Pathogen detection by core-shell type aptamer-magnetic preconcentration coupled to real-time PCR

Ozalp, V. Cengiz
Kavruk, Murat
Keskin, Batuhan B.
Öktem, Hüseyin Avni
The presence of pathogenic bacteria is a major health risk factor in food samples and the commercial food supply chain is susceptible to bacterial contamination. Thus, rapid and sensitive identification methods are in demand for the food industry. Quantitative polymerase chain reaction (PCR) is one of the reliable specific methods with reasonably fast assay times. However, many constituents in food samples interfere with PCR, resulting in false results and thus hindering the usability of the method. Therefore, we aimed to develop an aptamer-based magnetic separation system as a sample preparation method for subsequent identification and quantification of the contaminant bacteria by real-time PCR. To achieve this goal, magnetic beads were prepared via suspension polymerization and grafted with glycidylmethacrylate (GMA) brushes that were modified into high quantities of amino groups. The magnetic beads were decorated with two different aptamer sequences binding specifically to Escherichia coli or Salmonella typhimurium. The results showed that even 1.0% milk inhibited PCR, but our magnetic affinity system capture of bacteria from 100% milk samples allowed accurate determination of bacterial contamination at less than 2.0 h with limit of detection around 100 CFU/mL for both bacteria in spiked-milk samples.


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Flavonoids, present in fruits, vegetables and beverages derived from plants, have been described as health-promoting, disease-preventing dietary supplements, and have activity as cancer preventive agents. The cancer protective effects of flavonoids have been attributed to a wide variety of mechanisms, including modulating enzyme activities resulting in the decreased carcinogenicity of xenobiotics. Cytochrome P4501A1 (CYP1A1) is a Phase I enzyme which is known to be involved in the activation of procarcinoge...
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The conversion of the cellular form of the prion protein (PrPC) to an abnormal, alternatively folded isoform (PrPSc) is the central event in prion diseases or transmissible spongiform encephalopathies. Recent studies have demonstrated de novo generation of murine prions from recombinant prion protein (recPrP) after inoculation into transgenic and wild-type mice. These so-called synthetic prions lead to novel prion diseases with unique neuropathological and biochemical features. Moreover, the use of recPrP i...
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Cytochromes P450 are versatile heme-based enzymes responsible for vital life processes. Of these, P450cam (substrate camphor) has been most studied. Despite this, precise mechanisms of the key OO cleavage step remain partly elusive to date; effects observed in various enzyme mutants remain partly unexplained. We have carried out extended (to 1000 ns) MM-MD and follow-on quantum mechanics/molecular mechanics computations, both on the well-studied FeOO state and on Cpd(0) (compound 0). Our simulations include...
Production of an acetone-butanol-ethanol mixture from Clostridium acetobutylicum and its conversion to high-value biofuels
Sreekumar, Sanil; Baer, Zachary C.; Pazhamalai, Anbarasan; Günbaş, Emrullah Görkem; Grippo, Adam; Blanch, Harvey W.; Clark, Douglas S.; Toste, F. Dean (Springer Science and Business Media LLC, 2015-03-01)
Clostridium acetobutylicum is a bacterial species that ferments sugar to a mixture of organic solvents (acetone, butanol and ethanol). This protocol delineates a methodology to combine solventogenic clostridial fermentation and chemical catalysis via extractive fermentation for the production of biofuel blendstocks. Extractive fermentation of C. acetobutylicum is operated in fed-batch mode with a concentrated feed solution (500 grams per liter glucose and 50 grams per liter yeast extract) for 60 h, producin...
Citation Formats
V. C. Ozalp, G. BAYRAMOĞLU, M. Kavruk, B. B. Keskin, H. A. Öktem, and M. Y. ARICA, “Pathogen detection by core-shell type aptamer-magnetic preconcentration coupled to real-time PCR,” ANALYTICAL BIOCHEMISTRY, pp. 119–125, 2014, Accessed: 00, 2020. [Online]. Available: