Variable tree rooting strategies are key for modelling the distribution, productivity and evapotranspiration of tropical evergreen forests

A variety of modelling studies have suggested tree rooting depth as a key variable to explain evapotranspiration rates, productivity and the geographical distribution of evergreen forests in tropical South America. However, none of those studies have acknowledged resource investment, timing and physical constraints of tree rooting depth within a competitive environment, undermining the ecological realism of their results. Here, we present an approach of implementing variable rooting strategies and dynamic root growth into the LPJmL4.0 (Lund-Potsdam-Jena managed Land) dynamic global vegetation model (DGVM) and apply it to tropical and sub-tropical South America under contemporary climate conditions. We show how competing rooting strategies which underlie the trade-off between above- and below-ground carbon investment lead to more realistic simulation of intra-annual productivity and evapotranspiration and consequently of forest cover and spatial biomass distribution. We find that climate and soil depth determine a spatially heterogeneous pattern of mean rooting depth and below-ground biomass across the study region. Our findings support the hypothesis that the ability of evergreen trees to adjust their rooting systems to seasonally dry climates is crucial to explaining the current dominance, productivity and evapotranspiration of evergreen forests in tropical South America.Fil: Sakschewski, Boris. Potsdam Institute for Climate Impact Research; AlemaniaFil: Von Bloh, Werner. Humboldt-Universität zu Berlin; AlemaniaFil: Drüke, Markus. Humboldt-Universität zu Berlin; AlemaniaFil: Sörensson, Anna. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Centro de Investigaciones del Mar y la Atmósfera. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Centro de Investigaciones del Mar y la Atmósfera; ArgentinaFil: Ruscica, Romina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Centro de Investigaciones del Mar y la Atmósfera. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Centro de Investigaciones del Mar y la Atmósfera; ArgentinaFil: Langerwisch, Fanny. Universitat Potsdam; AlemaniaFil: Billing, Maik. Universidade Federal de Santa Catarina; BrasilFil: Bereswill, Sarah. Universidade Estadual de Campinas; BrasilFil: Hirota, Marina. Potsdam Institute for Climate Impact Research; AlemaniaFil: Oliveira, Rafael Silva. Potsdam Institute for Climate Impact Research; AlemaniaFil: Heinke, Jens. Potsdam Institute for Climate Impact Research; AlemaniaFil: Thonicke, Kirsten. Potsdam Institute for Climate Impact Research; Alemani

Variable tree rooting strategies are key for modelling the distribution, productivity and evapotranspiration of tropical evergreen forests

A variety of modelling studies have suggested tree rooting depth as a key variable to explain evapotranspiration rates, productivity and the geographical distribution of evergreen forests in tropical South America. However, none of those studies have acknowledged resource investment, timing and physical constraints of tree rooting depth within a competitive environment, undermining the ecological realism of their results. Here, we present an approach of implementing variable rooting strategies and dynamic root growth into the LPJmL4.0 (Lund-Potsdam-Jena managed Land) dynamic global vegetation model (DGVM) and apply it to tropical and sub-tropical South America under contemporary climate conditions. We show how competing rooting strategies which underlie the trade-off between above- and below-ground carbon investment lead to more realistic simulation of intra-annual productivity and evapotranspiration and consequently of forest cover and spatial biomass distribution. We find that climate and soil depth determine a spatially heterogeneous pattern of mean rooting depth and below-ground biomass across the study region. Our findings support the hypothesis that the ability of evergreen trees to adjust their rooting systems to seasonally dry climates is crucial to explaining the current dominance, productivity and evapotranspiration of evergreen forests in tropical South America

A Single Nucleotide Change Affects Fur-Dependent Regulation of sodB in H. pylori

Helicobacter pylori is a significant human pathogen that has adapted to survive the many stresses found within the gastric environment. Superoxide Dismutase (SodB) is an important factor that helps H. pylori combat oxidative stress. sodB was previously shown to be repressed by the Ferric Uptake Regulator (Fur) in the absence of iron (apo-Fur regulation) [1]. Herein, we show that apo regulation is not fully conserved among all strains of H. pylori. apo-Fur dependent changes in sodB expression are not observed under iron deplete conditions in H. pylori strains G27, HPAG1, or J99. However, Fur regulation of pfr and amiE occurs as expected. Comparative analysis of the Fur coding sequence between G27 and 26695 revealed a single amino acid difference, which was not responsible for the altered sodB regulation. Comparison of the sodB promoters from G27 and 26695 also revealed a single nucleotide difference within the predicted Fur binding site. Alteration of this nucleotide in G27 to that of 26695 restored apo-Fur dependent sodB regulation, indicating that a single base difference is at least partially responsible for the difference in sodB regulation observed among these H. pylori strains. Fur binding studies revealed that alteration of this single nucleotide in G27 increased the affinity of Fur for the sodB promoter. Additionally, the single base change in G27 enabled the sodB promoter to bind to apo-Fur with affinities similar to the 26695 sodB promoter. Taken together these data indicate that this nucleotide residue is important for direct apo-Fur binding to the sodB promoter

Cluster K Mycobacteriophages: Insights into the Evolutionary Origins of Mycobacteriophage TM4

Five newly isolated mycobacteriophages –Angelica, CrimD, Adephagia, Anaya, and Pixie – have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them – with the exception of TM4 – form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species

The Transcriptional Response of Drosophila melanogaster to Infection with the Sigma Virus (Rhabdoviridae)

Bacterial and fungal infections induce a potent immune response in Drosophila melanogaster, but it is unclear whether viral infections induce an antiviral immune response. Using microarrays, we examined the changes in gene expression in Drosophila that occur in response to infection with the sigma virus, a negative-stranded RNA virus (Rhabdoviridae) that occurs in wild populations of D. melanogaster. We detected many changes in gene expression in infected flies, but found no evidence for the activation of the Toll, IMD or Jak-STAT pathways, which control immune responses against bacteria and fungi. We identified a number of functional categories of genes, including serine proteases, ribosomal proteins and chorion proteins that were overrepresented among the differentially expressed genes. We also found that the sigma virus alters the expression of many more genes in males than in females. These data suggest that either Drosophila do not mount an immune response against the sigma virus, or that the immune response is not controlled by known immune pathways. If the latter is true, the genes that we identified as differentially expressed after infection are promising candidates for controlling the host's response to the sigma virus

Human cathelicidin production by the cervix

hCAP18/LL-37 is the sole human cathelicidin; a family of host defence peptides with key roles in innate host defence. hCAP18/LL-37 is expressed primarily by neutrophils and epithelial cells, but its production and function in the lower genital tract is largely uncharacterised. Despite the significant roles for cathelicidin in multiple organs and inflammatory processes, its impact on infections that could compromise fertility and pregnancy is unknown. The aim of this study was to investigate cathelicidin production, regulation and function in the cervix. hCAP18/LL-37 was found to be present in cervicovaginal secretions collected from women in the first trimester of pregnancy and to be expressed at significantly higher levels in samples from women with alterations in vaginal bacterial flora characteristic of bacterial vaginosis. In endocervical epithelial cell lines, expression of the gene encoding hCAP18/LL-37 (CAMP) was not affected by TLR agonists, but was found to be up-regulated by both 1, 25 hydroxyvitamin D3 and 25 hydroxyvitamin D3. However, no association was found between serum levels of vitamin D and hCAP18/LL-37 concentrations in cervicovaginal secretions (n = 116). Exposure to synthetic LL-37 had a pro-inflammatory effect on endocervical epithelial cell lines, increasing secretion of inflammatory cytokine IL-8. Together these data demonstrate inducible expression of hCAP18/LL-37 in the female lower reproductive tract in vivo and suggest the capacity for this peptide to modulate host defence to infection in this system. Further investigation will elucidate the effects of hCAP18/LL-37 on the physiology and pathophysiology of labour, and may lead to strategies for the prevention of infection-associated preterm birth

Coupling non‐invasive imaging and reactive transport modeling to investigate water and oxygen dynamics in the root zone

Abstract Oxygen (O2) availability in soils is vital for plant growth and productivity. The transport and consumption of O2 in the root zone is closely linked to soil moisture content, the spatial distribution of roots, as well as structure and heterogeneity of the surrounding soil. In this study, we measure three‐dimensional root system architecture and the spatiotemporal dynamics of soil moisture (θ) and O2 concentrations in the root zone of maize (Zea mays) via non‐invasive imaging, and then construct and parameterize a reactive transport model based on the experimental data. The combination of three non‐invasive imaging methods allowed for a direct comparison of simulation results with observations at high spatial and temporal resolution. In three different modeling scenarios, we investigated how the results obtained for different levels of conceptual complexity in the model were able to match measured θ and O2 concentration patterns. We found that the modeling scenario that considers heterogeneous soil structure and spatial variability of hydraulic parameters (permeability, porosity, and van Genuchten α and n), better reproduced the measured θ and O2 patterns relative to a simple model with a homogenous soil domain. The results from our combined imaging and modeling analysis reveal that experimental O2 and water dynamics can be reproduced quantitatively in a reactive transport model, and that O2 and water dynamics are best characterized when conditions unique to the specific system beyond the distribution of roots, such as soil structure and its effect on water saturation and macroscopic gas transport pathways, are considered

Altered antibody profiles against common infectious agents in chronic disease.

Despite the important diagnostic value of evaluating antibody responses to individual human pathogens, antibody profiles against multiple infectious agents have not been used to explore health and disease mainly for technical reasons.  We hypothesized that the interplay between infection and chronic disease might be revealed by profiling antibodies against multiple agents. Here, the levels of antibodies against a panel of 13 common infectious agents were evaluated with the quantitative Luciferase Immunoprecipitation Systems (LIPS) in patients from three disease cohorts including those with pathogenic anti-interferon-γ autoantibodies (IFN-γ AAB), HIV and Sjögren's syndrome (SjS) to determine if their antibody profiles differed from control subjects.  The IFN-γ AAB patients compared to controls demonstrated statistically higher levels of antibodies against VZV (p=0.0003), EBV (p=0.002), CMV (p=0.003), and C. albicans (p=0.03), but lower antibody levels against poliovirus (p=0.04). Comparison of HIV patients with blood donor controls revealed that the patients had higher levels of antibodies against CMV (p=0.0008), HSV-2 (p=0.0008), EBV (p=0.001), and C. albicans (p=0.01), but showed decreased levels of antibodies against coxsackievirus B4 (p=0.0008), poliovirus (p=0.0005),   and HHV-6B (p=0.002). Lastly, SjS patients had higher levels of anti-EBV antibodies (p=0.03), but lower antibody levels against several enteroviruses including a newly identified picornavirus, HCoSV-A (p=0.004), coxsackievirus B4 (p=0.04), and poliovirus (p=0.02). For the IFN-γ AAB and HIV cohorts, principal component analysis revealed unique antibody clusters that showed the potential to discriminate patients from controls.  The results suggest that antibody profiles against these and likely other common infectious agents may yield insight into the interplay between exposure to infectious agents, dysbiosis, adaptive immunity and disease activity