Annotation of primate miRNAs by high throughput sequencing of small RNA libraries

BACKGROUND: In addition to genome sequencing, accurate functional annotation of genomes is required in order to carry out comparative and evolutionary analyses between species. Among primates, the human genome is the most extensively annotated. Human miRNA gene annotation is based on multiple lines of evidence including evidence for expression as well as prediction of the characteristic hairpin structure. In contrast, most miRNA genes in non-human primates are annotated based on homology without any expression evidence. We have sequenced small-RNA libraries from chimpanzee, gorilla, orangutan and rhesus macaque from multiple individuals and tissues. Using patterns of miRNA expression in conjunction with a model of miRNA biogenesis we used these high-throughput sequencing data to identify novel miRNAs in non-human primates. RESULTS: We predicted 47 new miRNAs in chimpanzee, 240 in gorilla, 55 in orangutan and 47 in rhesus macaque. The algorithm we used was able to predict 64% of the previously known miRNAs in chimpanzee, 94% in gorilla, 61% in orangutan and 71% in rhesus macaque. We therefore added evidence for expression in between one and five tissues to miRNAs that were previously annotated based only on homology to human miRNAs. We increased from 60 to 175 the number miRNAs that are located in orthologous regions in humans and the four non-human primate species studied here. CONCLUSIONS: In this study we provide expression evidence for homology-based annotated miRNAs and predict de novo miRNAs in four non-human primate species. We increased the number of annotated miRNA genes and provided evidence for their expression in four non-human primates. Similar approaches using different individuals and tissues would improve annotation in non-human primates and allow for further comparative studies in the future

Drift estimation in sparse sequential dynamic imaging, with application to nanoscale fluorescence microscopy.

A major challenge in many modern superresolution fluorescence microscopy techniques at the nanoscale lies in the correct alignment of long sequences of sparse but spatially and temporally highly resolved images. This is caused by the temporal drift of the protein structure, e.g. due to temporal thermal inhomogeneity of the object of interest or its supporting area during the observation process. We develop a simple semiparametric model for drift correction in single-marker switching microscopy. Then we propose an M-estimator for the drift and show its asymptotic normality. This is used to correct the final image and it is shown that this purely statistical method is competitive with state of the art calibration techniques which require the incorporation of fiducial markers in the specimen. Moreover, a simple bootstrap algorithm allows us to quantify the precision of the drift estimate and its effect on the final image estimation. We argue that purely statistical drift correction is even more robust than fiducial tracking, rendering the latter superfluous in many applications. The practicability of our method is demonstrated by a simulation study and by a single-marker switching application. This serves as a prototype for many other typical imaging techniques where sparse observations with high temporal resolution are blurred by motion of the object to be reconstructed

Self-Sabotage Workshop: a starting point to unravel sabotaging of instruments as a design practice

Within the music improvisation and jazz scenes, playing a wrong note may be seen as a source of creativity and novelty, where an initially undesired factor (the mistaken note) invites the musician to leverage their skills to transform it into new musical material. How does this idea, however, translate into more experimental scenes like NIME, where control and virtuosity are not necessarily the performance's aim? Moreover, within NIME communities the addition of randomness or constraints to musical instruments is often an intended aesthetic decision rather than a source of mistakes. To explore this contrast, we invited four NIME practitioners to participate in the Self-Sabotage Workshop, where each practitioner had to build their own sabotaging elements for their musical instruments and to give a short demonstration with them. We gathered participants' impressions of self-sabotating in a focus group, inquiring about control and musicality, and also the strategies they developed for coping with the self-sabotaged instruments. We discuss the emergent ideas of planned and unplanned sabotaging, and we propose a starting point towards the idea of self-sabotaging as a continuous design and musical process where designers/musicians try to overcome barriers that they impose upon themselves

Genetic evidence of human adaptation to a cooked diet

Humans have been argued to be biologically adapted to a cooked diet, but this hypothesis has not been tested at the molecular level. Here, we combine controlled feeding experiments in mice with comparative primate genomics to show that consumption of a cooked diet influences gene expression and that affected genes bear signals of positive selection in the human lineage. Liver gene expression profiles in mice fed standardized diets of meat or tuber were affected by food type and cooking, but not by caloric intake or consumer energy balance. Genes affected by cooking were highly correlated with genes known to be differentially expressed in liver between humans and other primates, and more genes in this overlap set show signals of positive selection in humans than would be expected by chance. Sequence changes in the genes under selection appear before the split between modern humans and two archaic human groups, Neandertals and Denisovans, supporting the idea that human adaptation to a cooked diet had begun by at least 275,000 years ago

Design and testing of a co-rotating vibration excitation system

A vibration excitation system (VES) in a form of an active coupling is proposed, designed and manufactured. The system is equipped with a set of piezoelectric stack actuators uniformly distributed around the rotor axis and positioned parallel to each other. The actuator arrangement allows an axial displacement of the coupling halves as well as their rotation about any transverse axis. Through the application of the VES an aimed vibration excitation is realised in a co-rotating coordinate system, which enables a non-invasive and precise modal analysis of rotating components. As an example, the VES is applied for the characterisation of the structural dynamic behaviour of a generic steel rotor at different rotational speeds. The first results are promising for both stationary and rotating conditions

Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes

Despite advances in identifying the genetic basis of psychiatric and neurological disorders, fundamental questions about their evolutionary origins remain elusive. Here, introgressed variants from archaic humans such as Neandertals can serve as an intriguing research paradigm. We compared the number of associations for Neandertal variants to the number of associations of frequency-matched non-archaic variants with regard to human CNS disorders (neurological and psychiatric), nervous system drug prescriptions (as a proxy for disease), and related, non-disease phenotypes in the UK biobank (UKBB). While no enrichment for Neandertal genetic variants were observed in the UKBB for psychiatric or neurological disease categories, we found significant associations with certain behavioral phenotypes including pain, chronotype/sleep, smoking and alcohol consumption. In some instances, the enrichment signal was driven by Neandertal variants that represented the strongest association genome-wide. SNPs within a Neandertal haplotype that was associated with smoking in the UKBB could be replicated in four independent genomics datasets

Humanized Foxp2 accelerates learning by enhancing transitions from declarative to procedural performance

The acquisition of language and speech is uniquely human, but how genetic changes might have adapted the nervous system to this capacity is not well understood. Two human-specific amino acid substitutions in the transcription factor forkhead box P2 (FOXP2) are outstanding mechanistic candidates, as they could have been positively selected during human evolution and as FOXP2 is the sole gene to date firmly linked to speech and language development. When these two substitutions are introduced into the endogenous Foxp2 gene of mice (Foxp2[superscript hum]), cortico-basal ganglia circuits are specifically affected. Here we demonstrate marked effects of this humanization of Foxp2 on learning and striatal neuroplasticity. Foxp2[superscript hum/hum] mice learn stimulus–response associations faster than their WT littermates in situations in which declarative (i.e., place-based) and procedural (i.e., response-based) forms of learning could compete during transitions toward proceduralization of action sequences. Striatal districts known to be differently related to these two modes of learning are affected differently in the Foxp2[superscript hum/hum] mice, as judged by measures of dopamine levels, gene expression patterns, and synaptic plasticity, including an NMDA receptor-dependent form of long-term depression. These findings raise the possibility that the humanized Foxp2 phenotype reflects a different tuning of corticostriatal systems involved in declarative and procedural learning, a capacity potentially contributing to adapting the human brain for speech and language acquisition.Nancy Lurie Marks Family FoundationSimons Foundation (Autism Research Initiative Grant 137593)National Institutes of Health (U.S.) (Grant R01 MH060379)Wellcome Trust (London, England) (Grant 075491/Z/04)Wellcome Trust (London, England) (Grant 080971)Fondation pour la recherche medicaleMax Planck Society for the Advancement of Scienc

Computer-generated dot maps as an epidemiologic tool: investigating an outbreak of toxoplasmosis.

We used computer-generated dot maps to examine the spatial distribution of 94 Toxoplasma gondii infections associated with an outbreak in British Columbia, Canada. The incidence among patients served by one water distribution system was 3.52 times that of patients served by other sources. Acute T. gondii infection among 3, 812 pregnant women was associated with the incriminated distribution system

Measurement of the diffractive structure function in deep inelastic scattering at HERA

This paper presents an analysis of the inclusive properties of diffractive deep inelastic scattering events produced in $ep$ interactions at HERA. The events are characterised by a rapidity gap between the outgoing proton system and the remaining hadronic system. Inclusive distributions are presented and compared with Monte Carlo models for diffractive processes. The data are consistent with models where the pomeron structure function has a hard and a soft contribution. The diffractive structure function is measured as a function of \xpom, the momentum fraction lost by the proton, of $\beta$, the momentum fraction of the struck quark with respect to \xpom, and of $Q^2$. The \xpom dependence is consistent with the form \xpoma where $a~=~1.30~\pm~0.08~(stat)~^{+~0.08}_{-~0.14}~(sys)$ in all bins of $\beta$ and $Q^2$. In the measured $Q^2$ range, the diffractive structure function approximately scales with $Q^2$ at fixed $\beta$. In an Ingelman-Schlein type model, where commonly used pomeron flux factor normalisations are assumed, it is found that the quarks within the pomeron do not saturate the momentum sum rule.Comment: 36 pages, latex, 11 figures appended as uuencoded fil

Transcription Factors Are Targeted by Differentially Expressed miRNAs in Primates

MicroRNAs (miRNAs) are small RNA molecules involved in the regulation of mammalian gene expression. Together with other transcription regulators, miRNAs modulate the expression of genes and thereby potentially contribute to tissue and species diversity. To identify miRNAs that are differentially expressed between tissues and/or species, and the genes regulated by these, we have quantified expression of miRNAs and messenger RNAs in five tissues from multiple human, chimpanzee, and rhesus macaque individuals using high-throughput sequencing. The breadth of this tissue and species data allows us to show that downregulation of target genes by miRNAs is more pronounced between tissues than between species and that downregulation is more pronounced for genes with fewer binding sites for expressed miRNAs. Intriguingly, we find that tissue- and species-specific miRNAs target transcription factor genes (TFs) significantly more often than expected. Through their regulatory effect on transcription factors, miRNAs may therefore exert an indirect influence on a larger proportion of genes than previously thought