In Chapter 1, I discuss the background to the problems which confront a realist account of the growth of scientific knowledge. At the beginning of Chapter 2, I explain in what sense relativism constitutes a challenge to this account. Four interconnected questions are then posed which are said to underlie the realist position. The chapter finishes with an explanation of how some of them arise in an actual case study. Chapter 3 deals with a general argument of Quine's for the view that reference is inscrutable. In reply I maintain that the argument does not hold good, either with respect to interpreting our own language or when it comes to translating an alien language. With Chapter 4, I begin to answer the four questions. I explain how Tarski's theory of truth can be seen as a correspondence theory. It is argued, however, that Tarski's theory itself presupposes theories of reference and extension, and certain recent attempts to overcome this lacuna are criticized. In the next chapter I draw an analogy between natural kind predicates, which are of particular importance in science, and proper names, and offer cluster theories of reference for both. This answers the third most basic of the four questions. These theories are defended against criticisms made by Kripke and Putnam, Chapter 6 aims to answer the second most basic question by considering in detail how we can understand what earlier scientific theories were about. I develop some arguments of Davidson's as a counter to Quine's doctrine of the indeterminacy of translation of sentences. I claim that although translation might in fact be indeterminate, Quine, through concentrating on behavioural evidence to the exclusion of other physical evidence, has failed to show that it is, and that in any case indeterminacy of sentence translation does not imply inscrutability of reference of terms. Finally, in Chapter 7, I sum up ray explication of the realist's account of the growth of science with respect to natural kind predicates. I then consider two cases of theory change of different sorts and suggest how my work might be extended.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 1990. / Includes bibliographical references (p. 129-130). / Sponsored by NASA. NAGW-21 / Terrence W. Fong. / M.S.

Usando incorporação \"in vivo\" de 35S metionina tradução \"in vitro\" de RNA e eletroforese bidimensional, iniciamos um estudo do controle da síntese de proteínas durante duas fases distintas de diferenciação celular, a esporulação e a germinação, do fungo Blastocladiella emersonii. Durante a esporulação ocorre uma intensa variação no padrão de síntese proteica. Foi analisada a síntese de 108 proteínas, sendo verificado que o aumento na síntese de várias proteínas está associado com estágios definidos da esporulação. Um grande número de proteínas básicas é sintetizado exclusivamente no final da esporulação, que corresponde à fase de diferenciação dos zoósporos. Também foram detectadas drásticas variações na população de mRNAs ao longo de toda a esporulação. A síntese de várias proteínas típicas da esporulação parece ser controlada ao nível da transcrição. Além disso a maioria dos RNAs mensageiros específicos da esporulação não é conservada nos zoósporos maduros; o zoósporos contém mRNAs armazenados que provavelmente são sintetizados nos últimos 30 minutos da esporulação. Durante a transição dos zoósporos a células redondas, que ocorre nos primeiros 25 minutos após a indução da germinação em meio inorgânico, não foram verificadas diferenças qualitativas no padrão de síntese proteica, tanto na ausência como na presença de actinomicina D, indicando que os eventos precoces da germinação são inteiramente pré-programados pelo mRNA que está armazenado nos zoósporos. Contudo, na germinação tardia são verificadas profundas variações no padrão de síntese proteica. A síntese de algumas dessas proteínas (seis polipeptídios), provavelmente corresponde a uma tradução seletiva de mensagens armazenadas nos zoósporos, enquanto que a maioria das novas proteínas expressas (vinte e dois polipeptídios) corresponde a tradução de novos mRNAs. Assim, durante a germinação dos zoósporos, ocorrem múltiplos níveis de regulação da síntese proteica, envolvendo controles ao nível da tradução e transcrição. Durante o início da germinação também foi observado um controle ao nível de pós-traduçãoo, com várias proteínas dos zoósporos sendo especificamente degradadas ou modificadas. Também analisamos o padrão das proteínas sintetizadas durante a germinação em meio nutriente sendo observada a síntese de polipeptídios específicos desta condição de germinação e crescimento. Algumas proteínas cuja síntese é controlada pelo desenvolvimento foram identificadas. Utilizando anticorpos monoclonais comerciais contra actina, α e β-turbulinas foip-tubulinas foi possível identificar estas proteínas no perfil eletroforético de proteínas sintetizadas durante a esporulação. Comparando a cinética da síntese \"oin vitro\" destas proteínas com o acúmulo de seus respectivos mRNAs traduzidos \"in vitro\", o, foi possível demonstrar que o intenso aumento na síntese de actina, α e β-tubulinas que ocorre durante a esporulação apresenta uma correlação temporal com o aumento dos mRNAs correspondentes. Em paralelo ao aumento da síntese destas três proteínas citoesqueLéticas pôde ser detectado um aumento dos seus conteúdos em massa. Durante a germinação e crescimento ocorre uma sensível diminuição no conteúdo destas proteínas. Além disso, verificamos que as proteínas identificadas como α e β-tubulinas estão presentes no flagelo dos zoósporos. Muito interessante foi a observação de que três proteínas sintetizadas durante a esporulação correspondiam aparentemente a três proteínas, Hsp70, Hsp76 e Hsp39a, cuja síntese é induzida pelo choque térmico. Esta verificação decorreu do fato de estarmos investigando se em Blastocladiella a resposta ao choque térmico teria algum controle do desenvolvimento, uma vez que alguns dados da literatura sugeriam o envolvimento de certas proteínas de choque térmico (Hsps) no desenvolvimento normal de alguns organismos. Em Blastocladiella a resposta ao choque térmico é dependente do estágio do desenvolvimento. Células expostas a temperaturas elevadas nos diferentes estágios do desenvolvimento (esporulação, germinação e crescimento) mostram uma síntese diferencial de proteínas de choque térmico. Conjuntos específicos de Hsps (de um total de 22 Hsps) são induzidos em cada fase, demonstrando uma expressão não coordenada dos genes de choque térmico. A proteína de 70 kDa, sintetizada espontaneamente durante um certo intervalo da esporulação, apresenta mobilidade eletroforética em géis bidimensionais idêntica à Hsp70. A confirmação da identidade entre estas proteínas foi obtida através de análise dos seus peptídios resultantes de digestão enzimática parcial bem como pelo reconhecimento de ambas as proteínas por anticorpos contra a proteína DnaK (homóloga à Hsp70> de E. coli e contra a proteína Hsp70 de Drosophila. Utilizando tradução o\"in vitro\"o de RNA e hibridização de RNA com uma sonda do gene hsp70 de Drosophila, demonstramos que o aumento de síntese da Hsp70 que ocorre durante o choque térmico e espontaneamente durante a esporulação, está associado com a acumulação do mRNA desta proteína. Embora a síntese de Hsps seja controlada pelo desenvolvimento em Blastocladiella, a aquisição de termotolerância pode ser induzida em qualquer estágio do seu ciclo de vida. A indução da termotolerância em Blastocladiella é dependente da síntese de proteínas e está correlacionada com o aumento da síntese de algumas Hsps: Hsp82a, Hsp82b, Hsp76, Hsp70, Hsp60,Hsp25 e Hsp17b. As outras Hsps parecem não estar envolvidas especificamente com a termotolerância. As observações anteriores de que o estado de fosforilação da proteína ribossômica 56, em Blastocladiella, varia durante o desenvolvimento e em resposta a alterações do meio ambiente (Bonato et al., 1984, Eur. J. Biochem. 144:597-606) e a verificação de que a resposta ao choque térmico, em Blastocladiella, também está sob o controle do desenvolvimento proporcionou a oportunidade de verificar se os diferentes níveis de fosforilação de 56 poderiam ser correlacionados com a tradução de mensageiros específicos isto é, mRNAs normais ou de choque térmico durante o choque térmico, recuperação do choque térmico e indução de termotolerância nos diferentes estágios do ciclo de vida deste fungo. Assim foi observado que, independente do estado inicial de fosforilação de 56 (máximo ou intermediário>, ocorre uma rápida e completa desfosforilação de 56 durante o choque térmico, sendo que a 56 permanece desfosforilada durante a termotolerância. Durante a recuperação do choque térmico, ocorre a refosforilação de 56 para os níveis característicos de cada estágio do desenvolvimento, coincidentemente com a interrupção da síntese de proteínas de choque térmico. / Using 35S methionine pulse labeling in vitro translation and two-dimensional gel electrophoresis, we investigated the regulation of protein synthesis during two distinct phases of cell differentiation, sporulation and germination, in the aquatic fungus Blastocladiella emersonii. We have found dramatic changes in the spectrum of proteins synthesized during sporulation. Synthesis of 108 polypeptides was analyzed and a large increase in the synthesis of several proteins is associated with particular stages. A large number of basic proteins are synthesized exclusively during late sporulation. Changes in translatable mRNA species were also detected by in vitro translation of RNA prepared at different stages of sporulation. The synthesis of several proteins during sporulation seems to be transcriptionally controlled. Most of the sporulationspecific messages are not present in the mature zoospores; the zoospores contain stored mRNA, which is apparently synthesized in the last 30 min of sporulation.We analyzed the pattern of proteins synthesized during zoospore germination in an inorganic solution, in both the presence and absence of actinomycin D. During the transition from zoospore to round cells (the first 25 min), essentially no qualitative differences were noticeable, indicating that the earliest stages of germination are entirely preprogrammed with stored RNA. Later in germination (after 25 min), however, changes in the pattern of protein synthesis were found. Some of these proteins (a total of 6 polypeptides) correspond possibly to a selective translation of stored messages, whereas the majority of the changed proteins (22 polypeptides) corresponds to newly synthesized mRNA. Thus, multiple levels of protein synthesis regulation seem to occur during zoospore germination, involving both transcriptional and translational controls. We also analyzed the pattern of protein synthesis during germination in a nutrient medium; synthesis of specific polypeptides occurred during late germination. During early germination posttranslational control was also observed, several labeled proteins from zoospores being specifically degraded or charge modified. Some proteins whose expression is developmentally regulated were identified. Actin, α- and β-tubulin have been identified in the two-dimensional pattern of proteins synthesized during sporulation by using well characterized monoclonal antibodies and western blotting. We compared the kinetics of synthesis of these proteins, by pulse-labeling experiments with ‌35S‌methionine, with the accumulation of their corresponding mRNAs, translated in a cell-free system. Large increases occur in the rates of actin and α- and β-tubulin biosynthesis during sporulation and there is an accumulation of the corresponding mRNAs. In parallel to the increased synthesis, these cytoskeletal proteins accumulate during the late stage of sporulation. During germination and early growth there is a strong decrease in the level of these proteins. We also verified that α- and β-tubulin are present in flagellar axonemes of zoopores. Very interesting was the observation that three proteins spontaneously expressed during sporulation correspond possibly to three heat shock-induced proteins CHsp70, Hsp76, Hsp39a). This fact was noticed when we were investigating the heat shock-response during the development of Blastocladiella. The heat-shock response in Blastocladiella is dependent on the developmental stage. Cells exposed to elevated temperatures at different stages of life cycle (sporulation, germination or growth) show a differential synthesis of heat-shock proteins (Hsps). Of a total af 22 polypeptides induced, particular subsets of Hsps appear in each phase, demonstrating a non-coordinate heat-shock gene expression. By the criteria of two-dimensional gel electrophoresis and partial proteolysis mapping, the 70-kDa protein, whose synthesis is induced spontaneously during sporulation, is indistinguishable from the heat-inducible hsp70. Additional evidence in support of the identity between the 70-kDa protein and Hsp70 was provided by immunological cross-reaction of both proteins with antibodies against DnaK protein from E.coli and Hsp70 from Drosophila. The techniques of in vitro translation, and Northern analysis using a Drosophila hsp70 probe, demonstrated that enhanced synthesis of hsp70, which occurs during heat-shock treatment and spontaneously during sporulation, is associated with an accumulation of Hsp70 mRNA. Although the Hsps synthesis is developmentally regulated in Blastocladiella, the acquisition of thermotolerance can be induced at any stage of the life cycle. lhe development of thermotolerance is correlated with the enhanced synthesis of some heat-shock proteins: Hsp82a, Hsp82b, Hsp76, Hsp70, Hsp60, Hsp25, Hsp17b. Other Hsps are not specifically involved in thermotolerance. In B. emersonii the state of 56 phosphorylation changes depending on the developmental stage and environmental conditions (Bonato et al., 1984, Eur. J. Biochem. 144, 597-606). On the other hand, we verified that the heat-shock response is developmentally regulated. Then, we examined the changes in 56 phosphorylation during heat shock, thermotolerance, and recovery from heat shock at different stages of life cycle in order to investigate whether the different levels of 56 phosphorylation might be correlated with the translation of specific message subsets. We observed that independently of the initial state of 56 phosphorylation (maximal or intermediate), a rapid and complete dephosphorylation of 56 is induced by heat shock and 56 remains unphosphorylated during the acquired thermotolerance. During recovery from heat shock rephosphorylation of 56 occurs always to the levels characteristic of that particular stage, coincidently with the turn off of heat shock protein synthesis.

Usando incorporação \"in vivo\" de 35S metionina tradução \"in vitro\" de RNA e eletroforese bidimensional, iniciamos um estudo do controle da síntese de proteínas durante duas fases distintas de diferenciação celular, a esporulação e a germinação, do fungo Blastocladiella emersonii. Durante a esporulação ocorre uma intensa variação no padrão de síntese proteica. Foi analisada a síntese de 108 proteínas, sendo verificado que o aumento na síntese de várias proteínas está associado com estágios definidos da esporulação. Um grande número de proteínas básicas é sintetizado exclusivamente no final da esporulação, que corresponde à fase de diferenciação dos zoósporos. Também foram detectadas drásticas variações na população de mRNAs ao longo de toda a esporulação. A síntese de várias proteínas típicas da esporulação parece ser controlada ao nível da transcrição. Além disso a maioria dos RNAs mensageiros específicos da esporulação não é conservada nos zoósporos maduros; o zoósporos contém mRNAs armazenados que provavelmente são sintetizados nos últimos 30 minutos da esporulação. Durante a transição dos zoósporos a células redondas, que ocorre nos primeiros 25 minutos após a indução da germinação em meio inorgânico, não foram verificadas diferenças qualitativas no padrão de síntese proteica, tanto na ausência como na presença de actinomicina D, indicando que os eventos precoces da germinação são inteiramente pré-programados pelo mRNA que está armazenado nos zoósporos. Contudo, na germinação tardia são verificadas profundas variações no padrão de síntese proteica. A síntese de algumas dessas proteínas (seis polipeptídios), provavelmente corresponde a uma tradução seletiva de mensagens armazenadas nos zoósporos, enquanto que a maioria das novas proteínas expressas (vinte e dois polipeptídios) corresponde a tradução de novos mRNAs. Assim, durante a germinação dos zoósporos, ocorrem múltiplos níveis de regulação da síntese proteica, envolvendo controles ao nível da tradução e transcrição. Durante o início da germinação também foi observado um controle ao nível de pós-traduçãoo, com várias proteínas dos zoósporos sendo especificamente degradadas ou modificadas. Também analisamos o padrão das proteínas sintetizadas durante a germinação em meio nutriente sendo observada a síntese de polipeptídios específicos desta condição de germinação e crescimento. Algumas proteínas cuja síntese é controlada pelo desenvolvimento foram identificadas. Utilizando anticorpos monoclonais comerciais contra actina, α e β-turbulinas foip-tubulinas foi possível identificar estas proteínas no perfil eletroforético de proteínas sintetizadas durante a esporulação. Comparando a cinética da síntese \"oin vitro\" destas proteínas com o acúmulo de seus respectivos mRNAs traduzidos \"in vitro\", o, foi possível demonstrar que o intenso aumento na síntese de actina, α e β-tubulinas que ocorre durante a esporulação apresenta uma correlação temporal com o aumento dos mRNAs correspondentes. Em paralelo ao aumento da síntese destas três proteínas citoesqueLéticas pôde ser detectado um aumento dos seus conteúdos em massa. Durante a germinação e crescimento ocorre uma sensível diminuição no conteúdo destas proteínas. Além disso, verificamos que as proteínas identificadas como α e β-tubulinas estão presentes no flagelo dos zoósporos. Muito interessante foi a observação de que três proteínas sintetizadas durante a esporulação correspondiam aparentemente a três proteínas, Hsp70, Hsp76 e Hsp39a, cuja síntese é induzida pelo choque térmico. Esta verificação decorreu do fato de estarmos investigando se em Blastocladiella a resposta ao choque térmico teria algum controle do desenvolvimento, uma vez que alguns dados da literatura sugeriam o envolvimento de certas proteínas de choque térmico (Hsps) no desenvolvimento normal de alguns organismos. Em Blastocladiella a resposta ao choque térmico é dependente do estágio do desenvolvimento. Células expostas a temperaturas elevadas nos diferentes estágios do desenvolvimento (esporulação, germinação e crescimento) mostram uma síntese diferencial de proteínas de choque térmico. Conjuntos específicos de Hsps (de um total de 22 Hsps) são induzidos em cada fase, demonstrando uma expressão não coordenada dos genes de choque térmico. A proteína de 70 kDa, sintetizada espontaneamente durante um certo intervalo da esporulação, apresenta mobilidade eletroforética em géis bidimensionais idêntica à Hsp70. A confirmação da identidade entre estas proteínas foi obtida através de análise dos seus peptídios resultantes de digestão enzimática parcial bem como pelo reconhecimento de ambas as proteínas por anticorpos contra a proteína DnaK (homóloga à Hsp70> de E. coli e contra a proteína Hsp70 de Drosophila. Utilizando tradução o\"in vitro\"o de RNA e hibridização de RNA com uma sonda do gene hsp70 de Drosophila, demonstramos que o aumento de síntese da Hsp70 que ocorre durante o choque térmico e espontaneamente durante a esporulação, está associado com a acumulação do mRNA desta proteína. Embora a síntese de Hsps seja controlada pelo desenvolvimento em Blastocladiella, a aquisição de termotolerância pode ser induzida em qualquer estágio do seu ciclo de vida. A indução da termotolerância em Blastocladiella é dependente da síntese de proteínas e está correlacionada com o aumento da síntese de algumas Hsps: Hsp82a, Hsp82b, Hsp76, Hsp70, Hsp60,Hsp25 e Hsp17b. As outras Hsps parecem não estar envolvidas especificamente com a termotolerância. As observações anteriores de que o estado de fosforilação da proteína ribossômica 56, em Blastocladiella, varia durante o desenvolvimento e em resposta a alterações do meio ambiente (Bonato et al., 1984, Eur. J. Biochem. 144:597-606) e a verificação de que a resposta ao choque térmico, em Blastocladiella, também está sob o controle do desenvolvimento proporcionou a oportunidade de verificar se os diferentes níveis de fosforilação de 56 poderiam ser correlacionados com a tradução de mensageiros específicos isto é, mRNAs normais ou de choque térmico durante o choque térmico, recuperação do choque térmico e indução de termotolerância nos diferentes estágios do ciclo de vida deste fungo. Assim foi observado que, independente do estado inicial de fosforilação de 56 (máximo ou intermediário>, ocorre uma rápida e completa desfosforilação de 56 durante o choque térmico, sendo que a 56 permanece desfosforilada durante a termotolerância. Durante a recuperação do choque térmico, ocorre a refosforilação de 56 para os níveis característicos de cada estágio do desenvolvimento, coincidentemente com a interrupção da síntese de proteínas de choque térmico. / Using 35S methionine pulse labeling in vitro translation and two-dimensional gel electrophoresis, we investigated the regulation of protein synthesis during two distinct phases of cell differentiation, sporulation and germination, in the aquatic fungus Blastocladiella emersonii. We have found dramatic changes in the spectrum of proteins synthesized during sporulation. Synthesis of 108 polypeptides was analyzed and a large increase in the synthesis of several proteins is associated with particular stages. A large number of basic proteins are synthesized exclusively during late sporulation. Changes in translatable mRNA species were also detected by in vitro translation of RNA prepared at different stages of sporulation. The synthesis of several proteins during sporulation seems to be transcriptionally controlled. Most of the sporulationspecific messages are not present in the mature zoospores; the zoospores contain stored mRNA, which is apparently synthesized in the last 30 min of sporulation.We analyzed the pattern of proteins synthesized during zoospore germination in an inorganic solution, in both the presence and absence of actinomycin D. During the transition from zoospore to round cells (the first 25 min), essentially no qualitative differences were noticeable, indicating that the earliest stages of germination are entirely preprogrammed with stored RNA. Later in germination (after 25 min), however, changes in the pattern of protein synthesis were found. Some of these proteins (a total of 6 polypeptides) correspond possibly to a selective translation of stored messages, whereas the majority of the changed proteins (22 polypeptides) corresponds to newly synthesized mRNA. Thus, multiple levels of protein synthesis regulation seem to occur during zoospore germination, involving both transcriptional and translational controls. We also analyzed the pattern of protein synthesis during germination in a nutrient medium; synthesis of specific polypeptides occurred during late germination. During early germination posttranslational control was also observed, several labeled proteins from zoospores being specifically degraded or charge modified. Some proteins whose expression is developmentally regulated were identified. Actin, α- and β-tubulin have been identified in the two-dimensional pattern of proteins synthesized during sporulation by using well characterized monoclonal antibodies and western blotting. We compared the kinetics of synthesis of these proteins, by pulse-labeling experiments with ‌35S‌methionine, with the accumulation of their corresponding mRNAs, translated in a cell-free system. Large increases occur in the rates of actin and α- and β-tubulin biosynthesis during sporulation and there is an accumulation of the corresponding mRNAs. In parallel to the increased synthesis, these cytoskeletal proteins accumulate during the late stage of sporulation. During germination and early growth there is a strong decrease in the level of these proteins. We also verified that α- and β-tubulin are present in flagellar axonemes of zoopores. Very interesting was the observation that three proteins spontaneously expressed during sporulation correspond possibly to three heat shock-induced proteins CHsp70, Hsp76, Hsp39a). This fact was noticed when we were investigating the heat shock-response during the development of Blastocladiella. The heat-shock response in Blastocladiella is dependent on the developmental stage. Cells exposed to elevated temperatures at different stages of life cycle (sporulation, germination or growth) show a differential synthesis of heat-shock proteins (Hsps). Of a total af 22 polypeptides induced, particular subsets of Hsps appear in each phase, demonstrating a non-coordinate heat-shock gene expression. By the criteria of two-dimensional gel electrophoresis and partial proteolysis mapping, the 70-kDa protein, whose synthesis is induced spontaneously during sporulation, is indistinguishable from the heat-inducible hsp70. Additional evidence in support of the identity between the 70-kDa protein and Hsp70 was provided by immunological cross-reaction of both proteins with antibodies against DnaK protein from E.coli and Hsp70 from Drosophila. The techniques of in vitro translation, and Northern analysis using a Drosophila hsp70 probe, demonstrated that enhanced synthesis of hsp70, which occurs during heat-shock treatment and spontaneously during sporulation, is associated with an accumulation of Hsp70 mRNA. Although the Hsps synthesis is developmentally regulated in Blastocladiella, the acquisition of thermotolerance can be induced at any stage of the life cycle. lhe development of thermotolerance is correlated with the enhanced synthesis of some heat-shock proteins: Hsp82a, Hsp82b, Hsp76, Hsp70, Hsp60, Hsp25, Hsp17b. Other Hsps are not specifically involved in thermotolerance. In B. emersonii the state of 56 phosphorylation changes depending on the developmental stage and environmental conditions (Bonato et al., 1984, Eur. J. Biochem. 144, 597-606). On the other hand, we verified that the heat-shock response is developmentally regulated. Then, we examined the changes in 56 phosphorylation during heat shock, thermotolerance, and recovery from heat shock at different stages of life cycle in order to investigate whether the different levels of 56 phosphorylation might be correlated with the translation of specific message subsets. We observed that independently of the initial state of 56 phosphorylation (maximal or intermediate), a rapid and complete dephosphorylation of 56 is induced by heat shock and 56 remains unphosphorylated during the acquired thermotolerance. During recovery from heat shock rephosphorylation of 56 occurs always to the levels characteristic of that particular stage, coincidently with the turn off of heat shock protein synthesis.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2005. / Härtill 4 uppsatser.

A range of mesoporous materials based on SBA-15 have been prepared and characterised. The materials were templated by neutral block copolymer P123, and typically have a hexagonal (p6mm) pore structure, with high surface areas and narrow pore size distributions. The removal of the surfactant template by calcination and solvent extraction has been investigated. The aqueous stability of this material, and the hydrolysis of the surface was studied. Organic functional groups were incorporated into the silica surface by co-condensation, or by post synthesis grafting. A range of functional groups were incorporated, including amine, carboxy, allyl and thiol groups. The pore size of the materials was controlled by the addition of trimethoxybenzene during synthesis, which significantly increased the pore size and uptake capacity of the materials. The adsorption of CALB by SBA-15 was investigated, with support materials extracted by calcination or solvent extraction. Rapid uptake at high loading was observed, with a maximum loading of 450 mg g-1 measured. The leaching of the enzyme from the support was investigated, and found to be high with unfunctionalised supports. The leaching from functionalised supports incorporating sulfur groups was significantly reduced. The activity of the immobilised CALB was measured by tributyrin hydrolysis in aqueous media, and by enantioselective transesterification of (R)-1-phenylethanol in organic media. The effect of surface functionalisation for reusability and thermal stability in aqueous systems was investigated. Preliminary studies of supported CALB for dynamic kinetic resolution were carried out, with an investigation of acidic zeolites and a mesoporous supported catalyst for 1-phenylethanol racemisation. The encapsulation of immobilised CALB was investigated, and the activity and reusability of these systems studied.

This thesis is aimed at extending the spherical barotropic contour-advective semi-Lagrangian (CASL) Algorithm, written in 1996 by David Dritschel and Maarten Ambaum, to more complex test cases within the shallow-water context. This is an integral part for development of any numerical model and the accuracy obtained depends on many factors, including knowledge of the initial state of the atmosphere or ocean, the numerical methods applied, and the resolutions used. The work undertaken throughout this thesis is highly varied and produces important steps towards creating a versatile suite of programs to model all types of flow, quickly and accurately. This, as will be explained in later chapters, impacts both public safety and the world economy, since much depends on accurate medium range forecasting. There shall be an investigation of a series of tests which demonstrate certain aspects of a dynamical system and its progression into more unstable situations - including the generation and feedback of freely propagating inertia-gravity waves (hereafter “gravity waves"), which transmit throughout the system. The implications for increasing forecast accuracy will be discussed. Within this thesis two main CASL algorithms are outlined and tested, with the accuracy of the results compared with previous results. In addition, other dynamical fields (besides geopotential height and potential vorticity) are analysed in order to assess how well the models deal with gravity waves. We shall see that such waves are sensitive to the presence, or not, of sharp potential vorticity gradients, as well as to numerical parameter settings. In particular, large time-steps (convenient for semi-Lagrangian schemes) may not only seriously affect gravity waves, but may also have an adverse impact on the primary fields of height and velocity. These problems are exacerbated by a poor resolution of potential vorticity gradients, which we shall attempt to improve.

Activation of otherwise unreactive substrates is a common strategy in chemistry and in nature. Adenylate-forming enzymes use adenosine monophosphate to activate the hydroxyl of their carboxylic substrate, creating a better leaving group. In a second step this reactive group is replaced in a nucleophilic elimination reaction to form esters, amides or thioesters. Recent studies have revealed that NRPS- independent siderophore (NIS) synthetases are also adenylate-forming enzymes, but are not included in the current superfamily description. NIS enzymes are involved in biosynthesis of high-affinity iron chelators which are used for iron acquisition by many pathogenic microorganisms. This is an important area of study, not only for potential therapeutic intervention, but also to illuminate new enzyme chemistries. Here the structural and biochemical studies of AcsD from Pectobacterium chrysanthemi are reported. AcsD is a NIS synthetase involved in achromobactin biosynthesis. The co-complex structures of ATP and citrate provide a mechanism for the stereospecific formation of an enzyme-bound citryl-adenylate. This intermediate reacts with L-serine to form a likely achromobactin precursor. A detailed characterization of AcsD nucleophile profile showed that it can not only catalyze ester formation, but also amide and possibly thioester formation, creating new stereospecific citric acid derivatives. The structure of a N-citryl-ethylenediamine product co-complex identifies the residues that are important for both recognition of L-serine and for catalyzing ester formation. The structural studies on the processive enzyme AlcC, which is involved in the final step of alcaligin biosynthesis of Bordetella pertussis, show that it has a similar topology to AcsD. It also shows that ATP is coordinated in a manner similar to that seen in AcsD. Biochemical studies of a substrate analogue establish that AlcC is not only capable of synthesizing substrate dimers and trimers, but also able to assemble the respective dimer and trimer macrocycles. A series of docked binding models have been developed to illustrate the likely substrate coordination and the steps along dimerization and macrocyclization formation. Structural and mechanistic comparison of NIS enzymes with other adenylate-forming enzymes highlights the diversity of the fold, active site architecture, and metal coordination that has evolved. Hence, a new classification scheme for adenylate forming enzymes is proposed.

The mammalian Na+/H+ exchanger isoform 1 (NHE1) is a ubiquitously expressed membrane protein that regulates myocardial intracellular pH. Inhibition of NHE1 prevents hypertrophy and reduces ischemia-reperfusion (I/R) injury in animal models. To understand the regulation of NHE1 in the myocardium by phosphorylation we constructed adenoviruses, which express wild type or mutant cDNA for NHE1. Additionally, wild type and mutant NHE1 had mutations Leu163Phe/Gly174Ser, which increases NHE1 resistance to EMD87580 (NHE1 inhibitor) by 100-fold. This allowed measurement of exogenous NHE1 activity while inhibiting endogenous NHE1 activity. We examined the effects of a series of mutations of phosphorylation sites in the cytosolic domain of NHE1. Sustained intracellular acidosis and phenylephrine caused an ERK-dependent activation of NHE1 activity and phosphorylation levels. We demonstrated that amino acids Ser770 and Ser771 were essential for activation of NHE1 activity in isolated rat cardiomyocytes by sustained intracellular acidosis and phenylephrine. Furthermore, mutation of Ser770 and Ser771 to Ala prevented increased NHE1 phosphorylation by sustained intracellular acidosis and phenylephrine. This was found to occur in an ERK-dependent manner. Taken together, our results demonstrate that both sustained intracellular acidosis and phenylephrine rapidly activate the NHE1 protein in isolated cardiac cells via an ERK-dependent pathway that acts on the common amino acids Ser770 and Ser771 of the C-terminal tail of NHE1.

No description available.