The aim of this work is study of utilization of PHA producing bacteria in bioremediation technologies. For this study were used bacteria Pseudomonas putida KT2440 and two isolates from soil contaminated by petroleum - Pseudomonas gessardii (D2) a Pseudomonas fulva (D3). The experimental part describes especially study of feather biodegradation using selected microbial strains. All the tested bacterial strains were capable of feather degradation and utilization as the sole carbon source. During biodegradation experiment, we monitored weight loss of feather, protease and keratinase activity, concentration of bacterial biomass and PHA content as well as pH. The highest biodegradation ability and keratinase activity was observed in Pseudomonas putida. None of tested bacteria accumulated detectable amount of PHA during growth on waste feather, nevertheless, bacterial biomass grown during feather degradation can be used as an inoculum for PHA production on waste frying oil and octanoic acid. Using this experimental setup, high PHA content (54% of cell dry weight) was achiaved in Pseudomonas putida. Another part of the thesis deals with biodegradation of petroleum oil. The highest capability of growth on this carbon source were determined in Pseudomonas fulva.

Ziel dieser Arbeit war eine Untersuchung zur Häufigkeit des Wechsels von Legehennen zwischen Innen- und Außenbereichen, einschließlich der Aufenthaltsdauer außerhalb des Stalles, in Relation zum Federpicken und der Beschaffenheit des Integumentes. Der Einfluss der Haltungsbedingungen und der Einfluss des Genotyps wurden untersucht. Die Gruppe, die ohne Grünauslauf war, bewegte sich signifikant häufiger zwischen dem Stall und dem Wintergarten als andere Gruppen mit Grünauslauf. Die Aufenthaltsdauer im Stall und Wintergarten war in der Gruppe ohne Grünauslauf signifikant höher als bei anderen mit Grünauslauf (GA). Hennen, denen eine große Auslauffläche angeboten wurde (10m²/T) bewegten sich signifikant häufiger zu den Außenbereichen als andere mit einem Angebot von 2,5 m²/Tier. Hennen mit einem Angebot von 2,5 m²/Tier hielten sich länger auf dem Grünland auf als Hennen mit einer Besatzdichte von 10m²/T. Die höchsten Federpickaktivitäten waren in der Gruppe ohne GA im Vergleich zu den Gruppen mit GA. Im Vergleich zu anderen Gruppen mit GA, hatte die Gruppe ohne GA einen schlechteren Gefiederzustand. LSL Hennen bewegten sich im Vergleich zu den LT Hennen häufiger zwischen Innen- und Außenbereichen. LSL Hennen hielten sich im Vergleich zu den LT Hennen länger im Wintergarten auf. Dennoch hielten sich die LT Hennen im Vergleich länger auf dem Grünland auf. Die schlechteste Gefiederbeschaffenheit wiesen LSL Hennen im Vergleich zu LT Hennen auf. Die Resultate der vorliegenden Untersuchungen weisen darauf hin, dass die Auslaufnutzung einen positiven Einfluss auf den Gefieder- und Hautzustand hat. Die untersuchten Genotypen unterschieden sich in der Häufigkeit des Ortswechsels und der Aufenthaltsdauer im Grünauslauf. / The aim of this work was to investigate the frequency of movement of laying hens between indoor and outdoor enclosures and the time hens spent outside the hen house in relation to feather pecking and condition of the integument. The effect of housing condition and the genotype were studied. Hens that were offered a large space to outside open area (10m²/bird) moved significantly more frequently to the outdoor areas than others (2.5m²/bird). Frequency of movement between poultry house and winter garden was higher in the group without grassland. Hens kept at a higher density outdoors (2.5m²/bird) spent significantly more time in this area than hens were kept at a lower density (10m²/bird) on grassland. The high rates of feather pecking are observed in the group without grassland compared to groups stocked at 2.5m² or 10m² per bird on grassland The group without grassland had poorer feather condition compared to other groups that had 2.5m²/bird and 10m²/bird on grassland Lohmann Selected Leghorn (LSL) hens moved more frequently to the outdoor enclosures compared to Lohmann Tradition (LT). But LT hens spent significantly more time on grassland than LSL.The plumage condition was worse in LSL than LT hens. It is concluded that housing conditions might have a stronger influence on the development of feather pecking than the genetic aspect. Large differences between the genotypes examined were found in respect to the frequency of movement to the outdoor areas, the time spent outside and plumage and skin damage.

The aim of this study was to investigate the effect of additional enrichment materials (EMs; pecking stones and alfalfa bales) on the occurrence of plumage damage, skin injuries, and toe injuries, with an emphasis on the possible differences between commercial hybrid strains of laying hens. During rearing (weeks 1–18, 16 compartments, 4000 pullets) and laying periods (weeks 21–72, 24 compartments, 2808 hens) in a littered housing system, EMs were permanently provided to the study groups (EXP), while control groups (CON) did not receive additional EM. In a two-factorial study design (two groups with four strains) with 351 hens per variant, the brown egg-laying Lohmann Brown classic (LB) and Bovans Brown (BB) strains as well as the white egg-laying Lohmann Selected Leghorn classic (LSL) and Dekalb White (DW) strains were investigated. Compared to the CON, the EXP showed reduced body mass during rearing (p < 0.001) and reduced albumen consistency in the laying period (p < 0.001). Regarding integument condition, the LSL in the EXP showed more toe injuries than in the CON (p = 0.018). Remarkably, genotype-environment interactions between strains and groups were evident (p < 0.001). In groups with an EM supply, plumage damage decreased in LB (p ≤ 0.033) and LSL (p ≤ 0.005) but increased in BB (p ≤ 0.003). Moreover, there were fewer skin injuries in LSL (p = 0.001) but more in BB (p = 0.001) in groups with access to EM. In view of the diverging effects between strains, future practical recommendations for laying hen husbandry should be strain-specific.:Introduction Materials and Methods Results Discussions Author Contributions Funding Acknowledgments Conflicts of Interest References

Os derramamentos de petróleo são consequência inevitável e indesejável da produção e transporte do petróleo e seus derivados. A maioria desses derramamentos são relativamente pequenos, mas alguns deles são grandes o suficiente para causar significativo impacto ambiental. Nessas situações, os modelos computacionais são ferramentas importantes para estimar a trajetória, dimensionamento e comportamento do óleo derramado no ambiente marinho, sendo determinantes na elaboração de planos de ação e trabalho das equipes de resposta. O transporte e destino de óleo offshore derramado são regidos majoritariamente, no curto período, por processos de transporte e de transformação físico-químicos e no longo período por processos de degradação biológica, de acordo com as condições ambientais locais (oceânicas e atmosféricas). Os principais processos que atuam sobre as manchas de óleo offshore incluem, no curto período, advecção, difusão turbulenta, espalhamento superficial, evaporação, dissolução, emulsificação, sedimentação e a interação de mancha de óleo com a linha da costa. O STFM (Spill, Transport and Fate Model) foi o modelo computacional desenvolvido nesse trabalho. Os algoritmos foram desenvolvidos com base em formulações físico-químicas propostas na literatura, sendo testadas as proposições de diversos autores e selecionadas as equações que apresentaram melhores resultado para integrar o conjunto físico-químico que compõe o STFM. Os resultados do trabalho mostraram que o STFM apresentou desempenho superior aos demais modelos testados na descrição do espalhamento e difusão dando mais estabilidade à mancha por utilizar a derivação de Dodge para a proposta de espalhamento de Fay e substituir o método usual de Randon Walk por Randon Flight (avançado no tempo) na forma canônica dada por Lynch. O algoritmo do STFM também traz outra evolução importante ao incluir um modelo de evaporação baseado nas equações empíricas de Fingas, substituindo as atuais parametrizações baseadas no ADIOS2 e nos métodos de pseudocomponentes. / Oil and its by-products spills are an inevitable and undesirable consequence of their production and transportation. Even though these spills are relatively small, some of them are large enough to cause significant environmental impact. Taken this into account, the computational models are important tools to estimate the trajectory, dimensioning and behavior of the oil spilled in the marine environment, being also determinants to elaborate action plans for response teams work. The transportation and fate of oil spills are governed in the short term by physical-chemical transport and transformation processes and in the long term by biological degradation processes, according to local environmental conditions (oceanic and atmospheric). The main processes that act on offshore oil spills include, in the short term, advection, turbulent diffusion, surface scattering, evaporation, dissolution, emulsification, sedimentation and the interaction of oil slick according to the coast line. The Spill, Transport and Fate Model (STFM) was the computational model developed in this work. The algorithms were developed based on physicochemical formulations proposed in literature, being the propositions of several authors tested and the equations which presented the best results were selected to integrate the physical-chemical set that makes up the STFM. The STFM results presented superior performance, giving more stability to the stain, compared to the other models tested in the scattering and diffusion description, by using the Dodge derivation for the Fay spreading proposal and by replacing the usual \"Randon Walk\" method by \"Randon Flight\" (advanced in time) in the canonical form given by Lynch. The STFM algorithm also brings forward another important evolution by including an evaporation model based on Fingas empirical equations, replacing the current parameterizations based on ADIOS2 and pseudo component methods.

Os derramamentos de petróleo são consequência inevitável e indesejável da produção e transporte do petróleo e seus derivados. A maioria desses derramamentos são relativamente pequenos, mas alguns deles são grandes o suficiente para causar significativo impacto ambiental. Nessas situações, os modelos computacionais são ferramentas importantes para estimar a trajetória, dimensionamento e comportamento do óleo derramado no ambiente marinho, sendo determinantes na elaboração de planos de ação e trabalho das equipes de resposta. O transporte e destino de óleo offshore derramado são regidos majoritariamente, no curto período, por processos de transporte e de transformação físico-químicos e no longo período por processos de degradação biológica, de acordo com as condições ambientais locais (oceânicas e atmosféricas). Os principais processos que atuam sobre as manchas de óleo offshore incluem, no curto período, advecção, difusão turbulenta, espalhamento superficial, evaporação, dissolução, emulsificação, sedimentação e a interação de mancha de óleo com a linha da costa. O STFM (Spill, Transport and Fate Model) foi o modelo computacional desenvolvido nesse trabalho. Os algoritmos foram desenvolvidos com base em formulações físico-químicas propostas na literatura, sendo testadas as proposições de diversos autores e selecionadas as equações que apresentaram melhores resultado para integrar o conjunto físico-químico que compõe o STFM. Os resultados do trabalho mostraram que o STFM apresentou desempenho superior aos demais modelos testados na descrição do espalhamento e difusão dando mais estabilidade à mancha por utilizar a derivação de Dodge para a proposta de espalhamento de Fay e substituir o método usual de Randon Walk por Randon Flight (avançado no tempo) na forma canônica dada por Lynch. O algoritmo do STFM também traz outra evolução importante ao incluir um modelo de evaporação baseado nas equações empíricas de Fingas, substituindo as atuais parametrizações baseadas no ADIOS2 e nos métodos de pseudocomponentes. / Oil and its by-products spills are an inevitable and undesirable consequence of their production and transportation. Even though these spills are relatively small, some of them are large enough to cause significant environmental impact. Taken this into account, the computational models are important tools to estimate the trajectory, dimensioning and behavior of the oil spilled in the marine environment, being also determinants to elaborate action plans for response teams work. The transportation and fate of oil spills are governed in the short term by physical-chemical transport and transformation processes and in the long term by biological degradation processes, according to local environmental conditions (oceanic and atmospheric). The main processes that act on offshore oil spills include, in the short term, advection, turbulent diffusion, surface scattering, evaporation, dissolution, emulsification, sedimentation and the interaction of oil slick according to the coast line. The Spill, Transport and Fate Model (STFM) was the computational model developed in this work. The algorithms were developed based on physicochemical formulations proposed in literature, being the propositions of several authors tested and the equations which presented the best results were selected to integrate the physical-chemical set that makes up the STFM. The STFM results presented superior performance, giving more stability to the stain, compared to the other models tested in the scattering and diffusion description, by using the Dodge derivation for the Fay spreading proposal and by replacing the usual \"Randon Walk\" method by \"Randon Flight\" (advanced in time) in the canonical form given by Lynch. The STFM algorithm also brings forward another important evolution by including an evaporation model based on Fingas empirical equations, replacing the current parameterizations based on ADIOS2 and pseudo component methods.

The two main goals of my thesis were to further our understanding of how parental effort is related to life-history trade-offs and to see how parental investment is reflected in various potential measures of nestling quality. I looked at how fitness is maximized by examining (1) the trade-off between current and future reproduction, and (2) the trade-off between quantity and quality of offspring. To see how parents responded to energetic demands and whether each sex reacted in a similar way, I experimentally manipulated brood sizes and quantified provisioning rates. Both male and female parents with enlarged broods increased their feeding rates, but provisioning on a per nestling basis declined, so that parents fledged lighter nestlings with shorter wings. Although the incidence of mortality did not differ between control and enlarged broods, nestlings from enlarged broods were lighter than those from control broods with the same brood size, suggesting that clutch size may be individually optimized. I also looked at how nestlings responded to different levels of nutritional stress in the manipulated broods by quantifying size and body condition, plumage colouration, and the physiological measures of T-cell mediated immune responses, and corticosterone levels in nestling feathers as a long-term integrated measure of stress physiology. The size of melanin ornaments on feathers and the saturation and brightness of carotenoid colouration was associated with nestling mass in such a way that suggested that plumage characteristics reflect nestling quality. The immune function of nestlings was negatively related to brood size and nestlings in better body condition could mount greater immune responses to foreign antigens suggesting that immune responses are energetically costly. Corticosterone levels in the feathers were not related to nestling body condition and were unaffected by the experimental brood manipulation. The ii mass of male nestlings, which are the larger sex, was more compromised by brood size than female mass was. I also found sex-specific relationships between plumage characteristics and measures of physiological performance. These findings help to explain optimal clutch size and the classic trade-off between quality and quantity of offspring. They also offer new insights into the reliability of putative measures of quality in nestlings and relationships between physiological and morphological traits.

Avian cholera, caused by infection with Pasteurella multocida, is an important infectious disease of wild birds in North America Since it was first confirmed in 2005, annual outbreaks of avian cholera have had a dramatic effect on common eiders on East Bay Island, Nunavut, one of the largest breeding colonies of northern common eiders (Somateria mollissima borealis) in the eastern Arctic. I investigated potential avian and environmental reservoirs of P. multocida on East Bay Island and other locations in the eastern Canadian Arctic by collecting cloacal and oral swabs from live or harvested, apparently healthy, common eiders, lesser snow geese, Ross’s geese, king eiders, herring gulls, and snow buntings. Water and sediment from ponds on East Bay Island were sampled before and during outbreaks. Avian and environmental samples were tested using a real-time polymerase chain reaction (PCR) assay to detect P. multocida. PCR positive birds were found in every species except for snow buntings, and PCR positive common eiders were found in most locations, supporting the hypothesis that apparently healthy wild birds can act as a reservoir for avian cholera. In all years, P. multocida DNA was detected in ponds both before and after the avian cholera outbreak began each year, suggesting that the environment also plays a role in outbreak dynamics. Contrary to our expectations, model results revealed that ponds were generally more likely to be positive earlier in the season, before the outbreaks began. Whereas average air temperature at the beginning of the breeding season was not an important predictor for detecting P. multocida in ponds, eiders were more likely to be PCR positive under cooler conditions, pointing to an important link between disease and weather. Potential origins of P. multocida causing avian cholera in Arctic eider colonies were investigated by comparing eastern Arctic isolates of P. multocida to isolates from wild birds across Canada, and the central flyway in the United States. Using repetitive extragenic palindromic-PCR (REP-PCR) and multi-locus sequence typing (MLST), we detected a low degree of genetic diversity among isolates, and P. multocida genotypes were correlated with somatic serotype. Isolates from East Bay Island were distinct from P. multocida from eider colonies in the St. Lawrence Estuary, Quebec, however, East Bay Island isolates were indistinguishable from isolates collected from a 2007 pelagic avian cholera outbreak on the east coast of Canada. Isolates from East Bay Island and Nunavik shared sequence types, indicating possible transmission of isolates among eider colonies in the eastern Arctic. Previously, feather corticosterone in eiders was found to be significantly associated with environmental temperature during the moulting period. In my study, path analysis revealed that environmental conditions experienced during the moulting period had direct impacts on arrival date and pre-breeding body condition of common eiders during the subsequent breeding period on East Bay Island, with indirect impacts on both reproductive success and survival. Higher temperatures experienced during the fall moulting period appear to impose significant costs to eiders, with subsequent carry-over effects on both survival and reproduction many months later during avian cholera outbreaks. This thesis describes several important features of the host, agent and environmental dynamics of avian cholera in North America with a particular focus on the disease in the eastern Canadian Arctic. Continued exploration of infectious wildlife disease dynamics is needed to better predict, detect, manage, and mitigate disease emergence that can threaten human and animal health and species conservation.

Host-parasite associations are born by cospeciations or by host switches. Feather lice have traditionally been used as model parasites for studying these events and underlying ecological factors. By now tens of analyses have addressed comparisons of host and parasite phylogenies to study cospeciations and host switches in lice, however, these analyses are strongly biased towards the temperate zone. Tropical environment could provide new insight into the origin of host-parasite interactions, because it is ecologically unique. This work aims to supplement the knowledge of host-parasite associations in lice using coevolution analyses of two feather lice genera and their passerine hosts in tropical rainforest in Cameroon. It shows that lice in the tropics cospeciate rarely. To assess whether host switches are non-random and occur preferentially between hosts with specific traits, this work also analyses relations between parasite genetic distances and hosts' trait similarities. No effect of host morphology and spatial distribution was found. However, genetic distances of the lice strongly correlate with genetic distances of their hosts.

Immersion heaters are used by industries to heat fluids. The element of an immersion heater need to be fully immersed into the heated liquid, otherwise it could be subject to overheat. The main purpose of this thesis is to find a temperature sensor, which could signal in case the immersion heater is at risk to suffer from overheat due to low liquid level. A comparison of accuracy, size and cost between an analog and a digital sensor is held, to conclude whether either one is at an advantage for this application.An immersion heater with ceramic element and quartz glass tube and a water tank, both provided by Scandymet, is used during experiments. First, the position for the sensor inside the heater was examined, by placing the sensor at different positions. Next, measurements of the operating temperature of the immersion heater were made at different liquid levels. This resulted in a placement for the sensor near the head of the immersion heater and an approximate temperature range from 41 ℃ to 58 ℃. Both the analog and digital sensors is chosen with measurable ranges to match the result from previous experiments. A thermistor along with a linearizing series resistor make the analog design and a DS18B20+ with a pull-up resistor the digital design. The microcontroller for both designs is Adafruit Feather Adalogger M0, which is programmed in C/C++ using Arduino IDE software. It is concluded that it is possible to signal in case liquid level decrease below minimum level, by inserting a temperature sensing device into the immersion heater. The sensor should be placed above the maximum liquid level mark, close to the head of the heater. The analog design would be recommended as overheat protection, due to its smaller size, less expensive and, with further calibration, accurate response.

Les crinoïdes sont bien connus pour leurs fossiles, mais la biominéralisation de leurs stades larvaires n’est que peu documentée. La première partie du projet présente le développement des ossicules des trois stades larvaires du comatule Florometra serratissima : doliolaria, cystidienne et pentacrinoïde. Les ossicules du crinoïde démontraient de la plasticité phénotypique et de la désynchronisation dans leur développement. Les crinoïdes étant la classe basale des échinodermes modernes, ceci porte à croire que ces traits étaient aussi caractéristiques des échinodermes ancestraux et auraient joué un rôle dans la radiation hâtive et la grande disparité des échinodermes. Pour notre deuxième étude, comme les patrons de morphologie des crinoïdes et des autres échinodermes sont nombreux et sont régulés par des protéines spécifiques, nous avons vérifié la présence de quatre familles de protéines de la matrice de spicules (SMAP) connues chez les oursins dans les transcriptomes des autres échinodermes et d’autres deutérostomes. La famille des spicules matrix (SM) et l’anhydrase carbonique CARA7LA étaient absentes chez tout autre organisme que les oursins, les protéines spécifiques au mésenchyme (MSP130) étaient présentes en nombres différents chez tous les ambulacraires suggérant de multiples duplications et pertes, et les métalloprotéases étaient nombreuses chez chacun. Le développement des ossicules chez les échinodermes est un sujet qui a gagné en popularité au cours des dernières décennies, spécialement chez les oursins, et inclure les crinoïdes dans ce type d’étude permettra de nous renseigner sur l’origine et l’évolution des échinodermes modernes. / While the fossil record of crinoids is widespread and largely known, biomineralization of their larval stages is poorly documented. The first part of the project focuses on the ossicle development of the three larval stages of the feather star Florometra serratissima: doliolaria, cystidean and pentacrinoid. The ossicles of the crinoid showed phenotypic plasticity and asynchronous development. Crinoids form the basal class of living echinoderms; this prompts one to believe that these traits were also characteristic of the ancestral echinoderms and would have played a role in the early radiation and large disparity of the modern echinoderms. For the second study, as patterns of morphology of crinoids and of other echinoderms are numerous and are regulated by specific proteins, we verified the presence of four families of spicule matrix associated proteins (SMAPs) known among sea urchins in transcriptomes of the other echinoderms and deuterostomes. The family of spicule matrix (SMs) proteins and the carbonic anhydrase CARA7LA were absent in any other organism aside from sea urchins, mesenchyme specific proteins (MSP130s) were present in varying numbers in all ambulacrarians suggesting multiple duplications and losses and matrix metalloproteases were numerous in every organisms. The development of ossicles in echinoderms is a topic that has gained popularity in the last decades, especially in sea urchins, and including crinoids in this type of study will inform us about the origin and evolution of the modern echinoderms.