Dengue Virus RNA Structure Specialization Facilitates Host Adaptation

Many viral pathogens cycle between humans and insects. These viruses must have evolved strategies for rapid adaptation to different host environments. However, the mechanistic basis for the adaptation process remains poorly understood. To study the mosquito-human adaptation cycle, we examined changes in RNA structures of the dengue virus genome during host adaptation. Deep sequencing and RNA structure analysis, together with fitness evaluation, revealed a process of host specialization of RNA elements of the viral 3’UTR. Adaptation to mosquito or mammalian cells involved selection of different viral populations harvesting mutations in a single stem-loop structure. The host specialization of the identified RNA structure resulted in a significant viral fitness cost in the non-specialized host, posing a constraint during host switching. Sequence conservation analysis indicated that the identified host adaptable stem loop structure is duplicated in dengue and other mosquito-borne viruses. Interestingly, functional studies using recombinant viruses with single or double stem loops revealed that duplication of the RNA structure allows the virus to accommodate mutations beneficial in one host and deleterious in the other. Our findings reveal new concepts in adaptation of RNA viruses, in which host specialization of RNA structures results in high fitness in the adapted host, while RNA duplication confers robustness during host switching.     

Assessment of biofilm formation by Scedosporium apiospermum,S. aurantiacum,S. minutisporum and Lomentospora prolificans

Reported herein is the ability of Scedosporium apiospermum, S. aurantiacum, S. minutisporum and Lomentospora prolificans conidia to adhere, differentiate into hyphae and form biofilms on both polystyrene and lung epithelial cells. To different degrees, all of the fungi adhered to polystyrene after 4 h, with a predominance of those with germinated conidia. Prolonged fungi–polystyrene contact resulted in the formation of a monolayer of intertwined mycelia, which was identified as a typical biofilm structure due to the presence of a viable mycelial biomass, extracellular matrix and enhanced antifungal resistance. Ultrastructural details were revealed by SEM and CLSM, showing the dense compaction of the mycelial biomass and the presence of channels within the organized biofilm. A similar biofilm structure was observed following the co-culture of each fungus with A549 cells, revealing a mycelial trap covering all of the lung epithelial monolayer. Collectively, these results highlight the potential for biofilm formation by these clinically relevant fungal pathogens.     

Denitrifying population dynamic and evolution of nitrogen gas during a composting process

Abstract Little information exists about nitrogen losses through microbial activity during treatment of solid urban waste (SUW) by processes such as composting. In the present study, in addition to evaluating the pattern of nitrogen losses by denitrification at different stages of the process, a comparison between the method of Pochon and Tardieux, and an improved gas chromatographic method for estimating denitrifying populations was undertaken, Though the MPN (Most Probable Number) enumerations were higher using the colorimetric method than the gas chromatographic one, the patterns of the two graphs showing numbers of denitrifiers during composing were the same. The highest numbers were revealed immediately after loading the reactor (10⁷–10⁸/g d.w.), lower numbers of denitrifiers were found in the second sampling corresponding to the thermophilic phase (10³–10⁴/g d.w.). These numbers increased gradually as the waste material stabilized (10th to 123rd day of composting) to again reach values of 10⁷–10⁸/g d.w.     

Disregulation in TH1 and TH2 subsets of CD4+ T cells in peripheral blood of colorectal cancer patients and involvement in cancer establishment and progression

 Recent theories have established that, during an ongoing immune response, the lymphokines produced by TH1 and TH2 subsets of CD4⁺ T cells are critical to the effectiveness of that response. In vivo and in vitro studies have demonstrated that the type of environmental cytokines plays a determinant role in directing the development of naive T cells into TH1 or TH2 effector cells. Disregulated expansion of one or other subset may contribute to the development of certain diseases. To establish whether a similar situation might exist in the cells of the peripheral blood (PBMC) of colorectal cancer patients, we have performed immunological studies on a group of patients and a group of healthy subjects. We examined the interleukin-2 (IL-2), interferon γ (IFNγ), IL-4, IL-6 and tumour necrosis factor α levels in serum; the production of IL-4 and IL-2, with and without activating agents, by PBMC, tumour-draining lymph node lymphocytes and tumour cells; and the proliferative response of PBMC to IL-2, IL-4 and anti-CD3 monoclonal antibody (anti-CD3), which were variously combined. The data of the present study lead us to hypothesize that, because of suppressive effects probably due to environmental IL-4, in the peripheral blood of patients there seems to be a disregulation in the functionality of TH1 and TH2 subsets of CD4⁺ T cells, with an expansion in TH2 and a malfunction in TH1 cells. Moreover it seems that this disregulation increases with as the disease progresses through the stages, suggesting that it can be directly implicated in the mechanisms that allow the tumour to locate and progress in the host. Received: 27 June 1995 / Accepted: 13 November 1995     

Inferring Meaningful Communities from Topology-Constrained Correlation Networks

Community structure detection is an important tool in graph analysis. This can be done, among other ways, by solving for the partition set which optimizes the modularity scores . Here it is shown that topological constraints in correlation graphs induce over-fragmentation of community structures. A refinement step to this optimization based on Linear Discriminant Analysis (LDA) and a statistical test for significance is proposed. In structured simulation constrained by topology, this novel approach performs better than the optimization of modularity alone. This method was also tested with two empirical datasets: the Roll-Call voting in the 110th US Senate constrained by geographic adjacency, and a biological dataset of 135 protein structures constrained by inter-residue contacts. The former dataset showed sub-structures in the communities that revealed a regional bias in the votes which transcend party affiliations. This is an interesting pattern given that the 110th Legislature was assumed to be a highly polarized government. The -amylase catalytic domain dataset (biological dataset) was analyzed with and without topological constraints (inter-residue contacts). The results without topological constraints showed differences with the topology constrained one, but the LDA filtering did not change the outcome of the latter. This suggests that the LDA filtering is a robust way to solve the possible over-fragmentation when present, and that this method will not affect the results where there is no evidence of over-fragmentation.     

A new species of Rhytidognathus (Carabidae,?Migadopini) from Argentina

The Migadopini are a small tribe of Carabidae with 47 species that occur in South America, Australia, and New Zealand, in the sub-Antarctic areas. In South America, most of the genera inhabit areas related to sub-Antartic Nothofagus forest except two monogeneric genera, the Ecuadorian genus Aquilex Moret and the Pampean genus Rhytidognathus Chaudoir. These two genera are geographically isolated from the remaining five South American genera. New material of Rhytidognathus from the northeast of Buenos Aires province and from Entre Ríos province permits establishing that the previous records of Rhytidognathus ovalis (Dejean) for Argentina were erroneous and that it belongs to a new species. Based on external morphological characters and from male and female genitalia we describe Rhytidognathus platensis as a new species. In this contribution we provide illustrations, keys, habitat characteristics and some biogeographic considerations on the distribution of Rhytidognathus.     

The p53 isoforms are differentially modified by Mdm2

The discovery that the single p53 gene encodes several different p53 protein isoforms has initiated a flurry of research into the function and regulation of these novel p53 proteins. Full-length p53 protein level is primarily regulated by the E3-ligase Mdm2, which promotes p53 ubiquitination and degradation. Here, we report that all of the novel p53 isoforms are ubiquitinated and degraded to varying degrees in an Mdm2-dependent and -independent manner, and that high-risk human papillomavirus can degrade some but not all of the novel isoforms, demonstrating that full-length p53 and the p53 isoforms are differentially regulated. In addition, we provide the first evidence that Mdm2 promotes the NEDDylation of p53β. Altogether, our data indicates that Mdm2 can distinguish between the p53 isoforms and modify them differently.     

Relationship between laying dates of black kites Milvus migrans and spring temperatures in Italy: rapid response to climate change?

Many Holarctic bird species have been shown to be laying progressively earlier in response to global warming. Most studies have been conducted on small-bodied species at northern latitudes. In Italy, black kite Milvus migrans populations are concentrated near large pre-Alpine lakes, whose water temperatures have been increasing steadily in recent decades. Annual black kite laying dates have become 10–11 days earlier during the last nine years. This shift was related to temporal variations in spring air temperatures, with earlier laying in warmer springs. The progressive advancement in laying dates was not associated with an increase in population level productivity, despite the fact that productivity declined with laying date at the individual territory level within years. Avian response to climate change may be occurring more rapidly than previously thought, even in relatively long-lived species, and not only at the most northern latitudes or highest elevations. Because this change has occurred so rapidly, and because laying dates match annual variations in spring temperatures, the response must be facultatively driven by prevailing conditions, rather than genetic in response to natural selection.     

The effects of manipulation of sedimentary iron and organic matter on sediment biogeochemistry and seagrasses in a subtropical carbonate environment

The microbial metabolism of organic matter (OM) in seagrass beds can create sulfidic conditions detrimental to seagrass growth; iron (Fe) potentially has ameliorating effects through titration of the sulfides and the precipitation of iron-sulfide minerals into the sediment. In this study, the biogeochemical effects of Fe availability and its interplay with sulfur and OM on sulfide toxicity, phosphorous (P) availability, seagrass growth and community structure were tested. The availability of Fe and OM was manipulated in a 2 × 2 factorial experiment arranged in a Latin square, with four replicates per treatment. The treatments included the addition of Fe, the addition of OM, the addition of both Fe and OM as well as no addition. The experiment was conducted in an oligotrophic, iron-deficient seagrass bed. Fe had an 84.5% retention efficiency in the sediments with the concentration of Fe increasing in the seagrass leaves over the course of the experiment. Porewater chemistry was significantly altered with a dramatic decrease in sulfide levels in Fe addition plots while sulfide levels increased in the OM addition treatments. Phosphorus increased in seagrass leaves collected in the Fe addition plots. Decreased sulfide stress was evidenced by heavier δ³⁴S in leaves and rhizomes from plots to which Fe was added. The OM addition negatively affected seagrass growth but increased P availability; the reduced sulfide stress in Fe added plots resulted in elevated productivity. Fe availability may be an important determinant of the impact that OM has on seagrass vitality in carbonate sediments vegetated with seagrasses.