KRAS Promoter G-Quadruplexes from Sequences of Different Length: A Physicochemical Study

DNA G-quadruplexes (G4s) form in relevant genomic regions and intervene in several biological processes, including the modulation of oncogenes expression, and are potential anticancer drug targets. The human KRAS proto-oncogene promoter region contains guanine-rich sequences able to fold into G4 structures. Here, by using circular dichroism and differential scanning calorimetry as complementary physicochemical methodologies, we compared the thermodynamic stability of the G4s formed by a shorter and a longer version of the KRAS promoter sequence, namely 5′-AGGGCGGTGTGGGAATAGGGAA-3′ (KRAS 22RT) and 5′-AGGGCGGTGTGGGAAGAGGGAAGAGGGGGAGG-3′ (KRAS 32R). Our results show that the unfolding mechanism of KRAS 32R is more complex than that of KRAS 22RT. The different thermodynamic stability is discussed based on the recently determined NMR structures. The binding properties of TMPyP4 and BRACO-19, two well-known G4-targeting anticancer compounds, to the KRAS G4s were also investigated. The present physicochemical study aims to help in choosing the best G4 target for potential anticancer drugs.     

A novel mathematical formulation for solving the dynamic and discrete berth allocation problem by using the Bee Colony Optimisation algorithm

Applied Intelligence - Berth allocation is one of the crucial points for efficient management of ports. This problem is complex due to all possible combinations for assigning ships to available...     

Pharmacokinetics and Pharmacodynamics of Anthocyanins after Administration of Tart Cherry Juice to Individuals with Gout

Scope

Tart cherries (TCs) contain high levels of anthocyanins that exert potent antioxidant and antiinflammatory effects and potentially benefit individuals with gout.

Methods and results

This study aims to quantitate the major anthocyanins in TC Juice Concentrate (TCJC) and identify the pharmacokinetic (PK) and pharmacodynamic (PD) parameters of the major anthocyanin cyanidin-3-glucosylrutinoside (C3GR). A PK-PD study enrolling human subjects with a history of gout is performed. Subjects are randomized to receive either 60 or 120 mL of TCJC. Anthocyanins are quantitated using liquid chromatography-mass spectroscopy (LCMS). Antioxidant and antiinflammatory mRNA expression is measured using real-time qPCR before and after the administration of TCJC. A population PK model (popPK) is fit to the experimental data, and an indirect PD model (IDR) is constructed in Monolix.

Conclusion

Of the bioavailable anthocyanins, C3GR achieves the highest plasma concentration in a dose-dependent manner. A popPK predicts anthocyanin exposure, and an IDR produces reasonable approximations of PD effects.     

A trajectory-based algorithm to determine and refine Euler angles of projections in three-dimensional microscopy. Improvements and tests

An improvement of the trajectory matching algorithm is presented, which is based on the use of the derivative of trajectories and of the projection of experimental sinogram lines in the factor space determined by sinogram lines of projections of a model. The algorithm performance is illustrated by use of different phantom structures, to show the effect of symmetry on trajectory matching. A GroEL complex has also been reconstructed from both cryo-negatively stained and unstained frozen-hydrated samples. The refinement of this structure has been carried out by the trajectory matching algorithm as well as by conventional cross-correlation methods. Slight differences among the two results are discussed. The improved trajectory matching algorithm, based on chi2 distances, runs much faster than correlation analysis and looks satisfactory as for the quality of the reconstructed structures.     

An update procedure for an effective and simultaneous extraction of sesquiterpene lactones and phenolics from chicory

A new method for recovering and purifying sesquiterpene lactones (SLs) and optimise the solvent system for their extraction from freeze-dried chicory leaves was studied. Catalogna (leafy chicory) and Head Radicchio types were used as test samples. Solid phase extraction (SPE) employing silica-based cartridges allowed a fast and straightforward purification of SL from interfering phenolics, before HPLC determination. Under these conditions, SL were eluted during loading and washing steps whereas polar phenolic compounds were retained on silica stationary phase. Hydrophilic mixtures methanol/water acidified by small percentages of formic acid led to consistently higher SL recoveries in comparison to organic solvents and enabled the simultaneous extraction of phenolics. Phenolic recovery in crude extracts was assessed at levels higher than 95% for both Catalogna and Head Radicchio. Total, free and bound SL amounts detected in extract obtained by 2% (v/v) formic acid in methanol/water 4/1 (v/v) were 2223.4, 778.5 and 1444.9 mg/kg of dried product in Catalogna, and 401.2, 105.1 and 296.0 in Head Radicchio. In both cases, recoveries were consistently higher than those obtained with methanol alone.     

Characterization of the major whey proteins from milk of Mediterranean water buffalo (Bubalus bubalis)

In this work, the whey protein fractions from 120 Mediterranean water buffalo individual milks were analysed by microchip electrophoresis (MCE), reverse-phase high-performance liquid chromatography (RP-HPLC) and mass spectrometry (ESI-MS). Validation procedures were carried out for both MCE and HPLC. The chromatographic analysis allowed the complete separation of the whey protein fractions, resulting in a well-defined peak structure; the adopted RP-HPLC and ESI-MS protocols provided identification of β-lactoglobulin (18,266 Da), α-lactoalbumin (14,236 Da) and serum albumin (66,397 Da). The calculated mean concentrations were 4.04 g/l, 2.45 g/l and 0.35 g/l, respectively.     

Volatile compounds and compositional quality of virgin olive oil from Oueslati variety: Influence of geographical origin

Headspace solid-phase microextraction (HS-SPME) was applied to the analysis of volatile compounds of virgin olive oils from Oueslati variety cultivated in different geographical areas. Thus, olives at the same stage of maturation were harvested from seven regions in the Centre and the South of the country for oil extraction and analysis. Twenty-seven compounds were characterised by GC-FID and GC–MS. Compounds belonging mainly to alcohols, esters, aldehydes, ketones and hydrocarbons chemical classes characterised the volatile profiles. Significant differences in the proportion of volatiles from oils of different geographical origins were detected. The results suggest that, besides genetic factors, environmental conditions influence volatile formation.