Simultaneous analysis of multiple data types in pharmacogenomic studies using weighted sparse canonical correlation analysis

Variation in drug response results from a combination of factors that include differences in gender, ethnicity, and environment, as well as genetic variation that may result in differences in mRNA and protein expression. This article presents two integrative analytic approaches that make use of both genome-wide SNP and mRNA expression data available on the same set of subjects: a step-wise integrative approach and a comprehensive analysis using sparse canonical correlation analysis (SCCA). In addition to applying standard SCCA, we present a novel modification of SCCA which allows different weighting for the various pair-wise relationships in the SCCA. These integrative approaches are illustrated with both simulated data and data from a pharmacogenomic study of the drug gemcitabine. Results from these analyses found little overlap in terms of genes detected, possibly detecting different biological mechanisms. In addition, we found the proposed weighted SCCA to outperform its unweighted counterpart in detecting associations between the genomic features and phenotype. Further research is needed to develop and assess new integrative methods for pharmacogenomic studies, as these types of analyses may uncover novel insights into the relationship between genomic variation and drug response.     

Automatic segmentation and supervised learning-based selection of nuclei in cancer tissue images

Analysis of preferential localization of certain genes within the cell nuclei is emerging as a new technique for the diagnosis of breast cancer. Quantitation requires accurate segmentation of 100-200 cell nuclei in each tissue section to draw a statistically significant result. Thus, for large-scale analysis, manual processing is too time consuming and subjective. Fortuitously, acquired images generally contain many more nuclei than are needed for analysis. Therefore, we developed an integrated workflow that selects, following automatic segmentation, a subpopulation of accurately delineated nuclei for positioning of fluorescence in situ hybridization-labeled genes of interest. Segmentation was performed by a multistage watershed-based algorithm and screening by an artificial neural network-based pattern recognition engine. The performance of the workflow was quantified in terms of the fraction of automatically selected nuclei that were visually confirmed as well segmented and by the boundary accuracy of the well-segmented nuclei relative to a 2D dynamic programming-based reference segmentation method. Application of the method was demonstrated for discriminating normal and cancerous breast tissue sections based on the differential positioning of the HES5 gene. Automatic results agreed with manual analysis in 11 out of 14 cancers, all four normal cases, and all five noncancerous breast disease cases, thus showing the accuracy and robustness of the proposed approach. ? Published 2012 Wiley Periodicals, Inc.     

Inhibition of thymidine kinase activity by hydroxyurea during highly and less proliferative regions of rat brain

Hydroxyurea, when injected intraperitoneally, exerted marked inhibition on the activity of thymidine kinase in 5 day old postnatal cerebellum and 15 day old embryonic cerebrum. However, it failed to show any sustained inhibition on thymidine kinase activity in 5 day old postnatal cerebrum. In this case, the marginal decrease of thymidine kinase activity noticed during early intervals reversed back to more than normal value at a later time interval. These results along with our earlier findings are taken to indicate the differential action of this drug on thymidine kinase activity in rapidly and slowly proliferating regions of rat brain     

Mobilization and exudation of photo-assimilated14C by developing pods of groundnut (Arachis hypogaea L.)

Summary ‘Pod washings’ were collected from groundnut at three hour intervals for 24 hours after feeding the plants with¹⁴CO₂. Low radioactivity was found in the first four ‘Pod washings’ of 10 day old pods and the radioactivity increased with time. Highest radioactivity was found in washings of 20 and 30 day old pods and was twice the activity found in the washings of 50 day old pods. The radioactivity of both ethanol-soluble and insoluble fractions in pods was determined. The radioactivity mobilized into the pods increased with age and it was highest in 50 day old pods. The influence of the pod exudates on geocarposphere microflora during pod development is discussed.     

Axial dispersion in plate-pulsed columns

The residence time distribution (RTD) of the phase under continuous flow and dispersed flow was measured in a plate-pulsed column under countercurrent liquid-liquid flow, and modelled using (i) the axial dispersion model and (ii) the noninteger ideal stage cascade model. The axial mixing in the continuous phase was found to be significantly higher than in the dispersed phase. The model parameters were related to the operating conditions and system variables.     

Modeling of RNA nanotubes using molecular dynamics simulation

In this study, we construct novel RNA nanoclusters, RNA nanotubes made of several nanorings up to the size of 20 nm, utilizing the molecular dynamics simulation, and study their structural properties [i.e., the root mean square deviation, the radius of gyration and the radial distribution function (RDF)] in physiological solutions that can be used for drug delivery into the human body. The patterns of energy and temperature variations of the systems are also discussed. Furthermore, we study the concentration of ions around the tube as a function of time at a particular temperature. We have found that when the temperature increases, the number of ions increases within a certain distance of the tube. We report that the number of ions within this distance around the tubes decreases in quenched runs. This indicates that some ions evaporate with decrease in temperature, as has been observed in the case of the nanoring. RDF plots also demonstrate a similar trend with temperature, as was found in the case of RNA nanorings.     

Effects of sex hormones on enzymic esterification of 2-(N-hydroxyacetamido)-fluorene by rat liver cytosol

1. Enzymic esterifications of 2-(N-hydroxyacetamido)fluorene and several other hydroxamic acids by liver cytosol were studied. Determination of 2-acetamido-3-methylthiofluorene was used for the assay. 2. With rat liver cytosol, requirement for ATP, Mg²⁺ and SO₄²⁻ suggested formation of phosphate and sulphate esters of 2-(N-hydroxyacetamido)fluorene. 3. Rats showed sex and age differences in their activity. Liver from adult male rat was at least twice as active as liver from adult female rat. No such sex differences were found in mice, hamsters and guinea pigs. 4. Administration of testosterone (300μg/day) subcutaneously for 8 days increased the activity in the female rat by 100%, whereas diethylstilboestrol (100μg/day) had no effect. In the male rat diethylstilboestrol treatment decreased the activity by 60%, whereas testosterone pretreatment was without any effect. 5. Among various endocrine ablations such as adrenalectomy, castration, adrenalectomy–castration and hypophysectomy in the adult male rat, hypophysectomy was found to be the most effective in decreasing the activity of the liver to about 50% of control values. 6. Like 2-(N-hydroxyacetamido)fluorene, various other N-hydroxy derivatives of 2-acetamido-7-fluorofluorene, 2-acetamidophenanthrene, 4-acetamidobiphenyl and 4-acetamidostilbene were also shown to be esterified to different extents by rat liver cytosol.     

Optimization of parameters in the batch kinetic studies of glucose isomerisation by arthrobacter sp.

Vital parameters like temperature, pH and agitation are optimized in the kinetic studies of glucose isomerisation carried out in a batch fashion. A 4-litre fermentor with temperature, pH, agitation and other controls is used. It is found that the two parameters — temperature and pH, do not have an interacting effect on each other. A temperature of 60°C, a pH of 8.0 and a speed of 200 rpm are found to be better suited for the production of fructose syrups starting from glucose by arthrobacter sp. An upper limit of 20 minutes on the residence time is suggested for use in the design of flow reactors.