Evaluation of microarray data normalization procedures using spike-in experiments

Background  

Recently, a large number of methods for the analysis of microarray data have been proposed but there are few comparisons of their relative performances. By using so-called spike-in experiments, it is possible to characterize the analyzed data and thereby enable comparisons of different analysis methods.     

Effect of Selected Types of Beer on Bacteria of the Genus Arcobacter

The genus Arcobacter is related to the well-known human pathogen, Campylobacter jejuni, and has been linked to human diseases. In this study, the survival of Arcobacter spp. in various concentrations of ethanol, in various samples of beers, and in a model stomach has been investigated. For most of these bacteria, a concentration of 10 % ethanol was determined to be the minimum inhibitory concentration. The fact that these organisms are able to survive under these conditions may have an impact in the food processing industry. We studied the activity of beer against arcobacters. These bacteria were killed in all samples of beer within 30 min. A model stomach, containing a food matrix and a synthetic gastric fluid, was used to deduce the effect of beer against Arcobacter spp. during food consumption. Complete inactivation of all monitored arcobacters was detected usually within 15 min. However, the presence of beer does not potentiate the effect of gastric fluid against these bacteria. This is apparently the first study focusing upon the effect of beer on Arcobacter spp.     

An integrative approach to unravel the Ceratitis FAR (Diptera,Tephritidae) cryptic species complex: a review

This paper reviews all information gathered from different disciplines and studies to resolve the species status within the Ceratitis FAR (Ceratitis fasciventris, Ceratitis anonae, Ceratitis rosa) complex, a group of polyphagous fruit fly pest species (Diptera, Tephritidae) from Africa. It includes information on larval and adult morphology, wing morphometrics, cuticular hydrocarbons, pheromones, microsatellites, developmental physiology and geographic distribution. The general consensus is that the FAR complex comprises Ceratitis anonae, two species within Ceratitis rosa (so-called R1 and R2) and two putatitve species under Ceratitis fasciventris. The information regarding the latter is, however, too limited to draw final conclusions on specific status. Evidence for this recognition is discussed with reference to publications providing further details.     

Vitamin C for DNA damage prevention

The ability of vitamin C to affect genetic damage was reviewed in human studies that used molecular epidemiology methods, including analysis of DNA adducts, DNA strand breakage (using the Comet assay), oxidative damage measured as levels of 8-oxo-7,8-dihydroxy-2'-deoxyguanosine (8-oxodG), cytogenetic analysis of chromosomal aberrations and micronuclei, and the induction of DNA repair proteins. The protective effect of vitamin C was observed at plasma levels>50μmol/l. Vitamin C supplementation decreased the frequency of chromosomal aberrations in groups with insufficient dietary intake who were occupationally exposed to mutagens, and also decreased the sensitivity to mutagens as assessed using the bleomycin assay. High vitamin C levels in plasma decreased the frequency of genomic translocations in groups exposed to ionizing radiation or c-PAHs in polluted air. The frequency of micronuclei was decreased by vitamin C supplementation in smokers challenged with γ-irradiation, and higher vitamin C levels in plasma counteracted the damage induced by air pollution. The prevalence of DNA adducts inversely correlated with vitamin C levels in groups environmentally exposed to high concentrations of c-PAHs. Increased vitamin C levels decreased DNA strand breakage induced by air pollution. Oxidative damage (8-oxodG levels) was decreased by vitamin C supplementation in groups with plasma levels>50μmol/l exposed to PM2.5 and c-PAHs. Modulation of DNA repair by vitamin C supplementation was observed both in poorly nourished subjects and in groups with vitamin C plasma levels>50μmol/l exposed to higher concentrations of c-PAHs. It is possible that the impact of vitamin C on DNA damage depends both on background values of vitamin C in the individual as well as on the level of exposure to xenobiotics or oxidative stress.     

Postnatal development of phospholipids and their fatty acid profile in rat heart

The aim of this study was to determine the concentration of phospholipids (PL), plasmalogen components of choline (PC) and ethanolamine (PE) phosphoglycerides (PLPC, PLPE) and fatty acid profile of PL and triacylglycerols (TAG) in developing rat left ventricular myocardium between postnatal day (d) 2 and 100. The steepest increase of total PL (TPL) concentration occurs between d2 and d5, followed by a further slower increase between d20 and d40. Similar developmental changes were observed in PC and PE. The PLPE concentration rises by d10, whereas PLPC does not change during the whole period investigated, except for the transient decline on d5. The concentration of diphosphatidylglycerol (DPG) increases by d60; the steepest rise occurs between d20 and d40. Phosphatidylinositol (PI) concentration rises only by d5. The concentration of phosphatidylserine (PS) decreases between d5 and d10 and then it does not change. Sphingomyelin (SM) concentration is maintained till d10, it declines on d20 and does not change thereafter. The proportion of saturated fatty acids (SFA) increases by d5 in PC, PE, PS and TAG, and by d10 in DPG and PI. After d20 the SFA proportion gradually decline in all lipids. Monounsaturated FA (MUFA) proportion decreases in PC, PE, PI and PS from d2 till d10, and in the weaning period it tends to rise again. In contrast, in DPG and TAG the proportion of MUFA declines during the whole postnatal period. N-6 polyunsaturated FA (PUFA) decrease in all PL by d20 and rise again thereafter; in TAG they decline between d2 and d10 and return to the initial level by d100. N-3 PUFA increase in all PL during the suckling period and decline after weaning; in TAG they increase only by d5 and then they decline. This remodeling of myocardial PL and TAG composition during postnatal development may affect membrane properties and contribute to developmental changes in the function of membrane proteins and cell signaling.     

Modelling of β-d-glucopyranose ring distortion in different force fields: a metadynamics study

Modelling of carbohydrate conformations is a challenging task for force field developers. Three carbohydrate force fields, namely GLYCAM06, GROMOS 45a4 and OPLS were evaluated. Free energies of different ring conformations of β-d-glucopyranose were calculated using metadynamics in vacuum as well as in explicitly modelled water. All three force fields model the ⁴C₁ conformation as the most stable by at least 6 kJ/mol, as compared to other conformations. Interconversion from the ⁴C₁ to any other conformation is associated with a barrier of no lower than 26 kJ/mol. The free energy surface calculated in the GLYCAM06 force field is in remarkably good agreement with the recent Car-Parrinello metadynamics study. The effect of a water environment is relatively low and analogous in all tested force fields. Namely, the presence of water stabilizes the upper-left (^3,OB) versus bottom-right (B_3,O) area of Stoddard’s plot, relative to the situation in vacuum. Comparison of free and potential surfaces is also provided for vacuum calculations.     

Phylogeny of the leafy liverwort Ptilidium: cryptic speciation and shared haplotypes between the Northern and Southern Hemispheres

The small, phylogenetically isolated liverwort genus Ptilidium has been regarded as of cool-Gondwanic origin with the bipolar, terrestrial Ptilidium ciliare giving rise to the Northern Hemisphere epiphytes Ptilidium pulcherrimum and Ptilidium californicum. This hypothesis is examined using a dataset including three chloroplast DNA regions from 134 Ptilidium accessions and one accession each of its closest relatives Trichocoleopsis and Neotrichocolea. Maximum likelihood and parsimony analyses point to a close relationship between P. ciliare and P. pulcherrimum, whereas P. californicum is placed sister to the remainder of the genus, separated by a long branch. Haplotype analysis and our phylogeny indicate the presence of Southern Hemisphere haplotypes of P. ciliare in the Northern Hemisphere, and shared haplotypes of P. ciliare and P. pulcherrimum between Europe and North America. Based on our findings, we reject the Gondwana-scenario and propose recent long distance dispersal as an explanation for the bipolar disjunct range. Ptilidium ciliare is resolved as paraphyletic with P. pulcherrimum nested within it. An isolated Ptilidium lineage with the morphology of P. ciliare from the Himalaya region likely represents a hitherto unrecognized cryptic species. Ptilidium pulcherrimum splits into a Japanese clade and a clade with accessions from Europe and North America.     

Is there a signal transduction pathway that links events at the plasma membrane to the phosphorylation state of the mitochondrial pyruvate dehydrogenase complex?

Monoclonal antibodies against the E1α subunit of pyruvate dehydrogenase (PDH) were used to quantify the mitochondrial pyruvate dehydrogenase complex (mtPDC) by enzyme-linked immunosorbent assay (ELISA). Recombinant Arabidopsis thaliana PDH (E1) was used to calibrate the ELISA. Antibodies against a synthetic phosphopeptide corresponding to phosphorylation site one of E1α were used in an ELISA to quantify phospho-PDC (P-PDC). For calibration of the second ELISA, recombinant E1 was phosphorylated in vitro with recombinant A. thaliana E1-kinase. The two ELISA were used to quantify mitochondrial total- and P-PDC in clarified homogenates from Nicotiana tabacum BY-2 suspension cells. The level of mtPDC remained constant throughout the 7-day growth cycle at 25.1 g⁻¹ FW. During the lag (days 0–2) and stationary (day 7) stages of the growth cycle, the mtPDC was completely phosphorylated (inactive), whereas during the log-growth stage it was completely dephosphorylated (active). Exposure of 3- or 7-day posttransfer suspension cells to osmotic stress significantly decreased proportion of P-PDC. A series of pharmacological studies were undertaken to gain insight into the signal transduction pathways coupling osmotic stress perception with control of mitochondrial respiration. Results from these studies indicate a signal transduction pathway linking stress perception to control of mitochondrial respiration that includes protein kinases and phosphoprotein phosphatases.