Binding and degradation of fibrinogen by Bacteroides fragilis and characterization of a 54 kDa fibrinogen-binding protein

Bacteroides fragilis is a bacterium that resides in the normal human gastro-intestinal tract; however, it is also the most commonly isolated Gram-negative obligate anaerobe from human clinical infections, such as intra-abdominal abscesses, and the most common cause of anaerobic bacteraemia. Abscess formation is important in bacterial containment, limiting dissemination of infection and bacteraemia. In this study, we investigated B. fragilis binding and degradation of human fibrinogen, the major structural component involved in fibrin abscess formation. We have shown that B. fragilis NCTC9343 binds human fibrinogen. A putative Bacteroides fragilis fibrinogen-binding protein, designated BF-FBP, identified in the genome sequence of NCTC9343, was cloned and expressed in Escherichia coli. The purified recombinant BF-FBP bound primarily to the human fibrinogen Bß-chain. In addition, we have identified fibrinogenolytic activity in B. fragilis exponential phase culture supernatants, associated with fibrinogenolytic metalloproteases in NCTC9343 and 638R, and cysteine protease activity in YCH46. All nine clinical isolates of B. fragilis examined degraded human fibrinogen; with eight isolates, initial A-chain degradation was observed, with varying Bß-chain and -chain degradation. With one blood culture isolate, Bß-chain and -chain degradation occurred first, followed by subsequent A-chain degradation. Our data raise the possibility that the fibrinogen-binding protein of B. fragilis, along with a variety of fibrinogenolytic proteases, may be an important virulence factor that facilitates dissemination of infection via reduction or inhibition of abscess formation.

Antimicrobial and antibiofilm activities of 1-alkylquinolinium bromide ionic liquids

Quinoline derivatives are known to possess a range of bioactive and medicinal activities, which have been exploited in the design of antibacterial, antifungal and antimalarial compounds. In this study, we report on the microbiological toxicity of a series of 1-alkylquinolinium bromides against a range of clinically relevant microorganisms, in both planktonic and sessile (biofilm) cultures. A comparison of antimicrobial activity against planktonic bacteria and established biofilms is presented. In general, 1-alkylquinolinium ionic liquids possess excellent, broad spectrum antimicrobial activity against microorganisms grown in both the planktonic and sessile, or biofilm, mode of growth. Importantly, these compounds are potent against Gram positive and Gram negative bacteria, as well as fungi, with a clear dependency on length of the alkyl substituent for activity, with compounds containing twelve and fourteen carbons in the alkyl group exhibiting highest antimicrobial and antibiofilm activity. © 2010 The Royal Society of Chemistry.

Development of a novel DNA microarray to detect bacterial pathogens in patients with chronic obstructive pulmonary disease (COPD)

A novel microarray was constructed with DNA PCR product probes targeting species specific functional genes of nine clinically significant respiratory pathogens, including the Gram-positive organisms (Streptococcus pneumoniae, Streptococcus pyogenes), the Gram-negative organisms (Chlamydia pneumoniae, Coxiella burnetii Haemophilus spp., Legionella pneumophila, Moraxella catarrhalis, and Pseudomonas aeruginosa), as well as the atypical bacterium, Mycoplasma pneumoniae. In a "proof-of-concept" evaluation of the developed microarray, the microarray was compared with real-time PCR from 14 sputum specimens from COPD patients. All of the samples positive for bacterial species in real-time PCR were also positive for the same bacterial species using the microarray. This study shows that a microarray using PCR probes is a potentially useful method to monitor the populations of bacteria in respiratory specimens and can be tailored to specific clinical needs such as respiratory infections of particular patient populations, including patients with cystic fibrosis and bronchiectasis. (C) 2010 Elsevier B.V. All rights reserved.

Moving window kernel PCA for adaptive monitoring of nonlinear processes

This paper discusses the monitoring of complex nonlinear and time-varying processes. Kernel principal component analysis (KPCA) has gained significant attention as a monitoring tool for nonlinear systems in recent years but relies on a fixed model that cannot be employed for time-varying systems. The contribution of this article is the development of a numerically efficient and memory saving moving window KPCA (MWKPCA) monitoring approach. The proposed technique incorporates an up- and downdating procedure to adapt (i) the data mean and covariance matrix in the feature space and (ii) approximates the eigenvalues and eigenvectors of the Gram matrix. The article shows that the proposed MWKPCA algorithm has a computation complexity of O(N2), whilst batch techniques, e.g. the Lanczos method, are of O(N3). Including the adaptation of the number of retained components and an l-step ahead application of the MWKPCA monitoring model, the paper finally demonstrates the utility of the proposed technique using a simulated nonlinear time-varying system and recorded data from an industrial distillation column.

Turning Asteroids into Comets with ELTs

It is clear that ELTs will be able to detect extremely weak outgassing from Solar system bodies via a number of different methods. Occultations will allow probing for outgassing around 20 km main-belt asteroids. Imaging can reveal dust emission rates of only milligrams/second in the inner solar system, while sublimation rates of gasses should be measurable down to gram/second levels. Suitable targets will be identified via the coming all-sky surveys, through both the classical dynamical Tisserand Invariant and long-baseline lightcurves. It is possible that using these methods, ELTs may allow the discovery of much more activity throughout the Solar system than is presently known.

Incorporating Higher Moments into Value at Risk Forecasting

Value-at-risk (VaR) forecasting generally relies on a parametric density function of portfolio returns that ignores higher moments or assumes them constant. In this paper, we propose a simple approach to forecasting of a portfolio VaR. We employ the Gram-Charlier expansion (GCE) augmenting the standard normal distribution with the first four moments, which are allowed to vary over time. In an extensive empirical study, we compare the GCE approach to other models of VaR forecasting and conclude that it provides accurate and robust estimates of the realized VaR. In spite of its simplicity, on our dataset GCE outperforms other estimates that are generated by both constant and time-varying higher-moments models.

Effect of a pharmacist-led multicomponent intervention focussing on the medication monitoring phase to prevent potential adverse drug events in nursing homes

OBJECTIVES: To determine the extent to which the use of a clinical informatics tool that implements prospective monitoring plans reduces the incidence of potential delirium, falls, hospitalizations potentially due to adverse drug events, and mortality.

DESIGN: Randomized cluster trial.

SETTING: Twenty-five nursing homes serviced by two long-term care pharmacies.

PARTICIPANTS: Residents living in nursing homes during 2003 (1,711 in 12 intervention; 1,491 in 13 usual care) and 2004 (1,769 in 12 intervention; 1,552 in 13 usual care).

INTERVENTION: The pharmacy automatically generated Geriatric Risk Assessment MedGuide (GRAM) reports and automated monitoring plans for falls and delirium within 24 hours of admission or as part of the normal time frame of federally mandated drug regimen review.

MEASUREMENTS: Incidence of potential delirium, falls, hospitalizations potentially due to adverse drug events, and mortality.

RESULTS: GRAM triggered monitoring plans for 491 residents. Newly admitted residents in the intervention homes experienced a lower rate of potential delirium onset than those in usual care homes (adjusted hazard ratio (HR)=0.42, 95% confidence interval (CI)=0.35–0.52), overall hospitalization (adjusted HR=0.89, 95% CI=0.72–1.09), and mortality (adjusted HR=0.88, 95% CI=0.66–1.16). In longer stay residents, the effects of the intervention were attenuated, and all estimates included unity.

CONCLUSION: Using health information technology in long-term care pharmacies to identify residents who might benefit from the implementation of prospective medication monitoring care plans when complex medication regimens carry potential risks for falls and delirium may reduce adverse effects associated with appropriate medication use.

Limnonectins: A new class of antimicrobial peptides from the skin secretion of the Fujian large-headed frog (Limnonectes fujianensis)

Amphibian skin secretions are rich sources of biologically-active peptides with antimicrobial peptides predominating in many species. Several studies involving molecular cloning of biosynthetic precursor-encoding cDNAs from skin or skin secretions have revealed that these exhibit highly-conserved domain architectures with an unusually high degree of conserved nucleotide and resultant amino acid sequences within the signal peptides. This high degree of nucleotide sequence conservation has permitted the design of primers complementary to such sites facilitating “shotgun” cloning of skin or skin secretion-derived cDNA libraries from hitherto unstudied species. Here we have used such an approach using a skin secretion-derived cDNA library from an unstudied species of Chinese frog – the Fujian large-headed frog, Limnonectes fujianensis – and have discovered two 16-mer peptides of novel primary structures, named limnonectin-1Fa (SFPFFPPGICKRLKRC) and limnonectin-1Fb (SFHVFPPWMCKSLKKC), that represent the prototypes of a new class of amphibian skin antimicrobial peptide. Unusually these limnonectins display activity only against a Gram-negative bacterium (MICs of 35 and 70 µM) and are devoid of haemolytic activity at concentrations up to 160 µM. Thus the “shotgun” cloning approach described can exploit the unusually high degree of nucleotide conservation in signal peptide-encoding domains of amphibian defensive skin secretion peptide precursor-encoding cDNAs to rapidly expedite the discovery of novel and functional defensive peptides in a manner that circumvents specimen sacrifice without compromising robustness of data

Complete Genome Sequence of Propionibacterium acnes Type IB Strain 6609

Propionibacterium acnes is an anaerobic Gram-positive bacterium that forms part of the normal human cutaneous microbiota and is thought to play a central role in acne vulgaris, a chronic inflammatory disease of the pilosebaceous unit (I. Kurokawa et al., Exp. Dermatol. 18:821-832, 2009). Here we present the whole genome sequence of P. acnes type IB strain 6609, which was recovered from a skin sample from a woman with no recorded acne history and is thus considered a nonpathogenic strain (I. Nagy, Microbes Infect. 8:2195-2205, 2006).

DETECTION OF IRRADIATED CHICKEN MEAT BY ANALYSIS OF LIPID EXTRACTS FOR 2-SUBSTITUTED CYCLOBUTANONES USING AN ENZYME-LINKED-IMMUNOSORBENT-ASSAY

The means to detect the irradiation of food has been investigated for many years. In recent times radiolytic products, termed 2-alkylcyclobutanones (2-CBs), have been identified as excellent markers of irradiation in lipid-containing foods. An ELISA test was developed, which was capable of detecting a number of these compounds in irradiated chicken meat. A polyclonal antiserum was raised to a 2-CB containing a terminal carboxyl group conjugated to a carrier protein. This antiserum was highly specific for cyclobutanones containing C-10 and C-12 side chains. During assay validation the limit of detection of the assay was calculated to be 0.064 pg of 2-CB per gram of fat, within- and between-assay variations ranged from 6.7 to 18%. During experimental studies, chicken meat irradiated at doses ranging from 2.5 to 10 kGy were assayed and correctly identified as being treated. Quantitative comparisons between the ELISA and CC-MS revealed a good correlation (r(2) = 0.913) between the two methodologies in concentrations of 2-CB detected in irradiated samples.

Draft Genome Sequence of an Antibiotic-Resistant Propionibacterium acnes Strain, PRP-38, from the Novel Type IC Cluster

Propionibacterium acnes, a non-spore-forming, anaerobic Gram-positive bacterium, is most notably recognized for its association with acne vulgaris (I. Kurokawa et al., Exp. Dermatol. 18:821–832, 2009). We now present the draft genome sequence of an antibiotic-resistantP. acnesstrain, PRP-38, isolated from an acne patient in the United Kingdom and belonging to the novel type IC cluster. Copyright © 2012, American Society for Microbiology. All Rights Reserved.

Crossing the eukaryote-prokaryote divide:A ubiquitin homolog in the human commensal bacterium Bacteroides fragilis

The resident microbiota of the human gastrointestinal (GI) tract is comprised of ~2,000 bacterial species, the majority of which are anaerobes. Colonization of the GI tract is important for normal development of the immune system and provides a reservoir of catabolic enzymes that degrade ingested plant polysaccharides. Bacteroides fragilis is an important member of the microbiota because it contributes to T helper cell development, but is also the most frequently isolated Gram-negative anaerobe from clinical infections. During the annotation of the B. fragilis genome sequence, we identified a gene predicted to encode a homolog of the eukaryotic protein modifier, ubiquitin. Previously, ubiquitin had only been found in eukaryotes, indicating the bacterial acquisition as a potential inter-kingdom horizontal gene transfer event. Here we discuss the possible roles of B. fragilis ubiquitin and the implications for health and disease. © 2012 Landes Bioscience

Degradation of 1,3-dichloropropene by Pseudomonas cichorii 170

The gram-negative bacterium Pseudomonas cichorii 170, isolated from soil that was repeatedly treated with the nematocide 1,3-dichloropropene, could utilize low concentrations of 1,3-dichloropropene as a sole carbon and energy source, Strain 170 was also able to grow on 3-chloroallyl alcohol, 3-chloroacrylic acid, and several 1-halo-n-alkanes. This organism produced at least three different dehalogenases: a hydrolytic haloalkane dehalogenase specific for haloalkanes and two 3-chloroacrylic acid dehalogenases, one specific for cis-3-chloroacrylic acid and the other specific for trans-3-chloroacrylic acid. The haloalkane dehalogenase and the trans-3-chloroacrylic acid dehalogenase were expressed constitutively, whereas the cis-3-chloroacrylic acid dehalogenase was inducible, The presence of these enzymes indicates that 1,3-dichloropropene is hydrolyzed to 3-chloroallyl alcohol, which is oxidized in two steps to 3-chloroacrylic acid. The latter compound is then dehalogenated, probably forming malonic acid semialdehyde. The haloalkane dehalogenase gene, which is involved in the conversion of 1,3-dichloropropene to 3-chloroallyl alcohol, was cloned and sequenced, and this gene turned out to be identical to the previously studied dhaA gene of the gram-positive bacterium Rhodococcus rhodochrous NCIMB13063, Mutants resistant to the suicide substrate 1,2-dibromoethane lacked haloalkane dehalogenase activity and therefore could not utilize haloalkanes for growth. PCR analysis showed that these mutants had lost at least part of the dhaA gene.

Application of atmospheric pressure nonthermal plasma for the in vitro eradication of bacterial biofilms

The use of atmospheric pressure nonthermal plasma represents an interesting and novel approach for the decontamination of surfaces colonized with microbial biofilms that exhibit enhanced tolerance to antimicrobial challenge. In this study, the influence of an atmospheric pressure nonthermal plasma jet, operated in a helium and oxygen gas mixture under ambient pressure, was evaluated against biofilms of Bacillus cereus,Staphylococcus aureus,Escherichia coli and Pseudomonas aeruginosa. Within <4 min of plasma exposure, complete eradication of the two Gram-positive bacterial biofilms was achieved. Although Gram-negative biofilms required longer treatment time, their complete eradication was still possible with 10 min of exposure. Whilst this study provides useful proof of concept data on the use of atmospheric pressure plasmas for the eradication of bacterial biofilms in vitro, it also demonstrates the critical need for improved understanding of the mechanisms and kinetics related to such a potentially significant approach. © 2012 Federation of European Microbiological Societies.

Complete Genome Sequences of Three Propionibacterium acnes Isolates from the Type IA(2) Cluster

Propionibacterium acnes is an anaerobic Gram-positive bacterium that has been linked to a wide range of opportunistic human infections and conditions, most notably acne vulgaris (I. Kurokawa et al., Exp. Dermatol. 18:821-832, 2009). We now present the whole-genome sequences of three P. acnes strains from the type IA(2) cluster which were recovered from ophthalmic infections (A. McDowell et al., Microbiology 157:1990-2003, 2011).