1,115 research outputs found
tRNA signatures reveal polyphyletic origins of streamlined SAR11 genomes among the alphaproteobacteria
Phylogenomic analyses are subject to bias from compositional convergence and
noise from horizontal gene transfer (HGT). Compositional convergence is a
likely cause of controversy regarding phylogeny of the SAR11 group of
Alphaproteobacteria that have extremely streamlined, A+T-biased genomes. While
careful modeling can reduce artifacts caused by convergence, the most
consistent and robust phylogenetic signal in genomes may lie distributed among
encoded functional features that govern macromolecular interactions. Here we
develop a novel phyloclassification method based on signatures derived from
bioinformatically defined tRNA Class-Informative Features (CIFs). tRNA CIFs are
enriched for features that underlie tRNA-protein interactions. Using a simple
tRNA-CIF-based phyloclassifier, we obtained results consistent with those of
bias-corrected whole proteome phylogenomic studies, rejecting monophyly of
SAR11 and affiliating most strains with Rhizobiales with strong statistical
support. Yet SAR11 and Rickettsiales tRNA genes share distinct patterns of
A+T-richness, as expected from their elevated genomic A+T compositions. Using
conventional supermatrix methods on total tRNA sequence data, we could recover
the artifactual result of a monophyletic SAR11 grouping with Rickettsiales.
Thus tRNA CIF-based phyloclassification is more robust to base content
convergence than supermatrix phylogenomics on whole tRNA sequences. Also, given
the notoriously promiscuous HGT of aminoacyl-tRNA synthetases, tRNA CIF-based
phyloclassification may be relatively robust to HGT of network components. We
describe how unique features of tRNA-protein interaction networks facilitate
the mining of traits governing macromolecular interactions from genomic data,
and discuss why interaction-governing traits may be especially useful to solve
difficult problems in microbial classification and phylogeny
tRNA functional signatures classify plastids as late-branching cyanobacteria.
BackgroundEukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data.ResultsUsing Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies ("phyloclassifies") cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data.ConclusionsPhylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies
Defect and solute properties in dilute Fe-Cr-Ni austenitic alloys from first principles
We present results of an extensive set of first-principles density functional
theory calculations of point defect formation, binding and clustering energies
in austenitic Fe with dilute concentrations of Cr and Ni solutes.Comment: 24 pages, 10 figures, published in Phys. Rev.
A1-L12 interfacial free energies from data on coarsening in five binary Ni alloys, informed by thermodynamic phase diagram assessments
The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes
Many cases of non-standard genetic codes are known in mitochondrial genomes.
We carry out analysis of phylogeny and codon usage of organisms for which the
complete mitochondrial genome is available, and we determine the most likely
mechanism for codon reassignment in each case. Reassignment events can be
classified according to the gain-loss framework. The gain represents the
appearance of a new tRNA for the reassigned codon or the change of an existing
tRNA such that it gains the ability to pair with the codon. The loss represents
the deletion of a tRNA or the change in a tRNA so that it no longer translates
the codon. One possible mechanism is Codon Disappearance, where the codon
disappears from the genome prior to the gain and loss events. In the
alternative mechanisms the codon does not disappear. In the Unassigned Codon
mechanism, the loss occurs first, whereas in the Ambiguous Intermediate
mechanism, the gain occurs first. Codon usage analysis gives clear evidence of
cases where the codon disappeared at the point of the reassignment and also
cases where it did not disappear. Codon disappearance is the probable
explanation for stop to sense reassignments and a small number of reassignments
of sense codons. However, the majority of sense to sense reassignments cannot
be explained by codon disappearance. In the latter cases, by analysis of the
presence or absence of tRNAs in the genome and of the changes in tRNA
sequences, it is sometimes possible to distinguish between the Unassigned Codon
and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments
follow the same scenario and that it is necessary to consider the details of
each case carefully.Comment: 53 pages (45 pages, including 4 figures + 8 pages of supplementary
information). To appear in J.Mol.Evo
Thinking the unthinkable: Imagining an ‘un-American,’ Girl-friendly, Women- and Trans-Inclusive Alternative for Baseball
The purpose of this article is twofold: to capture the injustice inherent in the gendered bifurcation of baseball and softball via the prism of critical feminist sport studies; and to begin to imagine a girl-friendly/women-and trans-inclusive future for baseball that is less fertile for cooptation into post-911 United States security state discourses. In this article I link the "unthinkability" of the occupational segregation of baseball in North America to the dominance of the ideology of the two sex system and European disasporic morality. To illustrate the extent of this occupational segregation via the gendered bifurcation of baseball and softball, I draw on feminist sport studies to examine the exemplars or "texts" of three Canadian brother/sister baseball softball duos: Jason Bay and Lauren Bay Regula; Brett and Danielle Lawrie; and Mathew and Katie Reyes
Effect of Correlated tRNA Abundances on Translation Errors and Evolution of Codon Usage Bias
Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find a consistent positive correlation between tRNA abundances across the genetic code. This work challenges one of the fundamental assumptions made in over 30 years of research on CUB that codons with higher tRNA abundances have lower missense error rates and that missense errors are the primary selective force responsible for CUB
Search for long-lived, massive particles in events with displaced vertices and missing transverse momentum in s =13 TeV pp collisions with the ATLAS detector
A search for long-lived, massive particles predicted by many theories beyond the Standard Model is presented. The search targets final states with large missing transverse momentum and at least one high-mass displaced vertex with five or more tracks, and uses 32.8 fb-1 of s=13 TeV pp collision data collected by the ATLAS detector at the LHC. The observed yield is consistent with the expected background. The results are used to extract 95% C.L. exclusion limits on the production of long-lived gluinos with masses up to 2.37 TeV and lifetimes of O(10-2)-O(10) ns in a simplified model inspired by split supersymmetry
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