Diagnosis of Chlamydia trachomatis infections in a sexually transmitted disease clinic: evaluation of a urine sample tested by enzyme immunoassay and polymerase chain reaction in comparison with a cervical and/or a urethral swab tested by culture and polymerase chain reaction

AbstractObjective To evaluate the value of a urine sample for diagnosing Chlamydia trachomatis infection in an STD clinic in a prospective study of samples collected from 410 consecutive STD patients (167 female and 243 male).Methods Urine samples were tested by enzyme immunoassay (EIA) and polymerase chain reaction (PCR) in comparison with cervical and/or urethral swabs tested by PCR and cell culture. A questionnaire was completed for a total of 320 patients concerning symptoms, and determining whether they were controls, contacts or were being tested subsequent to legal abortion.Results The overall prevalence of C. trachomatis infection was 11.5%. At least 40% of patients were asymptomatic. Of the C. trachomatis-positive patients, 85% were diagnosed by testing urine, compared to 91% by testing swabs. For urine tests, the sensitivities of PCR were 66.7% and 71.9% for female and male patients, respectively, and the sensitivities of EIA were 40.0% and 62.5%, or 46.7% and 71.9%, for female and male patients, respectively, by including a 30% gray zone below the cut-off value. For swabs, the sensitivities of PCR were 93.3% and 87.5% for female and male patients, respectively, and equal to the sensitivities of culture. In total, 3.3% of controls and 35% of contacts were found to be C. trachomatis positive.Conclusion The use of urine samples for the diagnosis of C. trachomatis infections was effective, but urine samples should be additional to conventional swab(s) instead of replacing. Partner notification and a confirmation of cure is recommended

Structure calculation, refinement and validation using CcpNmr Analysis

CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological questions. This report describes how CcpNmr Analysis can seamlessly link together all of the tasks in the NMR structure-determination process. It details each of the stages from generating NMR restraints [distance, dihedral,hydrogen bonds and residual dipolar couplings (RDCs)],exporting these to and subsequently re-importing them from structure-calculation software (such as the programs CYANA or ARIA) and analysing and validating the results obtained from the structure calculation to, ultimately, the streamlined deposition of the completed assignments and the refined ensemble of structures into the PDBe repository. Until recently, such solution-structure determination by NMR has been quite a laborious task, requiring multiple stages and programs. However, with the new enhancements to CcpNmr Analysis described here, this process is now much more intuitive and efficient and less error-prone

FDG-PET staging and importance of lymph node SUV in head and neck cancer

OBJECTIVES: The role of positron emission tomography (PET) with fluoro-deoxy-glucose (FDG) in the staging of head and neck cancer (HNC) is unclear. The NCCN guidelines do not recommend FDG-PET as a part of standard workup. The purpose of this report is to examine the role of FDG-PET imaging in altering management and providing prognostic information for HNC. METHODS: Retrospective review of HNC patients who had a staging FDG-PET scan performed at either Thomas Jefferson University or University of Kansas Medical Center between the years 2001 and 2007. A total of 212 PET scans were performed in patients who went on to receive radiotherapy. RESULTS: The median follow-up time for all patients was 469 days. The PPV and NPV of PET imaging to correctly identify lymph node status was 94% and 89% respectively. Lymph nodes with extracapsular extension (ECE) had higher SUVs than nodes without ECE, 11.0 vs. 5.0 (p \u3c 0.0007). Maximum SUV for the primary tumor \u3e 8.0 was predictive of worse overall survival (p \u3c 0.045), while the SUV of the lymph nodes was predictive for distant recurrence at one year--with a mean SUV value of 10.4 for patients with distant failure vs. 7.0 without (p \u3c 0.05). CONCLUSIONS: FDG-PET staging in head and neck cancer has good positive and negative predictive values in determining lymph node status. The maximum SUV of the primary tumor is predictive of overall survival. This is the first report to find that the SUV of a lymph node is predictive for ECE and also for distant recurrence

FAD binding, cobinamide binding and active site communication in the corrin reductase (CobR)

Adenosylcobalamin, the coenzyme form of vitamin B12, is one Nature's most complex coenzyme whose de novo biogenesis proceeds along either an anaerobic or aerobic metabolic pathway. The aerobic synthesis involves reduction of the centrally chelated cobalt metal ion of the corrin ring from Co(II) to Co(I) before adenosylation can take place. A corrin reductase (CobR) enzyme has been identified as the likely agent to catalyse this reduction of the metal ion. Herein, we reveal how Brucella melitensis CobR binds its coenzyme FAD (flavin dinucleotide) and we also show that the enzyme can bind a corrin substrate consistent with its role in reduction of the cobalt of the corrin ring. Stopped-flow kinetics and EPR reveal a mechanistic asymmetry in CobR dimer that provides a potential link between the two electron reduction by NADH to the single electron reduction of Co(II) to Co(I)

Efficiency of Lift Production in Flapping and Gliding Flight of Swifts

Many flying animals use both flapping and gliding flight as part of their routine behaviour. These two kinematic patterns impose conflicting requirements on wing design for aerodynamic efficiency and, in the absence of extreme morphing, wings cannot be optimised for both flight modes. In gliding flight, the wing experiences uniform incident flow and the optimal shape is a high aspect ratio wing with an elliptical planform. In flapping flight, on the other hand, the wing tip travels faster than the root, creating a spanwise velocity gradient. To compensate, the optimal wing shape should taper towards the tip (reducing the local chord) and/or twist from root to tip (reducing local angle of attack). We hypothesised that, if a bird is limited in its ability to morph its wings and adapt its wing shape to suit both flight modes, then a preference towards flapping flight optimization will be expected since this is the most energetically demanding flight mode. We tested this by studying a well-known flap-gliding species, the common swift, by measuring the wakes generated by two birds, one in gliding and one in flapping flight in a wind tunnel. We calculated span efficiency, the efficiency of lift production, and found that the flapping swift had consistently higher span efficiency than the gliding swift. This supports our hypothesis and suggests that even though swifts have been shown previously to increase their lift-to-drag ratio substantially when gliding, the wing morphology is tuned to be more aerodynamically efficient in generating lift during flapping. Since body drag can be assumed to be similar for both flapping and gliding, it follows that the higher total drag in flapping flight compared with gliding flight is primarily a consequence of an increase in wing profile drag due to the flapping motion, exceeding the reduction in induced drag

A software framework for analysing solid-state MAS NMR data

Solid-state magic-angle-spinning (MAS) NMR of proteins has undergone many rapid methodological developments in recent years, enabling detailed studies of protein structure, function and dynamics. Software development, however, has not kept pace with these advances and data analysis is mostly performed using tools developed for solution NMR which do not directly address solid-state specific issues. Here we present additions to the CcpNmr Analysis software package which enable easier identification of spinning side bands, straightforward analysis of double quantum spectra, automatic consideration of non-uniform labelling schemes, as well as extension of other existing features to the needs of solid-state MAS data. To underpin this, we have updated and extended the CCPN data model and experiment descriptions to include transfer types and nomenclature appropriate for solid-state NMR experiments, as well as a set of experiment prototypes covering the experiments commonly employed by solid-sate MAS protein NMR spectroscopists. This work not only improves solid-state MAS NMR data analysis but provides a platform for anyone who uses the CCPN data model for programming, data transfer, or data archival involving solid-state MAS NMR data

Simulated moult reduces flight performance but overlap with breeding does not affect breeding success in a long-distance migrant

1.Long-distance migrants are time-constrained as they need to incorporate many annual cycle stages within a year. Migratory passerines moult in the short interval between breeding and migration. To widen this interval, moult may start while still breeding, but this results in flying with moulting wings when food provisioning.2.We experimentally simulated wing gaps in breeding male pied flycatchers by plucking two primary feathers from both wings. We quantified the nest visitations of both parents, proportion of high-quality food brought to the nestlings and adults and nestlings condition. Differences in oxidative damage caused by a possible reduction in flight efficiency were measured in amounts of ROMs and OXY in the blood. We also measured how flight performance was affected with recordings of the male`s escape flight using high-speed cameras. Finally, we collected data on adult survival, clutch size and laying date in the following year.3.“Plucked” males travelled a 5% shorter distance per wingbeat, showing that our treatment reduced flight performance. In line with this, “plucked” males visited their nests less often. Females of “plucked” males, however, visited the nest more often than controls, and fully compensated their partner's reduced visitation rate. As a result, there were no differences between treatments in food quality brought to the nest, adult or chick mass or number of successfully fledged chicks. Males did not differ in their oxidative damage or local survival to the following year. In contrast, females paired with plucked males tended to return less often to breed in the next year in comparison to controls, but this difference was not significant. For the birds that did return, there were no effects on breeding.4.Our results reveal that wing gaps in male pied flycatchers reduce their flight performance, but when it occurs during breeding they prioritise their future reproduction by reducing parental care. As a result, there is no apparent detriment to their condition during breeding. Because non-moulting females are able to compensate their partner's reduced care, there is also no immediate cost to the offspring, but females may pay the cost suffering from a reduced survival

The trans-activation domain of the sporulation response regulator Spo0A revealed by X-ray crystallography

Sporulation in Bacillus involves the induction of scores of genes in a temporally and spatially co-ordinated programme of cell development. Its initiation is under the control of an expanded two-component signal transduction system termed a phosphorelay. The master control element in the decision to sporulate is the response regulator, Spo0A, which comprises a receiver or phosphoacceptor domain and an effector or transcription activation domain. The receiver domain of Spo0A shares sequence similarity with numerous response regulators, and its structure has been determined in phosphorylated and unphosphorylated forms. However, the effector domain (C-Spo0A) has no detectable sequence similarity to any other protein, and this lack of structural information is an obstacle to understanding how DNA binding and transcription activation are controlled by phosphorylation in Spo0A. Here, we report the crystal structure of C-Spo0A from Bacillus stearothermophilus revealing a single alpha -helical domain comprising six alpha -helices in an unprecedented fold. The structure contains a helix-turn-helix as part of a three alpha -helical bundle reminiscent of the catabolite gene activator protein (CAP), suggesting a mechanism for DNA binding. The residues implicated in forming the sigma (A)-activating region clearly cluster in a flexible segment of the polypeptide on the opposite side of the structure from that predicted to interact with DNA. The structural results are discussed in the context of the rich array of existing mutational data

Enhanced flight performance by genetic manipulation of wing shape in Drosophila

Insect wing shapes are remarkably diverse and the combination of shape and kinematics determines both aerial capabilities and power requirements. However, the contribution of any specific morphological feature to performance is not known. Using targeted RNA interference to modify wing shape far beyond the natural variation found within the population of a single species, we show a direct effect on flight performance that can be explained by physical modelling of the novel wing geometry. Our data show that altering the expression of a single gene can significantly enhance aerial agility and that the Drosophila wing shape is not, therefore, optimized for certain flight performance characteristics that are known to be important. Our technique points in a new direction for experiments on the evolution of performance specialities in animals