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.     

Intracranial hydatidosis. Report of a case diagnosed on cerebrospinal fluid cytology

BACKGROUND: Hydatidosis occurs due to infestation with the larval stage of the Echinococcus species. Humans are incidental hosts. Symptoms and signs in humans are a slowly growing mass lesion, especially in the central nervous system. Diagnosis depends on the appropriate presentation and history with corroborative radiology and serology. Microscopic detection of characteristic parasitic scolices and hooklets is confirmatory. CASE: A 10-year-old girl presented with complaints of headaches and convulsions for the preceding several months. Computed tomography findings showed asymmetric dilatation of the right lateral ventricle by an intraventricular, focally calcified mass. The radiologic suspicion was an intraventricular tuberculoma, hydatid cyst or choroid plexus papilloma. Cytologic examination of cerebrospinal fluid (CSF) smears revealed characteristic echinococcal components. CONCLUSION: Intracranial hydatid cyst is a fairly uncommon manifestation of an echinococcal infestation and shares clinicoradiologic features with several intracranial, space-occupying lesions. Cytologic examination of CSF samples may be employed to detect confirmatory evidence of a clinical/radiologic suspicion.     

Light meromyosin paracrystal formation

Studies of paracrystal formation by column purified light meromyosin (LMM) prepared in a variety of ways led to the following conclusions: (a) different portions of the myosin rod may be coded for different stagger relationships. This was concluded from observations that paracrystals with different axial repeat periodicities could be obtained either with LMM framents of different lengths prepared with the same enzyme, or with LMM fragments of identical lengths but prepared with different enzymes. (b) Paracrystals with a 14-nm axial repeat periodicity are most likely formed by the aggregation of sheets with a 44-nm axial repeat within the sheets which are staggered by 14 nm. All of the axial repeat patterns expected from one sheet or aggregates of more than one sheet, on this basis, were observed in the same electron micrograph. (c) C-protein binding probably occurs preferentially to LMM molecules related in some specific way. This was concluded from the observation that the same axial repeat pattern was obtained in paracrystals formed from different LMM preparations in the presence of C-protein, regardless of differences in the axial repeat obtained in the absence of C-protein. (d) Nucleic acid is responsible for the 43-nm axial repeat patterns observed in paracrystals formed by the ethanol-resistant fraction of LMM. In the absence of nuclei acid, paracrystals with a 14nm axial repeat are obtained. (e) The 43-nm axial repeat pattern observed with the ethanol-resistant fraction of LMM is different for LMM preparations obtained by trypsin and papain digestions.     

梨头霉11α—羟基化制备16β—甲基—11α,17α21—三烃基孕甾—1, …

选育到一株对１６β－甲基－１７α,２１－二羟基孕甾－１,４＝－二烯－３,２０－二酮（Ⅱａ）１１α－羟基化活性强的梨头霉Ａ２８菌株,并发现底物２１－乙酰化（Ⅱｂ）可明显提高１１α－羟工 能力。在适宜的转化条件下,１１ｂ投料浓度０．５％,产物１６β－基１１α,１７α,２１－三羟基孕甾－１,４－二烯－３,２０－二酮（Ⅲ）收率为７３％,结构经波谱分析确认。     

Assessment of genetic and pheromonal diversity of the Cydia strobilella species complex (Lepidoptera: Tortricidae)

Combining pheromone trapping and genetic analyses can be useful when trying to resolve complexes of closely related insect taxa that are difficult to distinguish based on morphological characters. Nearctic and Palearctic populations of the spruce seed moth, Cydia strobilella L., have been considered taxonomically synonymous since 1983, but more recent work revealing distinct sex pheromones for Canadian and Swedish moths suggest that populations in the two regions belong to different species. In order to test this hypothesis, we performed field trapping using different pheromone lures at ten sites in North America, Europe and Asia, and reconstructed phylogenetic relationships among trapped moths using mitochondrial (cytochrome oxidase subunit I) and nuclear (elongation factor 1 alpha) DNA sequence data. Trapping data and tree topologies for both genes revealed distinct pherotypes in North America and Eurasia. A genetically distinct population from China was investigated further with respect to its sex pheromone. Electrophysiological data indicated that Chinese females produce a deviant ratio of the sex pheromone components (dienic acetates) compared to Swedish females. However, trapping experiments in both areas revealed a similar broad response profile in males to a wide range of acetate ratios, and these populations should be considered taxonomically synonymous. A previous suggestion of an agonistic effect on the attraction of C. strobilella males in Sweden when adding the corresponding alcohols to the binary acetate blend was also tested in Sweden as well as in China, with no observed effect on attraction of males. In conclusion, our study demonstrates the great potential of using pheromone trapping as a tool for identification and delimitation of taxa within cryptic species complexes. Based on our data, Nearctic and Palearctic populations of C. strobilella should be considered different species, and C. youngana Kearfott stat. rev. is resurrected here as valid name for North American populations, which was the case before the revision in 1983.     

Adiponectin Protects Against Hyperoxic Lung Injury and Vascular Leak

Adiponectin (Ad), an adipokine exclusively secreted by the adipose tissue, has emerged as a paracrine metabolic regulator as well as a protectant against oxidative stress. Pharmacological approaches of protecting against clinical hyperoxic lung injury during oxygen therapy/treatment are limited. We have previously reported that Ad inhibits the NADPH oxidase-catalyzed formation of superoxide from molecular oxygen in human neutrophils. Based on this premise, we conducted studies to determine whether (i) exogenous Ad would protect against the hyperoxia-induced barrier dysfunction in the lung endothelial cells (ECs) in vitro, and (ii) endogenously synthesized Ad would protect against hyperoxic lung injury in wild-type (WT) and Ad-overexpressing transgenic (AdTg) mice in vivo. The results demonstrated that exogenous Ad protected against the hyperoxia-induced oxidative stress, loss of glutathione (GSH), cytoskeletal reorganization, barrier dysfunction, and leak in the lung ECs in vitro. Furthermore, the hyperoxia-induced lung injury, vascular leak, and lipid peroxidation were significantly attenuated in AdTg mice in vivo. Also, AdTg mice exhibited elevated levels of total thiols and GSH in the lungs as compared with WT mice. For the first time, our studies demonstrated that Ad protected against the hyperoxia-induced lung damage apparently through attenuation of oxidative stress and modulation of thiol-redox status.     

Antiangiogenic properties of Koetjapic acid, a natural triterpene isolated from Sandoricum koetjaoe Merr

Background

Angiogenesis, the formation of new blood vessels, has become an important target in cancer therapy. Angiogenesis plays an important role in tumor growth and metastasis. Koetjapic acid (KA) is a seco-A-ring oleanene triterpene isolated from S. koetjape. The solvent extract of this plant species was shown previously to have strong antiangiogenic activity; however the active ingredient(s) that conferred the biological activity and the mode of action was not established. Given the high concentration of KA in S. koetjape, an attempt has been made in this study to investigate the antiangiogenic properties of KA.

Results

Treatment with 10-50 μg/ml KA resulted in dose dependent inhibition of new blood vessels growth in ex vivo rat aortic ring assay. KA was found to be non-cytotoxic against HUVECs with IC₅₀ 40.97 ± 0.37 μg/ml. KA inhibited major angiogenesis process steps, endothelial cell migration and differentiation as well as VEGF expression.

Conclusions

The non-cytotoxic compound, KA, may be a potent antiangiogenic agent; its activity may be attributed to inhibition of endothelial cells migration and differentiation as well VEGF suppression.     

Synthesis and anti-tumor evaluation of B-ring substituted steroidal pyrazoline derivatives

The synthesis and anti-tumor activity screening of new steroidal derivatives (4–18) containing pharmacologically attractive pyrazoline moieties are performed. During in vitro anticancer evaluation, the newly synthesized compounds displayed moderate to good cytotoxicity on cervical and leukemia cancer cell lines. In addition these compounds were found to be nontoxic to normal cell (PBMCs) (IC₅₀ > 50 μM). The structure–activity relationship is also discussed. The most effective anticancer compound 9 was found to be active with IC₅₀ value of 10.6 μM. It demonstrated significant antiproliferative influence on Jurkat cell lines. The morphological changes and growth characteristics of HeLa cells treated with compound 4 were analyzed by means of SEM.     

More than royal food - <Emphasis Type="Italic">Major royal jelly protein</Emphasis> genes in sexuals and workers of the honeybee <Emphasis Type="Italic">Apis mellifera</Emphasis>

Background

In the honeybee Apis mellifera, female larvae destined to become a queen are fed with royal jelly, a secretion of the hypopharyngeal glands of young nurse bees that rear the brood. The protein moiety of royal jelly comprises mostly major royal jelly proteins (MRJPs) of which the coding genes (mrjp1-9) have been identified on chromosome 11 in the honeybee’s genome.

Results

We determined the expression of mrjp1-9 among the honeybee worker caste (nurses, foragers) and the sexuals (queens (unmated, mated) and drones) in various body parts (head, thorax, abdomen). Specific mrjp expression was not only found in brood rearing nurse bees, but also in foragers and the sexuals.

Conclusions

The expression of mrjp1 to 7 is characteristic for the heads of worker bees, with an elevated expression of mrjp1-4 and 7 in nurse bees compared to foragers. Mrjp5 and 6 were higher in foragers compared to nurses suggesting functions in addition to those of brood food proteins. Furthermore, the expression of mrjp9 was high in the heads, thoraces and abdomen of almost all female bees, suggesting a function irrespective of body section. This completely different expression profile suggests mrjp9 to code for the most ancestral major royal jelly protein of the honeybee.