Molecular characterization of the human gut microbiota: the effect of aging

Age-related physiological changes in the gastrointestinal tract, as well as modification in lifestyle, nutritional behaviour, and functionality of the host immune system, inevitably affect the gut microbiota. The study presented here is focused on the application and comparison of two different microarray approaches for the characterization of the human gut microbiota, the HITChip and the HTF-Microb.Array, with particular attention to the effects of the aging process on the composition of this ecosystem. By using the Human Intestinal Tract Chip (HITChip), recently developed at the Wageningen University, The Netherland, we explored the age-related changes of gut microbiota during the whole adult lifespan, from young adults, through elderly to centenarians. We observed that the microbial composition and diversity of the gut ecosystem of young adults and seventy-years old people is highly similar but differs significantly from that of the centenarians. After 100 years of symbiotic association with the human host, the microbiota is characterized by a rearrangement in the Firmicutes population and an enrichment of facultative anaerobes. The presence of such a compromised microbiota in the centenarians is associated with an increased inflammation status, also known as inflamm-aging, as determined by a range of peripheral blood inflammatory markers. In parallel, we overtook the development of our own phylogenetic microarray with a lower number of targets, aiming the description of the human gut microbiota structure at high taxonomic level. The resulting chip was called High Taxonomic level Fingerprinting Microbiota Array (HTF-Microb.Array), and was based on the Ligase Detection Reaction (LDR) technology, which allowed us to develop a fast and sensitive tool for the fingerprint of the human gut microbiota in terms of presence/absence of the principal groups. The validation on artificial DNA mixes, as well as the pilot study involving eight healthy young adults, demonstrated that the HTF-Microb.Array can be used to successfully characterize the human gut microbiota, allowing us to obtain results which are in approximate accordance with the most recent characterizations. Conversely, the evaluation of the relative abundance of the target groups on the bases of the relative fluorescence intensity probes response still has some hindrances, as demonstrated by comparing the HTF.Microb.Array and HITChip high taxonomic level fingerprints of the same centenarians.

Fingerprint Recognition: Enhancement, Feature Extraction and Automatic Evaluation of Algorithms

The identification of people by measuring some traits of individual anatomy or physiology has led to a specific research area called biometric recognition. This thesis is focused on improving fingerprint recognition systems considering three important problems: fingerprint enhancement, fingerprint orientation extraction and automatic evaluation of fingerprint algorithms. An effective extraction of salient fingerprint features depends on the quality of the input fingerprint. If the fingerprint is very noisy, we are not able to detect a reliable set of features. A new fingerprint enhancement method, which is both iterative and contextual, is proposed. This approach detects high-quality regions in fingerprints, selectively applies contextual filtering and iteratively expands like wildfire toward low-quality ones. A precise estimation of the orientation field would greatly simplify the estimation of other fingerprint features (singular points, minutiae) and improve the performance of a fingerprint recognition system. The fingerprint orientation extraction is improved following two directions. First, after the introduction of a new taxonomy of fingerprint orientation extraction methods, several variants of baseline methods are implemented and, pointing out the role of pre- and post- processing, we show how to improve the extraction. Second, the introduction of a new hybrid orientation extraction method, which follows an adaptive scheme, allows to improve significantly the orientation extraction in noisy fingerprints. Scientific papers typically propose recognition systems that integrate many modules and therefore an automatic evaluation of fingerprint algorithms is needed to isolate the contributions that determine an actual progress in the state-of-the-art. The lack of a publicly available framework to compare fingerprint orientation extraction algorithms, motivates the introduction of a new benchmark area called FOE (including fingerprints and manually-marked orientation ground-truth) along with fingerprint matching benchmarks in the FVC-onGoing framework. The success of such framework is discussed by providing relevant statistics: more than 1450 algorithms submitted and two international competitions.

Spectroscopic investigation on photoreactivity, structure and polymorphism of organic molecular crystals

The study of the spectroscopic phenomena in organic solids, in combination with other techniques, is an effective tool for the understanding of the structural properties of materials based on these compounds. This Ph.D. work was dedicated to the spectroscopic investigation of some relevant processes occurring in organic molecular crystals, with the goal of expanding the knowledge on the relationship between structure, dynamics and photoreactivity of these systems. Vibrational spectroscopy has been the technique of choice, always in combination with X-ray diffraction structural studies and often the support of computational methods. The vibrational study of the molecular solid state reaches its full potential when it includes the low-wavenumber region of the lattice-phonon modes, which probe the weak intermolecular interactions and are the fingerprints of the lattice itself. Microscopy is an invaluable addition in the investigation of processes that take place in the micro-meter scale of the crystal micro-domains. In chemical and phase transitions, as well as in polymorph screening and identification, the combination of Raman microscopy and lattice-phonon detection has provided useful information. Research on the fascinating class of single-crystal-to-single-crystal photoreactions, has shown how the homogeneous mechanism of these transformations can be identified by lattice-phonon microscopy, in agreement with the continuous evolution of their XRD patterns. On describing the behavior of the photodimerization mechanism of vitamin K3, the focus was instead on the influence of its polymorphism in governing the product isomerism. Polymorphism is the additional degree of freedom of molecular functional materials, and by advancing in its control and properties, functionalities can be promoted for useful applications. Its investigation focused on thin-film phases, widely employed in organic electronics. The ambiguities in phase identification often emerging by other experimental methods were successfully solved by vibrational measurements.

Exploiting spectrally resolved satellite observations to assess the performance of climate models

The accurate representation of the Earth Radiation Budget by General Circulation Models (GCMs) is a fundamental requirement to provide reliable historical and future climate simulations. In this study, we found reasonable agreement between the integrated energy fluxes at the top of the atmosphere simulated by 34 state-of-the-art climate models and the observations provided by the Cloud and Earth Radiant Energy System (CERES) mission on a global scale, but large regional biases have been detected throughout the globe. Furthermore, we highlighted that a good agreement between simulated and observed integrated Outgoing Longwave Radiation (OLR) fluxes may be obtained from the cancellation of opposite-in-sign systematic errors, localized in different spectral ranges. To avoid this and to understand the causes of these biases, we compared the observed Earth emission spectra, measured by the Infrared Atmospheric Sounding Interferometer (IASI) in the period 2008-2016, with the synthetic radiances computed on the basis of the atmospheric fields provided by the EC-Earth GCM. To this purpose, the fast σ-IASI radiative transfer model was used, after its validation and implementation in EC-Earth. From the comparison between observed and simulated spectral radiances, a positive temperature bias in the stratosphere and a negative temperature bias in the middle troposphere, as well as a dry bias of the water vapor concentration in the upper troposphere, have been identified in the EC-Earth climate model. The analysis has been performed in clear-sky conditions, but the feasibility of its extension in the presence of clouds, whose impact on the radiation represents the greatest source of uncertainty in climate models, has also been proven. Finally, the analysis of simulated and observed OLR trends indicated good agreement and provided detailed information on the spectral fingerprints of the evolution of the main climate variables.