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

Diversity of a phosphate transporter gene among species and isolates of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) are a key group of beneficial obligate biotrophs, establishing a mutualistic symbiosis with the roots of most land plants. The molecular markers generally used for their characterization are mainly based on informative regions of nuclear rDNA (SSU-ITS-LSU), although protein-encoding genes have also been proposed. Within functional genes, those encoding for phosphate transporters (PT) are particularly important in AMF, given their primary ability to take up Pi from soil, and to differentially affect plant phosphate nutrition. In this work, we investigated the genetic diversity of PT1 gene sequences and sequences of the taxonomically relevant SSU-ITS-LSU region in two isolates of the species Funneliformis coronatus, three isolates of the species Funneliformis mosseae and two species of the genus Rhizoglomus, originated from geographically distant areas and cultured in vivo. Our results showed that partial PT1 sequences not only successfully differentiated AMF genera and species like ribosomal gene sequences but also highlighted intraspecific diversity among F. mosseae and F. coronatus isolates. The study of functional genes related to the uptake of key mineral nutrients for the assessment of AMF diversity represents a key step in the selection of efficient isolates to be used as inocula in sustainable agriculture

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

Ecological implications beyond the ecotoxicity of plastic debris on marine phytoplankton assemblage structure and functioning

none7noPlastic pollution is a global issue posing a threat to marine biota with ecological implications on ecosystem functioning. Micro and nanoplastic impact on phytoplankton autotrophic species (e.g., cell growth inhibition, decrease in chlorophyll a and photosynthetic efficiency and hetero-aggregates formation) have been largely documented. However, the heterogeneity of data makes rather difficult a comparison based on size (i.e. micro vs nano). In addition, knowledge gaps on the ecological impact on phytoplankton assemblage structure and functioning are evident. A new virtual meta-analysis on cause-effect relationships of micro and nanoplastics on phytoplankton species revealed the significant effect posed by polymer type on reducing cell density for tested PVC, PS and PE plastics. Linked with autotrophic phytoplankton role in atmospheric CO2 fixation, a potential impact of plastics on marine carbon pump is discussed. The understanding of the effects of microplastics and nanoplastics on the phytoplankton functioning is fundamental to raise awareness on the overall impact on the first level of marine food web. Interactions between micro and nanoplastics and phytoplankton assemblages have been quite documented by in vitro examinations; but, further studies considering natural plankton assemblages and/or large mesocosm experiments should be performed to evaluate and try predicting ecological impacts on primary producers.openCasabianca Silvia, Bellingeri Arianna, Capellacci Samuela, Sbrana Alice, Russo Tommaso, Corsi Ilaria, Penna AntonellaCasabianca, Silvia; Bellingeri, Arianna; Capellacci, Samuela; Sbrana, Alice; Russo, Tommaso; Corsi, Ilaria; Penna, Antonell

Comment on: ‘‘The dark nature of Somma-Vesuvius volcano:Evidence from the 3.5 ka BP Avellino eruption’’ by Milia A.Raspini A., Torrente M.M.,

We present here some criticism to the scientific content of the paper of Milia et al. [2007. The dark nature of Somma-Vesuvius volcano: evidence from the 3.5 ka B.P. Avellino eruption. Quaternary International, 173–174, 57–66] published in Quaternary International. Milia et al. (2007) interpreted seismic lines in the Gulf of Naples (southern Italy), and inferred the presence of deposits from a large debris avalanche which occurred just before the Avellino eruption of Somma-Vesuvius volcano. The authors supported their seismic profile interpretation with on-land stratigraphies and logs. However, we present here different on-land data that demonstrate the inconsistency of the occurrence of any debris avalanche before or after the Avellino eruption, and we provide also an alternative interpretation for the observed seismic facies offshore of Somma-Vesuvius