GObar: A Gene Ontology based analysis and visualization tool for gene sets

Background  

Microarray experiments, as well as other genomic analyses, often result in large gene sets containing up to several hundred genes. The biological significance of such sets of genes is, usually, not readily apparent.     

Three-dimensional structure of a regular surface layer from Pseudomonas acidovorans

The regular surface layer of Pseudomonas acidovorans was investigated by computer processing of a series of tilted view electron micrographs, and a reconstruction of the three-dimensional structure was obtained. The pattern is tetragonal and consists of massive identical subunits, block-like in face-view, which interlock loosely in a simple cobblestone pattern. The square unit cell has a lattice constant of 11 nm. The surface layer pattern of P. acidovorans appears to be more dependent on the underlying membrane for maintaining its integrity than those so far studied in other bacteria.     

Post-conception mating in wild long-tailed macaques (Macaca fascicularis): characterization, endocrine correlates and functional significance

In many anthropoid primates, mating activity is not restricted to the ovarian cycle but also occurs during pregnancy. Although it has been suggested that the main function of this post-conception mating is to confuse paternity, studies showing whether or not male primates can distinguish between the fertile phase of the conception cycle (FPCC) and the period of peak post-conception mating (peak PCM) are almost non-existent. Here, we examine whether the pattern of female sexual traits (specific sexual behaviors, sexual swelling) and female attractiveness to males differ between FPCC and peak PCM in 6 wild female long-tailed macaques. We also use fecal hormone analysis to investigate whether female traits during peak PCM are related to changes in female sex hormones. All females exhibited a distinct period of heightened mating activity around days 45-60 of gestation. During peak PCM, swelling size and frequency of female solicitations (but not reaching back) were significantly correlated with changes in the estrogen to progestogen ratio. Swelling size, frequency of female sexual behaviors and copulations and proportion of male-initiated copulations and ejaculations were not significantly different between FPCC and peak PCM. Although males spent significantly less time consorting females during peak PCM, all (particularly low-ranking and non-resident males) invested heavily in terms of reproductive costs associated with mate-guarding and mating during pregnancy. We conclude that post-conception mating in wild long-tailed macaques is not merely a by-product of endocrine changes and devoid of adaptive function. Our results more strongly support the hypothesis that it may form part of a female reproductive strategy to confuse paternity, which appears to apply particularly to low-ranking and extra-group males.     

Manipulation of male attractiveness induces rapid changes in avian maternal yolk androgen deposition

Avian eggs contain maternal androgens that may adjust offspringdevelopment to environmental conditions. We review evidenceand functional explanations for the relationship between androgenconcentrations in avian eggs and male attractiveness. Experimentalstudies in captive birds show generally positive relationships,but results from correlational and experimental field studiesare less consistent, perhaps because they lack a within-femaledesign to control for confounding between-female variation.We analyzed the effect of male attractiveness on yolk levelsof maternal androgens in a wild bird, using a correlationaland experimental approach with a within-female design. We manipulatedthe sexually selected UV coloration of the crown feathers ofmale blue tits (Cyanistes caeruleus) after their female hadlaid the second egg and measured the subsequent effect on androgenconcentrations (testosterone and androstenedione) in the fifth,seventh, and ninth eggs relative to that in the second egg.Levels of testosterone, but not androstenedione, in eggs 5 and7 were higher for control (attractive) than for UV-reduced (unattractive)males. This effect disappeared in the ninth egg, coincidingwith the recovery of UV coloration after manipulation. Thissuggests that females are capable of rapid adjustments of testosteronedeposition in response to changes in their mate's ornamentalplumage. However, androgen concentrations in the second eggand pretreatment male crown coloration were not correlated.Possibly, the combination of relatively small variation in UVcoloration before treatment and the influence of unknown confoundingvariables in the correlative approach resulted in insufficientstatistical power to detect such a correlation.     

Identification of endogenous sugar-binding proteins (lectins) in human placenta by histochemical localization and biochemical characterization

Human placentas of different stages of development were histochemically analyzed for expression of endogenous sugar-binding proteins using a panel of biotin-conjugated, chemically glycosylated probes with specificity for beta-galactosides, alpha-galactosides, alpha-mannosides, alpha-fucosides and alpha-glucosides. Temporal differences in the expression of sugar-binding proteins and different patterns of staining of the component cell types of human placenta were discerned, especially pronounced for alpha-fucoside-specific binding in the trophoblast and alpha-glucoside-specific binding in fetal and maternal macrophages. Fractionation of salt and detergent extracts from human placentas by affinity chromatography on columns with immobilized carbohydrates or glycoproteins substantiated the histochemically detectable temporal changes on the basis of alterations in the pattern of individual sugar-binding proteins, as determined by gel electrophoresis under denaturing conditions. Analysis of the trophoblastic layer primarily disclosed the presence of several additional sugar-binding proteins (lectins) in comparison to full-term placenta. The presence and developmental changes of such endogenous sugar receptors may lead to specific carbohydrate-protein interactions of physiological significance with similarly developmentally regulated carbohydrated portions of glyco-conjugates, already detected in human placenta by plant lectins.     

Comparison of an EMG-based and a stress-based method to predict shoulder muscle forces

The estimation of muscle forces in musculoskeletal shoulder models is still controversial. Two different methods are widely used to solve the indeterminacy of the system: electromyography (EMG)-based methods and stress-based methods. The goal of this work was to evaluate the influence of these two methods on the prediction of muscle forces, glenohumeral load and joint stability after total shoulder arthroplasty. An EMG-based and a stress-based method were implemented into the same musculoskeletal shoulder model. The model replicated the glenohumeral joint after total shoulder arthroplasty. It contained the scapula, the humerus, the joint prosthesis, the rotator cuff muscles supraspinatus, subscapularis and infraspinatus and the middle, anterior and posterior deltoid muscles. A movement of abduction was simulated in the plane of the scapula. The EMG-based method replicated muscular activity of experimentally measured EMG. The stress-based method minimised a cost function based on muscle stresses. We compared muscle forces, joint reaction force, articular contact pressure and translation of the humeral head. The stress-based method predicted a lower force of the rotator cuff muscles. This was partly counter-balanced by a higher force of the middle part of the deltoid muscle. As a consequence, the stress-based method predicted a lower joint load (16% reduced) and a higher superior–inferior translation of the humeral head (increased by 1.2 mm). The EMG-based method has the advantage of replicating the observed cocontraction of stabilising muscles of the rotator cuff. This method is, however, limited to available EMG measurements. The stress-based method has thus an advantage of flexibility, but may overestimate glenohumeral subluxation.     

Ligand-dependent differences in estrogen receptor beta-interacting proteins identified in lung adenocarcinoma cells corresponds to estrogenic responses

Background

A recent epidemiological study demonstrated a reduced risk of lung cancer mortality in breast cancer patients using antiestrogens. These and other data implicate a role for estrogens in lung cancer, particularly nonsmall cell lung cancer (NSCLC). Approximately 61% of human NSCLC tumors express nuclear estrogen receptor β (ERβ); however, the role of ERβ and estrogens in NSCLC is likely to be multifactorial. Here we tested the hypothesis that proteins interacting with ERβ in human lung adenocarcinoma cells that respond proliferatively to estradiol (E₂) are distinct from those in non-E₂-responsive cells.

Methods

FLAG affinity purification of FLAG-ERβ-interacting proteins was used to isolate ERβ-interacting proteins in whole cell extracts from E₂ proliferative H1793 and non-E₂-proliferative A549 lung adenocarcinoma cell lines. Following trypsin digestion, proteins were identified using liquid chromatography electrospray ionization tandem mass spectrometry (LC-MS/MS). Proteomic data were analyzed using Ingenuity Pathway Analysis. Select results were confirmed by coimmunoprecipitation.

Results

LC-MS/MS identified 27 non-redundant ERβ-interacting proteins. ERβ-interacting proteins included hsp70, hsp60, vimentin, histones and calmodulin. Ingenuity Pathway Analysis of the ERβ-interacting proteins revealed differences in molecular and functional networks between H1793 and A549 lung adenocarcinoma cells. Coimmunoprecipitation experiments in these and other lung adenocarcinoma cells confirmed that ERβ and EGFR interact in a gender-dependent manner and in response to E₂ or EGF. BRCA1 interacted with ERβ in A549 cell lines and in human lung adenocarcinoma tumors, but not normal lung tissue.

Conclusion

Our results identify specific differences in ERβ-interacting proteins in lung adenocarcinoma cells corresponding to ligand-dependent differences in estrogenic responses.

     

Different Patterns of White Matter Degeneration Using Multiple Diffusion Indices and Volumetric Data in Mild Cognitive Impairment and Alzheimer Patients

Alzheimeŕs disease (AD) represents the most prevalent neurodegenerative disorder that causes cognitive decline in old age. In its early stages, AD is associated with microstructural abnormalities in white matter (WM). In the current study, multiple indices of diffusion tensor imaging (DTI) and brain volumetric measurements were employed to comprehensively investigate the landscape of AD pathology. The sample comprised 58 individuals including cognitively normal subjects (controls), amnestic mild cognitive impairment (MCI) and AD patients. Relative to controls, both MCI and AD subjects showed widespread changes of anisotropic fraction (FA) in the corpus callosum, cingulate and uncinate fasciculus. Mean diffusivity and radial changes were also observed in AD patients in comparison with controls. After controlling for the gray matter atrophy the number of regions of significantly lower FA in AD patients relative to controls was decreased; nonetheless, unique areas of microstructural damage remained, e.g., the corpus callosum and uncinate fasciculus. Despite sample size limitations, the current results suggest that a combination of secondary and primary degeneration occurrs in MCI and AD, although the secondary degeneration appears to have a more critical role during the stages of disease involving dementia.     

Ca2+-dependent lipid binding and membrane integration of PopA, a harpin-like elicitor of the hypersensitive response in tobacco

PopA is released by type III secretion from the bacterial plant pathogen Ralstonia solanacearum and triggers the hypersensitive response (HR) in tobacco. The function of PopA remains obscure, mainly because mutants lacking this protein are not altered in their ability to interact with plants. In an attempt to identify the site of PopA activity in plant cells, we generated transgenic tobacco plants expressing the popA gene under the control of an inducible promoter. Immunocytologic analysis revealed that the HR phenotype of these plants correlated with the presence of PopA at the plant plasma membrane. Membrane localization was observed irrespective of whether the protein was designed to accumulate in the cytoplasm or to be secreted by the plant cell, suggesting a general lipid-binding ability. We found that the protein had a high affinity for sterols and sphingolipids in vitro and that it required Ca2+ for both lipid binding and oligomerization. In addition, the protein was integrated into liposomes and membranes from Xenopus laevis oocytes where it formed ion-conducting pores. These characteristics suggest that PopA is part of a system that aims to attach the host cell plasma membrane and to allow molecules cross this barrier.