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Bodenkontaminationen durch Mineralölkohlenwasserstoffe sind ein weltweites Umweltproblem. Die Kontaminatiosquellen stehen im Zusammenhang mit Förderung, Lagerung, Transport, Verteilung und Endlagerung von Erdöl und Erdölprodukten. Brasilien beginnt zurzeit einen Prozess der Altlastenerfassung und –erkundung und in Konsequenz dessen auch die Suche nach geeigneten Sanierungstechniken. Biologische Prozesse spielen eine immer stärkere Rolle insbesondere bei der Sanierung von Bodenkontaminationen mit organischen Substanzen. Diese Prozesse gelten als “ökologisch korrekter” und sind im Vergleich mit anderen Techniken mit geringeren Kosten und technischen Aufwand durchführbar. Ziel dieser Arbeit war es, die Anwendungsmöglichkeiten der biologischen Bodensanierung mittels des Terraferm® Verfahrens unter den Umweltbedingungen des Bundesstaates São Paulo, Brasilien zu überprüfen. Zu diesem Zweck wurde der Boden einer MKW-kontaminierte Fläche (Mina de Argila) in der Raffinerie REPLAN der PETROBRÁS S/A in Paulínia -SP ausgekoffert. Es wurden zehn Bodenproben in Bezug auf ihre physikalisch-chemischen Eigenschaften MKW, PAK, BTEX, Metalle (Cr, Zn, Pb, Ni, Cu, Cd, As, Hg, Fe, Ta), Wassergehalt, pH, Korngröße analysiert. Drei Proben mit durchschnittlichen MKW-gehalten wurden zur Überprüfung der biologischen Sanierbarkeit und der Bestimmung der Kontrollparameter für den später Sanierungsdurchführung Säulenversuchen unterzogen. Insgesamt wurden 72.384t kontaminierten Bodens ausgekoffert, wovon 21.050t der Abfallklasse II (nach NBR 10004) zugeordnet wurden und direkt auf eine Mülldeponie verbracht wurden. Es wurden 51.334t der Abfallklasse 1 in die Bodenreinigungsanlage der Firmen SAPOTEC/ESTRE in Paulínia - SP mittels des Terraferm® Verfahrens behandelt. Dieses Verfahren ist darauf ausgelegt, alle für den biologischen Abbau nötigen Prozessparameter im Optimum zu halten. Die Behandlung erfolgt in Hallen auf versiegeltem Untergrund und die dabei freigesetzten Schad- und Geruchsstoffe werden gefasst und einer Abluftreinigung zugeführt. Nach der Vorbehandlung (Aussortierung von Störstoffen, Zugabe von Strukturmaterial, Durchmischung) mittels speziellem Aufbereitungsaggregat wurden insgesamt elf Behandlungsmieten aufgesetzt. Der Sauerstoffgehalt, Bodenfeuchte und Nährstoffgehalte wurden im Optimalbereich gehalten. Die Analysen und die Säulenversuche bestätigten die biologische Sanierbarkeit des Bodens. Die Abbauraten in den Säulenversuchen lagenzwischen 70,2% und 88,6% in 14 Tagen. Diese hohen Abbauraten lassen sich durch die Zusammensetzung der MKW begründen, die sich hauptsächlich aus gut abbaubaren n-Alkanen und iso-Alkanen bestehen. Die durchschnittliche Abbaurate bei den elf Behandlungsmieten lag bei 80,88%, wobei die niedrigste bei 54,71% und die höchste Abbaurate bei 97,97% lagen. Die statistische Auswertung ergab, dass sich die Mittelwerte der MKW-gehalte während der Behandlung signifikant voneinander unterscheiden (<0,01). Die im Rahmen dieser Arbeit durchgeführten Versuche bestätigen den erfolgreichen Einsatz des Terraferm® Verfahrens unter Umweltbedingungen des Bundesstaates São Paulo, Brasilien. Die starke Variabilität der Abbauraten in den Behandlungsmieten deutet aber auf einen weiteren Forschungsbedarf, insbesondere hinsichtlich des Temperatur-einflusses, hin. / Contaminações de solos com hidrocarbonetos de petróleo são um problema ambiental com abrangência mundial devido à alta demanda de produtos refinados de petróleo. As fontes são múltiplas e estão relacionadas à exploração, produção, armazenamento, transporte, distribuição e à destinação final de petróleo e seus derivados. Hoje o Brasil está iniciando um processo de avaliação e cadastramento de suas áreas contaminadas e, conseqüentemente, está procurando alternativas para a remediação das mesmas. Processos biológicos estão ganhando cada vez mais importância no tratamento, especialmente de solos contaminados com compostos orgânicos. Estes métodos são favorecidos por serem mais limpos, com custos baixos e de mais fácil aplicação em escala industrial. Assim, com o objetivo de verificar a aplicabilidade da biorremediação através do processo Terraferm® às condições ambientais do Estado de São Paulo, Brasil, foi realizada a remediação ex situ de uma área contaminada com TPH, chamada Mina de Argila na Refinaria de Paulínia – REPLAN da PETROBRÁS S/A, em Paulínia - SP. Foram analisadas dez amostras de solo contaminado em relação aos parâmetros físico-químicos TPH, PAH, BTEX, metais (Cr, Zn, Pb, Ni, Cu, Cd, As, Hg, Fe, Ta), umidade, pH, oxigênio e granulometria. Três amostras com valores médios de TPH foram submetidas a ensaios de coluna para verificação da biotratabilidade do material e para definição de parâmetros de controle do processo em escala industrial. Foram removidos um total de 72.384t de material contaminado. Deste total, 21.050t foram classificadas como resíduo classe II segundo a NBR 10004 e encaminhadas para um aterro sanitário, e 51.334t foram classificadas como resíduo classe I, sendo destinadas à estação de biorremediação das empresas SAPOTEC/ESTRE, em Paulínia - SP. O solo contaminado foi tratado com o processo Terraferm®, que visa à otimização dos parâmetros que influenciam diretamente a atividade microbiana necessária para a biodegradação. O tratamento é feito em galpões com piso impermeabilizado e com um sistema de captação e tratamento das emissões geradas durante o processo de biodegradação. Após o pré-tratamento em máquina especial, que consiste na separação dos materiais não-tratáveis, na homogeneização e na adição de material estrutural, o solo contaminado foi colocado em onze pilhas de tratamento. Os fatores chave como o teor de oxigênio, a umidade e os nutrientes foram mantidos nas faixas consideradas ótimas. A caracterização química e o ensaio de coluna comprovaram a biotratabilidade do solo. Noensaio em coluna, obteve-se taxas de degradação entre 70,2% e 88,6% em 14 dias. Essas taxas altas são explicadas pela composição do TPH que consiste, neste caso, basicamente de n-alcanos e iso-alcanos considerados de fácil degradação biológica. A taxa média de degradação obtida no tratamento das onze pilhas foi de 80,88%, sendo a menor de 54,71% e a maior de 97,97%. Na análise estatística, verificou-se que as médias das concentrações de TPH durante cada período de tratamento diferem significativamente (<0,01). O trabalho conclui que o processo Terraferm® foi aplicado com sucesso nas condições ambientais do Estado de São Paulo, Brasil. Entretanto, os resultados do tratamento mostram uma alta variabilidade das taxas de degradação nas pilhas, que indica a necessidade de novas pesquisas, especialmente sobre a influência da temperatura no processo. / Soil contaminations with petroleum hydrocarbons are a worldwide environmental problem due to the high demand for refined petroleum products. Contamination sources are multiple and related to the exploration, production, storage, transportation, distribution, and final disposal of petroleum and its derivatives. Nowadays Brazil is starting to assess and record its contaminated areas and consequently search for alternatives for their remediation. Biological processes are gaining more and more importance, specially in the treatment of soils contaminated by organic compounds. These methods are favored for being cleaner, with lower costs, and more easily applicable to industrial scale. Therefore, with the objective of verifying the applicability of bioremediation to the environmental conditions of São Paulo State, Brazil, the ex situ remediation of a contaminated area by TPH was carried out by using the Terraferm® process. The area called Mina de Argila was located in the Paulínia Refinery – REPLAN, which belongs to PETROBRÁS S/A (the country's leader in the exploration, production, and distribution of petroleum products). Ten samples of contaminated soil were analyzed in relation to the physical-chemical parameters TPH, PAH, BTEX, metals (Cr, Zn, Pb, Ni, Cu, Cd, As, Hg, Fe, Ta), humidity, pH, oxygen and texture. Three samples with average values of TPH were submitted to column tests in order to assess the material biotreatability and define the control parameters of the process on industrial scale. A total of 72,384t of contaminated soil were removed. From this total, 21,050t were classified as class II waste according to NBR 10004 and sent to a landfill, and 51,334t were classified as class I waste and sent to the bioremediation plant of the companies SAPOTEC/ESTRE, in Paulínia – São Paulo State. The contaminated soil was treated with the Terraferm® process whose purpose is to optimize the parameters which directly influence the microbial activity necessary for biodegradation. The treatment was carried out in sheds with waterproof floor and a collection and treatment system for the emissions generated in the biodegradation process. After the treatment in a special machine, which consists in separating non-treatable materials, homogenizing, and adding structural material, the soil was placed into eleven treatment piles. The oxygen content, humidity, and nutrients were kept within a range considered optimum. The chemical characterization and the column test proved the soil biotreatability. In the column test, the degradation rates were between 70.2% and 88.6% in 14 days. These high rates are due to the TPHcomposition, which in this case basically consists in n-alkenes and iso-alkenes of easy biological degradation. The average degradation rate verified in the treatment of the eleven piles was of 80.88%, the lowest being 54.71% and the highest 97.97%. In the statistical analysis, it was verified that the average concentrations of TPH during each treatment period differ significantly (<0.01). The conclusion of this work is that the Terraferm® process was successfully applied to the environmental conditions of São Paulo State. However, the treatment results show a high variability in the degradation rates of the piles, which indicates the need for further research, specially on the influence of temperature on the process.

Bodenkontaminationen durch Mineralölkohlenwasserstoffe sind ein weltweites Umweltproblem. Die Kontaminatiosquellen stehen im Zusammenhang mit Förderung, Lagerung, Transport, Verteilung und Endlagerung von Erdöl und Erdölprodukten. Brasilien beginnt zurzeit einen Prozess der Altlastenerfassung und –erkundung und in Konsequenz dessen auch die Suche nach geeigneten Sanierungstechniken. Biologische Prozesse spielen eine immer stärkere Rolle insbesondere bei der Sanierung von Bodenkontaminationen mit organischen Substanzen. Diese Prozesse gelten als “ökologisch korrekter” und sind im Vergleich mit anderen Techniken mit geringeren Kosten und technischen Aufwand durchführbar. Ziel dieser Arbeit war es, die Anwendungsmöglichkeiten der biologischen Bodensanierung mittels des Terraferm® Verfahrens unter den Umweltbedingungen des Bundesstaates São Paulo, Brasilien zu überprüfen. Zu diesem Zweck wurde der Boden einer MKW-kontaminierte Fläche (Mina de Argila) in der Raffinerie REPLAN der PETROBRÁS S/A in Paulínia -SP ausgekoffert. Es wurden zehn Bodenproben in Bezug auf ihre physikalisch-chemischen Eigenschaften MKW, PAK, BTEX, Metalle (Cr, Zn, Pb, Ni, Cu, Cd, As, Hg, Fe, Ta), Wassergehalt, pH, Korngröße analysiert. Drei Proben mit durchschnittlichen MKW-gehalten wurden zur Überprüfung der biologischen Sanierbarkeit und der Bestimmung der Kontrollparameter für den später Sanierungsdurchführung Säulenversuchen unterzogen. Insgesamt wurden 72.384t kontaminierten Bodens ausgekoffert, wovon 21.050t der Abfallklasse II (nach NBR 10004) zugeordnet wurden und direkt auf eine Mülldeponie verbracht wurden. Es wurden 51.334t der Abfallklasse 1 in die Bodenreinigungsanlage der Firmen SAPOTEC/ESTRE in Paulínia - SP mittels des Terraferm® Verfahrens behandelt. Dieses Verfahren ist darauf ausgelegt, alle für den biologischen Abbau nötigen Prozessparameter im Optimum zu halten. Die Behandlung erfolgt in Hallen auf versiegeltem Untergrund und die dabei freigesetzten Schad- und Geruchsstoffe werden gefasst und einer Abluftreinigung zugeführt. Nach der Vorbehandlung (Aussortierung von Störstoffen, Zugabe von Strukturmaterial, Durchmischung) mittels speziellem Aufbereitungsaggregat wurden insgesamt elf Behandlungsmieten aufgesetzt. Der Sauerstoffgehalt, Bodenfeuchte und Nährstoffgehalte wurden im Optimalbereich gehalten. Die Analysen und die Säulenversuche bestätigten die biologische Sanierbarkeit des Bodens. Die Abbauraten in den Säulenversuchen lagenzwischen 70,2% und 88,6% in 14 Tagen. Diese hohen Abbauraten lassen sich durch die Zusammensetzung der MKW begründen, die sich hauptsächlich aus gut abbaubaren n-Alkanen und iso-Alkanen bestehen. Die durchschnittliche Abbaurate bei den elf Behandlungsmieten lag bei 80,88%, wobei die niedrigste bei 54,71% und die höchste Abbaurate bei 97,97% lagen. Die statistische Auswertung ergab, dass sich die Mittelwerte der MKW-gehalte während der Behandlung signifikant voneinander unterscheiden (<0,01). Die im Rahmen dieser Arbeit durchgeführten Versuche bestätigen den erfolgreichen Einsatz des Terraferm® Verfahrens unter Umweltbedingungen des Bundesstaates São Paulo, Brasilien. Die starke Variabilität der Abbauraten in den Behandlungsmieten deutet aber auf einen weiteren Forschungsbedarf, insbesondere hinsichtlich des Temperatur-einflusses, hin. / Contaminações de solos com hidrocarbonetos de petróleo são um problema ambiental com abrangência mundial devido à alta demanda de produtos refinados de petróleo. As fontes são múltiplas e estão relacionadas à exploração, produção, armazenamento, transporte, distribuição e à destinação final de petróleo e seus derivados. Hoje o Brasil está iniciando um processo de avaliação e cadastramento de suas áreas contaminadas e, conseqüentemente, está procurando alternativas para a remediação das mesmas. Processos biológicos estão ganhando cada vez mais importância no tratamento, especialmente de solos contaminados com compostos orgânicos. Estes métodos são favorecidos por serem mais limpos, com custos baixos e de mais fácil aplicação em escala industrial. Assim, com o objetivo de verificar a aplicabilidade da biorremediação através do processo Terraferm® às condições ambientais do Estado de São Paulo, Brasil, foi realizada a remediação ex situ de uma área contaminada com TPH, chamada Mina de Argila na Refinaria de Paulínia – REPLAN da PETROBRÁS S/A, em Paulínia - SP. Foram analisadas dez amostras de solo contaminado em relação aos parâmetros físico-químicos TPH, PAH, BTEX, metais (Cr, Zn, Pb, Ni, Cu, Cd, As, Hg, Fe, Ta), umidade, pH, oxigênio e granulometria. Três amostras com valores médios de TPH foram submetidas a ensaios de coluna para verificação da biotratabilidade do material e para definição de parâmetros de controle do processo em escala industrial. Foram removidos um total de 72.384t de material contaminado. Deste total, 21.050t foram classificadas como resíduo classe II segundo a NBR 10004 e encaminhadas para um aterro sanitário, e 51.334t foram classificadas como resíduo classe I, sendo destinadas à estação de biorremediação das empresas SAPOTEC/ESTRE, em Paulínia - SP. O solo contaminado foi tratado com o processo Terraferm®, que visa à otimização dos parâmetros que influenciam diretamente a atividade microbiana necessária para a biodegradação. O tratamento é feito em galpões com piso impermeabilizado e com um sistema de captação e tratamento das emissões geradas durante o processo de biodegradação. Após o pré-tratamento em máquina especial, que consiste na separação dos materiais não-tratáveis, na homogeneização e na adição de material estrutural, o solo contaminado foi colocado em onze pilhas de tratamento. Os fatores chave como o teor de oxigênio, a umidade e os nutrientes foram mantidos nas faixas consideradas ótimas. A caracterização química e o ensaio de coluna comprovaram a biotratabilidade do solo. Noensaio em coluna, obteve-se taxas de degradação entre 70,2% e 88,6% em 14 dias. Essas taxas altas são explicadas pela composição do TPH que consiste, neste caso, basicamente de n-alcanos e iso-alcanos considerados de fácil degradação biológica. A taxa média de degradação obtida no tratamento das onze pilhas foi de 80,88%, sendo a menor de 54,71% e a maior de 97,97%. Na análise estatística, verificou-se que as médias das concentrações de TPH durante cada período de tratamento diferem significativamente (<0,01). O trabalho conclui que o processo Terraferm® foi aplicado com sucesso nas condições ambientais do Estado de São Paulo, Brasil. Entretanto, os resultados do tratamento mostram uma alta variabilidade das taxas de degradação nas pilhas, que indica a necessidade de novas pesquisas, especialmente sobre a influência da temperatura no processo. / Soil contaminations with petroleum hydrocarbons are a worldwide environmental problem due to the high demand for refined petroleum products. Contamination sources are multiple and related to the exploration, production, storage, transportation, distribution, and final disposal of petroleum and its derivatives. Nowadays Brazil is starting to assess and record its contaminated areas and consequently search for alternatives for their remediation. Biological processes are gaining more and more importance, specially in the treatment of soils contaminated by organic compounds. These methods are favored for being cleaner, with lower costs, and more easily applicable to industrial scale. Therefore, with the objective of verifying the applicability of bioremediation to the environmental conditions of São Paulo State, Brazil, the ex situ remediation of a contaminated area by TPH was carried out by using the Terraferm® process. The area called Mina de Argila was located in the Paulínia Refinery – REPLAN, which belongs to PETROBRÁS S/A (the country's leader in the exploration, production, and distribution of petroleum products). Ten samples of contaminated soil were analyzed in relation to the physical-chemical parameters TPH, PAH, BTEX, metals (Cr, Zn, Pb, Ni, Cu, Cd, As, Hg, Fe, Ta), humidity, pH, oxygen and texture. Three samples with average values of TPH were submitted to column tests in order to assess the material biotreatability and define the control parameters of the process on industrial scale. A total of 72,384t of contaminated soil were removed. From this total, 21,050t were classified as class II waste according to NBR 10004 and sent to a landfill, and 51,334t were classified as class I waste and sent to the bioremediation plant of the companies SAPOTEC/ESTRE, in Paulínia – São Paulo State. The contaminated soil was treated with the Terraferm® process whose purpose is to optimize the parameters which directly influence the microbial activity necessary for biodegradation. The treatment was carried out in sheds with waterproof floor and a collection and treatment system for the emissions generated in the biodegradation process. After the treatment in a special machine, which consists in separating non-treatable materials, homogenizing, and adding structural material, the soil was placed into eleven treatment piles. The oxygen content, humidity, and nutrients were kept within a range considered optimum. The chemical characterization and the column test proved the soil biotreatability. In the column test, the degradation rates were between 70.2% and 88.6% in 14 days. These high rates are due to the TPHcomposition, which in this case basically consists in n-alkenes and iso-alkenes of easy biological degradation. The average degradation rate verified in the treatment of the eleven piles was of 80.88%, the lowest being 54.71% and the highest 97.97%. In the statistical analysis, it was verified that the average concentrations of TPH during each treatment period differ significantly (<0.01). The conclusion of this work is that the Terraferm® process was successfully applied to the environmental conditions of São Paulo State. However, the treatment results show a high variability in the degradation rates of the piles, which indicates the need for further research, specially on the influence of temperature on the process.

Bodenkontaminationen durch Mineralölkohlenwasserstoffe sind ein weltweites Umweltproblem. Die Kontaminatiosquellen stehen im Zusammenhang mit Förderung, Lagerung, Transport, Verteilung und Endlagerung von Erdöl und Erdölprodukten. Brasilien beginnt zurzeit einen Prozess der Altlastenerfassung und –erkundung und in Konsequenz dessen auch die Suche nach geeigneten Sanierungstechniken. Biologische Prozesse spielen eine immer stärkere Rolle insbesondere bei der Sanierung von Bodenkontaminationen mit organischen Substanzen. Diese Prozesse gelten als “ökologisch korrekter” und sind im Vergleich mit anderen Techniken mit geringeren Kosten und technischen Aufwand durchführbar. Ziel dieser Arbeit war es, die Anwendungsmöglichkeiten der biologischen Bodensanierung mittels des Terraferm® Verfahrens unter den Umweltbedingungen des Bundesstaates São Paulo, Brasilien zu überprüfen. Zu diesem Zweck wurde der Boden einer MKW-kontaminierte Fläche (Mina de Argila) in der Raffinerie REPLAN der PETROBRÁS S/A in Paulínia -SP ausgekoffert. Es wurden zehn Bodenproben in Bezug auf ihre physikalisch-chemischen Eigenschaften MKW, PAK, BTEX, Metalle (Cr, Zn, Pb, Ni, Cu, Cd, As, Hg, Fe, Ta), Wassergehalt, pH, Korngröße analysiert. Drei Proben mit durchschnittlichen MKW-gehalten wurden zur Überprüfung der biologischen Sanierbarkeit und der Bestimmung der Kontrollparameter für den später Sanierungsdurchführung Säulenversuchen unterzogen. Insgesamt wurden 72.384t kontaminierten Bodens ausgekoffert, wovon 21.050t der Abfallklasse II (nach NBR 10004) zugeordnet wurden und direkt auf eine Mülldeponie verbracht wurden. Es wurden 51.334t der Abfallklasse 1 in die Bodenreinigungsanlage der Firmen SAPOTEC/ESTRE in Paulínia - SP mittels des Terraferm® Verfahrens behandelt. Dieses Verfahren ist darauf ausgelegt, alle für den biologischen Abbau nötigen Prozessparameter im Optimum zu halten. Die Behandlung erfolgt in Hallen auf versiegeltem Untergrund und die dabei freigesetzten Schad- und Geruchsstoffe werden gefasst und einer Abluftreinigung zugeführt. Nach der Vorbehandlung (Aussortierung von Störstoffen, Zugabe von Strukturmaterial, Durchmischung) mittels speziellem Aufbereitungsaggregat wurden insgesamt elf Behandlungsmieten aufgesetzt. Der Sauerstoffgehalt, Bodenfeuchte und Nährstoffgehalte wurden im Optimalbereich gehalten. Die Analysen und die Säulenversuche bestätigten die biologische Sanierbarkeit des Bodens. Die Abbauraten in den Säulenversuchen lagenzwischen 70,2% und 88,6% in 14 Tagen. Diese hohen Abbauraten lassen sich durch die Zusammensetzung der MKW begründen, die sich hauptsächlich aus gut abbaubaren n-Alkanen und iso-Alkanen bestehen. Die durchschnittliche Abbaurate bei den elf Behandlungsmieten lag bei 80,88%, wobei die niedrigste bei 54,71% und die höchste Abbaurate bei 97,97% lagen. Die statistische Auswertung ergab, dass sich die Mittelwerte der MKW-gehalte während der Behandlung signifikant voneinander unterscheiden (<0,01). Die im Rahmen dieser Arbeit durchgeführten Versuche bestätigen den erfolgreichen Einsatz des Terraferm® Verfahrens unter Umweltbedingungen des Bundesstaates São Paulo, Brasilien. Die starke Variabilität der Abbauraten in den Behandlungsmieten deutet aber auf einen weiteren Forschungsbedarf, insbesondere hinsichtlich des Temperatur-einflusses, hin. / Contaminações de solos com hidrocarbonetos de petróleo são um problema ambiental com abrangência mundial devido à alta demanda de produtos refinados de petróleo. As fontes são múltiplas e estão relacionadas à exploração, produção, armazenamento, transporte, distribuição e à destinação final de petróleo e seus derivados. Hoje o Brasil está iniciando um processo de avaliação e cadastramento de suas áreas contaminadas e, conseqüentemente, está procurando alternativas para a remediação das mesmas. Processos biológicos estão ganhando cada vez mais importância no tratamento, especialmente de solos contaminados com compostos orgânicos. Estes métodos são favorecidos por serem mais limpos, com custos baixos e de mais fácil aplicação em escala industrial. Assim, com o objetivo de verificar a aplicabilidade da biorremediação através do processo Terraferm® às condições ambientais do Estado de São Paulo, Brasil, foi realizada a remediação ex situ de uma área contaminada com TPH, chamada Mina de Argila na Refinaria de Paulínia – REPLAN da PETROBRÁS S/A, em Paulínia - SP. Foram analisadas dez amostras de solo contaminado em relação aos parâmetros físico-químicos TPH, PAH, BTEX, metais (Cr, Zn, Pb, Ni, Cu, Cd, As, Hg, Fe, Ta), umidade, pH, oxigênio e granulometria. Três amostras com valores médios de TPH foram submetidas a ensaios de coluna para verificação da biotratabilidade do material e para definição de parâmetros de controle do processo em escala industrial. Foram removidos um total de 72.384t de material contaminado. Deste total, 21.050t foram classificadas como resíduo classe II segundo a NBR 10004 e encaminhadas para um aterro sanitário, e 51.334t foram classificadas como resíduo classe I, sendo destinadas à estação de biorremediação das empresas SAPOTEC/ESTRE, em Paulínia - SP. O solo contaminado foi tratado com o processo Terraferm®, que visa à otimização dos parâmetros que influenciam diretamente a atividade microbiana necessária para a biodegradação. O tratamento é feito em galpões com piso impermeabilizado e com um sistema de captação e tratamento das emissões geradas durante o processo de biodegradação. Após o pré-tratamento em máquina especial, que consiste na separação dos materiais não-tratáveis, na homogeneização e na adição de material estrutural, o solo contaminado foi colocado em onze pilhas de tratamento. Os fatores chave como o teor de oxigênio, a umidade e os nutrientes foram mantidos nas faixas consideradas ótimas. A caracterização química e o ensaio de coluna comprovaram a biotratabilidade do solo. Noensaio em coluna, obteve-se taxas de degradação entre 70,2% e 88,6% em 14 dias. Essas taxas altas são explicadas pela composição do TPH que consiste, neste caso, basicamente de n-alcanos e iso-alcanos considerados de fácil degradação biológica. A taxa média de degradação obtida no tratamento das onze pilhas foi de 80,88%, sendo a menor de 54,71% e a maior de 97,97%. Na análise estatística, verificou-se que as médias das concentrações de TPH durante cada período de tratamento diferem significativamente (<0,01). O trabalho conclui que o processo Terraferm® foi aplicado com sucesso nas condições ambientais do Estado de São Paulo, Brasil. Entretanto, os resultados do tratamento mostram uma alta variabilidade das taxas de degradação nas pilhas, que indica a necessidade de novas pesquisas, especialmente sobre a influência da temperatura no processo. / Soil contaminations with petroleum hydrocarbons are a worldwide environmental problem due to the high demand for refined petroleum products. Contamination sources are multiple and related to the exploration, production, storage, transportation, distribution, and final disposal of petroleum and its derivatives. Nowadays Brazil is starting to assess and record its contaminated areas and consequently search for alternatives for their remediation. Biological processes are gaining more and more importance, specially in the treatment of soils contaminated by organic compounds. These methods are favored for being cleaner, with lower costs, and more easily applicable to industrial scale. Therefore, with the objective of verifying the applicability of bioremediation to the environmental conditions of São Paulo State, Brazil, the ex situ remediation of a contaminated area by TPH was carried out by using the Terraferm® process. The area called Mina de Argila was located in the Paulínia Refinery – REPLAN, which belongs to PETROBRÁS S/A (the country's leader in the exploration, production, and distribution of petroleum products). Ten samples of contaminated soil were analyzed in relation to the physical-chemical parameters TPH, PAH, BTEX, metals (Cr, Zn, Pb, Ni, Cu, Cd, As, Hg, Fe, Ta), humidity, pH, oxygen and texture. Three samples with average values of TPH were submitted to column tests in order to assess the material biotreatability and define the control parameters of the process on industrial scale. A total of 72,384t of contaminated soil were removed. From this total, 21,050t were classified as class II waste according to NBR 10004 and sent to a landfill, and 51,334t were classified as class I waste and sent to the bioremediation plant of the companies SAPOTEC/ESTRE, in Paulínia – São Paulo State. The contaminated soil was treated with the Terraferm® process whose purpose is to optimize the parameters which directly influence the microbial activity necessary for biodegradation. The treatment was carried out in sheds with waterproof floor and a collection and treatment system for the emissions generated in the biodegradation process. After the treatment in a special machine, which consists in separating non-treatable materials, homogenizing, and adding structural material, the soil was placed into eleven treatment piles. The oxygen content, humidity, and nutrients were kept within a range considered optimum. The chemical characterization and the column test proved the soil biotreatability. In the column test, the degradation rates were between 70.2% and 88.6% in 14 days. These high rates are due to the TPHcomposition, which in this case basically consists in n-alkenes and iso-alkenes of easy biological degradation. The average degradation rate verified in the treatment of the eleven piles was of 80.88%, the lowest being 54.71% and the highest 97.97%. In the statistical analysis, it was verified that the average concentrations of TPH during each treatment period differ significantly (<0.01). The conclusion of this work is that the Terraferm® process was successfully applied to the environmental conditions of São Paulo State. However, the treatment results show a high variability in the degradation rates of the piles, which indicates the need for further research, specially on the influence of temperature on the process.

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Protonentherapie ist eine wichtige Behandlungsmodalität in der Radioonkologie. Aufgrund einer vorteilhaften Dosisverteilung im bestrahlten Volumen kann diese Bestrahlungsmethode das tumorumgebende Normalgewebe schützen. Dadurch können Nebenwirkungen in bestimmten Patientenpopulationen, zum Beispiel Kindern oder Patienten mit Gehirntumoren, verringert werden. Trotzdem können nach Protonenbestrahlung von Gehirntumorpatienten Normalgewebsschäden auftreten. Gründe dafür können der notwendige klinische Sicherheitssaum im Normalgewebe, der Einfluss der relativen biologischen Wirksamkeit RBE sowie eine erhöhte Strahlensensitivität bestimmter Gehirnregionen sein. Um diese Aspekte zu beleuchten, werden geeignete präklinische Modelle für die Normalgewebsreaktion im Gehirn nach Protonenbestrahlung benötigt. Darüber hinaus kann eine Risikostratifizierung der Patienten durch die Vorhersage von Nebenwirkungswahrscheinlichkeiten oder der Tumorantwort den Behandlungserfolg erhöhen. Auch hier können präklinische Modelle helfen, um neue prädiktive Biomarker zu finden und um die zugrunde liegenden Mechanismen strahleninduzierter Gehirnschäden besser zu verstehen. Das Ziel dieser Dissertation war die Etablierung und Charakterisierung von adäquaten präklinischen Modellen für die Untersuchung von strahleninduzierten Normalgewebsschäden im Gehirn. Diese Modelle bilden die Grundlage für zukünftige Studien zur Untersuchung von RBE Effekten, der spezifische Strahlensensitivität einzelner Gehirnregionen und neuer Biomarker. Die getesteten Modellsysteme waren in vitro Kulturen von adulten organotypischen Gehirnschnitten, Tumorschnittkultur sowie in vivo Bestrahlung von Gehirnsubvolumina, jeweils mit dem Modellorganismus Maus. Die Etablierung eines Bestrahlungssetups in der experimentellen Protonenanlage und dessen dosimetrische Charakterisierung waren von großer Bedeutung für die Durchführung der biologischen Experimente. Ein weiteres Hauptziel war die Definition klinisch relevanter Endpunkte für frühe und späte Nebenwirkungen. Die Gewebsschnitte wurden durch Messungen des Zellüberlebens und der Entzündungsreaktion, sowie mittels in situ Analyse von Zellmorphologie und DNA Schäden untersucht. Als ergänzendes Modell wurde die Tumorschnittkultur etabliert und ähnliche Endpunkte analysiert. Adulte Gehirnschnitte stellten sich als ungeeignet für präklinische Experimente in der Radioonkologie heraus. Die Messungen von Zelltod und Entzündungswerten zeigten eine starke Zellreaktion auf die Inkulturnahme, aber keine auf die Protonenbestrahlung. In der Histologie wurden gestörte Zellmorphologie, reduzierte Vitalität und eingeschränkte Reparaturfähigkeit von DNA Schäden beobachtet. Daher sollten für strahlenbiologische Experimente andere 3D Zellkulturmodelle in Betracht gezogen werden, wie zum Beispiel Organoide oder durch Tissue Engineering hergestellte Kulturen. Durch die Publikation der Daten leistet diese Dissertation einen wichtigen Beitrag zur aktuellen Forschung, da so künftig die limitierten Ressourcen, die für strahlenbiologische Experimente mit Protonen zur Verfügung stehen, auf relevantere Modelle verwendet werden können. Die Bestrahlung von Gehirnsubvolumina in Mäusen wurde mit dem Ziel etabliert, klinisch vergleichbare Felder zu erreichen. Das gewählte Zielvolumen war der rechte Hippocampus; der Protonenstrahl sollte in der Mitte des Gehirns stoppen. Im Rahmen des Projekts wurde ein Arbeitsablauf für präzise und reproduzierbare Bestrahlung entwickelt. Zur Verifizierung wurde der induzierte DNA Schaden ausgewertet und anschließend mit Monte-Carlos Dosissimulationen korreliert. Die Maushirnbestrahlung lieferte wertvolle Ergebnisse für frühe Zeitpunkte (d.h. innerhalb 24 h nach Bestrahlung). Im Verlauf des Projekts wurde ein Algorithmus erstellt, der schnell und zuverlässig die räumliche Verteilung des DNA Schadens in Relation zur Gesamtzellzahl analysiert. Diese Auswertung zeigte, wie bei der Bestrahlungsplanung vorgesehen, ein Stoppen des Protonenstrahls im Gehirn. Eine anschließende Korrelation der Schadensverteilung mit der applizierten Dosis weist nach, dass das Modell einen wichtigen Beitrag zur Untersuchung des RBE leisten kann. In einer darauf folgenden Studie wurde der Dosis-Zeitverlauf der beobachteten Strahlenreaktion des Normalgewebes genauer beleuchtet. Dafür wurden Untersuchungen des Allgemeinzustands der Versuchstiere, regelmäßige Magnetresonanztomografie (MRI) Messungen über einen Zeitraum von sechs Monaten, sowie abschließende Histologie korreliert. Die Volumenzunahme des Kontrastmittelaustritts, die den Zusammenbruch der Blut-Hirn-Schranke anzeigt, wurde konturiert; aus diesen Daten entstand ein prädiktives Dosis-Volumen Modell. Die Pilotstudie konnte eine dosisabhängige Strahlenreaktion nachweisen, die sich im Zusammenbruch der Blut-Hirn-Schranke, einer Hautreaktion mit vorrübergehender Alopezie, Gewichtsabnahme und zelluläre Veränderung äußerte. Das von den MRI Messungen abgeleitete Modell konnte zuverlässig das Eintreten der Nebenwirkungen, den Krankheitsverlauf, sowie die geschätzte Überlebensdauer der Mäuse vorhersagen. Zusätzlich konnte ein Zusammenhang zwischen den MRI Bildänderungen und den pathologischen Gewebsveränderungen beobachtet werden. Durch die außerordentlich homogene Strahlenreaktion der Tiere können aus den vorliegenden Daten künftig zuverlässig geeignete Dosen für spezifische experimentelle Endpunkte bestimmt werden. Zusammenfassend wurden in dieser Arbeit zwei präklinische Modelle für die Protonengehirnbestrahlung etabliert, nämlich organotypische Gewebsschnitte als 3D Zellkulturmodell sowie in vivo Bestrahlung von Gehirnsubvolumina in Mäusen. Während Zellkulturexperimente die Erwartungen nicht erfüllen konnten, stellen sich die Tierexperimente als hervorragendes Modell für translationale Radioonkologie heraus, welches zusätzlich für andere Strahlenqualitäten eingesetzt werden kann. Darauf basierend können aktuelle und zukünftige Studien die Ursachen von strahleninduzierten Normalgewebsschäden im Gehirn beleuchten, RBE Effekte untersuchen und neue prädiktive Biomarker erforschen.:Contents Abstract i Zusammenfassung v Publications ix List of Figures xiii List of Acronyms and Abbreviations xiv 1 Introduction 3 2 Background 5 2.1 Proton therapy for brain cancer treatment 5 2.1.1 Fundamentals of radiobiology 5 2.1.2 Proton therapy 6 2.1.3 Tumors of the central nervous system 8 2.2 Radiation effects on brain cells 8 2.2.1 Neurons and myelin 9 2.2.2 Blood-brain barrier 9 2.2.3 Astrocytes 10 2.2.4 Microglia 10 2.3 Principles of histology 11 2.3.1 Hematoxylin & eosin staining 12 2.3.2 Immunohistochemistry 13 2.3.3 Bioimage analysis 13 2.4 Techniques in medical imaging 14 2.4.1 Projectional radiography 14 2.4.2 Computed tomography 14 2.4.3 Magnetic resonance imaging 15 2.5 Preclinical models for radiation injury 17 2.5.1 Technical requirements 17 2.5.2 In vitro models 17 2.5.3 Small animal models 18 3 Applying Tissue Slice Culture in Cancer Research – Insights from Preclinical Proton Radiotherapy 19 3.1 Aim of the study 19 3.2 Conclusion 19 3.3 Author’s contribution 19 3.4 Publication 21 4 High-precision image-guided proton irradiation of mouse brain sub-volumes 41 4.1 Aim of the study 41 4.2 Conclusion 41 4.3 Author’s contribution 41 4.4 Publication 43 5 Late side effects in normal mouse brain tissue after proton irradiation 51 5.1 Aim of the study 51 5.2 Conclusion 51 5.3 Author’s contribution 52 5.4 Publication 53 6 Discussion 71 6.1 Establishment of preclinical models for radiooncology 71 6.1.1 3D cell culture 71 6.1.2 In vivo irradiation of brain subvolumes 73 6.2 Current applications of the mouse model 75 6.2.1 Ongoing data analysis 75 6.2.2 Innovating on-site imaging 76 6.2.3 RBE investigations 77 6.3 Future studies of radiation-induced brain tissue toxicities 79 Acknowledgement XV Supplementary Material XVII 1 Applying Tissue Slice Culture in Cancer Research – Insights from Preclinical Proton Radiotherapy XVII 2 High-precision image-guided proton irradiation of mouse brain sub-volumes XXVI 3 Late side effects in normal mouse brain tissue after proton irradiation XXXI / Proton therapy is an important modality in radiation oncology. Due to a favorable dose distribution in the irradiated volume, this treatment allows to spare tumor-surrounding normal tissue. Although this protection can lead to reduced side effects in certain patient populations, such as brain tumor or pediatric patients, normal tissue toxicities can occur to some extend. This could be due to clinical safety margins around the tumor that lead to dose deposition in the normal tissue. The underlying causes might also be related to relative biological effectiveness (RBE) variations or elevated radiosensitivity of certain brain regions. To address these issues, suitable preclinical models for normal brain tissue reaction after proton therapy are needed. In addition, patient stratification to predict the tumor response or the probability of side effects will contribute to increased treatment effectiveness. Preclinical models can improve the process of finding new predictive biomarkers and help to understand underlying mechanisms of radiation-induced brain injury. The aim of this thesis was to establish and characterize suitable preclinical models of brain tissue irradiation effects and set the base for future studies designed to reveal RBE effects, brain region specific radiation sensitivities, and novel biomarkers. The tested model systems were in vitro organotypic brain slice culture (OBSC) and in vivo irradiation of brain subvolumes, both on mouse brain tissue. Setup establishment at the experimental proton beam line and subsequent dosimetry built the foundation for conducting the biological experiments. Additionally, one main goal was defining clinically relevant endpoints for both short- and long-term effects. For OBSC, assays for cell death and inflammation, as well as in situ analysis of cell morphology and DNA damage induction were tested. As comparative model to OBSC, tumor slice culture was established and the results were also used for proton investigation. Adult OBSC turned out as inadequate model for preclinical experiments in radiation oncology. The assays measuring cell death and inflammation indicated a severe reaction during the first days in culture, but no response to irradiation. Histology revealed deficient cell morphology, reduced vitality and impaired DNA damage repair. In conclusion, other 3D cell culture models, such as organoids or tissue engineered constructs, should be considered for radiobiological experiments with protons. By publishing the observations, this thesis contributes to conserving the limited resources of proton radiobiology for more meaningful models. A methodology for irradiation of mouse brain subvolumes was established with a focus on creating fields comparable to clinical practice. The chosen target was the right hippocampus and the goal was to stop the proton beam in the middle of the brain. The project included a workflow for this precise irradiation in a robust and reproducible manner. Evaluation of the induced DNA damage and its correlation to Monte Carlo dose simulations were used for verification. Irradiation of mouse brain subvolumes yielded valuable results for early (i.e. within 24 h after irradiation) time points. An evaluation algorithm was designed for fast and robust analysis of spatial DNA damage distribution in relation to the total cell count. This ratio showed that the beam stopped in the brain tissue, in accordance to the treatment planning. Furthermore, the DNA damage could be reliably correlated with the dose simulation, which proves the value of the presented model for future RBE studies. In a follow-up experiment, the dose-time relationship of induced normal tissue reactions was analysed. For this, scoring of the animals' health status was combined with regular MRI measurements over the course of up to 6 months, and final histopathology. The volume increase of contrast agent leakage - representing breakdown of the blood brain barrier (BBB) - was contoured and the data was used to create a dose-volume response model. This pilot study on long-term radiation effects revealed dose-dependent normal tissue toxicities, including breakdown of the BBB, a skin reaction with temporary alopecia, weight reduction and changes on the cellular level. The model derived from MRI data reliably predicts onset of side effects, volume of brain damage as well as the expected animal survival. In addition, MRI image changes could be correlated to underlying tissue alterations by histopathology. Due to the uniform radiation response of the animals this data set enables to determine endpoint-specific dose values in future experiments. In conclusion, two preclinical models for proton brain irradiation were established, namely OBSC as 3D cell culture model and in vivo irradiation of mouse brain subvolumes. While the former could not yield the anticipated results, the latter emerged as excellent model for translational radiooncology, which can also be applied for experiments with other radiation types. Ongoing and future studies will focus on revealing the causes of normal brain tissue toxicities, studying RBE effects, and investigating new predictive biomarkers.:Contents Abstract i Zusammenfassung v Publications ix List of Figures xiii List of Acronyms and Abbreviations xiv 1 Introduction 3 2 Background 5 2.1 Proton therapy for brain cancer treatment 5 2.1.1 Fundamentals of radiobiology 5 2.1.2 Proton therapy 6 2.1.3 Tumors of the central nervous system 8 2.2 Radiation effects on brain cells 8 2.2.1 Neurons and myelin 9 2.2.2 Blood-brain barrier 9 2.2.3 Astrocytes 10 2.2.4 Microglia 10 2.3 Principles of histology 11 2.3.1 Hematoxylin & eosin staining 12 2.3.2 Immunohistochemistry 13 2.3.3 Bioimage analysis 13 2.4 Techniques in medical imaging 14 2.4.1 Projectional radiography 14 2.4.2 Computed tomography 14 2.4.3 Magnetic resonance imaging 15 2.5 Preclinical models for radiation injury 17 2.5.1 Technical requirements 17 2.5.2 In vitro models 17 2.5.3 Small animal models 18 3 Applying Tissue Slice Culture in Cancer Research – Insights from Preclinical Proton Radiotherapy 19 3.1 Aim of the study 19 3.2 Conclusion 19 3.3 Author’s contribution 19 3.4 Publication 21 4 High-precision image-guided proton irradiation of mouse brain sub-volumes 41 4.1 Aim of the study 41 4.2 Conclusion 41 4.3 Author’s contribution 41 4.4 Publication 43 5 Late side effects in normal mouse brain tissue after proton irradiation 51 5.1 Aim of the study 51 5.2 Conclusion 51 5.3 Author’s contribution 52 5.4 Publication 53 6 Discussion 71 6.1 Establishment of preclinical models for radiooncology 71 6.1.1 3D cell culture 71 6.1.2 In vivo irradiation of brain subvolumes 73 6.2 Current applications of the mouse model 75 6.2.1 Ongoing data analysis 75 6.2.2 Innovating on-site imaging 76 6.2.3 RBE investigations 77 6.3 Future studies of radiation-induced brain tissue toxicities 79 Acknowledgement XV Supplementary Material XVII 1 Applying Tissue Slice Culture in Cancer Research – Insights from Preclinical Proton Radiotherapy XVII 2 High-precision image-guided proton irradiation of mouse brain sub-volumes XXVI 3 Late side effects in normal mouse brain tissue after proton irradiation XXXI

Der Bericht fasst die Ergebnisse eines Forschungsprojektes zusammen, in dem Möglichkeiten zur Optimierung der maschinellen Unkrautregulierung untersucht wurden, um eine Reduzierung des Handarbeitsaufwands zu erreichen. Mit der erprobten Gerätekombination ist eine Senkung der Handarbeit gegenüber dem bisher in der Praxis üblichen Verfahren um 50 bis 60 Prozent möglich. In der optimalen Variante zur Unkrautregulierung wurde bei einem Ertrag von 98 dt/ha (2013) bzw. 108 dt/ha (2014) und einem kalkulierten Durchschnittserlös von 3,00 €/kg die Gewinnzone erreicht. Die Ergebnisse richten sich an Praktiker und Berater aus dem ökologischen und konventionellen Gartenbau.

Statische Rottereaktoren sind mit ihrem Festbett das vorherrschende technologische Konzept zur biologischen Behandlung von Restabfall (MBA) und zur Bioabfallkompostierung. Auftretende prozesstechnische Probleme beim Reaktorbetrieb waren die Motivation zur vorliegenden Arbeit. Untersucht wurde das Betriebsverhalten am Beispiel von MBA-Anlagen. Die Bedingungen und Vorgänge wurden im Kontext von Stoffsystem und technischem System unter Anwendung verfahrenstechnischer Methoden analysiert. Für Großanlagen geeignete experimentelle Methoden wurden entwickelt und das Betriebsverhalten im Istzustand und im modifizierten Anlagenzustand beschrieben. Es wurden signifikante Beeinflussungen der Rottebedingungen durch Stoffsystem und Prozessführung unter Einwirkung der Technik deutlich. Die prozessrelevanten Einflussfaktoren sowie deren Ursachen und Wirkungen auf das Betriebsverhalten konnten analysiert und zahlreiche konzeptions- und konstruktionsbedingte Probleme statischer Rottereaktoren identifiziert werden. Als besonders problematisch zeigten sich stochastisch und systematisch auftretende Vorzugsströmungen aufgrund der Heterogenität des Haufwerks und undefinierte Bedingungen zur Belüftung aufgrund schwankender Druckbedingungen im Prozessluftsystem und gegenseitiger Beeinflussungen. Aus den Ergebnissen wurden Maßnahmen für einen verbesserten Betrieb bestehender Anlagen und Lösungen für zukünftige Anlagen abgeleitet / With their fixed bed, static reactors are the predominant technological concept for the biological treatment of residual waste (MBT) and for the composting of bio-waste. Process-based problems in the reactor operation were the motivation for the present work. The operating behavior was examined using the example of MBT plants. The conditions and processes were analyzed in the context of the material system and the technical system using process engineering methods. Experimental methods suitable for real plants were developed and the operating behavior in the current state and in the modified plant state was described. Significant influences on the rotting conditions by the material system and process management under the effect of technology became apparent. The process-relevant influencing factors and their causes and effects on the operating behavior could be analyzed and numerous concept- and construction-conditioned problems of static reactors could be identified. Stochastic and systematic preference flows due to the heterogeneity of the material in the reactor and undefined conditions for ventilation due to fluctuating pressure conditions in the process air system and mutual influences were particularly problematic. Technical measures for improved operating behavior of existing plants and solutions for future plants were derived from the results.

Understanding the development, organization, and function of tissues is a central goal in developmental biology. With modern time-lapse microscopy, it is now possible to image entire tissues during development and thereby localize subcellular proteins. A particularly productive area of research is the study of single layer epithelial tissues, which can be simply described as a 2D manifold. For example, the apical band of cell adhesions in epithelial cell layers actually forms a 2D manifold within the tissue and provides a 2D outline of each cell. The Drosophila melanogaster wing has become an important model system, because its 2D cell organization has the potential to reveal mechanisms that create the final fly wing shape. Other examples include structures that naturally localize at the surface of the tissue, such as the ciliary components of planarians. Data from these time-lapse movies typically consists of mosaics of overlapping 3D stacks. This is necessary because the surface of interest exceeds the field of view of todays microscopes. To quantify cellular tissue dynamics, these mosaics need to be processed in three main steps: (a) Extracting, correcting, and stitching individ- ual stacks into a single, seamless 2D projection per time point, (b) obtaining cell characteristics that occur at individual time points, and (c) determine cell dynamics over time. It is therefore necessary that the applied methods are capable of handling large amounts of data efficiently, while still producing accurate results. This task is made especially difficult by the low signal to noise ratios that are typical in live-cell imaging. In this PhD thesis, I develop algorithms that cover all three processing tasks men- tioned above and apply them in the analysis of polarity and tissue dynamics in large epithelial cell layers, namely the Drosophila wing and the planarian epithelium. First, I introduce an efficient pipeline that preprocesses raw image mosaics. This pipeline accurately extracts the stained surface of interest from each raw image stack and projects it onto a single 2D plane. It then corrects uneven illumination, aligns all mosaic planes, and adjusts brightness and contrast before finally stitching the processed images together. This preprocessing does not only significantly reduce the data quantity, but also simplifies downstream data analyses. Here, I apply this pipeline to datasets of the developing fly wing as well as a planarian epithelium. I additionally address the problem of determining cell polarities in chemically fixed samples of planarians. Here, I introduce a method that automatically estimates cell polarities by computing the orientation of rootlets in motile cilia. With this technique one can for the first time routinely measure and visualize how tissue polarities are established and maintained in entire planarian epithelia. Finally, I analyze cell migration patterns in the entire developing wing tissue in Drosophila. At each time point, cells are segmented using a progressive merging ap- proach with merging criteria that take typical cell shape characteristics into account. The method enforces biologically relevant constraints to improve the quality of the resulting segmentations. For cases where a full cell tracking is desired, I introduce a pipeline using a tracking-by-assignment approach. This allows me to link cells over time while considering critical events such as cell divisions or cell death. This work presents a very accurate large-scale cell tracking pipeline and opens up many avenues for further study including several in-vivo perturbation experiments as well as biophysical modeling. The methods introduced in this thesis are examples for computational pipelines that catalyze biological insights by enabling the quantification of tissue scale phenomena and dynamics. I provide not only detailed descriptions of the methods, but also show how they perform on concrete biological research projects.

The majority of bacteria are organized in surface-associated communities, the so called biofilms. Crucial processes that drive the formation of such biofilms are the motility of bacteria on a substrate, enabling cells to reach each others vicinity, and attractive cell-cell-interactions, driving the formation of microcolonies. These colonies, aggregates consisting of thousands of cells, are the precursors of biofilms. In this thesis we investigate the role of cell appendages, called type IV pili, in the substrate motion of bacteria and the formation of bacterial microcolonies. Therefore, we study the bacterial dynamics with the help of experiments and theoretical models. We introduce a novel simulation tool in the tradition of Brownian dynamics simulations. In this computational model, that was developed alongside experimental observations, we study how explicit pili dynamics, pili-substrate and pili–pili interactions drive the cell dynamics. First, we apply our model to investigate how individual cells move on a substrate due to cycles of protrusion and retraction of type IV pili. We show that the characteristic features, in particular persistent motion, can solely originate from collective interactions of pili. Next, we perform experiments to study the coalescence of bacterial microcolonies. With the help of experiments and our computational model, we identify a spatially-dependent gradient of motility of cells within the colony as the origin of a separation of time scale, a feature which is in disagreement with the coalescence dynamics of fluid droplets. Additionally, we show that altering the force generation of pili can cause demixing of cells within bacterial aggregates. Finally, we combine our knowledge of the substrate motion of cells and of the pili-mediated interactions of colonies to identify the main processes (aggregation, fragmentation and cell divisions) that drive assembly of colonies. Starting from experiments, we develop a mathematical model and observe excellent qualitative and quantitative agreement to experimental data of the density of colonies of different sizes. In summary, hand in hand with experiments, we develop theoretical frameworks to unravel the role of type IV pili in bacterial surface motility, microcolony dynamics and colony formation.:1. Introduction 2. Computational model of bacterial motility and mechanics 3. Motility of single bacteria on a substrate 4. Coalescence and internal dynamics of bacterial microcolonies 5. Demixing of bacterial microcolonies 6. Self-assembly of microcolonies 7. Summary and Outlook A. Details of the Simulation model B. Experimental protocols C. Geometric estimation of the parameters of the stochastic model D. Solutions for simplified models of pili-mediated cell motion E. Image analysis of experimental data F. Simulations and data analysis G. The mean squared relative distance (MSRD)