The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies

Background  

Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers.     

Alpha-tocopherol amplifies benzoyl peroxide free radical decomposition in a chemical system

Benzoyl peroxide is commonly used in the treatment of acne, even though some adverse effects have been reported, probably mediated by the formation of peroxide-derived free radicals and the depletion of antioxidants. In the present work we have studied, in a chemical system, the effect of alpha-tocopherol on benzoyl peroxide radical decomposition to analyse the presence of an interaction between these two compounds, leading to an enhanced peroxide-cytotoxicity, as we have previously reported. Under our experimental conditions alpha-tocopherol strongly amplified the peroxide free radical decomposition occurring either in the presence or in the absence of UV irradiation, and lead to the formation of an unknown radical species in addition to benzoyloxy, phenyl and tocopheroxyl free radicals. The results of this study show that the enhancement of benzoyl peroxide toxicity in cells exposed simultaneously to this peroxide and alpha-tocopherol, is likely due to the generation of the detected radical species.     

Embryo recovery rate and recipients’ pregnancy rate after nonsurgical embryo transfer in donkeys

Sixty-three embryos were recovered out of 83 estrous cycles (75.9%) and 98 ovulations (64.3%) of five Pantesca jennies, 2 to 5 yr old, naturally mated or artificially inseminated with fresh semen. Embryo recovery rate was influenced by number of ovulations per cycle (133% and 63% for double and single ovulations, respectively), by the day of embryo recovery attempt (12%, 83%, and 75% at Days 7, 8, and 9 after ovulation, respectively), and by the repetition of the embryo recovery attempt on successive cycles (60%, 79%, and 100% for cycles 1 to 7, 8 to 14, and 15 to 24, respectively). All recovered embryos but three were classified as good or excellent. Of 58 nonsurgical embryo transfers to Ragusana jenny recipients, 13 (22.4%), 10 (17.2%), and 9 (15.5%) resulted in a pregnancy at Days 14, 25, and 50, respectively. Recipients’ pregnancy rate was not influenced by the evaluated parameters: embryo quality and age, media employed to wash embryos, days after ovulation of the recipient, experience of the operator. Between 14 and 50 d of pregnancy, 4 of 13 (30.7%) embryos were lost with an influence of the days from ovulation of the recipient: recipients at Days 5 or 6 kept all pregnancies (N = 7), whereas recipients at Days 7 or 8 lost 3 of 4 pregnancies, as one of the two recipients at Day 3. More studies are needed before embryo transfer could be considered a reliable tool to preserve endangered donkey breeds.     

Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1

The focus of this study was to analyze the content, distribution, and comparative genome relationships of 996 chromosome bin-mapped expressed sequence tags (ESTs) accounting for 2266 restriction fragments (loci) on the homoeologous group 3 chromosomes of hexaploid wheat (Triticum aestivum L.). Of these loci, 634, 884, and 748 were mapped on chromosomes 3A, 3B, and 3D, respectively. The individual chromosome bin maps revealed bins with a high density of mapped ESTs in the distal region and bins of low density in the proximal region of the chromosome arms, with the exception of 3DS and 3DL. These distributions were more localized on the higher-resolution group 3 consensus map with intermediate regions of high-mapped-EST density on both chromosome arms. Gene ontology (GO) classification of mapped ESTs was not significantly different for homoeologous group 3 chromosomes compared to the other groups. A combined analysis of the individual bin maps using 537 of the mapped ESTs revealed rearrangements between the group 3 chromosomes. Approximately 232 (44%) of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large- and small-scale differences in gene order. Of the group 3 mapped EST unigenes approximately 21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected.     

Parameter estimation in a model for multidimensional recording of neuronal data: a Gibbsian approximation approach

This article proposes improved numerical procedures for estimating parameters in a spatiotemporal lattice model introduced for the analysis of cortical activities monitored from arrays of diodes. The numerical algorithms are based on approximations inspired by statistical physics. Both Gibbsian and mean-field approximations are used; they allow for computing local conditional probabilities inside the lattice. The statistical procedures rely on the computation of pseudomaximum-likelihood estimators. The estimators are evaluated on the basis of Monte Carlo simulations. These simulations show that mean-field approximations are useful for reducing the variance of estimators when the data are recorded from arrays of 144 diodes (which are in accordance with standard practice). In light of these improved methods, we give new interpretations for a data set obtained from optical recording of a Guinea pig's auditory cortex in response to pure tone stimulations.     

Free radical generation during chemical depolymerization of heparin

Low-molecular weight heparins (LMWHs), as compared with unfractionated heparin (UFH), present superior bioavailability, much longer plasma half-life, and lower incidence of side effects. For these reasons, over the past two decades LMWHs have become the drugs of choice for the treatment of deep venous thrombosis, pulmonary embolism, arterial thrombosis, and unstable angina. Furthermore, their use in acute ischemic stroke is currently under study. LMWHs are obtained by UFH depolymerization, which can be performed using various methods, including nitrous acid depolymerization, cleavage by beta-elimination of benzyl ester, enzymatic depolymerization, and peroxyl radical-dependent depolymerization. This article addresses the chemical depolymerization, obtained by free radical attack (mainly hydroxyl radical), of heparin. The electron spin resonance (ESR) spectroscopy, coupled to the spin trapping technique, was employed to study this reaction. Free radical-mediated heparin depolymerization was performed under different chemical conditions. The final products of the reactions were purified and classified on the basis of their molecular weight and other characteristics. The level of heparin fragmentation was different depending on the type of depolymerization reaction used. Moreover, the level of reproducibility and the resulting radical species were different for every type of reaction performed.     

Plant regeneration from immature cotyledon explant cultures of bean (P. coccineus L.)

A method for plant regeneration, via organogenesis and somatic embryogenesis, from P. coccineus is described. Immature cotyledons from plants regenerated and cloned in previous experiments were used. The highest percentage of regeneration (37.5%) was observed from the cotyledons of clone C7 on a modified Murashige & Skoog basal medium to which (2-isopentenyl)adenine (2iP, 10 mg l^-1) and 2-naphthoxyacetic acid (NOA, 0.05 mg l^-1) were added. On average, the same medium gave the highest percentage of regeneration also from the cotyledons of the 7 clones of P. coccineus used in the experiment. Newly regenerated plants were normally fertile. The procedure described may serve for induction of somaclonal variation for in vitro selection of valuable genotypes and for genetic transformation by A. tumefaciens.Abbreviations 6BA 6-benzylaminopurine - CCC chlorocholine chloride - IAA indole-3-acetic acid - 2iP (2-isopentenyl)adenine - NOA 2-naphthoxyacetic acid     

Comparison between two peptide epitopes presented to cytotoxic T lymphocytes by HLA-A2. Evidence for discrete locations within HLA-A2

An influenza B virus nucleoprotein (BNP) peptide, residues 82-94, defined by limited sequence homology with an HLA-A2-restricted peptide from influenza A matrix protein, was recognized by HLA-A2-restricted CTL. Reciprocal inhibition of T cell recognition by the two peptides suggest that the BNP peptide may have lower avidity for HLA-A2 molecules than the matrix peptide. The interaction between this peptide and HLA-A2 was explored by studying the CTL recognition of BNP 82-94 presented by mutant HLA-A2 molecules. Mutations at residues 9, 99, 70, 74, 152 and 156 were found to abolish T cell recognition of the BNP peptide. These results were compared with results previously obtained with the influenza A matrix peptide and suggest that the two peptides bind differently in the peptide binding site.