An evolutionary approach to the design of experiments for combinatorial optimization with an application to enzyme engineering

In a large number of problems the high dimensionality of the search space, the vast number of variables and the economical constrains limit the ability of classical techniques to reach the optimum of a function, known or unknown. In this thesis we investigate the possibility to combine approaches from advanced statistics and optimization algorithms in such a way to better explore the combinatorial search space and to increase the performance of the approaches. To this purpose we propose two methods: (i) Model Based Ant Colony Design and (ii) Naïve Bayes Ant Colony Optimization. We test the performance of the two proposed solutions on a simulation study and we apply the novel techniques on an appplication in the field of Enzyme Engineering and Design.

Sleep-related changes in blood pressure in hypocretin-deficient narcoleptic mice

Objectives. Blood pressure (BP) physiologically has higher and lower values during the active and rest period, respectively. Subjects failing to show the appropriate BP decrease (10-20%) on passing form diurnal activity to nocturnal rest and sleep have increased risk of target organ damage at the cardiac, vascular and cerebrovascular levels. Hypocretin (HCRT) releasing neurons, mainly located in the lateral hypothalamus, project widely to the central nervous system. Thus HCRT neurons are involved in several autonomic functions, including BP regulation. HCRT neurons also play a key role in wake-sleep cycle regulation, the lack of which becomes evident in HCRT-deficient narcoleptic patients. I investigated whether chronic lack of HCRT signaling alters BP during sleep in mouse models of narcolepsy. Methods. The main study was performed on HCRT-ataxin3 transgenic mice (TG) with selective post-natal ablation of HCRT neurons, HCRT gene knockout mice (KO) with preserved HCRT neurons, and Wild-Type control mice (WT) with identical genetic background. Experiments where replicated on TG and WT mice with hybrid genetic background (hTG and hWT, respectively). Mice were implanted with a telemetric pressure transducer (TA11PA-C10, DSI) and electrodes for discriminating wakefulness (W), rapid-eye-movement sleep (REMS) and non-REMS (NREMS). Signals were recorded for 3 days. Mean BP values were computed in each wake-sleep state and analyzed by ANOVA and t-test with significance at p<0.05. Results. The decrease in BP between either NREMS or REMS and W was significantly blunted in TG and KO with respect to WT as well as in hTG with respect to hWT. Conclusions. Independently from the genetic background, chronic HCRT deficiency leads to a decreased BP difference between W and sleep potentially adverse in narcoleptic subjects. These data suggest that HCRT play an important role in the sleep-dependent cardiovascular control.

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).

Phytoplankton Response to Environmental Variables and Organic Pollutants. Laboratory Cultures and Numerical Simulations Experiments

Herbicides are becoming emergent contaminants in Italian surface, coastal and ground waters, due to their intensive use in agriculture. In marine environments herbicides have adverse effects on non-target organisms, as primary producers, resulting in oxygen depletion and decreased primary productivity. Alterations of species composition in algal communities can also occur due to the different sensitivity among the species. In the present thesis the effects of herbicides, widely used in the Northern Adriatic Sea, on different algal species were studied. The main goal of this work was to study the influence of temperature on algal growth in the presence of the triazinic herbicide terbuthylazine (TBA), and the cellular responses adopted to counteract the toxic effects of the pollutant (Chapter 1 and 2). The development of simulation models to be applied in environmental management are needed to organize and track information in a way that would not be possible otherwise and simulate an ecological prospective. The data collected from laboratory experiments were used to simulate algal responses to the TBA exposure at increasing temperature conditions (Chapter 3). Part of the thesis was conducted in foreign countries. The work presented in Chapter 4 was focused on the effect of high light on growth, toxicity and mixotrophy of the ichtyotoxic species Prymnesium parvum. In addition, a mesocosm experiment was conducted in order to study the synergic effect of the pollutant emamectin benzoate with other anthropogenic stressors, such as oil pollution and induced phytoplankton blooms (Chapter 5).

Leucemia Acuta Mieloide e signaling purinergico: possibili sviluppi terapeutici

I nucleotidi trifosfato sono, dal punto di vista evoluzionistico, tra le molecole più antiche e conservate tra le specie. Oltre al ruolo che ricoprono nella sintesi degli acidi nucleici e nel metabolismo energetico della cellula, negli ultimi anni è emerso sempre di più il loro coinvolgimento nella regolazione di numerose funzioni cellulari. Questi importanti mediatori cellulari sono presenti nel microambiente e cambiamenti nella loro concentrazione extracellulare possono modulare la funzionalità cellulare. I nucleotidi trifosfato ATP e UTP, presenti nel microambiente midollare, sono dei potenti stimolatori dei progenitori emopoietici. Essi stimolano la proliferazione e l’attecchimento delle cellule staminali emopoietiche, così come la loro capacità migratoria, attraverso l’attivazione di specifici recettori di membrana, i recettori purinergici (P2R). In questo studio abbiamo dimostrato che ATP e UTP esercitano un effetto opposto sul compartimento staminale leucemico di leucemia acuta mieloide (LAM). Abbiamo dimostrato che le cellule leucemiche esprimono i recettori P2 funzionalmente attivi. Studi di microarray hanno evidenziato che, a differenza di ciò che avviene nelle CD34+, la stimolazione di cellule leucemiche con ATP induce la down-regolazione dei geni coinvolti nella proliferazione e nella migrazione, mentre up-regola geni inibitori del ciclo cellulare. Abbiamo poi confermato a livello funzionale, mediante test in vitro, gli effetti osservati a livello molecolare. Studi di inibizione farmacologica, ci hanno permesso di capire che l’attività inibitoria dell’ATP sulla proliferazione si esplica attraverso l’attivazione del recettore P2X7, mentre i sottotipi recettoriali P2 prevalentemente coinvolti nella regolazione della migrazione sono i recettori P2Y2 e P2Y4. Esperimenti di xenotrapianto, hanno evidenziato che l’esposizione ad ATP e UTP sia dei blasti leucemici sia delle cellule staminali leucemiche CD38-CD34+ diminuisce la loro capacità di homing e di engraftment in vivo. Inoltre, il trattamento farmacologico con ATP, di topi ai quali è stata indotta una leucemia umana, ha diminuito lo sviluppo della leucemia in vivo.

Development of new tools and devices for CMB and foreground data analysis and future experiments

The discovery of the Cosmic Microwave Background (CMB) radiation in 1965 is one of the fundamental milestones supporting the Big Bang theory. The CMB is one of the most important source of information in cosmology. The excellent accuracy of the recent CMB data of WMAP and Planck satellites confirmed the validity of the standard cosmological model and set a new challenge for the data analysis processes and their interpretation. In this thesis we deal with several aspects and useful tools of the data analysis. We focus on their optimization in order to have a complete exploitation of the Planck data and contribute to the final published results. The issues investigated are: the change of coordinates of CMB maps using the HEALPix package, the problem of the aliasing effect in the generation of low resolution maps, the comparison of the Angular Power Spectrum (APS) extraction performances of the optimal QML method, implemented in the code called BolPol, and the pseudo-Cl method, implemented in Cromaster. The QML method has been then applied to the Planck data at large angular scales to extract the CMB APS. The same method has been applied also to analyze the TT parity and the Low Variance anomalies in the Planck maps, showing a consistent deviation from the standard cosmological model, the possible origins for this results have been discussed. The Cromaster code instead has been applied to the 408 MHz and 1.42 GHz surveys focusing on the analysis of the APS of selected regions of the synchrotron emission. The new generation of CMB experiments will be dedicated to polarization measurements, for which are necessary high accuracy devices for separating the polarizations. Here a new technology, called Photonic Crystals, is exploited to develop a new polarization splitter device and its performances are compared to the devices used nowadays.

An Integrated Transmission-Media Noise Calibration Software For Deep-Space Radio Science Experiments

The thesis describes the implementation of a calibration, format-translation and data conditioning software for radiometric tracking data of deep-space spacecraft. All of the available propagation-media noise rejection techniques available as features in the code are covered in their mathematical formulations, performance and software implementations. Some techniques are retrieved from literature and current state of the art, while other algorithms have been conceived ex novo. All of the three typical deep-space refractive environments (solar plasma, ionosphere, troposphere) are dealt with by employing specific subroutines. Specific attention has been reserved to the GNSS-based tropospheric path delay calibration subroutine, since it is the most bulky module of the software suite, in terms of both the sheer number of lines of code, and development time. The software is currently in its final stage of development and once completed will serve as a pre-processing stage for orbit determination codes. Calibration of transmission-media noise sources in radiometric observables proved to be an essential operation to be performed of radiometric data in order to meet the more and more demanding error budget requirements of modern deep-space missions. A completely autonomous and all-around propagation-media calibration software is a novelty in orbit determination, although standalone codes are currently employed by ESA and NASA. The described S/W is planned to be compatible with the current standards for tropospheric noise calibration used by both these agencies like the AMC, TSAC and ESA IFMS weather data, and it natively works with the Tracking Data Message file format (TDM) adopted by CCSDS as standard aimed to promote and simplify inter-agency collaboration.

Development Of New Toolkits For Orbit Determination Codes For Precise Radio Tracking Experiments

This thesis describes the developments of new models and toolkits for the orbit determination codes to support and improve the precise radio tracking experiments of the Cassini-Huygens mission, an interplanetary mission to study the Saturn system. The core of the orbit determination process is the comparison between observed observables and computed observables. Disturbances in either the observed or computed observables degrades the orbit determination process. Chapter 2 describes a detailed study of the numerical errors in the Doppler observables computed by NASA's ODP and MONTE, and ESA's AMFIN. A mathematical model of the numerical noise was developed and successfully validated analyzing against the Doppler observables computed by the ODP and MONTE, with typical relative errors smaller than 10%. The numerical noise proved to be, in general, an important source of noise in the orbit determination process and, in some conditions, it may becomes the dominant noise source. Three different approaches to reduce the numerical noise were proposed. Chapter 3 describes the development of the multiarc library, which allows to perform a multi-arc orbit determination with MONTE. The library was developed during the analysis of the Cassini radio science gravity experiments of the Saturn's satellite Rhea. Chapter 4 presents the estimation of the Rhea's gravity field obtained from a joint multi-arc analysis of Cassini R1 and R4 fly-bys, describing in details the spacecraft dynamical model used, the data selection and calibration procedure, and the analysis method followed. In particular, the approach of estimating the full unconstrained quadrupole gravity field was followed, obtaining a solution statistically not compatible with the condition of hydrostatic equilibrium. The solution proved to be stable and reliable. The normalized moment of inertia is in the range 0.37-0.4 indicating that Rhea's may be almost homogeneous, or at least characterized by a small degree of differentiation.

Visual-somatosensory interactions in mental representations of the body and the face

The body is represented in the brain at levels that incorporate multisensory information. This thesis focused on interactions between vision and cutaneous sensations (i.e., touch and pain). Experiment 1 revealed that there are partially dissociable pathways for visual enhancement of touch (VET) depending upon whether one sees one’s own body or the body of another person. This indicates that VET, a seeming low-level effect on spatial tactile acuity, is actually sensitive to body identity. Experiments 2-4 explored the effect of viewing one’s own body on pain perception. They demonstrated that viewing the body biases pain intensity judgments irrespective of actual stimulus intensity, and, more importantly, reduces the discriminative capacities of the nociceptive pathway encoding noxious stimulus intensity. The latter effect only occurs if the pain-inducing event itself is not visible, suggesting that viewing the body alone and viewing a stimulus event on the body have distinct effects on cutaneous sensations. Experiment 5 replicated an enhancement of visual remapping of touch (VRT) when viewing fearful human faces being touched, and further demonstrated that VRT does not occur for observed touch on non-human faces, even fearful ones. This suggests that the facial expressions of non-human animals may not be simulated within the somatosensory system of the human observer in the same way that the facial expressions of other humans are. Finally, Experiment 6 examined the enfacement illusion, in which synchronous visuo-tactile inputs cause another’s face to be assimilated into the mental self-face representation. The strength of enfacement was not affected by the other’s facial expression, supporting an asymmetric relationship between processing of facial identity and facial expressions. Together, these studies indicate that multisensory representations of the body in the brain link low-level perceptual processes with the perception of emotional cues and body/face identity, and interact in complex ways depending upon contextual factors.

Experiments on Pro-Sociality and Environmental Issues

The thesis comprises three essays that use experimental methods, one about other-regarding motivations in economic behavior and the others on pro-social behavior in two environmental economics problems. The first chapter studies how the expectations of the others and the concern to maintain a balance between effort exerted and rewards obtained interact in shaping the behavior in a modified dictator game. We find that dictators condition their choices on recipients' expectations only when there is a high probability that the the recipient will not be compensated for her effort. Otherwise, dictators tend to balance the efforts and rewards of the recipients, irrespective of the recipients' expectations. In the second chapter, I investigate the problem of local opposition to large public projects (e.g. landfills, incinerators, etc.). In particular, the experiment shows how the uncertainty about the project's quality makes the community living in the host site skeptical about the project. I also test whether side-transfers and costly information disclosure can help to increase the efficiency. Both tools succesfully make the host more willing to accept the project, but they lead to the realization of different types of projects. The last chapter is an experiment on climate negotiations. To avoid the global warming, countries are called to cooperate in the abatement of their emissions. We study whether the dynamic aspect of the climate change makes cooperation across countries behaviorally more difficult. We also consider inequality across countries as a possible factor that hinders international cooperation.