A top-r feature selection algorithm for microarray gene expression data

Most of the conventional feature selection algorithms have a drawback whereby a weakly ranked gene that could perform well in terms of classification accuracy with an appropriate subset of genes will be left out of the selection. Considering this shortcoming, we propose a feature selection algorithm in gene expression data analysis of sample classifications. The proposed algorithm first divides genes into subsets, the sizes of which are relatively small (roughly of size h), then selects informative smaller subsets of genes (of size r < h) from a subset and merges the chosen genes with another gene subset (of size r) to update the gene subset. We repeat this process until all subsets are merged into one informative subset. We illustrate the effectiveness of the proposed algorithm by analyzing three distinct gene expression data sets. Our method shows promising classification accuracy for all the test data sets. We also show the relevance of the selected genes in terms of their biological functions.     

Xanthohumol impairs autophagosome maturation through direct inhibition of valosin-containing protein

Autophagy is a bulk, nonspecific protein degradation pathway that is involved in the pathogenesis of cancer and neurodegenerative disease. Here, we observed that xanthohumol (XN), a prenylated chalcone present in hops (Humulus lupulus L.) and beer, modulates autophagy. By using XN-immobilized beads, valosin-containing protein (VCP) was identified as a XN-binding protein. VCP has been reported to be an essential protein for autophagosome maturation. Using an in vitro pull down assay, we showed that XN bound directly to the N domain, which is known to mediate cofactor and substrate binding to VCP. These data indicated that XN inhibited the function of VCP, thereby allowing the impairment of autophagosome maturation and resulting in the accumulation of microtubule-associated protein 1 light chain 3-II (LC3-II). This is the first report demonstrating XN as a VCP inhibitor that binds directly to the N domain of VCP. Our finding that XN bound to and inactivated VCP not only reveals the molecular mechanism of XN-modulated autophagy but may also explain how XN exhibits various biological activities that have been reported previously.     

Skewed Production of IL-6 and TGFβ by Cultured Salivary Gland Epithelial Cells from Patients with Sj?gren's Syndrome

Objective

To determine the cytokine production profile of cultured salivary gland epithelial (SGE) cells obtained from patients with Sjögren''s syndrome (SS).

Methods

SGE cells obtained from 9 SS patients and 6 normal controls were cultured in the presence of exogenous IFNγ. Cell proliferation and apoptosis in response to IFNγ were determined by WST1 assay and by FACS analysis. The concentrations of IL-6 and TGFβ secreted into culture supernatants were analyzed by ELISA.

Results

IFNγ did not significantly affect the proliferation or apoptosis of SGE cells. However, IL-6 concentrations were higher, and TGFβ concentrations were lower, in culture supernatants of SGE cells from SS patients than from normal controls.

Conclusion

Cytokine production by SGE cells from SS patients showed a skewed balance compared with normal controls, with increased IL-6 and decreased TGFβ secretion. This imbalance may be critical in the regulation of Treg/Th17 cells and may foster a pathogenic milieu that may be causative and predictive in SS.     

Corticosterone induces rapid spinogenesis via synaptic glucocorticoid receptors and kinase networks in hippocampus

Background

Modulation of dendritic spines under acute stress is attracting much attention. Exposure to acute stress induces corticosterone (CORT) secretion from the adrenal cortex, resulting in rapid increase of CORT levels in plasma and the hippocampus.

Methodology/Principal Findings

Here we demonstrated the mechanisms of rapid effect (∼1 h) of CORT on the density and morphology of spines by imaging neurons in adult male rat hippocampal slices. The application of CORT at 100–1000 nM induced a rapid increase in the density of spines of CA1 pyramidal neurons. The density of small-head spines (0.2–0.4 µm) was increased even at low CORT levels (100–200 nM). The density of middle-head spines (0.4–0.5 µm) was increased at high CORT levels between 400–1000 nM. The density of large-head spines (0.5–1.0 µm) was increased only at 1000 nM CORT. Co-administration of RU486, an antagonist of glucocorticoid receptor (GR), abolished the effect of CORT. Blocking a single kinase, such as MAPK, PKA, PKC or PI3K, suppressed CORT-induced enhancement of spinogenesis. Blocking NMDA receptors suppressed the CORT effect.

Conclusions/Significance

These results imply that stress levels of CORT (100–1000 nM) drive the spinogenesis via synaptic GR and multiple kinase pathways.     

The evolving proteome of a complex extracellular matrix, the Oikopleura house

Extracellular matrices regulate biological processes at the level of cells, tissues, and in some cases, entire multicellular organisms. The subphylum Urochordata exemplifies the latter case, where animals are partially or completely enclosed in "houses" or "tunics". Despite this common strategy, we show that the house proteome of the appendicularian, Oikopleura, has very little in common with the proteome of the sister class, ascidian, Ciona. Of 80 identified house proteins (oikosins), ～half lack domain modules or similarity to known proteins, suggesting de novo appearance in appendicularians. Gene duplication has been important in generating almost 1/3 of the current oikosin complement, with serial duplications up to 8 paralogs in one family. Expression pattern analyses revealed that individual oikosins are produced from specific fields of cells within the secretory epithelium, but in some cases, migrate up to at least 20 cell diameters in extracellular space to combine in defined house structures. Interestingly, peroxidasin and secretory phospholipase A(2) domains, implicated in innate immune defence are secreted from the anlage associated with the food-concentrating filter, suggesting that this extra-organismal structure may play, in part, such a role in Oikopleura. We also show that sulfation of proteoglycans is required for the hydration and inflation of pre-house rudiments into functional houses. Though correct proportioning in the production of oikosins would seem important in repetitive assembly of the complex house structure, the genomic organization of oikosin loci appears incompatible with common enhancers or locus control regions exerting such a coordinate regulatory role. Thus, though all tunicates employ extracellular matrices based on a cellulose scaffold as a defining feature of the subphylum, they have evolved radically different protein compositions associated with this common underlying structural theme.     

Introducing site-specific glycosylation using protein engineering techniques reduces the immunogenicity of β-lactoglobulin

To reduce the immunogenicity of β-lactoglobulin (BLG), we prepared wild-type bovine BLG variant A (wt) and three site-specifically glycosylated BLGs (D28N, D137N/A139S, and P153A), and expressed them in the methylotrophic yeast Pichia pastoris by fusion of the cDNA to the sequence coding for the α-factor signal peptide from Saccharomyces cerevisiae. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis indicated that the glycosylated BLGs were conjugated with a ~4 kDa high-mannose chain. Each glycosylated BLG retained ～80% of the retinol-binding activity of BLG. Structural analyses by intrinsic fluorescence, CD spectra, and ELISA with monoclonal antibodies indicated that the surface structure was slightly changed by using protein engineering techniques, but that the site-specifically glycosylated BLGs were covered by high-mannose chains without substantial disruption of wt conformation. Antibody responses to the glycosylated BLGs tended to be weaker in BALB/c, C57BL/6, and C3H/He mice. We conclude that site-specific glycosylation is an effective method to reduce the immunogenicity of BLG, and that masking of epitopes by high-mannose chains is effective to reduce immunogenicity.     

Competition between the cyanobacterium Microcystis aeruginosa and the diatom Cyclotella sp. under nitrogen-limited condition caused by dilution in eutrophic lake

The improvement of water quality in Lake Tega, Japan, has been carried out by dilution, causing the shift of dominant species from Microcystis aeruginosa to Cyclotella sp. in summer. The disappearance of Microcystis blooms would be related to dilution, but the detail effect has not been understood yet. In this study, the effect of nitrate concentration on the competition between M. aeruginosa and Cyclotella sp. was investigated through the single-species and the competitive culture experiments. The single-species culture experiment indicated that the half saturation constants for M. aeruginosa and Cyclotella sp. were 0.016 and 0.234?mg?N L^?1, representing that M. aeruginosa would possess a higher affinity to nitrate. On the other hand, the maximum growth rate for Cyclotella sp. was obtained as 0.418?day^?1, which did not represent a significant difference with 0.366?day^?1 obtained for M. aeruginosa. The competitive culture experiment revealed that Cyclotella sp. completely dominated over M. aeruginosa at the nitrate concentrations of 0.5 and 2.5?mg?N L^?1. The dominance of Cyclotella sp. could be attributed to the difference in the abilities of nitrate storage as well as nitrate uptake. One of the possibilities for the disappearance of Microcystis blooms caused by dilution as observed in Lake Tega could be due to the decrease in nitrate concentration, and the lower N:P ratio seemed not to relate to Microcystis blooms.     

Mitotic inheritance of endoplasmic reticulum in the primitive red alga Cyanidioschyzon merolae

Endoplasmic reticulum (ER) is a major site for secretory protein folding and lipid synthesis. Since ER cannot be synthesized de novo, it must be inherited during the cell cycle. Studying ER inheritance can however be difficult because the ER of typical plant and animal cells is morphologically complex. Therefore, our study used Cyanidioschyzon merolae, a species that has a simple ER structure, to investigate the inheritance of this organelle. Using immunofluorescence microscopy, we demonstrated that C. merolae contains a nuclear ER (nuclear envelope) and a small amount of peripheral ER extending from the nuclear ER. During mitosis, the nuclear ER became dumbbell-shaped and underwent division. Peripheral ER formed ring-like structures during the G1 and S phases, and extended toward the mitochondria and cell division planes during the M phase. These observations indicated that C. merolae undergoes closed mitosis, whereby the nuclear ER does not diffuse, and the peripheral ER contains cell cycle-specific structures.     

Rapid detection of gene mutations responsible for non-syndromic aortic aneurysm and dissection using two different methods: resequencing microarray technology and next-generation sequencing

Aortic aneurysm and/or dissection (AAD) is a life-threatening condition, and several syndromes are known to be related to AAD. In this study, two new technologies, resequencing array technology (ResAT) and next-generation sequencing (NGS), were used to analyze eight genes associated with syndromic AAD in 70 patients with non-syndromic AAD. Eighteen sequence variants were detected using both ResAT and NGS. In addition one of these sequence variants was detected by ResAT only and two additional variants by NGS only. Three of the 18 variants are likely to be pathogenic (in 4.3% of AAD patients and in 8.6% of a subset of patients with thoracic AAD), highlighting the importance of genetic analysis in non-syndromic AAD. ResAT and NGS similarly detected most, but not all, of the variants. Resequencing array technology was a rapid and efficient method for detecting most nucleotide substitutions, but was unable to detect short insertions/deletions, and it is impractical to update custom arrays frequently. Next-generation sequencing was able to detect almost all types of mutation, but requires improved informatics methods.