Evolutionary dynamics of retrotransposons following autopolyploidy in the Buckler Mustard species complex

Long terminal repeat retrotransposons (LTR‐RTs) represent a major fraction of plant genomes, but processes leading to transposition bursts remain elusive. Polyploidy expectedly leads to LTR‐RT proliferation, as the merging of divergent diploids provokes a genome shock activating LTR‐RTs and/or genetic redundancy supports the accumulation of active LTR‐RTs through relaxation of selective constraints. Available evidence supports interspecific hybridization as the main trigger of genome dynamics, but few studies have addressed the consequences of intraspecific polyploidy (i.e. autopolyploidy), where the genome shock is expectedly minimized. The dynamics of LTR‐RTs was thus here evaluated through low coverage 454 sequencing of three closely related diploid progenitors and three independent autotetraploids from the young Biscutella laevigata species complex. Genomes from this early diverging Brassicaceae lineage presented a minimum of 40% repeats and a large diversity of transposable elements. Differential abundances and patterns of sequence divergence among genomes for 37 LTR‐RT families revealed contrasted dynamics during species diversification. Quiescent LTR‐RT families with limited genetic variation among genomes were distinguished from active families (37.8%) having proliferated in specific taxa. Specific families proliferated in autopolyploids only, but most transpositionally active families in polyploids were also differentiated among diploids. Low expression levels of transpositionally active LTR‐RT families in autopolyploids further supported that genome shock and redundancy are non‐mutually exclusive triggers of LTR‐RT proliferation. Although reputed stable, autopolyploid genomes show LTR‐RT fractions presenting analogies with polyploids between widely divergent genomes.     

Characterization and structural analyses of nonspecific lipid transfer protein 1 from mung bean

Plant nonspecific lipid transfer proteins (nsLTPs) are thermal stable proteins that are capable of transferring lipid molecules between bilayers in vitro. This family of proteins, abundant in plants, is proposed to be involved in defense, pollination, and germination; the in vivo biological function remains, however, elusive. Here we report the purification and sequencing of an nsLTP1 from mung bean sprouts. We have also determined the solution structure of this nsLTP1, which represents the first 3D structure of the dicotyledonous nsLTP1 family. The global fold of mung bean nsLTP1 is similar to those of the monocotyledonous nsLTP1 structures and consists of four alpha-helices stabilized by four disulfide bonds. There are, however, some notable differences in the C-terminal tails and internal hydrophobic cavities. Circular dichroism and fluorescence spectroscopy were used to compare the thermodynamics and lipid transfer properties of mung bean nsLTP1 with those of rice nsLTP1. Docking of a lipid molecule into the solution structure of mung bean nsLTP1 reveals similar binding cavities and hydrophobic interactions as in rice nsLTP1, consistent with their comparable lipid transfer properties measured experimentally.     

Autophagic Cell Death in Dictyostelium Requires the Receptor Histidine Kinase DhkM

Dictyostelium constitutes a genetically tractable model for the analysis of autophagic cell death (ACD). During ACD, Dictyostelium cells first transform into paddle cells and then become round, synthesize cellulose, vacuolize, and die. Through random insertional mutagenesis, we identified the receptor histidine kinase DhkM as being essential for ACD. Surprisingly, different DhkM mutants showed distinct nonvacuolizing ACD phenotypes. One class of mutants arrested ACD at the paddle cell stage, perhaps through a dominant-negative effect. Other mutants, however, progressed further in the ACD program. They underwent rounding and cellulose synthesis but stopped before vacuolization. Moreover, they underwent clonogenic but not morphological cell death. Exogenous 8-bromo-cAMP restored vacuolization and death. A role for a membrane receptor at a late stage of the ACD pathway is puzzling, raising questions as to which ligand it is a receptor for and which moieties it phosphorylates. Together, DhkM is the most downstream-known molecule required for this model ACD, and its distinct mutants genetically separate previously undissociated late cell death events.     

Personalized Modeling for Prediction with Decision-Path Models

Deriving predictive models in medicine typically relies on a population approach where a single model is developed from a dataset of individuals. In this paper we describe and evaluate a personalized approach in which we construct a new type of decision tree model called decision-path model that takes advantage of the particular features of a given person of interest. We introduce three personalized methods that derive personalized decision-path models. We compared the performance of these methods to that of Classification And Regression Tree (CART) that is a population decision tree to predict seven different outcomes in five medical datasets. Two of the three personalized methods performed statistically significantly better on area under the ROC curve (AUC) and Brier skill score compared to CART. The personalized approach of learning decision path models is a new approach for predictive modeling that can perform better than a population approach.     

Psychometric Validation Study of the Liebowitz Social Anxiety Scale - Self-Reported Version for Brazilian Portuguese

Social Anxiety Disorder (SAD) is prevalent and rarely diagnosed due to the difficulty in recognizing its symptoms as belonging to a disorder. Therefore, the evaluation/screening scales are of great importance for its detection, with the most used being the Liebowitz Social Anxiety Scale (LSAS). Thus, this study proposed to evaluate the psychometric properties of internal consistency and convergent validity, as well as the confirmatory factorial analysis and reliability of the self-reported version of the LSAS (LSAS-SR), translated into Brazilian Portuguese, in a sample of the general population (N = 413) and in a SAD clinical sample (N = 252). The convergent validity with specific scales for the evaluation of SAD and a general anxiety scale presented correlations ranging from 0.21 to 0.84. The confirmatory factorial analysis did not replicate the previously indicated findings of the literature, with the difficulty being in obtaining a consensus factorial structure common to the diverse cultures in which the instrument was studied. The LSAS-SR presented excellent internal consistency (α = 0.90–0.96) and test-retest reliability (Intraclass Correlation Coefficient = 0.81; Pearson’s = 0.82). The present findings support those of international studies that attest to the excellent psychometric properties of the LSAS-SR, endorsing its status as the gold standard.     

Integrative taxonomy of Flatbill Flycatchers (Tyrannidae) reveals a new species from the Amazonian lowlands

Integrative taxonomic studies continue to reveal that many current polytypic species of birds are in fact constituted by two or more species and therefore have been central in uncovering ‘hidden’ or ‘cryptic’ biodiversity. The Olivaceous Flatbill (Aves: Tyrannidae: Rhynchocyclus olivaceus) currently has nine recognized subspecies distributed throughout the Neotropics, but so far, no complete phylogenetic hypothesis exists to test the validity and evolutionary relationships among them. To remedy this, we conducted a multi-character integrative taxonomic revision of the genus Rhynchocyclus, focusing on the polytypic R. olivaceus. The combination of a taxonomically dense sampled multilocus phylogeny (including three mitochondrial and two nuclear genes) with phenotypic analyses including morphological and vocal characters pointed to several taxonomic inconsistencies within R. olivaceus. The analyses strongly support that R. olivaceus is paraphyletic, with an exclusively cis-Andean clade (where the topotypic R. olivaceus is found) clustering as sister to Rhynchocyclus fulvipectus, to the exclusion of a clade grouping trans-Andean and western Amazonian populations currently placed in R. olivaceus—one of which is unnamed and fully diagnosable based on vocal and genetic characters. Consistent with the phylogenetic results, our vocal analyses identified at least four morphologically cryptic lineages within R. olivaceus that can be mutually diagnosed from each other by different loudsongs and call parameters. Therefore, we provide evidence for splitting these four groups into separate species, two of which are sympatric but not syntopic in western Amazonia, including an unnamed species described herein—Rhynchocyclus cryptus, sp. nov. urn:lsid:zoobank.org:act:2DC17190-2BDD-49EC-88E6-4CF2FC2562A3.