacle anatomy, physiology, adaptive significance and evolution to help put into context the following chapters that present original research. The second chapter describes the dynamics of blood flow through the spectacle vasculature of colubrid snakes, demonstrating three main points: (1) that the spectacle vasculature exhibits cycles of regular dilation and constriction, (2) that the visual perception of a threat induces vasoconstriction of its vessels, and (3) that spectacle vessels remain dilated throughout the renewal phase. The implications of these points are discussed. The third chapter describes the spectral transmittance of the shed spectacle scale, the only keratinized structure in the animal kingdom to contribute to the dioptric apparatus of the eye, as well as its thickness. Spectacle scale transmittance and thickness was found to differ dramatically between snakes and geckos and found in snakes to vary between families. The adaptive significance of the observed variation is discussed. The fourth chapter describes biochemical analyses of the shed spectacle scales of snakes and geckos and compares their composition to other scales in the integument. Spectacle scales were found to differ significantly from other scales in their keratin composition, and gecko spectacle scales in particular were found to lack ß keratin, that hard corneous protein thought to be common to all reptile scales. The concluding chapter will discuss where this research has brought the state of our knowledge on the spectacle and offers thoughts on potentially useful avenues for further research.

The eyes of snakes and most geckos, as well as a number of other disparate squamate taxa, are shielded beneath a layer of transparent integument referred to as the “reptilian spectacle.” Derived from the embryonic fusion of palpebral tissues, the spectacle contains a number of specializations of the skin to benefit vision while still allowing it to function as the primary barrier to the environment. For example, in nearly all species that possess it, it is markedly thinned compared to the surrounding integument and its keratinized scale is optically transparent. While the spectacle may thus seem ideally adapted to vision in allowing the eyes to be always unoccluded, it does have a few drawbacks. One such drawback is its vascularity, the implications of which are still not fully understood, but are explored herein. As no recent synthesis exists of the body of knowledge on reptilian spectacles, the first chapter of this thesis consists of a review of spectacle anatomy, physiology, adaptive significance and evolution to help put into context the following chapters that present original research. The second chapter describes the dynamics of blood flow through the spectacle vasculature of colubrid snakes, demonstrating three main points: (1) that the spectacle vasculature exhibits cycles of regular dilation and constriction, (2) that the visual perception of a threat induces vasoconstriction of its vessels, and (3) that spectacle vessels remain dilated throughout the renewal phase. The implications of these points are discussed. The third chapter describes the spectral transmittance of the shed spectacle scale, the only keratinized structure in the animal kingdom to contribute to the dioptric apparatus of the eye, as well as its thickness. Spectacle scale transmittance and thickness was found to differ dramatically between snakes and geckos and found in snakes to vary between families. The adaptive significance of the observed variation is discussed. The fourth chapter describes biochemical analyses of the shed spectacle scales of snakes and geckos and compares their composition to other scales in the integument. Spectacle scales were found to differ significantly from other scales in their keratin composition, and gecko spectacle scales in particular were found to lack ß keratin, that hard corneous protein thought to be common to all reptile scales. The concluding chapter will discuss where this research has brought the state of our knowledge on the spectacle and offers thoughts on potentially useful avenues for further research.

No description available.

The ubiquitous abundance of organic compounds in natural and anthorpogenically influenced eco-systems has put these compounds into the focus of atmospheric research. Organic compounds have an impact on air quality, climate, and human health. Moreover, they affect particle growth, secondary organic aerosol (SOA) formation, and the global radiation budget by altering particle properties. To investigate the multiphase chemistry of organic compounds and interactions with the aqueous phase in the troposphere, modelling can provide a useful tool. The oxidation of larger organic molecules to the final product CO2 can involve a huge number of intermediate compounds and tens of thousands of reactions. Therefore, the creation of explicit mechanisms relies on automated mechanism construction. Estimation methods for the prediction of the kinetic data needed to describe the degradation of these intermediates are inevitable due to the infeasibility of an experimental determination of all necessary data. Current aqueous phase descriptions of organic chemistry lag behind the gas phase descriptions in atmospheric chemical mechanisms despite its importance for the multiphase chemistry of organic compounds. In this dissertation, the gas phase mechanism Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) has been advanced by a protocol for the description of the oxidation of organic compounds in the aqueous phase. Therefore, a database with kinetic data of 465 aqueous phase hydroxyl radical and 129 aqueous phase nitrate radical reactions with organic compounds has been compiled and evaluated. The database was used to evaluate currently available estimation methods for the prediction of aqueous phase kinetic data of reactions of organic compounds. Among the investigated methods were correlations of gas and aqueous kinetic data, kinetic data of homologous series of various compound classes, reactivity comparisons of inorganic radical oxidants, Evans-Polanyi-type correlations, and structure-activity relationships (SARs). Evans-Polanyi-type correlations have been improved for the purpose of automated mechanism self-generation of mechanisms with large organic molecules. A protocol has been designed based on SARs for hydroxyl radical reactions and the improved Evans-Polanyi-type correlations for nitrate radical reactions with organic compounds. The protocol was assessed in a series of critical sensitivity studies, where uncertainties of critical parameters were investigated. The advanced multiphase generator GECKO-A was used to generate mechanisms, which were applied in box model studies and validated against two sets of aerosol chamber experiments. Experiments differed by the initial compounds used (hexane and trimethylbenzene) and the experimental conditions (UV-C lights off/on and additional in-situ hydroxyl radical source no/yes). Reasonable to good agreement of the modelled and experimental results was achieved in these studies. Finally, GECKO-A was used to create two new CAPRAM version, where, for the first time, branchingratios for different reaction pathways were introduced and the chemistry of compounds with up to four carbon atoms has been extended. The most detailed mechanism comprises 4174 compounds and 7145 processes. Detailed investigations were performed under real tropospheric conditions in urban and remote continental environments. Model results showed significant improvements, especially in regard to the formation of organic aerosol mass. Detailed investigations of concentration-time profiles and chemical fluxes refined the current knowledge of the multiphase processing of organic compounds in the troposphere, but also pointed at current limitations of the generator protocol, the mechanisms created, and current understanding of aqueous phase processes of organic compounds. / Das zahlreiche Vorkommen organischer Verbindungen in natürlichen und anthropogen beeinflussten Ökosystemen hat diese Verbindungen in den Fokus der Atmosphärenforschung gerückt. Organische Verbindungen beeinträchtigen die Luftqualität, die menschliche Gesundheit und das Klima. Weiterhin werden Partikelwachstum und -eigenschaften, sekundäre organische Partikelbildung und dadurch der globale Strahlungshaushalt durch sie beeinflusst. Um die troposphärische Multiphasenchemie organischer Verbindungen und Wechselwirkungen mit der Flüssigphase zu untersuchen, sind Modellstudien hilfreich. Die Oxidation großer organischer Moleküle führt zu einer Vielzahl an Zwischenprodukten. Der Abbau erfolgt in unzähligen Reaktionen bis hin zum Endprodukt CO2. Bei der Entwicklung expliziter Mechanismen muss deshalb für diese Verbindungen auf computergestützte, automatisierte Methoden zurückgegriffen werden. Abschätzungsmethoden für die Vorhersage kinetischer Daten zur Beschreibung des Abbaus der Zwischenprodukte sind unabdingbar, da eine experimentelle Bestimmung aller benötigten Daten nicht realisierbar ist. Die derzeitige Beschreibung der Flüssigphasenchemie unterliegt deutlich den Beschreibungen der Gasphase in atmosphärischen Chemiemechanismen trotz deren Relevanz für die Multiphasenchemie. In dieser Arbeit wurde der Gasphasenmechanismusgenerator GECKO-A (“Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere”) um ein Protokoll zur Oxidation organischer Verbindungen in der Flüssigphase erweitert. Dazu wurde eine Datenbank mit kinetischen Daten von 465 Hydroxylradikal- und 129 Nitratradikalreaktionen mit organischen Verbindungen angelegt und evaluiert. Mit Hilfe der Datenbank wurden derzeitige Abschätzungsmethoden für die Vorhersage kinetischer Daten von Flüssigphasenreaktionen organischer Verbindungen evaluiert. Die untersuchten Methoden beinhalteten Korrelationen kinetischer Daten aus Gas- und Flüssigphase, homologer Reihen verschiedener Stoffklassen, Reaktivitätsvergleiche, Evans-Polanyi-Korrelationen und Struktur-Reaktivitätsbeziehungen. Für die Mechanismusgenerierung großer organischer Moleküle wurden die Evans-Polanyi-Korrelationen in dieser Arbeit weiterentwickelt. Es wurde ein Protokol für die Mechanismusgenerierung entwickelt, das auf Struktur-Reaktivitätsbeziehungen bei Reaktionen von organischen Verbindungen mit OH-Radikalen und auf den erweiterten Evans-Polanyi-Korrelationen bei NO3-Radikalreaktionen beruht. Das Protokoll wurde umfangreich in einer Reihe von Sensitivitätsstudien getestet, um Unsicherheiten kritischer Parameter abzuschätzen. Der erweiterte Multiphasengenerator GECKO-A wurde dazu verwendet, neue Mechanismen zu generieren, die in Boxmodellstudien gegen Aerosolkammerexperimente evaluiert wurden. Die Experimentreihen unterschieden sich sowohl in der betrachteten Ausgangssubstanz (Hexan und Trimethylbenzen) und dem Experimentaufbau (ohne oder mit UV-C-Photolyse und ohne oder mit zusätzlicher partikulärer Hydroxylradikalquelle). Bei den Experimenten konnte eine zufriedenstellende bis gute Übereinstimmung der experimentellen und Modellergebnisse erreicht werden. Weiterhin wurde GECKO-A verwendet, um zwei neue CAPRAM-Versionen mit bis zu 4174 Verbindungen und 7145 Prozessen zu generieren. Erstmals wurden Verzweigungsverhältnisse in CAPRAM eingeführt. Außerdem wurde die Chemie organischer Verbindungen mit bis zu vier Kohlenstoffatomen erweitert. Umfangreiche Untersuchungen unter realistischen troposphärischen Bedingungen in urbanen und ländlichen Gebieten haben deutliche Verbesserungen der erweiterten Mechanismen besonders in Bezug auf Massenzuwachs des organischen Aerosolanteils gezeigt. Das Verständnis der organischen Multiphasenchemie konnte durch detaillierte Untersuchungen zu den Konzentrations-Zeit-Profilen und chemischen Flüssen vertieft werden, aber auch gegenwärtige Limitierungen des Generators, der erzeugten Mechanismen und unseres Verständnisses für Flüssigphasenprozesse organischer Verbindungen aufgezeigt werden.

The ubiquitous abundance of organic compounds in natural and anthorpogenically influenced eco-systems has put these compounds into the focus of atmospheric research. Organic compounds have an impact on air quality, climate, and human health. Moreover, they affect particle growth, secondary organic aerosol (SOA) formation, and the global radiation budget by altering particle properties. To investigate the multiphase chemistry of organic compounds and interactions with the aqueous phase in the troposphere, modelling can provide a useful tool. The oxidation of larger organic molecules to the final product CO2 can involve a huge number of intermediate compounds and tens of thousands of reactions. Therefore, the creation of explicit mechanisms relies on automated mechanism construction. Estimation methods for the prediction of the kinetic data needed to describe the degradation of these intermediates are inevitable due to the infeasibility of an experimental determination of all necessary data. Current aqueous phase descriptions of organic chemistry lag behind the gas phase descriptions in atmospheric chemical mechanisms despite its importance for the multiphase chemistry of organic compounds. In this dissertation, the gas phase mechanism Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) has been advanced by a protocol for the description of the oxidation of organic compounds in the aqueous phase. Therefore, a database with kinetic data of 465 aqueous phase hydroxyl radical and 129 aqueous phase nitrate radical reactions with organic compounds has been compiled and evaluated. The database was used to evaluate currently available estimation methods for the prediction of aqueous phase kinetic data of reactions of organic compounds. Among the investigated methods were correlations of gas and aqueous kinetic data, kinetic data of homologous series of various compound classes, reactivity comparisons of inorganic radical oxidants, Evans-Polanyi-type correlations, and structure-activity relationships (SARs). Evans-Polanyi-type correlations have been improved for the purpose of automated mechanism self-generation of mechanisms with large organic molecules. A protocol has been designed based on SARs for hydroxyl radical reactions and the improved Evans-Polanyi-type correlations for nitrate radical reactions with organic compounds. The protocol was assessed in a series of critical sensitivity studies, where uncertainties of critical parameters were investigated. The advanced multiphase generator GECKO-A was used to generate mechanisms, which were applied in box model studies and validated against two sets of aerosol chamber experiments. Experiments differed by the initial compounds used (hexane and trimethylbenzene) and the experimental conditions (UV-C lights off/on and additional in-situ hydroxyl radical source no/yes). Reasonable to good agreement of the modelled and experimental results was achieved in these studies. Finally, GECKO-A was used to create two new CAPRAM version, where, for the first time, branchingratios for different reaction pathways were introduced and the chemistry of compounds with up to four carbon atoms has been extended. The most detailed mechanism comprises 4174 compounds and 7145 processes. Detailed investigations were performed under real tropospheric conditions in urban and remote continental environments. Model results showed significant improvements, especially in regard to the formation of organic aerosol mass. Detailed investigations of concentration-time profiles and chemical fluxes refined the current knowledge of the multiphase processing of organic compounds in the troposphere, but also pointed at current limitations of the generator protocol, the mechanisms created, and current understanding of aqueous phase processes of organic compounds.:1 Introduction and motivation 2 Theoretical background 2.1 General overview of the tropospheric multiphase chemistry of organic compounds 2.1.1 Gas phase chemistry 2.1.2 Phase transfer 2.1.3 Aqueous phase chemistry 2.2 Tropospheric multiphase chemistry mechanisms 2.2.1 Gas phase mechanisms 2.2.2 Aqueous phase mechanisms 2.2.3 The multiphase mechanism MCMv3.1-CAPRAM 3.0n 2.2.3.1 MCMv3.1 2.2.3.2 CAPRAM 3.0n 2.3 Multiphase chemistry box models 2.3.1 Overview 2.3.2 The model SPACCIM 2.3.2.1 Overview 2.3.2.2 The microphysical scheme 2.3.2.3 The chemical and phase transfer scheme 2.3.2.4 The coupling scheme 2.4 Prediction of aqueous phase kinetic data 2.4.1 Simple correlations 2.4.2 Evans-Polanyi-correlations 2.4.3 Structure-activity relationships 2.5 The generator GECKO-A 3 Evaluation of kinetic data and prediction methods 3.1 Compilation and evaluation of aqueous phase kinetic data 3.2 Extrapolation of gas phase rate constants to the aqueous phase 3.3 Homologous series of compound classes 3.4 Radical reactivity comparisons 3.5 Evans-Polanyi-type correlations 3.5.1 OH rate constant prediction 3.5.2 NO3 rate constant prediction 3.5.3 Development of an advanced Evans-Polanyi-type correlation 3.6 Structure-activity relationships 3.7 Conclusions from the evaluation process 4 Development of the new aqueous phase protocol and its implementation into GECKO-A 4.1 Initialisation and workflow of GECKO-A 4.2 Estimation of phase transfer data 4.3 OH reactions of stable compounds 4.4 NO3 reactions of stable compounds 4.5 Hydration of carbonyl compounds 4.6 Hydrolysis of carbonyl nitrates 4.7 Dissociation of carboxylic acids 4.8 Degradation of radical compounds 4.8.1 RO2 recombinations and cross-reactions 4.8.2 HO2 elimination of ff-hydroxy peroxy radicals 4.8.3 Degradation of acylperoxy radicals 4.8.4 Degradation of fi-carboxyl peroxy radicals 4.8.5 Degradation of alkoxy radicals 4.8.6 Degradation of acyloxy radicals 5 Investigation and refinement of crucial parameters in GECKO-A and CAPRAM mechanism development 5.1 Formation and degradation of polycarbonyl compounds in the protocol 5.2 Influence of the mass accommodation coefficient on the organic multiphase chemistry and composition 5.3 Influence of the cut-off parameter for minor reaction pathways 5.4 Influence of the chosen SAR in the protocol 5.5 Processing of organic mass fraction in the protocol 5.5.1 Parameterisations for radical attack of the overall organic mass fraction 5.5.2 Detailed studies of organic nitrate sinks and sources 5.5.3 Phase transfer of oxygenated organic compounds in the protocol 5.5.4 Decay of alkoxy radicals in the protocol 5.5.5 Revision of the GROMHE thermodynamic database 5.6 Influence of the nitrate radical chemistry 5.7 The final protocol for aqueous phase mechanism self-generation 5.8 CAPRAM mechanism development 5.8.1 CAPRAM 3.0 5.8.2 CAPRAM 3.5 5.8.3 CAPRAM 4.0 6 Model results and discussion 6.1 Comparisons of model results with aerosol chamber experiments 6.1.1 Design of the aerosol chamber experiments 6.1.1.1 Hexane oxidation experiment 6.1.1.2 Trimethylbenzene oxidation experiment 6.1.2 Mechanism generation and model setup 6.1.2.1 Hexane oxidation experiment 6.1.2.2 Trimethylbenzene oxidation experiment 6.1.3 Evaluation of the model versus aerosol chamber results 6.1.3.1 Hexane oxidation experiment 6.1.3.2 Trimethylbenzene oxidation experiment 6.2 Simulations with a ‘real atmosphere’ scenario 6.2.1 Model setup 6.2.2 Meteorological and microphysical parameters 6.2.3 Influence of the extended organic scheme on the particle acidity and SOA formation 6.2.3.1 Particle acidity 6.2.3.2 Particle mass 6.2.4 Influence of the extended organic scheme on inorganic radical oxidants 6.2.4.1 OH chemistry 6.2.4.2 NO3 chemistry 6.2.4.3 Comparison of OH and NO3 chemistry 6.2.4.4 HO2/O2- chemistry 6.2.5 Influence of the extended organic scheme on inorganic non-radical oxidants 6.2.5.1 H2O2 chemistry 6.2.5.2 O3 chemistry 6.2.6 Influence of the extended organic scheme on inorganic particulate matter 6.2.6.1 Sulfate chemistry 6.2.6.2 Nitrate chemistry 6.2.6.3 TMI chemistry 6.2.7 Detailed investigations of selected organic subsystems 6.2.7.1 Monofunctional organic compounds 6.2.7.2 Carbonyl compounds 6.2.7.3 Dicarboxylic acids and functionalised monocarboxylic acids 7 Conclusions References Glossary Acronyms List of symbols List of Figures List of Tables Acknowledgements Curriculum Vitae List of relevant publications Peer-reviewed publications Oral conference contributions Poster conference contributions Appendix A Overview of selected compound classes of tropospheric relevance B Detailed description of the function of SARs C The kinetic database C.1 Reactions of hydroxyl radicals with organic compounds C.2 Reactions of nitrate radicals with organic compounds D Detailed information about the evaluation of prediction methods D.1 Rate data used for the derivation and evaluation of gas-aqueous phase correlations D.2 Explanation of the use of box plots D.3 Additional correlations of homologous series of various compound classes D.4 Additional information of Evans-Polanyi-type correlations D.5 Additional information of structure-activity relationships E Additional information for the development of the protocol of GECKO-A E.1 Investigations on the decay of acylperoxy radicals E.2 Additional information about the sensitivity of mass accomodation coefficients E.3 Additional information about the sensitivity studies concerning the decay of polycarbonyls E.4 Additional information about the sensitivity studies concerning the omission of minor reaction pathways E.5 Additional information about the sensitivity studies concerning the processing of the organic mass fraction E.6 Additional information about the influence of the nitrate radical chemistry F Additional information about the mechanism generation and model initialisation F.1 List of primary compounds used for the generation of CAPRAM 3.5 F.2 List of primary compounds used for the generation of CAPRAM 4.0 F.3 Model initialization of the ‘real atmosphere’ scenarios G The CAPRAM oxidation scheme G.1 Photolysis processes G.2 Inorganic chemistry G.2.1 Phase transfer processes G.2.2 Chemical conversions G.3 Organic chemistry G.3.1 Phase transfer processes G.3.2 Chemical conversions H Detailed information about the model validation with chamber experiments H.1 Additional information about the initialisation of the hexane oxidation experiment H.2 Additional model results from the hexane oxidation experiment H.3 Additional information about the sensitivity runs used in the trimethylbenzene oxidation experiment H.4 Additional results from the TMB oxidation experiment I Additional results from the ‘real atmosphere’ scenario I.1 Particle acidity and SOA formation I.2 Radical oxidants I.3 Organic compounds References of the Appendix / Das zahlreiche Vorkommen organischer Verbindungen in natürlichen und anthropogen beeinflussten Ökosystemen hat diese Verbindungen in den Fokus der Atmosphärenforschung gerückt. Organische Verbindungen beeinträchtigen die Luftqualität, die menschliche Gesundheit und das Klima. Weiterhin werden Partikelwachstum und -eigenschaften, sekundäre organische Partikelbildung und dadurch der globale Strahlungshaushalt durch sie beeinflusst. Um die troposphärische Multiphasenchemie organischer Verbindungen und Wechselwirkungen mit der Flüssigphase zu untersuchen, sind Modellstudien hilfreich. Die Oxidation großer organischer Moleküle führt zu einer Vielzahl an Zwischenprodukten. Der Abbau erfolgt in unzähligen Reaktionen bis hin zum Endprodukt CO2. Bei der Entwicklung expliziter Mechanismen muss deshalb für diese Verbindungen auf computergestützte, automatisierte Methoden zurückgegriffen werden. Abschätzungsmethoden für die Vorhersage kinetischer Daten zur Beschreibung des Abbaus der Zwischenprodukte sind unabdingbar, da eine experimentelle Bestimmung aller benötigten Daten nicht realisierbar ist. Die derzeitige Beschreibung der Flüssigphasenchemie unterliegt deutlich den Beschreibungen der Gasphase in atmosphärischen Chemiemechanismen trotz deren Relevanz für die Multiphasenchemie. In dieser Arbeit wurde der Gasphasenmechanismusgenerator GECKO-A (“Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere”) um ein Protokoll zur Oxidation organischer Verbindungen in der Flüssigphase erweitert. Dazu wurde eine Datenbank mit kinetischen Daten von 465 Hydroxylradikal- und 129 Nitratradikalreaktionen mit organischen Verbindungen angelegt und evaluiert. Mit Hilfe der Datenbank wurden derzeitige Abschätzungsmethoden für die Vorhersage kinetischer Daten von Flüssigphasenreaktionen organischer Verbindungen evaluiert. Die untersuchten Methoden beinhalteten Korrelationen kinetischer Daten aus Gas- und Flüssigphase, homologer Reihen verschiedener Stoffklassen, Reaktivitätsvergleiche, Evans-Polanyi-Korrelationen und Struktur-Reaktivitätsbeziehungen. Für die Mechanismusgenerierung großer organischer Moleküle wurden die Evans-Polanyi-Korrelationen in dieser Arbeit weiterentwickelt. Es wurde ein Protokol für die Mechanismusgenerierung entwickelt, das auf Struktur-Reaktivitätsbeziehungen bei Reaktionen von organischen Verbindungen mit OH-Radikalen und auf den erweiterten Evans-Polanyi-Korrelationen bei NO3-Radikalreaktionen beruht. Das Protokoll wurde umfangreich in einer Reihe von Sensitivitätsstudien getestet, um Unsicherheiten kritischer Parameter abzuschätzen. Der erweiterte Multiphasengenerator GECKO-A wurde dazu verwendet, neue Mechanismen zu generieren, die in Boxmodellstudien gegen Aerosolkammerexperimente evaluiert wurden. Die Experimentreihen unterschieden sich sowohl in der betrachteten Ausgangssubstanz (Hexan und Trimethylbenzen) und dem Experimentaufbau (ohne oder mit UV-C-Photolyse und ohne oder mit zusätzlicher partikulärer Hydroxylradikalquelle). Bei den Experimenten konnte eine zufriedenstellende bis gute Übereinstimmung der experimentellen und Modellergebnisse erreicht werden. Weiterhin wurde GECKO-A verwendet, um zwei neue CAPRAM-Versionen mit bis zu 4174 Verbindungen und 7145 Prozessen zu generieren. Erstmals wurden Verzweigungsverhältnisse in CAPRAM eingeführt. Außerdem wurde die Chemie organischer Verbindungen mit bis zu vier Kohlenstoffatomen erweitert. Umfangreiche Untersuchungen unter realistischen troposphärischen Bedingungen in urbanen und ländlichen Gebieten haben deutliche Verbesserungen der erweiterten Mechanismen besonders in Bezug auf Massenzuwachs des organischen Aerosolanteils gezeigt. Das Verständnis der organischen Multiphasenchemie konnte durch detaillierte Untersuchungen zu den Konzentrations-Zeit-Profilen und chemischen Flüssen vertieft werden, aber auch gegenwärtige Limitierungen des Generators, der erzeugten Mechanismen und unseres Verständnisses für Flüssigphasenprozesse organischer Verbindungen aufgezeigt werden.:1 Introduction and motivation 2 Theoretical background 2.1 General overview of the tropospheric multiphase chemistry of organic compounds 2.1.1 Gas phase chemistry 2.1.2 Phase transfer 2.1.3 Aqueous phase chemistry 2.2 Tropospheric multiphase chemistry mechanisms 2.2.1 Gas phase mechanisms 2.2.2 Aqueous phase mechanisms 2.2.3 The multiphase mechanism MCMv3.1-CAPRAM 3.0n 2.2.3.1 MCMv3.1 2.2.3.2 CAPRAM 3.0n 2.3 Multiphase chemistry box models 2.3.1 Overview 2.3.2 The model SPACCIM 2.3.2.1 Overview 2.3.2.2 The microphysical scheme 2.3.2.3 The chemical and phase transfer scheme 2.3.2.4 The coupling scheme 2.4 Prediction of aqueous phase kinetic data 2.4.1 Simple correlations 2.4.2 Evans-Polanyi-correlations 2.4.3 Structure-activity relationships 2.5 The generator GECKO-A 3 Evaluation of kinetic data and prediction methods 3.1 Compilation and evaluation of aqueous phase kinetic data 3.2 Extrapolation of gas phase rate constants to the aqueous phase 3.3 Homologous series of compound classes 3.4 Radical reactivity comparisons 3.5 Evans-Polanyi-type correlations 3.5.1 OH rate constant prediction 3.5.2 NO3 rate constant prediction 3.5.3 Development of an advanced Evans-Polanyi-type correlation 3.6 Structure-activity relationships 3.7 Conclusions from the evaluation process 4 Development of the new aqueous phase protocol and its implementation into GECKO-A 4.1 Initialisation and workflow of GECKO-A 4.2 Estimation of phase transfer data 4.3 OH reactions of stable compounds 4.4 NO3 reactions of stable compounds 4.5 Hydration of carbonyl compounds 4.6 Hydrolysis of carbonyl nitrates 4.7 Dissociation of carboxylic acids 4.8 Degradation of radical compounds 4.8.1 RO2 recombinations and cross-reactions 4.8.2 HO2 elimination of ff-hydroxy peroxy radicals 4.8.3 Degradation of acylperoxy radicals 4.8.4 Degradation of fi-carboxyl peroxy radicals 4.8.5 Degradation of alkoxy radicals 4.8.6 Degradation of acyloxy radicals 5 Investigation and refinement of crucial parameters in GECKO-A and CAPRAM mechanism development 5.1 Formation and degradation of polycarbonyl compounds in the protocol 5.2 Influence of the mass accommodation coefficient on the organic multiphase chemistry and composition 5.3 Influence of the cut-off parameter for minor reaction pathways 5.4 Influence of the chosen SAR in the protocol 5.5 Processing of organic mass fraction in the protocol 5.5.1 Parameterisations for radical attack of the overall organic mass fraction 5.5.2 Detailed studies of organic nitrate sinks and sources 5.5.3 Phase transfer of oxygenated organic compounds in the protocol 5.5.4 Decay of alkoxy radicals in the protocol 5.5.5 Revision of the GROMHE thermodynamic database 5.6 Influence of the nitrate radical chemistry 5.7 The final protocol for aqueous phase mechanism self-generation 5.8 CAPRAM mechanism development 5.8.1 CAPRAM 3.0 5.8.2 CAPRAM 3.5 5.8.3 CAPRAM 4.0 6 Model results and discussion 6.1 Comparisons of model results with aerosol chamber experiments 6.1.1 Design of the aerosol chamber experiments 6.1.1.1 Hexane oxidation experiment 6.1.1.2 Trimethylbenzene oxidation experiment 6.1.2 Mechanism generation and model setup 6.1.2.1 Hexane oxidation experiment 6.1.2.2 Trimethylbenzene oxidation experiment 6.1.3 Evaluation of the model versus aerosol chamber results 6.1.3.1 Hexane oxidation experiment 6.1.3.2 Trimethylbenzene oxidation experiment 6.2 Simulations with a ‘real atmosphere’ scenario 6.2.1 Model setup 6.2.2 Meteorological and microphysical parameters 6.2.3 Influence of the extended organic scheme on the particle acidity and SOA formation 6.2.3.1 Particle acidity 6.2.3.2 Particle mass 6.2.4 Influence of the extended organic scheme on inorganic radical oxidants 6.2.4.1 OH chemistry 6.2.4.2 NO3 chemistry 6.2.4.3 Comparison of OH and NO3 chemistry 6.2.4.4 HO2/O2- chemistry 6.2.5 Influence of the extended organic scheme on inorganic non-radical oxidants 6.2.5.1 H2O2 chemistry 6.2.5.2 O3 chemistry 6.2.6 Influence of the extended organic scheme on inorganic particulate matter 6.2.6.1 Sulfate chemistry 6.2.6.2 Nitrate chemistry 6.2.6.3 TMI chemistry 6.2.7 Detailed investigations of selected organic subsystems 6.2.7.1 Monofunctional organic compounds 6.2.7.2 Carbonyl compounds 6.2.7.3 Dicarboxylic acids and functionalised monocarboxylic acids 7 Conclusions References Glossary Acronyms List of symbols List of Figures List of Tables Acknowledgements Curriculum Vitae List of relevant publications Peer-reviewed publications Oral conference contributions Poster conference contributions Appendix A Overview of selected compound classes of tropospheric relevance B Detailed description of the function of SARs C The kinetic database C.1 Reactions of hydroxyl radicals with organic compounds C.2 Reactions of nitrate radicals with organic compounds D Detailed information about the evaluation of prediction methods D.1 Rate data used for the derivation and evaluation of gas-aqueous phase correlations D.2 Explanation of the use of box plots D.3 Additional correlations of homologous series of various compound classes D.4 Additional information of Evans-Polanyi-type correlations D.5 Additional information of structure-activity relationships E Additional information for the development of the protocol of GECKO-A E.1 Investigations on the decay of acylperoxy radicals E.2 Additional information about the sensitivity of mass accomodation coefficients E.3 Additional information about the sensitivity studies concerning the decay of polycarbonyls E.4 Additional information about the sensitivity studies concerning the omission of minor reaction pathways E.5 Additional information about the sensitivity studies concerning the processing of the organic mass fraction E.6 Additional information about the influence of the nitrate radical chemistry F Additional information about the mechanism generation and model initialisation F.1 List of primary compounds used for the generation of CAPRAM 3.5 F.2 List of primary compounds used for the generation of CAPRAM 4.0 F.3 Model initialization of the ‘real atmosphere’ scenarios G The CAPRAM oxidation scheme G.1 Photolysis processes G.2 Inorganic chemistry G.2.1 Phase transfer processes G.2.2 Chemical conversions G.3 Organic chemistry G.3.1 Phase transfer processes G.3.2 Chemical conversions H Detailed information about the model validation with chamber experiments H.1 Additional information about the initialisation of the hexane oxidation experiment H.2 Additional model results from the hexane oxidation experiment H.3 Additional information about the sensitivity runs used in the trimethylbenzene oxidation experiment H.4 Additional results from the TMB oxidation experiment I Additional results from the ‘real atmosphere’ scenario I.1 Particle acidity and SOA formation I.2 Radical oxidants I.3 Organic compounds References of the Appendix

Scar-free wound healing and regeneration are uncommon phenomena permitting the near complete restoration of damaged tissues, organs and structures. Although rare in mammals, many lizards are able to undergo scarless healing and regeneration following loss of the tail. This study investigated the spontaneous and intrinsic capacity of the leopard gecko (Eublepharis macularius) tail to undergo scar-free wound healing and regeneration following two different forms of tail loss: autotomy, a voluntary and evolved mechanism of tail shedding at fracture planes; and surgical amputation, involuntary loss of the tail outside the fracture planes. Furthermore, I investigated the ability of the regenerate tail to regenerate by amputating a regenerate tail (previously lost by autotomy). To investigate these phenomena I imaged wound healing and regenereating tails daily (following autotomy and amputation) to document gross morphological changes. I used histochemistry to document tissue structure and immunohistochemistry to determine the tissue/cellular location of my five proteins of interest (PCNA, MMP-9, WE6, α-sma, TGF-β3). Each of these proteins of interest has been previously documented during wound healing and/or regeneration in other wound healing/regeneration model organisms (e.g. mice, urodeles, lizards, zebrafish). Scar-free wound healing and regeneration occurred following autotomy, amputation of the original tail and amputation of the regenerate tail, indicating that the leopard gecko tail has an instrinsic scar-free wound healing and regenerative capacity that is independent of the mode of tail loss (autotomy or amputation). Furthermore immunohistochemistry revealed a conserved sequence and location of the expression of the five proteins of interest following both forms of tail loss. These results provide the basis for further studies investigating scar-free wound healing and regeneration in a novel amniote model, the leopard gecko. / NSERC

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