The majority of genes in the pathogenic Neisseria species are present in non-pathogenic Neisseria lactamica, including those designated as virulence genes: response

A response to Snyder LA, Saunders NJ: The majority of genes in the pathogenic Neisseria species are present in non-pathogenic Neisseria lactamica, including those designated as virulence genes. BMC Genomics 2006, 7:128

Empirical Bayesian models for analysing molecular serotyping microarrays.

BACKGROUND: Microarrays offer great potential as a platform for molecular diagnostics, testing clinical samples for the presence of numerous biomarkers in highly multiplexed assays. In this study applied to infectious diseases, data from a microarray designed for molecular serotyping of Streptococcus pneumoniae was used, identifying the presence of any one of 91 known pneumococcal serotypes from DNA extracts. This microarray incorporated oligonucleotide probes for all known capsular polysaccharide synthesis genes and required a statistical analysis of the microarray intensity data to determine which serotype, or combination of serotypes, were present within a sample based on the combination of genes detected. RESULTS: We propose an empirical Bayesian model for calculating the probabilities of combinations of serotypes from the microarray data. The model takes into consideration the dependencies between serotypes, induced by genes they have in common, and by homologous genes which, although not identical, are similar to each other in sequence. For serotypes which are very similar in capsular gene composition, extra probes are included on the microarray, providing additional information which is integrated into the Bayesian model. For each serotype combination with high probability, a second model, a Bayesian random effects model is applied to determine the relative abundance of each serotype. CONCLUSIONS: To assess the accuracy of the proposed analysis we applied our methods to experimental data from samples containing individual serotypes and samples containing combinations of serotypes with known levels of abundance. All but two of the known serotypes of S. pneumoniae that were tested as individual samples could be uniquely determined by the Bayesian model. The model also enabled the presence of combinations of serotypes within samples to be determined. Serotypes with very low abundance within a combination of serotypes can be detected (down to 2% abundance in this study). As well as detecting the presence of serotype combinations, an approximate measure of the percentage abundance of the serotypes within the combination can be obtained.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

An Integrated Surface Seismic/Seismic Profile Case Study: Simonette Area, Alberta

On the basis of conventional surface seismic data, the 13-15-63-25W5M exploratory well was drilled into a low-relief Leduc Formation reef (Devonian Wood-bend Group) in the Simonette area, west-central Alberta, Canada. The well was expected to intersect the crest of the reef and encounter about 50-60 m of pay; unfortunately it was drilled into a flank position and abandoned. The decision to abandon the well, as opposed to whipstocking in the direction of the reef crest, was made after the acquisition and interpretive processing of both near-and far-offset (252 and 524 m, respectively) vertical seismic profile (VSP) data, and after the reanalysis of existing surface seismic data

Selective reduction of coliforms in constructed wetlands

The University Archives has determined that this item is of continuing value to OSU's history

A partial characterization of the deoxyribonucleic acid found in the thoracic muscles of the tobacco hornworm moth (Manducta sexta)

The DNAs (deoxyribonucleic acids) of the thoracic tissue of the tobacco hornworm, Manducta sexta, were studied by physical and chemical means. The adult moth was considered to be fully formed two days after emergence from the pupal case, as indicated by its ability to fly and the integrity of the dorsal longitudinal flight muscle as seen in electron micrographs. The dorsal longitudinal flight muscle development was followed by assaying for total RNA (ribonucleic acid), DNA and protein during the period of time four days prior to emergence and two days after, α-glycerolphosphate dehydrogenase and cytochrome C oxidase were used as mitochondrial marker enzymes, and to follow the development of the mitochondria over a similar period of time. The enzyme assays also showed that the majority of activity was in the mitochondrial fraction. Once it was established that the insect tissue was developing normally and that an adult moth could be considered fully developed at the end of two days the DNA from the thoracic muscles was isolated and characterized. The material isolated from the nuclear (and debris) fraction was identified as DNA and characterized by its buoyant density in CsC1 gradients, purine and pyrimidine composition, melting temperature (hyperchromicity), spectral analysis and molecular weight. The genome size was estimated from renaturation kinetics and the amount of rapidly reassociating material (repeated sequences) was determined. DNA was isolated from the mitochondrial fraction in impure form but was identified on analytical CsC1 gradients and its buoyant density determined. The number and presence of super coils was estimated by reversible denaturation experiments (snap back). The molecular weight of the DNA was determined by two different methods; 1) from its band width in CsC1 gradients and 2) from contour lengths, measured on electron micrographs, of the circular and super coil forms. Circles and super coils were readily identified in the electron micrographs. The molecular weight found by band width analysis is 10.4 x 10⁶ daltons and the molecular weight range as determined from the electron micrographic studies is 7.9 x 10⁶ to 16.8 x 10⁶ daltons. The molecular circumference of the mitochond rial DNA, on formvar coated grids, is 4.0μ

Development and application of the active surveillance of pathogens microarray to monitor bacterial gene flux

BACKGROUND: Human and animal health is constantly under threat by emerging pathogens that have recently acquired genetic determinants that enhance their survival, transmissibility and virulence. We describe the construction and development of an Active Surveillance of Pathogens (ASP) oligonucleotide microarray, designed to 'actively survey' the genome of a given bacterial pathogen for virulence-associated genes. RESULTS: The microarray consists of 4958 reporters from 151 bacterial species and include genes for the identification of individual bacterial species as well as mobile genetic elements (transposons, plasmid and phage), virulence genes and antibiotic resistance genes. The ASP microarray was validated with nineteen bacterial pathogens species, including Francisella tularensis, Clostridium difficile, Staphylococcus aureus, Enterococcus faecium and Stenotrophomonas maltophilia. The ASP microarray identified these bacteria, and provided information on potential antibiotic resistance (eg sufamethoxazole resistance and sulfonamide resistance) and virulence determinants including genes likely to be acquired by horizontal gene transfer (e.g. an alpha-haemolysin). CONCLUSION: The ASP microarray has potential in the clinic as a diagnostic tool, as a research tool for both known and emerging pathogens, and as an early warning system for pathogenic bacteria that have been recently modified either naturally or deliberately

Coherence length of an elongated condensate: a study by matter-wave interferometry

We measure the spatial correlation function of Bose-Einstein condensates in the cross-over region between phase-coherent and strongly phase-fluctuating condensates. We observe the continuous path from a gaussian-like shape to an exponential-like shape characteristic of one-dimensional phase-fluctuations. The width of the spatial correlation function as a function of the temperature shows that the condensate coherence length undergoes no sharp transition between these two regimes.Comment: 8 pages, 6 figure, submitted to EPJ

Recommended Personal Protective Equipment for Cochlear Implant and Other Mastoid Surgery During the COVID-19 Era

© 2020 American Laryngological, Rhinological and Otological Society Inc, "The Triological Society" and American Laryngological Association (ALA) Objectives/Hypothesis: The overall aim of this study was to evaluate personal protective equipment (PPE) that may facilitate the safe recommencement of cochlear implantation in the COVID-19 era, with the broader goal of minimizing the period of auditory deprivation in prelingually deaf children and reducing the risk of cochlear ossification in individuals following meningitis. Methods: The study design comprised 1) an objective assessment of mastoid drilling-induced droplet spread conducted during simulated cochlear implant (CI) surgery and its mitigation via the use of a protective drape tent and 2) an evaluation of three PPE configurations by otologists while performing mastoid drilling on ex vivo temporal bones. The various PPE solutions were assessed in terms of their impact on communication, vital physiological parameters, visual acuity and fields, and acceptability to surgeons using a systematic risk-based approach. Results: Droplet spread during simulated CI surgery extended over 2 m, a distance greater than previously reported. A drape tent significantly reduced droplet spread. The ensemble of a half-face mask and safety spoggles (foam lined safety goggles) had consistently superior performance across all aspects of clinical usability. All other PPE options were found to substantially restrict the visual field, making them unsafe for microsurgery. Conclusions: The results of this preclinical study indicate that the most viable solution to enable the safe conduct of CI and other mastoid surgery is a combination of a filtering facepiece (FFP)3 mask or half-face respirator with safety spoggles as PPE. Prescription spoggles are an option for surgeons who need to wear corrective glasses to operate. A drape tent reduces droplet spread. A multicenter clinical trial to evaluate the effectiveness of PPE should be the next step toward safely performing CI surgery during the COVID-19 era. Level of Evidence: 4 Laryngoscope, 2020

Social and non-social autism symptom and trait domains are genetically dissociable

The core diagnostic criteria for autism comprise two symptom domains – social and communication difficulties, and unusually repetitive and restricted behaviour, interests and activities. There is some evidence to suggest that these two domains are dissociable, yet, this hypothesis has not been tested using molecular genetics. We test this using a GWAS of a non-social autistic trait, systemizing (N = 51,564), defined as the drive to analyse and build systems. We demonstrate that systemizing is heritable and genetically correlated with autism. In contrast, we do not identify significant genetic correlations between social autistic traits and systemizing. Supporting this, polygenic scores for systemizing are significantly positively associated with restricted and repetitive behaviour but not with social difficulties in autistic individuals. These findings strongly suggest that the two core domains of autism are genetically dissociable, and point at how to fractionate the genetics of autism

Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum

As nonreplicating tubercle bacilli are tolerant to the cidal action of antibiotics and resistant to multiple stresses, identification of this persister-like population of tubercle bacilli in sputum presents exciting and tractable new opportunities to investigate both responses to chemotherapy and the transmission of tuberculosis