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author:("Lu, xinjin")
1.  Metagenomic Identification of Bacterioplankton Taxa and Pathways Involved in Microcystin Degradation in Lake Erie 
PLoS ONE  2013;8(4):e61890.
Cyanobacterial harmful blooms (CyanoHABs) that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera) and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax) of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr) were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems.
doi:10.1371/journal.pone.0061890
PMCID: PMC3634838  PMID: 23637924
2.  A rapid low-cost real-time PCR for the detection of klebsiella pneumonia carbapenemase genes 
Background
Klebsiella pneumonia carbapenemases (KPCs) are able to hydrolyze the carbapenems, which cause many bacteria resistance to multiple classes of antibiotics, so the rapid dissemination of KPCs is worrisome. Laboratory identification of KPCs-harboring clinical isolates would be a key to limit the spread of the bacteria. This study would evaluate a rapid low-cost real-time PCR assay to detect KPCs.
Methods
Real-time PCR assay based on SYBR GreenIwas designed to amplify a 106bp product of the blaKPC gene from the159 clinical Gram-negative isolates resistant to several classes of -lactam antibiotics through antimicrobial susceptibility testing. We confirmed the results of real-time PCR assay by the conventional PCR-sequencing. At the same time, KPCs of these clinical isolates were detected by the modified Hodge test (MHT). Then we compared the results of real-time PCR assay with those of MHT from the sensitivity and specificity. Moreover, we evaluated the sensitivity of the real-time PCR assay.
Results
The sensitivity and specificity of the results of the real-time PCR assay compared with those of MHT was 29/29(100%) and 130/130(100%), respectively. The results of the real-time PCR and the MHT were strongly consistent (Exact Sig. (2-tailed) =1. 000; McNemar test). The real-time PCR detection limit was about 0.8cfu using clinical isolates.
Conclusion
The real-time PCR assay could rapidly and accurately detect KPCs -harboring strains with high analytical sensitivity and specificity.
doi:10.1186/1476-0711-11-9
PMCID: PMC3377543  PMID: 22545713
Real-time polymerase chain reaction; Klebsiella pneumonia carbapenemase
3.  Qualitative Analysis of Models with Different Treatment Protocols to Prevent Antitbiotic Resistance 
Mathematical biosciences  2010;227(1):56-67.
This paper is concerned with the qualitative analysis of two models (Bonhoeffer et al., Proc. Natl. Acad. Sci. USA 94 (1997), 12106–12111) for different treatment protocols to prevent antibiotic resistance. Detailed qualitative analysis about the local or global stability of the equilibria of both models is carried out in term of the basic reproduction number R0. For the model with a single antibiotic therapy, we show that if R0 < 1, then the disease-free equilibrium is globally asymptotically stable; if R0 > 1, then the disease endemic equilibrium is globally asymptotically stable. For the model with multiple antibiotic therapies, stabilities of various equilibria are analyzed and combining treatment is shown better than cycling treatment. Numerical simulations are performed to show that the dynamical properties depend intimately upon the parameters.
doi:10.1016/j.mbs.2010.06.002
PMCID: PMC2925136  PMID: 20600160
Antibiotic resistance; mathematical model; basic reproduction number; equilibrium; stability

Results 1-3 (3)