Genome sequencing and functional characterization of the non-pathogenic Klebsiella pneumoniae KpGe bacteria

Klebsiella pneumoniae is an extensively studied human pathogen responsible for a wide variety of infections. Dictyostelium discoideum is a model host organism employed to study many facets of the complex interactions between phagocytic cells and bacteria. Historically, a non-pathogenic strain of K. pneumoniae has been used to feed Dictyostelium amoebae, and more recently to study cellular mechanisms involved in bacterial recognition, ingestion and killing. Here we provide the full genome sequence and functional characterization of this non-pathogenic KpGe strain.     

PCSK9 reduces the protein levels of the LDL receptor in mouse brain during development and after ischemic stroke

Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a major role in cholesterol homeostasis through enhanced degradation of the LDL receptor (LDLR) in liver. As novel inhibitors/silencers of PCSK9 are now being tested in clinical trials to treat hypercholesterolemia, it is crucial to define the physiological consequences of the lack of PCSK9 in various organs. LDLR regulation by PCSK9 has not been extensively described during mouse brain development and injury. Herein, we show that PCSK9 and LDLR are co-expressed in mouse brain during development and at adulthood. Although the protein levels of LDLR and apolipoprotein E (apoE) in the adult brain of Pcsk9(-/-) mice are similar to those of wild-type (WT) mice, LDLR levels increased and were accompanied by a reduction of apoE levels during development. This suggests that the upregulation of LDLR protein levels in Pcsk9(-/-) mice enhances apoE degradation. Upon ischemic stroke, PCSK9 was expressed in the dentate gyrus between 24 h and 72 h following brain reperfusion. Although mouse behavior and lesion volume were similar, LDLR protein levels dropped ～2-fold less in the Pcsk9(-/-)-lesioned hippocampus, without affecting apoE levels and neurogenesis. Thus, PCSK9 downregulates LDLR levels during brain development and following transient ischemic stroke in adult mice.     

Fungal adenylyl cyclase integrates CO2 sensing with cAMP signaling and virulence

The ascomycete Candida albicans is the most common fungal pathogen in immunocompromised patients . Its ability to change morphology, from yeast to filamentous forms, in response to host environmental cues is important for virulence . Filamentation is mediated by second messengers such as cyclic adenosine 3',5'-monophosphate (cAMP) synthesized by adenylyl cyclase . The distantly related basidiomycete Cryptococcus neoformans is an encapsulated yeast that predominantly infects the central nervous system in immunocompromised patients . Similar to the morphological change in C. albicans, capsule biosynthesis in C. neoformans, a major virulence attribute, is also dependent upon adenylyl cyclase activity . Here we demonstrate that physiological concentrations of CO2/HCO3- induce filamentation in C. albicans by direct stimulation of cyclase activity. Furthermore, we show that CO2/HCO3- equilibration by carbonic anhydrase is essential for pathogenesis of C. albicans in niches where the available CO2 is limited. We also demonstrate that adenylyl cyclase from C. neoformans is sensitive to physiological concentrations of CO2/HCO3-. These data demonstrate that the link between cAMP signaling and CO2/HCO3- sensing is conserved in fungi and reveal CO2 sensing to be an important mediator of fungal pathogenesis. Novel therapeutic agents could target this pathway at several levels to control fungal infections.     

Osteoprotegerin decreases human osteoclast apoptosis by inhibiting the TRAIL pathway

Osteoprotegerin (OPG) is a secreted decoy receptor that recognizes RANKL, and blocks the interaction between RANK and RANKL, leading to the inhibition of osteoclast differentiation and activation. As OPG is a major inhibitor of bone resorption, we wondered whether OPG could modulate osteoclast survival/apoptosis. Osteoclast apoptosis was evaluated by adding various doses of OPG to human osteoclast cultures obtained from cord blood monocytes. Surprisingly, apoptosis decreased after adding the OPG. We hypothesized that OPG may block its second ligand, TRAIL, which is involved in osteoclast apoptosis. We showed that osteoclasts expressed TRAIL, and that TRAIL levels in the culture medium dose-dependently decreased in presence of OPG, as did the level of activated caspase-8 in osteoclasts. In addition, the expression of TRAIL by osteoclasts was not affected in the presence of OPG. Our findings suggest that OPG inhibits osteoclast apoptosis, at least in part, by binding and thus inhibiting endogenously produced TRAIL in human osteoclast cultures. TRAIL could be an autocrine factor for the regulation of osteoclast survival/apoptosis.     

Evaluation of the taxonomic accuracy and pathogenicity prediction power of 16 primer sets amplifying single copy marker genes in the Pseudomonas syringae species complex

The Pseudomonas syringae species complex is composed of several closely related species of bacterial plant pathogens. Here, we used in silico methods to assess 16 PCR primer sets designed for broad identification of isolates throughout the species complex. We evaluated their in silico amplification rate in 2161 publicly available genomes, the correlation between pairwise amplicon sequence distance and whole genome average nucleotide identity, and trained naive Bayes classification models to quantify classification resolution. Furthermore, we show the potential for using single amplicon sequence data to predict type III effector protein repertoires, which are important determinants of host specificity and range.     

Invasive knotweed modifies predator–prey interactions in the soil food web

Biological Invasions - Invasive plants often modify the structure of the community of native plants and animals, but their potential impact on the plant–soil interface is poorly studied. In...     

Demographic analysis of a dominant shrub (Cytisus scoparius): Prospects for encroachment control

Shrub encroachment in pastoral areas subsequent to land-use changes has become a major problem for biodiversity and pastoral resource conservation. Controlling encroachment by grazing is the most promising prospect at this time, but the impact of small domestic ruminants on the population dynamics of dominant shrubby species is still poorly understood. To control the rapid densification of dominant shrub populations means that we have to focus on the early stages of shrub colonisation. In this paper, we present a modelling approach that includes deterministic matrix modelling to understand demography strategy at the very beginning of shrub population growth and to identify potential targeted life stages for control. We collected demographic data over a period of 5 years on the European dominant shrub, Cytisus scoparius (Scotch broom; Fabaceae), which is often part of the heathlands that establish themselves on former permanent grasslands in Europe. Our results reveal a very high variation in flowering frequency between years and a large contribution of the seed bank to the total number of seedlings that emerge each year. Modelling shows that population growth is very vigorous and is not stopped by repeated “bad years” for seed production. Sensitivity analyses indicate that early life stage survival (seedling, juvenile) has the greatest impact on population growth. These results make it possible to identify juveniles as one of the best targets for control since they combine a high degree of sensitivity in terms of population demography, good palatability for domestic herbivores and easy accessibility within a management schedule.     

Adult asthmatics display exaggerated IFNgamma responses to human metapneumovirus and respiratory syncytial virus.

Human metapneumovirus and respiratory syncytial virus are RNA viruses associated with lower respiratory tract infections. Regular symptomatic re-infection and sequelae are common, particularly in individuals with pre-existing respiratory diseases, such as asthma. Our understanding of virus-dependent cytokine responses and potential differences between allergic asthmatics and non-asthmatics is limited. To test our hypothesis that adults with mild allergic asthma, the most common form of this disease, exhibit distinct pro-inflammatory responses, we developed a model using acute in vitro infection of fresh peripheral blood mononuclear cells. For both viruses, the production of innate-immunity-associated IL-6 and IL-10 was indistinguishable in the 2 populations. Type 1 cytokine production dominated adaptive immune responses in both asthmatic and non-asthmatic individuals. Surprisingly, asthmatics exhibited stronger pro-inflammatory IFNgamma production in response to human metapneumovirus than non-asthmatic adults (p = 0.01), with a similar, but statistically nonsignificant trend in the respiratory-syncytial-virus-stimulated response. Neutralizing IL-10 did not enhance the intensity of IFNgamma responses, demonstrating that this pro-inflammatory bias is not counter-regulated by IL-10. Finally, anti-TLR4 blocked lipopolysaccharide, but not respiratory-syncytial-virus-driven cytokine production. Collectively, the data demonstrate that asthma is characterized by markedly stronger pro-inflammatory IFNgamma responses to pneumoviruses than their non-asthmatic counterparts. This distinctive pattern of viral immunity may contribute to a worsening of asthma symptoms during respiratory virus infections.     

Influence of taxonomic resolution on mutualistic network properties

1. Ecologists are increasingly interested in plant–pollinator networks that synthesize in a single object the species and the interactions linking them within their ecological context. Numerous indices have been developed to describe the structural properties and resilience of these networks, but currently, these indices are calculated for a network resolved to the species level, thus preventing the full exploitation of numerous datasets with a lower taxonomic resolution. Here, we used datasets from the literature to study whether taxonomic resolution has an impact on the properties of plant–pollinator networks.
2. For a set of 41 plant–pollinator networks from the literature, we calculated nine network index values at three different taxonomic resolutions: species, genus, and family. We used nine common indices assessing the structural properties or resilience of networks: nestedness (estimated using the nestedness index based on overlap and decreasing fill [NODF], weighted NODF, discrepancy [BR], and spectral radius [SR]), connectance, modularity, robustness to species loss, motifs frequencies, and normalized degree.
3. We observed that modifying the taxonomic resolution of these networks significantly changes the absolute values of the indices that describe their properties, except for the spectral radius and robustness. After the standardization of indices measuring nestedness with the Z‐score, three indices—NODF, BR, and SR for binary matrices—are not significantly different at different taxonomic resolutions. Finally, the relative values of all indices are strongly conserved at different taxonomic resolutions.
4. We conclude that it is possible to meaningfully estimate the properties of plant–pollinator interaction networks with a taxonomic resolution lower than the species level. We would advise using either the SR or robustness on untransformed data, or the NODF, discrepancy, or SR (for weighted networks only) on Z‐scores. Additionally, connectance and modularity can be compared between low taxonomic resolution networks using the rank instead of the absolute values.