Divergent MicroRNA Targetomes of Closely Related Circulating Strains of a Polyomavirus

Hundreds of virus-encoded microRNAs (miRNAs) have been uncovered, but an in-depth functional understanding is lacking for most. A major challenge for the field is separating those miRNA targets that are biologically relevant from those that are not advantageous to the virus. Here, we show that miRNAs from related variants of the polyomavirus simian vacuolating virus 40 (SV40) have differing host target repertoires (targetomes) while their direct autoregulatory activity on virus-encoded early gene products is completely preserved. These results underscore the importance of miRNA-mediated viral gene autoregulation in some polyomavirus life cycles. More broadly, these findings imply that some host targets of virus-encoded miRNAs are likely to be of little selective advantage to the virus, and our approach provides a strategy for prioritizing relevant targets.     

Two new species (Gustavia johnclarkii and G. hubbardiorum) and other contributions to the systematics of Gustavia (Lecythidaceae)

Gustavia johnclarkii and G. hubbardiorum, two new species from the wet forests of northwestern and Amazonian Ecuador, are described and illustrated. In addition, the two subspecies of both G. speciosa and G. macarenensis are elevated to species, and the new combination Gustavia paucisperma is provided. A justification for these changes is presented.     

Occupancy modelling as a new approach to assess supranational trends using opportunistic data: a pilot study for the damselfly Calopteryx splendens

There is limited information available on changes in biodiversity at the European scale, because there is a lack of data from standardised monitoring for most species groups. However, a great number of observations made without a standardised field protocol is available in many countries for many species. Such opportunistic data offer an alternative source of information, but unfortunately such data suffer from non-standardised observation effort and geographical bias. Here we describe a new approach to compiling supranational trends using opportunistic data which adjusts for these two major imperfections. The non-standardised observation effort is dealt with by occupancy modelling, and the unequal geographical distribution of sites by a weighting procedure. The damselfly Calopteryx splendens was chosen as our test species. The data were collected from five countries (Ireland, Great Britain, the Netherlands, Belgium and France), covering the period 1990–2008. We used occupancy models to estimate the annual number of occupied 1 × 1 km sites per country. Occupancy models use presence-absence data, account for imperfect detection of species, and thereby correct for between-year variability in observation effort. The occupancy models were run per country in a Bayesian mode of inference using JAGS. The occupancy estimates per country were then aggregated to assess the supranational trend in the number of occupied 1 × 1 km². To adjust for the unequal geographical distribution of surveyed sites, we weighted the countries according to the number of sites surveyed and the range of the species per country. The distribution of C. splendens has increased significantly in the combined five countries. Our trial demonstrated that a supranational trend in distribution can be derived from opportunistic data, while adjusting for observation effort and geographical bias. This opens new perspectives for international monitoring of biodiversity.     

Niche breadth and range area in North American trees

Identifying factors affecting species distribution is a longstanding goal in ecology and evolution that is accentuated by our need to anticipate climate change impacts. We sought to test whether any phylogenetic effect can be detected in either the environmental characteristics or range attributes of North American trees, and to explore the existence of a general interspecific pattern in the environmental factors influencing species range size. To do so we tested prevailing hypotheses relating climatic and edaphic characteristics to species range size in the North American arboflora (n = 598), using spatial null models to test for the relevance of observed patterns. We found that interspecific variation in the range area of North American trees is strongly related to the environmental regimes characteristic of the species range. Linear models and phylogenetic regressions involving six environmental characteristics explained 83% of the variance in species range area, and affirmed a positive relationship between niche breadth and range size. Tree species that can tolerate a larger variability in local climatic conditions, deal with harsher edaphic conditions, and weak levels of environmental energy tend to have larger range area; this can account for the greater geographic range of species at higher latitudes, the Rapoport effect. There is a significant phylogenetic signal for both range area and limits in North American trees, and for climatic limits, but not for energy or edaphic characteristics associated with species range. These findings highlight the possibility that species with small geographic ranges may be more sensitive to the effects of climate change.     

Gossypol and an HMT G9a inhibitor act in synergy to induce cell death in pancreatic cancer cells

The histone methyltransferase G9a is overexpressed in a variety of cancer types, including pancreatic adenocarcinoma, and promotes tumor invasiveness and metastasis. We recently reported the discovery of BRD4770, a small-molecule inhibitor of G9a that induces senescence in PANC-1 cells. We observed that the cytotoxic effects of BRD4770 were dependent on genetic background, with cell lines lacking functional p53 being relatively resistant to compound treatment. To understand the mechanism of genetic selectivity, we used two complementary screening approaches to identify enhancers of BRD4770. The natural product and putative BH3 mimetic gossypol enhanced the cytotoxicity of BRD4770 in a synergistic manner in p53-mutant PANC-1 cells but not in immortalized non-tumorigenic pancreatic cells. The combination of gossypol and BRD4770 increased LC3-II levels and the autophagosome number in PANC-1 cells, and the compound combination appears to act in a BNIP3 (B-cell lymphoma 2 19-kDa interacting protein)-dependent manner, suggesting that these compounds act together to induce autophagy-related cell death in pancreatic cancer cells.     

Discovery of the Inhibitory Effect of a Phosphatidylinositol Derivative on P-Glycoprotein by Virtual Screening Followed by In Vitro Cellular Studies

P-glycoprotein is capable of effluxing a broad range of cytosolic and membrane penetrating xenobiotic substrates, thus leading to multi-drug resistance and posing a threat for the therapeutic treatment of several diseases, including cancer and central nervous disorders. Herein, a virtual screening campaign followed by experimental validation in Caco-2, MDKCII, and MDKCII mdr1 transfected cell lines has been conducted for the identification of novel phospholipids with P-gp transportation inhibitory activity. Phosphatidylinositol-(1,2-dioctanoyl)-sodium salt (8∶0 PI) was found to significantly inhibit transmembrane P-gp transportation in vitro in a reproducible-, cell line-, and substrate-independent manner. Further tests are needed to determine whether this and other phosphatidylinositols could be co-administered with oral drugs to successfully increase their bioavailability. Moreover, as phosphatidylinositols and phosphoinositides are present in the human diet and are known to play an important role in signal transduction and cell motility, our finding could be of substantial interest for nutrition science as well.     

Focused Examination of the Intestinal Epithelium Reveals Transcriptional Signatures Consistent with Disturbances in Enterocyte Maturation and Differentiation during the Course of SIV Infection

The Gastrointestinal (GI) tract plays a pivotal role in AIDS pathogenesis as it is the primary site for viral transmission, replication and CD4⁺ T cell destruction. Accordingly, GI disease (enteropathy) has become a well-known complication and a driver of AIDS progression. To better understand the molecular mechanisms underlying GI disease we analyzed global gene expression profiles sequentially in the intestinal epithelium of the same animals before SIV infection and at 21 and 90 days post infection (DPI). More importantly we obtained sequential excisional intestinal biopsies and examined distinct mucosal components (epithelium. intraepithelial lymphocytes, lamina propria lymphocytes, fibrovascular stroma) separately. Here we report data pertaining to the epithelium. Overall genes associated with epithelial cell renewal/proliferation/differentiation, permeability and adhesion were significantly down regulated (<1.5–7 fold) at 21 and 90DPI. Genes regulating focal adhesions (n = 6), gap junctions (n = 3), ErbB (n = 3) and Wnt signaling (n = 4) were markedly down at 21DPI and the number of genes in each of these groups that were down regulated doubled between 21 and 90DPI. Notable genes included FAK, ITGA6, PDGF, TGFβ3, Ezrin, FZD6, WNT10A, and TCF7L2. In addition, at 90DPI genes regulating ECM-receptor interactions (laminins and ITGB1), epithelial cell gene expression (PDX1, KLF6), polarity/tight junction formation (PARD3B&6B) and histone demethylase (JMJD3) were also down regulated. In contrast, expression of NOTCH3, notch target genes (HES4, HES7) and EZH2 (histone methyltransferase) were significantly increased at 90DPI. The altered expression of genes linked to Wnt signaling together with decreased expression of PDX1, PARD3B, PARD6B and SDK1 suggests marked perturbations in intestinal epithelial function and homeostasis leading to breakdown of the mucosal barrier. More importantly, the divergent expression patterns of EZH2 and JMJD3 suggests that an epigenetic mechanism involving histone modifications may contribute to the massive decrease in gene expression at 90DPI leading to defects in enterocyte maturation and differentiation.     

Multigeneration Cross-Contamination of Mail with Bacillus anthracis Spores

The release of biological agents, including those which could be used in biowarfare or bioterrorism in large urban areas, has been a concern for governments for nearly three decades. Previous incidents from Sverdlosk and the postal anthrax attack of 2001 have raised questions on the mechanism of spread of Bacillus anthracis spores as an aerosol or contaminant. Prior studies have demonstrated that Bacillus atrophaeus is easily transferred through simulated mail handing, but no reports have demonstrated this ability with Bacillus anthracis spores, which have morphological differences that may affect adhesion properties between spore and formite. In this study, equipment developed to simulate interactions across three generations of envelopes subjected to tumbling and mixing was used to evaluate the potential for cross-contamination of B. anthracis spores in simulated mail handling. In these experiments, we found that the potential for cross-contamination through letter tumbling from one generation to the next varied between generations while the presence of a fluidizer had no statistical impact on the transfer of material. Likewise, the presence or absence of a fluidizer had no statistically significant impact on cross-contamination levels or reaerosolization from letter opening.