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).

Advanced spectroscopic techniques and chemometric analysis for atmospheric organic aerosol characterization and source apportionment

Atmospheric aerosol particles directly impact air quality and participate in controlling the climate system. Organic Aerosol (OA) in general accounts for a large fraction (10–90%) of the global submicron (PM1) particulate mass. Chemometric methods for source identification are used in many disciplines, but methods relying on the analysis of NMR datasets are rarely used in atmospheric sciences. This thesis provides an original application of NMR-based chemometric methods to atmospheric OA source apportionment. The method was tested on chemical composition databases obtained from samples collected at different environments in Europe, hence exploring the impact of a great diversity of natural and anthropogenic sources. We focused on sources of water-soluble OA (WSOA), for which NMR analysis provides substantial advantages compared to alternative methods. Different factor analysis techniques are applied independently to NMR datasets from nine field campaigns of the project EUCAARI and allowed the identification of recurrent source contributions to WSOA in European background troposphere: 1) Marine SOA; 2) Aliphatic amines from ground sources (agricultural activities, etc.); 3) Biomass burning POA; 4) Biogenic SOA from terpene oxidation; 5) “Aged” SOAs, including humic-like substances (HULIS); 6) Other factors possibly including contributions from Primary Biological Aerosol Particles, and products of cooking activities. Biomass burning POA accounted for more than 50% of WSOC in winter months. Aged SOA associated with HULIS was predominant (> 75%) during the spring-summer, suggesting that secondary sources and transboundary transport become more important in spring and summer. Complex aerosol measurements carried out, involving several foreign research groups, provided the opportunity to compare source apportionment results obtained by NMR analysis with those provided by more widespread Aerodyne aerosol mass spectrometers (AMS) techniques that now provided categorization schemes of OA which are becoming a standard for atmospheric chemists. Results emerging from this thesis partly confirm AMS classification and partly challenge it.

Gait analysis using a single wearable inertial measurement unit

Procedures for quantitative walking analysis include the assessment of body segment movements within defined gait cycles. Recently, methods to track human body motion using inertial measurement units have been suggested. It is not known if these techniques can be readily transferred to clinical measurement situations. This work investigates the aspects necessary for one inertial measurement unit mounted on the lower back to track orientation, and determine spatio-temporal features of gait outside the confines of a conventional gait laboratory. Apparent limitations of different inertial sensors can be overcome by fusing data using methods such as a Kalman filter. The benefits of optimizing such a filter for the type of motion are unknown. 3D accelerations and 3D angular velocities were collected for 18 healthy subjects while treadmill walking. Optimization of Kalman filter parameters improved pitch and roll angle estimates when compared to angles derived using stereophotogrammetry. A Weighted Fourier Linear Combiner method for estimating 3D orientation angles by constructing an analytical representation of angular velocities and allowing drift free integration is also presented. When tested this method provided accurate estimates of 3D orientation when compared to stereophotogrammetry. Methods to determine spatio-temporal features from lower trunk accelerations generally require knowledge of sensor alignment. A method was developed to estimate the instants of initial and final ground contact from accelerations measured by a waist mounted inertial device without rigorous alignment. A continuous wavelet transform method was used to filter and differentiate the signal and derive estimates of initial and final contact times. The technique was tested with data recorded for both healthy and pathologic (hemiplegia and Parkinson’s disease) subjects and validated using an instrumented mat. The results show that a single inertial measurement unit can assist whole body gait assessment however further investigation is required to understand altered gait timing in some pathological subjects.

Analysis of the Slow Food movement impact on the farmers and rural areas’ sustainable development

The evaluation of the farmers’ communities’ approach to the Slow Food vision, their perception of the Slow Food role in supporting their activity and their appreciation and expectations from participating in the event of Mother Earth were studied. The Unified Theory of Acceptance and Use of Technology (UTAUT) model was adopted in an agro-food sector context. A survey was conducted, 120 questionnaires from farmers attending the Mother Earth in Turin in 2010 were collected. The descriptive statistical analysis showed that both Slow Food membership and participation to Mother Earth Meeting were much appreciated for the support provided to their business and the contribution to a more sustainable and fair development. A positive social, environmental and psychological impact on farmers also resulted. Results showed also an interesting perspective on the possible universality of the Slow Food and Mother Earth values. Farmers declared that Slow Food is supporting them by preserving the biodiversity and orienting them to the use of local resources and reducing the chemical inputs. Many farmers mentioned the language/culture and administration/bureaucratic issues as an obstacle to be a member in the movement and to participate to the event. Participation to Mother Earth gives an opportunity to exchange information with other farmers’ communities and to participate to seminars and debates, helpful for their business development. The absolute majority of positive answers associated to the farmers’ willingness to relate to Slow Food and participate to the next Mother Earth editions negatively influenced the UTAUT model results. A factor analysis showed that the variables associated to the UTAUT model constructs Performance Expectancy and Effort Expectancy were consistent, able to explain the construct variability, and their measurement reliable. Their inclusion in a simplest Technology Acceptance Model could be considered in future researches.

Institutional Processes and Discursive Strategies: Rhetoric and Vocabulary Analysis of CSR and Sustainability

The candidate tackled an important issue in contemporary management: the role of CSR and Sustainability. The research proposal focused on a longitudinal and inductive research, directed to specify the evolution of CSR and contribute to the new institutional theory, in particular institutional work framework, and to the relation between institutions and discourse analysis. The documental analysis covers all the evolution of CSR, focusing also on a number of important networks and associations. Some of the methodologies employed in the thesis have been employed as a consequence of data analysis, in a truly inductive research process. The thesis is composed by two section. The first section mainly describes the research process and the analyses results. The candidates employed several research methods: a longitudinal content analysis of documents, a vocabulary research with statistical metrics as cluster analysis and factor analysis, a rhetorical analysis of justifications. The second section puts in relation the analysis results with theoretical frameworks and contributions. The candidate confronted with several frameworks: Actor-Network-Theory, Institutional work and Boundary Work, Institutional Logic. Chapters are focused on different issues: a historical reconstruction of CSR; a reflection about symbolic adoption of recurrent labels; two case studies of Italian networks, in order to confront institutional and boundary works; a theoretical model of institutional change based on contradiction and institutional complexity; the application of the model to CSR and Sustainability, proposing Sustainability as a possible institutional logic.

Movement Analysis by means of inertial sensors: from bench to bedside

in the everyday clinical practice. Having this in mind, the choice of a simple setup would not be enough because, even if the setup is quick and simple, the instrumental assessment would still be in addition to the daily routine. The will to overcome this limit has led to the idea of instrumenting already existing and widely used functional tests. In this way the sensor based assessment becomes an integral part of the clinical assessment. Reliable and validated signal processing methods have been successfully implemented in Personal Health Systems based on smartphone technology. At the end of this research project there is evidence that such solution can really and easily used in clinical practice in both supervised and unsupervised settings. Smartphone based solution, together or in place of dedicated wearable sensing units, can truly become a pervasive and low-cost means for providing suitable testing solutions for quantitative movement analysis with a clear clinical value, ultimately providing enhanced balance and mobility support to an aging population.

Sensory analysis as a tool to improve the quality of aquaculture products

Sensory analysis is a scientific discipline used to evoke, measure, analyse and interpret the responses to products that are perceived by the senses of sight, smell, taste, touch and hearing. This science is used to highlight the strengths and characteristics of a product, such as in the case of research and development products where alternative ingredients, food waste or by-products are used. It can also be used to evaluate the same characteristics over time, to highlight alterations in one of the sensory components at a given time or over time. This doctoral thesis deals with the valorisation, through characterisation, of various aquaculture fish products. In particular, the products covered by this study were analysed, depending on the objective pursued, with different sensory methods using trained judges and in one case consumers. Therefore, the sensory characterisation of the products was useful for investigating the foods considered in this doctoral research. In particular, specific research topics were taken: 1. The study of alternative ingredients, such as the outcomes of different levels of inclusion of insect larvae (Hermetia illucens) meal on the quality of sea bream (Sparus aurata) fillets. 2. The study of consumer expectations and perceptions on the use of insect meal as a feed for aquaculture products. In particular, this study was done after the characterisation by Quantitative Descriptive analysis (QDA) of the products to exclude sensory differences. 3. Development of a non-destructive and cheap device based on dielectric spectroscopy for assessing fish freshness. In particular in this study, the developed device was evaluated in correlation with a sensory method for assessing the freshness of fish product, the Quality Index Method (QIM)