Soil enzyme activities and biochemical indexes to assess soil quality in agronomic and forested ecosystems

The soil carries out a wide range of functions and it is important study the effects of land use on soil quality in order to provide most sustainable practices. Three fields trial have been considered to assess soil quality and functionality after human alteration, and to determine the power of soil enzymatic activities, biochemical indexes and mathematical model in the evaluation of soil status. The first field was characterized by conventional and organic management in which were tested also tillage effects. The second was characterized by conventional, organic and agro-ecological management. Finally, the third was a beech forest where was tested the effects of N deposition on soil organic carbon sequestration. Results highlight that both enzyme activities and biochemical indexes could be valid parameters for soil quality evaluation. Conventional management and plowing negatively affected soil quality and functionality with intensive tillage that lead to the downturn of microbial biomass and activity. Both organic and agro-ecological management revealed to be good practices for the maintenance of soil functionality with better microbial activity and metabolic efficiency. This positively affected also soil organic carbon content. At the eutrophic forest, enzyme activities and biochemical indexes positively respond to the treatments but one year of experimentation resulted to be not enough to observe variation in soil organic carbon content. Mathematical models and biochemical indicators resulted to be valid tools for assess soil quality, nonetheless it would be better including the microbial component in the mathematical model and consider more than one index if the aim of the work is to evaluate the overall soil quality and functionality. Concluding, the forest site is the richest one in terms of organic carbon, microbial biomass and activity while, the organic and the agro-ecological management seem to be the more sustainable but without taking in consideration the yield.

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.

Astronomical site testing in the era of the extremely large telescopes

The quality of astronomical sites is the first step to be considered to have the best performances from the telescopes. In particular, the efficiency of large telescopes in UV, IR, radio etc. is critically dependent on atmospheric transparency. It is well known that the random optical effects induced on the light propagation by turbulent atmosphere also limit telescope’s performances. Nowadays, clear appears the importance to correlate the main atmospheric physical parameters with the optical quality reachable by large aperture telescopes. The sky quality evaluation improved with the introduction of new techniques, new instrumentations and with the understanding of the link between the meteorological (or synoptical parameters and the observational conditions thanks to the application of the theories of electromagnetic waves propagation in turbulent medias: what we actually call astroclimatology. At the present the site campaigns are evolved and are performed using the classical scheme of optical seeing properties, meteorological parameters, sky transparency, sky darkness and cloudiness. New concept are added and are related to the geophysical properties such as seismicity, microseismicity, local variability of the climate, atmospheric conditions related to the ground optical turbulence and ground wind regimes, aerosol presence, use of satellite data. The purpose of this project is to provide reliable methods to analyze the atmospheric properties that affect ground-based optical astronomical observations and to correlate them with the main atmospheric parameters generating turbulence and affecting the photometric accuracy. The first part of the research concerns the analysis and interpretation of longand short-time scale meteorological data at two of the most important astronomical sites located in very different environments: the Paranal Observatory in the Atacama Desert (Chile), and the Observatorio del Roque de Los Muchachos(ORM) located in La Palma (Canary Islands, Spain). The optical properties of airborne dust at ORM have been investigated collecting outdoor data using a ground-based dust monitor. Because of its dryness, Paranal is a suitable observatory for near-IR observations, thus the extinction properties in the spectral range 1.00-2.30 um have been investigated using an empirical method. Furthermore, this PhD research has been developed using several turbulence profilers in the selection of the site for the European Extremely Large Telescope(E-ELT). During the campaigns the properties of the turbulence at different heights at Paranal and in the sites located in northern Chile and Argentina have been studied. This given the possibility to characterize the surface layer turbulence at Paranal and its connection with local meteorological conditions.

A candidate gene approach to identify DNA markers associated with meat quality and production traits: investigation of several cathepsin genes in Italian heavy pigs.

The cathepsin enzymes represent an important family of lysosomal proteinases with a broad spectrum of functions in many, if not in all, tissues and cell types. In addition to their primary role during the normal protein turnover, they possess highly specific proteolytic activities, including antigen processing in the immune response and a direct role in the development of obesity and tumours. In pigs, the involvement of cathepsin enzymes in proteolytic processes have important effects during the conversion of muscle to meat, due to their influence on meat texture and sensory characteristics, mainly in seasoned products. Their contribution is fundamental in flavour development of dry-curing hams. However, several authors have demonstrated that high cathepsin activity, in particular of cathepsin B, is correlated to defects of these products, such as an excessive meat softness together with abnormal free tyrosine content, astringent or metallic aftertastes and formation of a white film on the cut surface. Thus, investigation of their genetic variability could be useful to identify DNA markers associated with these dry cured hams parameters, but also with meat quality, production and carcass traits in Italian heavy pigs. Unfortunately, no association has been found between cathepsin markers and meat quality traits so far, in particular with cathepsin B activity, suggesting that other genes, besides these, affect meat quality parameters. Nevertheless, significant associations were observed with several carcass and production traits in pigs. A recent study has demonstrated that different single nucleotide polymorphisms (SNPs) localized in cathepsin D (CTSD), F (CTSF), H and Z genes were highly associated with growth, fat deposition and production traits in an Italian Large White pig population. The aim of this thesis was to confirm some of these results in other pig populations and identify new cathepsin markers in order to evaluate their effects on cathepsin activity and other production traits. Furthermore, starting from the data obtained in previous studies on CTSD gene, we also analyzed the known polymorphism located in the insulin-like growth factor 2 gene (IGF2 intron3-g.3072G>A). This marker is considered the causative mutation for the quantitative trait loci (QTL) affecting muscle mass and fat deposition in pigs. Since IGF2 maps very close to CTSD on porcine chromosome (SSC) 2, we wanted to clarify if the effects of the CTSD marker were due to linkage disequilibrium with the IGF2 intron3-g.3072G>A mutation or not. In the first chapter, we reported the results from these two SSC2 gene markers. First of all, we evaluated the effects of the IGF2 intron3-g.3072G>A polymorphism in the Italian Large White breed, for which no previous studies have analysed this marker. Highly significant associations were identified with all estimated breeding values for production and carcass traits (P<0.00001), while no effects were observed for meat quality traits. Instead, the IGF2 intron3-g.3072G>A mutation did not show any associations with the analyzed traits in the Italian Duroc pigs, probably due to the low level of variability at this polymorphic site for this breed. In the same Duroc pig population, significant associations were obtained for the CTSD marker for all production and carcass traits (P < 0.001), after excluding possible confounding effects of the IGF2 mutation. The effects of the CTSD g.70G>A polymorphism were also confirmed in a group of Italian Large White pigs homozygous for the IGF2 intron3-g.3072G allele G (IGF2 intron3-g.3072GG) and by haplotype analysis between the markers of the two considered genes. Taken together, all these data indicated that the IGF2 intron3-g.3072G>A mutation is not the only polymorphism affecting fatness and muscle deposition in pigs. In the second chapter, we reported the analysis of two new SNPs identified in cathepsin L (CTSL) and cathepsin S (CTSS) genes and the association results with meat quality parameters (including cathepsin B activity) and several production traits in an Italian Large White pig population. Allele frequencies of these two markers were evaluated in 7 different pig breeds. Furthermore, we mapped using a radiation hybrid panel the CTSS gene on SSC4. Association studies with several production traits, carried out in 268 Italian Large White pigs, indicated positive effects of the CTSL polymorphism on average daily gain, weight of lean cuts and backfat thickness (P<0.05). The results for these latter traits were also confirmed using a selective genotype approach in other Italian Large White pigs (P<0.01). In the 268 pig group, the CTSS polymorphism was associated with feed:gain ratio and average daily gain (P<0.05). Instead, no association was observed between the analysed markers and meat quality parameters. Finally, we wanted to verify if the positive results obtained for the cathepsin L and S markers and for other previous identified SNPs (cathepsin F, cathepsin Z and their inhibitor cystatin B) were confirmed in the Italian Duroc pig breed (third chapter). We analysed them in two groups of Duroc pigs: the first group was made of 218 performance-tested pigs not selected by any phenotypic criteria, the second group was made of 100 Italian Duroc pigs extreme and divergent for visible intermuscular fat trait. In the first group, the CTSL polymorphism was associated with weight of lean cuts (P<0.05), while suggestive associations were obtained for average daily gain and backfat thickness (P<0.10). Allele frequencies of the CTSL gene marker also differed positively among the visible intermuscular extreme tails. Instead, no positive effects were observed for the other DNA markers on the analysed traits. In conclusion, in agreement with the present data and for the biological role of these enzymes, the porcine CTSD and CTSL markers: a) may have a direct effect in the biological mechanisms involved in determining fat and lean meat content in pigs, or b) these markers could be very close to the putative functional mutation(s) present in other genes. These findings have important practical applications, in particular the CTSD and CTSL mutations could be applied in a marker assisted selection (MAS) both in the Italian Large White and Italian Duroc breeds. Marker assisted selection could also increase in efficiency by adding information from the cathepsin S genotype, but only in the Italian Large White breed.