Effect of Group IIC Introns on Host Gene Expression in S. cerevisiae

Group II introns are self-splicing ribozymes believed to be the evolutionary ancestors to eukaryotic spliceosomal introns. They are found in bacteria, archaea, and eukaryotic organelles but not in eukaryotic nuclear genomes. Group IIA and IIB introns introduced to nuclei in Saccharomyces cerevisiae are able to transcribe and splice, but post-transcriptionally silence their host genes. It has been shown that both RNA-RNA interactions and pre-mRNA cytoplasmic mislocalization contribute to the silencing of the genes. RNA-RNA interactions include binding between the exon-binding sequences (EBS) in the intron and intron-binding sequences (IBS) in the ligated exons. Group IIC introns contain reduced EBS-IBS sequences compared to their group IIA and group IIB counterparts; thus it is worthwhile to investigate if IIC introns will function differently in yeast, either causing no silencing or using a distinct silencing mechanism. To this end, a group IIC-reporter cassette was prepared and transformed into yeast. Phenotype screening of the yeast was carried out to determine if silencing occurs. Mechanisms, including the presence of RNA-RNA interactions and their impact on the host genes were investigated. Primer extension assays conducted show that group IIC-reporter constructs can splice in vivo in S. cerevisiae, although exon ligation does not occur. This is a noteworthy distinction in silencing mechanism between the closely related group IIA, IIB, and IIC introns. This information will assist in establishing the evolutionary narrative of the expulsion of group II introns from nuclear genomes and the evolution of group II introns to ancestrally-related spliceosomal introns

Finding Scientific Gems with Google

We apply the Google PageRank algorithm to assess the relative importance of all publications in the Physical Review family of journals from 1893--2003. While the Google number and the number of citations for each publication are positively correlated, outliers from this linear relation identify some exceptional papers or "gems" that are universally familiar to physicists.Comment: 6 pages, 4 figures, 2 tables, 2-column revtex4 forma

Production of human recombinant proapolipoprotein A-I in Escherichia coli: purification and biochemical characterization

A human liver cDNA library was used to isolate a clone coding for apolipoprotein A-I (Apo A-I). The clone carries the sequence for the prepeptide (18 amino acids), the propeptide (6 amino acids), and the mature protein (243 amino acids). A coding cassette for the proapo A-I molecule was reconstructed by fusing synthetic sequences, chosen to optimize expression and specifying the amino-terminal methionine and amino acids -6 to +14, to a large fragment of the cDNA coding for amino acids 15-243. The module was expressed in pOTS-Nco, an Escherichia coli expression vector carrying the regulatable X P^ promoter, leading to the production of proapolipoprotein A-I at up to 10% of total soluble proteins. The recombinant polypeptide was purified and characterized in terms of apparent molecular mass, isoelectric point, and by both chemical and enzymatic peptide mapping. In addition, it was assayed in vitro for the stimulation of the enzyme lecithin: cholesterol acyltransferase. The data show for the first time that proapo A-I can be produced efficiently in E. coli as a stable and undegraded protein having physical and functional properties indistinguishable from those of the natural product

Happiness is assortative in online social networks

Social networks tend to disproportionally favor connections between individuals with either similar or dissimilar characteristics. This propensity, referred to as assortative mixing or homophily, is expressed as the correlation between attribute values of nearest neighbour vertices in a graph. Recent results indicate that beyond demographic features such as age, sex and race, even psychological states such as "loneliness" can be assortative in a social network. In spite of the increasing societal importance of online social networks it is unknown whether assortative mixing of psychological states takes place in situations where social ties are mediated solely by online networking services in the absence of physical contact. Here, we show that general happiness or Subjective Well-Being (SWB) of Twitter users, as measured from a 6 month record of their individual tweets, is indeed assortative across the Twitter social network. To our knowledge this is the first result that shows assortative mixing in online networks at the level of SWB. Our results imply that online social networks may be equally subject to the social mechanisms that cause assortative mixing in real social networks and that such assortative mixing takes place at the level of SWB. Given the increasing prevalence of online social networks, their propensity to connect users with similar levels of SWB may be an important instrument in better understanding how both positive and negative sentiments spread through online social ties. Future research may focus on how event-specific mood states can propagate and influence user behavior in "real life".Comment: 17 pages, 9 figure

Measuring health inequality among children in developing countries: does the choice of the indicator of economic status matter?

Background Currently, poor-rich inequalities in health in developing countries receive a lot of attention from both researchers and policy makers. Since measuring economic status in developing countries is often problematic, different indicators of wealth are used in different studies. Until now, there is a lack of evidence on the extent to which the use of different measures of economic status affects the observed magnitude of health inequalities. Methods This paper provides this empirical evidence for 10 developing countries, using the Demographic and Health Surveys data-set. We compared the World Bank asset index to three alternative wealth indices, all based on household assets. Under-5 mortality and measles immunisation coverage were the health outcomes studied. Poor-rich inequalities in under-5 mortality and measles immunisation coverage were measured using the Relative Index of Inequality. Results Comparing the World Bank index to the alternative indices, we found that (1) the relative position of households in the national wealth hierarchy varied to an important extent with the asset index used, (2) observed poor-rich inequalities in under-5 mortality and immunisation coverage often changed, in some cases to an important extent, and that (3) the size and direction of this change varied per country, index, and health indicator. Conclusion Researchers and policy makers should be aware that the choice of the measure of economic status influences the observed magnitude of health inequalities, and that differences in health inequalities between countries or time periods, may be an artefact of different wealth measures used

Mutant and chimeric recobinant plasminogen activatorsproduction in eukaryotic cellsand preliminary characterization

Mutant urokinase-type plasminogen activator (u-PA) genes and hybrid genes between tissue-type plasminogen activator (t-PA) and u-PA have been designed to direct the synthesis of new plasminogen activators and to investigate the structure-function relationship in these molecules. The following classes of constructs were made starting from cDNA encoding human t-PA or u-PA: 1) u-PA mutants in which the Arg156 and Lys158 were substituted with threonine, thus preventing cleavage by thrombin and plasmin; 2) hybrid molecules in which the NH2-terminal regions of t-PA (amino acid residues 1-67, 1-262, or 1-313) were fused with the COOH-terminal region of u-PA (amino acids 136-411, 139-411, or 195-411, respectively); and 3) a hybrid molecule in which the second kringle of t-PA (amino acids 173-262) was inserted between amino acids 130 and 139 of u-PA. In all cases but one, the recombinant proteins, produced by transfected eukaryotic cells, were efficiently secreted in the culture medium. The translation products have been tested for their ability to activate plasminogen after in situ binding to an insolubilized monoclonal antibody directed against urokinase. All recombinant enzymes were shown to be active, except those in which Lys158 of u-PA was substituted with threonine. Recombination of structural regions derived from t-PA, such as the finger, the kringle 2, or most of the A-chain sequences, with the protease part or the complete u-PA molecule did not impair the catalytic activity of the hybrid polypeptides. This observation supports the hypothesis that structural domains in t-PA and u-PA fold independently from one to another