Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 Å resolution

KH (hnRNP K homology) domains, consisting of ∼70 amino acid residues, are present in a variety of nucleic-acid-binding proteins. Among these are poly(C)-binding proteins (PCBPs), which are important regulators of mRNA stability and posttranscriptional regulation in general. All PCBPs contain three different KH domains and recognize poly(C)-sequences with high affinity and specificity. To reveal the molecular basis of poly(C)-sequence recognition, we have determined the crystal structure, at 1.6 Å resolution, of PCBP2 KH3 domain in complex with a 7-nt DNA sequence (5′-AACCCTA-3′) corresponding to one repeat of the C-rich strand of human telomeric DNA. The domain assumes a type-I KH fold in a βααββα configuration. The protein–DNA interface could be studied in unprecedented detail and is made up of a series of direct and water-mediated hydrogen bonds between the protein and the DNA, revealing an especially dense network involving several structural water molecules for the last 2 nt in the core recognition sequence. Unlike published KH domain structures, the protein crystallizes without protein–protein contacts, yielding new insights into the dimerization properties of different KH domains. A nucleotide platform, an interesting feature found in some RNA molecules, was identified, evidently for the first time in DNA

Biomass Burning Plumes in the Vicinity of the California Coast: Airborne Characterization of Physicochemical Properties, Heating Rates, and Spatiotemporal Features

This study characterizes in situ airborne properties associated with biomass burning (BB) plumes in the vicinity of the California coast. Out of 231 total aircraft soundings in July–August 2013 and 2016, 81 were impacted by BB layers. A number of vertical characteristics of BB layers are summarized in this work (altitude, location relative to cloud top height, thickness, number of vertically adjacent layers, interlayer distances) in addition to differences in vertical aerosol concentration profiles due to either surface type (e.g., land or ocean) or time of day. Significant BB layer stratification occurred, especially over ocean versus land, with the majority of layers in the free troposphere and within 100 m of the boundary layer top. Heating rate profiles demonstrated the combined effect of cloud and BB layers and their mutual interactions, with enhanced heating in BB layers with clouds present underneath. Aerosol size distribution data are summarized below and above the boundary layer, with a notable finding being enhanced concentrations of supermicrometer particles in BB conditions. A plume aging case study revealed the dominance of organics in the free troposphere, with secondary production of inorganic and organic species and coagulation as a function of distance from fire source up to 450 km. Rather than higher horizontal and vertical resolution, a new smoke injection height method was the source of improved agreement for the vertical distribution of BB aerosol in the Navy Aerosol Analysis and Prediction System model when compared to airborne data

The 3′ Untranslated Region of the Rabies Virus Glycoprotein mRNA Specifically Interacts with Cellular PCBP2 Protein and Promotes Transcript Stability

Viral polymerase entry and pausing at intergenic junctions is predicted to lead to a defined polarity in the levels of rhabdovirus gene expression. Interestingly, we observed that the rabies virus glycoprotein mRNA is differentially over-expressed based on this model relative to other transcripts during infection of 293T cells. During infection, the rabies virus glycoprotein mRNA also selectively interacts with the cellular poly(rC)-binding protein 2 (PCBP2), a factor known to influence mRNA stability. Reporter assays performed both in electroporated cells and in a cell-free RNA decay system indicate that the conserved portion of the 3′ UTR of the rabies virus glycoprotein mRNA contains an RNA stability element. PCBP2 specifically interacts with reporter transcripts containing this 72 base 3′ UTR sequence. Furthermore, the PCBP2 interaction is directly associated with the stability of reporter transcripts. Therefore, we conclude that PCBP2 specifically and selectively interacts with the rabies virus glycoprotein mRNA and that this interaction may contribute to the post-transcriptional regulation of glycoprotein expression

Patterns of Loss and Regeneration of Tropical Dry Forest in Madagascar: The Social Institutional Context

Loss of tropical forests and changes in land-use/land-cover are of growing concern worldwide. Although knowledge exists about the institutional context in which tropical forest loss is embedded, little is known about the role of social institutions in influencing regeneration of tropical forests. In the present study we used Landsat images from southern Madagascar from three different years (1984, 1993 and 2000) and covering 5500 km(2), and made a time-series analysis of three distinct large-scale patterns: 1) loss of forest cover, 2) increased forest cover, and 3) stable forest cover. Institutional characteristics underlying these three patterns were analyzed, testing the hypothesis that forest cover change is a function of strength and enforcement of local social institutions. The results showed a minor decrease of 7% total forest cover in the study area during the whole period 1984–2000, but an overall net increase of 4% during the period 1993–2000. The highest loss of forest cover occurred in a low human population density area with long distances to markets, while a stable forest cover occurred in the area with highest population density and good market access. Analyses of institutions revealed that loss of forest cover occurred mainly in areas characterized by insecure property rights, while areas with well-defined property rights showed either regenerating or stable forest cover. The results thus corroborate our hypothesis. The large-scale spontaneous regeneration dominated by native endemic species appears to be a result of a combination of changes in precipitation, migration and decreased human population and livestock grazing pressure, but under conditions of maintained and well-defined property rights. Our study emphasizes the large capacity of a semi-arid system to spontaneously regenerate, triggered by decreased pressures, but where existing social institutions mitigate other drivers of deforestation and alternative land-use

Detection and Characterization of Wolbachia Infections in Natural Populations of Aphids: Is the Hidden Diversity Fully Unraveled?

Aphids are a serious threat to agriculture, despite being a rather small group of insects. The about 4,000 species worldwide engage in highly interesting and complex relationships with their microbial fauna. One of the key symbionts in arthropods is Wolbachia, an α-Proteobacterium implicated in many important biological processes and believed to be a potential tool for biological control. Aphids were thought not to harbour Wolbachia; however, current data suggest that its presence in aphids has been missed, probably due to the low titre of the infection and/or to the high divergence of the Wolbachia strains of aphids. The goal of the present study is to map the Wolbachia infection status of natural aphids populations, along with the characterization of the detected Wolbachia strains. Out of 425 samples from Spain, Portugal, Greece, Israel and Iran, 37 were found to be infected. Our results, based mainly on 16S rRNA gene sequencing, indicate the presence of two new Wolbachia supergroups prevailing in aphids, along with some strains belonging either to supergroup B or to supergroup A