Finding smORFs: getting closer

Millions of small open reading frames exist in eukaryotes. We do not know how many, or which are translated, but bioinformatics is getting us closer to the answer. See related Research article: http://www.genomebiology.com/2015/16/1/179

Phenotypic and genotypic characterisation of Burkholderia cenocepacia J2315 mutants affected in homoserine lactone and diffusible signal factor-based quorum sensing systems suggests interplay between both types of systems

Many putative virulence factors of Burkholderia cenocepacia are controlled by various quorum sensing (QS) circuits. These QS systems either use N-acyl homoserine lactones (AHL) or cis-2-dodecenoic acid ("Burkholderia diffusible signal factor'', BDSF) as signalling molecules. Previous work suggested that there is little cross-talk between both types of systems. We constructed mutants in B. cenocepacia strain J2315, in which genes encoding CepI (BCAM1870), CciI (BCAM0239a) and the BDSF synthase (BCAM0581) were inactivated, and also constructed double (Delta cepI Delta BCAM0581, Delta cciI Delta BCAM0581 and Delta cepI Delta cciI) mutants and a triple (Delta cepI Delta cciI Delta BCAM0581) mutant. Subsequently we investigated phenotypic properties (antibiotic susceptibility, biofilm formation, production of AHL and BDSF, protease activity and virulence in Caenorhabditis elegans) and measured gene expression in these mutants, and this in the presence and absence of added BDSF, AHL or both. The triple mutant was significantly more affected in biofilm formation, antimicrobial susceptibility, virulence in C. elegans, and protease production than either the single or double mutants. The Delta BCAM0581 mutant and the Delta cepI Delta BCAM0581 and Delta cciI Delta BCAM0581 double mutants produced significantly less AHL compared to the WT strain and the Delta cepI and Delta cciI single mutant, respectively. The expression of cepI and cciI in Delta BCAM0581, was approximately 3-fold and 7-fold (p < 0.05) lower than in the WT, respectively. The observed differences in AHL production, expression of cepI and cciI and QS-controlled phenotypes in the Delta BCAM0581 mutant could (at least partially) be restored by addition of BDSF. Our data suggest that, in B. cenocepacia J2315, AHL and BDSF-based QS systems co-regulate the same set of genes, regulate different sets of genes that are involved in the same phenotypes and/or that the BDSF system controls the AHL-based QS system. As the expression of the gene encoding the C6-HSL synthase CciI (and to a lesser extent the C8-HSL synthase CepI) is partially controlled by BDSF, it seems likely that the BDSF QS systems controls AHL production through this system

Experimental and calculated circular dichroism spectra of monoaza[5]helicenes

Circular dichroism (CD) spectra have been measured in the range of 400–200 nm on CH3OH solutions of both enantiomers for the almost complete series of monoaza[5]helicenes, namely the molecules where the hetero N atom occupies positions 1, 3, 4, 5, 6, and 7, respectively (the 2 isomer is missing due to difficulties in the synthesis). CD spectra recorded at controlled room temperature allow one to define precise racemization rates, that are nicely interpreted on the basis of DFT molecular orbital calculations. Time-dependent DFT methods provide us with calculated CD and UV spectra, that are compared with the corresponding experimental data. We discuss the role of the N atom in determining the height of the racemization barrier and in shaping the appearance of the CD spectra

A database of microRNA expression patterns in Xenopus laevis

MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides. In addition we carried out small RNA-seq on different stages of early Xenopus development, identified 44 miRNAs belonging to 29 new families and characterized the expression of 5 of these. Our analyses identified miRNA expression in many organs of the developing embryo. In particular a large number were expressed in neural tissue and in the somites. Surprisingly none of the miRNAs we have looked at show expression in the heart. Our results have been made freely available as a resource in both XenMARK and Xenbase

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

Thousands of small Open Reading Frames (smORFs) with the potential to encode small peptides of fewer than 100 amino acids exist in our genomes. However, the number of smORFs actually translated, and their molecular and functional roles are still unclear. In this study, we present a genome-wide assessment of smORF translation by ribosomal profiling of polysomal fractions in Drosophila. We detect two types of smORFs bound by multiple ribosomes and thus undergoing productive translation. The 'longer' smORFs of around 80 amino acids resemble canonical proteins in translational metrics and conservation, and display a propensity to contain transmembrane motifs. The 'dwarf' smORFs are in general shorter (around 20 amino-acid long), are mostly found in 5'-UTRs and non-coding RNAs, are less well conserved, and have no bioinformatic indicators of peptide function. Our findings indicate that thousands of smORFs are translated in metazoan genomes, reinforcing the idea that smORFs are an abundant and fundamental genome component

What Do You look for in a Prospective Date?: Reexamining the Preferences of Men and Women Who Differ in Self-Monitoring Propensities

Abstract unavailabl

Resisting Temptation Revisited: Devaluation versus Enhancement of an Attractive Suitor by Exclusive and Nonexclusive Daters

Individuals committed to exclusive relationships often evaluate attractive, opposite-sex targets less favorably than do less committed individuals. This devaluative distortion of alternatives has been interpreted as relationship maintenance by exclusive daters. Two experiments evaluated an alternative hypothesis: Less committed individuals may more favorably evaluate attractive, other-sex targets because they are seeking a relationship. In Experiment 1, exclusive and nonexclusive daters imagined a scenario in which an attractive stranger showed interest in the participant (high threat/high opportunity) or in his or her best friend (low threat/low opportunity). In Experiment 2, exclusive and nonexclusive daters anticipated interacting with an attractive target who was either available/seeking a relationship (high threat/high opportunity) or unavailable for a relationship (low threat/low opportunity). As predicted, nonexclusive daters evaluated available targets more favorably than unavailable ones, showing clear evidence of relationship-seeking motives. However, exclusive daters showed little evidence of devaluing available targets in the interest of relationship maintenance

Investigating the Social-Adjustive and Value-Expressive Functions of Well-Grounded Attitudes: Implications for Change and for Subsequent Behavior

Recent demonstrations of the plausibility of functional theories of persuasion have occurred within advertising contexts or have targeted potentially nebulous or uninvolving attitudes, and may thus have demonstrated the utility of functional explanations of attitude formation rather than attitude change. In the present study, attitudes that participants have acted on and consider important (i.e., the criteria they use to select dating partners) were the targets of persuasion. High and low self-monitoring individuals, who hold different dating attitudes that serve different functions, were exposed to functionally relevant or functionally irrelevant messages that reached either proattitudinal or counter attitudinal conclusions. As anticipated by functional theory, (a) low self-monitoring individuals changed their dating attitudes only after hearing a counter attitudinal message that addressed the value-expressive functions their dating attitudes served, whereas (b) high self-monitoring individuals changed their opinions only after hearing a counter attitudinal message that addressed the social-adjustive functions served by their dating attitudes. Although the data revealed that important attitudes can be changed via a functionally relevant appeal, only the low self-monitoring individuals subsequently used their changed attitudes to guide their behavior in a subsequent couple-matching task. Implications of these results for functional theories of persuasion and for variations in attitude/behavior consistency were discussed

Who Smokes in Hollywood? Characteristics of Smokers in Popular Films from 1940 to 1989

We examined how smokers were depicted in 100 popular films spanning 5 decades. Smokers were depicted as more romantically and sexually active than nonsmokers and as marginally more intelligent than nonsmokers. Smokers and nonsmokers did not differ in terms of attractiveness, goodness, socioeconomic status, aggression, friendliness, or outcome at film’s end. Thus, if anything, smokers are depicted a bit more positively than nonsmokers. We compared Hollywood’s depiction of smokers to real-world demographics on smoking and found that Hollywood’s depiction of smoking tends to ignore the negative consequences and correlates (e.g., ill health, low socioeconomic status, aggressive behavior) of smoking