Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays

Background: Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples. Results: We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2 of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log(2) units (6 of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators. Conclusions: This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells.

Endocannabinoids in neuroendopsychology: multiphasic control of mitochondrial function

The endocannabinoid system (ECS) is a construct based on the discovery of receptors that are modulated by the plant compound tetrahydrocannabinol and the subsequent identification of a family of nascent ligands, the 'endocannabinoids'. The function of the ECS is thus defined by modulation of these receptors-in particular, by two of the best-described ligands (2-arachidonyl glycerol and anandamide), and by their metabolic pathways. Endocannabinoids are released by cell stress, and promote both cell survival and death according to concentration. The ECS appears to shift the immune system towards a type 2 response, while maintaining a positive energy balance and reducing anxiety. It may therefore be important in resolution of injury and inflammation. Data suggest that the ECS could potentially modulate mitochondrial function by several different pathways; this may help explain its actions in the central nervous system. Dose-related control of mitochondrial function could therefore provide an insight into its role in health and disease, and why it might have its own pathology, and possibly, new therapeutic directions.

Approximating a class of combinatorial problems with rational objective function

In the late seventies, Megiddo proposed a way to use an algorithm for the problem of minimizing a linear function a(0) + a(1)x(1) + ... + a(n)x(n) subject to certain constraints to solve the problem of minimizing a rational function of the form (a(0) + a(1)x(1) + ... + a(n)x(n))/(b(0) + b(1)x(1) + ... + b(n)x(n)) subject to the same set of constraints, assuming that the denominator is always positive. Using a rather strong assumption, Hashizume et al. extended Megiddo`s result to include approximation algorithms. Their assumption essentially asks for the existence of good approximation algorithms for optimization problems with possibly negative coefficients in the (linear) objective function, which is rather unusual for most combinatorial problems. In this paper, we present an alternative extension of Megiddo`s result for approximations that avoids this issue and applies to a large class of optimization problems. Specifically, we show that, if there is an alpha-approximation for the problem of minimizing a nonnegative linear function subject to constraints satisfying a certain increasing property then there is an alpha-approximation (1 1/alpha-approximation) for the problem of minimizing (maximizing) a nonnegative rational function subject to the same constraints. Our framework applies to covering problems and network design problems, among others.

Burrows with Chimneys of the Fiddler Crab Uca thayeri: Construction, Occurrence, and Function

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Ovary peltate trichomes of Zeyheria montana (Bignoniaceae): Developmental ultrastructure and secretion in relation to function

center dot Background and Aims Nectar production in the Bignoniaceae species lacking a nectariferous functional disc is ascribed to trichomatic glands around the ovary base and/or on the inner corolla wall. Nevertheless, knowledge about the secretion and function of these glands is very incomplete. The purpose of this paper is to study, from a developmental viewpoint, the ultrastructure, histochemistry and secretory process of the peltate trichomes on the ovary of Zeyheria montana, a species in the Bignoniaceae which has a rudimentary disc.center dot Methods Samples of the gynoecium at various developmental stages were fixed and processed for light and electron microscopy. Histochemistry and cytochemistry tests were performed to examine the chemical composition of exudates. Thin layer chromatography was used to determine the presence of alkaloids and terpenes in gynoecium and fruit extracts, and in fresh nectar stored in the nectar chamber.center dot Key Results Peltate trichomes at different developmental stages appear side by side from floral budding up to pre-dispersal fruit. Large plastids with an extensive internal membrane system consisting of tubules filled with lipophilic material, abundant smooth endoplasmic reticulum, few Golgi bodies, lipophilic deposits in the smooth endoplasmic reticulum and mitochondria, and scattered cytoplasmic oil droplets are the main characteristics of mature head cells. The secretion which accumulates in the subcuticular space stains positively for hydrophilic and lipophilic substances, with lipids prevailing for fully peltate trichomes. Histochemistry and thin layer chromatography detected terpenes and alkaloids. Fehling's test to detect of sugars in the secretion was negative.center dot Conclusions the continuous presence and activity of peltate trichomes on the ovary of Z. montana from early budding through to flowering and fruiting set, and its main chemical components, alkaloids and terpenes, suggest that they serve a protective function and are not related to the floral nectar source or to improving nectar quality.

Impairment of adult male reproductive function in rats exposed to ethanol since puberty

The objective of this work was to evaluate reproductive function in adult male rats exposed to ethanol since puberty. Male Wistar rats, 50 days old, received a liquid diet with 36% of the daily calories derived from ethanol or an isocaloric control diet for 55 days. The ethanol treatment impaired sexual behavior and only 22% of these rats reached ejaculation. The fertility of ethanol-treated animals was significantly reduced, mainly after natural mating. Serum testosterone levels, daily sperm production and sperm count in the epididymis were also significantly diminished after ethanol treatment, associated with an acceleration of the sperm transit time in the cauda epididymidis, decrease in sperm motility and increased percentage of abnormal shaped sperm cells. The results showed that chronic consumption of ethanol beginning at puberty impairs the reproductive function of adult male rats. (c) 2006 Elsevier B.V. All rights reserved.

New insights regarding HCV-NS5A structure/function and indication of genotypic differences

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Black hole partition function using the hybrid formalism of superstrings

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The high-eccentricity asymmetric expansion of the disturbing function for non-planar resonant problems

In this paper we present an extension to the nonplanar case of the asymmetric expansion of the averaged resonant disturbing function of Ferraz-Mello & Sato (1989, A&A 225, 541-547). Comparions with the exact averaged disturbing function are also presented. The expansion gives a good approximation of the exact function in a wide region around the center of expansion.

Relative contributions of beta-cell function and tissue insulin sensitivity to fasting and postglucose-load glycemia

We performed hyperglycemic clamps in 283 nondiabetic Caucasians and, with multiple linear regression, determined the contribution of beta-cell function and tissue insulin sensitivity to variations in glycemia and insulinemia during oral glucose tolerance tests (OGTTs). Impaired glucose tolerance (IGT) subjects had reduced insulin sensitivity(P < .02) and beta-cell function (P < .0001). Normal glucose tolerance (NGT) subjects with first-degree type 2 diabetic relatives had reduced first and second phase insulin secretion (both, P < .05), but normal insulin sensitivity(P = .37). beta-Cell function and insulin sensitivity accounted for one fourth of the variability in glucose tolerance. Fasting plasma glucose in subjects with NGT (n = 185) was a function of both phases of insulin secretion and of insulin sensitivity tall, P < .05), whereas, in IGT subjects (n = 98), it was a function of first phase insulin secretion and insulin sensitivity(P < .01). Two-hour glycemia was a function of second phase secretion and insulin sensitivity (P < .01). Fasting and 2-hour plasma insulin levels were determined by insulin sensitivity land glycemia) in NGT subjects (P < .001), but by second phase secretion in IGT (P < .001). We conclude that beta-cell function is reduced in subjects with IGT; glycemia and insulinemia are not regulated by the same mechanisms in IGT and NGT; insulin sensitivity does not contribute to insulinemia in IGT; family history of diabetes influences beta-cell function, but not insulin sensitivity in Caucasians. Copyright (C) 2000 by W.B. Saunders Company.

Time evolution of the structure function and dynamical scaling in porous SnO2 dry gels

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Ant-tended hemiptera in Amazonian myrmecophytes: Patterns of abundance and implications for mutualism function (Hymenoptera: Formicidae)

We assessed how the abundance of ant-tended Hemiptera associated with two Amazonian myrmecophytes, Tococa bullifera and Maieta guianensis, varied as a function of resident ant species. We collected five species or morpho-species of adult hemiptera in the domatia of M. guianensis, with four of these species also found in Tococa bullifera. Maieta guianensis plants inhabited by Crematogaster laevis had over four-fold more hemiptera in them than plants inhabited by Pheidole minutula. In contrast, the density of hemiptera in Tococa bullifera domatia was independent of the species of ant resident. For each of the two ant species inhabiting Maieta guianensis, there was a positive and significant relationship between the abundance of hemiptera and workers inhabiting a plant. This relationship was also significant and positive for the Tococa bullifera plants inhabited by C. laevis. However, there was no relationship between Azteca worker and hemipteran density, although there was a trend towards a positive relationship. Our results indicate that hemipteran abundance can vary significantly between different myrmecophyte species, but that the nature of this relationship is mediated by the identity of the ant associate. Because hemipterans are herbivores, the costs and benefits of different ant partners to the host plant may vary in ways that are often overlooked.

eIF5A has a function in the cotranslational translocation of proteins into the ER

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Immediate and long-term effects of psychological stress during adolescence in cardiovascular function: comparison of homotypic vs heterotypic stress regimens

Adolescence has been proposed as an ontogenic period of vulnerability to stress. Nevertheless, the impact of stressful events during adolescence in cardiovascular activity is poorly understood. Therefore, the purpose of this study was to investigate the immediate and long-lasting effects of exposure to stressful events during adolescence in cardiovascular function of rats. To this end, we compared the impact of 10-days exposure to two chronic stress protocols: the repeated restraint stress (RRS, homotypic) and chronic variable stress (CVS, heterotypic). Independent groups of animals were tested 24 h (immediate) or three weeks (long-lasting) following completion of stress period. Exposure to CVS, but not RRS, during adolescence increased basal HR values without affecting arterial pressure, which was followed by augmented power of oscillatory component at low frequency (sympathetic-related) of the pulse interval (PI). RRS enhanced variance of the PI with an increase in the power of both low and high (parasympathetic-related) frequency components. RRS also increased the baroreflex gain. Neither RRS nor CVS affected systolic arterial pressure variability. The RRS-evoked changes in PI variability were long-lasting and persisted into adulthood while all alterations evoked by the CVS were reversed in adulthood. These findings indicate a stress type-specific influence in immediate and long-term effects of stress during adolescence in cardiovascular function. While immediate changes in cardiovascular function were mainly observed following CVS, long-lasting autonomic consequences in adulthood were observed only in animals exposed to RRS during adolescence.

Measurement of differential cross sections for the production of a pair of isolated photons in pp collisions at root s=7TeV

A measurement of differential cross sections for the production of a pair of isolated photons in proton-proton collisions at root s = 7 TeV is presented. The data sample corresponds to an integrated luminosity of 5.0 fb(-1) collected with the CMS detector. A data-driven isolation template method is used to extract the prompt diphoton yield. The measured cross section for two isolated photons, with transverse energy above 40 and 25 GeV respectively, in the pseudorapidity range vertical bar eta vertical bar < 2.5, vertical bar eta vertical bar (sic) [1.44, 1.57] and with an angular separation Delta R > 0.45, is 17.2 +/-0.2 (stat) +/-1.9 (syst) +/- 0.4 (lumi) pb. Differential cross sections are measured as a function of the diphoton invariant mass, the diphoton transverse momentum, the azimuthal angle difference between the two photons, and the cosine of the polar angle in the Collins-Soper reference frame of the diphoton system. The results are compared to theoretical predictions at leading, next-to-leading, and next-to-next-to-leading order in quantum chromodynamics.