56 research outputs found

    Computational expression deconvolution in a complex mammalian organ

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    BACKGROUND: Microarray expression profiling has been widely used to identify differentially expressed genes in complex cellular systems. However, while such methods can be used to directly infer intracellular regulation within homogeneous cell populations, interpretation of in vivo gene expression data derived from complex organs composed of multiple cell types is more problematic. Specifically, observed changes in gene expression may be due either to changes in gene regulation within a given cell type or to changes in the relative abundance of expressing cell types. Consequently, bona fide changes in intrinsic gene regulation may be either mimicked or masked by changes in the relative proportion of different cell types. To date, few analytical approaches have addressed this problem. RESULTS: We have chosen to apply a computational method for deconvoluting gene expression profiles derived from intact tissues by using reference expression data for purified populations of the constituent cell types of the mammary gland. These data were used to estimate changes in the relative proportions of different cell types during murine mammary gland development and Ras-induced mammary tumorigenesis. These computational estimates of changing compartment sizes were then used to enrich lists of differentially expressed genes for transcripts that change as a function of intrinsic intracellular regulation rather than shifts in the relative abundance of expressing cell types. Using this approach, we have demonstrated that adjusting mammary gene expression profiles for changes in three principal compartments – epithelium, white adipose tissue, and brown adipose tissue – is sufficient both to reduce false-positive changes in gene expression due solely to changes in compartment sizes and to reduce false-negative changes by unmasking genuine alterations in gene expression that were otherwise obscured by changes in compartment sizes. CONCLUSION: By adjusting gene expression values for changes in the sizes of cell type-specific compartments, this computational deconvolution method has the potential to increase both the sensitivity and specificity of differential gene expression experiments performed on complex tissues. Given the necessity for understanding complex biological processes such as development and carcinogenesis within the context of intact tissues, this approach offers substantial utility and should be broadly applicable to identifying gene expression changes in tissues composed of multiple cell types

    Biochemical characterization of patients with dihydrolipoamide dehydrogenase deficiency

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    Dihydrolipoamide dehydrogenase (DLD; E3) oxidizes lipoic acid. Restoring the oxidized state allows lipoic acid to act as a necessary electron sink for the four mitochondrial keto-acid dehydrogenases: pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase, branched-chain α-keto-acid dehydrogenase, and 2-oxoadipate dehydrogenase. DLD deficiency (DLDD) is caused by biallelic pathogenic variants i

    Genomic analysis of early murine mammary gland development using novel probe-level algorithms

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    We describe a novel algorithm (ChipStat) for detecting gene-expression changes utilizing probe-level comparisons of replicate Affymetrix oligonucleotide microarray data. A combined detection approach is shown to yield greater sensitivity than a number of widely used methodologies including SAM, dChip and logit-T. Using this approach, we identify alterations in functional pathways during murine neonatal-pubertal mammary development that include the coordinate upregulation of major urinary proteins and the downregulation of loci exhibiting reciprocal imprinting

    The Impact of Tobacco Control Policies on Smoking Among Socioeconomic Groups in Nine European Countries, 1990-2007

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    Background: It is uncertain whether tobacco control policies have contributed to a narrowing or widening of socioeconomic inequalities in smoking in European countries during the past two decades. This paper aims to investigate the impact of price and non-price related population-wide tobacco control policies on smoking by socioeconomic group in nine European countries between 1990 and 2007. Methods: Individual-level education, occupation and smoking status were obtained from nationally representative surveys. Country-level price-related tobacco control policies were measured by the relative price of cheapest cigarettes and of cigarettes in the most popular price category. Country-level non-price policies were measured by a summary score covering four policy domains: smoking bans or restrictions in public places and workplaces, bans on advertising and promotion, health warning labels, and cessation services. The associations between policies and smoking were explored using logistic regressions, stratified by education and occupation, and adjusted for age, Gross Domestic Product, period and country fixed effects. Results: The price of popular cigarettes and non-price policies were negatively associated with smoking among men. The price of the cheapest cigarettes was negatively associated with smoking among women. While these favorable effects were generally in the same direction for all socioeconomic groups, they were larger and statistically significant in lower socioeconomic groups only. Conclusions: Tobacco control policies as implemented in nine European countries, have probably helped to reduce the prevalence of smoking in the total population, particularly in lower socioeconomic groups. Widening inequalities in smoking may be explained by other factors. Policies with larger effects on lower socioeconomic groups are needed to reverse this trend. Implications: Socioeconomic inequalities in smoking widened between the 1990s and the 2000s in Europe. During the same period, there were intensified tobacco control policies in many European countries. It is uncertain whether tobacco control policies have contributed to a narrowing or widening of socioeconomic inequalities in smoking in European countries. This study shows that tobacco control policies as implemented in the available European countries have helped to reduce the prevalence of smoking in the total population, particularly in lower socioeconomic groups. Widening inequalities in smoking may be explained by other factors.Peer reviewe

    Networked T Cell Death following Macrophage Infection by Mycobacterium tuberculosis

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    <div><h3>Background</h3><p>Depletion of T cells following infection by <em>Mycobacterium tuberculosis</em> (Mtb) impairs disease resolution, and interferes with clinical test performance that relies on cell-mediated immunity. A number of mechanisms contribute to this T cell suppression, such as activation-induced death and trafficking of T cells out of the peripheral circulation and into the diseased lungs. The extent to which Mtb infection of human macrophages affects T cell viability however, is not well characterised.</p> <h3>Methodology/Principal Findings</h3><p>We found that lymphopenia (<1.5×10<sup>9</sup> cells/l) was prevalent among culture-positive tuberculosis patients, and lymphocyte counts significantly improved post-therapy. We previously reported that Mtb-infected human macrophages resulted in death of infected and uninfected bystander macrophages. In the current study, we sought to examine the influence of infected human alveolar macrophages on T cells. We infected primary human alveolar macrophages (the primary host cell for Mtb) or PMA-differentiated THP-1 cells with Mtb H37Ra, then prepared cell-free supernatants. The supernatants of Mtb-infected macrophages caused dose-dependent, caspase-dependent, T cell apoptosis. This toxic effect of infected macrophage secreted factors did not require TNF-α or Fas. The supernatant cytotoxic signal(s) were heat-labile and greater than 50 kDa in molecular size. Although ESAT-6 was toxic to T cells, other Mtb-secreted factors tested did not influence T cell viability; nor did macrophage-free Mtb bacilli or broth from Mtb cultures. Furthermore, supernatants from <em>Mycobacterium bovis</em> Bacille de Calmette et Guerin (BCG)- infected macrophages also elicited T cell death suggesting that ESAT-6 itself, although cytotoxic, was not the principal mediator of T cell death in our system.</p> <h3>Conclusions</h3><p>Mtb-Infected macrophages secrete heat-labile factors that are toxic to T cells, and may contribute to the immunosuppression seen in tuberculosis as well as interfere with microbial eradication in the granuloma.</p> </div

    "The End of Immortality!" Eternal Life and the Makropulos Debate

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    Responding to a well-known essay by Bernard Williams, philosophers (and a few theologians) have engaged in what I call “the Makropulos debate,” a debate over whether immortality—“living forever”—would be desirable for beings like us. Lacking a firm conceptual grounding in the religious contexts from which terms such as “immortality” and “eternal life” gain much of their sense, the debate has consisted chiefly in a battle of speculative fantasies. Having presented my four main reasons for this assessment, I examine an alternative and neglected conception, the idea of eternal life as a present possession, derived in large part from Johannine Christianity. Without claiming to argue for the truth of this conception, I present its investigation as exemplifying a conceptually fruitful direction of inquiry into immortality or eternal life, one which takes seriously the religious and ethical surroundings of these concepts
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