A multiplex real-time PCR assay for rapid detection and differentiation of 25 bacterial and fungal pathogens from whole blood samples

Early detection of bloodstream infections (BSI) is crucial in the clinical setting. Blood culture remains the gold standard for diagnosing BSI. Molecular diagnostic tools can contribute to a more rapid diagnosis in septic patients. Here, a multiplex real-time PCR-based assay for rapid detection of 25 clinically important pathogens directly from whole blood in <6 h is presented. Minimal analytical sensitivity was determined by hit rate analysis from 20 independent experiments. At a concentration of 3 CFU/ml a hit rate of 50% was obtained for E. aerogenes and 100% for S. marcescens, E. coli, P. mirabilis, P. aeruginosa, and A. fumigatus. The hit rate for C. glabrata was 75% at 30 CFU/ml. Comparing PCR identification results with conventional microbiology for 1,548 clinical isolates yielded an overall specificity of 98.8%. The analytical specificity in 102 healthy blood donors was 100%. Although further evaluation is warranted, our assay holds promise for more rapid pathogen identification in clinical sepsis.

Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution

Transmission electron microscopy has provided most of what is known about the ultrastructural organization of tissues, cells, and organelles. Due to tremendous advances in crystallography and magnetic resonance imaging, almost any protein can now be modeled at atomic resolution. To fully understand the workings of biological "nanomachines" it is necessary to obtain images of intact macromolecular assemblies in situ. Although the resolution power of electron microscopes is on the atomic scale, in biological samples artifacts introduced by aldehyde fixation, dehydration and staining, but also section thickness reduces it to some nanometers. Cryofixation by high pressure freezing circumvents many of the artifacts since it allows vitrifying biological samples of about 200 mum in thickness and immobilizes complex macromolecular assemblies in their native state in situ. To exploit the perfect structural preservation of frozen hydrated sections, sophisticated instruments are needed, e.g., high voltage electron microscopes equipped with precise goniometers that work at low temperature and digital cameras of high sensitivity and pixel number. With them, it is possible to generate high resolution tomograms, i.e., 3D views of subcellular structures. This review describes theory and applications of the high pressure cryofixation methodology and compares its results with those of conventional procedures. Moreover, recent findings will be discussed showing that molecular models of proteins can be fitted into depicted organellar ultrastructure of images of frozen hydrated sections. High pressure freezing of tissue is the base which may lead to precise models of macromolecular assemblies in situ, and thus to a better understanding of the function of complex cellular structures.

Evaluating the relationship between moisture induced expansion and horizontal stress orientation in samples from the nonesuch formation

High horizontal stresses can cause numerous ground control problems in mines and other underground structures ultimately impacting worker safety, productivity and the economics of an underground operation. Mine layout and design can be optimized when the presence and orientation of these stresses are recognized and their impact minimized. A simple technique for correlating the principal horizontal stress direction in a sedimentary rock mass with the preferential orientation of moisture induced expansion in a sample of the same rock was introduced in the 1970s and has since gone un-reported and unused. This procedure was reexamined at a locality near the original test site at White Pine, Michigan in order to validate the original research and to consider its usefulness in mining and civil engineering applications in high horizontal stress conditions. This procedure may also be useful as an economical means for characterizing regional stress fields.

INVESTIGATION OF AIR JIGGING AND AIR CLASSIFICATION TO RECOVER METALLIC PARTICLES FROM ANALYTICAL SAMPLES

Analyzing “nuggety” gold samples commonly produces erratic fire assay results, due to random inclusion or exclusion of coarse gold in analytical samples. Preconcentrating gold samples might allow the nuggets to be concentrated and fire assayed separately. In this investigation synthetic gold samples were made using similar density tungsten powder and silica, and were preconcentrated using two approaches: an air jig and an air classifier. Current analytical gold sampling method is time and labor intensive and our aim is to design a set-up for rapid testing. It was observed that the preliminary air classifier design showed more promise than the air jig in terms of control over mineral recovery and preconcentrating bulk ore sub-samples. Hence the air classifier was modified with the goal of producing 10-30 grams samples aiming to capture all of the high density metallic particles, tungsten in this case. Effects of air velocity and feed rate on the recovery of tungsten from synthetic tungsten-silica mixtures were studied. The air classifier achieved optimal high density metal recovery of 97.7% at an air velocity of 0.72 m/s and feed rate of 160 g/min. Effects of density on classification were investigated by using iron as the dense metal instead of tungsten and the recovery was seen to drop from 96.13% to 20.82%. Preliminary investigations suggest that preconcentration of gold samples is feasible using the laboratory designed air classifier.

COMPARISON OF NON-HEATING PALEOINTENSITY TECHNIQUES USING BASALTS FROM LEMPTÉGY VOLCANO, FRANCE AND SYNTHETIC MAGNETITE-BEARING SAMPLES

Data of the strength of Earth’s magnetic field (paleointensity) in the geological past are crucial for understanding the geodynamo. Conventional paleointensity determination methods require heating a sample to a high temperature in one or more steps. Consequently, many rocks are unsuitable for these methods due to a heating-induced experimental alteration. Alternative non-heating paleointensity methods are investigated to assess their effectiveness and reliability using both natural samples from Lemptégy Volcano, France, and synthetic samples. Paleointensity was measured from the natural and synthetic samples using the Pseudo-Thellier, ARM, REM, REMc, REM’, and Preisach methods. For the natural samples, only the Pseudo-Thellier method was able to produce a reasonable paleointensity estimate consistent with previous paleointensity data. The synthetic samples yielded more successful estimates using all the methods, with the Pseudo-Thellier and ARM methods producing the most accurate results. The Pseudo-Thellier method appears to be the best alternative to the heating-based paleointensity methods.

Assessment of a real-time PCR test to diagnose syphilis from diverse biological samples

OBJECTIVES: To investigate the contribution of a real-time PCR assay for the detection of Treponema pallidum in various biological specimens with the secondary objective of comparing its value according to HIV status. METHODS: Prospective cohort of incident syphilis cases from three Swiss hospitals (Geneva and Bern University Hospitals, Outpatient Clinic for Dermatology of Triemli, Zurich) diagnosed between January 2006 and September 2008. A case-control study was nested into the cohort. Biological specimens (blood, lesion swab or urine) were taken at diagnosis (as clinical information) and analysed by real-time PCR using the T pallidum 47 kDa gene. RESULTS: 126 specimens were collected from 74 patients with primary (n = 26), secondary (n = 40) and latent (n = 8) syphilis. Among primary syphilis, sensitivity was 80% in lesion swabs, 28% in whole blood, 55% in serum and 29% in urine, whereas among secondary syphilis, it was 20%, 36%, 47% and 44%, respectively. Among secondary syphilis, plasma and cerebrospinal fluid were also tested and provided a sensitivity of 100% and 50%, respectively. The global sensitivity of T pallidum by PCR (irrespective of the compartment tested) was 65% during primary, 53% during secondary and null during latent syphilis. No difference regarding serology or PCR results was observed among HIV-infected patients. Specificity was 100%. CONCLUSIONS: Syphilis PCR provides better sensitivity in lesion swabs from primary syphilis and displays only moderate sensitivity in blood from primary and secondary syphilis. HIV status did not modify the internal validity of PCR for the diagnosis of primary or secondary syphilis.

[Urinary specific gravity--comparative measurements using reagent strips and refractometer in 340 morning urine samples]

The specific gravity of urine (SG) indicates the number and weight of solute particles in urine; its measurement is helpful in interpreting proteinuria detected by dipstick tests and in monitoring adequate hydration in patients with nephrolithiasis. Four methods for measuring SG or osmolality of urine are currently available (depression of the freezing-point, urometry, refractometry, cation exchange on a reagent strip). Using a recently developed reagent strip, we have measured SG in morning urines of 340 non-selected outpatients and compared the results with SG measurements by refractometry of the same urines. In 86.2% of all urines, a good positive correlation between SG measured by reagent strip and refractometry was noted (r = 0.913, p = 0.0001). In 13.8% of the urines, however, the SG measured by reagent strip deviated by more than +/- 5 from the value obtained by refractometry; in 90% of these urines, glucosuria (reagent strip values too low or too high), proteinuria (values too high), or bacteriuria/leukocyturia (values too low or too high) could be found. In alkaline urine (pH > 7.0), SG values obtained by reagent strip have to be corrected by +5.