Bioremediation of PAHs - Limitations and soultions

Introduction 1.1 Occurrence of polycyclic aromatic hydrocarbons (PAH) in the environment Worldwide industrial and agricultural developments have released a large number of natural and synthetic hazardous compounds into the environment due to careless waste disposal, illegal waste dumping and accidental spills. As a result, there are numerous sites in the world that require cleanup of soils and groundwater. Polycyclic aromatic hydrocarbons (PAHs) are one of the major groups of these contaminants (Da Silva et al., 2003). PAHs constitute a diverse class of organic compounds consisting of two or more aromatic rings with various structural configurations (Prabhu and Phale, 2003). Being a derivative of benzene, PAHs are thermodynamically stable. In addition, these chemicals tend to adhere to particle surfaces, such as soils, because of their low water solubility and strong hydrophobicity, and this results in greater persistence under natural conditions. This persistence coupled with their potential carcinogenicity makes PAHs problematic environmental contaminants (Cerniglia, 1992; Sutherland, 1992). PAHs are widely found in high concentrations at many industrial sites, particularly those associated with petroleum, gas production and wood preserving industries (Wilson and Jones, 1993). 1.2 Remediation technologies Conventional techniques used for the remediation of soil polluted with organic contaminants include excavation of the contaminated soil and disposal to a landfill or capping - containment - of the contaminated areas of a site. These methods have some drawbacks. The first method simply moves the contamination elsewhere and may create significant risks in the excavation, handling and transport of hazardous material. Additionally, it is very difficult and increasingly expensive to find new landfill sites for the final disposal of the material. The cap and containment method is only an interim solution since the contamination remains on site, requiring monitoring and maintenance of the isolation barriers long into the future, with all the associated costs and potential liability. A better approach than these traditional methods is to completely destroy the pollutants, if possible, or transform them into harmless substances. Some technologies that have been used are high-temperature incineration and various types of chemical decomposition (for example, base-catalyzed dechlorination, UV oxidation). However, these methods have significant disadvantages, principally their technological complexity, high cost , and the lack of public acceptance. Bioremediation, on the contrast, is a promising option for the complete removal and destruction of contaminants. 1.3 Bioremediation of PAH contaminated soil & groundwater Bioremediation is the use of living organisms, primarily microorganisms, to degrade or detoxify hazardous wastes into harmless substances such as carbon dioxide, water and cell biomass Most PAHs are biodegradable unter natural conditions (Da Silva et al., 2003; Meysami and Baheri, 2003) and bioremediation for cleanup of PAH wastes has been extensively studied at both laboratory and commercial levels- It has been implemented at a number of contaminated sites, including the cleanup of the Exxon Valdez oil spill in Prince William Sound, Alaska in 1989, the Mega Borg spill off the Texas coast in 1990 and the Burgan Oil Field, Kuwait in 1994 (Purwaningsih, 2002). Different strategies for PAH bioremediation, such as in situ , ex situ or on site bioremediation were developed in recent years. In situ bioremediation is a technique that is applied to soil and groundwater at the site without removing the contaminated soil or groundwater, based on the provision of optimum conditions for microbiological contaminant breakdown.. Ex situ bioremediation of PAHs, on the other hand, is a technique applied to soil and groundwater which has been removed from the site via excavation (soil) or pumping (water). Hazardous contaminants are converted in controlled bioreactors into harmless compounds in an efficient manner. 1.4 Bioavailability of PAH in the subsurface Frequently, PAH contamination in the environment is occurs as contaminants that are sorbed onto soilparticles rather than in phase (NAPL, non aqueous phase liquids). It is known that the biodegradation rate of most PAHs sorbed onto soil is far lower than rates measured in solution cultures of microorganisms with pure solid pollutants (Alexander and Scow, 1989; Hamaker, 1972). It is generally believed that only that fraction of PAHs dissolved in the solution can be metabolized by microorganisms in soil. The amount of contaminant that can be readily taken up and degraded by microorganisms is defined as bioavailability (Bosma et al., 1997; Maier, 2000). Two phenomena have been suggested to cause the low bioavailability of PAHs in soil (Danielsson, 2000). The first one is strong adsorption of the contaminants to the soil constituents which then leads to very slow release rates of contaminants to the aqueous phase. Sorption is often well correlated with soil organic matter content (Means, 1980) and significantly reduces biodegradation (Manilal and Alexander, 1991). The second phenomenon is slow mass transfer of pollutants, such as pore diffusion in the soil aggregates or diffusion in the organic matter in the soil. The complex set of these physical, chemical and biological processes is schematically illustrated in Figure 1. As shown in Figure 1, biodegradation processes are taking place in the soil solution while diffusion processes occur in the narrow pores in and between soil aggregates (Danielsson, 2000). Seemingly contradictory studies can be found in the literature that indicate the rate and final extent of metabolism may be either lower or higher for sorbed PAHs by soil than those for pure PAHs (Van Loosdrecht et al., 1990). These contrasting results demonstrate that the bioavailability of organic contaminants sorbed onto soil is far from being well understood. Besides bioavailability, there are several other factors influencing the rate and extent of biodegradation of PAHs in soil including microbial population characteristics, physical and chemical properties of PAHs and environmental factors (temperature, moisture, pH, degree of contamination). Figure 1: Schematic diagram showing possible rate-limiting processes during bioremediation of hydrophobic organic contaminants in a contaminated soil-water system (not to scale) (Danielsson, 2000). 1.5 Increasing the bioavailability of PAH in soil Attempts to improve the biodegradation of PAHs in soil by increasing their bioavailability include the use of surfactants , solvents or solubility enhancers.. However, introduction of synthetic surfactant may result in the addition of one more pollutant. (Wang and Brusseau, 1993).A study conducted by Mulder et al. showed that the introduction of hydropropyl-ß-cyclodextrin (HPCD), a well-known PAH solubility enhancer, significantly increased the solubilization of PAHs although it did not improve the biodegradation rate of PAHs (Mulder et al., 1998), indicating that further research is required in order to develop a feasible and efficient remediation method. Enhancing the extent of PAHs mass transfer from the soil phase to the liquid might prove an efficient and environmentally low-risk alternative way of addressing the problem of slow PAH biodegradation in soil.

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

Higher order Sobolev Spaces and polyharmonic boundary value problems in Carnot Groups

The main task of this work is to present a concise survey on the theory of certain function spaces in the contexts of Hörmander vector fields and Carnot Groups, and to discuss briefly an application to some polyharmonic boundary value problems on Carnot Groups of step 2.

Proposta di traduzione di un capitolo di The To-Do List di Mike Gayle

Scopo principale del seguente elaborato è quello di fornire una possibile traduzione di un capitolo dell’opera di Mike Gayle, The To-Do List. Al fine di contestualizzare e rendere più comprensibile, specie per un lettore italiano, la proposta di traduzione in questione, verranno descritti dapprima l’autore ed il genere letterario al quale appartiene il libro, quindi la trama del libro stesso. Seguirà il commento della traduzione, nel quale si evidenzieranno alcuni degli elementi particolarmente difficili da rendere in italiano – talvolta dal punto di vista lessicale, più spesso dal punto di vista culturale. La scelta di affrontare l’opera di Gayle nasce soprattutto dall’interesse verso uno dei corsi svolti all’università, grazie al quale ho avuto l’occasione di scoprire, in lingua inglese, il genere letterario comunemente chiamato Chick Lit; The To-Do List, che appartiene a quella che potremmo definire come “Chick Lit maschile”e che presenta moltissimi riferimenti alla cultura britannica, rappresentava la fonte perfetta per mettermi alla prova ed effettuare una traduzione che fosse, oltre che fedele al testo originale, comprensibile e immediata per un ipotetico lettore italiano.

Reproduction and artificial restocking of Acipenser naccarii (Bonaparte, 1836). Genetic and physiological characterization through microsatellite markers and radioimmunoassay of sexual steroids

The Adriatic sturgeon, Acipenser naccarii (Bonaparte, 1836), is a highly threatened species due to human activities, particularly overfishing and habitat destruction. Its peculiar ecology and biology (restricted areal and anadromy) makes this species particularly vulnerable. In March 2010 the IUCN has identified the Adriatic sturgeon as a critically endangered species according to the Red List of Threatened Species. Due to its rapid decline, starting from the 80s, at present there is no evidence of natural reproduction in wild environment, which makes the Adriatic sturgeon dependenton captive breeding programs that need to be improved in order to be effective for the survival of the species. For this purpose this study aims to characterize artificial restocking population of Adriatic sturgeon, with both genetic and physiological analysis in order to establish an efficient restocking program for future reproductions. The research is structured on two levels: First genetically, by analyzing 9 microsatellite loci. This gives information relatively about parent allocation and kinship between individuals that were sampled for this study. Hence to predict which reproduction events are the most optimal in terms of incrementing genetic diversity, by the estimation of multilocus pairwise band sharing coefficients. Second step, physiological analysis: testosterone (T) concentration levels in each individual were measured for sexing, without sacrificing the lives of the animals with the use of an invasive examination of the gonads. The combination of interdisciplinary analysis is important to obtain an overall picture in order to indicate the main broodstock participating in reproduction events and future optimal potential participants, in order to ensure a valid management for restocking program and their monitoring.

Estrazione terminologica automatica: sistemi a confronto

In any terminological study, candidate term extraction is a very time-consuming task. Corpus analysis tools have automatized some processes allowing the detection of relevant data within the texts, facilitating term candidate selection as well. Nevertheless, these tools are (normally) not specific for terminology research; therefore, the units which are automatically extracted need manual evaluation. Over the last few years some software products have been specifically developed for automatic term extraction. They are based on corpus analysis, but use linguistic and statistical information to filter data more precisely. As a result, the time needed for manual evaluation is reduced. In this framework, we tried to understand if and how these new tools can really be an advantage. In order to develop our project, we simulated a terminology study: we chose a domain (i.e. legal framework for medicinal products for human use) and compiled a corpus from which we extracted terms and phraseologisms using AntConc, a corpus analysis tool. Afterwards, we compared our list with the lists extracted automatically from three different tools (TermoStat Web, TaaS e Sketch Engine) in order to evaluate their performance. In the first chapter we describe some principles relating to terminology and phraseology in language for special purposes and show the advantages offered by corpus linguistics. In the second chapter we illustrate some of the main concepts of the domain selected, as well as some of the main features of legal texts. In the third chapter we describe automatic term extraction and the main criteria to evaluate it; moreover, we introduce the term-extraction tools used for this project. In the fourth chapter we describe our research method and, in the fifth chapter, we show our results and draw some preliminary conclusions on the performance and usefulness of term-extraction tools.

"La scienza in cucina e l'arte di mangiar bene" di Pellegrino Artusi. Proposta di glossario culinario italiano-russo

L'obiettivo della tesi è la compilazione del glossario culinario italiano-russo che “racchiudere” termini culinari artusiani e propone una versione russa basandosi anche sulla traduzione parziale del libro in lingua russa. La tesi si divide in sette parti: introduzione, capitoli primo, secondo, terzo e quarto, conclusione e bibliografia. Il primo capitolo introduce la figura di Pellegrino Artusi con brevi cenni sulla sua vita e tratteggia, altresì, le peripezie ed il successo internazionale della sua opera ed il suo approdo in Russia. Il secondo capitolo è dedicato alla ricerca terminologica e alle fasi propedeutiche alla creazione del glossario. Inoltre, vengono spiegate le risorse usate per la creazione dei corpora. Avendo a disposizione la traduzione parziale de “La scienza in cucina e l'arte di mangiar bene” in russo (traduzione di I. Alekberova) fornita dalla Casa Artusi, si cerca di spiegare la scelta dei termini italiani messi a confronto con quelli esistenti nella traduzione russa. Il terzo capitolo introduce il glossario stesso preceduto da una breve spiegazione. Ogni “entrata” contiene il termine, la sua categoria grammaticale e la sua definizione in entrambe le lingue, seguita nella maggior parte dei casi dalle collocazioni o dagli esempi d'uso oppure dai sinonimi. Il quarto capitolo presenta commenti alla compilazione del glossario. Qui vengono analizzati i problemi riscontrati durante la fase compilativa, si presentano le soluzioni trovate e si forniscono esempi concreti. Ci sono anche commenti alle voci non presenti nel glossario. Infine, vi è una breve conclusione del percorso affrontato seguita dalla bibliografia e dalla sitografia. ENGLISH The purpose of this dissertation is to present a bilingual Italian-Russian glossary based on the culinary terms drawn from Artusi's cooking book "The Science of Cooking and the Art of Fine dining". The dissertation consists of an introduction, 4 chapters, conclusions and a list of bibliography. An introduction presents an overview of the entire dissertation. The first chapter includes a presentation of Pellegrino Artusi, brief introduction to his life, his book and the success it has had around the world and mainly in Russia. The second chapter focuses on the creation and use of comparable and parallel corpora that have been created ad hoc for the purpose of the glossary. It also describes the different programs that have been used in order to select the terminology. The third chapter presents the structure of the bilingual culinary glossary followed by the glossary itself. Each entry contains the term, its gramatical category and the definition in both languages followed by, in most but not all cases, collocation, synonyms and additional notes. The fourth chapter presents an analysis of the compilation of the glossary combined with comments and examples. This chapter is followed by final conclusions of the present dissertation. The last part contains a bibliography that includes all the resources that have been used for the completion of this dissertation followed by the webliography.

Analysis of Lead-Acid batteries with a third-order dynamical model

Electrical energy storage is a really important issue nowadays. As electricity is not easy to be directly stored, it can be stored in other forms and converted back to electricity when needed. As a consequence, storage technologies for electricity can be classified by the form of storage, and in particular we focus on electrochemical energy storage systems, better known as electrochemical batteries. Largely the more widespread batteries are the Lead-Acid ones, in the two main types known as flooded and valve-regulated. Batteries need to be present in many important applications such as in renewable energy systems and in motor vehicles. Consequently, in order to simulate these complex electrical systems, reliable battery models are needed. Although there exist some models developed by experts of chemistry, they are too complex and not expressed in terms of electrical networks. Thus, they are not convenient for a practical use by electrical engineers, who need to interface these models with other electrical systems models, usually described by means of electrical circuits. There are many techniques available in literature by which a battery can be modeled. Starting from the Thevenin based electrical model, it can be adapted to be more reliable for Lead-Acid battery type, with the addition of a parasitic reaction branch and a parallel network. The third-order formulation of this model can be chosen, being a trustworthy general-purpose model, characterized by a good ratio between accuracy and complexity. Considering the equivalent circuit network, all the useful equations describing the battery model are discussed, and then implemented one by one in Matlab/Simulink. The model has been finally validated, and then used to simulate the battery behaviour in different typical conditions.

Generic wind estimation and compensation based on residual generators and higher-order sliding mode schemes

This master thesis proposes a solution to the approach problem in case of unknown severe microburst wind shear for a fixed-wing aircraft, accounting for both longitudinal and lateral dynamics. The adaptive controller design for wind rejection is also addressed, exploiting the wind estimation provided by suitable estimators. It is able to successfully complete the final approach phase even in presence of wind shear, and at the same time aerodynamic envelope protection is retained. The adaptive controller for wind compensation has been designed by a backstepping approach and feedback linearization for time-varying systems. The wind shear components have been estimated by higher-order sliding mode schemes. At the end of this work the results are provided, an autonomous final approach in presence of microburst is discussed, performances are analyzed, and estimation of the microburst characteristics from telemetry data is examined.