Reconstructing the free energy landscape of a polyprotein by single-molecule experiments

The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is investigated by using atomic force microscopy. Exploiting a fluctuation relation, the equilibrium free energy as a function of the molecule elongation is estimated from pulling experiments. Such a free energy exhibits a regular shape that sets a typical unfolding length at zero force of the order of 20 nm. This length scale turns out to be much larger than the kinetic unfolding length that is also estimated by analyzing the typical rupture force of the molecule under dynamic loading

A CONTRIBUTION TO THE STUDY OF A PISA ALLUVIAL PLAIN SECTOR FOR LOW TEMPERATURE GEOTHERMAL ASSESSMENT

The target of this work is to evaluate the possible feeding of the east sector of the Pisa plain hydrogeological system by the Monte Pisano meteoric waters, using a geochemical and geological approach. The study was made considering the Calci basin and the area of the sedimentary plain adjacent at the Calci fan, where spring and well waters have been sampled and analyzed. The analyses of the major and minor elements of the well waters have confirmed a common origin with the springs above the Calci major alluvial fan, showing the same geochemical fingerprint. The isotopic analyses (δD-δ18O) allowed to compute the average altitude of infiltration of the waters. The altitudes obtained for the groundwaters sampled close to the alluvial fan are comparable with the average altitude of the Monte Pisano, confirming the hypothesis of the feeding of this aquifer sector by the Calci alluvial fan. The meteoric waters infiltrate through the debris-alluvial bodies that cover the south-western side of the Monte Pisano slopes reaching the aquifers at the foot of the hills. A possible water contribution to the feeding of about 5*106 m3/yr has been estimated from the hydrologic budget of the drainage basin above the Calci alluvial fan

Arbuscular mycorrhizal fungi affect total phenolics content and antioxidant activity in leaves of oak leaf lettuce varieties

Plant secondary metabolites are considered key bioactive compounds for a healthy diet. Arbuscular mycorrhizal fungi (AMF) may interact with host plant metabolism, inducing the accumulation of health-promoting phytochemicals and antioxidant molecules. Lettuce is a largely consumed vegetable, which may interact with AMF to alter its content of secondary metabolites and natural antioxidants molecules, as previously shown in cultivars belonging to var. capitata or var. longifolia. In this study, the effects of red and green leaf Lactuca sativa var. crispa inoculation with different AMF species, Rhizoglomus irregulare and Funneliformis mosseae, were investigated, by assessing the total phenolics and anthocyanins content, and the antioxidant activity of leaf tissue. A significant increase of antioxidant activity and of phenolics were observed in plants of both cultivars inoculated with R. irregulare, compared to non inoculated plants. Likewise, anthocyanins (in red leaf lettuce) were more abundant in inoculated plants than in controls. Altogether, the results indicate that R. irregulare strain showed a stronger ability than F. mosseae in affecting plant metabolism and that mycorrhizal inoculation may be used to enhance concentration of phenolics in leaf type lettuces, provided that a suitable AMF is selected

Contact-dependent Stimulation and Inhibition of Dendritic Cells by Natural Killer Cells

Natural killer (NK) cells and dendritic cells (DCs) are two distinct cell types of innate immunity. It is known that the in vitro interaction of human NK cells with autologous DCs results in DC lysis. Here we show that contact-dependent interactions between activated human NK cells and immature DCs (iDCs) provides a “control switch” for the immune system. At low NK/DC ratios, this interaction dramatically amplifies DC responses, whereas at high ratios it completely turns off their responses. Specifically, culture of activated human NK cells with iDCs, at low NK/DC ratios (1:5), led to exponential increases in DC cytokine production, which were completely dependent on cell-to-cell contact. DC maturation was also driven by cognate interactions with NK cells and maturation was dependent on endogenously produced TNF-α in the culture. At slightly higher NK/DC ratios (5:1), inhibition of DC functions was the dominant feature due to potent killing by the autologous NK cells. Resting NK cells also stimulated autologous DC maturation in a TNF-α/contact-dependent manner, however, increasing the NK/DC ratio only led to an enhancement of this effect

Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis

Background: Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in carcinogenesis. We discuss a genome-wide approach based on graph theory and Gene Ontology vocabulary for the functional characterization of common fragile sites and for the identification of genes that contribute to tumour cell biology. Results: Common fragile sites were assembled in a network based on a simple measure of correlation among common fragile site patterns of expression. By applying robust measurements to capture in quantitative terms the non triviality of the network, we identified several topological features clearly indicating departure from the Erdos-Renyi random graph model. The most important outcome was the presence of an unexpected large connected component far below the percolation threshold. Most of the best characterized common fragile sites belonged to this connected component. By filtering this connected component with Gene Ontology, statistically significant shared functional features were detected. Common fragile sites were found to be enriched for genes associated to the immune response and to mechanisms involved in tumour progression such as extracellular space remodeling and angiogenesis. Moreover we showed how the internal organization of the graph in communities and even in very simple subgraphs can be a starting point for the identification of new factors of instability at common fragile sites. Conclusion: We developed a computational method addressing the fundamental issue of studying the functional content of common fragile sites. Our analysis integrated two different approaches. First, data on common fragile site expression were analyzed in a complex networks framework. Second, outcomes of the network statistical description served as sources for the functional annotation of genes at common fragile sites by means of the Gene Ontology vocabulary. Our results support the hypothesis that fragile sites serve a function; we propose that fragility is linked to a coordinated regulation of fragile genes expression

Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis

Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in carcinogenesis. We discuss a genome-wide approach based on graph theory and Gene Ontology vocabulary for the functional characterization of common fragile sites and for the identification of genes that contribute to tumour cell biology. CFS were assembled in a network based on a simple measure of correlation among common fragile site patterns of expression. By applying robust measurements to capture in quantitative terms the non triviality of the network, we identified several topological features clearly indicating departure from the Erdos-Renyi random graph model. The most important outcome was the presence of an unexpected large connected component far below the percolation threshold. Most of the best characterized common fragile sites belonged to this connected component. By filtering this connected component with Gene Ontology, statistically significant shared functional features were detected. Common fragile sites were found to be enriched for genes associated to the immune response and to mechanisms involved in tumour progression such as extracellular space remodeling and angiogenesis. Our results support the hypothesis that fragile sites serve a function; we propose that fragility is linked to a coordinated regulation of fragile genes expression.Comment: 18 pages, accepted for publication in BMC Bioinformatic

Testing of Roller-Crimper-and-Undercutting-Blade-Equipped Prototype for Plants Termination

The use of roller crimpers to terminate plants and obtain a natural mulch before cash crop establishment has been identified as a valid and sustainable approach to control weeds. Several enhancements have been evaluated to improve and speed up plant termination to avoid delays in cash crop planting and consequent yield losses, which can occur with standard roller crimpers. In the present study, a new prototype machine provided with a roller crimper and an undercutting blade, allowing it to simultaneously crimp plant stems and cut root systems, has been designed, realized, and tested. The aim of the research was therefore to evaluate the effectiveness of the prototype for plant termination and to compare it with a commercial roller crimper. The termination was performed on a spontaneous vegetation cover (weeds). A monophasic exponential decay model to evaluate the weed termination rate over time was performed. The fitted model showed that the prototype is able to achieve a greater and faster weed devitalization compared to the commercial roller crimper, with a lower plateau (0.23 vs. 5.35 % of greenness of plant material, respectively) and higher constant of decay (1.45 vs. 0.39 day−1, respectively). Further studies are needed to evaluate the prototype’s effectiveness in relation to different soil textures, moisture conditions, and amounts of plant biomass to manage, to further improve the machine and extend its use in a broad range of situations, including cover crop termination

Organic farming systems for adaptation to and mitigation of climate change: Effects on soil fertility and resource use efficiency

Organic farming is pointed as one of the most sustainable farming practices in terms of environmental sustainability and climate change mitigation potential. At the core of organic farming practices there are practices aimed at improving soil fertility, increasing soil C content and enhancing system biodiversity. A long-term field experiment (LTE) (MASCOT) was started on 2001 in San Piero a Grado, Pisa (Italy) with the aim to compare two different cropping systems, one managed organically and one conventionally, in terms of agronomical, economic and environmental sustainability. In 2016, the MASCOT was redesigned as a full system trial and the organic system was reshaped according to up to date agroecological standards. Climate change adaptation capacity of the two systems is being assessed through agronomic and economic parameters, whilst greenhouse gas emission mitigation potential is mainly expressed in terms of soil C sequestration

“Once upon a Time in the Mediterranean”. Long Term Trends of Mediterranean Fisheries Resources Based on Fishers’ Traditional Ecological Knowledge

We investigate long-term changes in the Mediterranean marine resources driving the trawl fisheries by analysing fishers’ perceptions (Traditional Ecological Knowledge, TEK) throughout the Mediterranean Sea for the last 80 years. To this end, we conducted an extended set of interviews with old experienced fishers that enabled us to classify species (or taxa) as 'decreasing' or 'increasing' both in terms of abundance, as well as average size in the catch. The aspect that most clearly emerged in all the investigated areas over time was the notable increase of fishing capacity indicators, such as engine power and fishing depth range. Atlantic mackerel, poor cod, scorpionfishes, striped seabream, and John Dory demonstrated a decreasing trend in the fishers' perceived abundance, while Mediterranean parrotfish, common pandora, cuttlefish, blue and red shrimp, and mullets gave indications of an increasing temporal trend. Although, as a rule, trawler captains did not report any cataclysmic changes (e.g. extinctions), when they were invited to estimate total overall catches, a clear decreasing pattern emerged; this being a notable finding taking into account the steep escalation of fishing efficiency during the past century. The overall deteriorating status of stocks in most Mediterranean regions calls for responsible management and design of rebuilding plans. This should include historical information accounting for past exploitation patterns that could help defining a baseline of fish abundance prior to heavy industrial fisheries exploitation.JRC.G.3-Maritime affair