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

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

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