scholarly journals An Exon-Capture System for the Entire Class Ophiuroidea

2015 ◽  
Vol 33 (1) ◽  
pp. 281-294 ◽  
Author(s):  
Andrew F. Hugall ◽  
Timothy D. O’Hara ◽  
Sumitha Hunjan ◽  
Roger Nilsen ◽  
Adnan Moussalli
Keyword(s):  
Entire Class ◽  
Exon Capture

scholarly journals An exon-capture system for the entire class Ophiuroidea

2015 ◽  
Author(s):  
Andrew Forrest Hugall ◽  
Timothy D O'Hara ◽  
Sumitha Hunjan ◽  
Roger Nilsen ◽  
Adnan Moussalli
Keyword(s):  
Phylogenetic Diversity ◽  
Marine Invertebrates ◽  
Orthologous Genes ◽  
Crown Group ◽  
Group Key ◽  
Entire Class ◽  
Exon Capture ◽  
Allelic Differences ◽  
Key Features ◽  
Ancestral States

We present an exon-capture system for an entire class of marine invertebrates, the Ophiuroidea, built upon a phylogenetically diverse transcriptome foundation. The system captures ~90 percent of the 1552 exon target, across all major lineages of the quarter-billion year old extant crown group. Key features of our system are: 1) basing the target on an alignment of orthologous genes determined from 52 transcriptomes spanning the phylogenetic diversity and trimmed to remove anything difficult to capture, map or align, 2) use of multiple artificial representatives based on ancestral states rather than exemplars to improve capture and mapping of the target, 3) mapping reads to a multi-reference alignment, and 4) using patterns of site polymorphism to distinguish among paralogy, polyploidy, allelic differences and sample contamination. The resulting data gives a well-resolved tree (currently standing at 417 samples, 275,352 bp, 91% data-complete) that will transform our understanding of ophiuroid evolution and biogeography.

THE POLITICS OF DANCE: EUNOMIA AND THE EXCEPTION OF DIONYSUS IN PLATO'S LAWS

2020 ◽  
pp. 1-15
Author(s):  
Kenneth W. Yu
Keyword(s):  
Recent Work ◽  
Social Relations ◽  
The Body ◽  
Entire Class ◽  
A Site

How to inculcate virtue in the citizens of Magnesia by means of the dance component of choreia constitutes one of the principal concerns in the Laws (= Leg.), revealing Plato's evolving ideas about the expediency of music and paideia for the construction of his ideal city since the Republic. Indeed, a steady stream of monographs and articles on the Laws has enriched our understanding of how Plato theorizes the body as a site of intervention and choral dance as instrumental in solidifying social relations and in conditioning the ethical and political self. As one scholar has aptly put it: ‘a city and its sociopolitical character [are] effectively danced into existence.’ Drawing on this recent work, I focus on an enigmatic passage in Laws Book 7 that merits more attention than it has received, in which Plato curiously singles out Bacchic dances from those that are ‘without controversy’ (815b7–d4): τὴν τοίνυν ἀμφισβητουμένην ὄρχησιν δεῖ πρῶτον χωρὶς τῆς ἀναμφισβητήτου διατεμεῖν. τίς οὖν αὕτη, καὶ πῇ δεῖ χωρὶς τέμνειν ἑκατέραν; ὅση μὲν βακχεία τ᾽ ἐστὶν καὶ τῶν ταύταις ἑπομένων, ἃς Νύμφας τε καὶ Πᾶνας καὶ Σειληνοὺς καὶ Σατύρους ἐπονομάζοντες, ὥς φασιν, μιμοῦνται κατῳνωμένους, περὶ καθαρμούς τε καὶ τελετάς τινας ἀποτελούντων, σύμπαν τοῦτο τῆς ὀρχήσεως τὸ γένος οὔθ᾽ ὡς εἰρηνικὸν οὔθ᾽ ὡς πολεμικὸν οὔθ᾽ ὅτι ποτὲ βούλεται ῥᾴδιον ἀφορίσασθαι: διορίσασθαι μήν μοι ταύτῃ δοκεῖ σχεδὸν ὀρθότατον αὐτὸ εἶναι, χωρὶς μὲν πολεμικοῦ, χωρὶς δὲ εἰρηνικοῦ θέντας, εἰπεῖν ὡς οὐκ ἔστι πολιτικὸν τοῦτο τῆς ὀρχήσεως τὸ γένος, ἐνταῦθα δὲ κείμενον ἐάσαντας κεῖσθαι, νῦν ἐπὶ τὸ πολεμικὸν ἅμα καὶ εἰρηνικὸν ὡς ἀναμφισβητήτως ἡμέτερον ὂν ἐπανιέναι. So, first of all, we should separate questionable dancing far from dancing that is without controversy. Which is the controversial kind, and how are the two to be distinguished? All the dancing that is of a Bacchic kind and cultivated by those who indulge in intoxicated imitations of Nymphs, Pans, Sileni and Satyrs (as they name them), when performing certain rites of expiation and initiation—this entire class of dancing cannot easily be marked off either as pacific or as warlike, nor as of any one particular kind. The most correct way of defining it appears to me to be this—to place it away from both pacific and warlike dancing, and to pronounce that this type of dancing is οὐ πολιτικόν; having thus set aside and dismissed it, we will now return to the warlike and pacific types, which without controversy belong to us.

scholarly journals Mimicry and mitonuclear discordance in nudibranchs: New insights from exon capture phylogenomics

2020 ◽  
Vol 10 (21) ◽  
pp. 11966-11982
Author(s):  
Kara K. S. Layton ◽  
Jose I. Carvajal ◽  
Nerida G. Wilson
Keyword(s):  
Exon Capture

scholarly journals Is Sexual Conflict a Driver of Speciation? A Case Study With a Tribe of Brush-footed Butterflies

2020 ◽  
Author(s):  
Ana Paula S Carvalho ◽  
Ryan A St Laurent ◽  
Emmanuel F A Toussaint ◽  
Caroline Storer ◽  
Kelly M Dexter ◽  
...  
Keyword(s):  
Sexual Conflict ◽  
Abiotic Factors ◽  
Evolutionary Mechanisms ◽  
Diversification Rates ◽  
Exon Capture ◽  
Key Driver ◽  
Underlying Mechanisms ◽  
Analytical Approaches ◽  
Acting In Concert

Abstract Understanding the evolutionary mechanisms governing the uneven distribution of species richness across the tree of life is a great challenge in biology. Scientists have long argued that sexual conflict is a key driver of speciation. This hypothesis, however, has been highly debated in light of empirical evidence. Recent advances in the study of macroevolution make it possible to test this hypothesis with more data and increased accuracy. In the present study, we use phylogenomics combined with four different diversification rate analytical approaches to test whether sexual conflict is a driver of speciation in brush-footed butterflies of the tribe Acraeini. The presence of a sphragis, an external mating plug found in most species among Acraeini, was used as a proxy for sexual conflict. Diversification analyses statistically rejected the hypothesis that sexual conflict is associated with shifts in diversification rates in Acraeini. This result contrasts with earlier studies and suggests that the underlying mechanisms driving diversification are more complex than previously considered. In the case of butterflies, natural history traits acting in concert with abiotic factors possibly play a stronger role in triggering speciation than does sexual conflict. [Acraeini butterflies; arms race; exon capture phylogenomics; Lepidoptera macroevolution; sexual selection; sphragis.]

HOW TO MAKE HORIZONTAL DEMONSTRATIONS VISIBLE TO AN ENTIRE CLASS

Science ◽  
1930 ◽  
Vol 72 (1873) ◽  
pp. 533-534
Author(s):  
E. J. Wimmer
Keyword(s):  
Entire Class

scholarly journals Limited ER quality control for GPI-anchored proteins

2016 ◽  
Vol 213 (6) ◽  
pp. 693-704 ◽  
Author(s):  
Natalia Sikorska ◽  
Leticia Lemus ◽  
Auxiliadora Aguilera-Romero ◽  
Javier Manzano-Lopez ◽  
Howard Riezman ◽  
...  
Keyword(s):  
Quality Control ◽  
Endoplasmic Reticulum ◽  
Protein Folding ◽  
Misfolded Proteins ◽  
Control Mechanisms ◽  
Gpi Anchor ◽  
Er Quality Control ◽  
Entire Class ◽  
Er Export ◽  
Export Signal

Endoplasmic reticulum (ER) quality control mechanisms target terminally misfolded proteins for ER-associated degradation (ERAD). Misfolded glycophosphatidylinositol-anchored proteins (GPI-APs) are, however, generally poor ERAD substrates and are targeted mainly to the vacuole/lysosome for degradation, leading to predictions that a GPI anchor sterically obstructs ERAD. Here we analyzed the degradation of the misfolded GPI-AP Gas1* in yeast. We could efficiently route Gas1* to Hrd1-dependent ERAD and provide evidence that it contains a GPI anchor, ruling out that a GPI anchor obstructs ERAD. Instead, we show that the normally decreased susceptibility of Gas1* to ERAD is caused by canonical remodeling of its GPI anchor, which occurs in all GPI-APs and provides a protein-independent ER export signal. Thus, GPI anchor remodeling is independent of protein folding and leads to efficient ER export of even misfolded species. Our data imply that ER quality control is limited for the entire class of GPI-APs, many of them being clinically relevant.

scholarly journals Exon capture optimization in large-genome amphibians

2015 ◽  
Author(s):  
Evan McCartney-Melstad ◽  
Genevieve G. Mount ◽  
H. Bradley Shaffer
Keyword(s):  
Model Organisms ◽  
Tiger Salamander ◽  
Illumina Hiseq ◽  
F1 Hybrid ◽  
Large Genome ◽  
Sequence Capture ◽  
Exon Capture ◽  
Target Capture ◽  
Individual Input ◽  
Enrichment Efficiency

Background Gathering genomic-scale data efficiently is challenging for non-model species with large, complex genomes. Transcriptome sequencing is accessible for even large-genome organisms, and sequence capture probes can be designed from such mRNA sequences to enrich and sequence exonic regions. Maximizing enrichment efficiency is important to reduce sequencing costs, but, relatively little data exist for exon capture experiments in large-genome non-model organisms. Here, we conducted a replicated factorial experiment to explore the effects of several modifications to standard protocols that might increase sequence capture efficiency for large-genome amphibians. Methods We enriched 53 genomic libraries from salamanders for a custom set of 8,706 exons under differing conditions. Libraries were prepared using pools of DNA from 3 different salamanders with approximately 30 gigabase genomes: California tiger salamander (Ambystoma californiense), barred tiger salamander (Ambystoma mavortium), and an F1 hybrid between the two. We enriched libraries using different amounts of c0t-1 blocker, individual input DNA, and total reaction DNA. Enriched libraries were sequenced with 150 bp paired-end reads on an Illumina HiSeq 2500, and the efficiency of target enrichment was quantified using unique read mapping rates and average depth across targets. The different enrichment treatments were evaluated to determine if c0t-1 and input DNA significantly impact enrichment efficiency in large-genome amphibians. Results Increasing the amounts of c0t-1 and individual input DNA both reduce the rates of PCR duplication. This reduction led to an increase in the percentage of unique reads mapping to target sequences, essentially doubling overall efficiency of the target capture from 10.4% to nearly 19.9%. We also found that post-enrichment DNA concentrations and qPCR enrichment verification were useful for predicting the success of enrichment. Conclusions Increasing the amount of individual sample input DNA and the amount of c0t-1 blocker both increased the efficiency of target capture in large-genome salamanders. By reducing PCR duplication rates, the number of unique reads mapping to targets increased, making target capture experiments more efficient and affordable. Our results indicate that target capture protocols can be modified to efficiently screen large-genome vertebrate taxa including amphibians.

scholarly journals A Novel Class of RanGTP Binding Proteins

1997 ◽  
Vol 138 (1) ◽  
pp. 65-80 ◽  
Author(s):  
Dirk Görlich ◽  
Marylena Dabrowski ◽  
F. Ralf Bischoff ◽  
Ulrike Kutay ◽  
Peer Bork ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Nuclear Import ◽  
Cell Cycle Progression ◽  
Binding Proteins ◽  
Nuclear Pore ◽  
Sequence Motif ◽  
Nucleotide Exchange ◽  
Direct Function ◽  
Entire Class ◽  
Dependent Transport

The importin-α/β complex and the GTPase Ran mediate nuclear import of proteins with a classical nuclear localization signal. Although Ran has been implicated also in a variety of other processes, such as cell cycle progression, a direct function of Ran has so far only been demonstrated for importin-mediated nuclear import. We have now identified an entire class of ∼20 potential Ran targets that share a sequence motif related to the Ran-binding site of importin-β. We have confirmed specific RanGTP binding for some of them, namely for two novel factors, RanBP7 and RanBP8, for CAS, Pse1p, and Msn5p, and for the cell cycle regulator Cse1p from Saccharomyces cerevisiae. We have studied RanBP7 in more detail. Similar to importin-β, it prevents the activation of Ran's GTPase by RanGAP1 and inhibits nucleotide exchange on RanGTP. RanBP7 binds directly to nuclear pore complexes where it competes for binding sites with importin-β, transportin, and apparently also with the mediators of mRNA and U snRNA export. Furthermore, we provide evidence for a Ran-dependent transport cycle of RanBP7 and demonstrate that RanBP7 can cross the nuclear envelope rapidly and in both directions. On the basis of these results, we propose that RanBP7 might represent a nuclear transport factor that carries an as yet unknown cargo, which could apply as well for this entire class of related RanGTP-binding proteins.

18. Sleeping Car Porters in Canada (1917-1964)

2016 ◽  
Author(s):  
Sonja Moroz ◽  
Gillian Craig
Keyword(s):  
Entire Class ◽  
Race And Racialization

The following posters are a result of research done by the students in Dr. Cynthia Levine-Rasky’s Sociology 233: ‘Race’ and Racialization course. These ten posters were chosen by the entire class to be exhibited at I@Q.

17. Islamophobia in Canada

2016 ◽  
Author(s):  
Darcy Vidler
Keyword(s):  
Entire Class ◽  
Race And Racialization

The following posters are a result of research done by the students in Dr. Cynthia Levine-Rasky’s Sociology 233: ‘Race’ and Racialization course. These ten posters were chosen by the entire class to be exhibited at I@Q.

Sign in / Sign up

Export Citation Format

Share Document