Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

ABSTRACT: BACKGROUND: Gene-set enrichment analyses (GEA or GSEA) are commonly used for biological characterization of an experimental gene-set. This is done by finding known functional categories, such as pathways or Gene Ontology terms, that are over-represented in the experimental set; the assessment is based on an overlap statistic. Rich biological information in terms of gene interaction network is now widely available, but this topological information is not used by GEA, so there is a need for methods that exploit this type of information in high-throughput data analysis. RESULTS: We developed a method of network enrichment analysis (NEA) that extends the overlap statistic in GEA to network links between genes in the experimental set and those in the functional categories. For the crucial step in statistical inference, we developed a fast network randomization algorithm in order to obtain the distribution of any network statistic under the null hypothesis of no association between an experimental gene-set and a functional category. We illustrate the NEA method using gene and protein expression data from a lung cancer study. CONCLUSIONS: The results indicate that the NEA method is more powerful than the traditional GEA, primarily because the relationships between gene sets were more strongly captured by network connectivity rather than by simple overlaps.     

Single-Step Purification of Two Functional Human Apolipoprotein E Variants Hyperexpressed inEscherichia coli

We have cloned, from total human liver RNA, the cDNA encoding apolipoprotein E3 (apoE3). Site-directed mutagenesis was used to obtain the cDNA encoding the apoE4 isoform, a major variant of this apolipoprotein in man. These two cDNAs were subcloned into the procaryotic expression vector pAHRS. A polyhistidine tag was added at the NH₂-termini of the recombinant proteins (apoE3 and apoE4) to enable rapid purification. The resulting plasmids (pAHRS-apoE3 and pAHRS-apoE4) were introduced into theEscherichia colistrain BL21(DE3). Recombinant strains were grown at 37°C in a Luria and Bertani medium and the addition of isopropyl β-thiogalactoside resulted in the expression of large amounts of apoE protein (40.5 kDa), representing at least 15% of cellular proteins. The recombinant apoE isoforms were purified, under denaturating conditions, in one step by affinity chromatography on a Ni-chelated agarose column, yielding to about 20 mg of 96% pure protein per liter of culture. Compared to plasma apoE3 purified from human very low density lipoproteins, the two renatured recombinant apoE isoforms have the same secondary structure content, as revealed by circular dichroism measurement. Moreover, the recombinant apoE3 isoform shares similar properties for the association with lipids, compared to the human protein, indicating that the addition of the amino-terminal polyhistidine peptide does not influence the structure and the lipid binding properties of this recombinant apoE isoform. No differences in the secondary structure of recombinant apoE4 were detected, whereas this isoform presents specific reactivity with lipids. This simple and rapid procedure for the expression and the purification of functional recombinant apoE should therefore enable structural and physiological studies requiring large amounts of these apolipoproteins.     

Why People Drink Shampoo? Food Imitating Products Are Fooling Brains and Endangering Consumers for Marketing Purposes

A Food Imitating Product (FIP) is a household cleaner or a personal care product that exhibits food attributes in order to enrich consumption experience. As revealed by many cases worldwide, such a marketing strategy led to unintentional self-poisonings and deaths. FIPs therefore constitute a very serious health and public policy issue. To understand why FIPs are a threat, we first conducted a qualitative analysis on real-life cases of household cleaners and personal care products-related phone calls at a poison control center followed by a behavioral experiment. Unintentional self-poisoning in the home following the accidental ingestion of a hygiene product by a healthy adult is very likely to result from these products being packaged like foodstuffs. Our hypothesis is that FIPs are non-verbal food metaphors that could fool the brain of consumers. We therefore conducted a subsequent functional neuroimaging (fMRI) experiment that revealed how visual processing of FIPs leads to cortical taste inferences. Considered in the grounded cognition perspective, the results of our studies reveal that healthy adults can unintentionally categorize a personal care product as something edible when a food-like package is employed to market nonedible and/or dangerous products. Our methodology combining field (qualitative) and laboratory (behavioral and functional neuroimaging) findings could be of particular relevance for policy makers, as it can help screening products prior to their market release – e.g. the way they are packaged and how they can potentially confuse the mind of consumers – and therefore save lives.     

Energy requirement for biosynthesis of DNA in Escherichia coli: Role of membrane-bound energy-transducing ATPase (coupling factor)

A mutant of Escherichia coli missing energy-transducing ATPase and known to be defective in a variety of membrane functions from earlier studies (Yamamoto, T. H., Mével-Ninio, M. and Valentine, R. C. (1973) Biochim. Biophys. Acta 314, 267–275; Thipayathasana, P. and Valentine, R. C. (1974) Biochim. Biophys. Acta 347, 464–468; Mével-Ninio, M. and Yamamoto, T. (1974) Biochim. Biophys. Acta 357, 63–66) has been found to be blocked for anaerobic DNA synthesis. The rate of anaerobic DNA synthesis in the mutant, measured as radioactive adenine incorporation into the alkali-resistant fraction of whole cells, is about 1/6 the rate of DNA synthesis in the wild type culture under similar conditions. Addition of NO₃^- or O₂ restores DNA biosynthesis in the mutant. The entry of radioactive adenine is not appreciably affected in the mutant by anaerobiosis. It is concluded that coupling factor plays a role in some step(s) of DNA biosynthesis.     

Transport characteristics of a novel local drug delivery system using nordihydroguaiaretic acid (NDGA)-polymerized collagen fibers

The use of nordihydroguaiaretic acid (NDGA)-polymerized collagen fibers as a novel local drug delivery system is introduced. The drug loading of these biocompatible fibers is illustrated with the anti-inflammatory agents dexamethasone and dexamethasone 21-phosphate. Capillary zone electrophoresis was used to measure the amount of drug released from the fibers into phosphate buffered saline with time. From these measurements and the use of a mathematical model, we were able to determine the diffusion coefficients for dexamethasone (D = 1.86 x 10(-14) m2/s) and dexamethasone 21-phosphate (D = 2.36 x 10(-13) m2/s) in the NDGA collagen fibers. These values have not been previously reported. These fibers can be used to load other agents as well. The diffusion coefficient of any agent loaded in these fibers can be determined using the techniques and mathematical method described. The rate of drug release from the fibers can be controlled using a PLGA coating. The overall importance of this paper is the potential broad application of this novel drug delivery system for the treatment of various human diseases.