Chlamydia trachomatis Genital Tract Infections: When Host Immune Response and the Microbiome Collide

© 2016 Genital infections with Chlamydia trachomatis continue to be a major health problem worldwide. While some individuals clear their infection (presumed to be the result of an effective Th1/interferon-γ response), others develop chronic infections and some are prone to repeat infections. In females in particular, chronic asymptomatic infections are common and can lead to pelvic inflammatory disease and infertility. Recent studies suggest that the genital tract microbiota could be a significant factor and explain person-to-person variation in C. trachomatis infections. One hypothesis suggests that C. trachomatis can use its trpBA genes to rescue tryptophan from indole, which is a product of anaerobic members of the genital tract microbiota. Women with particular microbiota types, such as seen in bacterial vaginosis, have increased numbers of anaerobes, and this would enable the chlamydia in these individuals to overcome the host's interferon-γ attempts to eliminate it, resulting in more repeat and/or chronic infections

kt Effects in Direct-Photon Production

We discuss the phenomenology of initial-state parton-kt broadening in direct-photon production and related processes in hadron collisions. After a brief summary of the theoretical basis for a Gaussian-smearing approach, we present a systematic study of recent results on fixed-target and collider direct-photon production, using complementary data on diphoton and pion production to provide empirical guidance on the required amount of kt broadening. This approach provides a consistent description of the observed pattern of deviation of next-to-leading order QCD calculations relative to the direct-photon data, and accounts for the shape and normalization difference between fixed-order perturbative calculations and the data. We also discuss the uncertainties in this phenomenological approach, the implications of these results on the extraction of the gluon distribution of the nucleon, and the comparison of our findings to recent related work.Comment: LaTeX, uses revtex and epsf, 37 pages, 15 figure

Effects of Higher-Order Threshold Corrections in High-E_T Jet Production

Results for higher-order threshold enhancements in high-E_T jet production in hadron-hadron collisions are presented. Expressions are given for the next-to-next-to-leading order (NNLO) threshold corrections to the single-jet inclusive cross section at next-to-leading logarithmic (NLL) accuracy. The corrections are found to be small for the specific choice of E_T/2 for the factorization and renormalization scales, and the corrected cross section shows a substantial reduction of the scale dependence. A comparison to experimental results from the Tevatron is presented.Comment: 24 pages LaTeX, 5 figure

In vitro rescue of genital strains of Chlamydia trachomatis from interferon-γ and tryptophan depletion with indole-positive, but not indole-negative Prevotella spp.

© 2016 The Author(s). Background: The natural course of sexually transmitted infections caused by Chlamydia trachomatis varies between individuals. In addition to parasite and host effects, the vaginal microbiota might play a key role in the outcome of C. trachomatis infections. Interferon-gamma (IFN-γ), known for its anti-chlamydial properties, activates the expression of indoleamine 2,3-dioxygenase (IDO1) in epithelial cells, an enzyme that catabolizes the amino acid L- tryptophan into N-formylkynurenine, depleting the host cell's pool of tryptophan. Although C. trachomatis is a tryptophan auxotroph, urogenital strains (but not ocular strains) have been shown in vitro to have the ability to produce tryptophan from indole using the tryptophan synthase (trpBA) gene. It has been suggested that indole producing bacteria from the vaginal microbiota could influence the outcome of Chlamydia infection. Results: We used two in vitro models (treatment with IFN-γ or direct limitation of tryptophan), to study the effects of direct rescue by the addition of exogenous indole, or by the addition of culture supernatant from indole-positive versus indole-negative Prevotella strains, on the growth and infectivity of C. trachomatis. We found that only supernatants from the indole-positive strains, P. intermedia and P. nigrescens, were able to rescue tryptophan-starved C. trachomatis. In addition, we analyzed vaginal secretion samples to determine physiological indole concentrations. In spite of the complexity of vaginal secretions, we demonstrated that for some vaginal specimens with higher indole levels, there was a link to higher recovery of the Chlamydia under tryptophan-starved conditions, lending preliminary support to the critical role of the IFN-γ-tryptophan-indole axis in vivo. Conclusions: Our data provide evidence for the ability of both exogenous indole as well as supernatant from indole producing bacteria such as Prevotella, to rescue genital C. trachomatis from tryptophan starvation. This adds weight to the hypothesis that the vaginal microbiota (particularly from women with lower levels of lactobacilli and higher levels of indole producing anaerobes) may be intrinsically linked to the outcome of chlamydial infections in some women

Prompt photons at RHIC

We calculate the inclusive cross section for prompt photon production in heavy-ion collisions at RHIC energies ($\sqrt{s}=130$ GeV and $\sqrt{s}=200$ GeV) in the central rapidity region including next-to-leading order, $O(\alpha_{em}\alpha_s^2)$, radiative corrections, initial state nuclear shadowing and parton energy loss effects. We show that there is a significant suppression of the nuclear cross section, up to $\sim 30$ at $\sqrt{s}=200$ GeV, due to shadowing and medium induced parton energy loss effects. We find that the next-to-leading order contributions are large and have a strong $p_t$ dependence.Comment: 9 pages, 5 figures, expanded discussion of the K facto

A simplified structure for the second order cosmological perturbation equations

Increasingly accurate observations of the cosmic microwave background and the large scale distribution of galaxies necessitate the study of nonlinear perturbations of Friedmann-Lemaitre cosmologies, whose equations are notoriously complicated. In this paper we present a new derivation of the governing equations for second order perturbations within the framework of the metric-based approach that is minimal, as regards amount of calculation and length of expressions, and flexible, as regards choice of gauge and stress-energy tensor. Because of their generality and the simplicity of their structure our equations provide a convenient starting point for determining the behaviour of nonlinear perturbations of FL cosmologies with any given stress-energy content, using either the Poisson gauge or the uniform curvature gauge.Comment: 30 pages, no figures. Changed title to the one in published version and some minor changes and addition

A New Scintillator Tile/Fiber Preshower Detector for the CDF Central Calorimeter

A detector designed to measure early particle showers has been installed in front of the central CDF calorimeter at the Tevatron. This new preshower detector is based on scintillator tiles coupled to wavelength-shifting fibers read out by multi-anode photomultipliers and has a total of 3,072 readout channels. The replacement of the old gas detector was required due to an expected increase in instantaneous luminosity of the Tevatron collider in the next few years. Calorimeter coverage, jet energy resolution, and electron and photon identification are among the expected improvements. The final detector design, together with the R&D studies that led to the choice of scintillator and fiber, mechanical assembly, and quality control are presented. The detector was installed in the fall 2004 Tevatron shutdown and started collecting colliding beam data by the end of the same year. First measurements indicate a light yield of 12 photoelectrons/MIP, a more than two-fold increase over the design goals.Comment: 5 pages, 10 figures (changes are minor; this is the final version published in IEEE-Trans.Nucl.Sci.

Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent

© 2015 Roulis et al. Background: The obligate intracellular bacterium Chlamydia pneumoniae is a common respiratory pathogen, which has been found in a range of hosts including humans, marsupials and amphibians. Whole genome comparisons of human C. pneumoniae have previously highlighted a highly conserved nucleotide sequence, with minor but key polymorphisms and additional coding capacity when human and animal strains are compared. Results: In this study, we sequenced three Australian human C. pneumoniae strains, two of which were isolated from patients in remote indigenous communities, and compared them to all available C. pneumoniae genomes. Our study demonstrated a phylogenetically distinct human C. pneumoniae clade containing the two indigenous Australian strains, with estimates that the most recent common ancestor of these strains predates the arrival of European settlers to Australia. We describe several polymorphisms characteristic to these strains, some of which are similar in sequence to animal C. pneumoniae strains, as well as evidence to suggest that several recombination events have shaped these distinct strains. Conclusions: Our study reveals a greater sequence diversity amongst both human and animal C. pneumoniae strains, and suggests that a wider range of strains may be circulating in the human population than current sampling indicates

Inclusive Jet Production, Parton Distributions, and the Search for New Physics

Jet production at the Tevatron probes some of the smallest distance scales currently accessible. A gluon distribution that is enhanced at large x compared to previous determinations provides a better description of the Run 1b jet data from both CDF and D0. However, considerable uncertainty still remains regarding the gluon distribution at high x. In this paper, we examine the effects of this uncertainty, and of the remaining uncertainties in the NLO QCD theory, on jet cross section comparisons to Run 1b data. We also calculate the range of contributions still possible from any new physics. Predictions are also made for the expanded kinematic range expected for the ongoing Run 2 at the Tevatron and for the LHC.Comment: 50 pages, 31 figures, RevTe

Examination of direct-photon and pion production in proton-nucleon collisions

We present a study of inclusive direct-photon and pion production in hadronic interactions, focusing on a comparison of the ratio of gamma/pi0 yields with expectations from next-to-leading order perturbative QCD (NLO pQCD). We also examine the impact of a phenomenological model involving k_T smearing (which approximates effects of additional soft-gluon emission) on absolute predictions for photon and pion production and their ratio.Comment: 20 pages, 12 figures. Minor changes in wording and in figure