A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

Background  

Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement error associated with each feature and the choice of preprocessing method. Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide. Furthermore, the estimated expression values also vary depending on the selected preprocessing scheme. In microarray breast cancer classification studies, however, these two forms of feature variability are almost always ignored and hence their exact role is unclear.     

The effect of constant moisture and aeration levels in soil on Fusarium wilt of tomatoes

Soil patches on opposite sides of Pseudoroegneria spicata plants in the field were treated with either distilled water or a nutrient solution containing N, P, or K. Roots from these enriched and control patches were tested three days later for their capacities of ammonium, phosphate, and potassium uptake. When phosphate was augmented in the enriched patches, rates of phosphate uptake increased significantly, but not rates of ammonium or potassium uptake. When the enriched patches were augmented with nitrogen, uptake capacities of both ammonium and potassium increased significantly (mean increases of up to 88% and 71% for ammonium and potassium, respectively). Potassium augmentation did not lead to increased soil-available K and, correspondingly, did not induce changes in the capacity for uptake of K, N, or P. The potential importance of nutrient uptake kinetics in the exploitation of nutrient-rich soil patches is discussed.     

Studies on phenotypic complementation of ataxia-telangiectasia cells by chromosome transfer.

Cells derived from patients with the cancer-prone inherited disorder ataxia-telangiectasia (A-T) show an abnormal response to ionizing radiation-induced DNA damage, such as an increased cell killing and a diminished inhibition of DNA synthesis. The enhanced killing of A-T (group D) cells by X-rays can be corrected by multiple cDNAs, mapping to different chromosomes (6, 11, 17, and 18). In order to examine whether genes located on these chromosomes complement AT-D cells, normal neo-tagged chromosomes 6, 11, 17, and 18 were introduced into AT-D cells by microcell-mediated chromosome transfer. However, correction of the enhanced killing of AT-D cells by X-rays could only be achieved by chromosome 11 and by none of the other chromosomes tested. The enhanced killing of A-T (complementation group C) cells was also corrected by chromosome 11. Usually, but not in all microcell hybrid clones, chromosome 11 also corrected the radioresistant DNA synthesis (RDS) phenotype of AT-D and AT-C cells. These results (i) confirm findings by others suggesting assignment of the ATD and ATC genes to chromosome 11, (ii) demonstrate that several genes can modify the cellular radiation response when they are taken out of their normal genomic context and/or control, and (iii) indicate that the RDS phenotype and the enhanced cell killing in A-T are independent pleiotropic features resulting from the primary mutations in A-T. Also, our findings underscore that, in establishing cDNAs as candidate genes for A-T, microcell-mediated chromosome transfer studies are needed to exclude nonspecific correcting effects of these candidate cDNA genes.     

Effects of varying pollen load on fruit set,seed set and seedling performance in apple and pear

Two apple crosses and one pear cross were carried out using three different pollen densities. In one of the apple crosses, both fruit and seed set decreased when a mixture of pollen and powder (diluted pollen treatment) was used for pollination. Also, seedlings from the undiluted treatment were more vigorous than those originating from pollination with diluted pollen. In the other apple cross, however, no effect on fruit set, seed set or growth in the first year was found. Mean diameter after the second year differed among treatments, but did not seem to be related to pollen density. For pear, the number of good seeds decreased and the number of deaf, probably unfertilized, seeds increased with decreasing pollen density. However, there was no apparent significant effect of pollen density on seedling growth. With respect to scab resistance and mildew attack in both apple crosses, no differences among treatments were found. The results indicate that gametophytic competition may occur in apple crosses, but that it is probably weaker in pear.     

Severe Blunt Muscle Trauma in Rats: Only Marginal Hypoxia in the Injured Area

Background

After severe muscle trauma, hypoxia due to microvascular perfusion failure is generally believed to further increase local injury and to impair healing. However, detailed analysis of hypoxia at the cellular level is missing. Therefore, in the present work, spectroscopic measurements of microvascular blood flow and O₂ supply were combined with immunological detection of hypoxic cells to estimate O₂ conditions within the injured muscle area.

Materials and Methods

Severe blunt muscle trauma was induced in the right Musculus gastrocnemius of male Wistar rats by a standardized “weight-drop” device. Microvascular blood flow, relative hemoglobin amount, and hemoglobin O₂ saturation were determined by laser Doppler and white-light spectroscopy. Hypoxic cells were detected by histologic evaluation of covalent binding of pimonidazole and expression of HIF-1α.

Results

Directly after trauma and until the end of experiment (480 minutes), microvascular blood flow and relative hemoglobin amount were clearly increased. In contrast to blood flow and relative hemoglobin amount, there was no immediate but a delayed increase of microvascular hemoglobin O₂ saturation. Pimonidazole immunostaining revealed a hypoxic fraction (percentage area of pimonidazole-labelled muscle cells within the injured area) between 8 to 3%. There was almost no HIF-1α expression detectable in the muscle cells under each condition studied.

Conclusions

In the early phase (up to 8 hours) after severe blunt muscle trauma, the overall microvascular perfusion of the injured area and thus its O₂ supply is clearly increased. This increased O₂ supply is obviously sufficient to ensure normoxic (or even hyperoxic) conditions in the vast majority of the cells.     

A gene that regulates DNA replication in response to DNA damage is located on human chromosome 4q.

Inhibition of replicative DNA synthesis following gamma-irradiation is observed in eukaryotic cells but is defective in cells derived from patients with the cancer-prone inherited disorder ataxia-telangiectasia (A-T) and in A-T-like Chinese hamster cell mutants. Chinese hamster cells show a less pronounced inhibition of DNA synthesis after gamma-irradiation when compared to irradiated human HeLa or mouse A9 cells. Therefore, to identify new human genes involved in the regulation of DNA replication in response to ionizing radiation in mammalian cells, single human chromosomes were introduced into Chinese hamster cells by microcell-mediated chromosome transfer. It is found that a new gene on human chromosome 4q inhibits DNA synthesis following gamma- and UV irradiation in hamster cells. However, this delay of DNA replication did not improve cell survival or the level of chromosomal aberrations induced by X-rays, indicating that the lack of the inhibition of DNA synthesis after X-irradiation is not a prerequisite for the X-ray sensitivity and chromosomal instability, which is observed in A-T and A-T-like hamster cells.     

The role of host immune cells and <Emphasis Type="Italic">Borrelia burgdorferi</Emphasis> antigens in the etiology of Lyme disease

Lyme disease is a zoonosis caused by infection with bacteria belonging to the Borrelia burgdorferi species after the bite of an infected tick. Even though an infection by this bacterium can be effectively treated with antibiotics, when the infection stays unnoticed B. burgdorferi can persist and chronic post-treatment Lyme disease syndrome is able to develop. Although a cellular and humoral response is observed after an infection with the Borrelia bacteria, these pathogens are still capable to stay alive. Several immune evasive mechanisms have been revealed and explained and much work has been put into the understanding of the contribution of the innate and adaptive immune response. This review provides an overview with the latest findings regarding the cells of the innate and adaptive immune systems, how they recognize contribute and mediate in the killing of the B. burgdorferi spirochete. Moreover, this review also elaborates on the antigens that are expressed by on the spirochete. Since antigens drive the adaptive and, indirectly, the innate response, this review will discuss briefly the most important antigens that are described to date. Finally, there will be a brief elaboration on the escape mechanisms of B. burgdorferi with a focus on tick salivary proteins and spirochete antigens.