Identification of commonly expressed exoproteins and proteolytic cleavage events by proteomic mining of clinically relevant UK isolates of Staphylococcus aureus

The range of exoproteins and core exoproteome of 14 Staphylococcus aureus isolates representing major lineages associated with asymptomatic carriage and clinical disease in the UK was identified by MS proteomics using a combined database incorporating sequences derived from 39 S. aureus genomes. In all, 632 different proteins were identified and, of these, only 52 (8 %) were found in all 14 isolates whereas 144 (23 %) were found in just a single isolate. Comparison of the observed mass of each protein (based on migration by SDS-PAGE) with its predicted mass (based on amino acid sequence) suggested that 95 % of the proteins identified were not subject to any major post-translational modification. Migration of 5 % of the proteins was not as expected: 1 % of the proteins migrated at a mass greater than predicted, while 4 % appeared to have undergone proteolytic cleavage; these included SsaA2, Aur, SspP, Ebh as well as BlaR1, MecR1, FsH, OatA and LtaS. Intriguingly, a truncated SasG was produced by a single CC8 USA300-like strain. The analysis provided evidence of the marked heterogeneity in protein expression by S. aureus in broth, while yielding a core but narrow common exoproteome

Streptococcal superantigen‐induced expansion of human tonsil T cells leads to altered T follicular helper cell phenotype, B cell death and reduced immunoglobulin release

Streptococcal pyrogenic exotoxin (Spe) A expression is epidemiologically linked to streptococcal tonsillo‐pharyngitis and outbreaks of scarlet fever, although the mechanisms by which superantigens confer advantage to Streptococcus pyogenes are unclear. S. pyogenes is an exclusively human pathogen. As the leucocyte profile of tonsil is unique, the impact of SpeA production on human tonsil cell function was investigated. Human tonsil cells from routine tonsillectomy were co‐incubated with purified streptococcal superantigens or culture supernatants from isogenic streptococcal isolates, differing only in superantigen production. Tonsil cell proliferation was quantified by tritiated thymidine incorporation, and cell surface characteristics assessed by flow cytometry. Soluble mediators including immunoglobulin were measured using enzyme‐linked immunosorbent assay. Tonsil T cells proliferated in response to SpeA and demonstrated typical release of proinflammatory cytokines. When cultured in the absence of superantigen, tonsil preparations released large quantities of immunoglobulin over 7 days. In contrast, marked B cell apoptosis and abrogation of total immunoglobulin (Ig)A, IgM, and IgG production occurred in the presence of SpeA and other superantigens. In SpeA‐stimulated cultures, T follicular helper (Tfh) cells showed a reduction in C‐X‐C chemokine receptor (CXCR)5 (CD185) expression, but up‐regulation of OX40 (CD134) and inducible T cell co‐stimulator (ICOS) (CD278) expression. The phenotypical change in the Tfh population was associated with impaired chemotactic response to CXCL13. SpeA and other superantigens cause dysregulated tonsil immune function, driving T cells from Tfh to a proliferating phenotype, with resultant loss of B cells and immunoglobulin production, providing superantigen‐producing bacteria with a probable survival advantage

Extracellular bacterial lymphatic metastasis drives Streptococcus pyogenes systemic infection

Unassisted metastasis through the lymphatic system is a mechanism of dissemination thus far ascribed only to cancer cells. Here, we report that Streptococcus pyogenes also hijack lymphatic vessels to escape a local infection site, transiting through sequential lymph nodes and efferent lymphatic vessels to enter the bloodstream. Contrasting with previously reported mechanisms of intracellular pathogen carriage by phagocytes, we show S. pyogenes remain extracellular during transit, first in afferent and then efferent lymphatics that carry the bacteria through successive draining lymph nodes. We identify streptococcal virulence mechanisms important for bacterial lymphatic dissemination and show that metastatic streptococci within infected lymph nodes resist and subvert clearance by phagocytes, enabling replication that can seed intense bloodstream infection. The findings establish the lymphatic system as both a survival niche and conduit to the bloodstream for S. pyogenes, explaining the phenomenon of occult bacteraemia. This work provides new perspectives in streptococcal pathogenesis with implications for immunity

Impact of contusion injury on intramuscular emm1 group a streptococcus infection and lymphatic spread.

Invasive group A Streptococcus (iGAS) is frequently associated with emm1 isolates, with an attendant mortality of around 20%. Cases occasionally arise in previously healthy individuals with a history of upper respiratory tract infection, soft tissue contusion, and no obvious portal of entry. Using a new murine model of contusion, we determined the impact of contusion on iGAS bacterial burden and phenotype. Calibrated mild blunt contusion did not provide a focus for initiation or seeding of GAS that was detectable following systemic GAS bacteremia, but instead enhanced GAS migration to the local draining lymph node following GAS inoculation at the same time and site of contusion. Increased migration to lymph node was associated with emergence of mucoid bacteria, although was not specific to mucoid bacteria. In one study, mucoid colonies demonstrated a significant increase in capsular hyaluronan that was not linked to a covRS or rocA mutation, but to a deletion in the promoter of the capsule synthesis locus, hasABC, resulting in a strain with increased fitness for lymph node migration. In summary, in the mild contusion model used, we could not detect seeding of muscle by GAS. Contusion promoted bacterial transit to the local lymph node. The consequences of contusion-associated bacterial lymphatic migration may vary depending on the pathogen and virulence traits selected

Strong coupling constant from τ\tau decay within renormalization scheme invariant treatment

We extract a numerical value for the strong coupling constant \alpha_s from the \tau-lepton decay rate into nonstrange particles. A new feature of our procedure is the explicit use of renormalization scheme invariance in analytical form in order to perform the actual analysis in a particular renormalization scheme. For the reference coupling constant in the \MSsch-scheme we obtain \alpha_s(M_\tau)= 0.3184 \pm 0.0060_{exp} which corresponds to \al_s(M_Z)= 0.1184 \pm 0.0007_{exp} \pm 0.0006_{hq mass}. This new numerical value is smaller than the standard value from $\tau$-data quoted in the literature and is closer to \al_s(M_Z)-values obtained from high energy experiments.Comment: 8 page

Habitat filtering across tree life stages in tropical forest communities

Tropical tree communities are shaped by local-scale habitat heterogeneity in the form of topographic and edaphic variation, but the life-history stage at which habitat associations develop remains poorly understood. This is due, in part, to the fact that previous studies have not accounted for the widely disparate sample sizes number of stems that result when trees are divided into size classes. We demonstrate that the observed habitat structuring of a community is directly related to the number of individuals in the community. We then compare the relative importance of habitat heterogeneity to tree community structure for saplings, juveniles and adult trees within seven large 24-50 ha tropical forest dynamics plots while controlling for sample size. Changes in habitat structuring through tree life stages were small and inconsistent among life stages and study sites. Where found, these differences were an order of magnitude smaller than the findings of previous studies that did not control for sample size. Moreover, community structure and composition were very similar among tree sub-communities of different life stages. We conclude that the structure of these tropical tree communities is established by the time trees are large enough to be included in the census 1 cm diameter at breast height, which indicates that habitat filtering occurs during earlier life stages. © 2013 The Authors Published by the Royal Society. All rights reserved

SPIDER: Probing the Early Universe with a Suborbital Polarimeter

We evaluate the ability of SPIDER, a balloon-borne polarimeter, to detect a divergence-free polarization pattern ("B-modes") in the Cosmic Microwave Background (CMB). In the inflationary scenario, the amplitude of this signal is proportional to that of the primordial scalar perturbations through the tensor-to-scalar ratio r. We show that the expected level of systematic error in the SPIDER instrument is significantly below the amplitude of an interesting cosmological signal with r=0.03. We present a scanning strategy that enables us to minimize uncertainty in the reconstruction of the Stokes parameters used to characterize the CMB, while accessing a relatively wide range of angular scales. Evaluating the amplitude of the polarized Galactic emission in the SPIDER field, we conclude that the polarized emission from interstellar dust is as bright or brighter than the cosmological signal at all SPIDER frequencies (90 GHz, 150 GHz, and 280 GHz), a situation similar to that found in the "Southern Hole." We show that two ~20-day flights of the SPIDER instrument can constrain the amplitude of the B-mode signal to r<0.03 (99% CL) even when foreground contamination is taken into account. In the absence of foregrounds, the same limit can be reached after one 20-day flight.Comment: 29 pages, 8 figures, 4 tables; v2: matches published version, flight schedule updated, two typos fixed in Table 2, references and minor clarifications added, results unchange

Phylogenetic turnover along local environmental gradients in tropical forest communities

© 2016, Springer-Verlag Berlin Heidelberg. While the importance of local-scale habitat niches in shaping tree species turnover along environmental gradients in tropical forests is well appreciated, relatively little is known about the influence of phylogenetic signal in species’ habitat niches in shaping local community structure. We used detailed maps of the soil resource and topographic variation within eight 24–50 ha tropical forest plots combined with species phylogenies created from the APG III phylogeny to examine how phylogenetic beta diversity (indicating the degree of phylogenetic similarity of two communities) was related to environmental gradients within tropical tree communities. Using distance-based redundancy analysis we found that phylogenetic beta diversity, expressed as either nearest neighbor distance or mean pairwise distance, was significantly related to both soil and topographic variation in all study sites. In general, more phylogenetic beta diversity within a forest plot was explained by environmental variables this was expressed as nearest neighbor distance versus mean pairwise distance (3.0–10.3 % and 0.4–8.8 % of variation explained among plots, respectively), and more variation was explained by soil resource variables than topographic variables using either phylogenetic beta diversity metric. We also found that patterns of phylogenetic beta diversity expressed as nearest neighbor distance were consistent with previously observed patterns of niche similarity among congeneric species pairs in these plots. These results indicate the importance of phylogenetic signal in local habitat niches in shaping the phylogenetic structure of tropical tree communities, especially at the level of close phylogenetic neighbors, where similarity in habitat niches is most strongly preserved

Body size, trophic position, and the coupling of different energy pathways across a saltmarsh landscape

Body size is considered an important structuring mechanism of food webs because consumers are usually larger and more mobile than their prey and may couple energy among habitats. We explored the links among trophic position (TP), body size, and the coupling of different energy channels (phytoplankton and C4-marsh plants) in a saltmarsh landscape in the northern Gulf of Mexico—a dynamic system considered weakly shaped by biotic interactions. Body size was positively associated with TP, and this relationship was stronger in the phytoplankton pathway vs. the C4-marsh pathway. There was a gradual increase in the coupling of phytoplankton and C4-marsh plants at larger body sizes and higher TP. Phytoplankton supported longer food chains and larger body sizes than C4-marsh plants. Results support predictions of the landscape theory for food web architecture and indicate that the role of body size in determining trophic interactions may vary across food web compartments

Calculations of binding energies and masses of heavy quarkonia using renormalon cancellation

We use various methods of Borel integration to calculate the binding ground energies and masses of b-bbar and t-tbar quarkonia. The methods take into account the leading infrared renormalon structure of the hard+soft part of the binding energies E(s), and of the corresponding quark pole masses m_q, where the contributions of these singularities in M(s) = 2 m_q + E(s) cancel. Beforehand, we carry out the separation of the binding energy into its hard+soft and ultrasoft parts. The resummation formalisms are applied to expansions of m_q and E(s) in terms of quantities which do not involve renormalon ambiguity, such as MSbar quark mass, and alpha_s. The renormalization scales are different in calculations of m_q, E(s) and E(us). The MSbar mass of b quark is extracted, and the binding energies of t-tbar and the peak (resonance) energies for (t+tbar) production are obtained.Comment: 23 pages, 8 double figures, revtex4; the version to appear in Phys.Rev.D; extended discussion between Eqs.(25) and (26); the paragraph between Eqs.(32) and (33) is new and explains the numerical dependence of the residue parameter on the factorization scale; several new references were added; acknowledgments were modified; the numerical results are unchange