PASTA: splice junction identification from RNA-Sequencing data

Background: Next generation transcriptome sequencing (RNA-Seq) is emerging as a powerful experimental tool for the study of alternative splicing and its regulation, but requires ad-hoc analysis methods and tools. PASTA (Patterned Alignments for Splicing and Transcriptome Analysis) is a splice junction detection algorithm specifically designed for RNA-Seq data, relying on a highly accurate alignment strategy and on a combination of heuristic and statistical methods to identify exon-intron junctions with high accuracy. Results: Comparisons against TopHat and other splice junction prediction software on real and simulated datasets show that PASTA exhibits high specificity and sensitivity, especially at lower coverage levels. Moreover, PASTA is highly configurable and flexible, and can therefore be applied in a wide range of analysis scenarios: it is able to handle both single-end and paired-end reads, it does not rely on the presence of canonical splicing signals, and it uses organism-specific regression models to accurately identify junctions. Conclusions: PASTA is a highly efficient and sensitive tool to identify splicing junctions from RNA-Seq data. Compared to similar programs, it has the ability to identify a higher number of real splicing junctions, and provides highly annotated output files containing detailed information about their location and characteristics. Accurate junction data in turn facilitates the reconstruction of the splicing isoforms and the analysis of their expression levels, which will be performed by the remaining modules of the PASTA pipeline, still under development. Use of PASTA can therefore enable the large-scale investigation of transcription and alternative splicing

Moment-based metrics for global sensitivity analysis of hydrological systems

We propose new metrics to assist global sensitivity analysis, GSA, of hydrological and Earth systems. Our approach allows assessing the impact of uncertain parameters on main features of the probability density function, pdf, of a target model output, y. These include the expected value of y, the spread around the mean and the degree of symmetry and tailedness of the pdf of y. Since reliable assessment of higher order statistical moments can be computationally demanding, we couple our GSA approach with a surrogate model, approximating the full model response at a reduced computational cost. Here, we consider the generalized Polynomial Chaos Expansion (gPCE), other model reduction techniques being fully compatible with our theoretical framework. We demonstrate our approach through three test cases, including an analytical benchmark, a simplified scenario mimicking pumping in a coastal aquifer, and a laboratory-scale conservative transport experiment. Our results allow ascertaining which parameters can impact some moments of the model output pdf while being uninfluential to others. We also investigate the error associated with the evaluation of our sensitivity metrics by replacing the original system model through a gPCE. Our results indicate that the construction of a surrogate model with increasing level of accuracy might be required depending on the statistical moment considered in the GSA. Our approach is fully compatible with (and can assist the development of) analysis techniques employed in the context of reduction of model complexity, model calibration, design of experiment, uncertainty quantification and risk assessment

Le acque sotterranee del Cansiglio

Il Cansiglio è un altipiano carsico, con un’estensione di circa 100 km2 e un’altitudine media di circa 1000 m; esso è situato al confine tra due regioni (Veneto e Friuli Venezia Giulia) e tre provincie (Treviso, Belluno e Pordenone). Questo importante sistema carsico non è mai stato oggetto di approfonditi studi idrogeologici, nonostante la presenza di rilevanti sorgenti alla sua base (Meschio, Molinetto, Santissima e Gorgazzo). L’occasione si è presentata con l’esplorazione, da parte del Gruppo Speleologico Ferrarese in collaborazione con altri gruppi speleologici, di quella che è tuttora la grotta più profonda della zona: l’Abisso Col de la Rizza (904/FR410) (circa 800 m di profondità per 4 km di sviluppo). Con la collaborazione del Dipartimento di Scienze della Terra dell’Università di Ferrara, è stato, quindi, progettato e realizzato un multi- tracciamento delle acque sotterranee, con due iniezioni in parallelo: fluoresceina sodica all’Abisso Col de la Rizza e tinopal CBS-X al Bus de la Genziana (V-TV1000) (la cavità più sviluppata della zona, con circa 5 km di sviluppo per 600 m di profondità). Il monitoraggio è stato eseguito alle sorgenti del Molinetto, Santissima e Gorgazzo, mediante campionatori di acqua automatici (alle sorgenti Molinetto e Gorgazzo) e con un impegnativo programma di prelievi manuali di campioni d’acqua e di fluocaptori (carboni attivi e garze di cotone) in 3-4 punti di ogni sorgente monitorata. Al termine del tracciamento risultavano positive alla fluoresceina sodica le sorgenti Molinetto e Santissima, mentre nessuna delle sorgenti monitorate era positiva al tinopal CBS-X. Le curve di arrivo del tracciante, permettevano il calcolo delle velocità medie di transito in entrambe le sorgenti positive alla fluoresceina sodica, pari a circa: 250 m giorno-1, in fase di magra, e 1100 m giorno-1, in fase di piena.Cansiglio is a limestone plateau with an extent of about 100 km2 and a mean altitude of 1000 m; it is located on the border between two regions (Veneto and Friuli Venezia Giulia) and three provinces (Treviso, Belluno and Pordenone). The hydrogeology of this important karst system is poorly known, despite it probably feeds three important springs located at its south-eastern border (Molinetto, Santissima and Gorgazzo) that form Livenza River. Gruppo Speleologico Ferrarese, in collaboration with other speleological team, explored the deepest cave of Cansiglio: Abisso Col de la Rizza (904/FR410) (about 800 m deep and with 4 km of extent), which provided the opportunity to perform a tracer test. In collaboration with the Earth Sciences Department of Ferrara University, a multi-tracer test was made with two contemporary injections of fluorescent dyes in groundwaters: uranine in Abisso Col de la Rizza and tinopal CBS-X in Bus de la Genziana (V-TV1000) (600 m deep and 5 km of extent). The monitoring at Molinetto, Santissima and Gorgazzo springs was performed by means of automated samplers (at Gorgazzo and Molinetto springs) and an intense discrete sampling survey, which included water samples, charcoal bags and cotton lints collection. Molinetto and Santissima springs resulted positive to uranine, while any springs was positive to tinopal CBS-X. The breakthrough curves make possible the determination of the mean velocity of uranine: about 250 m day-1, during low flow conditions, and 1100 m day-1, after an intense rainfall event

Solute concentration at a well in non-Gaussian aquifers under constant and time-varying pumping schedule

Our study is keyed to the analysis of the interplay between engineering factors (i.e., transient pumping rates versus less realistic but commonly analyzed uniform extraction rates) and the heterogeneous structure of the aquifer (as expressed by the probability distribution characterizing transmissivity) on contaminant transport. We explore the joint influence of diverse (a) groundwater pumping schedules (constant and variable in time) and (b) representations of the stochastic heterogeneous transmissivity (T) field on temporal histories of solute concentrations observed at an extraction well. The stochastic nature of T is rendered by modeling its natural logarithm, Y = ln T, through a typical Gaussian representation and the recently introduced Generalized sub-Gaussian (GSG) model. The latter has the unique property to embed scale-dependent non-Gaussian features of the main statistics of Y and its (spatial) increments, which have been documented in a variety of studies. We rely on numerical Monte Carlo simulations and compute the temporal evolution at the well of low order moments of the solute concentration (C), as well as statistics of the peak concentration (Cp), identified as the environmental performance metric of interest in this study. We show that the pumping schedule strongly affects the pattern of the temporal evolution of the first two statistical moments of C, regardless the nature (Gaussian or non-Gaussian) of the underlying Y field, whereas the latter quantitatively influences their magnitude. Our results show that uncertainty associated with C and Cpestimates is larger when operating under a transient extraction scheme than under the action of a uniform withdrawal schedule. The probability density function (PDF) of Cpdisplays a long positive tail in the presence of time-varying pumping schedule. All these aspects are magnified in the presence of non-Gaussian Y fields. Additionally, the PDF of Cpdisplays a bimodal shape for all types of pumping schemes analyzed, independent of the type of heterogeneity considered

Celecoxib inhibits proliferation and survival of chronic myelogeous leukemia (CML) cells via AMPK-dependent regulation of β-catenin and mTORC1/2.

CML is effectively treated with tyrosine kinase inhibitors (TKIs). However, the efficacy of these drugs is confined to the chronic phase of the disease and development of resistance to TKIs remains a pressing issue. The anti-inflammatory COX2 inhibitor celecoxib has been utilized as anti-tumour drug due to its anti-proliferative activity. However, its effects in hematological malignancies, in particular CML, have not been investigated yet. Thus, we tested biological effects and mechanisms of action of celecoxib in Philadelphia-positive (Ph+) CML and ALL cells.We show here that celecoxib suppresses the growth of Ph+ cell lines by increasing G1-phase and apoptotic cells and reducing S- and G2-phase cells. These effects were independent of COX2 inhibition but required the rapid activation of AMP-activated protein kinase (AMPK) and the consequent inhibition mTORC1 and 2. Treatment with celecoxib also restored GSK3β function and led to down-regulation of β-catenin activity through transcriptional and post-translational mechanisms, two effects likely to contribute to Ph+ cell growth suppression by celecoxib.Celecoxib inhibited colony formation of TKI-resistant Ph+ cell lines including those with the T315I BCR-ABL mutation and acted synergistically with imatinib in suppressing colony formation of TKI-sensitive Ph+ cell lines. Finally, it suppressed colony formation of CD34+ cells from CML patients, while sparing most CD34+ progenitors from healthy donors, and induced apoptosis of primary Ph+ ALL cells.Together, these findings indicate that celecoxib may serve as a COX2-independent lead compound to simultaneously target the mTOR and β-catenin pathways, key players in the resistance of CML stem cells to TKIs

SIOUX project: a simultaneous multiband camera for exoplanet atmospheres studies

The exoplanet revolution is well underway. The last decade has seen order-of-magnitude increases in the number of known planets beyond the Solar system. Detailed characterization of exoplanetary atmospheres provide the best means for distinguishing the makeup of their outer layers, and the only hope for understanding the interplay between initial composition chemistry, temperature-pressure atmospheric profiles, dynamics and circulation. While pioneering work on the observational side has produced the first important detections of atmospheric molecules for the class of transiting exoplanets, important limitations are still present due to the lack of sys- tematic, repeated measurements with optimized instrumentation at both visible (VIS) and near-infrared (NIR) wavelengths. It is thus of fundamental importance to explore quantitatively possible avenues for improvements. In this paper we report initial results of a feasibility study for the prototype of a versatile multi-band imaging system for very high-precision differential photometry that exploits the choice of specifically selected narrow-band filters and novel ideas for the execution of simultaneous VIS and NIR measurements. Starting from the fundamental system requirements driven by the science case at hand, we describe a set of three opto-mechanical solutions for the instrument prototype: 1) a radial distribution of the optical flux using dichroic filters for the wavelength separation and narrow-band filters or liquid crystal filters for the observations; 2) a tree distribution of the optical flux (implying 2 separate foci), with the same technique used for the beam separation and filtering; 3) an exotic solution consisting of the study of a complete optical system (i.e. a brand new telescope) that exploits the chromatic errors of a reflecting surface for directing the different wavelengths at different foci