183 research outputs found

    Selective Enrichment and Sequencing of Whole Mitochondrial Genomes in the Presence of Nuclear Encoded Mitochondrial Pseudogenes (Numts)

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    Numts are an integral component of many eukaryote genomes offering a snapshot of the evolutionary process that led from the incorporation of an α-proteobacterium into a larger eukaryotic cell some 1.8 billion years ago. Although numt sequence can be harnessed as molecular marker, these sequences often remain unidentified and are mistaken for genuine mtDNA leading to erroneous interpretation of mtDNA data sets. It is therefore indispensable that during the process of amplifying and sequencing mitochondrial genes, preventive measures are taken to ensure the exclusion of numts to guarantee the recovery of genuine mtDNA. This applies to mtDNA analyses in general but especially to studies where mtDNAs are sequenced de novo as the launch pad for subsequent mtDNA-based research. By using a combination of dilution series and nested rolling circle amplification (RCA), we present a novel strategy to selectively amplify mtDNA and exclude the amplification of numt sequence. We have successfully applied this strategy to de novo sequence the mtDNA of the Black Field Cricket Teleogryllus commodus, a species known to contain numts. Aligning our assembled sequence to the reference genome of Teleogryllus emma (GenBank EU557269.1) led to the identification of a numt sequence in the reference sequence. This unexpected result further highlights the need of a reliable and accessible strategy to eliminate this source of error

    Toward a General Theory of Standards of Proof

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    Which standard of proof is best for a particular type of case This deceptively simple question has been much discussed but the current state of understanding is unsatisfactory Statisticians posed a general answer philosophers and others launched an assault on that answer practically oriented scholars draw on both strains unsystematically and courts generally offer little or no reasoning for their decisions The goal of this article is to outline a systematic and complete justification for selecting one probabilistic standard of proof over another By training a microscope on one small corner of the law incapacity will contests this article demonstrates the relevance of old factors identifies several new factors and integrates the factors into an approach that will hopefully guide future inquiry One important implication is that the choice of proof standard will almost necessarily be tentative too much is unknown or unknowabl

    Review of Coronal Oscillations - An Observer's View

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    Recent observations show a variety of oscillation modes in the corona. Early non-imaging observations in radio wavelengths showed a number of fast-period oscillations in the order of seconds, which have been interpreted as fast sausage mode oscillations. TRACE observations from 1998 have for the first time revealed the lateral displacements of fast kink mode oscillations, with periods of ~3-5 minutes, apparently triggered by nearby flares and destabilizing filaments. Recently, SUMER discovered with Doppler shift measurements loop oscillations with longer periods (10-30 minutes) and relatively short damping times in hot (7 MK) loops, which seem to correspond to longitudinal slow magnetoacoustic waves. In addition, propagating longitudinal waves have also been detected with EIT and TRACE in the lowest density scale height of loops near sunspots. All these new observations seem to confirm the theoretically predicted oscillation modes and can now be used as a powerful tool for ``coronal seismology'' diagnostic.Comment: 5 Figure

    The Exclusion of Felons from Jury Service

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    Host selection by an insect herbivore with spatially variable density dependence

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    Many species of phytophagous insects do not oviposit preferentially on plants that yield high offspring performance. One proposed explanation is that negatively density-dependent offspring performance would select for females that disperse eggs among plants to minimize competition. Recent work showing larval density dependence often varies substantially among plants suggests that ovipositing females should not only respond to the density of competitors but also to traits predictive of the strength of density dependence mediated by plants. In this study, we used field and greenhouse experiments to examine oviposition behavior in an insect herbivore that experiences density-dependent larval performance and variability in the strength of that density dependence among host-plant individuals. We found females moved readily among plants in the field and had strong preferences for plants that mediate weak offspring density dependence. Females, however, did not avoid plants with high densities of competitors, despite the fact that offspring performance declines steeply with density on most plants in natural populations. This means females minimize the effects of density dependence on their offspring by choosing plants that mediate only weak larval density dependence, not by choosing plants with low densities of competitors. Our results suggest that explaining the lack of positive preference-performance correlations in many systems may not be as simple as invoking density dependence. Resource selection behavior may depend not just on the presence or absence of density-dependent offspring performance but also on variation in the strength of offspring density dependence among sites within populations
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