In vitro nuclear interactome of the HIV-1 Tat protein

<p>Abstract</p> <p>Background</p> <p>One facet of the complexity underlying the biology of HIV-1 resides not only in its limited number of viral proteins, but in the extensive repertoire of cellular proteins they interact with and their higher-order assembly. HIV-1 encodes the regulatory protein Tat (86–101aa), which is essential for HIV-1 replication and primarily orchestrates HIV-1 provirus transcriptional regulation. Previous studies have demonstrated that Tat function is highly dependent on specific interactions with a range of cellular proteins. However they can only partially account for the intricate molecular mechanisms underlying the dynamics of proviral gene expression. To obtain a comprehensive nuclear interaction map of Tat in T-cells, we have designed a proteomic strategy based on affinity chromatography coupled with mass spectrometry.</p> <p>Results</p> <p>Our approach resulted in the identification of a total of 183 candidates as Tat nuclear partners, 90% of which have not been previously characterised. Subsequently we applied <it>in silico </it>analysis, to validate and characterise our dataset which revealed that the Tat nuclear interactome exhibits unique signature(s). First, motif composition analysis highlighted that our dataset is enriched for domains mediating protein, RNA and DNA interactions, and helicase and ATPase activities. Secondly, functional classification and network reconstruction clearly depicted Tat as a polyvalent protein adaptor and positioned Tat at the nexus of a densely interconnected interaction network involved in a range of biological processes which included gene expression regulation, RNA biogenesis, chromatin structure, chromosome organisation, DNA replication and nuclear architecture.</p> <p>Conclusion</p> <p>We have completed the <it>in vitro </it>Tat nuclear interactome and have highlighted its modular network properties and particularly those involved in the coordination of gene expression by Tat. Ultimately, the highly specialised set of molecular interactions identified will provide a framework to further advance our understanding of the mechanisms of HIV-1 proviral gene silencing and activation.</p

Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches

Evolutionary histories are now being inferred from unprecedented, genome-scale datasets for a broad range of organismal groups. While phylogenomic data has helped in resolving a number of difficult, long-standing questions, constructing appropriate datasets from genomes is not straightforward, particularly in non-model groups. Here we explore the utility of phylogenomic data to infer robust phylogenies for a lineage of closely related lichen-forming fungal species. We assembled multiple, distinct nuclear phylogenomic datasets, ranging from ca. 25 Kb to 16.8 Mb and inferred topologies using both concatenated gene tree approaches and species tree methods based on the multispecies coalescent model. In spite of evidence for rampant incongruence among individual loci, these genome-scale datasets provide a consistent, well-supported phylogenetic hypothesis using both concatenation and multispecies coalescent approaches (ASTRAL-II and SVDquartets). However, the popular full hierarchical coalescent approach implemented in *BEAST provided inconsistent inferences, both in terms of nodal support and topology, with smaller subsets of the phylogenomic data. While comparable, well-supported topologies can be accurately inferred with only a small fraction of the overall genome, consistent results across a variety of datasets and methodological approaches provide reassurance that phylogenomic data can effectively be used to provide robust phylogenies for closely related lichen-forming fungal lineages

Biogeography, ecology, and spatial patterns of patagonian lizards

Patagonia has a great diversity of lizards, including 6 families, 11 genera and 163 species. The majority of this diversity with documented geographical records corresponds to the Liolaemidae family (Phymaturus and Liolaemus). Latitudinally, lizard richness is higher between 37° to 39° S, decreasing gradually until latitude 54° S; longitudinally, it is higher between 69° and 71° W. The georeferenced records and the number of collected specimens have some biases, with higher values in the northern regions (up to latitude 42° S). However, there are areas up to latitude 45° S with species richness similar to others with a greater number of collected individuals. The vegetation units with the highest species richness (S) in Argentinean Patagonia are the northern and central areas reaching west of Chubut Province: Western District (S = 60) and Typical Southern Monte (S = 49), passing through areas with intermediate richness and with only one species (Wet Magellanic Steppe) or none (Evergreen shrub, Monte?s Mountains and Valleys, Western Interior Pampa, and Peat Bogs). There is a general trend towards lower species richness in vegetation units located in the extreme south of Argentina and south of latitude 41° S in Chile. We evaluated differences in lizard diversity and evenness among vegetation units through a dendrogram based on species incidences and found 6 clusters. Then, we compared species richness between members of each cluster with rarefaction curves. Species marginally distributed in Patagonia have a narrower altitudinal range than Patagonian endemics. Species in genus Liolaemus have small differences in altitudinal range, but species of Phymaturus have pronounced differences in altitudinal ranges. Our spatial analyses, based on intensive systematic-taxonomic activity over the last two decades, shed light into the understanding of lizard distributions in one of the regions with the greatest diversity of reptiles in the world. We also provide ecological and spatial metrics for an updated list of Patagonian lizards. We highlight that the usefulness of discretizing large volumes of information and geographic space into a synthetic framework allows using quantitative results for the study of spatial patterns of biodiversity, decision-making for design studies, use of resources and creation of protected areas.Fil: Minoli, Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; ArgentinaFil: Perez, Cristian Hernan Fulvio. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Centro Nacional Patagonico. Unidad de Administracion Territorial.; ArgentinaFil: Morando, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; ArgentinaFil: Avila, Luciano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; Argentin