Periphyton biomass on artificial strips was observed monthly to see the impacts of nutrient differences on periphyton and periphyton-macroinvertebrates interaction. The experiment was conducted for four months in a mesocosm which were runned at six countries at the same time and with the same steps. Eight enclosures at two meters depth were used that four of them had high nutrient level and the other four had low nutrient level. Sediment, macrophyte, fish, plankton, benthic invertebrates and water were added at the same time and with the same way in all of the countries. Periphyton growth which formed on artificial 32 cm2 strips for June, July, August and September were brushed to filtered mesocosm water and dry mass, ash free dry mass, phosphorus content and chlorophyl-a concentrations were measured. Grazer pressure on the periphyton was observed with a laboratory experiment for July, August and September months. At the end of the mesocosm experiment macrophytes and fish were harvested. Macrophytes&rsquo / dry mass and fish&rsquo / abundance were measured. Moreover at the end of the experiment epiphyton was also measured. Three kajak cores were taken from sediment for macroinvertebrates at the end of the experiment and identified. All physical features of mesocosm enclosures and PVI data were recorded for every 2 weeks. Periphyton biomass was higher concentrations in HN enclosures than LN tanks. Only dry mass of periphyton biomass showed the opposite because of the marl deposition in LN tanks. This finding was also reinforced by epiphyton samples which was taken at the end of the experiment. LN enclosures had the more abundance of macroinvertebrate. The groups we found in sediment which had big grazer effect on periphyton such as gastropods and Chironomidae. Grazer experiment showed that grazer effect on periphyton increased in time. Although this raise, periphyton growth also increased in LN enclosures with nutrient increasing. This may be indicate that nutrient effect has a stronger effect than grazer pressure on periphyton. As it is explained before in the beginning of the experiment all of the conditions were the same except nutrient level. Thus, bottom-up effect changed the top-down control and at the end of the experiment we saw the more periphyton less macroinvertebrate and more fish in HN tanks while the opposite was seen in LN tanks.

Proteomics serves an important role at the systems-level in understanding of biological functioning. Mass spectrometry proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. In the most widely used bottom-up approach to MS-based high-throughput quantitative proteomics, complex mixtures of proteins are first subjected to enzymatic cleavage, the resulting peptide products are separated based on chemical or physical properties and then analyzed using a mass spectrometer. The three fundamental challenges in the analysis of bottom-up MS-based proteomics are as follows: (i) Identifying the proteins that are present in a sample, (ii) Aligning different samples on elution (retention) time, mass, peak area (intensity) and etc, (iii) Quantifying the abundance levels of the identified proteins after alignment. Each of these challenges requires knowledge of the biological and technological context that give rise to the observed data, as well as the application of sound statistical principles for estimation and inference. In this dissertation, we present a set of statistical methods in bottom-up proteomics towards protein identification, alignment and quantification. We describe a fully Bayesian hierarchical modeling approach to peptide and protein identification on the basis of MS/MS fragmentation patterns in a unified framework. Our major contribution is to allow for dependence among the list of top candidate PSMs, which we accomplish with a Bayesian multiple component mixture model incorporating decoy search results and joint estimation of the accuracy of a list of peptide identifications for each MS/MS fragmentation spectrum. We also propose an objective criteria for the evaluation of the False Discovery Rate (FDR) associated with a list of identifications at both peptide level, which results in more accurate FDR estimates than existing methods like PeptideProphet. Several alignment algorithms have been developed using different warping functions. However, all the existing alignment approaches suffer from a useful metric for scoring an alignment between two data sets and hence lack a quantitative score for how good an alignment is. Our alignment approach uses "Anchor points" found to align all the individual scan in the target sample and provides a framework to quantify the alignment, that is, assigning a p-value to a set of aligned LC-MS runs to assess the correctness of alignment. After alignment using our algorithm, the p-values from Wilcoxon signed-rank test on elution (retention) time, M/Z, peak area successfully turn into non-significant values. Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein's associated spectral peaks. However, typical mass spectrometry-based proteomics data sets have substantial proportions of missing observations, due at least in part to censoring of low intensities. This complicates intensity-based differential expression analysis. We outline a statistical method for protein differential expression, based on a simple Binomial likelihood. By modeling peak intensities as binary, in terms of "presence / absence", we enable the selection of proteins not typically amendable to quantitative analysis; e.g., "one-state" proteins that are present in one condition but absent in another. In addition, we present an analysis protocol that combines quantitative and presence / absence analysis of a given data set in a principled way, resulting in a single list of selected proteins with a single associated FDR.

Les réseaux trophiques jouent un rôle primordial dans la régulation des flux de matière et d'énergie au sein des écosystèmes. Dans le cadre des pratiques de recharge artificielle des aquifères, les biocénoses souterraines sont pleinement sollicitées et leur capacité à dégrader les flux de matière organique de surface conditionne le maintien de la qualité des eaux souterraines. L'objectif de ce travail est de déterminer l'influence d'une augmentation des flux de carbone organique dissous sur l'intensité des interactions trophiques entre les communautés microbiennes et les assemblages d'invertébrés au toit des nappes phréatiques rechargées artificiellement avec des eaux de ruissellement pluvial. A travers une approche expérimentale de terrain et de laboratoire, ce travail permet d'évaluer l'intensité des relations existant entre les flux de carbone organique dissous, les conditions environnementales, l'activité et la diversité de communautés microbiennes et l'abondance des communautés d'invertébrés.

Tetranychus urticae es una especie plaga importante en cítricos que puede también alimentarse de otras especies asociadas a la cubierta vegetal de este cultivo. Para determinar el efecto de la gestión de la cubierta vegetal en el control biológico de este ácaro, hemos estudiado la dinámica tanto de ácaros Tetranychidae como Phytoseiidae en cuatro parcelas comerciales de mandarino clementino en las que se aplicó tres estrategias diferentes de gestión de la cubierta vegetal: (1) suelo desnudo, (2) cubierta espontánea y (3) cubierta sembrada de Festuca arundinacea. Los resultados apuntan a que tanto los enemigos naturales (mecanismos "top-down") como la planta huésped (mecanismos "bottom-up") juegan un papel importante en la regulación de los ácaros Tetranychidae. Por un lado, la selección de dos razas de T. urticae especializadas en F. arundinacea y en Citrus clementina, en la cubierta y en el árbol respectivamente, cuando esta gramínea se utiliza como cubierta podría explicar en parte los resultados obtenidos (regulación "bottom-up") ya que esto impediría a los especímenes de una planta huésped colonizar con éxito la otra. Los ensayos de trasplante recíproco realizados muestran que las dos demos de T. urticae recogidas de clementina y F. arundinacea difieren considerablemente en su éxito en el desarrollo en el huésped alternativo y esto indica la existencia de fenómenos de adaptación local. Esta adaptación se traduciría en mecanismos "bottom-up" que evitarían que los ácaros que habitan en la cubierta colonicen con éxito la copa de los árboles. Por otro lado, la composición cualitativa de las comunidades de Phytoseiidae asociados a las diferentes cubiertas podría ser clave en la regulación de las poblaciones de T. urticae y Panonychus citri (regulación "top-down"). Los ácaros Phytoseiidae tipo I y II, depredadores especializados en Tetranychidae, se encuentran de manera consistente en la cubierta de F. arundinacea y esto puede explicar la mejor regulación de las poblaciones de ácaros Tetranychidae en los árboles asociados a esta cubierta. Por el contrario, la disposición más regular de fuentes de alimentación alternativas (polen) en la cubierta natural en relación con la cubierta de F. arundinacea, podría explicar la mayor abundancia de Phytoseiidae tipo IV en la primera. Como consecuencia, los Phytoseiidae tipo I y II, más eficaces en el control de Tetranychidae, podrían sufrir las consecuencias de ser competitivamente inferiores que el Phytoseiidae generalista tipo IV que explota el polen en la cubierta espontánea. Este hecho, en combinación con los períodos de escasez de presa, podría dar lugar a su desaparición del agroecosistema y resultar en un deficiente control de los ácaros Tetranychidae en los árboles asociados a una cubierta natural. Haciendo balance de gastos e ingresos, la cubierta más favorable fue la de F. arundinacea (entre 44,4 y 74,5% de reducción de costes en relación con la más cara). Festuca arundinacea como cubierta vegetal es una estrategia de control biológico por conservación muy recomendable para los productores de clementina. Aunque su uso no redujo las poblaciones de ácaros en los árboles por debajo del umbral económico, la disminución en la necesidad de tratamientos, hace que la adopción de esta táctica sea una alternativa beneficiosa tanto ecológica como económicamente. Nuestros resultados apuntan a la cubierta de F. arundinacea, que no permitió el establecimiento de Tetranychus evansi y ofrece una mejor regulación de P. citri y T. urticae que en suelo desnudo o cubierta natural, como la más adecuada para un control más sostenible de los ácaros Tetranychidae en cítricos.

A wide range of additional forward chaining applications could be realized with deductive databases, if their rule formalism, their immediate consequence operator, and their fixpoint iteration process would be more flexible. Deductive databases normally represent knowledge using stratified Datalog programs with default negation. But many practical applications of forward chaining require an extensible set of user–defined built–in predicates. Moreover, they often need function symbols for building complex data structures, and the stratified fixpoint iteration has to be extended by aggregation operations. We present an new language Datalog*, which extends Datalog by stratified meta–predicates (including default negation), function symbols, and user–defined built–in predicates, which are implemented and evaluated top–down in Prolog. All predicates are subject to the same backtracking mechanism. The bottom–up fixpoint iteration can aggregate the derived facts after each iteration based on user–defined Prolog predicates.

Despite tremendous advances in mass spectrometry instrumentation and mass spectrometry-based methodologies, global protein profiling of organellar, cellular, tissue and body fluid proteomes in different organisms remains a challenging task due to the complexity of the samples and the wide dynamic range of protein concentrations. In addition, large amounts of produced data make result exploitation difficult. To overcome these issues, further advances in sample preparation, mass spectrometry instrumentation as well as data processing and data analysis are required. The presented study focuses as first on the improvement of the proteolytic digestion of proteins in in-gel based proteomic approach (Gel-LCMS). To this end commonly used bovine trypsin (BT) was modified with oligosaccharides in order to overcome its main disadvantages, such as weak thermostability and fast autolysis at basic pH. Glycosylated trypsin derivates maintained their cleavage specifity and showed better thermostability, autolysis resistance and less autolytic background than unmodified BT. In line with the “accelerated digestion protocol” (ADP) previously established in our laboratory modified enzymes were tested in in-gel digestion of proteins. Kinetics of in-gel digestion was studied by MALDI TOF mass spectrometry using 18O-labeled peptides as internal standards as well as by label-free quantification approach, which utilizes intensities of peptide ions detected by nanoLC-MS/MS. In the performed kinetic study the effect of temperature, enzyme concentration and digestion time on the yield of digestion products was characterized. The obtained results showed that in-gel digestion of proteins by glycosylated trypsin conjugates was less efficient compared to the conventional digestion (CD) and achieved maximal 50 to 70% of CD yield, suggesting that the attached sugar molecules limit free diffusion of the modified trypsins into the polyacrylamide gel pores. Nevertheless, these thermostable and autolysis resistant enzymes can be regarded as promising candidates for gel-free shotgun approach. To address the reliability issue of proteomic data I further focused on protein identifications with borderline statistical confidence produced by database searching. These hits are typically produced by matching a few marginal quality MS/MS spectra to database peptide sequences and represent a significant bottleneck in proteomics. A method was developed for rapid validation of borderline hits, which takes advantage of the independent interpretation of the acquired tandem mass spectra by de novo sequencing software PepNovo followed by mass-spectrometry driven BLAST (MS BLAST) sequence similarity searching that utilize all partially accurate, degenerate and redundant proposed peptide sequences. It was demonstrated that a combination of MASCOT software, de novo sequencing software PepNovo and MS BLAST, bundled by a simple scripted interface, enabled rapid and efficient validation of a large number of borderline hits, produced by matching of one or two MS/MS spectra with marginal statistical significance.

La thèse répond à deux problématiques, d'une part la quantification des effacements de consommation d'électricité par technologies gaz dans l'habitat et d'autre part de l'intégration de leurs valorisations dans une perspective de planification des infrastructures. Ces travaux se justifient dans un contexte d'augmentation de la pointe électrique, à l'origine d'une hausse du risque de défaillance du système, et de la baisse des consommations de gaz naturel conduisant à une sous utilisation du réseau de distribution. Pourtant, alors que la demande en gaz naturel croît du fait de l'installation de centrales à cycle combiné sur le réseau de transport, l'interaction des réseaux de distribution gaz/électricité n'est pas exploitée.Ce manuscrit envisage l'intégration des technologies gaz comme moyen de Maîtrise de la Demande en Électricité dans le processus de planification des réseaux. Ainsi les effacements de consommations d'électricité lors des périodes dimensionnantes par des micro-cogénérateurs ou des chaudières hybrides sont des solutions alternatives aux solutions de renforcement de réseaux.Pour quantifier le gisement d'effacement, nous nous intéressons à l'impact marginal des systèmes sur la demande en termes de modification de la quantité d'Énergie Non Distribuée potentielle. Les estimations des impacts de systèmes de chauffage sur la demande sont donc des prérequis à cette approche. Nous modélisons les courbes de charge régionales par une approche Bottom-Up permettant de déterminer les profils de demande marginale de chauffage en fonction des systèmes. La mise en application de cette méthode est à fiabiliser par des études socio-technico-économiques permettant de réduire les incertitudes sur les déterminants des besoins de chauffage. Une calibration en puissance des profils générés a été proposée mais n'a pu être réalisée. En revanche, nous apportons une contribution à l'analyse des courbes de charge agrégées en montrant que le modèle d'estimation actuellement utilisé par le gestionnaire de réseau s'apparente à un modèle simplifié de bâtiment

Det finns nu ingen tvekan om att det är vi människor, och vårt användande av fossila bränslen, som bidrar till den förstärkta växthuseffekten. Rättvisande metoder till att mäta växthusgasutsläpp är nödvändiga för att kunna fatta framtida beslut. Vägtrafiken är en av de största källorna till utsläpp av växthusgaser och den ökar hela tiden i omfattning. Den här studien fokuserar på olika metoder som används för att uppskatta koldioxidemissioner från vägtrafiken genom att först uppskatta mängderna diesel, från ett kritiskt perspektiv. Som hjälp till detta har en alternativ metod, för att uppskatta dieselkonsumtionen från vägtrafiken i Sverige, skapats. Resultaten visar skillnader mellan olika metoders uppskattningar, några av dessa i motsättning till varandra. Studien visar att resultat från modellen HBEFA 3.1 samvarierar med statistiken över levererad diesel i Sverige men visar lägre volymer. De alternativa metoderna, som skapats för den här studien, kan förklara sänkningarna av dieselkonsumtionen år 2008-2009 men kan inte förklara sänkningarna år 1999-2000 och 2011-2012. Mera studier som undersöker skillnaderna mellan resultaten från National inventory report Sweden och statistisk information över levererade mängder diesel i Sverige, och vad som orsakar dessa, behövs. / There is now no doubt about that it is humans, and our usage of fossil fuels, that contributes to the global warming. Accurate methods of measuring greenhouse gases are vital for future decision making. Road traffic is one of the major sources for greenhouse gases and it is increasing in volume. This study focus on different methods, used to estimate carbon dioxide emissions from road traffic by first estimating the quantity of diesel, from a critical point of view. For that purpose an alternative method used to estimate diesel consumption from road traffic in Sweden is created. The results show differences between methods estimates, some of them in contradiction to each other. The study shows that the results from the model HBEFA 3.1 covariate with both sources of statistics on delivered diesel in Sweden but show lower volumes. The alternative methods created in this study can explain the decrease of diesel consumption in the year 2008-2009 but can’t explain the decrease in the years 1999-2000 and 2011-2012. More studies on differences between the results in the National inventory report Sweden and statistical information on deliveries of diesel, and what is causing them, are needed.

This study looks at political culture and socialisation responses to Integrated Water Resource Management (IWRM). It identifies political culture and socialisation as part of a process, the development of a political culture with specific attitudes, cognitions, and feelings towards the political system. Political culture and socialisation impart the knowledge of how to act politically, i.e. how to apply values in formulating demands and making claims on the political system. They form a connecting link between micro- and macro-politics. The study maintains that political orientations are handed down from one generation to another, through the process of political socialisation. Top-down and bottom-up influences come into play to augment a discourse on the global nature of political socialisation and the political culture of international societies with regard to IWRM and governance ideologies. It is argued that these international ideas become relevant in the national political agenda, civil society organisations and trans-national networks. The IWRM aspects of water as an economic good and a basic human right have become a two-edged sword in the South African context. The study reveals that politics stand at the epicentre of water problems, and that IWRM is a political-ethical issue which challenges power bases in many communities. The IWRM global norms of equitable, efficient and sustainable use of water resources have become a major problem in a water-scarce country burdened with economic inequalities and abject poverty. This is a pressing issue because there is an increasing demand for water to sustain the development necessary to redress the draconian ills of the apartheid past. This becomes evident in the fundamental legislative overhaul that has taken place since 1994, embracing a transformation culture that glorifies the norm of water not only as a fundamental human right, but also as a commodity that is necessary to sustain human dignity. It is here that water is politicised. Violent protests have erupted in reaction to perceived neo-liberal attempts to deny the poor their access to this resource. The political culture and socialisation responses as far as IWRM is concerned appear within fragmented lines, i.e. mainly black and poor communities embrace a culture of non-payment for services and resort to violent protests as a viable method to raise their concerns. In contrast, the white and middle-class communities manifest a tendency to form parallel local government structures; they then withhold rate payments and provide services for themselves through ratepayer associations. Finally, the study considers the South African context with regard to the manifestations of political culture, and how this influences water resources. It is evident that there is too much emphasis on politics at the expense of discussions on IWRM. Civil society organisations make very little attempt to encourage public participation in water management structures. It also appears that political elites who are disillusioned with civil society organisations tend to derail their efforts to educate the public on water management structures. / MA, Political Studies, North-West University, Vaal Triangle Campus, 2011

Le modalità attuali di produzione, distribuzione e consumo dei servizi elettrico, idrico e d’igiene urbana sono largamente insostenibili. Alla luce del crescente impatto ambientale di tali attività, aziende di servizio, istituzioni e cittadini-consumatori si dichiarano preoccupati e disponibili a riorientare strategie, politiche e pratiche sulla base di principi di sostenibilità ambientale. Il presente lavoro si propone di analizzare i processi di trasformazione in senso ecologico di alcune filiere della produzione e del consumo di servizi pubblici locali secondo una prospettiva disciplinare di sociologia dell’ambiente, attraverso uno studio di caso avente per oggetto le politiche ambientali della maggiore local utility italiana e una indagine qualitativa delle pratiche sociali di consumo di servizi di un campione di stakeholders/clienti della medesima Società. La ricerca assegna ampio spazio all’analisi dell’attuale scenario socio-ambientale nel quale trovano posto discorsi e strategie ambientali di multiutilities orientate a un incremento della complessità organizzativa e delle performance sociali, economiche, ambientali, e cambiamenti nelle modalità di consumo/fruizione finale dei servizi che ridefiniscono, sul piano simbolico e pratico, gli importanti nessi tra produzione e consumo e tra fattori come tecnologia e stile di vita. In particolare dalla ricerca sembrano emergere con insistenza due percorsi che si propongono come obiettivo la sostenibilità ambientale. Uno di tipo istituzionale che prospetta cambiamenti secondo uno schema di intervento dall’alto verso il basso (top-down), e un altro, animato da priorità molto diverse, che è portatore di un rinnovamento partecipativo dal basso. A fronte di queste contrastanti vie della sostenibilità, il modello teorico più noto e diffuso nell’ambito della sociologia dell’ambiente per la lettura del mutamento in senso ecologico nel campo dei servizi pubblici locali mostra la propria inadeguatezza e l’esigenza di una riformulazione. Sul piano delle risultanze empiriche la separazione e il difficile riconoscimento tra i soggetti portatori di strategie top-down e quelli che elaborano percorsi bottom up mostra la problematica presenza di logiche di azione molto diverse in campo ambientale che sembrano difficili da conciliare. A un’ultima analisi emerge come nel conseguimento di principi di sostenibilità ambientale sia la via dall’alto che quella dal basso, accanto e indubbie potenzialità, possiedono rilevanti elementi di incertezza e ambiguità che per il momento sembrano rendere indefinibile da parte dei produttori e consumatori dei servizi elettrico, idrico e ambientale un percorso efficace e condiviso per la transizione verso un futuro sostenibile. / The sustainable management of common-pool resources will be among the main challenges that people will have to solve in the next years. In spite of all that, unsustainability of the current energy, water and waste production–consumption models are evident. In the last years socio-technical utility systems such as electricity, water and waste, have been subjected to many transformation in managerial (liberalization), organizational (multiutility model) and socio-cultural (new orientation for consumption) dimensions. Since the utility systems are closely intertwined with society and nature their transformation to play a leading role in the making of environmental sustainable future for society. In the first section this paper introduces an analysis of theoretic position on utility system’s transformation, and highlight weak point and perspective of this dynamic change’s riding. In the second section the paper proposes a sociological integrated framework for interpretation of the ecological transformation of the energy and water consumption and waste management. The sociological analysis shows that in socio-environmental field there are two sustainable paths (top down strategy versus bottom up way) but they seem weak and uncertain and don’t enough for building a sustainable future.