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  • 1
    Publication Date: 2013-04-02
    Description: The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo . To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2'-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5'-splice site forms intramolecular base pairs that are removed by this structural change, which likely allows splice site recognition and exon inclusion. Genome-wide analyses show that pyrvinium pamoate regulates 〉300 alternative exons that form secondary structures enriched in A–U base pairs. Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2014-12-17
    Description: Homologous non-coding RNAs frequently exhibit domain insertions, where a branch of secondary structure is inserted in a sequence with respect to its homologs. Dynamic programming algorithms for common secondary structure prediction of multiple RNA homologs, however, do not account for these domain insertions. This paper introduces a novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures. The algorithm is implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs. This update is accomplished with negligible increase in computational cost. Benchmarks on ncRNA families with domain insertions validate the method. Over base pairs occurring in inserted domains, Dynalign II improves accuracy over Dynalign, attaining 80.8% sensitivity (compared with 14.4% for Dynalign) and 91.4% positive predictive value (PPV) for tRNA; 66.5% sensitivity (compared with 38.9% for Dynalign) and 57.0% PPV for RNase P RNA; and 50.1% sensitivity (compared with 24.3% for Dynalign) and 58.5% PPV for SRP RNA. Compared with Dynalign, Dynalign II also exhibits statistically significant improvements in overall sensitivity and PPV. Dynalign II is available as a component of RNAstructure, which can be downloaded from http://rna.urmc.rochester.edu/RNAstructure.html .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2012-02-28
    Description: With discovery of diverse roles for RNA, its centrality in cellular functions has become increasingly apparent. A number of algorithms have been developed to predict RNA secondary structure. Their performance has been benchmarked by comparing structure predictions to reference secondary structures. Generally, algorithms are compared against each other and one is selected as best without statistical testing to determine whether the improvement is significant. In this work, it is demonstrated that the prediction accuracies of methods correlate with each other over sets of sequences. One possible reason for this correlation is that many algorithms use the same underlying principles. A set of benchmarks published previously for programs that predict a structure common to three or more sequences is statistically analyzed as an example to show that it can be rigorously evaluated using paired two-sample t -tests. Finally, a pipeline of statistical analyses is proposed to guide the choice of data set size and performance assessment for benchmarks of structure prediction. The pipeline is applied using 5S rRNA sequences as an example.
    Keywords: Nucleic acid structure, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2012-03-20
    Description: Motivation: Many RNA molecules function without being translated into proteins, and function depends on structure. Pseudoknots are motifs in RNA secondary structures that are difficult to predict but are also often functionally important. Results: TurboKnot is a new algorithm for predicting the secondary structure, including pseudoknotted pairs, conserved across multiple sequences. TurboKnot finds 81.6% of all known base pairs in the systems tested, and 75.6% of predicted pairs were found in the known structures. Pseudoknots are found with half or better of the false-positive rate of previous methods. Availability: The program is available for download under an open-source license as part of the RNAstructure package at: http://rna.urmc.rochester.edu . Contact: david_mathews@urmc.rochester.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 5
    Publication Date: 2014-12-10
    Description: Modern high-power, large-aperture (HPLA) radars have been used in a variety of investigations including the investigation of meteoroid fragmentation. The identification of fragmentation has been based on a detailed interpretation, based on radio science, of head- and trail-echo properties. We now extend the discussion of fragmenting meteoroids to include apparent high-altitude (130–180 km) meteors observed at the Jicamarca Radio Observatory (JRO). While there have been a few reports of high-altitude meteors observed both optically and with radar, the meteor radar community has remained sceptical, with suspicions of antenna side-lobe contamination being the most commonly raised objection. We report results from two sets of meteor observations carried out at JRO in 2010 April. Our findings include meteoroid fragmentation results that are similar to those from the Arecibo VHF radar. These findings lead to the conclusions that fragmentation is not only observed at the JRO but that k B scattering adds an interesting additional radio science dimension to the issue. We also report on apparent high-altitude meteor events that, if ultimately confirmed, offer insight into sputtering as a source of the meteor ionization, and perhaps indicate the unique importance of magnetic field geometry in these head-echo observations. Also, new, apparently high-altitude transient events, likely related to the meteoroid flux, have been identified. In presenting these results, we note our careful calibration of the JRO radar, utilizing satellite returns in order to largely, if not totally, exclude side-lobe contamination and other possible error sources, as reported in our companion paper.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2014-12-10
    Description: The Jicamarca Radio Observatory (JRO) main 50-MHz array antenna radar system with multiple receivers is being used to study meteors via two interferometric receiving modes. One of the major challenges in these studies is the phase calibration of the various receiver (interferometric) channels (legs). While investigating some ambiguous features in meteor head-echo results, we developed a ‘new’ calibration technique that employs satellite observations to produce more accurate phase and pattern measurements than were previously available. This calibration technique, which resolves head-echo ambiguities, uses the fact that Earth-orbiting satellites are in gravitationally well-defined orbits and thus the pulse-to-pulse radar returns must be consistent (coherent) for an entire satellite pass through the radar beam. In particular, the satellite yields a reliable point source for phase and thus interferometry-derived range, Doppler and trajectory calibration. Using several satellites observed during standard meteor observations, we derive satellite orbital parameters by matching the observed and modelled three-dimensional trajectory and Doppler results. This approach uncovered subtle phase distortions that led to interferometry-derived trajectory distortions that are important only to point targets such as meteor head-echoes. We present the array calibration and radar imaging of satellite passes from our meteor observations of 2010 April 15/16. Future observations of a priori known satellites would likely yield significantly more accurate calibrations, especially of distant side lobes.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
    Publication Date: 2013-03-16
    Description: Recent hydrostatic X-ray studies of the hot interstellar medium (ISM) in early-type galaxies underestimate the gravitating mass as compared to stellar dynamics, implying modest, but significant deviations from exact hydrostatic equilibrium. We present a method for combining X-ray measurements and stellar dynamical constraints in the context of Bayesian statistics that allows the radial distribution of the implied non-thermal pressure or bulk motions in the hot ISM to be constrained. We demonstrate the accuracy of the method with hydrodynamical simulations tailored to produce a realistic galaxy model. Applying the method to the nearby elliptical galaxy NGC 4649, we find a significant but subdominant non-thermal pressure fraction (0.27 ± 0.06) in the central (5 kpc) part of the galaxy, similar to the level of deviations from hydrostatic equilibrium expected in galaxy clusters. Plausible sources of systematic error, if important, may reduce this fraction. Our results imply ~360 km s –1 random turbulence or a magnetic field B = (39 ± 6)( n e /0.1 cm – 3 ) 0.59 ± 0.09 μG, whereas gas rotation alone is unlikely to explain the detailed non-thermal profile. Future observations with Astro-H will allow turbulence or gas rotation at this level to be detected.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 8
    Publication Date: 2013-06-23
    Description: RNAstructure is a software package for RNA secondary structure prediction and analysis. This contribution describes a new set of web servers to provide its functionality. The web server offers RNA secondary structure prediction, including free energy minimization, maximum expected accuracy structure prediction and pseudoknot prediction. Bimolecular secondary structure prediction is also provided. Additionally, the server can predict secondary structures conserved in either two homologs or more than two homologs. Folding free energy changes can be predicted for a given RNA structure using nearest neighbor rules. Secondary structures can be compared using circular plots or the scoring methods, sensitivity and positive predictive value. Additionally, structure drawings can be rendered as SVG, postscript, jpeg or pdf. The web server is freely available for public use at: http://rna.urmc.rochester.edu/RNAstructureWeb .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2010-12-30
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 10
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