Gene microarray analysis using angular distribution decomposition.

Clustering techniques have been widely used in the analysis of microarray data to group genes with similar expression profiles. The similarity of expression profiles and hence the results of clustering greatly depend on how the data has been transformed. We present a method that uses the relative expression changes between pairs of conditions and an angular transformation to define the similarity of gene expression patterns. The pairwise comparisons of experimental conditions can be chosen to reflect the purpose of clustering allowing control the definition of similarity between genes. A variational Bayes mixture modeling approach is then used to find clusters within the transformed data. The purpose of microarray data analysis is often to locate groups genes showing particular patterns of expression change and within these groups to locate specific target genes that may warrant further experimental investigation. We show that the angular transformation maps data to a representation from which information, in terms of relative regulation changes, can be automatically mined. This information can be then be used to understand the "features" of expression change important to different clusters allowing potentially interesting clusters to be easily located. Finally, we show how the genes within a cluster can be visualized in terms of their expression pattern and intensity change, allowing potential target genes to be highlighted within the clusters of interest.     

A primary subcutaneous infection with Paracoccidioides brasiliensis leads to immunoprotection or exacerbated disease depending on the route of challenge

In human and experimental paracoccidioidomycosis the severe disease is characterized by depressed cellular immunity whereas the mild disease is associated with persistent T cell immunity. Since the subcutaneous route of antigen inoculation is an efficient inducer of cellular immunity, we decided to study this route of infection and verify its effect on a lethal secondary infection of susceptible hosts. It was observed that the s.c. infection induces positive delayed type hypersensitivity (DTH) responses in 9 different mouse strains, is a self healing process and susceptible mice develop more intense DTH reactions than resistant mice to Paracoccidioides brasiliensis infection. Unexpectedly, the previous s.c. infection of susceptible mice led to immunoprotection or disease exacerbation depending on the route of fungal challenge. Immunoprotection was achieved after intraperitoneal challenge and was associated with persistent cell-mediated immunity and a mixed type-1/type-2 immunity. Exacerbated disease was found after intravenous challenge, was associated with cellular immunity anergy and prevalent type-2 immune response. As a whole, our work demonstrates that susceptibility to P. brasiliensis infection cannot be ascribed to intrinsic inability to mount cellular immune responses, that a single immunization procedure can result in opposite disease outcomes and immunoprotection can be achieved by a balanced Th1/Th2 immunity.     

MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets

MPP is a Java application, encompassing both new and established algorithms, for the analysis of gene and marker content datasets arising from high-throughput microarray techniques. MPP analyses flat file output from microarray experiments to determine the probability of the presence or absence of genes or markers within a genome. MPP can construct gene or marker content datasets for a number of genomes and can use the data to estimate an evolutionary tree or network. Results from gene content analyses may be validated by comparing them to known gene contents. MPP was initially developed to analyse data derived from comparative genome hybridization (CGH) microarray experiments in fungi and bacteria. It has recently been adapted to analyse retrotransposon-based insertion polymorphism (RBIP) marker scores derived from tagged microarray marker (TAM) experiments in pea. New analytical procedures may be added easily to MPP as plugins in order to increase the scope of the software. AVAILABILITY: MPP source code, executables and online help are available at http://cbr.jic.ac.uk/dicks/software/     

Susceptibility of compound 48/80-sensitized Pseudomonas aeruginosa to the hydrophobic biocide triclosan

Pseudomonas aeruginosa is intrinsically resistant to the hydrophobic biocide triclosan, and yet it can be sensitized to low concentrations by permeabilization of the outer membrane using compound 48/80. A selective plating assay revealed that compound 48/80-permeabilized YM64, a triclosan-recognizing efflux pump-deficient variant, was unable to initiate growth on a medium containing triclosan. Macrobroth dilution assay data revealed that treatment with compound 48/80 synergistically decreased minimal inhibitory concentrations of the hydrophobic antibacterial agents rifamycin SV and chloramphenicol for all cell envelope variant strains examined. A low concentration of triclosan exerted a transient bactericidal effect on permeabilized wild-type strain PAO1, after which exponential growth resumed within 4 h. Permeabilized strain YM64 was unable to overcome the inhibition; yet, both strains remained susceptible to chloramphenicol for as long as 6 h, thereby suggesting that the outer membrane remained permeable to nonpolar compounds. These data support the notion that the transitory nature of compound 48/80 sensitization to triclosan in P. aeruginosa does not involve obviation of the hydrophobic diffusion pathway through the outer membrane. The inability of strain YM64 to overcome the synergistic effect of compound 48/80 and triclosan strongly suggests that triclosan-recognizing efflux pumps are involved in maintaining viability in wild-type cells whose outer membranes are otherwise compromised.     

PD98059 enhanced insulin, cytokine, and growth factor activation of xanthine oxidoreductase in epithelial cells involves STAT3 and the glucocorticoid receptor

PD98059 and U0126 are organic compound inhibitors frequently used to block the activity of the MEK-1/2 protein kinase. In the present work, promoter activation analyses of xanthine oxidoreductase (XOR) in epithelial cells uncovered the unexpected opposite effect of these inhibitors on activation of XOR. Activation of an XOR-luciferase fusion gene was studied in stably transfected epithelial cells. The XOR reporter gene was activated by the epidermal growth factors (EGF), prolactin, and dexamethasone and by the acute phase cytokines (APC) IL-1, IL-6, and TNFalpha as previously reported for its native gene, and insulin further stimulated activation induced with acute phase cytokines or growth factors. Activation of the proximal promoter was blocked by inhibitors of the glucocorticoid receptor (GR), p38 MAP kinase, and U0126. Unexpectedly, PD98059 activated the promoter and significantly enhanced expression induced by insulin, APC, or growth factors. Analysis of the XOR upstream DNA and proximal promoter revealed primary roles for the GR and STAT3 in mediating the effects of PD98059 on XOR activation and protein complex formation with the promoter. STAT3 phosphotyrosine-705 was rapidly induced by PD98059, dexamethasone, and insulin. XOR activation by PD98059, dexamethasone, or insulin was superinduced by a constitutively active derivative of STAT3, while a dominant negative derivative of STAT3 blocked the enhancing effect of PD98059 on XOR activation. These data demonstrate a previously unrecognized effect of PD98059 on STAT3 and the GR that could have unanticipated consequences when used to infer the involvement of the MEK-1/2 protein kinase.     

Chromosome doubling in a <Emphasis Type="Italic">Rosa rugosa</Emphasis> Thunb. hybrid by exposure of in vitro nodes to oryzalin: the effects of node length,oryzalin concentration and exposure time

Chromosome doubling was induced in vitro in a diploid hybrid of Rosa rugosa Thunb. using oryzalin as the spindle inhibitor. Nodal sections, 2 mm long, were exposed to 2.5 or 5 μM oryzalin and 10 mm nodal sections were exposed to 5 μM oryzalin for 0 (controls), 6, 12, 24 and 48 h. The ploidy of the emergent shoots was determined by flow cytometry. The frequency of tetraploid and mixoploid leaves that developed from 2 mm nodal sections exposed to 5 μM oryzalin peaked at 12 h exposure, when 35% of the leaves were tetraploid, but fell after longer exposures. Fewer tetraploid and mixoploid leaves were found when 2 mm nodes were exposed to 2.5 μM oryzalin for 6 and 12 h, indicating that it took longer for a spindle inhibiting concentration of oryzalin to build up in the meristem. However, the frequencies of tetraploid and mixoploid leaves continued to rise after 12 h and were highest at 48 h, when 44% were tetraploid. In treatments with 5 μM oryzalin, the frequencies of tetraploid and mixoploid leaves were lower, at equivalent exposure times, in 10 mm nodes than 2 mm nodes. This suggests that oryzalin diffused to the meristem mainly via the cut surfaces and that access via the epidermis and cuticle was impeded.     

Plant Growth Regulators and Induction of Leaf Senescence in Nitrogen-Deprived Wheat Plants

The sequence of events and the signals that regulate the remobilization of nitrogen (N) reserves during senescence induced by N starvation were studied in leaf 3, the last fully expanded leaf, in 17-day-old wheat (Triticum aestivum L.) plants. The first event observed was a rapid decrease in the isopentenyl adenosine (iPA) concentration during the first 24 h of N starvation. No differences in t-zeatin riboside and dihydrozeatin riboside concentrations were observed until the end of the assay. During the following 6 days, a decrease in soluble amino acids, chlorophyll, and protein, as well as an increase in soluble sugar concentration and endoproteolytic activity, could be observed. At day 3 of the experiment, the abscisic acid (ABA) concentration in the leaves of N-deprived plants started to increase. After 6 days of N deprivation there was a rise in oxidative stress, as indicated by the increase in malondialdehyde concentration, as well as a decrease in the activities of antioxidant enzymes catalase and ascorbate peroxidase. To analyze interactions with leaf development, the first, second, third, and fourth leaves were studied. iPA concentration decreased in all the leaf stages, including leaf 4, which was not fully expanded. A linear correlation between iPA and protein concentration was determined. These results suggest that the sharp fall in iPA could be the earliest event that induces protein degradation during the development of senescence induced by N deficiency, and that only later is ABA accumulated and oxidative stress developed.     

Sphingosine-1-phosphate initiates rapid retraction of pseudopodia by localized RhoA activation

Lysophosphatidic acid (LPA) stimulates sphingosine-1-phosphate (S1P)-sensitive motility in NIH3T3 clone7 cells. S1P inhibits motility only when added to the bottom well of the Boyden chamber, suggesting that pseudopodia can respond to their microenvironment. In order to study and localize this effect, we utilized a Transwell insert system to isolate pseudopodia. LPA stimulates protrusion of pseudopodia that are enriched in RhoA compared to cell bodies. Removal of LPA results in slow retraction with loss of vinculin-rich adhesion complexes and prolonged activation of RhoA. However, RhoA, ROCK and mDia are not required for this process. In contrast, rapid retraction, induced by adding S1P to the bottom well, is associated with a quick spike of activated RhoA and coalescence of adhesion complexes that colocalize with the ends of stress fibers. S1P-induced retraction requires RhoA and ROCK but is only delayed by inhibition of mDia. These data indicate that pseudopodia sense and integrate signals initiated by localized bioactive lipids, affecting both cellular polarity and their own function in motility.     

Co-composting of hair waste from the tanning industry with de-inking and municipal wastewater sludges

Production of waste hair in the leather manufacturing industry is increasing every year due to the adoption of hair-save unhairing techniques, leaving the tanners with the problem of coping with yet another solid by-product. Numerous potential strategies for hair utilisation have been proposed. However, the use of hair waste as agricultural fertiliser is one of its most promising applications due to the high nitrogen content of hair. Agricultural value of hair can be increased by composting. This paper deals with the composting of hair from the unhairing of bovine hide. Results indicated that hair cannot be either composted on its own or co-composted with de-inking sludge, a chemical complementary co-substrate. However, good results were obtained when co-composted with raw sludge from a municipal wastewater treatment plant at hair:raw sludge weight ratios 1:1, 1:2 and, 1:4 in lab scale and pilot plant scale composters. In all cases, a more stable product was achieved at the end of the process. Composting in the pilot plant composter was effectively monitored using Static Respiration Indices determined at process temperature at sampling (SRI _T ) and at 37°C (SRI₃₇). Notably, SRI _T values were more sensitive to changes in the biological activity. In contrast, Respiratory Quotient (RQ) values were not adequate to follow the development of the process.