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Molecules (Basel, Switzerland) Dec 2013The organophosphorous hydrolase (PTE) from Brevundimonas diminuta is capable of degrading extremely toxic organophosphorous compounds with a high catalytic turnover and...
The organophosphorous hydrolase (PTE) from Brevundimonas diminuta is capable of degrading extremely toxic organophosphorous compounds with a high catalytic turnover and broad substrate specificity. Although the natural substrate for PTE is unknown, its loop remodeling (loop 7-2/H254R) led to the emergence of a homoserine lactonase (HSL) activity that is undetectable in PTE (kcat/km values of up to 2 × 10(4)), with only a minor decrease in PTE paraoxonase activity. In this study, homology modeling and molecular dynamics simulations have been undertaken seeking to explain the reason for the substrate specificity for the wild-type and the loop 7-2/H254R variant. The cavity volume estimated results showed that the active pocket of the variant was almost two fold larger than that of the wild-type (WT) enzyme. pKa calculations for the enzyme (the WT and the variant) showed a significant pKa shift from WT standard values (ΔpKa = 3.5 units) for the His254 residue (in the Arg254 variant). Molecular dynamics simulations indicated that the displacement of loops 6 and 7 over the active site in loop 7-2/H254R variant is useful for N-acyl-L-homoserine lactone (C4-HSL) with a large aliphatic chain to site in the channels easily. Thence the expanding of the active pocket is beneficial to C4-HSL binding and has a little effect on paraoxon binding. Our results provide a new theoretical contribution of loop remodeling to the rapid divergence of new enzyme functions.
Topics: 4-Butyrolactone; Amino Acid Sequence; Binding Sites; Hydrogen Bonding; Models, Molecular; Molecular Docking Simulation; Molecular Dynamics Simulation; Molecular Sequence Data; Paraoxon; Phosphoric Triester Hydrolases; Protein Binding; Protein Conformation; Reproducibility of Results; Sequence Alignment; Substrate Specificity
PubMed: 24352010
DOI: 10.3390/molecules181215501 -
FEMS Microbiology Ecology Mar 2003Trifluralin (alpha,alpha,alpha-trifluoro-2,6-dinitro-N,N-dipropyl-p-toluidine; TFL) is a pre-emergence, soil-incorporated herbicide that has been in agricultural use...
Trifluralin (alpha,alpha,alpha-trifluoro-2,6-dinitro-N,N-dipropyl-p-toluidine; TFL) is a pre-emergence, soil-incorporated herbicide that has been in agricultural use since the early 1960s and is moderately persistent in soil. The purpose of this study was to isolate and characterise TFL-resistant bacteria from a soil in which this pesticide has been used for the last four decades and to determine their ability to degrade TFL using HPLC. Eight bacteria were isolated by repeated subculture in liquid medium with TFL as carbon source and a ninth (isolate 9) from growth around TFL crystals on solid medium. The bacteria from enriched liquid culture were identified by biochemical tests and 16S rDNA sequencing. In a mineral salts medium with 0.1% succinate, 0.1% yeast extract and 50 mg l(-1) TFL, reductions in the level of pesticide of 24.6% for Klebsiella sp., 16.4% for Herbaspirillum sp., 25.0% and 16.0% for two strains of Bacillus sp. and 21.0% for unidentified isolate number 9 were obtained after 30 days. These were similar to the level obtained using a known TFL-degrading bacterium, Brevundimonas diminuta (NCIMB 10329). Three Pseudomonas sp. and one Bacillus sp. reduced levels by less than 5%. The five positive isolates can be used to study the biochemical and molecular biology of TFL biodegradation with the aim of optimising the degradative ability of one or more of the isolates for future use in bioremediation processes.
PubMed: 19719679
DOI: 10.1111/j.1574-6941.2003.tb01058.x -
Journal of Periodontology Sep 2009This study compared the subgingival microbiota of subjects with refractory periodontitis (RP) to those in subjects with treatable periodontitis (GRs = good responders)... (Comparative Study)
Comparative Study
Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray.
BACKGROUND
This study compared the subgingival microbiota of subjects with refractory periodontitis (RP) to those in subjects with treatable periodontitis (GRs = good responders) or periodontal health (PH) using the Human Oral Microbe Identification Microarray (HOMIM).
METHODS
At baseline, subgingival plaque samples were taken from 47 subjects with periodontitis and 20 individuals with PH and analyzed for the presence of 300 species by HOMIM. The subjects with periodontitis were classified as having RP (n = 17) based on mean attachment loss (AL) and/or more than three sites with AL >or=2.5 mm after scaling and root planing, surgery, and systemically administered amoxicillin and metronidazole or as GRs (n = 30) based on mean attachment gain and no sites with AL >or=2.5 mm after treatment. Significant differences in taxa among the groups were sought using the Kruskal-Wallis and chi(2) tests.
RESULTS
More species were detected in patients with disease (GR or RP) than in those without disease (PH). Subjects with RP were distinguished from GRs or those with PH by a significantly higher frequency of putative periodontal pathogens, such as Parvimonas micra (previously Peptostreptococcus micros or Micromonas micros), Campylobacter gracilis, Eubacterium nodatum, Selenomonas noxia, Tannerella forsythia (previously T. forsythensis), Porphyromonas gingivalis, Prevotella spp., Treponema spp., and Eikenella corrodens, as well as unusual species (Pseudoramibacter alactolyticus, TM7 spp. oral taxon [OT] 346/356, Bacteroidetes sp. OT 272/274, Solobacterium moorei, Desulfobulbus sp. OT 041, Brevundimonas diminuta, Sphaerocytophaga sp. OT 337, Shuttleworthia satelles, Filifactor alocis, Dialister invisus/pneumosintes, Granulicatella adiacens, Mogibacterium timidum, Veillonella atypica, Mycoplasma salivarium, Synergistes sp. cluster II, and Acidaminococcaceae [G-1] sp. OT 132/150/155/148/135) (P <0.05). Species that were more prevalent in subjects with PH than in patients with periodontitis included Actinomyces sp. OT 170, Actinomyces spp. cluster I, Capnocytophaga sputigena, Cardiobacterium hominis, Haemophilus parainfluenzae, Lautropia mirabilis, Propionibacterium propionicum, Rothia dentocariosa/mucilaginosa, and Streptococcus sanguinis (P <0.05).
CONCLUSION
As determined by HOMIM, patients with RP presented a distinct microbial profile compared to patients in the GR and PH groups.
Topics: Adult; Amoxicillin; Anti-Bacterial Agents; Bacteria; Bacteroides; Bacteroidetes; Campylobacter; Chronic Periodontitis; Dental Plaque; Dental Scaling; Eikenella corrodens; Eubacterium; Female; Gram-Negative Bacteria; Gram-Positive Bacteria; Humans; Male; Metronidazole; Microarray Analysis; Middle Aged; Peptostreptococcus; Periodontitis; Periodontium; Porphyromonas gingivalis; Prevotella; Proteobacteria; Root Planing; Selenomonas; Treponema
PubMed: 19722792
DOI: 10.1902/jop.2009.090185 -
Journal of Clinical Microbiology Aug 2012In the literature, only three Brevundimonas diminuta environmental isolates carrying metallo-β-lactamase genes were recently published. However, so far, no B. diminuta...
In the literature, only three Brevundimonas diminuta environmental isolates carrying metallo-β-lactamase genes were recently published. However, so far, no B. diminuta clinical isolates carrying these carbapenem resistance genes have been described. Here we report the first VIM-2 metallo-β-lactamase-producing B. diminuta clinical isolate obtained from an immunocompromised patient.
Topics: Anti-Bacterial Agents; Caulobacteraceae; DNA, Bacterial; DNA, Ribosomal; Female; Gram-Negative Bacterial Infections; Humans; Immunocompromised Host; Microbial Sensitivity Tests; Middle Aged; RNA, Ribosomal, 16S; Sequence Analysis, DNA; beta-Lactam Resistance; beta-Lactamases; beta-Lactams
PubMed: 22692741
DOI: 10.1128/JCM.00924-12 -
Journal of Clinical Sleep Medicine :... Dec 2007The treatment of choice for obstructive sleep apnea (OSA) is nasal continuous positive airway pressure (nCPAP) during sleep, but dryness of the upper airway compromises...
RATIONALE
The treatment of choice for obstructive sleep apnea (OSA) is nasal continuous positive airway pressure (nCPAP) during sleep, but dryness of the upper airway compromises compliance. Heated humidifiers may mitigate such noncompliance; however, recent observations suggest that their use, particularly if not cleaned, increases the risk of respiratory infections. Humidifier water may be contaminated, but the long-held view that passive humidifiers cannot aerosolize water may obscure the perception of risk of infection.
OBJECTIVES
This study challenges the long-held view that "passover" humidifiers do not aerosolize water. With such evidence, this study characterizes the performance of filters to reduce the potential risk of contamination.
METHODS
Heated humidifier water contaminated with bacteria was studied under conditions simulating week-long use of nCPAP for OSA.
RESULTS
Bacteria were recovered in 9 of 11 tests from the breathing tubes of CPAP devices fitted with heated humidifiers with water contaminated with Brevundimonas diminuta or Serratia marcescens. Recoverable bacteria ranged from tens to thousands of colony forming units when tested at air flow rates of 60 liters per minute for 90 minutes. Neither organism was recovered from the circuit tubing when a hydrophobic breathing-circuit filter was positioned between the humidifier and face-mask tubing with a commercially available nCPAP machine tested under simulated-use conditions.
CONCLUSION
Data suggest that patients with OSA being treated with nCPAP fitted with humidifiers may be aerosolizing bacteria, putting them at risk for developing respiratory infections and that the use of a hydrophobic filter may attenuate the passage of microbes from contaminated humidifier water.
Topics: Aerosols; Bacterial Infections; Bacteriological Techniques; Caulobacteraceae; Colony Count, Microbial; Colony-Forming Units Assay; Continuous Positive Airway Pressure; Equipment Design; Heating; Humans; Humidity; Micropore Filters; Respiratory Tract Infections; Serratia marcescens; Water Microbiology
PubMed: 18198803
DOI: No ID Found -
Applied and Environmental Microbiology Aug 2000The validation of sterilization-grade membranes is integral to ensuring the efficient and safe use of microfiltration systems. Here validation refers to the production...
The validation of sterilization-grade membranes is integral to ensuring the efficient and safe use of microfiltration systems. Here validation refers to the production of sterile filtrate for sterilizing-grade membranes under challenge test conditions. Current validation methods require 48 h of culture for results to become available, which creates time delays within the manufacturing process and quality control (QC) backlogs. This work compares four methods for the production of filter challenge test data, to the desired test sensitivity, within 24 h using bioluminescent and fluorescent recombinant strains of the test organism Brevundimonas diminuta. These methods should provide a way to implement more rapid QC test regimens for filters.
Topics: Alphaproteobacteria; Colony Count, Microbial; Evaluation Studies as Topic; Filtration; Green Fluorescent Proteins; Luciferases; Luminescence; Luminescent Proteins; Micropore Filters; Plasmids; Recombination, Genetic; Reproducibility of Results; Sensitivity and Specificity; Sterilization
PubMed: 10919803
DOI: 10.1128/AEM.66.8.3432-3437.2000