Quality Assessment and Data Analysis for microRNA Expression Arrays

MicroRNAs are small (~22 nt) RNAs that regulate gene expression and play important roles in both normal and disease physiology. The use of microarrays for global characterization of microRNA expression is becoming increasingly popular and has the potential to be a widely used and valuable research tool. However, microarray profiling of microRNA expression raises a number of data analytic challenges that must be addressed in order to obtain reliable results. We introduce here a universal reference microRNA reagent set as well as a series of nonhuman spiked-in synthetic microRNA controls, and demonstrate their use for quality control and between-array normalization of microRNA expression data. We also introduce diagnostic plots designed to assess and compare various normalization methods. We anticipate that the reagents and analytic approach presented here will be useful for improving the reliability of microRNA microarray experiments.     

Generalized binding phenomena in an allosteric macromolecule

A general macromolecular partition function is developed in terms of chemical ligand activity, temperature and pressure for systems described by an array of species which are characterized by their state of allosteric conformation and ligand stoichiometry. The effects of chemical ligand binding, enthalpy change, and volume change are treated in a parallel manner. From a broad viewpoint all of these effects can be regarded as specific cases of generalized binding phenomena. This approach provides a general method for analyzing calorimetric and ligand binding experiments. Several applications are given: (1) Thermal scanning data for tRNAphe (P.L. Privalov and V.V. Filimonov, J. Mol. Biol. 122 (1978) 447) are shown to fit a general model with six conformational states. By application of linkage theory it is shown that sodium chloride is expelled as the molecule denatures. (2) The results of calorimetric titrations on the arabinose binding protein (H. Fukada, J.M. Sturtevant and F.A. Quiocho, J. Mol. Biol. 258 (1983) 13193) are shown to fit a simple two-state allosteric model. (3) A thermal binding curve is simulated for an unusual respiratory protein, trout I hemoglobin (B.G. Barisas and S.J. Gill, Biophys. Chem. 9 (1979) 235), in order to illustrate both the similarities and differences between enthalpy and chemical ligand binding processes.     

Antitumour activities of levans produced by Zymomonas mobilis strains

Levans produced by four Zymomonas mobilis strains showed antitumour activity against sarcoma 180 and Ehrlich carcinoma in Swiss albino mice. Levans from two strains (ZAP and CP4) had the highest effects. NMR analysis showed that the polymers were composed only of fructose units. The results suggested that the antineoplasic effect is associated to the polysaccharide molecular weight and that a particular molecular weight range may be responsible for this effect.     

Nuclear DNA content variation in seeds from 22 half-sib families of jack pine (Pinus banksiana,Pinaceae)

In order to understand the amount of DNA content variation and its potential roles, both absolute DNA amount and cell cycle phases in 22 half-sib families of jack pine were examined using flow cytometry. When the variability due to differences in speed of germination was taken into account, embryos from superior families (classified on the basis of height growth during field trials) had significantly higher levels of all nuclei classes greater than 4C. Mean DNA contents per nucleus were significantly lower in embryos from superior families compared to inferior ones. Analysis of megagametophyte tissue showed that the mother trees of these embryos expressed a similar pattern. Absolute DNA values were also established on the emerging radicle and the hypocotyl + cotyledons region (HC) separately in five of the families. Nuclei isolated from the emerging radicles had significantly lower levels of DNA than those isolated from the HC region. For three of these families, absolute DNA values from nuclei of the hypocotyl + cotyledons region were established on individual embryos with varying cotyledon numbers. In all three families total DNA amount per nucleus decreased with increasing cotyledon number. A better understanding of differences observed in DNA content during germination, as well as in total DNA content per nuclei among different half-sib families of jack pine, may help in the identification of factors that influence growth and adaptation of this species.