Copy Number Analysis of 24 Oncogenes: MDM4 Identified as a Putative Marker for Low Recurrence Risk in Non Muscle Invasive Bladder Cancer

Patients with non-muscle invasive bladder cancer (NMIBC) generally have a high risk of relapsing locally after primary tumor resection. The search for new predictive markers of local recurrence thus represents an important goal for the management of this disease. We studied the copy number variations (CNVs) of 24 oncogenes (MDM4, MYCN, ALK, PDGFRA, KIT, KDR, DHFR, EGFR, MET, SMO, FGFR1, MYC, ABL1, RET, CCND1, CCND2, CDK4, MDM2, AURKB, ERBB2, TOP2A, AURKA, AR and BRAF) using multiplex ligation probe amplification technique to verify their role as predictive markers of recurrence. Formalin-fixed paraffin-embedded tissue samples from 43 patients who underwent transurethral resection of the bladder (TURB) were used; 23 patients had relapsed and 20 were disease-free after 5 years. Amplification frequencies were analyzed for all genes and MDM4 was the only gene that showed significantly higher amplification in non recurrent patients than in recurrent ones (0.65 vs. 0.3; Fisher’s test p = 0.023). Recurrence-free survival analysis confirmed the predictive role of MDM4 (log-rank test p = 0.041). Our preliminary results indicate a putative role for the MDM4 gene in predicting local recurrence of bladder cancer. Confirmation of this hypothesis is needed in a larger cohort of NMIBC patients.     

The mineral profile affects the coagulation pattern and cheese-making efficiency of bovine milk

Natural variations in milk minerals, their relationships, and their associations with the coagulation process and cheese-making traits present an opportunity for the differentiation of milk destined for high-quality natural products, such as traditional specialties or Protected Designation of Origin (PDO) cheeses. The aim of this study was to quantify the effects of the native contents of Ca, P, Na, K, and Mg on 18 traits describing traditional milk coagulation properties (MCP), curd firming over time (CF_t) equation parameters, cheese yield (CY) measures, and nutrient recoveries in the curd (REC) using models that either included or omitted the simultaneous effects of milk fat and casein contents. The results showed that, by including milk fat and casein and the minerals in the statistical model, we were able to determine the specific effects of each mineral on coagulation and cheese-making efficiency. In general, about two-thirds of the apparent effects of the minerals on MCP and the CF_t equation parameters are actually mediated by their association with milk composition, especially casein content, whereas only one-third of the effects are direct and independent of milk composition. In the case of cheese-making traits, the effects of the minerals were mediated only negligibly by their association with milk composition. High Ca content had a positive effect on the coagulation pattern and cheese-making traits, favoring water retention in the curd in particular. Phosphorus positively affected the cheese-making traits in that it was associated with an increase in CY in terms of curd solids, and in all the nutrient recovery traits. However, a very high P content in milk was associated with lower fat recovery in the curd. The variation in the Na content in milk only mildly affected coagulation, whereas with regard to cheese-making, protein recovery was negatively associated with high concentrations of this mineral. Potassium seemed not to be actively involved in coagulation and the cheese-making process. Magnesium content tended to slow coagulation and reduce CY measures. Further studies on the relationships of minerals with casein and protein fractions could deepen our knowledge of the role of all minerals in coagulation and the cheese-making process.     

Increasing Cold Tolerance of Cactus Pear Fruit by High-Temperature Conditioning and Film Wrapping

Pre-storage high-temperature conditioning (HTC, 38 °C, and 95% RH for 24 h) and individual film wrapping (IFW) with a perforated polyolefinic heat-shrinkable film were used as individual treatments or in combination to mitigate chilling injury of first crop cactus pear cv ‘Gialla’. The fruit was stored for 21 days at either 2 or 8 °C (CS) plus 1 week of simulated marketing conditions (SMC) at 20 °C. The reduction in peel disorders and decay in HTC-treated fruit stored at 2 °C was comparable to that detected in control fruit stored at 8 °C. IFW was more efficient than HTC in reducing peel disorders, almost completely inhibited weight loss, and preserved freshness in fruit stored at 8 °C as well as in those stored at 8 °C. The internal quality of the fruit (pH, total soluble solids, titratable acidity, vitamin C, polyphenols, betaxanthins, antioxidant capacity, acetaldehyde, and ethanol) was slightly affected by treatments. Combining HTC with IFW did not improve fruit tolerance to low temperature but reduced decay with respect to individual treatments. IFW with a perforated film in combination with HTC is a good means of overcoming the stringent conditions of cold quarantine treatments, maintaining fruit freshness and reducing decay in cold-stored cactus pears.     

Preclinical Development of FA5, a Novel AMP-Activated Protein Kinase (AMPK) Activator as an Innovative Drug for the Management of Bowel Inflammation

Acadesine (ACA), a pharmacological activator of AMP-activated protein kinase (AMPK), showed a promising beneficial effect in a mouse model of colitis, indicating this drug as an alternative tool to manage IBDs. However, ACA displays some pharmacodynamic limitations precluding its therapeutical applications. Our study was aimed at evaluating the in vitro and in vivo effects of FA-5 (a novel direct AMPK activator synthesized in our laboratories) in an experimental model of colitis in rats. A set of experiments evaluated the ability of FA5 to activate AMPK and to compare the efficacy of FA5 with ACA in an experimental model of colitis. The effects of FA-5, ACA, or dexamethasone were tested in rats with 2,4-dinitrobenzenesulfonic acid (DNBS)-induced colitis to assess systemic and tissue inflammatory parameters. In in vitro experiments, FA5 induced phosphorylation, and thus the activation, of AMPK, contextually to the activation of SIRT-1. In vivo, FA5 counteracted the increase in spleen weight, improved the colon length, ameliorated macroscopic damage score, and reduced TNF and MDA tissue levels in DNBS-treated rats. Of note, FA-5 displayed an increased anti-inflammatory efficacy as compared with ACA. The novel AMPK activator FA-5 displays an improved anti-inflammatory efficacy representing a promising pharmacological tool against bowel inflammation.     

More concise representation of regular languages by automata and regular expressions

We consider two formalisms for representing regular languages: constant height pushdown automata and straight line programs for regular expressions. We constructively prove that their sizes are polynomially related. Comparing them with the sizes of finite state automata and regular expressions, we obtain optimal exponential and double exponential gaps, i.e., a more concise representation of regular languages.     

Characterization and catalytic activity of soft-templated NiO-CeO2 mixed oxides for CO and CO2 co-methanation

Nanosized NiO,CeO₂ and NiO-CeO₂ mixed oxides with different Ni/Ce molar ratios were prepared by the soft template method.All the samples were characterized by different techniques as to their chemical composition,structure,morphology and texture.On the catalysts submitted to the same reduction pretreatment adopted for the activity tests the surface basic properties and specific metal surface area were also determined.NiO and CeO₂ nanocrystals of about 4 nm in size were obtained,regardless of the Ni/Ce molar ratio.The Raman and X-ray photoelectron spectroscopy results proved the formation of defective sites at the NiO-CeO₂ interface,where Ni species are in strong interaction with the support.The microcalorimetric and Fourier transform infrared analyses of the reduced samples highlighted that,unlike metallic nickel,CeO₂ is able to effectively adsorb CO₂,forming carbonates and hydrogen carbonates.After reduction in H2 at 400°C for 1 h,the catalytic performance was studied in the CO and CO₂ co-methanation reaction.Catalytic tests were performed at atmospheric pressure and 300°C,using CO/CO₂/H₂ molar compositions of 1/1/7 or 1/1/5,and space velocities equal to 72000 or 450000 cm³?h^-1?gcat^-1.Whereas CO was almost completely hydrogenated in any investigated experimental conditions,CO₂ conversion was strongly affected by both the CO/CO₂/H₂ ratio and the space velocity.The faster and definitely preferred CO hydrogenation was explained in the light of the different mechanisms of CO and CO₂ methanation.On a selected sample,the influence of the reaction temperature and of a higher number of space velocity values,as well as the stability,were also studied.Provided that the Ni content is optimized,the NiCe system investigated was very promising,being highly active for the CO_x co-methanation reaction in a wide range of operating conditions and stable(up to 50 h)also when submitted to thermal stress.     

Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications

Nanoscale biosensors, a highly promising technique in clinical analysis, can provide sensitive yet label-free detection of biomolecules. The spatial and chemical specificity of the surface coverage, the proper immobilization of the bioreceptor as well as the underlying interfacial phenomena are crucial elements for optimizing the performance of a biosensor. Due to experimental limitations at the microscopic level, integrated cross-disciplinary approaches that combine in silico design with experimental measurements have the potential to present a powerful new paradigm that tackles the issue of developing novel biosensors. In some cases, computational studies can be seen as alternative approaches to assess the microscopic working mechanisms of biosensors. Nonetheless, the complex architecture of a biosensor, associated with the collective contribution from “substrate–receptor–analyte” conjugate in a solvent, often requires extensive atomistic simulations and systems of prohibitive size which need to be addressed. In silico studies of functionalized surfaces also require ad hoc force field parameterization, as existing force fields for biomolecules are usually unable to correctly describe the biomolecule/surface interface. Thus, the computational studies in this field are limited to date. In this review, we aim to introduce fundamental principles that govern the absorption of biomolecules onto functionalized nanomaterials and to report state-of-the-art computational strategies to rationally design nanoscale biosensors. A detailed account of available in silico strategies used to drive and/or optimize the synthesis of functionalized nanomaterials for biosensing will be presented. The insights will not only stimulate the field to rationally design functionalized nanomaterials with improved biosensing performance but also foster research on the required functionalization to improve biomolecule–surface complex formation as a whole.