Molecular epidemiology of multidrug resistant extended spectrum beta-lactamase producing Klebsiella pneumoniae at a Jamaican hospital, 2000 - 2004

<p>Abstract</p> <p>Background</p> <p>The accurate identification of a pathogen beyond the species level is critical in epidemiological studies and investigations of nosocomial outbreaks of infection. The clonal relatedness of 66 multidrug resistant (MDR) strains of extended spectrum beta-lactamase (ESBL) producing <it>K. pneumoniae </it>isolated from clinical specimens from hospitalized patients at a Jamaican hospital during a 5 year period were determined by pulsed field gel electrophoresis (PFGE).</p> <p>Results</p> <p>A total 10 different ESBL producing <it>K. pneumoniae </it>genotypes designated Clones I-X were found. The most frequently occurring strains belonged to Clones I (21/66, 32%), II (15/66, 26%), III (13/66, 20%) and IV (8/66, 12%) which accounted for 86% (57/66) of ESBL producing <it>K. pneumoniae </it>strains over the 5 year period. The remaining 9 (14%) cases of ESBL producing <it>K. pneumoniae </it>were due to strains of Clones V-X. The 4 predominant clones persisted for several years in the hospital.</p> <p>Conclusions</p> <p>The clonal and temporal distribution of the MDR ESBL producing <it>K. pneumoniae </it>strains among clinical service areas did not suggest outbreaks of the organism during the period of study. Instead the molecular epidemiology of ESBL producing <it>K. pneumoniae </it>at this hospital was more representative of an endemic persistence of clones of the organism with limited dissemination from patient to patient. Further studies to investigate the factors which determine the emergence and persistence of MDR ESBL producing <it>K. pneumoniae </it>in Jamaican hospitals and their impact on clinical and economic outcomes at such institutions would be useful.</p

Evaluation of bioluminescence-based assays of anti-malarial drug activity

Transgenic Plasmodium falciparum expressing luciferase offers an attractive bioluminescence-based assay platform for the investigation of the pharmacological properties of anti-malarial drugs. Here a side-by-side comparison of bioluminescence and fluorescence-based assays, utilizing a luciferase reporter cassette that confers a strong temporal pattern of luciferase expression during the S-phase of intraerythrocytic development, is reported

The functional analysis of nonsense suppressors derived from in vitro engineered \u3ci\u3eSaccharomyces cerevisiae\u3c/i\u3e tRNA\u3csup\u3eTrp\u3c/sup\u3e genes

Nonsense suppressors derived from Saccharomyces cerevisiae tRNATrp genes have not been identified by classical genetic screens, although one can construct efficient amber (am) suppressors from them by making the appropriate anticodon mutation in vitro. Herein, a series of in vitro constructed putative suppressor genes was produced to test if pre-tRNATrp processing difficulties could help to explain the lack of classical tRNATrp-based suppressors. It is clear that inefficient processing of in-trons from precursor tRNATrp, or inaccurate overall processing, may explain why some of these constructs fail to promote nonsense suppression in vivo. However, deficient processing must be only one of the reasons why classical tRNATrp-based suppressors have not been characterized, as suppres-sion may still be extremely weak or absent in instances where the in vitro construct can lead to an accumulation of mature tRNATrp. Furthermore, suppression is also very weak in strains transformed with an intronless derivative of a putative tRNATrp ochre (oc) suppressor gene, wherein intron removal cannot pose a problem

The functional analysis of nonsense suppressors derived from in vitro engineered \u3ci\u3eSaccharomyces cerevisiae\u3c/i\u3e tRNA\u3csup\u3eTrp\u3c/sup\u3e genes

Nonsense suppressors derived from Saccharomyces cerevisiae tRNATrp genes have not been identified by classical genetic screens, although one can construct efficient amber (am) suppressors from them by making the appropriate anticodon mutation in vitro. Herein, a series of in vitro constructed putative suppressor genes was produced to test if pre-tRNATrp processing difficulties could help to explain the lack of classical tRNATrp-based suppressors. It is clear that inefficient processing of in-trons from precursor tRNATrp, or inaccurate overall processing, may explain why some of these constructs fail to promote nonsense suppression in vivo. However, deficient processing must be only one of the reasons why classical tRNATrp-based suppressors have not been characterized, as suppres-sion may still be extremely weak or absent in instances where the in vitro construct can lead to an accumulation of mature tRNATrp. Furthermore, suppression is also very weak in strains transformed with an intronless derivative of a putative tRNATrp ochre (oc) suppressor gene, wherein intron removal cannot pose a problem

Identifying Old Tidal Dwarf Irregulars

We examine the observational consequences of the two possible origins for irregular galaxies: formation from collapse of a primordial cloud of gas early in the age of the Universe, and formation from tidal tails in an interaction that could have occured any time in the history of the Universe. Because the formation from tidal tails could have occurred a long time ago, proximity to larger galaxies is not sufficient to distinguish tidal dwarfs from traditional dwarfs. We consider the effects of little or no dark matter on rotation speeds and the Tully-Fisher relationship, the metallicity-luminosity relationship, structure, and stellar populations. From these selection criteria, we identify a small list of dwarf irregular galaxies that are candidates for having formed as tidal dwarfs.Comment: ApJ, to appear September 20, 200

The Local Group Census: planetary nebulae in Sextans B

Five planetary nebulae (PNe) have been discovered in the nearby dwarf irregular galaxy. Emission line images were obtained using the Wide Field Camera of the 2.5m Isaac Newton Telescope (INT) at La Palma (Spain). The candidate PNe were identified by their point-like appearance and relatively strong [OIII] emission-line fluxes. They are located within a galactocentric distance of 2.8 arcmin, corresponding to 1.1 kpc at the distance of Sextans B. Luminosities are in the range 1800--5600Lsolar. Sextans B is one of the smallest dwarf irregular galaxies with a PN population. The number of PNe detected suggest an enhanced star formation rate between 1 and 5 Gyr ago.Comment: 7 pages, 2 figure

Optical Counterparts of Ultra-Luminous X-ray Sources identified from Archival Hubble Space Telescope/WFPC2

We present a systematic analysis of archival HST WFPC2 ``Association'' data sets that correlate with the Chandra positions of a set of 44 ultra-luminous X-ray sources (ULXs) of nearby galaxies. We have improved the Chandra-HST relative astrometry whenever possible. Disparate numbers of potential ULX counterparts are found, and in some cases none are found. The lack of or low number of counterparts in some cases may be due to insufficient depth in the WFPC2 images. Particularly in late-type galaxies, the HST image in the ULX region was often complex or crowded. We therefore address various scenarios for the nature of the ULX since it is not known which, if any, of the sources found are true counterparts. The optical luminosities of the sources are typically in the range 10^4-6 L_sun. In several cases color information is available, with the colors roughly tending to be more red in early-type galaxies. This suggests that, in general, the (potential) counterparts found in early-type galaxies are likely to be older stellar populations, and are probably globular clusters. Several early-type galaxy counterparts have blue colors, which may be due to younger stellar populations in the host galaxies, however these could also be background sources. In spiral galaxies the sources may also be due to localized structure in the disks rather than bound stellar systems. Alternatively some of the counterparts in late-type galaxies may be isolated supergiant stars. The observed X-ray/optical flux ratio is diluted by the optical emission of the cluster in cases where the system is an X-ray binary in a cluster, particularly in the case of a low-mass X-ray binaries in old cluster. (abridged)Comment: 35 pages with 9 figures formatted with emulateapj. Only subset of figures 1 and 2 are shown, for full version see http://xassist.pha.jhu.edu/ptak/hst_ulx_pape

Systematic review of antiepileptic drugs’ safety and effectiveness in feline epilepsy

Understanding the efficacy and safety profile of antiepileptic drugs (AEDs) in feline epilepsy is a crucial consideration for managing this important brain disease. However, there is a lack of information about the treatment of feline epilepsy and therefore a systematic review was constructed to assess current evidence for the AEDs’ efficacy and tolerability in cats. The methods and materials of our former systematic reviews in canine epilepsy were mostly mirrored for the current systematic review in cats. Databases of PubMed, CAB Direct and Google scholar were searched to detect peer-reviewed studies reporting efficacy and/or adverse effects of AEDs in cats. The studies were assessed with regards to their quality of evidence, i.e. study design, study population, diagnostic criteria and overall risk of bias and the outcome measures reported, i.e. prevalence and 95% confidence interval of the successful and affected population in each study and in total

MGMR: leveraging RNA-Seq population data to optimize expression estimation

<p>Abstract</p> <p>Background</p> <p>RNA-Seq is a technique that uses Next Generation Sequencing to identify transcripts and estimate transcription levels. When applying this technique for quantification, one must contend with reads that align to multiple positions in the genome (multireads). Previous efforts to resolve multireads have shown that RNA-Seq expression estimation can be improved using probabilistic allocation of reads to genes. These methods use a probabilistic generative model for data generation and resolve ambiguity using likelihood-based approaches. In many instances, RNA-seq experiments are performed in the context of a population. The generative models of current methods do not take into account such population information, and it is an open question whether this information can improve quantification of the individual samples</p> <p>Results</p> <p>In order to explore the contribution of population level information in RNA-seq quantification, we apply a hierarchical probabilistic generative model, which assumes that expression levels of different individuals are sampled from a Dirichlet distribution with parameters specific to the population, and reads are sampled from the distribution of expression levels. We introduce an optimization procedure for the estimation of the model parameters, and use HapMap data and simulated data to demonstrate that the model yields a significant improvement in the accuracy of expression levels of paralogous genes.</p> <p>Conclusions</p> <p>We provide a proof of principal of the benefit of drawing on population commonalities to estimate expression. The results of our experiments demonstrate this approach can be beneficial, primarily for estimation at the gene level.</p