Molecular probe technology detects bacteria without culture

<p>Abstract</p> <p>Background</p> <p>Our ultimate goal is to detect the entire human microbiome, in health and in disease, in a single reaction tube, and employing only commercially available reagents. To that end, we adapted molecular inversion probes to detect bacteria using solely a massively multiplex molecular technology. This molecular probe technology does not require growth of the bacteria in culture. Rather, the molecular probe technology requires only a sequence of forty sequential bases unique to the genome of the bacterium of interest. In this communication, we report the first results of employing our molecular probes to detect bacteria in clinical samples.</p> <p>Results</p> <p>While the assay on Affymetrix GenFlex Tag16K arrays allows the multiplexing of the detection of the bacteria in each clinical sample, one Affymetrix GenFlex Tag16K array must be used for each clinical sample. To multiplex the clinical samples, we introduce a second, independent assay for the molecular probes employing Sequencing by Oligonucleotide Ligation and Detection. By adding one unique oligonucleotide barcode for each clinical sample, we combine the samples after processing, but before sequencing, and sequence them together.</p> <p>Conclusions</p> <p>Overall, we have employed 192 molecular probes representing 40 bacteria to detect the bacteria in twenty-one vaginal swabs as assessed by the Affymetrix GenFlex Tag16K assay and fourteen of those by the Sequencing by Oligonucleotide Ligation and Detection assay. The correlations among the assays were excellent.</p

An evidence-based approach to assessing surgical versus clinical diagnosis of symptomatic endometriosis

Challenges intrinsic to the accurate diagnosis of endometriosis contribute to an extended delay between the onset of symptoms and clinical confirmation. Intraoperative visualization, preferably with histologic verification, is considered by many professional organizations to be the gold standard by which endometriosis is diagnosed. Clinical diagnosis of symptomatic endometriosis via patient history, physical examination, and noninvasive tests, though more easily executed, is generally viewed as less accurate than surgical diagnosis. Technological advances and increased understanding of the pathophysiology of endometriosis warrant continuing reevaluation of the standard method for diagnosing symptomatic disease. A review of the published literature was therefore performed with the goal of comparing the accuracy of clinical diagnostic measures with that of surgical diagnosis. The current body of evidence suggests that clinical diagnosis of symptomatic endometriosis is more reliable than previously recognized and that surgical diagnosis has limitations that could be underappreciated. Regardless of the methodology used, women with suspected symptomatic endometriosis would be well served by a diagnostic paradigm that is reliable, conveys minimal risk of under- or over-diagnosis, lessens the time from symptom development to diagnosis, and guides the appropriate use of medical and surgical management strategies.</p

A condensed global photochemical mechanism for two-dimensional atmospheric models

A condensed chemical mechanism that represents the reactions of organic compounds in the atmosphere is developed and tested using a one-dimensional model. Due to the differences between the full and condensed mechanisms, the reduced version cannot be considered an accurate predictor of globally important trace species concentrations. The condensed mechanism must be improved before it can be used with confidence in two-dimensional models. Appendix contains both full and reduced mechanisms of photolysis and thermal reactions as well as species profile comparisons. 3 refs., 8 figs

Quantified estimates of total GWPs for greenhouse gases taking into account tropospheric chemistry

The purpose of this report is to give interim account of the progress being made at Lawrence Livermore National Laboratory (LLNL) in developing an improved capability for assessing the direct and indirect effects on Global Warming Potentials. Much of our current efforts are being devoted to improving the capability for modeling of global tropospheric processes in our state-of-the-art zonally-averaged chemical-radiative-transport model of the troposphere and stratosphere. These efforts are in preparation for an improved evaluation and better quantification of the indirect GWPs resulting from effects on tropospheric ozone from ethane and other gases with significant human-related emissions. There are three major findings that should result from this project that should have significant impacts on EPA and its programs. First, the current and ongoing studies of the direct and indirect GWPs should have a significant influence on the continuing national and international assessments of climate change. Second, the improved capability for modeling of chemical and physical processes should lead to enhanced understanding of the controlling factors influencing ozone, hydroxyl and other key tropospheric constituents. Third, the enhanced modeling capability should be important to future studies of human-related influences on tropospheric and stratospheric chemical processes

A Model for Shear Stress Sensing and Transmission in Vascular Endothelial Cells

AbstractArterial endothelial cell (EC) responsiveness to flow is essential for normal vascular function and plays a role in the development of atherosclerosis. EC flow responses may involve sensing of the mechanical stimulus at the cell surface with subsequent transmission via cytoskeleton to intracellular transduction sites. We had previously modeled flow-induced deformation of EC-surface flow sensors represented as viscoelastic materials with standard linear solid behavior (Kelvin bodies). In the present article, we extend the analysis to arbitrary networks of viscoelastic structures connected in series and/or parallel. Application of the model to a system of two Kelvin bodies in parallel reveals that flow induces an instantaneous deformation followed by creeping to the asymptotic response. The force divides equally between the two bodies when they have identical viscoelastic properties. When one body is stiffer than the other, a larger fraction of the applied force is directed to the stiffer body. We have also probed the impact of steady and oscillatory flow on simple sensor-cytoskeleton-nucleus networks. The results demonstrated that, consistent with the experimentally observed temporal chronology of EC flow responses, the flow sensor attains its peak deformation faster than intracellular structures and the nucleus deforms more rapidly than cytoskeletal elements. The results have also revealed that a 1-Hz oscillatory flow induces significantly smaller deformations than steady flow. These results may provide insight into the mechanisms behind the experimental observations that a number of EC responses induced by steady flow are not induced by oscillatory flow

O{sub 3} and stratospheric H{sub 2}O radiative forcing resulting from a supersonic jet transport emission scenario

The tropospheric radiative forcing has been calculated for ozone and water vapor perturbations caused by a realistic High Speed Civil Transport (HSCT) aircraft emission scenario. Atmospheric profiles of water vapor and ozone were obtained using the LLNL 2-D chemical-radiative-transport model (CRT) of the global troposphere and stratosphere. IR radiative forcing calculations were made with the LLNL correlated k-distribution radiative transfer model. UV-Visible-Near IR radiative forcing calculations were made with the LLNL two stream solar radiation model. For the case of water vapor the IR and Near IR radiative forcing was determined at five different latitudes and then averaged using an appropriate latitudinal average to obtain the global average value. Global average values of radiative forcing were approximately 1.2--2.6 10{sup {minus}3} W/m{sup 2}, depending on the background atmospheric water vapor profile. This result is consistent with prior published values for a similar aircraft scenario and supports the conclusion that the water vapor climate forcing effect is very small. The radiative forcing in the IR and UV-Visible spectral ranges, due to the ozone perturbation, was calculated for the globally averaged atmosphere. Global average values of the radiative forcing were 0.034 W/m{sup 2} for the UV-Visible spectral range and 0.006 W/m{sup 2} for the IR spectral range (0.04 W/m{sup 2} total). This result is also consistent with the range of published values obtained for a similar HSCT scenario. As was the case for water vapor, the ozone forcing is too small to be of major consequence