Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity.

BACKGROUND: Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Ct strain-specific differences in clinical trachoma suggest that genetic polymorphisms in Ct may contribute to the observed variability in severity of clinical disease. METHODS: Using Ct whole genome sequences obtained directly from conjunctival swabs, we studied Ct genomic diversity and associations between Ct genetic polymorphisms with ocular localization and disease severity in a treatment-naïve trachoma-endemic population in Guinea-Bissau, West Africa. RESULTS: All Ct sequences fall within the T2 ocular clade phylogenetically. This is consistent with the presence of the characteristic deletion in trpA resulting in a truncated non-functional protein and the ocular tyrosine repeat regions present in tarP associated with ocular tissue localization. We have identified 21 Ct non-synonymous single nucleotide polymorphisms (SNPs) associated with ocular localization, including SNPs within pmpD (odds ratio, OR = 4.07, p* = 0.001) and tarP (OR = 0.34, p* = 0.009). Eight synonymous SNPs associated with disease severity were found in yjfH (rlmB) (OR = 0.13, p* = 0.037), CTA0273 (OR = 0.12, p* = 0.027), trmD (OR = 0.12, p* = 0.032), CTA0744 (OR = 0.12, p* = 0.041), glgA (OR = 0.10, p* = 0.026), alaS (OR = 0.10, p* = 0.032), pmpE (OR = 0.08, p* = 0.001) and the intergenic region CTA0744-CTA0745 (OR = 0.13, p* = 0.043). CONCLUSIONS: This study demonstrates the extent of genomic diversity within a naturally circulating population of ocular Ct and is the first to describe novel genomic associations with disease severity. These findings direct investigation of host-pathogen interactions that may be important in ocular Ct pathogenesis and disease transmission.

Organ involvement other than lupus nephritis in childhood-onset systemic lupus erythematosus.

In this review we critically analyze pulmonary, gastrointestinal and cardiac manifestations of childhood-onset systemic lupus erythematosus (cSLE). Clinical manifestations of these organ systems may be the initial manifestation of cSLE; frequently occur with very active cSLE; and are potential life-threatening manifestations often presenting to the emergency department and requiring admission to the intensive care unit. Early recognition and treatment of the pulmonary, gastrointestinal and cardiac manifestations of cSLE will result in improved prognosis and better outcomes.

Supercooling of Atoms in an Optical Resonator.

We investigate laser cooling of an ensemble of atoms in an optical cavity. We demonstrate that when atomic dipoles are synchronized in the regime of steady-state superradiance, the motion of the atoms may be subject to a giant frictional force leading to potentially very low temperatures. The ultimate temperature limits are determined by a modified atomic linewidth, which can be orders of magnitude smaller than the cavity linewidth. The cooling rate is enhanced by the superradiant emission into the cavity mode allowing reasonable cooling rates even for dipolar transitions with ultranarrow linewidth.

Conditional ramsey spectroscopy with synchronized atoms.

We investigate Ramsey spectroscopy performed on a synchronized ensemble of two-level atoms. The synchronization is induced by the collective coupling of the atoms to a heavily damped mode of an optical cavity. We show that, in principle, with this synchronized system it is possible to observe Ramsey fringes indefinitely, even in the presence of spontaneous emission and other sources of individual-atom dephasing. This could have important consequences for atomic clocks and a wide range of precision metrology applications.

Synchronization of two ensembles of atoms.

We propose a system for observing the correlated phase dynamics of two mesoscopic ensembles of atoms through their collective coupling to an optical cavity. We find a dynamical quantum phase transition induced by pump noise and cavity output coupling. The spectral properties of the superradiant light emitted from the cavity show that at a critical pump rate the system undergoes a transition from the behavior of two independent oscillators to the phase locking that is the signature of quantum synchronization.

Host genetic studies in human ocular Chlamydial infection.

Several human and animal models and methods have been used to dissect genetic contributions to immunity and pathogenesis of chlamydial diseases. Considerable achievements have been made in this field of host genetics. The hope is that these studies will lead to medical applications by helping to elicit the function of genes that are involved in host defense against chlamydia and in progression to severe sequelae. In the present article, we review a selection of findings in the forward genetics of ocular Chlamydia trachomatis infection in humans.

Atomtronic circuits of diodes and transistors.

We illustrate that open quantum systems composed of neutral, ultracold atoms in one-dimensional optical lattices can exhibit behavior analogous to semiconductor electronic circuits. A correspondence is demonstrated for bosonic atoms, and the experimental requirements to realize these devices are established. The analysis follows from a derivation of a quantum master equation for this general class of open quantum systems.

Application of the Laboratory Risk Indicator in Necrotising Fasciitis (LRINEC) score to patients in a tropical tertiary referral centre.

The objective of this study was to assess the applicability and usefulness of the Laboratory Risk Indicator in Necrotising Fasciitis (LRINEC) score in patients from our institution. A retrospective analysis was undertaken of the case notes of all patients admitted to our facility between January 2002 and December 2005 with the admission diagnosis of necrotising fasciitis and the application of the LRINEC score upon the initial blood tests. The sensitivity, specificity and likelihood ratios were then calculated for patients with a LRINEC score of > or = 6 compared with the findings of a surgical biopsy. Twenty-eight patients were identified as having the admission diagnosis of necrotising fasciitis on the hospital database and were eligible for the study. Ten of these had biopsy-proven necrotising fasciitis. With a cut-off score of > or = 6, the LRINEC score had a sensitivity of 80%, specificity of 67%, a positive predictive value of 57% and a negative predictive value of 86% in distinguishing the patients with proven necrotising fasciitis from those with severe soft tissue infections. The likelihood ratio of a positive biopsy was 2.4 and the likelihood ratio of a negative biopsy was 0.3. A cut-off value of > or = 6 of the LRINEC score was not overly sensitive or specific, and the likelihood ratios suggest that, at this cut-off level, the LRINEC score would have only a very small effect on the post-test probability of the patients in the studied population having necrotising fasciitis.

Prospects for a millihertz-linewidth laser.

We propose a new light source based on having alkaline-earth atoms in an optical lattice collectively emit photons on an ultranarrow clock transition into the mode of a high Q resonator. The resultant optical radiation has an extremely narrow linewidth in the mHz range, even smaller than that of the clock transition itself due to collective effects. A power level of order 10;{-12} W is possible, sufficient for phase locking a slave optical local oscillator. Realizing this light source has the potential to improve the stability of the best clocks by 2 orders of magnitude.

Risk factors for active trachoma in The Gambia.

Trachoma has been endemic in The Gambia for decades but national surveys indicate that the prevalence is falling. Risk factor data can help guide trachoma control efforts. This study investigated risk factors for active trachoma and ocular Chlamydia trachomatis infection in children aged below 10 years in two Gambian regions. The overall prevalence of C. trachomatis infection was only 0.3% (3/950) compared with 10.4% (311/2990) for active trachoma, therefore analyses were only performed for active trachoma. After adjustment, increased risk of trachoma was associated with being aged 1-2 years (odds ratio (OR) 2.20, 95% CI 1.07-4.52) and 3-5 years (OR 3.62, 95% CI 1.80-7.25) compared with <1 year, nasal discharge (OR 2.07, 95% CI 1.53-2.81), ocular discharge (OR 2.68, 95% CI 1.76-4.09) and there being at least one other child in the household with active trachoma (OR 11.28, 95% CI 8.31-15.31). Compared with other occupations, children of traders had reduced risk (OR 0.53, 95% CI 0.30-0.94). At the household level, only the presence of another child in the household with active trachoma was associated with increased risk of active trachoma, suggesting that current trachoma control interventions are effective at this level. In contrast, child-level factors were associated with increased risk after adjustment, indicating a need to increase control efforts at the child level.

FOXP3 gene expression in a tuberculosis case contact study.

Regulatory T lymphocytes (T(regs)) that express FOXP3 are involved in the beneficial attenuation of immunopathology, but are also implicated in down-regulation of protective responses to infection. Their role in tuberculosis (TB) is unknown. We classified 1272 healthy TB contacts according to their tuberculin skin test (TST) and interferon (IFN)-gamma enzyme-linked immunospot (ELISPOT) results and 128 TB cases, and studied the expression of FOXP3 and interleukin (IL)-10 in blood samples. Compared to the uninfected contact group (TST(-), ELISPOT(-)), we observed higher levels of FOXP3 mRNA in blood from TB patients (< 0.001), but IL-10 expression was slightly lower (P = 0.04). In contrast, FOXP3 expression levels were significantly lower (P = 0.001) in the recently infected contacts (TST(+), ELISPOT(+)) but there was no difference for IL-10 (P = 0.74). We hypothesize that during early/subclinical TB, most of which will become latent, FOXP3(+) T(regs) may be sequestered in the lungs, but when TB becomes progressive, FOXP3 reappears at increased levels in the periphery. While these findings do not reveal the role, beneficial or harmful, of T(regs) in TB, they emphasize the probable importance of these cells.

Genetic variation at the TNF locus and the risk of severe sequelae of ocular Chlamydia trachomatis infection in Gambians.

Tumor necrosis factor (TNF) is thought to be a key mediator of the inflammatory and fibrotic response to Chlamydia trachomatis (Ct) infection. A large matched-pair case-control study investigated putative functional single nucleotide polymorphisms (SNPs) across the major histocompatibility complex (MHC) class III region, including TNF and its immediate neighbors nuclear factor of kappa light polypeptide gene enhancer in B cells (IkappaBL), inhibitor like 1 and lymphotoxin alpha (LTA) in relation to the risk of scarring sequelae of ocular Ct infection. Haplotype and linkage disequilibrium analysis demonstrated two haplotypes, differing at position TNF-308, conferring an increased risk of trichiasis. The TNF-308A allele, and its bearing haplotype, correlated with increased TNF production in lymphocyte cultures stimulated with chlamydial elementary body antigen. Thus TNF-308A may determine directly, or be a marker of a high TNF producer phenotype associated with increased risk of sequelae of chlamydial infection. Multivariate analysis provided evidence for the presence of additional risk-associated variants near the TNF locus.

Bose-Einstein condensates in rotating lattices.

Strongly interacting bosons in a two-dimensional rotating square lattice are investigated via a modified Bose-Hubbard Hamiltonian. Such a system corresponds to a rotating lattice potential imprinted on a trapped Bose-Einstein condensate. Second-order quantum phase transitions between states of different symmetries are observed at discrete rotation rates. For the square lattice we study, there are four possible ground-state symmetries.

Temporal cytokine gene expression patterns in subjects with trachoma identify distinct conjunctival responses associated with infection.

Ocular chlamydial disease is clinically diagnosed by the appearance of characteristic inflammatory changes and development of lymphoid follicles in the conjunctiva. Nucleic acid amplification tests and relatively non-invasive methods of sampling the conjunctival surface can be used to quantify the expression of chlamydial and host genes. Using quantitative real-time polymerase chain reaction to detect the presence of Chlamydia trachomatis (CT) 16S rRNA and human interleukin (IL)-1beta, IL-10, IL-12p40, interferon (IFN)-gamma and tumour necrosis factor (TNF)-alpha transcripts we examined the immune response at the conjunctival surface in a cohort of children living in a trachoma-endemic village in The Gambia. Elevated cytokine transcript levels were associated with the presence of CT 16S rRNA. Subclinical infection (CT infection without clinical signs of disease) elicited an immune response that is proinflammatory in nature, with elevations in the transcription of IL-1beta, IFN-gamma and IL-12p40. Clinically apparent infections were associated with the elevation of mRNA for the multi-functional cytokine TNF-alpha (fibrotic, type 1 inflammatory and regulatory) and the counter regulatory cytokine, IL-10, in addition to the other proinflammatory cytokines. A positive correlation between IFN-gamma transcript levels and the amount of CT 16S rRNA expressed in conjunctiva was found.

Risk of trachomatous scarring and trichiasis in Gambians varies with SNP haplotypes at the interferon-gamma and interleukin-10 loci.

Experimental evidence implicates interferon gamma (IFNgamma) in protection from and resolution of chlamydial infection. Conversely, interleukin 10 (IL10) is associated with susceptibility and persistence of infection and pathology. We studied genetic variation within the IL10 and IFNgamma loci in relation to the risk of developing severe complications of human ocular Chlamydia trachomatis infection. A total of 651 Gambian subjects with scarring trachoma, of whom 307 also had potentially blinding trichiasis and pair-matched controls with normal eyelids, were screened for associations between single-nucleotide polymorphisms (SNPs), SNP haplotypes and the risk of disease. MassEXTEND (Sequenom) and MALDI-TOF mass spectrometry were used for detection and analysis of SNPs and the programs PHASE and SNPHAP used to infer haplotypes from population genetic data. Multivariate conditional logistic regression analysis identified IL10 and IFNgamma SNP haplotypes associated with increased risk of both trachomatous scarring and trichiasis. SNPs in putative IFNgamma and IL10 regulatory regions lay within the disease-associated haplotypes. The IFNgamma +874A allele, previously linked to lower IFNgamma production, lies in the IFNgamma risk haplotype and was more common among cases than controls, but not significantly so. The promoter IL10-1082G allele, previously associated with high IL10 expression, is in both susceptibility and resistance haplotypes.

An index of community ocular Chlamydia trachomatis load for control of trachoma.

Quantitative PCR (Q-PCR) technology has recently been applied to the measurement of ocular loads of Chlamydia trachomatis. We present an index called the community ocular C. trachomatis load (COCTL) which is similar to the community microfilarial load (CMFL) of onchocerciasis. Our index has the advantage of being scale-independent so that, for example, percentage changes are the same whether calculated per eye swab or per Q-PCR capillary. The COCTL for a population or subgroup is formed by adding the arbitrary concentration of 1 organism per ml to each individual Q-PCR quantification, calculating the geometric mean, and finally subtracting 1 per ml again. The use of the COCTL is illustrated in a study of trachoma in northern Tanzania. The COCTL is higher in people with clinical trachoma than those without (5.8 organisms per swab vs. 0.1), and in children aged six months to ten years than in the overall population (1.1 vs. 0.4). The COCTL index is potentially useful for sentinel sites, operational research and calibration of clinical measures of trachoma.

Plasmodium falciparum infection of the placenta affects newborn immune responses.

The effects of exposure to placental malaria infection on newborn immunological responses, in particular Th1/Th2 cytokines and antigen-presenting cell (APC) function, were compared between cord blood mononuclear cells (CBMC) from parasitized and non-parasitized placentas of Gambian women. Cells were analysed in vitro for their ability to respond to mitogens [phorbol myristate acetate (PMA)/ionomycin, phytohaemagglutinin (PHA)], a malaria-unrelated test antigen [purified protein derivative of Mycobacterium tuberculin[purified protein derivative (PPD)] and Plasmodium falciparum schizont extracts. Mitogens induced strong proliferation and secretion of high concentrations of both IL-13 and sCD30 in CBMC from both groups. Conversely, significantly lower amounts of IFN-gamma were induced in the parasitized group in response to low doses of PHA. Protein antigens induced very low amounts of all tested cytokines, in particular IFN-gamma. However, a significantly higher release of sCD30 was observed in response to schizont extracts in the parasitized group. Addition of LPS to activate APC to low doses of PHA or schizont extracts increased the IFN-gamma production in both groups but levels remained lower in CBMC from the parasitized group. This result correlates with the lower production of IL-12 found following lipopolysaccharide (LPS) stimulation in this group. Taken together, these data show that placental infection with P. falciparum affects Th1 differentiation and sCD30 priming of neonatal lymphocytes and that the probable mode of action is via APC.

Ramsey fringes in a Bose-Einstein condensate between atoms and molecules.

In a recent experiment, a Feshbach scattering resonance was exploited to observe Ramsey fringes in a 85Rb Bose-Einstein condensate. The oscillation frequency corresponded to the binding energy of the molecular state. We show that the observations are remarkably consistent with predictions of a resonance field theory in which the fringes arise from oscillations between atoms and molecules.

Signatures of resonance superfluidity in a quantum Fermi gas.

We predict a direct and observable signature of the superfluid phase in a quantum Fermi gas, in a temperature regime already accessible in current experiments. We apply the theory of resonance superfluidity to a gas confined in a harmonic potential and demonstrate that a significant increase in density will be observed in the vicinity of the trap center.

Quantitation of Na+-K+-2Cl- cotransport splice variants in human tissues using kinetic polymerase chain reaction.

A kinetic reverse transcription-polymerase chain reaction (RT-PCR)-based assay is described that can discriminate and quantitate differentially spliced mRNAs. This assay should be generally applicable for high-throughput quantitation of differentially spliced transcripts. The utility of this method was assessed for spliced transcripts encoded by the human Na+-K+-2Cl- cotransporter gene hNKCC1. Evidence is presented that the NKCC1 isoform of the human Na+-K+-2Cl- cotransporter is differentially spliced analogous to that recently described for the mouse Na+-K+-2Cl- cotransporter gene BSC2. The nucleotide sequences of the two human splice variants predict Na+-K+-2Cl- cotransporter proteins differing only in length. Stable transfectants expressing these human splice variants, designated NKCC1a or NKCC1b, were constructed. Both splice variants produce functional Na+-K+-2Cl- cotransporters in vivo. The abundance of NKCC1 mRNA and patterns of differential splicing in 10 different tissue types and three cell lines were quantitated using the kRT-PCR assay. The results showed that the total amount of NKCC1 mRNA varied by more than 30-fold in the human tissues and cell lines examined. The ratio of NKCC1a/NKCC1b varied nearly 70-fold among these same tissues and cell lines suggesting that differential splicing of the NKCC1 transcript may play a regulatory role in human tissues.