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.

Finte pelli per interni auto in PVC: adeguamento ai requisiti REACH

Le finte pelli sono sistemi costituiti da vari strati, il cui componente principale è il PVC. La produzione delle finte pelli richiede l’utilizzo di un elevato numero di additivi; per ognuno di essi occorre valutare la quantità da utilizzare, l’efficienza in rapporto al suo costo e, non di minore importanza, il suo grado di tossicità. Gli additivi attualmente utilizzati nella produzione delle finte pelli, che presentano problemi legati alla sicurezza sono: gli ftalati (plastificanti), l’azodicarbonammide (agente espandente) e il triossido di antimonio (agente antifiamma). Il lavoro di tesi è stato incentrato sullo studio di queste materie prime allo scopo di trovare delle valide alternative rispetto ai composti standard, in relazione agli attuali (e probabili futuri) requisiti del REACH e produrre una finta pelle “migliorata” in termini di prestazioni e sicurezza.

OpenMP task scheduling strategies to mitigate hardware variability in tightly-coupled shared memory clusters

In questa tesi sono stati apportati due importanti contributi nel campo degli acceleratori embedded many-core. Abbiamo implementato un runtime OpenMP ottimizzato per la gestione del tasking model per sistemi a processori strettamente accoppiati in cluster e poi interconnessi attraverso una network on chip. Ci siamo focalizzati sulla loro scalabilità e sul supporto di task di granularità fine, come è tipico nelle applicazioni embedded. Il secondo contributo di questa tesi è stata proporre una estensione del runtime di OpenMP che cerca di prevedere la manifestazione di errori dati da fenomeni di variability tramite una schedulazione efficiente del carico di lavoro.

Physiologie eines erlernten Körpermodells in Drosophila melanogaster

In der vorliegenden Dissertation wird ein Körpergrößengedächtnis untersucht. Es wird dargestellt, wie diese Information über die Reichweite der Fliege beim Lückenklettern unter kotrollierten Umweltbedingungen erworben und prozessiert wird. Zusätzlich wird geklärt, welche biochemischen Signale benötigt werden, um daraus ein lang anhalten-des Gedächtnis zu formen. Adulte Fliegen sind in der Lage, ihre Körperreichweite zu lernen. Naive Fliegen, die in der Dunkelheit gehalten wurden, versuchen erfolglos, zu breite Lücken zu überqueren, während visuell erfahrene Fliegen die Kletterversuche an ihre Körpergröße anpassen. Erfahrene kleine Fliegen scheinen Kenntnis ihres Nachteils zu haben. Sie kehren an Lückenbreiten um, welche ihre größeren Artgenos-sen durchaus noch versuchen. Die Taufliegen lernen die größenabhängige Reichweite über die visuelle Rückmeldung während des Laufens (aus Parallaxenbewegung). Da-bei reichen 15 min in strukturierter, heller Umgebung aus. Es gibt keinen festgelegten Beginn der sensiblen Phase. Nach 2 h ist das Gedächtnis jedoch konsolidiert und kann durch Stress nicht mehr zerstört oder durch sensorische Eingänge verändert werden. Dunkel aufgezogene Fliegen wurden ausgewählten Streifenmustern mit spezifischen Raumfrequenzen ausgesetzt. Nur die Insekten, welche mit einem als „optimal“ klassi-fizierten Muster visuell stimuliert wurden, sind in der Lage, die Körperreichweite einzu-schätzen, indem die durchschnittliche Schrittlänge in Verbindung mit der visuellen Wahrnehmung gebracht wird. Überraschenderweise ist es sogar mittels partieller Kompensation der Parallaxen möglich, naive Fliegen so zu trainieren, dass sie sich wie kleinere Exemplare verhalten. Da die Experimente ein Erlernen der Körperreich-weite vermuten lassen, wurden lernmutante Stämme beim Lückenüberwinden getes-tet. Sowohl die Ergebnisse von rut1- und dnc1-Mutanten, als auch das defizitäre Klet-tern von oc1-Fliegen ließ eine Beteiligung der cAMP-abhängigen Lernkaskade in der Protocerebralbrücke (PB) vermuten. Rettungsexperimente der rut1- und dnc1-Hinter-gründe kartierten das Gedächtnis in unterschiedliche Neuronengruppen der PB, wel-che auch für die visuelle Ausrichtung des Kletterns benötigt werden. Erstaunlicher-weise haben laterale lokale PB-Neurone und PFN-Neurone (Projektion von der PB über den fächerförmigen Körper zu den Noduli) verschiedene Erfordernisse für cAMP-Signale. Zusammenfassend weisen die Ergebnisse darauf hin, dass hohe Mengen an cAMP/PKA-Signalen in den latero-lateralen Elementen der PB benötigt werden, wäh-rend kolumnäre PFN-Neurone geringe oder keine Mengen an cAMP/PKA erfordern. Das Körperreichweitengedächtnis ist vermutlich das am längsten andauernde Ge-dächtnis in Drosophila. Wenn es erst einmal konsolidiert ist hält es länger als drei Wo-chen.rnAußerdem kann die Fruchtliege Drosophila melanogaster trainiert werden, die kom-plexe motorische Aufgabe des Lückenkletterns zu optimieren. Die trainierten Fliegen werden erfolgreicher und schneller beim Überqueren von Lücken, welche größer sind als sie selbst. Dabei existiert eine Kurzeitkomponente (STM), die 40 min nach dem ersten Training anhält. Nach weiteren vier Trainingsdurchläufen im Abstand von 20 min wird ein Langzeitgedächtnis (LTM) zum Folgetag geformt. Analysen mit Mutati-onslinien wiesen eine Beteiligung der cAMP-abhängigen Lernkaskade an dieser Ge-dächtnisform auf. Rettungsexperimente des rut2080-Hintergrunds kartierten sowohl das STM, als auch das LTM in PFN-Neuronen. Das STM kann aber ebenso in den alpha- und beta- Loben der Pilzkörper gerettet werden.rnLetztendlich sind wildtypische Fliegen sogar in der Lage, sich an einen Verlust eines Mittelbeintarsuses und dem einhergehenden Fehlen des Adhäsionsorgans am Tarsusende anzupassen. Das Klettern wird zwar sofort schlechter, erholt sich aber bis zum Folgetag wieder auf ein normales Niveau. Dieser neue Zustand erfordert ein Ge-dächtnis für die physischen Möglichkeiten, die nur durch plastische Veränderungen im Nervensystem des Insekts erreicht werden können.

Ricostruzione delle sorgenti corticali da segnali EEG in task di discriminazione visiva: Effetto di training multisensoriale

I neuroni in alcune regioni del nostro cervello mostrano una risposta a stimoli multisensoriali (ad es. audio-visivi) temporalmente e spazialmente coincidenti maggiore della risposta agli stessi stimoli presi singolarmente (integrazione multisensoriale). Questa abilità può essere sfruttata per compensare deficit unisensoriali, attraverso training multisensoriali che promuovano il rafforzamento sinaptico all’interno di circuiti comprendenti le regioni multisensoriali stimolate. Obiettivo della presente tesi è stato quello di studiare quali strutture e circuiti possono essere stimolate e rinforzate da un training multisensoriale audio-visivo. A tale scopo, sono stati analizzati segnali elettroencefalografici (EEG) registrati durante due diversi task di discriminazione visiva (discriminazione della direzione di movimento e discriminazione di orientazione di una griglia) eseguiti prima e dopo un training audio-visivo con stimoli temporalmente e spazialmente coincidenti, per i soggetti sperimentali, o spazialmente disparati, per i soggetti di controllo. Dai segnali EEG di ogni soggetto è stato ricavato il potenziale evento correlato (ERP) sullo scalpo, di cui si è analizzata la componente N100 (picco in 140÷180 ms post stimolo) verificandone variazioni pre/post training mediante test statistici. Inoltre, è stata ricostruita l’attivazione delle sorgenti corticali in 6239 voxel (suddivisi tra le 84 ROI coincidenti con le Aree di Brodmann) con l’ausilio del software sLORETA. Differenti attivazioni delle ROI pre/post training in 140÷180 ms sono state evidenziate mediante test statistici. I risultati suggeriscono che il training multisensoriale abbia rinforzato i collegamenti sinaptici tra il Collicolo Superiore e il Lobulo Parietale Inferiore (nell’area Area di Brodmann 7), una regione con funzioni visuo-motorie e di attenzione spaziale.

Prognosis of Atrial Fibrillation in Patients with Symptomatic Peripheral Arterial Disease: Data from the REduction of Atherothrombosis for Continued Health (REACH) Registry

BACKGROUND: Atrial fibrillation (AF) is a significant risk factor for cardiovascular (CV) mortality. This study aims to evaluate the prognostic implication of AF in patients with peripheral arterial disease (PAD). METHODS: The International Reduction of Atherothrombosis for Continued Health (REACH) Registry included 23,542 outpatients in Europe with established coronary artery disease, cerebrovascular disease (CVD), PAD and/or >/=3 risk factors. Of these, 3753 patients had symptomatic PAD. CV risk factors were determined at baseline. Study end point was a combination of cardiac death, non-fatal myocardial infarction (MI) and stroke (CV events) during 2 years of follow-up. Cox regression analysis adjusted for age, gender and other risk factors (i.e., congestive heart failure, coronary artery re-vascularisation, coronary artery bypass grafting (CABG), MI, hypertension, stroke, current smoking and diabetes) was used. RESULTS: Of 3753 PAD patients, 392 (10%) were known to have AF. Patients with AF were older and had a higher prevalence of CVD, diabetes and hypertension. Long-term CV mortality occurred in 5.6% of patients with AF and in 1.6% of those without AF (p<0.001). Multivariable analyses showed that AF was an independent predictor of late CV events (hazard ratio (HR): 1.5; 95% confidence interval (CI): 1.09-2.0). CONCLUSION: AF is common in European patients with symptomatic PAD and is independently associated with a worse 2-year CV outcome.

Differences in management and outcomes between male and female patients with atherothrombotic disease: results from the REACH Registry in Europe

Although guidelines recommend similar evaluation and treatment for both sexes, differences in approach and outcomes have been reported.

Influence of polyvascular disease on cardiovascular event rates. Insights from the REACH Registry

Cardiovascular event rates have been shown to increase substantially with the number of symptomatic disease locations. We sought to assess the risk profile, management and subsequent event rates of polyvascular disease patients. Consecutive outpatients were assessed for atherosclerotic risk factors and medications in the REACH Registry. A total of 19,117 symptomatic patients in Europe completed a 2-year follow-up: 77.2% with single arterial bed disease (coronary artery or cerebrovascular or peripheral arterial disease) and 22.8% with polyvascular disease (>/= 1 disease location). Polyvascular disease patients were older (68.5 +/- 9.4 vs 66.3 +/- 9.9 years, p < 0.0001), more often current or former smokers (64.9% vs 58.7%, p < 0.0001), and more often suffered from hypertension (59.5% vs 46.6%, p < 0.0001) and diabetes (34.5% vs 25.9%, p < 0.0001) than single arterial bed disease patients. Despite more intense medical therapy, risk factors (smoking, hypertension, low fasting glucose, and low fasting total cholesterol) were less often controlled in polyvascular disease patients. This was associated with substantially more events over 2 years compared with single arterial bed disease patients (cMACCE [cardiovascular death/non-fatal stroke/non-fatal MI] odds ratio, 1.63 [95% CI, 1.45-1.83], p < 0.0001). In conclusion, polyvascular disease patients have more cardiovascular risk factors, and the prognosis for these patients is significantly worse than for patients with single arterial bed disease. This suggests a need to improve detection and consequent medical treatment of polyvascular disease.

Effects of adherence to guidelines for the control of major cardiovascular risk factors on outcomes in the REduction of Atherothrombosis for Continued Health (REACH) Registry Europe

To examine the impact of cardiovascular risk factor control on 3-year cardiovascular event rates in patients with stable symptomatic atherothrombotic disease in Europe.