Luminous Intensity for Traffic Signals: A Scientific Basis for Performance Specifications

Humnan factors experiments on visual responses to simulated traffic signals using incandescent lamps and light-emitting diodes are described

Strategies for Intracellular Survival of Burkholderia pseudomallei

Burkholderia pseudomallei is the causative agent of melioidosis, a disease with high mortality that is prevalent in tropical regions of the world. A key component of the pathogenesis of melioidosis is the ability of B. pseudomallei to enter, survive, and replicate within mammalian host cells. For non-phagocytic cells, bacterial adhesins have been identified both on the bacterial surface and associated with Type 4 pili. Cell invasion involves components of one or more of the three Type 3 Secretion System clusters, which also mediate, at least in part, the escape of bacteria from the endosome into the cytoplasm, where bacteria move by actin-based motility. The mechanism of actin-based motility is not clearly understood, but appears to differ from characterized mechanisms in other bacterial species. A small proportion of intracellular bacteria is targeted by host cell autophagy, involving direct recruitment of LC3 to endosomes rather than through uptake by canonical autophagosomes. However, the majority of bacterial cells are able to circumvent autophagy and other intracellular defense mechanisms such as the induction of inducible nitric oxide synthase, and then replicate in the cytoplasm and spread to adjacent cells via membrane fusion, resulting in the formation of multi-nucleated giant cells. A potential role for host cell ubiquitin in the autophagic response to bacterial infection has recently been proposed

Fis Is Essential for Capsule Production in Pasteurella multocida and Regulates Expression of Other Important Virulence Factors

P. multocida is the causative agent of a wide range of diseases of animals, including fowl cholera in poultry and wild birds. Fowl cholera isolates of P. multocida generally express a capsular polysaccharide composed of hyaluronic acid. There have been reports of spontaneous capsule loss in P. multocida, but the mechanism by which this occurs has not been determined. In this study, we identified three independent strains that had spontaneously lost the ability to produce capsular polysaccharide. Quantitative RT-PCR showed that these strains had significantly reduced transcription of the capsule biosynthetic genes, but DNA sequence analysis identified no mutations within the capsule biosynthetic locus. However, whole-genome sequencing of paired capsulated and acapsular strains identified a single point mutation within the fis gene in the acapsular strain. Sequencing of fis from two independently derived spontaneous acapsular strains showed that each contained a mutation within fis. Complementation of these strains with an intact copy of fis, predicted to encode a transcriptional regulator, returned capsule expression to all strains. Therefore, expression of a functional Fis protein is essential for capsule expression in P. multocida. DNA microarray analysis of one of the spontaneous fis mutants identified approximately 30 genes as down-regulated in the mutant, including pfhB_2, which encodes a filamentous hemagglutinin, a known P. multocida virulence factor, and plpE, which encodes the cross protective surface antigen PlpE. Therefore these experiments define for the first time a mechanism for spontaneous capsule loss in P. multocida and identify Fis as a critical regulator of capsule expression. Furthermore, Fis is involved in the regulation of a range of other P. multocida genes including important virulence factors

Detecting ancient life: Investigating the nature and origin of possible stromatolites and associated calcite from a one billion year old lake

Putative stromatolites and associated carbonate minerals in 1.1 Ga Stoer Group lacustrine sedimentary rocks were analysed to deduce their likely origins. Potential stromatolite examples included finely laminated and sometimes wrinkled carbonate-siliciclastic rocks of the Clachtoll Formation at Clachtoll and Bay of Stoer, and laminated limestone domes of the Poll a’Mhuilt Member (Bay of Stoer Formation) from Enard Bay. Petrography shows that the lamination and wrinkling of Clachtoll Formation specimens can most logically be explained by abiotic siliclastic sedimentary processes, namely rippling and soft-sediment deformation probably related to de-watering. Electron backscatter diffraction shows that the carbonate in these laminated Clachtoll Formation specimens was calcite, and petrography combined with clumped isotope palaeothermometry indicates it was likely to be part syn-depositional and part burial diagenetic in origin. The laminated domes of the Poll a’Mhuilt Member are shown to comprise clasts of limestone interlayered with clay, quartz, Na-rich feldspars and micas. Cathodoluminescence revealed the limestone clasts to be composite and built of sub-grains that must have been derived from an earlier, potentially Palaeoproterozoic, carbonate unit. Support for this hypothesis comes from clumped isotope palaeotemperature measurements that indicate the limestone clasts were precipitated or recrystallized under higher temperature conditions than the burial diagenetic calcite found in the Clachtoll Formation. Raman spectra of an organic carbon particle within a laminated dome of the Poll a’Mhuilt Member at Enard Bay are consistent with the organic carbon having been re-worked from the ∼2 Ga Loch Maree Group, and we speculate that this might also be true of the calcite. Microbial fossils are well known from elsewhere in the Stoer Group, but no conclusive examples were found within the thin-sections examined herein. No conclusive evidence was found to suggest that any of the examined putative stromatolites were biogenic, leading to the conclusion that they are best considered stromatolite-like sedimentary rocks (pseudostromatolites)

Comparative transcriptomic analysis of Porphyromonas gingivalis biofilm and planktonic cells

<p>Abstract</p> <p>Background</p> <p><it>Porphyromonas gingivalis </it>in subgingival dental plaque, as part of a mature biofilm, has been strongly implicated in the onset and progression of chronic periodontitis. In this study using DNA microarray we compared the global gene expression of a <it>P. gingivalis </it>biofilm with that of its planktonic counterpart grown in the same continuous culture.</p> <p>Results</p> <p>Approximately 18% (377 genes, at 1.5 fold or more, <it>P</it>-value < 0.01) of the <it>P. gingivalis </it>genome was differentially expressed when the bacterium was grown as a biofilm. Genes that were down-regulated in biofilm cells, relative to planktonic cells, included those involved in cell envelope biogenesis, DNA replication, energy production and biosynthesis of cofactors, prosthetic groups and carriers. A number of genes encoding transport and binding proteins were up-regulated in <it>P. gingivalis </it>biofilm cells. Several genes predicted to encode proteins involved in signal transduction and transcriptional regulation were differentially regulated and may be important in the regulation of biofilm growth.</p> <p>Conclusion</p> <p>This study analyzing global gene expression provides insight into the adaptive response of <it>P. gingivalis </it>to biofilm growth, in particular showing a down regulation of genes involved in growth and metabolic activity.</p

Polymyxin Resistance in Acinetobacter baumannii: Genetic Mutations and Transcriptomic Changes in Response to Clinically Relevant Dosage Regimens

Polymyxins are often last-line therapeutic agents used to treat infections caused by multidrug-resistant A. baumannii. Recent reports of polymyxin-resistant A. baumannii highlight the urgent need for research into mechanisms of polymyxin resistance. This study employed genomic and transcriptomic analyses to investigate the mechanisms of polymyxin resistance in A. baumannii AB307-0294 using an in vitro dynamic model to mimic four different clinically relevant dosage regimens of polymyxin B and colistin over 96 h. Polymyxin B dosage regimens that achieved peak concentrations above 1 mg/L within 1 h caused significant bacterial killing (~5 log10CFU/mL), while the gradual accumulation of colistin resulted in no bacterial killing. Polymyxin resistance was observed across all dosage regimens; partial reversion to susceptibility was observed in 6 of 8 bacterial samples during drug-free passaging. Stable polymyxin-resistant samples contained a mutation in pmrB. The transcriptomes of stable and non-stable polymyxin-resistant samples were not substantially different and featured altered expression of genes associated with outer membrane structure and biogenesis. These findings were further supported via integrated analysis of previously published transcriptomics data from strain ATCC19606. Our results provide a foundation for understanding the mechanisms of polymyxin resistance following exposure to polymyxins and the need to explore effective combination therapies

Dynamic enhancement of drug product labels to support drug safety, efficacy, and effectiveness

Out-of-date or incomplete drug product labeling information may increase the risk of otherwise preventable adverse drug events. In recognition of these concerns, the United States Federal Drug Administration (FDA) requires drug product labels to include specific information. Unfortunately, several studies have found that drug product labeling fails to keep current with the scientific literature. We present a novel approach to addressing this issue. The primary goal of this novel approach is to better meet the information needs of persons who consult the drug product label for information on a drug’s efficacy, effectiveness, and safety. Using FDA product label regulations as a guide, the approach links drug claims present in drug information sources available on the Semantic Web with specific product label sections. Here we report on pilot work that establishes the baseline performance characteristics of a proof-of-concept system implementing the novel approach. Claims from three drug information sources were linked to the Clinical Studies, Drug Interactions, and Clinical Pharmacology sections of the labels for drug products that contain one of 29 psychotropic drugs. The resulting Linked Data set maps 409 efficacy/effectiveness study results, 784 drug-drug interactions, and 112 metabolic pathway assertions derived from three clinically-oriented drug information sources (ClinicalTrials.gov, the National Drug File – Reference Terminology, and the Drug Interaction Knowledge Base) to the sections of 1,102 product labels. Proof-of-concept web pages were created for all 1,102 drug product labels that demonstrate one possible approach to presenting information that dynamically enhances drug product labeling. We found that approximately one in five efficacy/effectiveness claims were relevant to the Clinical Studies section of a psychotropic drug product, with most relevant claims providing new information. We also identified several cases where all of the drug-drug interaction claims linked to the Drug Interactions section for a drug were potentially novel. The baseline performance characteristics of the proof-of-concept will enable further technical and user-centered research on robust methods for scaling the approach to the many thousands of product labels currently on the market

Luminous Intensity for Traffic Signals: A Scientific Basis for Performance Specifications - Appendices

Luminous Intensity for Traffic Signals: A Scientific Basis for Performance Specifications - Appendice

Genomic-scale Analysis of Bacterial Gene and Protein Expression in the Host

DNA microarrays and proteomics are used to study bacterial gene and protein expression during infections

Evaluation of a patient self-stratification methodology to identify those in need of shielding during COVID-19

The logistical challenges of rapidly and accurately identifying those patients who needed to shield during the COVID-19 pandemic were unprecedented. We report our experiences of meeting this challenge for &gt;9,000 patients with rheumatic and musculoskeletal disease at our centre, incorporating an element of guided patient self-stratification. Our results indicate that patients are able to stratify their own risk accurately using the BSR COVID-19 risk stratification guidance.</p