La smoltification est un évènement métamorphique chez le saumon qui initie la migration de dévalaison et pré-adapte le juvénile à l’entrée en mer. Cette thèse a pour objectif d’étudier les régulations endocrines et environnementales de la smoltification chez le saumon Atlantique de la longue rivière Loire-Allier, population qui est en danger. Nous montrons la présence et la divergence fonctionnelle de deux paralogues de la sous-unité ß (tshßa & tshßb) de la thyrotropine (TSH) chez le saumon Atlantique et observons un pic d’expression de tshßb dans l’hypophyse à la smoltification, pic concomitant à l’initiation de la migration de dévalaison. Ce résultat est le premier à mettre en relation l’expression hypophysaire de TSH avec la smoltification et le comportement migratoire de dévalaison. L’exposition expérimentale à une photopériode constante de jours courts ou à une température augmentée n’affecte pas nettement le pic de tshßb ni l’initiation de la migration de dévalaison, ce qui met en évidence l’importance de contrôles endogènes. Cette étude apporte de nouvelles connaissances fondamentales sur le cycle de vie du saumon Atlantique avec la découverte de nouveaux acteurs dans le processus de smoltification et avec des implications dans le domaine de la conservation. / Smoltification is a metamorphic event in salmon, which initiates downstream migration and pre-adapts juvenile for seawater entry. The PhD aimed at investigating endocrine and environmental regulation of smoltification in the endangered long-river Loire-Allier Atlantic salmon. We report the presence and functional divergence of thyrotropin ß-subunit paralogs (tshßa & tshßb) in Atlantic salmon and showed a peak pituitary expression of tshßb at smoltification which was concomitant with the initiation of downstream migration. This is the first time pituitary TSH expression is related to smoltification and downstream migratory behavior. Experimental exposure to constant short-day photoperiod or to increased temperature did not markedly affect the peak of tshßb nor the initiation of downstream migration, highlighting the importance of endogenous controls. This study brings new insights to the life cycle of Atlantic salmon with the discovery of novel components of the smoltification process, and with implications for conservation.

Made available in DSpace on 2017-07-10T17:31:15Z (GMT). No. of bitstreams: 1 Constantino_Eleutherio_Luz.pdf: 2845155 bytes, checksum: f9e51c3d07bfcebf178a79ea1cc6f916 (MD5) Previous issue date: 2011-11-23 / The dissertation examines the downstream finning phenomenon as it operates in the bottom sediments in the Marrecas river, located in South West region of Parana state, Brazil. The area of basin has 865,43 km2 and encompasses he municipalities of Francisco Beltrão, Marmeleiro, Flor da Serra do Sul, Verê and Itapejara D Oeste. The Marrecas river basin inserted in Cretaceous age rock composed of basaltic rocks of the Serra Geral Formation with plateaus characterized by dissecting medium and high, elongated tops and slopes convex and straight. Were calculated the main basin morphometric index based on 1:260,000 scale map and longitudinal thalweg profile of the main channel based on 1:50,000 scale topographic maps. The botton sediments samples was performed in December 2009 and January 2010 with a van Veen samples in a location preferably located in the vicinity of the main tributaries of Marrecas river and easy access to river banks. The sandy and coarse sediments were analyzed by sieving techniques and use of gravelometer device. Were calculated grain-size statistical parameters: mean, median, sorting, skewness and kurtosis as defined by Folk & Ward (1957). The sphericity of the coarse sediments was defined by adopting the classification of Zingg (1935). The trends observed particle size showed a clear downstream finning of botton sediments in the downstream direction, changed locally due to the contribution of sediments by tributaries. The sorting showed no trend with values ranged from moderately to very poorly. Skewness shows a trend of variation of positive values in the upper reaches of the Marrecas river for negative values in the lower reaches, while the kurtosis showed a slight tendency passing values platikurtic to leptokurtic. The predominance of spherical shape in bottom sediments was attributed to spheroidal weathering and low resistance to abrasion of the rock. / A presente dissertação trata sobre a variação longitudinal das características texturais dos sedimentos de fundo no rio Marrecas, localizado na região Sudoeste do Paraná. A área da bacia do rio Marrecas possui 865,43 km2 e abarca parte dos municípios de Francisco Beltrão, Marmeleiro, Flor da Serra do Sul, Verê e Itapejara D Oeste. O total da bacia do rio Marrecas está inserida em terrenos de idade cretácea formada por rochas basálticas da formação Serra Geral que formam planaltos caracterizados por dissecação média e alta, topos alongados, vertentes convexas e retilíneas. Foram calculados os principais índices morfométricos da bacia baseados em mapas em escala 1:260.000 e elaborado perfil longitudinal do canal principal com base em cartas topográficas em escala 1:50.000. A coleta de sedimentos de fundo foi executada em dezembro de 2009 e janeiro de 2010, com amostrador de mandíbula tipo Van Veen em locais situados preferentemente nas imediações dos principais afluentes do rio Marrecas e em trechos de acesso fácil às margens do rio. Os sedimentos arenosos e rudáceos foram analisados mediante técnicas de peneiramento e emprego de cascalhômetro. Foram calculados os seguintes parâmetros estatísticos: diâmetro médio, mediana, grau de seleção, assimetria e curtose segundo a definição de Folk & Ward (1957). A esfericidade dos sedimentos rudáceos foi definida adotando a classificação de Zingg (1935). As tendências granulométricas observadas mostraram uma nítida granodecrescência dos sedimentos de fundo em direção à jusante, alterada localmente devido ao aporte de sedimentos pelos afluentes. O grau de seleção não mostrou nenhuma tendência e variou de moderadamente a muito pobremente selecionado. A assimetria mostra uma tendência de variação de valores positivos nos trechos superiores do rio Marrecas para valores negativos nos trechos inferiores, enquanto que a curtose exibiu uma passagem de valores platicúrticos para leptocúrticos em direção à jusante. O predomínio da forma esférica nos sedimentos de fundo foi atribuído a decomposição esferoidal do basalto e a baixa resistência desta rocha à abrasão.

Made available in DSpace on 2017-05-12T14:42:47Z (GMT). No. of bitstreams: 1 Constantino_Eleutherio_Luz.pdf: 2845155 bytes, checksum: f9e51c3d07bfcebf178a79ea1cc6f916 (MD5) Previous issue date: 2011-11-23 / The dissertation examines the downstream finning phenomenon as it operates in the bottom sediments in the Marrecas river, located in South West region of Parana state, Brazil. The area of basin has 865,43 km2 and encompasses he municipalities of Francisco Beltrão, Marmeleiro, Flor da Serra do Sul, Verê and Itapejara D Oeste. The Marrecas river basin inserted in Cretaceous age rock composed of basaltic rocks of the Serra Geral Formation with plateaus characterized by dissecting medium and high, elongated tops and slopes convex and straight. Were calculated the main basin morphometric index based on 1:260,000 scale map and longitudinal thalweg profile of the main channel based on 1:50,000 scale topographic maps. The botton sediments samples was performed in December 2009 and January 2010 with a van Veen samples in a location preferably located in the vicinity of the main tributaries of Marrecas river and easy access to river banks. The sandy and coarse sediments were analyzed by sieving techniques and use of gravelometer device. Were calculated grain-size statistical parameters: mean, median, sorting, skewness and kurtosis as defined by Folk & Ward (1957). The sphericity of the coarse sediments was defined by adopting the classification of Zingg (1935). The trends observed particle size showed a clear downstream finning of botton sediments in the downstream direction, changed locally due to the contribution of sediments by tributaries. The sorting showed no trend with values ranged from moderately to very poorly. Skewness shows a trend of variation of positive values in the upper reaches of the Marrecas river for negative values in the lower reaches, while the kurtosis showed a slight tendency passing values platikurtic to leptokurtic. The predominance of spherical shape in bottom sediments was attributed to spheroidal weathering and low resistance to abrasion of the rock. / A presente dissertação trata sobre a variação longitudinal das características texturais dos sedimentos de fundo no rio Marrecas, localizado na região Sudoeste do Paraná. A área da bacia do rio Marrecas possui 865,43 km2 e abarca parte dos municípios de Francisco Beltrão, Marmeleiro, Flor da Serra do Sul, Verê e Itapejara D Oeste. O total da bacia do rio Marrecas está inserida em terrenos de idade cretácea formada por rochas basálticas da formação Serra Geral que formam planaltos caracterizados por dissecação média e alta, topos alongados, vertentes convexas e retilíneas. Foram calculados os principais índices morfométricos da bacia baseados em mapas em escala 1:260.000 e elaborado perfil longitudinal do canal principal com base em cartas topográficas em escala 1:50.000. A coleta de sedimentos de fundo foi executada em dezembro de 2009 e janeiro de 2010, com amostrador de mandíbula tipo Van Veen em locais situados preferentemente nas imediações dos principais afluentes do rio Marrecas e em trechos de acesso fácil às margens do rio. Os sedimentos arenosos e rudáceos foram analisados mediante técnicas de peneiramento e emprego de cascalhômetro. Foram calculados os seguintes parâmetros estatísticos: diâmetro médio, mediana, grau de seleção, assimetria e curtose segundo a definição de Folk & Ward (1957). A esfericidade dos sedimentos rudáceos foi definida adotando a classificação de Zingg (1935). As tendências granulométricas observadas mostraram uma nítida granodecrescência dos sedimentos de fundo em direção à jusante, alterada localmente devido ao aporte de sedimentos pelos afluentes. O grau de seleção não mostrou nenhuma tendência e variou de moderadamente a muito pobremente selecionado. A assimetria mostra uma tendência de variação de valores positivos nos trechos superiores do rio Marrecas para valores negativos nos trechos inferiores, enquanto que a curtose exibiu uma passagem de valores platicúrticos para leptocúrticos em direção à jusante. O predomínio da forma esférica nos sedimentos de fundo foi atribuído a decomposição esferoidal do basalto e a baixa resistência desta rocha à abrasão.

This thesis explores Centralised Demand Information Sharing (CDIS) in supply chains. CDIS is an information sharing approach where supply chain members forecast based on the downstream member’s demand. The Bullwhip Effect is a demand variance amplification phenomenon: as the demand moves upstream in supply chains, its variability increases. Many papers in the literature show that, if supply chain members forecast using the less variable downstream member’s demand, this amplification can be reduced leading to a reduction in inventory cost. These papers, using strict model assumptions, discuss three demand information sharing approaches: No Information Sharing (NIS), Downstream Demand Inference (DDI) and Demand Information Sharing (DIS). The mathematical analysis in this stream of research is restricted to the Minimum Mean Squared Error (MMSE) forecasting method. A major motivation for this PhD research is to improve the above approaches, and assess those using less restrictive supply chain assumptions. In this research, apart from using the MMSE forecasting method, we also utilise two non-optimal forecasting methods, Simple Moving Averages (SMA) and Single Exponential Smoothing (SES). The reason for their inclusion is the empirical evidence of their high usage, familiarity and satisfaction in practice. We first fill some gaps in the literature by extending results on upstream demand translation for ARMA (p, q) processes to SMA and SES. Then, by using less restrictive assumptions, we show that the DDI approach is not feasible, while the NIS and DIS approaches can be improved. The two new improved approaches are No Information Sharing – Estimation (NIS-Est) and Centralised Demand Information Sharing (CDIS). It is argued in this thesis that if the supply chain strategy is not to share demand information, NIS-Est results in less inventory cost than NIS for an Order Up To policy. On the other hand, if the strategy is to share demand information, the CDIS approach may be used, resulting in lower inventory cost than DIS. These new approaches are then compared to the traditional approaches on theoretically generated data. NIS-Est improves on NIS, while CDIS improves on the DIS approach in terms of the bullwhip ratio, forecast error (as measured by Mean Squared Error), inventory holding and inventory cost. The results of simulation show that the performance of CDIS is the best among all four approaches in terms of these performance metrics. Finally, the empirical validity of the new approaches is assessed on weekly sales data of a European superstore. Empirical findings and theoretical results are consistent regarding the performance of CDIS. Thus, this research concludes that the inventory cost of an upstream member is reduced when their forecasts are based on a Centralised Demand Information Sharing (CDIS) approach.

<p>The importance of chemical use is enormous for areas such as agriculture, industry and medicine and hence a prerequisite for our modern society. In order to protect humans and the environment from the negative effects of chemical use, chemical regulations have been used at a relatively early stage in our history. The purpose of REACH, the new chemical regulation of the European Union, is to generate new knowledge of chemicals within the European market and to increase the responsibilities of the enterprises when it comes to risk management. Whether the enterprises will implement the regulations or not will be of vital importance for the realization of the law’s intentions.</p><p>The purpose of this study was to identify possibilities and problems that can occur when a downstream-user SME is about to implement REACH. Case study is the method by which this study has been carried out. Further, the study includes 20 smaller interviews with focus on smaller enterprises to address the generalization of the case study and to investigate the knowledge about REACH within this group of enterprises. The results from the case study showed three aspects that were important for this enterprise in the implementation process; the chosen enterprise had an active trade organization, the enterprise was a formulator and the size of the enterprise. The results from the telephone interviews showed that 12 of 20 enterprises were not aware of the new legislation but that there are differences between the subgroups of downstream-users. All of the interviewed formulators were aware of the legislation and had also started to work active towards implementing it, within the group of professional users only one of the enterprises were aware of the legislation. Further the telephone interviews did not show any clearly connection between the size of the enterprises and the level of knowledge about the new regulation, something that has been shown in earlier studies. Hence, there is a risk that the lack of knowledge will have a negative impact on the overall goal of REACH; to contribute to a sustainable development. From the results of this study it is motivated with directed information within this group of enterprises to overcome the lack of knowledge and to increase the chance that REACH will be a valuable contribution to a sustainable development within the chemical sector.</p>

<p>In prokaryotes, several mRNA sequences surrounding the initiation codon have been found to influence the translation process; these include the downstream region and its codon context, the Shine-Dalgarno sequence and the S1 ribosomal protein-binding site. In this thesis, the purpose has been to study the role of the downstream region and Shine-Dalgarno-like sequences on early translation elongation and gene expression in <i>Escherichia coli</i>.</p><p>The downstream region (DR) after the initiation codon (around five to seven codons), has an important role in the initiation of translation. We find that most of the codons which give very low gene expression at +2 (considering AUG as +1), reach 5 to 10 fold higher expression when those codons are positioned posteriori to +2, with the exception of the NGG codons. The NGG codons abort the translation process if located within the first five codons of the DR, due to peptidyl-tRNA drop-off. However, when the NGG codons are situated further down from the DR, the protein expression was increased at the same level of expression as in the presence of any other codon.</p><p>The Shine-Dalgarno (SD) is an important region of initiation in translation of bacteria. In spite of this, it has been found that Gram-negative bacteria could translate mRNAs with weak or non-functional SD, while the DR carries out a main role in the efficiency of translation. In addition, positions of SD and SD-like sequences are very important to direct initiation of translation in the choice between two possible initiation codons. A strong SD between two initiation sites will favor the second initiation site if it consists of a canonical start codon followed by a good DR.</p><p>The results suggest that the mRNA sequences surrounding the initiation codon: the downstream region and the Shine-Dalgarno and SD-like sequences, are very important contributors to the translation level and gene expression in <i>Escherichia coli</i>.</p>

<p>The passage efficiency of downstream migrating brown trout (Salmo trutta) smolts past two hydropower plants in the River Emån, southeastern Sweden, was evaluated by telemetry. From 26 April to 17 May 2005, 40 wild brown trout smolts were radio-tagged, and their positions were recorded daily until 14 June. Approximately 45% of the individuals passed both power plants, and 15% made it to the sea, some 28 km downstream of the power plants. About 20% of the individuals ceased migrating, residing in a lotic habitat. Mortality due to predation was 33%, and the predation rate was higher in the power plant dams than it was downstream of the power plants. Turbine-induced mortality was greater in the upper power plant (40%) than in the lower one (13%). Fish that chose the alternative routes, through the gates, swam past the upper dam faster than fish that swam through the turbines. The results confirm previous work in the river, namely that measures need to be taken to improve passage efficiency past the power plants, particularly passage of the upper power plant. Such measures are of crucial importance if the nature-like bypass channels at the power plants in Finsjö are going to have any long-term effects on the brown trout population.</p> / <p>Passageeffektiviteten för nedströms vandrande havsöringssmolt (Salmo trutta) förbi två vattenkraftverk i Emån, i sydöstra Sverige, utvärderades med telemetri. Från 26 april till och med 17 maj 2005 märktes 40 vilda havsöringssmolt med radiosändare och de positionsbestämdes dagligen till och med 14 juni. Ungefär 45% av individerna passerade båda kraftverken, och 15% klarade sig till havet, cirka 28 km nedströms kraftverken. Omkring 20% av individerna avbröt vandringen och stannade i ett lotiskt habitat. Mortalitet på grund av predation uppgick till 33%, och predationshastigheten var högre i kraftverksdammarna än nedströms kraftverken. Den turbininducerade mortaliteten var högre i det övre kraftverket (40%) än i det nedre (13%). Det gick fortare att passera den övre kraftverksdammen för fisk som valde de alternativa rutterna, genom dammluckorna, jämfört med att passera genom turbinerna. Dessa resultat bekräftar tidigare studier i ån, nämligen att åtgärder krävs för att förbättra passageeffektiviteten förbi kraftverken, i synnerhet passagen av det övre kraftverket. Sådana åtgärder är av avgörande betydelse om de naturlika fiskvägarna vid kraftverken i Finsjö ska få några långsiktiga effekter på havsöringspopulationen.</p>

In the middle of the 1990’s the microarray technology was introduced. The technology allowed for genome wide analysis of gene expression in one experiment. Since its introduction similar high through-put methods have been developed in other fields of molecular biology. These high through-put methods provide measurements for hundred up to millions of variables in a single experiment and a rigorous data analysis is necessary in order to answer the underlying biological questions. Further complications arise in data analysis as technological variation is introduced in the data, due to the complexity of the experimental procedures in these experiments. This technological variation needs to be removed in order to draw relevant biological conclusions from the data. The process of removing the technical variation is referred to as normalization or pre-processing. During the last decade a large number of normalization and data analysis methods have been proposed. In this thesis, data from two types of high through-put methods are used to evaluate the effect pre-processing methods have on further analyzes. In areas where problems in current methods are identified, novel normalization methods are proposed. The evaluations of known and novel methods are performed on simulated data, real data and data from an in-house produced spike-in experiment.

In prokaryotes, several mRNA sequences surrounding the initiation codon have been found to influence the translation process; these include the downstream region and its codon context, the Shine-Dalgarno sequence and the S1 ribosomal protein-binding site. In this thesis, the purpose has been to study the role of the downstream region and Shine-Dalgarno-like sequences on early translation elongation and gene expression in Escherichia coli. The downstream region (DR) after the initiation codon (around five to seven codons), has an important role in the initiation of translation. We find that most of the codons which give very low gene expression at +2 (considering AUG as +1), reach 5 to 10 fold higher expression when those codons are positioned posteriori to +2, with the exception of the NGG codons. The NGG codons abort the translation process if located within the first five codons of the DR, due to peptidyl-tRNA drop-off. However, when the NGG codons are situated further down from the DR, the protein expression was increased at the same level of expression as in the presence of any other codon. The Shine-Dalgarno (SD) is an important region of initiation in translation of bacteria. In spite of this, it has been found that Gram-negative bacteria could translate mRNAs with weak or non-functional SD, while the DR carries out a main role in the efficiency of translation. In addition, positions of SD and SD-like sequences are very important to direct initiation of translation in the choice between two possible initiation codons. A strong SD between two initiation sites will favor the second initiation site if it consists of a canonical start codon followed by a good DR. The results suggest that the mRNA sequences surrounding the initiation codon: the downstream region and the Shine-Dalgarno and SD-like sequences, are very important contributors to the translation level and gene expression in Escherichia coli.

Transgenic plant systems have been proposed as bioreactors in the production of pharmaceutical and industrial proteins. The economic benefits of inexpensive plant production systems could be erased if the downstream processing ends up being expensive. To avoid monoclonal antibody (mAb) modification or fouling of chromatography resins, removal of phenolics from plant extracts is desirable. Removal of major phenolics in Lemna extracts was evaluated by adsorption to PVPP, XAD-4, IRA-402 and Q-Sepharose resins. Analysis of phenolics adsorption to XAD-4, IRA-402 and Q-Sepharose showed superior dynamic binding capacities at pH 4.5 than at 7.5. The economic analysis using SuperPro Designer 7.0 indicated that addition of a phenolics adsorption step would increase mAb production cost only 20% by using IRA-402 compared to 35% for XAD-4 resin. The overall mAb processing cost can be reduced by implementing a phenolics removal step. To understand phenolics-resin interactions, adsorption isotherms of phenolic compounds (chlorogenic acid, ferulic acid, rutin, syringic acid and vitexin-2-O-rhamnoside) from different phenolic classes on three resins (IRA-402, PVPP, XAD-4) at pH 4.5 and 7.5 were determined. Differences in adsorption with the type of phenolics were observed, and PVPP was not efficient for phenolics removal. Screening of sugarcane lines for bovine lysozyme (BvLz) accumulation indicated that expression levels are still inadequate for commercial development. To maximize BvLz extraction, pH and ionic strength were evaluated; five conditions resulted in equivalent BvLz/TSP ratio. Membrane filtration process using BvLz extracts attained partial removal of native proteins by the 100 kDa membrane step, but also BvLz loss (21-29%). Regardless of the extraction condition, at least 47% of the starting BvLz was lost during the membrane processing. None of the evaluated extraction conditions caused a substantial recovery of BvLz in the concentrate. Alternative purification options for the IEX+HIC process, which achieved 95% BvLz purity, were tested. Direct loading of sugarcane extract concentrate on HIC and XAD-4 pretreatment of juice did not recovered BvLz as effectively as the IEX chromatography. Pure BvLz was obtained by the XAD+HIC process, but higher purification fold and HIC yield were achieved by the IEX+HIC process, due to the complete separation of BvLz and 18-kDa protein.