Biomedical subjects

Kjell-Arild Høgda

Publications and source records attributed to Kjell-Arild Høgda.

3 recordsLinked to original sources

PubMed2006

Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables.

BACKGROUND: Two-dimensional gel electrophoresis (2DE) is a powerful technique to examine post-translational modifications of complexly modulated proteins. Currently, spot detection is a necessary step to assess relations between spots and biological variables. This often proves time consuming and difficult when working with non-perfect gels. We developed an analysis technique to measure correlation between 2DE images and biological variables on a pixel by pixel basis. After image alignment and normalization, the biological parameters and pixel values are replaced by their specific rank. These rank adjusted images and parameters are then put into a standard linear Pearson correlation and further tested for significance and variance. RESULTS: We validated this technique on a set of simulated 2DE images, which revealed also correct working under the presence of normalization factors. This was followed by an analysis of p53 2DE immunoblots from cancer cells, known to have unique signaling networks. Since p53 is altered through these signaling networks, we expected to find correlations between the cancer type (acute lymphoblastic leukemia and acute myeloid leukemia) and the p53 profiles. A second correlation analysis revealed a more complex relation between the differentiation stage in acute myeloid leukemia and p53 protein isoforms. CONCLUSION: The presented analysis method measures relations between 2DE images and external variables without requiring spot detection, thereby enabling the exploration of biosignatures of complex signaling networks in biological systems.

Algorithms↗

PubMed2006

Adaptive contrast enhancement of two-dimensional electrophoretic protein gel images facilitates visualization, orientation and alignment.

2-DE is a powerful technique to discriminate post-translationally modified protein isoforms. However, all steps of 2-DE preparation and gel-staining may introduce unwanted artefacts, including inconsistent variation of background intensity over the entire 2-DE gel image. Background intensity variations limit the accuracy of gel orientation, overlay alignment and spot detection methods. We present a compact and efficient denoising algorithm that adaptively enhances the image contrast and then, through thresholding and median filtering, removes the gray-scale range covering the background. Applicability of the algorithm is demonstrated on immunoblots, isotope-labeled gels, and protein-stained gels. Validation is performed in contexts of (i) automatic gel orientation based on Hough transformation, (ii) overlay alignment based on cross correlation and (iii) spot detection. In gel stains with low background variability, e.g. Sypro Ruby, denoising will lower the spot detection sensitivity. In gel regions with high background levels denoising enhances spot detection. We propose that the denoising algorithm prepares images with high background for further automatic analysis, without requiring manual input on a gel-to-gel basis.

Algorithms↗

PubMed2006

The length of growing season and adult sex ratio affect sexual size dimorphism in moose.

While factors affecting body growth have been extensively studied, very little is known about the factors likely to affect the sexual size dimorphism (SSD) in polygynous mammals. Based on the carcass mass of 24420 male and female moose recorded in 14 Norwegian populations, we examine three hypotheses to explain geographical variation in SSD. First, SSD is expected to decrease when the relative density of animals (for a given habitat quality) increases, because resource limitation at high population densities is assumed to affect body growth of males more than females. Second, because males are selected to invest in growth more than females, environmental seasonality and related improvement of the forage quality during the short and intense growing season are expected to increase SSD. Third, by decreasing the proportion of adult males in the population, resulting in start of rutting earlier in life, hunting may decrease the SSD by increasing the reproductive cost of young males. We found that males grew faster and for a longer time of their life than did females and thus were heavier (-24%) when they reached adulthood. Sexual size dimorphism was independent of density but was higher in areas with short growing seasons. The low SSD in populations with largely adult female-biased sex ratios (males per female) shows that male body growth decreases with a decreasing proportion of adult males in the population. Our results indicate that geographical variation in moose SSD is influenced by divergent responses in the sexes to ecological factors affecting body growth.

Animal Feed↗