Bioinformatic methods in applied genomic research

Here I will focus on three main topics that best address and include the projects I have been working in during my three year PhD period that I have spent in different research laboratories addressing both computationally and practically important problems all related to modern molecular genomics. The first topic is the use of livestock species (pigs) as a model of obesity, a complex human dysfunction. My efforts here concern the detection and annotation of Single Nucleotide Polymorphisms. I developed a pipeline for mining human and porcine sequences. Starting from a set of human genes related with obesity the platform returns a list of annotated porcine SNPs extracted from a new set of potential obesity-genes. 565 of these SNPs were analyzed on an Illumina chip to test the involvement in obesity on a population composed by more than 500 pigs. Results will be discussed. All the computational analysis and experiments were done in collaboration with the Biocomputing group and Dr.Luca Fontanesi, respectively, under the direction of prof. Rita Casadio at the Bologna University, Italy. The second topic concerns developing a methodology, based on Factor Analysis, to simultaneously mine information from different levels of biological organization. With specific test cases we develop models of the complexity of the mRNA-miRNA molecular interaction in brain tumors measured indirectly by microarray and quantitative PCR. This work was done under the supervision of Prof. Christine Nardini, at the “CAS-MPG Partner Institute for Computational Biology” of Shangai, China (co-founded by the Max Planck Society and the Chinese Academy of Sciences jointly) The third topic concerns the development of a new method to overcome the variety of PCR technologies routinely adopted to characterize unknown flanking DNA regions of a viral integration locus of the human genome after clinical gene therapy. This new method is entirely based on next generation sequencing and it reduces the time required to detect insertion sites, decreasing the complexity of the procedure. This work was done in collaboration with the group of Dr. Manfred Schmidt at the Nationales Centrum für Tumorerkrankungen (Heidelberg, Germany) supervised by Dr. Annette Deichmann and Dr. Ali Nowrouzi. Furthermore I add as an Appendix the description of a R package for gene network reconstruction that I helped to develop for scientific usage (http://www.bioconductor.org/help/bioc-views/release/bioc/html/BUS.html).

Procedures of quality control and data analysis of multi-site ground-based observations for the absolute flux calibration of Gaia

The Gaia space mission is a major project for the European astronomical community. As challenging as it is, the processing and analysis of the huge data-flow incoming from Gaia is the subject of thorough study and preparatory work by the DPAC (Data Processing and Analysis Consortium), in charge of all aspects of the Gaia data reduction. This PhD Thesis was carried out in the framework of the DPAC, within the team based in Bologna. The task of the Bologna team is to define the calibration model and to build a grid of spectro-photometric standard stars (SPSS) suitable for the absolute flux calibration of the Gaia G-band photometry and the BP/RP spectrophotometry. Such a flux calibration can be performed by repeatedly observing each SPSS during the life-time of the Gaia mission and by comparing the observed Gaia spectra to the spectra obtained by our ground-based observations. Due to both the different observing sites involved and the huge amount of frames expected (≃100000), it is essential to maintain the maximum homogeneity in data quality, acquisition and treatment, and a particular care has to be used to test the capabilities of each telescope/instrument combination (through the “instrument familiarization plan”), to devise methods to keep under control, and eventually to correct for, the typical instrumental effects that can affect the high precision required for the Gaia SPSS grid (a few % with respect to Vega). I contributed to the ground-based survey of Gaia SPSS in many respects: with the observations, the instrument familiarization plan, the data reduction and analysis activities (both photometry and spectroscopy), and to the maintenance of the data archives. However, the field I was personally responsible for was photometry and in particular relative photometry for the production of short-term light curves. In this context I defined and tested a semi-automated pipeline which allows for the pre-reduction of imaging SPSS data and the production of aperture photometry catalogues ready to be used for further analysis. A series of semi-automated quality control criteria are included in the pipeline at various levels, from pre-reduction, to aperture photometry, to light curves production and analysis.

A molecular phylogeny of bivalve mollusks: ancient radiations and divergences as revealed by mitochondrial genes

The main scope of my PhD is the reconstruction of the large-scale bivalve phylogeny on the basis of four mitochondrial genes, with samples taken from all major groups of the class. To my knowledge, it is the first attempt of such a breadth in Bivalvia. I decided to focus on both ribosomal and protein coding DNA sequences (two ribosomal encoding genes -12s and 16s -, and two protein coding ones - cytochrome c oxidase I and cytochrome b), since either bibliography and my preliminary results confirmed the importance of combined gene signals in improving evolutionary pathways of the group. Moreover, I wanted to propose a methodological pipeline that proved to be useful to obtain robust results in bivalves phylogeny. Actually, best-performing taxon sampling and alignment strategies were tested, and several data partitioning and molecular evolution models were analyzed, thus demonstrating the importance of molding and implementing non-trivial evolutionary models. In the line of a more rigorous approach to data analysis, I also proposed a new method to assess taxon sampling, by developing Clarke and Warwick statistics: taxon sampling is a major concern in phylogenetic studies, and incomplete, biased, or improper taxon assemblies can lead to misleading results in reconstructing evolutionary trees. Theoretical methods are already available to optimize taxon choice in phylogenetic analyses, but most involve some knowledge about genetic relationships of the group of interest, or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. The method I proposed measures the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, it also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses.

Genetic Manipulation, Gene Silencing and Biomarker Development in Multiple Experimental Models.

The thesis is set in three different parts, according to the relative experimental models. First, the domestic pig (Sus scrofa) is part of the study on reproductive biotechnologies: the transgenesis technique of Sperm Mediated Gene Transfer is widely studied starting from the quality of the semen, through the study of multiple uptakes of exogenous DNA and lastly used in the production of multi-transgenic blastocysts. Finally we managed to couple the transgenesis pipeline with sperm sorting and therefore produced transgenic embryos of predetermined sex. In the second part of the thesis the attention is on the fruit fly (Drosophila melanogaster) and on its derived cell line: the S2 cells. The in vitro and in vivo models are used to develop and validate an efficient way to knock down the myc gene. First an efficient in vitro protocol is described, than we demonstrate how the decrease in myc transcript remarkably affects the ribosome biogenesis through the study of Polysome gradients, rRNA content and qPCR. In vivo we identified two optimal drivers for the conditional silencing of myc, once the flies are fed with RU486: the first one is throughout the whole body (Tubulin), while the second is a head fat body driver (S32). With these results we present a very efficient model to study the role of myc in multiple aspects of translation. In the third and last part, the focus is on human derived lung fibroblasts (hLF-1), mouse tail fibroblasts and mouse tissues. We developed an efficient assay to quantify the total protein content of the nucleus on a single cell level via fluorescence. We coupled the protocol with classical immunofluorescence so to have at the same time general and particular information, demonstrating that during senescence nuclear proteins increase by 1.8 fold either in human cells, mouse cells and mouse tissues.

Una base dati per il knowledge discovery in genetica medica

L'innovazione delle tecnologie di sequenziamento negli ultimi anni ha reso possibile la catalogazione delle varianti genetiche nei campioni umani, portando nuove scoperte e comprensioni nella ricerca medica, farmaceutica, dell'evoluzione e negli studi sulla popolazione. La quantità di sequenze prodotta è molto cospicua, e per giungere all'identificazione delle varianti sono necessari diversi stadi di elaborazione delle informazioni genetiche in cui, ad ogni passo, vengono generate ulteriori informazioni. Insieme a questa immensa accumulazione di dati, è nata la necessità da parte della comunità scientifica di organizzare i dati in repository, dapprima solo per condividere i risultati delle ricerche, poi per permettere studi statistici direttamente sui dati genetici. Gli studi su larga scala coinvolgono quantità di dati nell'ordine dei petabyte, il cui mantenimento continua a rappresentare una sfida per le infrastrutture. Per la varietà e la quantità di dati prodotti, i database giocano un ruolo di primaria importanza in questa sfida. Modelli e organizzazione dei dati in questo campo possono fare la differenza non soltanto per la scalabilità, ma anche e soprattutto per la predisposizione al data mining. Infatti, la memorizzazione di questi dati in file con formati quasi-standard, la dimensione di questi file, e i requisiti computazionali richiesti, rendono difficile la scrittura di software di analisi efficienti e scoraggiano studi su larga scala e su dati eterogenei. Prima di progettare il database si è perciò studiata l’evoluzione, negli ultimi vent’anni, dei formati quasi-standard per i flat file biologici, contenenti metadati eterogenei e sequenze nucleotidiche vere e proprie, con record privi di relazioni strutturali. Recentemente questa evoluzione è culminata nell’utilizzo dello standard XML, ma i flat file delimitati continuano a essere gli standard più supportati da tools e piattaforme online. È seguita poi un’analisi dell’organizzazione interna dei dati per i database biologici pubblici. Queste basi di dati contengono geni, varianti genetiche, strutture proteiche, ontologie fenotipiche, relazioni tra malattie e geni, relazioni tra farmaci e geni. Tra i database pubblici studiati rientrano OMIM, Entrez, KEGG, UniProt, GO. L'obiettivo principale nello studio e nella modellazione del database genetico è stato quello di strutturare i dati in modo da integrare insieme i dati eterogenei prodotti e rendere computazionalmente possibili i processi di data mining. La scelta di tecnologia Hadoop/MapReduce risulta in questo caso particolarmente incisiva, per la scalabilità garantita e per l’efficienza nelle analisi statistiche più complesse e parallele, come quelle riguardanti le varianti alleliche multi-locus.

Identification of stock units of Mullus barbatus (Linnaeus, 1758) in the Italian seas: development of genomic 2b-RAD markers and biological variation analysis.

This thesis is settled within the STOCKMAPPING project, which represents one of the studies that were developed in the framework of RITMARE Flagship project. The main goals of STOCKMAPPING were the creation of a genomic mapping for stocks of demersal target species and the assembling of a database of population genomic, in order to identify stocks and stocks boundaries. The thesis focuses on three main objectives representing the core for the initial assessment of the methodologies and structure that would be applied to the entire STOCKMAPPING project: individuation of an analytical design to identify and locate stocks and stocks boundaries of Mullus barbatus, application of a multidisciplinary approach to validate biological methods and an initial assessment and improvement for the genotyping by sequencing technique utilized (2b-RAD). The first step is the individuation of an analytical design that has to take in to account the biological characteristics of red mullet and being representative for STOCKMAPPING commitments. In this framework a reduction and selection steps was needed due to budget reduction. Sampling areas were ranked according the individuation of four priorities. To guarantee a multidisciplinary approach the biological data associated to the collected samples were used to investigate differences between sampling areas and GSAs. Genomic techniques were applied to red mullet for the first time so an initial assessment of molecular protocols for DNA extraction and 2b-RAD processing were needed. At the end 192 good quality DNAs have been extracted and eight samples have been processed with 2b-RAD. Utilizing the software Stacks for sequences analyses a great number of SNPs markers among the eight samples have been identified. Several tests have been performed changing the main parameter of the Stacks pipeline in order to identify the most explicative and functional sets of parameters.

Metodi computazionali per l'annotazione di genomi e proteomi

Il progresso tecnologico nel campo della biologia molecolare, pone la comunità scientifica di fronte all’esigenza di dare un’interpretazione all’enormità di sequenze biologiche che a mano a mano vanno a costituire le banche dati, siano esse proteine o acidi nucleici. In questo contesto la bioinformatica gioca un ruolo di primaria importanza. Un nuovo livello di possibilità conoscitive è stato introdotto con le tecnologie di Next Generation Sequencing (NGS), per mezzo delle quali è possibile ottenere interi genomi o trascrittomi in poco tempo e con bassi costi. Tra le applicazioni del NGS più rilevanti ci sono senza dubbio quelle oncologiche che prevedono la caratterizzazione genomica di tessuti tumorali e lo sviluppo di nuovi approcci diagnostici e terapeutici per il trattamento del cancro. Con l’analisi NGS è possibile individuare il set completo di variazioni che esistono nel genoma tumorale come varianti a singolo nucleotide, riarrangiamenti cromosomici, inserzioni e delezioni. Va però sottolineato che le variazioni trovate nei geni vanno in ultima battuta osservate dal punto di vista degli effetti a livello delle proteine in quanto esse sono le responsabili più dirette dei fenotipi alterati riscontrabili nella cellula tumorale. L’expertise bioinformatica va quindi collocata sia a livello dell’analisi del dato prodotto per mezzo di NGS ma anche nelle fasi successive ove è necessario effettuare l’annotazione dei geni contenuti nel genoma sequenziato e delle relative strutture proteiche che da esso sono espresse, o, come nel caso dello studio mutazionale, la valutazione dell’effetto della variazione genomica. È in questo contesto che si colloca il lavoro presentato: da un lato lo sviluppo di metodologie computazionali per l’annotazione di sequenze proteiche e dall’altro la messa a punto di una pipeline di analisi di dati prodotti con tecnologie NGS in applicazioni oncologiche avente come scopo finale quello della individuazione e caratterizzazione delle mutazioni genetiche tumorali a livello proteico.

Data management and data analysis in the large European projects GEHA (GEnetics of Healthy Aging) and NU-AGE (NUtrition and AGEing): a bioinformatic approach

The aging process is characterized by the progressive fitness decline experienced at all the levels of physiological organization, from single molecules up to the whole organism. Studies confirmed inflammaging, a chronic low-level inflammation, as a deeply intertwined partner of the aging process, which may provide the “common soil” upon which age-related diseases develop and flourish. Thus, albeit inflammation per se represents a physiological process, it can rapidly become detrimental if it goes out of control causing an excess of local and systemic inflammatory response, a striking risk factor for the elderly population. Developing interventions to counteract the establishment of this state is thus a top priority. Diet, among other factors, represents a good candidate to regulate inflammation. Building on top of this consideration, the EU project NU-AGE is now trying to assess if a Mediterranean diet, fortified for the elderly population needs, may help in modulating inflammaging. To do so, NU-AGE enrolled a total of 1250 subjects, half of which followed a 1-year long diet, and characterized them by mean of the most advanced –omics and non –omics analyses. The aim of this thesis was the development of a solid data management pipeline able to efficiently cope with the results of these assays, which are now flowing inside a centralized database, ready to be used to test the most disparate scientific hypotheses. At the same time, the work hereby described encompasses the data analysis of the GEHA project, which was focused on identifying the genetic determinants of longevity, with a particular focus on developing and applying a method for detecting epistatic interactions in human mtDNA. Eventually, in an effort to propel the adoption of NGS technologies in everyday pipeline, we developed a NGS variant calling pipeline devoted to solve all the sequencing-related issues of the mtDNA.

Sustainable improvement of water networks : to achieve best decisions for rehabilitation plans using advanced GIS and statistical techniques

Many of developing countries are facing crisis in water management due to increasing of population, water scarcity, water contaminations and effects of world economic crisis. Water distribution systems in developing countries are facing many challenges of efficient repair and rehabilitation since the information of water network is very limited, which makes the rehabilitation assessment plans very difficult. Sufficient information with high technology in developed countries makes the assessment for rehabilitation easy. Developing countries have many difficulties to assess the water network causing system failure, deterioration of mains and bad water quality in the network due to pipe corrosion and deterioration. The limited information brought into focus the urgent need to develop economical assessment for rehabilitation of water distribution systems adapted to water utilities. Gaza Strip is subject to a first case study, suffering from severe shortage in the water supply and environmental problems and contamination of underground water resources. This research focuses on improvement of water supply network to reduce the water losses in water network based on limited database using techniques of ArcGIS and commercial water network software (WaterCAD). A new approach for rehabilitation water pipes has been presented in Gaza city case study. Integrated rehabilitation assessment model has been developed for rehabilitation water pipes including three components; hydraulic assessment model, Physical assessment model and Structural assessment model. WaterCAD model has been developed with integrated in ArcGIS to produce the hydraulic assessment model for water network. The model have been designed based on pipe condition assessment with 100 score points as a maximum points for pipe condition. As results from this model, we can indicate that 40% of water pipeline have score points less than 50 points and about 10% of total pipes length have less than 30 score points. By using this model, the rehabilitation plans for each region in Gaza city can be achieved based on available budget and condition of pipes. The second case study is Kuala Lumpur Case from semi-developed countries, which has been used to develop an approach to improve the water network under crucial conditions using, advanced statistical and GIS techniques. Kuala Lumpur (KL) has water losses about 40% and high failure rate, which make severe problem. This case can represent cases in South Asia countries. Kuala Lumpur faced big challenges to reduce the water losses in water network during last 5 years. One of these challenges is high deterioration of asbestos cement (AC) pipes. They need to replace more than 6500 km of AC pipes, which need a huge budget to be achieved. Asbestos cement is subject to deterioration due to various chemical processes that either leach out the cement material or penetrate the concrete to form products that weaken the cement matrix. This case presents an approach for geo-statistical model for modelling pipe failures in a water distribution network. Database of Syabas Company (Kuala Lumpur water company) has been used in developing the model. The statistical models have been calibrated, verified and used to predict failures for both networks and individual pipes. The mathematical formulation developed for failure frequency in Kuala Lumpur was based on different pipeline characteristics, reflecting several factors such as pipe diameter, length, pressure and failure history. Generalized linear model have been applied to predict pipe failures based on District Meter Zone (DMZ) and individual pipe levels. Based on Kuala Lumpur case study, several outputs and implications have been achieved. Correlations between spatial and temporal intervals of pipe failures also have been done using ArcGIS software. Water Pipe Assessment Model (WPAM) has been developed using the analysis of historical pipe failure in Kuala Lumpur which prioritizing the pipe rehabilitation candidates based on ranking system. Frankfurt Water Network in Germany is the third main case study. This case makes an overview for Survival analysis and neural network methods used in water network. Rehabilitation strategies of water pipes have been developed for Frankfurt water network in cooperation with Mainova (Frankfurt Water Company). This thesis also presents a methodology of technical condition assessment of plastic pipes based on simple analysis. This thesis aims to make contribution to improve the prediction of pipe failures in water networks using Geographic Information System (GIS) and Decision Support System (DSS). The output from the technical condition assessment model can be used to estimate future budget needs for rehabilitation and to define pipes with high priority for replacement based on poor condition. rn

Simulations for Gravitational Lensing of 21 cm Radiation at EoR and Post-EoR Redshifts

21 cm cosmology opens an observational window to previously unexplored cosmological epochs such as the Epoch of Reionization (EoR), the Cosmic Dawn and the Dark Ages using powerful radio interferometers such as the planned Square Kilometer Array (SKA). Among all the other applications which can potentially improve the understanding of standard cosmology, we study the promising opportunity given by measuring the weak gravitational lensing sourced by 21 cm radiation. We performed this study in two different cosmological epochs, at a typical EoR redshift and successively at a post-EoR redshift. We will show how the lensing signal can be reconstructed using a three dimensional optimal quadratic lensing estimator in Fourier space, using single frequency band or combining multiple frequency band measurements. To this purpose, we implemented a simulation pipeline capable of dealing with issues that can not be treated analytically. Considering the current SKA plans, we studied the performance of the quadratic estimator at typical EoR redshifts, for different survey strategies and comparing two thermal noise models for the SKA-Low array. The simulation we performed takes into account the beam of the telescope and the discreteness of visibility measurements. We found that an SKA-Low interferometer should obtain high-fidelity images of the underlying mass distribution in its phase 1 only if several bands are stacked together, covering a redshift range that goes from z=7 to z=11.5. The SKA-Low phase 2, modeled in order to improve the sensitivity of the instrument by almost an order of magnitude, should be capable of providing images with good quality even when the signal is detected within a single frequency band. Considering also the serious effect that foregrounds could have on this detections, we discussed the limits of these results and also the possibility provided by these models of measuring an accurate lensing power spectrum.

Algorithmen zur labelfreien quantitativen Proteomanalyse auf Basis datenunabhängig-akquirierter LC-MS-Daten

Moderne ESI-LC-MS/MS-Techniken erlauben in Verbindung mit Bottom-up-Ansätzen eine qualitative und quantitative Charakterisierung mehrerer tausend Proteine in einem einzigen Experiment. Für die labelfreie Proteinquantifizierung eignen sich besonders datenunabhängige Akquisitionsmethoden wie MSE und die IMS-Varianten HDMSE und UDMSE. Durch ihre hohe Komplexität stellen die so erfassten Daten besondere Anforderungen an die Analysesoftware. Eine quantitative Analyse der MSE/HDMSE/UDMSE-Daten blieb bislang wenigen kommerziellen Lösungen vorbehalten. rn| In der vorliegenden Arbeit wurden eine Strategie und eine Reihe neuer Methoden zur messungsübergreifenden, quantitativen Analyse labelfreier MSE/HDMSE/UDMSE-Daten entwickelt und als Software ISOQuant implementiert. Für die ersten Schritte der Datenanalyse (Featuredetektion, Peptid- und Proteinidentifikation) wird die kommerzielle Software PLGS verwendet. Anschließend werden die unabhängigen PLGS-Ergebnisse aller Messungen eines Experiments in einer relationalen Datenbank zusammengeführt und mit Hilfe der dedizierten Algorithmen (Retentionszeitalignment, Feature-Clustering, multidimensionale Normalisierung der Intensitäten, mehrstufige Datenfilterung, Proteininferenz, Umverteilung der Intensitäten geteilter Peptide, Proteinquantifizierung) überarbeitet. Durch diese Nachbearbeitung wird die Reproduzierbarkeit der qualitativen und quantitativen Ergebnisse signifikant gesteigert.rn| Um die Performance der quantitativen Datenanalyse zu evaluieren und mit anderen Lösungen zu vergleichen, wurde ein Satz von exakt definierten Hybridproteom-Proben entwickelt. Die Proben wurden mit den Methoden MSE und UDMSE erfasst, mit Progenesis QIP, synapter und ISOQuant analysiert und verglichen. Im Gegensatz zu synapter und Progenesis QIP konnte ISOQuant sowohl eine hohe Reproduzierbarkeit der Proteinidentifikation als auch eine hohe Präzision und Richtigkeit der Proteinquantifizierung erreichen.rn| Schlussfolgernd ermöglichen die vorgestellten Algorithmen und der Analyseworkflow zuverlässige und reproduzierbare quantitative Datenanalysen. Mit der Software ISOQuant wurde ein einfaches und effizientes Werkzeug für routinemäßige Hochdurchsatzanalysen labelfreier MSE/HDMSE/UDMSE-Daten entwickelt. Mit den Hybridproteom-Proben und den Bewertungsmetriken wurde ein umfassendes System zur Evaluierung quantitativer Akquisitions- und Datenanalysesysteme vorgestellt.

L'importanza del gas naturale liquefatto e le prospettive dei rigassificatori in italia

Questo elaborato vuole illustrare l’importanza del gas naturale liquefatto, attraverso l’analisi della Strategia Energetica Nazionale e del Bilancio Energetico Nazionale, sostenendo la necessità di costruire ulteriori rigassificatori sul suolo italiano per permettere al nostro Paese, in previsione di una futura ripresa economica, di svincolarsi dalla quasi totale dipendenza di importazioni attraverso “pipeline” che vincolano in modo rigido e monopolistico il Paese importatore a quello esportatore e ai Paesi che vengono attraversati dalla condotta stessa

Studio di Flow-Assurance e sensitivity analysis in sistemi di distribuzione di petrolio e gas naturale

Argomento del lavoro è stato lo studio di problemi legati alla Flow-Asurance. In particolare, si focalizza su due aspetti: i) una valutazione comparativa delle diverse equazioni di stato implementate nel simulatore multifase OLGA, per valutare quella che porta a risultati più conservativi; ii) l’analisi della formazione di idrati, all’interno di sistemi caratterizzati dalla presenza di gas ed acqua. Il primo argomento di studio nasce dal fatto che per garantire continuità del flusso è necessario conoscere il comportamento volumetrico del fluido all’interno delle pipelines. Per effettuare tali studi, la Flow-Assurance si basa sulle Equazioni di Stato cubiche. In particolare, sono state confrontate: -L’equazione di Soave-Redlich-Kwong; -L’equazione di Peng-Robinson; -L’equazione di Peng-Robinson modificata da Peneloux. Sono stati analizzati 4 fluidi idrocarburici (2 multifase, un olio e un gas) con diverse composizioni e diverse condizioni di fase. Le variabili considerate sono state pressione, temperatura, densità e viscosità; sono state poi valutate le perdite di carico, parametro fondamentale nello studio del trasporto di un fluido, valutando che l'equazione di Peng-Robinson è quella più adatta per caratterizzare termodinamicamente il fluido durante una fase di design, in quanto fornisce l'andamento più conservativo. Dopo aver accertato la presenza di idrati nei fluidi multifase, l’obiettivo del lavoro è stato analizzare come il sistema rispondesse all’aggiunta di inibitori chimici per uscire dalla regione termodinamica di stabilità dell’idrato. Gli inibitori utilizzati sono stati metanolo e mono-etilen-glicole in soluzione acquosa. L’analisi è stata effettuata confrontando due metodi: -Metodo analitico di Hammerschmidt; -Metodo iterativo con PVTSim. I risultati ottenuti hanno dimostrato che entrambi gli inibitori utilizzati risolvono il problema della formazione di idrato spostando la curva di stabilità al di fuori delle pressioni e temperature che si incontrano nella pipeline. Valutando le quantità da iniettare, il metodo di Hammerschmidt risulta quello più conservativo, indicando portate maggiori rispetto al PVTsim, soprattutto aggiungendo metanolo.

Studio, analisi e progettazione di un prototipo di infrastructure as code

La tesi inserita in un periodo di forte transizione dai sistemi On­premises a sistemi Cloud ha avuto l'esigenza di risolvere alcune problematiche legate alla definizione delle infrastrutture. Come poter scalare le risorse all'evenienza ricreando gli stessi ambienti, monitorandoli e mettendo in sicurezza i dati critici delle applicazioni? La tesi ha risposto proprio a questa domanda definendo un nuovo paradigma nel concepire le infrastrutture chiamato Infrastructure as Code. La tesi ha approfondito le pratiche e le metodologie che si sono legate maggiormente all'Infrastructure as Code tra le quali Version Control, Configuration Management, Continuous Integration e Continuous Delivery. La tesi inoltre ha previsto la realizzazione di un prototipo finale nato dallo studio del flusso di sviluppo software aziendale, definendo gli ambienti in accordo ai sistemi di Version Control e Configuration Management, applicando pratiche di integrazione continua per giungere ad una deployment pipeline funzionale.

Stem cell-based therapeutic applications in retinal degenerative diseases

Retinal degenerative diseases that target photoreceptors or the adjacent retinal pigment epithelium (RPE) affect millions of people worldwide. Retinal degeneration (RD) is found in many different forms of retinal diseases including retinitis pigmentosa (RP), age-related macular degeneration (AMD), diabetic retinopathy, cataracts, and glaucoma. Effective treatment for retinal degeneration has been widely investigated. Gene-replacement therapy has been shown to improve visual function in inherited retinal disease. However, this treatment was less effective with advanced disease. Stem cell-based therapy is being pursued as a potential alternative approach in the treatment of retinal degenerative diseases. In this review, we will focus on stem cell-based therapies in the pipeline and summarize progress in treatment of retinal degenerative disease.