Genome-wide comparative analysis of microRNAs in three non-human primates

Abstract Background MicroRNAs (miRNAs) are negative regulators of gene expression in multicellular eukaryotes. With the recently completed sequencing of three primate genomes, the study of miRNA evolution within the primate lineage has only begun and may be expected to provide the genetic and molecular explanations for many phenotypic differences between human and non-human primates. Findings We scanned all three genomes of non-human primates, including chimpanzee (Pan troglodytes), orangutan (Pongo pygmaeus), and rhesus monkey (Macaca mulatta), for homologs of human miRNA genes. Besides sequence homology analysis, our comparative method relies on various postprocessing filters to verify other features of miRNAs, including, in particular, their precursor structure or their occurrence (prediction) in other primate genomes. Our study allows direct comparisons between the different species in terms of their miRNA repertoire, their evolutionary distance to human, the effects of filters, as well as the identification of common and species-specific miRNAs in the primate lineage. More than 500 novel putative miRNA genes have been discovered in orangutan that show at least 85 percent identity in precursor sequence. Only about 40 percent are found to be 100 percent identical with their human ortholog. Conclusion Homologs of human precursor miRNAs with perfect or near-perfect sequence identity may be considered to be likely functional in other primates. The computational identification of homologs with less similar sequence, instead, requires further evidence to be provided.</p

Evidence of Novel Quasiparticles in a Strongly Interacting Two-Dimensional Electron System: Giant Thermopower and Metallic Behaviour

We report thermopower ($S$) and electrical resistivity ($\rho_{2DES}$) measurements in low-density (10$^{14}$ m$^{-2}$), mesoscopic two-dimensional electron systems (2DESs) in GaAs/AlGaAs heterostructures at sub-Kelvin temperatures. We observe at temperatures $\lesssim$ 0.7 K a linearly growing $S$ as a function of temperature indicating metal-like behaviour. Interestingly this metallicity is not Drude-like, showing several unusual characteristics: i) the magnitude of $S$ exceeds the Mott prediction valid for non-interacting metallic 2DESs at similar carrier densities by over two orders of magnitude; and ii) $\rho_{2DES}$ in this regime is two orders of magnitude greater than the quantum of resistance $h/e^2$ and shows very little temperature-dependence. We provide evidence suggesting that these observations arise due to the formation of novel quasiparticles in the 2DES that are not electron-like. Finally, $\rho_{2DES}$ and $S$ show an intriguing decoupling in their density-dependence, the latter showing striking oscillations and even sign changes that are completely absent in the resistivity.Comment: QFS2012 Conference proceedings, Journal of Low Temperature Physics, accepted (figure and discussion added upon referee suggestions

Animal snoRNAs and scaRNAs with exceptional structures

The overwhelming majority of small nucleolar RNAs (snoRNAs) fall into two clearly defined classes characterized by distinctive secondary structures and sequence motifs. A small group of diverse ncRNAs, however, shares the hallmarks of one or both classes of snoRNAs but differs substantially from the norm in some respects. Here, we compile the available information on these exceptional cases, conduct a thorough homology search throughout the available metazoan genomes, provide improved and expanded alignments, and investigate the evolutionary histories of these ncRNA families as well as their mutual relationships