Unveiling the tartrazine binding mode with ds-DNA by UV-visible spectroscopy, electrochemical, and QM/MM methods.

Here, we studied the interaction between the food colorant tartrazine (TZ) and double stranded DNA (dsDNA), using spectroscopic, electrochemical, and computational methods such as QM/MM combined with TD-DFT. Despite the UV-vis spectroscopy is widely used to study the interaction between molecules, for the case of TZ there are discrepancies in the analyses presented in the literature available, presenting both hyperchromic and hypochromic effects and consequently different rationalizations for their results. Herein we propose the combination of UV-vis experiments with the design of high-level computational models capable of reproducing the experimental behavior to finally define the proper binding mode at the molecular scale together with the rationalization of the experimental optical response due to the complex formation. To complement the UV-vis experiments, we propose the use of electrochemical measurements, to support the results obtained through UV-vis spectroscopy, as it has been successfully used for the determination of interaction modes between small molecules and biomolecules in any condition. Our UV-vis spectroscopy experiments showed only a hypochromic effect of the absorption spectra of TZ after interaction with DNA, indicative of TZ being deeply buried in the DNA structure. The effect of ionic strength in the experimental procedures led to the dissociation of TZ, thus indicating that the interaction mode was groove binding. On the other hand, the electrochemical studies showed an irreversible reduction peak of TZ, which after the interaction with DNA exhibited a positive shift in potential that can be attributed to groove binding. The binding constant for TZ-DNA was calculated as 4.45x104M-1 (UV-vis) and 5.75x104M-1 (electrochemistry), in line with other groove binder azo dyes. Finally, through the QM/MM calculations we found that the minor-groove binding mode interacting in zones rich in adenine and thymine was the model best suited to reproduce the experimental UV-vis response.

Using variable precision rough set for selection and classification of biological knowledge integrated in DNA gene expression.

DNA microarrays have contributed to the exponential growth of genomic and experimental data in the last decade. This large amount of gene expression data has been used by researchers seeking diagnosis of diseases like cancer using machine learning methods. In turn, explicit biological knowledge about gene functions has also grown tremendously over the last decade. This work integrates explicit biological knowledge, provided as gene sets, into the classication process by means of Variable Precision Rough Set Theory (VPRS). The proposed model is able to highlight which part of the provided biological knowledge has been important for classification. This paper presents a novel model for microarray data classification which is able to incorporate prior biological knowledge in the form of gene sets. Based on this knowledge, we transform the input microarray data into supergenes, and then we apply rough set theory to select the most promising supergenes and to derive a set of easy interpretable classification rules. The proposed model is evaluated over three breast cancer microarrays datasets obtaining successful results compared to classical classification techniques. The experimental results shows that there are not significant differences between our model and classical techniques but it is able to provide a biological-interpretable explanation of how it classifies new samples.

Effect of substitution of sugarbeet pulp for barley in diets for finishing rabbits on growth performance and on energy and nitrogen efficiency.

One hundred forty New Zealand White x California weanling rabbits were used to study the influence of increasing dietary contents of digestible fiber replacing nonstructural carbohydrates on feed efficiency and growth performance. Four diets, formulated by replacing sugarbeet pulp (SBP) for barley grain, and two slaughter weights (2 or 2.5 kg) were used in a 4 x 2 factorial arrangement. Inclusion of 15% SBP decreased dietary energy and CP digestibilities by 6% (P < .001), but nonsignificant effects were found on growth performance, empty body composition, and DE and digestible CP efficiencies for growth. Higher levels of SBP (35 and 50%) led to leaner animals and did not affect DE intake but greatly impaired (P < .001) DE and nitrogen efficiencies, NEg intake, growth rate, and dressing percentage in relation to the control diet. Inclusion of SBP increased the weight of gut contents (P < .001) and decreased cecal pH (P < .001), with no significant effect on mortality. Slaughter weight did not affect growth rate or energy efficiency but impaired (by 13%, P < .001) feed conversion rate. Higher (P < .001) energy content in live weight gain (12.5%) and dressing percentage (3.2%) were observed for rabbits slaughtered at 2.5 kg than for those slaughtered at 2 kg. Our data indicate that SBP can replace 15% of barley grain without decreasing growth performance, although energy and nitrogen efficiencies were impaired by 5%.

Effect of diet on chemical composition of rabbits slaughtered at fixed body weights.

Four hundred and thirty-two Spanish Giant rabbits were fed 12 diets of variable energy to protein ratio [kcal digestible energy (DE)/g digestible crude protein (DCP)] from weaning to slaughter, both at different ages and weights. Body composition analysis for various chemical components indicated that body weight accounted for the greatest part of the variation in these constituents. Sex influenced only the N content (P less than .05). Dietary E/P accounted for greater variability in body composition than crude protein or crude fiber content of the diet. High dietary E/P increased (P less than .001) the proportion of body fat and reduced the proportion of body protein. This effect was made more obvious by adjustment to equal rate of weight gain and it showed that there may be a greater influence of dietary E/P on body composition than previously recognized.