Biomedical subjects

Barbara Pawlak

Publications and source records attributed to Barbara Pawlak.

4 recordsLinked to original sources

PubMed2005

Detection of Salmonella in environmental water and sediment by a nested-multiplex polymerase chain reaction assay.

From 1995 to 2002, 53 serovars of Salmonella were isolated in the Seine estuary (France). The 3 serovars most frequently found were S. enterica serovar Typhimurium, S. enterica serovar Infantis and S. enterica serovar Virchow. A nested multiplex PCR (nm-PCR) assay was developed to detect the presence of Salmonella in estuarine water and sediment samples. The target gene used was the phase 1 flagellin fliC chromosomal gene, present in all Salmonella serovars. A set of 4 primers was first used to amplify an 890-bp sequence of the fliC gene, and then a second set of 3 primers was used for the nested PCR. The nmPCR method has been successfully tested for 28 serovars, 13 of which are of epidemiological significance. The detection limit of the assay, without any pre-enrichment step, was estimated at 1 CFU in deionized water, and at 4-5 CFU in the reaction mixture when tested on estuarine water seeded with a Salmonella strain. When the nmPCR was used together with the classical culture method in environmental samples, it gave additional positive results for 11.3% of the sediment samples and 20% of the water samples despite a high background of other bacteria. Overall, the results demonstrated that this molecular approach informed us about the contamination by Salmonella of estuarine water and sediment samples. Positive amplifications suggested the presence of Salmonella DNA and could thus provide information about a recent (culturable) or past (non-culturable, released DNA) contamination of environmental samples by this pathogenic bacteria.

DNA Primers↗

PubMed2005

Density estimation for positron emission tomography.

PET (positron emission tomography) scans are still in the experimental phase, as one of the newest breast cancer diagnostic techniques. There are two traditional approaches to the computation of images from data collected in PET. In the first, standard CT (computed tomography) algorithms are used on rays designated by pairs of detectors receiving coincidence events. The problem generated by this approach is that generally only the mean can be used by such algorithms. With the relatively small numbers of events in PET, and with Poisson statistics for which variance equals the mean, the noise sensitivity of standard CT algorithms becomes limiting. This is exasperated further by 3D imaging with cylindrical arrays of detectors. Statistical CT algorithms take the variance into account. As in the list-mode approach, we consider each coincidence event individually. However, we estimate the location of the annihilation event that caused each coincidence event, one by one, based on the previously assigned location of events processed earlier. The estimated annihilation locations form the image. To accomplish this, we construct a probability distribution along each coincidence line. This is generated from previous annihilation points by density estimation. In this paper we present our density estimation approach to positron emission tomography. Nonparametric methods of density estimation are overviewed followed by numerical examples. Our goal here is to determine which density estimation approach is most suitable for PET.

Algorithms↗

PubMed2004

Coordination sphere vibrations in copper(II), nickel(II) and cobalt(II) complexes with 4-imidazoleacetic acid; metal isotope, deuteration, and density functional study.

Low-frequency vibrational spectra of Cu(II), Ni(II) and Co(II) complexes with 4-imidazoleacetic acid (HIA) are discussed. Metal isotope and deuteration effects were measured and used to assign the metal-ligand vibrations. These effects were included in density functional calculations carried out for the [Cu(IA)2] complex.

Cobalt↗

PubMed2004

Phylogenetic relationships between environmental and clinical isolates of Pseudomonas fluorescens and related species deduced from 16S rRNA gene and OprF protein sequences.

The major surface protein of the genus Pseudomonas, OprF, is a non-specific porin that plays an important role in maintenance of cell shape, in growth in a low osmolarity environment, and in adhesion to various supports. The objectives of our study were (i) to carry out a comparative analysis of phylogenies obtained from the OprF protein and from the 16S rRNA gene in 41 isolates from various sources (water, soil, milk and the hospital) and (ii) to investigate the physiological characteristics correlated with the phylogeny of OprF. We report here an important incongruence between the phylogenies of the 16S rRNA gene and the OprF protein. Phylogenetic analysis of 16S rRNA genes grouped Pseudomonas fluorescens isolates into one cluster (termed fluorescens r-cluster) whilst the phylogeny of the OprF protein divided Pseudomonas fluorescens isolates into two quite distinct clusters (termed fluorescens 1 o-cluster and fluorescens 2 o-cluster) that may be related to the original habitat of the strain. The fluorescens 1 o-cluster contained the majority of non-rhizospheric soil isolates, while the fluorescens 2 o-cluster contained all our clinical isolates and most of the rhizospheric isolates (which are fixed to the roots). In order to check this correlation, we studied two physiological characteristics: the range of growth temperature and the capacity for non-specific adhesion to polystyrene. The temperature range study for strains did not explain the existence of the two o-clusters but it did confirm the capacity of certain P. fluorescens strains to grow at 37 degrees C. The adhesion capacities of the isolates in the two o-clusters seems to be correlated with ecological niche.

Bacterial Adhesion↗