HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics

Background  

Accurate interpretation of data obtained by unsupervised analysis of large scale expression profiling studies is currently frequently performed by visually combining sample-gene heatmaps and sample characteristics. This method is not optimal for comparing individual samples or groups of samples. Here, we describe an approach to visually integrate the results of unsupervised and supervised cluster analysis using a correlation plot and additional sample metadata.     

Phylogenetic analysis of slippage-like sequence variation in the V4 rRNA expansion segment in tiger beetles (Cicindelidae)

Sequence variation in the middle part of the small-subunit rRNA was studied for representatives of the major groups in the family Cicindelidae (Coleoptera). All taxa exhibited a much expanded segment in variable region V4 compared to D. melanogaster. This expanded segment was not found in other groups of beetles, including three taxa in the closely related Carabidae. Secondary structure predictions indicate that the expanded segment folds into a single stem-loop structure in all taxa. Despite its structural conservation, the fragment differs strongly in primary sequence, even between closely related sister taxa. Several features of these sequences are consistent with slippage replication as the mechanism that has generated this sequence variation: the level of internal sequence repetition as measured by the relative simplicity factor (RSF), its variation in length between close relatives, and the strong nucleotide bias compared to the remainder of the gene. With few exceptions, there was also a correlation between sequence length and the level of sequence repetition, frequently interpreted as the result of slippage. Phylogenies inferred from the expansion segment were not consistent with existing hypotheses from other molecular data for the group. This indicates that DNA sequences in this region are not homologous throughout the entire Cicindelidae, but it leaves open the possibility that this expansion segment can be used for phylogeny reconstruction within subgroups. The implications of a phylogenetic approach to the understanding of slippage-like evolution are discussed.      

Imaging human epithelial properties with polarized light-scattering spectroscopy.

Biomedical imaging with light-scattering spectroscopy (LSS) is a novel optical technology developed to probe the structure of living epithelial cells in situ without need for tissue removal. LSS makes it possible to distinguish between single backscattering from epithelial-cell nuclei and multiply scattered light. The spectrum of the single backscattering component is further analyzed to provide quantitative information about the epithelial-cell nuclei such as nuclear size, degree of pleomorphism, degree of hyperchromasia and amount of chromatin. LSS imaging allows mapping these histological properties over wide areas of epithelial lining. Because nuclear enlargement, pleomorphism and hyperchromasia are principal features of nuclear atypia associated with precancerous and cancerous changes in virtually all epithelia, LSS imaging can be used to detect precancerous lesions in optically accessible organs.     

Electrical activity of the brain during isocapnic hyperventilation with cold air

The influence of hyperventilation on the electrical activity of the brain has conventionally been the subject of study of physiologists. The role of the brain in the adaptation to the inhalation of cold air remains to be understood in more detail. The aim of the study was to determine certain features of the cerebral response to isocapnic hyperventilation with cold air and to reveal the correlation of its electric activity in different modes of ventilation, with the pattern of quiet breathing and the forced expiration parameters. Twenty-one apparently healthy volunteers were subjected to comprehensive functional examination. Qualitative differences in the ?-rhythm relative power were revealed under the conditions of isocapnic hyperventilation with cold air. The specific features of the correlation of the electrical activity of the brain provoked by cold with the breathing pattern and the bronchomotor tone were revealed.     

A model of the mechanism of enzyme action in terms of protein conformational relaxation

A theoretical model of enzymatic reaction is formulated in which the modulation of the reaction coordinates by low-frequency conformational motions of the enzyme molecule causes the lowering of the activation energy barriers until they completely disappear. If the rates of electron transitions in the enzyme-substrate complex exceed the characteristic frequencies of conformational motions then the rate of the elementary enzymatic reaction shows hysteresis dependence on temperature and substrate concentration.