Leaving out control groups: an internal contrast analysis of gene expression profiles in atrial fibrillation patients--a systems biology approach to clinical categorization.

Atrial fibrillation (AF) is a frequent chronic dysrythmia with an incidence that increases with age (>40). Because of its medical and socio-economic impacts it is expected to become an increasing burden on most health care systems. AF is a multi-factorial disease for which the identification of subtypes is warranted. Novel approaches based on the broad concepts of systems biology may overcome the blurred notion of normal and pathological phenotype, which is inherent to high throughput molecular arrays analysis. Here we apply an internal contrast algorithm on AF patient data with an analytical focus on potential entry pathways into the disease. We used a RMA (Robust Multichip Average) normalized Affymetrix micro-array data set from 10 AF patients (geo_accession #GSE2240). Four series of probes were selected based on physiopathogenic links with AF entryways: apoptosis (remodeling), MAP kinase (cell remodeling), OXPHOS (ability to sustain hemodynamic workload) and glycolysis (ischemia). Annotated probe lists were polled with Bioconductor packages in R (version 2.7.1). Genetic profile contrasts were analysed with hierarchical clustering and principal component analysis. The analysis revealed distinct patient groups for all probe sets. A substantial part (54% till 67%) of the variance is explained in the first 2 principal components. Genes in PC1/2 with high discriminatory value were selected and analyzed in detail. We aim for reliable molecular stratification of AF. We show that stratification is possible based on physiologically relevant gene sets. Genes with high contrast value are likely to give pathophysiological insight into permanent AF subtypes.

Biomarker discovery with SELDI-TOF MS in human urine associated with early renal injury: evaluation with computational analytical tools.

BACKGROUND: Urine proteomics is one of the key emerging technologies to discover new biomarkers for renal disease, which may be used in the early diagnosis, prognosis and treatment of patients. In the present study, we validated surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) for biomarker discovery in patients with mild ischaemic kidney injury. METHODS: We used first-morning mid-stream urine samples from healthy volunteers, and from intensive care unit patients we collected urine 12-24 h after coronary artery bypass graft (CABG) surgery. Samples of 50 volunteers were mixed to establish a reference sample (master pool). Urine samples were analysed with constant creatinine levels. RESULTS: The average intra- and interchip variation was found to be in the normal experimental range (CV of 10 to 30%). Computational analysis revealed (i) low intra-individual day-to-day variation in individual healthy volunteers; (ii) high concordance between the master pool sample and individual samples. Machine learning techniques for classification of CABG condition vs healthy patients showed that (iii) in the 3-20 kDa range, the joint activity of four protein peaks effectively discriminated the two classes, (iv) in the 20-70 kDa range, a single m/z marker was sufficient to achieve perfect separation. CONCLUSIONS: Our results substantiate the effectiveness of Seldi-TOF MS-based computational analysis as a tool for discovering potential biomarkers in urine samples associated with early renal injury.

Visual pigment spectra of the comma butterfly, Polygonia c-album, derived from in vivo epi-illumination microspectrophotometry.

The visual pigments in the compound eye of the comma butterfly, Polygonia c-album, were investigated in a specially designed epi-illumination microspectrophotometer. Absorption changes due to photochemical conversions of the visual pigments, or due to light-independent visual pigment decay and regeneration, were studied by measuring the eye shine, i.e., the light reflected from the tapetum located in each ommatidium proximal to the visual pigment-bearing rhabdom. The obtained absorbance difference spectra demonstrated the dominant presence of a green visual pigment. The rhodopsin and its metarhodopsin have absorption peak wavelengths at 532 nm and 492 nm, respectively. The metarhodopsin is removed from the rhabdom with a time constant of 15 min and the rhodopsin is regenerated with a time constant of 59 min (room temperature). A UV rhodopsin with metarhodopsin absorbing maximally at 467 nm was revealed, and evidence for a blue rhodopsin was obtained indirectly.

Analyzing the reflections from single ommatidia in the butterfly compound eye with Voronoi diagrams.

This paper presents a robust method for the automated segmentation and quantitative measurement of reflections from single ommatidia in the butterfly compound eye. Digital pictures of the butterfly eye shine recorded with a digital camera are processed to yield binary images from which single facet centers can be extracted using a morphological image analysis procedure. The location of the facet centers is corrected by fitting in-line facet centers to a second-order polynomial. Based on the new centers a Voronoi diagram is constructed. In the case of the eye shine images, the Voronoi diagram defines a hexagonal lattice that overlaps with the original facet borders, allowing instantaneous quantification of the reflections from single ommatidia. We provide two typical examples to demonstrate that the developed technique may be a powerful tool to characterize in vivo the heterogeneity of butterfly eyes and to study the dynamic control of the light flux by the pupil mechanism.

Ommatidial heterogeneity in the compound eye of the male small white butterfly, Pieris rapae crucivora.

The ommatidia in the ventral two-thirds of the compound eye of male Pieris rapae crucivora are not uniform. Each ommatidium contains nine photoreceptor cells. Four cells (R1-4) form the distal two-thirds of the rhabdom, four cells (R5-8) approximately occupy the proximal one-third of the rhabdom, and the ninth cell (R9) takes up a minor basal part of the rhabdom. The R5-8 photoreceptor cells contain clusters of reddish pigment adjacent to the rhabdom. From the position of the pigment clusters, three types of ommatidia can be identified: the trapezoidal (type I), square (type II), and rectangular type (type III). Microspectrophotometry with an epi-illumination microscope has revealed that the reflectance spectra of type I and type III ommatidia peak at 635 nm and those of type II ommatidia peak at 675 nm. The bandwith of the reflectance spectra is 40-50 nm. Type II ommatidia strongly fluoresce under ultra-violet and violet epi-illumination. The three types of ommatidia are randomly distributed. The ommatidial heterogeneity is presumably crucial for color discrimination.