Gene Expression Profile in Response to Doxorubicin-Rapamycin Combined Treatment of HER-2-Overexpressing Human Mammary Epithelial Cell Lines

HER-2-positive breast cancers frequently sustain elevated AKT/mTOR signaling, which has been associated with resistance to doxorubicin treatment. Here, we investigated whether rapamycin, an mTOR inhibitor, increased the sensitivity to doxorubicin therapy in two HER-2-overexpressing cell lines: C5.2, which was derived from the parental HB4a by transfection with HER-2 and SKBR3, which exhibits HER-2 amplification. The epithelial mammary cell line HB4a was also analyzed. The combined treatment using 20 nmol/L of rapamycin and 30 nmol/L of doxorubicin arrested HB4a and C5.2 cells in S to G(2)-M, whereas SKBR3 cells showed an increase in the G(0)-G(1) phase. Rapamycin increased the sensitivity to doxorubicin in HER-2-overexpressing cells by approximately 2-fold, suggesting that the combination displayed a more effective antiproliferative action. Gene expression profiling showed that these results might reflect alterations in genes involved in canonical pathways related to purine metabolism, oxidative phosphorylation, protein ubiquitination, and mitochondrial dysfunction. A set of 122 genes modulated by the combined treatment and specifically related to HER-2 overexpression was determined by finding genes commonly regulated in both C5.2 and SKBR3 that were not affected in HB4a cells. Network analysis of this particular set showed a smaller subgroup of genes in which coexpression pattern in HB4a cells was disrupted in C5.2 and SKBR3. Altogether, our data showed a subset of genes that might be more robust than individual markers in predicting the response of HER-2-overexpressing breast cancers to doxorubicin and rapamycin combination. Mol Cancer Ther; 11(2); 464-74. (C) 2011 AACR.

Transverse sphericity of primary charged particles in minimum bias proton-proton collisions at root s=0.9, 2.76 and 7 TeV

Measurements of the sphericity of primary charged particles in minimum bias proton-proton collisions at root s = 0.9, 2.76 and 7 TeV with the ALICE detector at the LHC are presented. The observable is measured in the plane perpendicular to the beam direction using primary charged tracks with p(T) > 0.5 GeV/c in vertical bar eta vertical bar < 0.8. The mean sphericity as a function of the charged particle multiplicity at mid-rapidity (N-ch) is reported for events with different p(T) scales ("soft" and "hard") defined by the transverse momentum of the leading particle. In addition, the mean charged particle transverse momentum versus multiplicity is presented for the different event classes, and the sphericity distributions in bins of multiplicity are presented. The data are compared with calculations of standard Monte Carlo event generators. The transverse sphericity is found to grow with multiplicity at all collision energies, with a steeper rise at low N-ch, whereas the event generators show an opposite tendency. The combined study of the sphericity and the mean p(T) with multiplicity indicates that most of the tested event generators produce events with higher multiplicity by generating more back-to-back jets resulting in decreased sphericity (and isotropy). The PYTHIA6 generator with tune PERUGIA-2011 exhibits a noticeable improvement in describing the data, compared to the other tested generators.

Effects of light intensity and temperature on Cylindrospermopsis raciborskii (Cyanobacteria) with straight and coiled trichomes: growth rate and morphology

Cylindrospermopsis raciborskii (Woloszynska) Seenayya et Subba Raju (Ordem Nostocales) is one of the most troublesome bloom-forming species in Brazil. Understanding the population dynamics of the different morphotypes of C. raciborskii (straight and coiled) could assist in the prediction of favourable conditions for the proliferation of this potentially toxin-producing species. The aim of the present study was to assess the effects of two different light intensities and temperatures on the growth rate and morphology of the trichomes of the straight and coiled morphotypes. For such, two non-toxin producing strains of C. raciborskii were used - one with a coiled trichome (ITEP31) and another with a straight trichome (ITEP28). The strains were cultured in BG-11 medium in a climatic chamber under controlled conditions. Two light intensities (30 and 90 mu mol.m(-2).s(-1)) were combined at temperatures of 21 and 31 degrees C and the growth rate and morphological changes were analysed. The morphotypes responded differently to the different temperatures and light intensities. Both strains exhibited faster growth velocities when submitted to higher light intensity and temperature. The lower temperature and higher luminosity hampered the development of both strains. Variations in cellular morphology and an absence of akinetes in both strains were related to the lower temperature (21 C). The coiled morphotype demonstrated considerable phenotype plasticity, changing the morphology of trichome throughout its growth curve. Although molecular analysis does not sustain the separation of the morphotypes as distinct species, their different eco-physiological responses should be considered further knowledge of extreme importance for the population control of these potentially toxic organisms.

Identification of protein-coding and non-coding RNA expression profiles in CD34+ and in stromal cells in refractory anemia with ringed sideroblasts

Abstract Background Myelodysplastic syndromes (MDS) are a group of clonal hematological disorders characterized by ineffective hematopoiesis with morphological evidence of marrow cell dysplasia resulting in peripheral blood cytopenia. Microarray technology has permitted a refined high-throughput mapping of the transcriptional activity in the human genome. Non-coding RNAs (ncRNAs) transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression, and in the regulation of exon-skipping and intron retention. Characterization of ncRNAs in progenitor cells and stromal cells of MDS patients could be strategic for understanding gene expression regulation in this disease. Methods In this study, gene expression profiles of CD34+ cells of 4 patients with MDS of refractory anemia with ringed sideroblasts (RARS) subgroup and stromal cells of 3 patients with MDS-RARS were compared with healthy individuals using 44 k combined intron-exon oligoarrays, which included probes for exons of protein-coding genes, and for non-coding RNAs transcribed from intronic regions in either the sense or antisense strands. Real-time RT-PCR was performed to confirm the expression levels of selected transcripts. Results In CD34+ cells of MDS-RARS patients, 216 genes were significantly differentially expressed (q-value ≤ 0.01) in comparison to healthy individuals, of which 65 (30%) were non-coding transcripts. In stromal cells of MDS-RARS, 12 genes were significantly differentially expressed (q-value ≤ 0.05) in comparison to healthy individuals, of which 3 (25%) were non-coding transcripts. Conclusions These results demonstrated, for the first time, the differential ncRNA expression profile between MDS-RARS and healthy individuals, in CD34+ cells and stromal cells, suggesting that ncRNAs may play an important role during the development of myelodysplastic syndromes.

Chemical composition and enzymatic digestibility of sugarcane clones selected for varied lignin content

Abstract Background The recalcitrance of lignocellulosic materials is a major limitation for their conversion into fermentable sugars. Lignin depletion in new cultivars or transgenic plants has been identified as a way to diminish this recalcitrance. In this study, we assessed the success of a sugarcane breeding program in selecting sugarcane plants with low lignin content, and report the chemical composition and agronomic characteristics of eleven experimental hybrids and two reference samples. The enzymatic digestion of untreated and chemically delignified samples was evaluated to advance the performance of the sugarcane residue (bagasse) in cellulosic-ethanol production processes. Results The ranges for the percentages of glucan, hemicellulose, lignin, and extractive (based on oven-dry biomass) of the experimental hybrids and reference samples were 38% to 43%, 25% to 32%, 17% to 24%, and 1.6% to 7.5%, respectively. The samples with the smallest amounts of lignin did not produce the largest amounts of total polysaccharides. Instead, a variable increase in the mass of a number of components, including extractives, seemed to compensate for the reduction in lignin content. Hydroxycinnamic acids accounted for a significant part of the aromatic compounds in the samples, with p-coumaric acid predominating, whereas ferulic acid was present only in low amounts. Hydroxycinnamic acids with ester linkage to the hemicelluloses varied from 2.3% to 3.6%. The percentage of total hydroxycinnamic acids (including the fraction linked to lignin through ether linkages) varied from 5.0% to 9.2%, and correlated to some extent with the lignin content. These clones released up to 31% of glucose after 72 hours of digestion with commercial cellulases, whereas chemically delignified samples led to cellulose conversion values of more than 80%. However, plants with lower lignin content required less delignification to reach higher efficiencies of cellulose conversion during the enzymatic treatment. Conclusion Some of the experimental sugarcane hybrids did have the combined characteristics of high biomass and high sucrose production with low lignin content. Conversion of glucan to glucose by commercial cellulases was increased in the samples with low lignin content. Chemical delignification further increased the cellulose conversion to values of more than 80%. Thus, plants with lower lignin content required less delignification to reach higher efficiencies of cellulose conversion during the enzymatic treatment.

The putative role of ovary removal and progesterone when considering the effect of formaldehyde exposure on lung inflammation induced by ovalbumin

OBJECTIVE: Formaldehyde exposure during the menstrual cycle is known to affect the course of allergic lung inflammation. Because our previous data demonstrated that formaldehyde combined with an ovariectomy reduced allergic lung inflammation, we investigated the putative role of ovary removal and progesterone treatment when considering the effect of formaldehyde on allergic lung inflammation. METHOD: Ovariectomized rats and their matched controls were exposed to formaldehyde (1%, 3 days, 90 min/day) or vehicle, and immediately after exposure, the rats were sensitized to ovalbumin by a subcutaneous route. After 1 week, the rats received a booster by the same route, and after an additional week, the rats were challenged with ovalbumin (1%) by an aerosol route. The leukocyte numbers, interleukin-10 (IL-10) release, myeloperoxidase activity, vascular permeability, ex vivo tracheal reactivity to methacholine and mast cell degranulation were determined 24 h later. RESULTS: Our results showed that previous exposure to formaldehyde in allergic rats decreased lung cell recruitment, tracheal reactivity, myeloperoxidase activity, vascular permeability and mast cell degranulation while increasing IL-10 levels. Ovariectomy only caused an additional reduction in tracheal reactivity without changing the other parameters studied. Progesterone treatment reversed the effects of formaldehyde exposure on ex vivo tracheal reactivity, cell influx into the lungs and mast cell degranulation. CONCLUSION: In conclusion, our study revealed that formaldehyde and ovariectomy downregulated allergic lung inflammation by IL-10 release and mast cell degranulation. Progesterone treatment increased eosinophil recruitment and mast cell degranulation, which in turn may be responsible for tracheal hyperreactivity and allergic lung inflammation

Studies of Inorganic Layer and Framework Structures Using Time-, Temperature- and Pressure-Resolved Powder Diffraction Techniques

This thesis is concerned with in-situ time-, temperature- and pressure-resolved synchrotron X-ray powder diffraction investigations of a variety of inorganic compounds with twodimensional layer structures and three-dimensional framework structures. In particular, phase stability, reaction kinetics, thermal expansion and compressibility at non-ambient conditions has been studied for 1) Phosphates with composition MIV(HPO4)2·nH2O (MIV = Ti, Zr); 2) Pyrophosphates and pyrovanadates with composition MIVX2O7 (MIV = Ti, Zr and X = P, V); 3) Molybdates with composition ZrMo2O8. The results are compiled in seven published papers and two manuscripts. Reaction kinetics for the hydrothermal synthesis of α-Ti(HPO4)2·H2O and intercalation of alkane diamines in α-Zr(HPO4)2·H2O was studied using time-resolved experiments. In the high-temperature transformation of γ-Ti(PO4)(H2PO4)·2H2O to TiP2O7 three intermediate phases, γ'-Ti(PO4)(H2PO4)·(2-x)H2O, β-Ti(PO4)(H2PO4) and Ti(PO4)(H2P2O7)0.5 were found to crystallise at 323, 373 and 748 K, respectively. A new tetragonal three-dimensional phosphate phase called τ-Zr(HPO4)2 was prepared, and subsequently its structure was determined and refined using the Rietveld method. In the high-temperature transformation from τ-Zr(HPO4)2 to cubic α-ZrP2O7 two new orthorhombic intermediate phases were found. The first intermediate phase, ρ-Zr(HPO4)2, forms at 598 K, and the second phase, β-ZrP2O7, at 688 K. Their respective structures were solved using direct methods and refined using the Rietveld method. In-situ high-pressure studies of τ-Zr(HPO4)2 revealed two new phases, tetragonal ν-Zr(HPO4)2 and orthorhombic ω-Zr(HPO4)2 that crystallise at 1.1 and 8.2 GPa. The structure of ν-Zr(HPO4)2 was solved and refined using the Rietveld method. The high-pressure properties of the pyrophosphates ZrP2O7 and TiP2O7, and the pyrovanadate ZrV2O7 were studied up to 40 GPa. Both pyrophosphates display smooth compression up to the highest pressures, while ZrV2O7 has a phase transformation at 1.38 GPa from cubic to pseudo-tetragonal β-ZrV2O7 and becomes X-ray amorphous at pressures above 4 GPa. In-situ high-pressure studies of trigonal α-ZrMo2O8 revealed the existence of two new phases, monoclinic δ-ZrMo2O8 and triclinic ε-ZrMo2O8 that crystallises at 1.1 and 2.5 GPa, respectively. The structure of δ-ZrMo2O8 was solved by direct methods and refined using the Rietveld method.

Combined low initial DNA damage and high radiation-induced apoptosis confers clinical resistance to long-term toxicity in breast cancer patients treated with high-dose radiotherapy

[EN] Background: Either higher levels of initial DNA damage or lower levels of radiation-induced apoptosis in peripheral blood lymphocytes have been associated to increased risk for develop late radiation-induced toxicity. It has been recently published that these two predictive tests are inversely related. The aim of the present study was to investigate the combined role of both tests in relation to clinical radiation-induced toxicity in a set of breast cancer patients treated with high dose hyperfractionated radical radiotherapy. Methods: Peripheral blood lymphocytes were taken from 26 consecutive patients with locally advanced breast carcinoma treated with high-dose hyperfractioned radical radiotherapy. Acute and late cutaneous and subcutaneous toxicity was evaluated using the Radiation Therapy Oncology Group morbidity scoring schema. The mean follow-up of survivors (n = 13) was 197.23 months. Radiosensitivity of lymphocytes was quantified as the initial number of DNA double-strand breaks induced per Gy and per DNA unit (200 Mbp). Radiation-induced apoptosis (RIA) at 1, 2 and 8 Gy was measured by flow cytometry using annexin V/propidium iodide. Results: Mean DSB/Gy/DNA unit obtained was 1.70 ± 0.83 (range 0.63-4.08; median, 1.46). Radiation-induced apoptosis increased with radiation dose (median 12.36, 17.79 and 24.83 for 1, 2, and 8 Gy respectively). We observed that those "expected resistant patients" (DSB values lower than 1.78 DSB/Gy per 200 Mbp and RIA values over 9.58, 14.40 or 24.83 for 1, 2 and 8 Gy respectively) were at low risk of suffer severe subcutaneous late toxicity (HR 0.223, 95%CI 0.073-0.678, P = 0.008; HR 0.206, 95%CI 0.063-0.677, P = 0.009; HR 0.239, 95%CI 0.062-0.929, P = 0.039, for RIA at 1, 2 and 8 Gy respectively) in multivariate analysis. Conclusions: A radiation-resistant profile is proposed, where those patients who presented lower levels of initial DNA damage and higher levels of radiation induced apoptosis were at low risk of suffer severe subcutaneous late toxicity after clinical treatment at high radiation doses in our series. However, due to the small sample size, other prospective studies with higher number of patients are needed to validate these results.

Multiwavelenght study of cluster mergers and consequences for the radio emission properties of galaxy clusters

In the present thesis a thourough multiwavelength analysis of a number of galaxy clusters known to be experiencing a merger event is presented. The bulk of the thesis consists in the analysis of deep radio observations of six merging clusters, which host extended radio emission on the cluster scale. A composite optical and X–ray analysis is performed in order to obtain a detailed and comprehensive picture of the cluster dynamics and possibly derive hints about the properties of the ongoing merger, such as the involved mass ratio, geometry and time scale. The combination of the high quality radio, optical and X–ray data allows us to investigate the implications of the ongoing merger for the cluster radio properties, focusing on the phenomenon of cluster scale diffuse radio sources, known as radio halos and relics. A total number of six merging clusters was selected for the present study: A3562, A697, A209, A521, RXCJ 1314.4–2515 and RXCJ 2003.5–2323. All of them were known, or suspected, to possess extended radio emission on the cluster scale, in the form of a radio halo and/or a relic. High sensitivity radio observations were carried out for all clusters using the Giant Metrewave Radio Telescope (GMRT) at low frequency (i.e. ≤ 610 MHz), in order to test the presence of a diffuse radio source and/or analyse in detail the properties of the hosted extended radio emission. For three clusters, the GMRT information was combined with higher frequency data from Very Large Array (VLA) observations. A re–analysis of the optical and X–ray data available in the public archives was carried out for all sources. Propriety deep XMM–Newton and Chandra observations were used to investigate the merger dynamics in A3562. Thanks to our multiwavelength analysis, we were able to confirm the existence of a radio halo and/or a relic in all clusters, and to connect their properties and origin to the reconstructed merging scenario for most of the investigated cases. • The existence of a small size and low power radio halo in A3562 was successfully explained in the theoretical framework of the particle re–acceleration model for the origin of radio halos, which invokes the re–acceleration of pre–existing relativistic electrons in the intracluster medium by merger–driven turbulence. • A giant radio halo was found in the massive galaxy cluster A209, which has likely undergone a past major merger and is currently experiencing a new merging process in a direction roughly orthogonal to the old merger axis. A giant radio halo was also detected in A697, whose optical and X–ray properties may be suggestive of a strong merger event along the line of sight. Given the cluster mass and the kind of merger, the existence of a giant radio halo in both clusters is expected in the framework of the re–acceleration scenario. • A radio relic was detected at the outskirts of A521, a highly dynamically disturbed cluster which is accreting a number of small mass concentrations. A possible explanation for its origin requires the presence of a merger–driven shock front at the location of the source. The spectral properties of the relic may support such interpretation and require a Mach number M < ∼ 3 for the shock. • The galaxy cluster RXCJ 1314.4–2515 is exceptional and unique in hosting two peripheral relic sources, extending on the Mpc scale, and a central small size radio halo. The existence of these sources requires the presence of an ongoing energetic merger. Our combined optical and X–ray investigation suggests that a strong merging process between two or more massive subclumps may be ongoing in this cluster. Thanks to forthcoming optical and X–ray observations, we will reconstruct in detail the merger dynamics and derive its energetics, to be related to the energy necessary for the particle re–acceleration in this cluster. • Finally, RXCJ 2003.5–2323 was found to possess a giant radio halo. This source is among the largest, most powerful and most distant (z=0.317) halos imaged so far. Unlike other radio halos, it shows a very peculiar morphology with bright clumps and filaments of emission, whose origin might be related to the relatively high redshift of the hosting cluster. Although very little optical and X–ray information is available about the cluster dynamical stage, the results of our optical analysis suggest the presence of two massive substructures which may be interacting with the cluster. Forthcoming observations in the optical and X–ray bands will allow us to confirm the expected high merging activity in this cluster. Throughout the present thesis a cosmology with H0 = 70 km s−1 Mpc−1, m=0.3 and =0.7 is assumed.

Bioremediation of PAHs - Limitations and soultions

Introduction 1.1 Occurrence of polycyclic aromatic hydrocarbons (PAH) in the environment Worldwide industrial and agricultural developments have released a large number of natural and synthetic hazardous compounds into the environment due to careless waste disposal, illegal waste dumping and accidental spills. As a result, there are numerous sites in the world that require cleanup of soils and groundwater. Polycyclic aromatic hydrocarbons (PAHs) are one of the major groups of these contaminants (Da Silva et al., 2003). PAHs constitute a diverse class of organic compounds consisting of two or more aromatic rings with various structural configurations (Prabhu and Phale, 2003). Being a derivative of benzene, PAHs are thermodynamically stable. In addition, these chemicals tend to adhere to particle surfaces, such as soils, because of their low water solubility and strong hydrophobicity, and this results in greater persistence under natural conditions. This persistence coupled with their potential carcinogenicity makes PAHs problematic environmental contaminants (Cerniglia, 1992; Sutherland, 1992). PAHs are widely found in high concentrations at many industrial sites, particularly those associated with petroleum, gas production and wood preserving industries (Wilson and Jones, 1993). 1.2 Remediation technologies Conventional techniques used for the remediation of soil polluted with organic contaminants include excavation of the contaminated soil and disposal to a landfill or capping - containment - of the contaminated areas of a site. These methods have some drawbacks. The first method simply moves the contamination elsewhere and may create significant risks in the excavation, handling and transport of hazardous material. Additionally, it is very difficult and increasingly expensive to find new landfill sites for the final disposal of the material. The cap and containment method is only an interim solution since the contamination remains on site, requiring monitoring and maintenance of the isolation barriers long into the future, with all the associated costs and potential liability. A better approach than these traditional methods is to completely destroy the pollutants, if possible, or transform them into harmless substances. Some technologies that have been used are high-temperature incineration and various types of chemical decomposition (for example, base-catalyzed dechlorination, UV oxidation). However, these methods have significant disadvantages, principally their technological complexity, high cost , and the lack of public acceptance. Bioremediation, on the contrast, is a promising option for the complete removal and destruction of contaminants. 1.3 Bioremediation of PAH contaminated soil & groundwater Bioremediation is the use of living organisms, primarily microorganisms, to degrade or detoxify hazardous wastes into harmless substances such as carbon dioxide, water and cell biomass Most PAHs are biodegradable unter natural conditions (Da Silva et al., 2003; Meysami and Baheri, 2003) and bioremediation for cleanup of PAH wastes has been extensively studied at both laboratory and commercial levels- It has been implemented at a number of contaminated sites, including the cleanup of the Exxon Valdez oil spill in Prince William Sound, Alaska in 1989, the Mega Borg spill off the Texas coast in 1990 and the Burgan Oil Field, Kuwait in 1994 (Purwaningsih, 2002). Different strategies for PAH bioremediation, such as in situ , ex situ or on site bioremediation were developed in recent years. In situ bioremediation is a technique that is applied to soil and groundwater at the site without removing the contaminated soil or groundwater, based on the provision of optimum conditions for microbiological contaminant breakdown.. Ex situ bioremediation of PAHs, on the other hand, is a technique applied to soil and groundwater which has been removed from the site via excavation (soil) or pumping (water). Hazardous contaminants are converted in controlled bioreactors into harmless compounds in an efficient manner. 1.4 Bioavailability of PAH in the subsurface Frequently, PAH contamination in the environment is occurs as contaminants that are sorbed onto soilparticles rather than in phase (NAPL, non aqueous phase liquids). It is known that the biodegradation rate of most PAHs sorbed onto soil is far lower than rates measured in solution cultures of microorganisms with pure solid pollutants (Alexander and Scow, 1989; Hamaker, 1972). It is generally believed that only that fraction of PAHs dissolved in the solution can be metabolized by microorganisms in soil. The amount of contaminant that can be readily taken up and degraded by microorganisms is defined as bioavailability (Bosma et al., 1997; Maier, 2000). Two phenomena have been suggested to cause the low bioavailability of PAHs in soil (Danielsson, 2000). The first one is strong adsorption of the contaminants to the soil constituents which then leads to very slow release rates of contaminants to the aqueous phase. Sorption is often well correlated with soil organic matter content (Means, 1980) and significantly reduces biodegradation (Manilal and Alexander, 1991). The second phenomenon is slow mass transfer of pollutants, such as pore diffusion in the soil aggregates or diffusion in the organic matter in the soil. The complex set of these physical, chemical and biological processes is schematically illustrated in Figure 1. As shown in Figure 1, biodegradation processes are taking place in the soil solution while diffusion processes occur in the narrow pores in and between soil aggregates (Danielsson, 2000). Seemingly contradictory studies can be found in the literature that indicate the rate and final extent of metabolism may be either lower or higher for sorbed PAHs by soil than those for pure PAHs (Van Loosdrecht et al., 1990). These contrasting results demonstrate that the bioavailability of organic contaminants sorbed onto soil is far from being well understood. Besides bioavailability, there are several other factors influencing the rate and extent of biodegradation of PAHs in soil including microbial population characteristics, physical and chemical properties of PAHs and environmental factors (temperature, moisture, pH, degree of contamination). Figure 1: Schematic diagram showing possible rate-limiting processes during bioremediation of hydrophobic organic contaminants in a contaminated soil-water system (not to scale) (Danielsson, 2000). 1.5 Increasing the bioavailability of PAH in soil Attempts to improve the biodegradation of PAHs in soil by increasing their bioavailability include the use of surfactants , solvents or solubility enhancers.. However, introduction of synthetic surfactant may result in the addition of one more pollutant. (Wang and Brusseau, 1993).A study conducted by Mulder et al. showed that the introduction of hydropropyl-ß-cyclodextrin (HPCD), a well-known PAH solubility enhancer, significantly increased the solubilization of PAHs although it did not improve the biodegradation rate of PAHs (Mulder et al., 1998), indicating that further research is required in order to develop a feasible and efficient remediation method. Enhancing the extent of PAHs mass transfer from the soil phase to the liquid might prove an efficient and environmentally low-risk alternative way of addressing the problem of slow PAH biodegradation in soil.

Numerical simulations of magma chamber dynamics at Campi Flegrei, and associated seismicity, deformation and gravity changes

Understanding the complex relationships between quantities measured by volcanic monitoring network and shallow magma processes is a crucial headway for the comprehension of volcanic processes and a more realistic evaluation of the associated hazard. This question is very relevant at Campi Flegrei, a volcanic quiescent caldera immediately north-west of Napoli (Italy). The system activity shows a high fumarole release and periodic ground slow movement (bradyseism) with high seismicity. This activity, with the high people density and the presence of military and industrial buildings, makes Campi Flegrei one of the areas with higher volcanic hazard in the world. In such a context my thesis has been focused on magma dynamics due to the refilling of shallow magma chambers, and on the geophysical signals detectable by seismic, deformative and gravimetric monitoring networks that are associated with this phenomenologies. Indeed, the refilling of magma chambers is a process frequently occurring just before a volcanic eruption; therefore, the faculty of identifying this dynamics by means of recorded signal analysis is important to evaluate the short term volcanic hazard. The space-time evolution of dynamics due to injection of new magma in the magma chamber has been studied performing numerical simulations with, and implementing additional features in, the code GALES (Longo et al., 2006), recently developed and still on the upgrade at the Istituto Nazionale di Geofisica e Vulcanologia in Pisa (Italy). GALES is a finite element code based on a physico-mathematical two dimensional, transient model able to treat fluids as multiphase homogeneous mixtures, compressible to incompressible. The fundamental equations of mass, momentum and energy balance are discretised both in time and space using the Galerkin Least-Squares and discontinuity-capturing stabilisation technique. The physical properties of the mixture are computed as a function of local conditions of magma composition, pressure and temperature.The model features enable to study a broad range of phenomenologies characterizing pre and sin-eruptive magma dynamics in a wide domain from the volcanic crater to deep magma feeding zones. The study of displacement field associated with the simulated fluid dynamics has been carried out with a numerical code developed by the Geophysical group at the University College Dublin (O’Brien and Bean, 2004b), with whom we started a very profitable collaboration. In this code, the seismic wave propagation in heterogeneous media with free surface (e.g. the Earth’s surface) is simulated using a discrete elastic lattice where particle interactions are controlled by the Hooke’s law. This method allows to consider medium heterogeneities and complex topography. The initial and boundary conditions for the simulations have been defined within a coordinate project (INGV-DPC 2004-06 V3_2 “Research on active volcanoes, precursors, scenarios, hazard and risk - Campi Flegrei”), to which this thesis contributes, and many researchers experienced on Campi Flegrei in volcanological, seismic, petrological, geochemical fields, etc. collaborate. Numerical simulations of magma and rock dynamis have been coupled as described in the thesis. The first part of the thesis consists of a parametric study aimed at understanding the eect of the presence in magma of carbon dioxide in magma in the convection dynamics. Indeed, the presence of this volatile was relevant in many Campi Flegrei eruptions, including some eruptions commonly considered as reference for a future activity of this volcano. A set of simulations considering an elliptical magma chamber, compositionally uniform, refilled from below by a magma with volatile content equal or dierent from that of the resident magma has been performed. To do this, a multicomponent non-ideal magma saturation model (Papale et al., 2006) that considers the simultaneous presence of CO2 and H2O, has been implemented in GALES. Results show that the presence of CO2 in the incoming magma increases its buoyancy force promoting convection ad mixing. The simulated dynamics produce pressure transients with frequency and amplitude in the sensitivity range of modern geophysical monitoring networks such as the one installed at Campi Flegrei . In the second part, simulations more related with the Campi Flegrei volcanic system have been performed. The simulated system has been defined on the basis of conditions consistent with the bulk of knowledge of Campi Flegrei and in particular of the Agnano-Monte Spina eruption (4100 B.P.), commonly considered as reference for a future high intensity eruption in this area. The magmatic system has been modelled as a long dyke refilling a small shallow magma chamber; magmas with trachytic and phonolitic composition and variable volatile content of H2O and CO2 have been considered. The simulations have been carried out changing the condition of magma injection, the system configuration (magma chamber geometry, dyke size) and the resident and refilling magma composition and volatile content, in order to study the influence of these factors on the simulated dynamics. Simulation results allow to follow each step of the gas-rich magma ascent in the denser magma, highlighting the details of magma convection and mixing. In particular, the presence of more CO2 in the deep magma results in more ecient and faster dynamics. Through this simulations the variation of the gravimetric field has been determined. Afterward, the space-time distribution of stress resulting from numerical simulations have been used as boundary conditions for the simulations of the displacement field imposed by the magmatic dynamics on rocks. The properties of the simulated domain (rock density, P and S wave velocities) have been based on data from literature on active and passive tomographic experiments, obtained through a collaboration with A. Zollo at the Dept. of Physics of the Federici II Univeristy in Napoli. The elasto-dynamics simulations allow to determine the variations of the space-time distribution of deformation and the seismic signal associated with the studied magmatic dynamics. In particular, results show that these dynamics induce deformations similar to those measured at Campi Flegrei and seismic signals with energies concentrated on the typical frequency bands observed in volcanic areas. The present work shows that an approach based on the solution of equations describing the physics of processes within a magmatic fluid and the surrounding rock system is able to recognise and describe the relationships between geophysical signals detectable on the surface and deep magma dynamics. Therefore, the results suggest that the combined study of geophysical data and informations from numerical simulations can allow in a near future a more ecient evaluation of the short term volcanic hazard.

Bioengineering of exercise: biomechanical and metabolic aspects

The field of research of this dissertation concerns the bioengineering of exercise, in particular the relationship between biomechanical and metabolic knowledge. This relationship can allow to evaluate exercise in many different circumstances: optimizing athlete performance, understanding and helping compensation in prosthetic patients and prescribing exercise with high caloric consumption and minimal joint loading to obese subjects. Furthermore, it can have technical application in fitness and rehabilitation machine design, predicting energy consumption and joint loads for the subjects who will use the machine. The aim of this dissertation was to further understand how mechanical work and metabolic energy cost are related during movement using interpretative models. Musculoskeletal models, when including muscle energy expenditure description, can be useful to address this issue, allowing to evaluate human movement in terms of both mechanical and metabolic energy expenditure. A whole body muscle-skeletal model that could describe both biomechanical and metabolic aspects during movement was identified in literature and then was applied and validated using an EMG-driven approach. The advantage of using EMG driven approach was to avoid the use of arbitrary defined optimization functions to solve the indeterminate problem of muscle activations. A sensitivity analysis was conducted in order to know how much changes in model parameters could affect model outputs: the results showed that changing parameters in between physiological ranges did not influence model outputs largely. In order to evaluate its predicting capacity, the musculoskeletal model was applied to experimental data: first the model was applied in a simple exercise (unilateral leg press exercise) and then in a more complete exercise (elliptical exercise). In these studies, energy consumption predicted by the model resulted to be close to energy consumption estimated by indirect calorimetry for different intensity levels at low frequencies of movement. The use of muscle skeletal models for predicting energy consumption resulted to be promising and the use of EMG driven approach permitted to avoid the introduction of optimization functions. Even though many aspects of this approach have still to be investigated and these results are preliminary, the conclusions of this dissertation suggest that musculoskeletal modelling can be a useful tool for addressing issues about efficiency of movement in healthy and pathologic subjects.

Effect of rearing techniques and feed composition on productive traits, bird welfare and quality of poultry products

The PhD project was focused on the study of the poultry welfare conditions and improvements. The project work was divided into 3 main research activities. A) Field evaluation of chicken meat rearing conditions kept in intensive farms. Considering the lack of published reports concerning the overall Italian rearing conditions of broiler chickens, a survey was carried out to assess the welfare conditions of broiler reared in the most important poultry companies in Italy to verify if they are in accordance with the advices given in the European proposal COM (2005) 221 final. Chicken farm conditions, carcass lesions and meat quality were investigated. 1. The densities currently used in Italy are in accordance with the European proposal COM 221 final (2005) which suggests to keep broilers at a density lower than 30-32 kg live weight/m2 and to not exceed 38-40 kg live weight/m2. 2. The mortality rates in summer and winter agree with the mortality score calculated following the formula reported in the EU Proposal COM 221 final (2005). 3. The incidence of damaged carcasses was very low and did not seem related to the stocking density. 4. The FPD scores were generally above the maximum limit advised by the EU proposal COM 221 final (2005), although the stocking densities were lower than 30-32 kg live weight per m2. 5. It can be stated that the control of the environmental conditions, particularly litter quality, appears a key issue to control the onset of foot dermatitis. B) Manipulation of several farm parameters, such litter material and depth, stocking density and light regimen to improve the chicken welfare conditions, in winter season. 1. Even though 2 different stocking densities were established in this study, the performances achieved from the chickens were almost identical among groups. 2. The FCR was significantly better in Standard conditions contrarily to birds reared in Welfare conditions with lower stocking density, more litter material and with a light program of 16 hours light and 8 hours dark. 3. In our trial, in Standard groups we observed a higher content of moisture, nitrogen and ammonia released from the litter. Therefore it can be assumed that the environmental characteristics have been positively changed by the improvements of the rearing conditions adopted for Welfare groups. 4. In Welfare groups the exhausted litters of the pens were dryer and broilers showed a lower occurrence of FPD. 5. The prevalence of hock burn lesions, like FPD, is high with poor litter quality conditions. 6. The combined effect of a lower stocking density, a greater amount of litter material and a photoperiod similar to the natural one, have positively influenced the chickens welfare status, as a matter of fact the occurrence of FPD in Welfare groups was the lowest keeping the score under the European threshold of the proposal COM 221 final(2005). C) The purpose of the third research was to study the effect of high or low stocking density of broiler chickens, different types of litter and the adoption of short or long lighting regimen on broiler welfare through the evaluation of their productivity and incidence of foot pad dermatitis during the hot season. 1. The feed efficiency was better for the Low Density than for High Density broilers. 2. The appearance of FPD was not influenced by stocking density. 3. The foot examination revealed that the lesions occurred more in birds maintained on chopped wheat straw than on wood shaving. 4. In conclusion, the adoptions of a short light regimen similar to that occurring in nature during summer reduces the feed intake without modify the growth rate thus improving the feed efficiency. Foot pad lesion were not affected neither by stocking densities nor by light regimens whereas wood shavings exerted a favourable effect in preserving foot pad in good condition. D) A study was carried out to investigate more widely the possible role of 25-hydroxycholecalciferol supplemented in the diet of a laying hen commercial strain (Lohmann brown) in comparison of diets supplemented with D3 or with D3 + 25- hydroxycholecalciferol. Egg traits during a productive cycle as well as the bone characteristics of the layers have been as well evaluated to determine if there the vitamin D3 may enhance the welfare status of the birds. 1. The weight of the egg and of its components is often greater in hens fed a diet enriched with 25-hydroxycholecalciferol. 2. Since eggs of treated groups are heavier and a larger amount of shell is needed, a direct effect on shell strength is observed. 3. At 30 and at 50 wk of age hens fed 25 hydroxycholecalciferol exhibited greater values of bone breaking force. 4. Radiographic density values obtained in the trial are always higher in hens fed with 25-hydroxycholecalciferol of both treatments: supplemented for the whole laying cycle (25D3) or from 40 weeks of age onward (D3+25D3).

Modelling the effects of nitrogen deposition and carbon dioxide enrichment on forest carbon balance

Atmospheric CO2 concentration ([CO2]) has increased over the last 250 years, mainly due to human activities. Of total anthropogenic emissions, almost 31% has been sequestered by the terrestrial biosphere. A considerable contribution to this sink comes from temperate and boreal forest ecosystems of the northern hemisphere, which contain a large amount of carbon (C) stored as biomass and soil organic matter. Several potential drivers for this forest C sequestration have been proposed, including increasing atmospheric [CO2], temperature, nitrogen (N) deposition and changes in management practices. However, it is not known which of these drivers are most important. The overall aim of this thesis project was to develop a simple ecosystem model which explicitly incorporates our best understanding of the mechanisms by which these drivers affect forest C storage, and to use this model to investigate the sensitivity of the forest ecosystem to these drivers. I firstly developed a version of the Generic Decomposition and Yield (G’DAY) model to explicitly investigate the mechanisms leading to forest C sequestration following N deposition. Specifically, I modified the G’DAY model to include advances in understanding of C allocation, canopy N uptake, and leaf trait relationships. I also incorporated a simple forest management practice subroutine. Secondly, I investigated the effect of CO2 fertilization on forest productivity with relation to the soil N availability feedback. I modified the model to allow it to simulate short-term responses of deciduous forests to environmental drivers, and applied it to data from a large-scale forest Free-Air CO2 Enrichment (FACE) experiment. Finally, I used the model to investigate the combined effects of recent observed changes in atmospheric [CO2], N deposition, and climate on a European forest stand. The model developed in my thesis project was an effective tool for analysis of effects of environmental drivers on forest ecosystem C storage. Key results from model simulations include: (i) N availability has a major role in forest ecosystem C sequestration; (ii) atmospheric N deposition is an important driver of N availability on short and long time-scales; (iii) rising temperature increases C storage by enhancing soil N availability and (iv) increasing [CO2] significantly affects forest growth and C storage only when N availability is not limiting.

Advances in understanding of osmotic dehydration and vacuum impregnation of fruits

Osmotic Dehydration and Vacuum Impregnation are interesting operations in the food industry with applications in minimal fruit processing and/or freezing, allowing to develop new products with specific innovative characteristics. Osmotic dehydration is widely used for the partial removal of water from cellular tissue by immersion in hypertonic (osmotic) solution. The driving force for the diffusion of water from the tissue is provided by the differences in water chemical potential between the external solution and the internal liquid phase of the cells. Vacuum Impregnation of porous products immersed in a liquid phase consist of reduction of pressure in a solid-liquid system (vacuum step) followed by the restoration of atmospheric pressure (atmospheric step). During the vacuum step the internal gas in the product pores is expanded and partially flows out while during the atmospheric step, there is a compression of residual gas and the external liquid flows into the pores (Fito, 1994). This process is also a very useful unit operation in food engineering as it allows to introduce specific solutes in the tissue which can play different functions (antioxidants, pH regulators, preservatives, cryoprotectants etc.). The present study attempts to enhance our understanding and knowledge of fruit as living organism, interacting dynamically with the environment, and to explore metabolic, structural, physico-chemical changes during fruit processing. The use of innovative approaches and/or technologies such as SAFES (Systematic Approach to Food Engineering System), LF-NMR (Low Frequency Nuclear Magnetic Resonance), GASMAS (Gas in Scattering Media Absorption Spectroscopy) are very promising to deeply study these phenomena. SAFES methodology was applied in order to study irreversibility of the structural changes of kiwifruit during short time of osmotic treatment. The results showed that the deformed tissue can recover its initial state 300 min after osmotic dehydration at 25 °C. The LF-NMR resulted very useful in water status and compartmentalization study, permitting to separate observation of three different water population presented in vacuole, cytoplasm plus extracellular space and cell wall. GASMAS techniques was able to study the pressure equilibration after Vacuum Impregnation showing that after restoration of atmospheric pressure in the solid-liquid system, there was a reminding internal low pressure in the apple tissue that slowly increases until reaching the atmospheric pressure, in a time scale that depends on the vacuum applied during the vacuum step. The physiological response of apple tissue on Vacuum Impregnation process was studied indicating the possibility of vesicular transport within the cells. Finally, the possibility to extend the freezing tolerance of strawberry fruits impregnated with cryoprotectants was proven.