A meteo-hydrological prediction system based on a multi-model approach for precipitation forecasting

International audienceThe precipitation forecasted by a numerical weather prediction model, even at high resolution, suffers from errors which can be considerable at the scales of interest for hydrological purposes. In the present study, a fraction of the uncertainty related to meteorological prediction is taken into account by implementing a multi-model forecasting approach, aimed at providing multiple precipitation scenarios driving the same hydrological model. Therefore, the estimation of that uncertainty associated with the quantitative precipitation forecast (QPF), conveyed by the multi-model ensemble, can be exploited by the hydrological model, propagating the error into the hydrological forecast. The proposed meteo-hydrological forecasting system is implemented and tested in a real-time configuration for several episodes of intense precipitation affecting the Reno river basin, a medium-sized basin located in northern Italy (Apennines). These episodes are associated with flood events of different intensity and are representative of different meteorological configurations responsible for severe weather affecting northern Apennines. The simulation results show that the coupled system is promising in the prediction of discharge peaks (both in terms of amount and timing) for warning purposes. The ensemble hydrological forecasts provide a range of possible flood scenarios that proved to be useful for the support of civil protection authorities in their decision

Peptide Nucleic Acids as miRNA Target Protectors for the Treatment of Cystic Fibrosis

Cystic Fibrosis (CF) is one of the most common life shortening conditions in Caucasians. CF is caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene which result in reduced or altered CFTR functionality. Several microRNAs (miRNAs) downregulate the expression of CFTR, thus causing or exacerbating the symptoms of CF. In this context, the design of anti-miRNA agents represents a valid functional tool, but its translation to the clinic might lead to unpredictable side effects because of the interference with the expression of other genes regulated by the same miRNAs. Herein, for the first time, is proposed the use of peptide nucleic acids (PNAs) to protect specific sequences in the 3'UTR (untranslated region) of the CFTR messenger RNA (mRNA) by action of miRNAs. Two PNAs (7 and 13 bases long) carrying the tetrapeptide Gly-SerP-SerP-Gly at their C-end, fully complementary to the 3'UTR sequence recognized by miR-509-3p, have been synthesized and the structural features of target PNA/RNA heteroduplexes have been investigated by spectroscopic and molecular dynamics studies. The co-transfection of the pLuc-CFTR-3´UTR vector with different combinations of PNAs, miR-509-3p, and controls in A549 cells demonstrated the ability of the longer PNA to rescue the luciferase activity by up to 70% of the control, thus supporting the use of suitable PNAs to counteract the reduction in the CFTR expression

Teaching for conceptual change and conceptual discrimination with year 8 science students: An exploratory study of the topic \u27respiration\u27

Research has shown that despite formal education, secondary and tertiary students hold a host of misconceptions about respiration. This exploratory study investigated whether a four phase conceptual change teaching strategy could overcome conceptual problems typically associated with respiration, in a Year 8 science class from a school in Perth, Western Australia. The strategy consisted of a Conceptual Awareness Phase, an Exposition Phase, a Misconception Awareness Phase and an Application Phase. Two-tier multiple choice test items used in previous studies to identify misconceptions about respiration were also used in this study, together with interviews. The encouraging results suggest that the implemented conceptual change strategy was successful in developing in Year 8 students an acceptable scientific conception of respiration, and an awareness that the term \u27respiration\u27 is used differently by the lay, medical and scientific communities. The strategy was also found to be successful in reducing the incidence of misconceptions typically associated with respiration. Implications and recommendations for educators, textbook authors and curriculum writers, and the need for future research are discussed

Receptor tyrosine kinase-dependent PI3K activation is an escape mechanism to vertical suppression of the EGFR/RAS/MAPK pathway in KRAS-mutated human colorectal cancer cell lines

Abstract BACKGROUND: Previous studies showed that the combination of an anti-Epidermal growth factor (EGFR) and a MEK-inhibitor is able to prevent the onset of resistance to anti-EGFR monoclonal antibodies in KRAS-wild type colorectal cancer (CRC), while the same combination reverts anti-EGFR primary resistance in KRAS mutated CRC cell lines. However, rapid onset of resistance is a limit to combination therapies in KRAS mutated CRC. METHODS: We generated four different KRAS mutated CRC cell lines resistant to a combination of cetuximab (an anti-EGFR antibody) and refametinib (a selective MEK-inhibitor) after continuous exposure to increasing concentration of the drugs. We characterized these resistant cell lines by evaluating the expression and activation status of a panel of receptor tyrosine kinases (RTKs) and intracellular transducers by immunoblot and qRT-PCR. Oncomine comprehensive assay and microarray analysis were carried out to investigate new acquired mutations or transcriptomic adaptation, respectively, in the resistant cell lines. Immunofluorescence assay was used to show the localization of RTKs in resistant and parental clones. RESULTS: We found that PI3K-AKT pathway activation acts as an escape mechanism in cell lines with acquired resistance to combined inhibition of EGFR and MEK. AKT pathway activation is coupled to the activation of multiple RTKs such as HER2, HER3 and IGF1R, though its pharmacological inhibition is not sufficient to revert the resistant phenotype. PI3K pathway activation is mediated by autocrine loops and by heterodimerization of multiple receptors. CONCLUSIONS: PI3K activation plays a central role in the acquired resistance to the combination of anti-EGFR and MEK-inhibitor in KRAS mutated colorectal cancer cell lines. PI3K activation is cooperatively achieved through the activation of multiple RTKs such as HER2, HER3 and IGF1R

Challenges of drug resistance in the management of pancreatic cancer

The current treatment of choice for metastatic pancreatic cancer involves single agent gemcitabine or combination of gemcitabine with capecitabine and erlotinib (tyrosine kinase inhibitor). Only 25-30% of patients respond to this treatment and patients who do respond initially ultimately exhibit disease progression. Median survival for pancreatic cancer patients has reached a plateau due to inherent and acquired resistance to these agents. Key molecular factors implicated in this resistance include: deficiencies in drug uptake, alteration of drug targets, activations of DNA repair pathways, resistance to apoptosis, and the contribution of the tumor microenvironment. Moreover, for newer agents including tyrosine kinase inhibitors, over expression of signaling proteins, mutations in kinase domains, activation of alternative pathways, mutations of genes downstream of the target, and/or amplification of the target represent key challenges for treatment efficacy. Here we will review the contribution of known mechanisms and markers of resistance to key pancreatic cancer drug treatments

Structural Model of the hUbA1-UbcH10 Quaternary Complex: In Silico and Experimental Analysis of the Protein-Protein Interactions between E1, E2 and Ubiquitin

UbcH10 is a component of the Ubiquitin Conjugation Enzymes (Ubc; E2) involved in the ubiquitination cascade controlling the cell cycle progression, whereby ubiquitin, activated by E1, is transferred through E2 to the target protein with the involvement of E3 enzymes. In this work we propose the first three dimensional model of the tetrameric complex formed by the human UbA1 (E1), two ubiquitin molecules and UbcH10 (E2), leading to the transthiolation reaction. The 3D model was built up by using an experimentally guided incremental docking strategy that combined homology modeling, protein-protein docking and refinement by means of molecular dynamics simulations. The structural features of the in silico model allowed us to identify the regions that mediate the recognition between the interacting proteins, revealing the active role of the ubiquitin crosslinked to E1 in the complex formation. Finally, the role of these regions involved in the E1–E2 binding was validated by designing short peptides that specifically interfere with the binding of UbcH10, thus supporting the reliability of the proposed model and representing valuable scaffolds for the design of peptidomimetic compounds that can bind selectively to Ubcs and inhibit the ubiquitylation process in pathological disorders

AXL is an oncotarget in human colorectal cancer

AXL is a tyrosine kinase receptor activated by GAS6 and regulates cancer cell proliferation migration and angiogenesis. We studied AXL as new therapeutic target in colorectal cancer (CRC). Expression and activation of AXL and GAS6 were evaluated in a panel of human CRC cell lines. AXL gene silencing or pharmacologic inhibition with foretinib suppressed proliferation, migration and survival in CRC cells. In an orthotopic colon model of human HCT116 CRC cells overexpressing AXL, foretinib treatment caused significant inhibition of tumour growth and peritoneal metastatic spreading. AXL and GAS6 overexpression by immunohistochemistry (IHC) were found in 76,7% and 73.5%, respectively, of 223 human CRC specimens, correlating with less differentiated histological grading. GAS6 overexpression was associated with nodes involvement and tumour stage. AXL gene was found amplified by Fluorescence in situ hybridization (FISH) in 8/146 cases (5,4%) of CRC samples. Taken together, AXL inhibition could represent a novel therapeutic approach in CRC

Detecting Markovianity of Quantum Processes via Recurrent Neural Networks

We present a novel methodology utilizing Recurrent Neural Networks (RNNs) to classify Markovian and non-Markovian quantum processes, leveraging time series data derived from Choi states. The model exhibits exceptional accuracy, surpassing 95%, across diverse scenarios, encompassing dephasing and Pauli channels in an arbitrary basis, and generalized amplitude damping dynamics. Additionally, the developed model shows efficient forecasting capabilities for the analyzed time series data. These results suggest the potential of RNNs in discerning and predicting the Markovian nature of quantum processes

Spectral Gap Superposition States

This work introduces a novel NISQ-friendly procedure for estimating spectral gaps in quantum systems. By leveraging Adiabatic Thermalization, we are able to create the Spectral Gap Superposition state, a newly defined quantum state exhibiting observable fluctuations in time that allow for the accurate estimation of any energy gap. Our method is tested by estimating the energy gap between the ground and the first excited state for the 1D and 2D Ising model, the Hydrogen molecule H2 and Helium molecule He2. Despite limiting our circuit design to have at most 40 Trotter steps, our numerical experiments of both noiseless and noisy devices for the presented systems give relative errors in the order of $10^{-2}$ and $10^{-1}$. Further experiments on the IonQ Aria device lead to spectral gap estimations with a relative error of $10^{-2}$ for a 4-site Ising chain, demonstrating the validity of the procedure for NISQ devices and charting a path towards a new way of calculating energy gaps

Computational methods applied to drug discovery: the rational design of dual inhibitors of FAAH and COX

The search for effective and safe drugs in pain-relief treatment represents a great challenge for medicinal chemists. Lipid derived mediators, such as endocannabinoids, may have different roles as agonists of cannabinoid receptors, relieving pain, or as substrates of cyclooxygenase (COX), generating the pro-inflammatory prostamides. Moreover, the tissue-protective endocannabinoid anandamide is metabolised by fatty acid amide hydrolase (FAAH). Therefore, a new challenging approach in pain-relief might be the development of dual action FAAH/COX inhibitors. The purpose of this thesis is to apply computational methods in drug discovery to assist medicinal chemistry studies targeting the rational design of novel FAAH/COX inhibitors, and to exploit structural studies relative to two side projects on other biological targets. The wider project of this thesis explores the mechanism of action and the rational design of novel FAAH/COX dual inhibitors. The reversible mixed type inhibitors Flu-AM1 and Ibu-AM5, derivatives of flurbiprofen and ibuprofen, respectively, retain similar COX inhibitory properties and are more potent FAAH inhibitors than the parent compounds. Applying a combination of molecular docking, MD simulations and free energy evaluation of the ligand-receptor complex, the binding mode of the enantiomer forms of Flu-AM1 and Ibu-AM5 has been found in the substrate access channel of FAAH and has been supported by studies of site-directed mutagenesis. The substitution of the isobutyl group of Ibu-AM5 with 4-(2-(trifluoromethyl)pyridin-4-yl)amino group led to the design of TPA5 derivative, which showed an inhibitory activity (IC50 = 0.59 μM) similar to the lead compound (Ibu-AM5, IC50 = 0.52 μM). Kinetic studies of TPA5 revealed that it is a pure competitive inhibitor of rat FAAH and molecular modeling studies supported a binding mode that overlap the anandamide analog MAFP. Among TPA5 derivatives, compound TPA27 exhibited a 10-fold enhancement in the inhibitory profile against FAAH (IC50 = 0.058 μM). Thermodynamic Integration calculations performed to complete the transformation of TPA5 in TPA27 yielded a free energy difference of 0.3 kcal/mol, which indicates a slight lower affinity of TPA27 with respect to TPA5, in the competitive binding site. Kinetics studies showed that TPA27 could be considered the first non-competitive reversible FAAH inhibitor reported so far, and that it more likely binds to an allosteric site. Differences in the inhibitory potency against rat and mouse FAAH for all compounds studied suggested different aminoacid composition of both competitive and non-competitive binding sites. This information was used as criteria of selection for a putative allosteric site found between the cytosolic port and the interface of the FAAH monomers. Computational studies in the allosteric site allowed the definition of the binding mode of Ibu-AM5 and TPA27. Nevertheless, a series of derivatives of Ibu-AM5 and Flu-AM1 were designed in order to get more information on the structure-activity relationships, leading to the identification of novel derivatives with improved activity against FAAH (Ibu-AM56, IC50 = 0.08 μM; Ibu-AM57, IC50 = 0.1 μM; Flu-AM3, IC50 = 0.02 μM. Finally, the thesis also reports the results of two other projects: i) the design of potential anticancer peptides that interfere in the formation of the tetrameric complex hUbA1/UbcH10/Ub2, key intermediate of the ubiquitination cascade.; ii) structural studies on the hybridization of PNA of different length with miR-509-3p, involved in regulating the expression of the CFTR gene, as a way to validate a potential new strategy for the treatment of Cystic Fibrosis