Multiscale iterative voting for differential analysis of stress response for 2D and 3D cell culture models.

Three-dimensional (2D) cell culture models have emerged as the basis for improved cell systems biology. However, there is a gap in robust computational techniques for segmentation of these model systems that are imaged through confocal or deconvolution microscopy. The main issues are the volume of data, overlapping subcellular compartments and variation in scale or size of subcompartments of interest, which lead to ambiguities for quantitative analysis on a cell-by-cell basis. We address these ambiguities through a series of geometric operations that constrain the problem through iterative voting and decomposition strategies. The main contributions of this paper are to (i) extend the previously developed 2D radial voting to an efficient 3D implementation, (ii) demonstrate application of iterative radial voting at multiple subcellular and molecular scales, and (iii) investigate application of the proposed technology to two endpoints between 2D and 3D cell culture models. These endpoints correspond to kinetics of DNA damage repair as measured by phosphorylation of γH2AX, and the loss of the membrane-bound E-cadherin protein as a result of ionizing radiation. Preliminary results indicate little difference in the kinetics of the DNA damage protein between 2D and 3D cell culture models; however, differences between membrane-bound E-cadherin are more pronounced.

BioSig: an imaging bioinformatics system for phenotypic analysis.

Organisms express their genomes in a cell-specific manner, resulting in a variety of cellular phenotypes or phenomes. Mapping cell phenomes under a variety of experimental conditions is necessary in order to understand the responses of organisms to stimuli. Representing such data requires an integrated view of experimental and informatic protocols. The proposed system, named BioSig, provides the foundation for cataloging cellular responses as a function of specific conditioning, treatment, staining, etc., for either fixed tissue or living cell studies. A data model has been developed to capture experimental variables and map them to image collections and their computed representation. This representation is hierarchical and spans across sample tissues, cells, and organelles, which are imaged with light microscopy. At each layer, content is represented with an attributed graph, which contains information about cellular morphology, protein localization, and cellular organization in tissue or cell culture. The Web-based multilayer informatics architecture uses the data model to provide guided workflow access for content exploration.

New in vitro assay based on glucose consumption for determining intraconazole and amphotericin B activities against Aspergillus fumigatus.

We developed a new in vitro method of evaluating antifungal molecules. Fungal growth was determined by measuring glucose consumption, the only carbon source in a synthetic medium. First, the growth of 12 Aspergillus fumigatus strains was studied. Glucose consumption was an excellent indicator of fungal growth. Second, the partial inhibition of growth was calculated in terms of the 90% or 50% inhibitory concentration for the 12 strains after treatment with itraconazole and amphotericin B. With a 3-day incubation time, the calculated 90% and 50% inhibitory concentrations agreed with those obtained by a macromethod and with those reported in previous publications. In each case the high degrees of efficacy of itraconazole and amphotericin B against A. fumigatus were confirmed. Partial inhibition induced by low concentrations of antifungal agents was quantifiable by this new method.