A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets

Background  

Gene selection is an important step when building predictors of disease state based on gene expression data. Gene selection generally improves performance and identifies a relevant subset of genes. Many univariate and multivariate gene selection approaches have been proposed. Frequently the claim is made that genes are co-regulated (due to pathway dependencies) and that multivariate approaches are therefore per definition more desirable than univariate selection approaches. Based on the published performances of all these approaches a fair comparison of the available results can not be made. This mainly stems from two factors. First, the results are often biased, since the validation set is in one way or another involved in training the predictor, resulting in optimistically biased performance estimates. Second, the published results are often based on a small number of relatively simple datasets. Consequently no generally applicable conclusions can be drawn.     

Ecological effects of low-level phosphorus additions on two plant communities in a neotropical freshwater wetland ecosystem

We conducted a low-level phosphorus (P) enrichment study in two oligotrophic freshwater wetland communities (wet prairies [WP] and sawgrass marsh [SAW]) of the neotropical Florida Everglades. The experiment included three P addition levels (0, 3.33, and 33.3 mg P m^–2 month^–1), added over 2 years, and used in situ mesocosms located in northeastern Everglades National Park, Fla., USA. The calcareous periphyton mat in both communities degraded quickly and was replaced by green algae. In the WP community, we observed significant increases in net aboveground primary production (NAPP) and belowground biomass. Aboveground live standing crop (ALSC) did not show a treatment effect, though, because stem turnover rates of Eleocharis spp., the dominant emergent macrophyte in this community, increased significantly. Eleocharis spp. leaf tissue P content decreased with P additions, causing higher C:P and N:P ratios in enriched versus unenriched plots. In the SAW community, NAPP, ALSC, and belowground biomass all increased significantly in response to P additions. Cladium jamaicense leaf turnover rates and tissue nutrient content did not show treatment effects. The two oligotrophic communities responded differentially to P enrichment. Periphyton which was more abundant in the WP community, appeared to act as a P buffer that delayed the response of other ecosystem components until after the periphyton mat had disappeared. Periphyton played a smaller role in controlling ecosystem dynamics and community structure in the SAW community. Our data suggested a reduced reliance on internal stores of P by emergent macrophytes in the WP that were exposed to P enrichment. Eleocharis spp. rapidly recycled P through more rapid aboveground turnover. In contrast, C. jamaicense stored added P by initially investing in belowground biomass, then shifting growth allocation to aboveground tissue without increasing leaf turnover rates. Our results suggest that calcareous wetland systems throughout the Caribbean, and oligotrophic ecosystems in general, respond rapidly to low-level additions of their limiting nutrient.     

Guanine nucleotides differentiate agonist and antagonist interactions with opiate receptors.

Opiate receptor binding is regulated by guanine nucleotides differentially for agonists and antagonists. Guanosine-5′-triphosphate (GTP), its stable analogue guanyl-5′-yl-imidodiphosphate (Gpp(NH)p) and GDP inhibit binding of the ³H-agonists dihydromorphine, etorphine and enkephalins but not the ³H-antagonists naloxone or diprenorphine. GMP, ATP, ADP and AMP fail to alter either agonist or antagonist binding. Effects are more pronounced in the presence than in the absence of sodium.     

Synthesis of methylphenidate analogues and their binding affinities at dopamine and serotonin transport sites

The rhodium(II)-catalyzed intermolecular C-H insertion of methyl aryldiazoacetates with either N-Boc-piperidine or N-Boc-pyrrolidine followed by deprotection with trifluoroacetic acid is a very direct method for the synthesis of methylphenidate analogues. By using either dirhodium tetraacetate or dirhodium tetraprolinate derivatives as catalyst, either the racemic or enantioenriched methylphenidate analogues can be prepared. The binding affinities of the methylphenidate analogues to both the dopamine and the serotonin transporters are described. The most notable compounds are the erythro-(2-naphthyl) analogues which display high binding affinity and selectivity for the serotonin transporter.     

Segmental identity and cerebellar granule cell induction in rhombomere 1

Background  

Cerebellar granule cell precursors are specifically generated within the hindbrain segment, rhombomere 1, which is bounded rostrally by the midbrain/hindbrain isthmus and caudally by the boundary of the Hoxa2 expression domain. While graded signals from the isthmus have a demonstrable patterning role within this region, the significance of segmental identity for neuronal specification within rhombomere 1 is unexplored. We examined the response of granule cell precursors to the overexpression of Hoxa2, which normally determines patterns of development specific to the hindbrain. How much does the development of the cerebellum, a midbrain/hindbrain structure, reflect its neuromeric origin as a hindbrain segment?     

Arterial Levels of Oxygen Stimulate Intimal Hyperplasia in Human Saphenous Veins via a ROS-Dependent Mechanism

Saphenous veins used as arterial grafts are exposed to arterial levels of oxygen partial pressure (pO₂), which are much greater than what they experience in their native environment. The object of this study is to determine the impact of exposing human saphenous veins to arterial pO₂. Saphenous veins and left internal mammary arteries from consenting patients undergoing coronary artery bypass grafting were cultured ex vivo for 2 weeks in the presence of arterial or venous pO₂ using an established organ culture model. Saphenous veins cultured with arterial pO₂ developed intimal hyperplasia as evidenced by 2.8-fold greater intimal area and 5.8-fold increase in cell proliferation compared to those freshly isolated. Saphenous veins cultured at venous pO₂ or internal mammary arteries cultured at arterial pO₂ did not develop intimal hyperplasia. Intimal hyperplasia was accompanied by two markers of elevated reactive oxygen species (ROS): increased dihydroethidium associated fluorescence (4-fold, p<0.05) and increased levels of the lipid peroxidation product, 4-hydroxynonenal (10-fold, p<0.05). A functional role of the increased ROS saphenous veins exposed to arterial pO₂ is suggested by the observation that chronic exposure to tiron, a ROS scavenger, during the two-week culture period, blocked intimal hyperplasia. Electron paramagnetic resonance based oximetry revealed that the pO₂ in the wall of the vessel tracked that of the atmosphere with a ~30 mmHg offset, thus the cells in the vessel wall were directly exposed to variations in pO₂. Monolayer cultures of smooth muscle cells isolated from saphenous veins exhibited increased proliferation when exposed to arterial pO₂ relative to those cultured at venous pO₂. This increased proliferation was blocked by tiron. Taken together, these data suggest that exposure of human SV to arterial pO₂ stimulates IH via a ROS-dependent pathway.     

Brevipalpus mites (Acari: Tenuipalpidae): vectors of invasive, non-systemic cytoplasmic and nuclear viruses in plants

Multi-directional interactions occur among plant hosts, Brevipalpus mites and the plant viruses they transmit. Such interactions should be considered when evaluating the severity of a disease such as citrus leprosis. The current understanding of Brevipalpus-transmitted viruses relies on the capability of the vector to transmit the disease, the persistence of the virus in the host plant and the ability of the disease to spread. Previously, we discussed the Citrus leprosis virus (CiLV) and its importance and spread over the past decade into new areas of South and Central America, most recently into southern Mexico and Belize. Here, we address key questions to better understand the biology of the mite vector, fitness costs, and the peculiarities of Brevipalpus mite reproduction, virus survival, transmissibility and spread, and the expansion of the host plant range of Brevipalpus species vectoring the disease.