Detection of Gram-negative bacterial outer membrane vesicles using DNA aptamers

Shin, Hye-Su; Gedi, Vinayakumar; Kim, Joon-Ki; Lee, Dong-Ki

doi:10.1038/s41598-019-49755-0

Cited by 47 publications

(36 citation statements)

References 39 publications

(44 reference statements)

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“…A challenge for the FCM will be the very low numbers of such organisms of concern in the water, possibly requiring a concentration step. The development of advanced specific bacteria monitoring tools with online FCM combined with bacteria-specific fluorescent probes such as an antibody 57 , nucleic acid probes 58 , and aptamers 59,60 could be suggested in further studies. Fig.…”

Section: Resultsmentioning

confidence: 99%

Online characterization of bacterial processes in drinking water systems

2020

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The use of traditional drinking water microbial quality monitoring methods, including heterotrophic plate counts (HPCs) and total coliform counts, are not only laborious and time-consuming but also do not readily allow identification of risk areas in the network. Furthermore, if areas of concern are identified, and mitigation measures are taken, it takes days before the effectiveness of these measures is known. This study identified flow cytometry (FCM) as an online sensor technology for bacterial water quality monitoring in the distribution network. We monitored the total bacterial cell numbers and biodiversity in a drinking water distribution system (DWDS) using an online FCM. Two parallel online FCM monitoring systems were installed on two different locations at a drinking water treatment plant (DWTP; Saudi Arabia) supplying chlorinated water to the distribution and in the network 3.6 km away from the DWTP. The FCMs were operated at the same time in parallel to assess the biological stability in DWDSs. The flow cytometric data was compared with the conventional water quality detection methods (HPC and total coliforms). HPC and total coliforms were constantly below the detection limits, while the FCM provided detectable total cell count data and enabled the quantification of changes in the drinking water both with time and during distribution. Results demonstrate the value of FCM as a tool for compliance monitoring and risk assessment of DWDSs.

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Section: Resultsmentioning

confidence: 99%

Online characterization of bacterial processes in drinking water systems

2020

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“…Of interest, newer SELEX-based approaches (e.g., capillary electrophoresis-SELEX; cell-SELEX; magnetic bead-SELEX; microfluidic-SELEX, et al; reviewed in 34 ), many of which do not require use of radioactivity, have been developed in order to obtain aptamers. For example, aptamers that target part of the surface of whole live cells such as cancer cells 35 or bacteria 36,37 can be selected (see 38 for a review) using various biochemical or biophysical approaches. Aptamers targeting the surface of a protein can be selected using an ELISA-based approach.…”

Section: Discussionmentioning

confidence: 99%

Introducing SELEX via a semester‐long course‐based undergraduate research experience (CURE)

Kushner

2021

Biochem Molecular Bio Educ

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With the growing importance of the field of RNA biology, undergraduates need to perform RNA-related research. Systematic evolution of ligands by exponential enrichment (SELEX) has become an important method in RNA biology. The principles of SELEX were applied to a semester-long course-based undergraduate research experience (CURE) in which two rounds of in vivo functional selection of regions of a viral RNA were performed. As the labwork had an unknown outcome, students indicated that they were excited by the work and became invested in the experience. By completing two rounds of SELEX, the students repeated molecular methods (e.g., RNA extraction, RT-PCR, agarose gel electrophoresis, DNA purification, cloning, and sequence analysis) and reported that repetition reinforced their learning and helped them build confidence in their lab abilities. Students also appreciated that they did not learn a "technique-per-week" without context, but rather they understood why certain methods were used for certain molecular tasks. Results from a 19-question multiple-choice assessment indicated increased comprehension of theory underlying methods performed. Details regarding experimental methods and timeline, and assessment and attitudinal results from three student cohorts, are described herein.

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“…The nanomaterials conjugated with aptamers facilitate recognition, rapid enrichment, and separation of targets. Aptamer-based affinity approaches have been used in the analysis of peptides and proteins in bacterial cells and human samples [ 15 , 16 , 17 , 18 ]. A recent report revealed the application of enzyme-linked DNA aptamer to the detection of outer membrane vesicles in Gram-negative bacterial cells for the early diagnosis of bacterial infections [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Selective Capture and Identification of Methicillin-Resistant Staphylococcus aureus by Combining Aptamer-Modified Magnetic Nanoparticles and Mass Spectrometry

Liu

Katragunta

et al. 2021

IJMS

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A nucleic acid aptamer that specifically recognizes methicillin-resistant Staphylococcus aureus (MRSA) has been immobilized on magnetic nanoparticles to capture the target bacteria prior to mass spectrometry analysis. After the MRSA species were captured, they were further eluted from the nanoparticles and identified using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The combination of aptamer-based capture/enrichment and MS analysis of microorganisms took advantage of the selectivity of both techniques and should enhance the accuracy of MRSA identification. The capture and elution efficiencies for MRSA were optimized by examining factors such as incubation time, temperature, and elution solvents. The aptamer-modified magnetic nanoparticles showed a capture rate of more than 90% under the optimized condition, whereas the capture rates were less than 11% for non-target bacteria. The as-prepared nanoparticles exhibited only a 5% decrease in the capture rate and a 9% decrease in the elution rate after 10 successive cycles of utilization. Most importantly, the aptamer-modified nanoparticles revealed an excellent selectivity towards MRSA in bacterial mixtures. The capture of MRSA at a concentration of 102 CFU/mL remained at a good percentage of 82% even when the other two species were at 104 times higher concentration (106 CFU/mL). Further, the eluted MRSA bacteria were successfully identified using MALDI mass spectrometry.

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Detection of Gram-negative bacterial outer membrane vesicles using DNA aptamers

Cited by 47 publications

References 39 publications

Online characterization of bacterial processes in drinking water systems

Online characterization of bacterial processes in drinking water systems

Introducing SELEX via a semester‐long course‐based undergraduate research experience (CURE)

Selective Capture and Identification of Methicillin-Resistant Staphylococcus aureus by Combining Aptamer-Modified Magnetic Nanoparticles and Mass Spectrometry

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