A systematic approach to the interrogation and sharing of standardised biofilm signatures

Publicado em "6th International Conference on Practical Applications of Computational Biology & Bioinformatics", ISBN 978-3-642-28838-8The study of microorganism consortia, also known as biofilms, is associated to a number of applications in biotechnology, ecotechnology and clinical domains. A public repository on existing biofilm studies would aid in the design of new studies as well as promote collaborative and incremental work. However, bioinformatics approaches are hampered by the limited access to existing data. Scientific publications summarise the studies whilst results are kept in researchers’ private ad hoc files. Since the collection and ability to compare existing data is imperative to move forward in biofilm analysis, the present work has addressed the development of a systematic computer-amenable approach to biofilm data organisation and standardisation. A set of in-house studies involving pathogens and employing different state-of-the-art devices and methods of analysis was used to validate the approach. The approach is now supporting the activities of BiofOmics, a public repository on biofilm signatures (http://biofomics.org).The authors thank, among others, Rosario Oliveira, Maria Joao Vieira, Idalina Machado, Nuno Cerca, Mariana Henriques, Pilar Teixeira, Douglas Monteiro, Melissa Negri, Susana Lopes, Carina Almeida and Helder Lopes, for submitting their data. The financial support from IBB-CEB, Fundacao para a Ciencia e Tecnologia (FCT) and European Community fund FEDER (Program COMPETE), project PTDC/SAU-ESA/646091/2006/FCOMP-01-0124-FEDER-007480, are also gratefully acknowledged

Detection of specific antibodies in cord blood, infant and maternal saliva and breast milk to staphylococcal toxins implicated in sudden infant death syndrome (SIDS)

The common bacterial toxins hypothesis of sudden infant death syndrome (SIDS) is that nasopharyngeal bacterial toxins can trigger events leading to death in infants with absent/low levels of antibody that can neutralise the toxins. The aim of this study was to investigate nasopharyngeal carriage of Staphylococcus aureus and determine levels of immunity in the first year of life to toxic shock syndrome toxin (TSST-1) and staphylococcal enterotoxin C (SEC). Both toxins have been implicated in SIDS cases. Seventy-three mothers and their infants (39 males and 34 females) were enrolled onto the study. The infants had birth dates spread evenly throughout the year. In infants, S. aureus carriage decreased significantly with age (P < 0.001). Between 40% and 50% of infants were colonised with S. aureus in the first three months of life and 49% of the isolates produced one or both of the staphylococcal toxins. There was a significant correlation between nasopharyngeal carriage of S. aureus in mothers and infants in the three months following the birth (P < 0.001). Carriage of S. aureus in infants and their mothers was not significantly associated with levels of antibody to TSST-1 or SEC in cord blood, adult saliva or breast milk. Infants colonised by S. aureus had higher levels of salivary IgA to TSST-1 than infants who were culture negative. Analysis of cord blood samples by a quantitative ELISA detected IgG bound to TSST-1 and SEC in 95.5% and 91.8% of cases respectively. There was a marked variation in levels of maternal IgG to both TSST-1 and SEC among cord blood samples. Maternal age, birth weight, and seasonality significantly affected the levels of IgG binding to TSST-1 or SEC. Analysis of infant saliva samples detected IgA to TSST-1 and SEC in the first month after birth; 11% of samples tested positive for salivary IgA to TSST-1 and 5% for salivary IgA to SEC. By the age of two months these proportions had increased to 36% and 33% respectively. More infants who used a dummy tested positive for salivary IgA to TSST-1 compared to infants who did not use a dummy. Levels of IgA to TSST-1 and SEC detected in the breast-milk samples varied greatly among mothers. There was a trend for infants receiving breast milk with low levels of antibody to TSST-1 or SEC to have higher levels of salivary antibody to the toxins. In conclusion, passive immunity to toxins implicated in SIDS cases varies greatly among infants. Infants are able to mount an active mucosal immune response to TSST-1 and SEC in the first month of life. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved

Prediction of elastic modulus plus anisotropy using X-ray and electron backscattered diffraction texture quantification and ultrasonic (Electromagnetic acoustic transducer) measurements in aluminum sheets

Crystallographic texture is generally measured using X-ray diffraction, performed off-line using small samples determining near-surface texture only; electron backscattered diffraction (EBSD) can also be used, but only samples relatively small areas. Ultrasonic methods determine elastic property anisotropy and texture, via orientation distribution coefficients (ODCs), and while there is substantial literature comparing ultrasonically determined properties with X-ray or neutron diffraction texture, there is little discussion about texture inhomogeneity (place to place in a sheet or through thickness) and sampling volume effects (X-ray compared to EBSD) on the accuracy of the correlations. In this article, the crystallographic texture of nominally pure aluminum and commercial aluminum alloy sheets has been determined by X-ray diffraction and EBSD and used to calculate the elastic anisotropy, which is then compared to ultrasonic electromagnetic acoustic transducer (EMAT) velocity anisotropy taking into account through-thickness texture variations. Significant and consistent spatial variability in texture occurs in the aluminum sheet samples (sheet edge to center and through thickness). Predictions of elastic anisotropy based on surface texture determination, as characterized by X-ray diffraction or surface EBSD, gave poor correlations with EMAT velocity anisotropy when the sample contained significant through thickness texture variations; however, accounting for this using multiple EBSD scans through thickness gave good correlations

Quantifying damage, saturation and anisotropy in cracked rocks by inverting elastic wave velocities

Crack damage results in a decrease of elastic wave velocities and in the development of anisotropy. Using non-interactive crack effective medium theory as a fundamental tool, we calculate dry and wet elastic properties of cracked rocks in terms of a crack density tensor, average crack aspect ratio and mean crack fabric orientation from the solid grains and fluid elastic properties. Using this same tool, we show that both the anisotropy and shear-wave splitting of elastic waves can be derived. Two simple crack distributions are considered for which the predicted anisotropy depends strongly on the saturation, reaching up to 60% in the dry case. Comparison with experimental data on two granites, a basalt and a marble, shows that the range of validity of the non-interactive effective medium theory model extends to a total crack density of approximately 0.5, considering symmetries up to orthorhombic. In the isotropic case, Kachanov's (1994) non-interactive effective medium model was used in order to invert elastic wave velocities and infer both crack density and aspect ratio evolutions. Inversions are stable and give coherent results in terms of crack density and aperture evolution. Crack density variations can be interpreted in terms of crack growth and/or changes of the crack surface contact areas as cracks are being closed or opened respectively. More importantly, the recovered evolution of aspect ratio shows an exponentially decreasing aspect ratio (and therefore aperture) with pressure, which has broader geophysical implications, in particular on fluid flow. The recovered evolution of aspect ratio is also consistent with current mechanical theories of crack closure. In the anisotropic cases—both transverse isotropic and orthorhombic symmetries were considered—anisotropy and saturation patterns were well reproduced by the modelling, and mean crack fabric orientations we recovered are consistent with in situ geophysical imaging. Our results point out that: (1) It is possible to predict damage, anisotropy and saturation in terms of a crack density tensor and mean crack aspect ratio and orientation; (2) using well constrained wave velocity data, it is possible to extrapolate the contemporaneous evolution of crack density, anisotropy and saturation using wave velocity inversion as a tool; 3) using such an inversion tool opens the door in linking elastic properties, variations to permeability

Cross-Laboratory Standardization of Preclinical Lipidomics Using Differential Mobility Spectrometry and Multiple Reaction Monitoring

Modern biomarker and translational research as well as personalized health care studies rely heavily on powerful omics' technologies, including metabolomics and lipidomics. However, to translate metabolomics and lipidomics discoveries into a high-throughput clinical setting, standardization is of utmost importance. Here, we compared and benchmarked a quantitative lipidomics platform. The employed Lipidyzer platform is based on lipid class separation by means of differential mobility spectrometry with subsequent multiple reaction monitoring. Quantitation is achieved by the use of 54 deuterated internal standards and an automated informatics approach. We investigated the platform performance across nine laboratories using NIST SRM 1950-Metabolites in Frozen Human Plasma, and three NIST Candidate Reference Materials 8231-Frozen Human Plasma Suite for Metabolomics (high triglyceride, diabetic, and African-American plasma). In addition, we comparatively analyzed 59 plasma samples from individuals with familial hypercholesterolemia from a clinical cohort study. We provide evidence that the more practical methyl-tert-butyl ether extraction outperforms the classic Bligh and Dyer approach and compare our results with two previously published ring trials. In summary, we present standardized lipidomics protocols, allowing for the highly reproducible analysis of several hundred human plasma lipids, and present detailed molecular information for potentially disease relevant and ethnicity-related materials.Proteomic