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Fast and highly specific DNA-based multiplex detection on a solid support. Appl Microbiol Biotechnol 2014; 99:413-23. [PMID: 25472437 DOI: 10.1007/s00253-014-6246-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/14/2014] [Accepted: 11/17/2014] [Indexed: 10/24/2022]
Abstract
Highly specific and fast multiplex detection methods are essential to conduct reasonable DNA-based diagnostics and are especially important to characterise infectious diseases. More than 1000 genetic targets such as antibiotic resistance genes, virulence factors and phylogenetic markers have to be identified as fast as possible to facilitate the correct treatment of a patient. In the present work, we developed a novel ligation-based DNA probe concept that was combined with the microarray technology and used it for the detection of bacterial pathogens. The novel linear chain (LNC) probes identified all tested species correctly within 1 h based on their 16S rRNA gene in a 25-multiplex reaction. Genomic DNA was used directly as template in the ligation reaction identifying as little as 10(7) cells without any pre-amplification. The high specificity was further demonstrated characterising a single nucleotide polymorphism leading to no false positive fluorescence signals of the untargeted single nucleotide polymorphism (SNP) variants. In comparison to conventional microarray probes, the sensitivity of the novel LNC3 probes was higher by a factor of 10 or more. In summary, we present a fast, simple, highly specific and sensitive multiplex detection method adaptable for a wide range of applications.
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2
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Kersting S, Rausch V, Bier FF, von Nickisch-Rosenegk M. Multiplex isothermal solid-phase recombinase polymerase amplification for the specific and fast DNA-based detection of three bacterial pathogens. Mikrochim Acta 2014; 181:1715-1723. [PMID: 25253912 PMCID: PMC4167443 DOI: 10.1007/s00604-014-1198-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 01/30/2014] [Indexed: 12/24/2022]
Abstract
We report on the development of an on-chip RPA (recombinase polymerase amplification) with simultaneous multiplex isothermal amplification and detection on a solid surface. The isothermal RPA was applied to amplify specific target sequences from the pathogens Neisseria gonorrhoeae, Salmonella enterica and methicillin-resistant Staphylococcus aureus (MRSA) using genomic DNA. Additionally, a positive plasmid control was established as an internal control. The four targets were amplified simultaneously in a quadruplex reaction. The amplicon is labeled during on-chip RPA by reverse oligonucleotide primers coupled to a fluorophore. Both amplification and spatially resolved signal generation take place on immobilized forward primers bount to expoxy-silanized glass surfaces in a pump-driven hybridization chamber. The combination of microarray technology and sensitive isothermal nucleic acid amplification at 38 °C allows for a multiparameter analysis on a rather small area. The on-chip RPA was characterized in terms of reaction time, sensitivity and inhibitory conditions. A successful enzymatic reaction is completed in <20 min and results in detection limits of 10 colony-forming units for methicillin-resistant Staphylococcus aureus and Salmonella enterica and 100 colony-forming units for Neisseria gonorrhoeae. The results show this method to be useful with respect to point-of-care testing and to enable simplified and miniaturized nucleic acid-based diagnostics. The combination of multiplex isothermal nucleic acid amplification with RPA and spatially-resolved signal generation on specific immobilized oligonucleotides ![]()
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Affiliation(s)
- Sebastian Kersting
- Fraunhofer Institute for Biomedical Engineering IBMT, Branch Potsdam, Am Muehlenberg 13, 14476 Potsdam-Golm, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
| | - Valentina Rausch
- Fraunhofer Institute for Biomedical Engineering IBMT, Branch Potsdam, Am Muehlenberg 13, 14476 Potsdam-Golm, Germany
| | - Frank F. Bier
- Fraunhofer Institute for Biomedical Engineering IBMT, Branch Potsdam, Am Muehlenberg 13, 14476 Potsdam-Golm, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
| | - Markus von Nickisch-Rosenegk
- Fraunhofer Institute for Biomedical Engineering IBMT, Branch Potsdam, Am Muehlenberg 13, 14476 Potsdam-Golm, Germany
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3
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Andresen D, Nickisch-Rosenegk MV, Bier FF. Helicase-dependent amplification: use in OnChip amplification and potential for point-of-care diagnostics. Expert Rev Mol Diagn 2014; 9:645-50. [DOI: 10.1586/erm.09.46] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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4
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Schulze H, Barl T, Vase H, Baier S, Thomas P, Giraud G, Crain J, Bachmann TT. Enzymatic on-chip enhancement for high resolution genotyping DNA microarrays. Anal Chem 2012; 84:5080-4. [PMID: 22548504 DOI: 10.1021/ac3007945] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Antibiotic resistance among pathogenic microorganisms is emerging as a major human healthcare concern. While there are a variety of resistance mechanisms, many can be related to single nucleotide polymorphisms and for which DNA microarrays have been widely deployed in bacterial genotyping. However, genotyping by means of allele-specific hybridization can suffer from the drawback that oligonucleotide probes with different nucleotide composition have varying thermodynamic parameters. This results in unpredictable hybridization behavior of mismatch probes. Consequently, the degree of discrimination between perfect match and mismatch probes is insufficient in some cases. We report here an on-chip enzymatic procedure to improve this discrimination in which false-positive hybrids are selectively digested. We find that the application of CEL1 Surveyor nuclease, a mismatch-specific endonuclease, significantly enhances the discrimination fidelity, as demonstrated here on a microarray for the identification of variants of carbapenem resistant Klebsiella pneumoniae carbapenemases and monitored by end point detection of fluorescence intensity. Further fundamental investigations applying total internal reflection fluorescence detection for kinetic real-time measurements confirmed the enzymatic enhancement for SNP discrimination.
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Affiliation(s)
- Holger Schulze
- Division of Pathway Medicine, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland, UK
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Pierik A, Boamfa M, van Zelst M, Clout D, Stapert H, Dijksman F, Broer D, Wimberger-Friedl R. Real time quantitative amplification detection on a microarray: towards high multiplex quantitative PCR. LAB ON A CHIP 2012; 12:1897-1902. [PMID: 22473033 DOI: 10.1039/c2lc20740k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Quantitative real-time polymerase chain reaction (qrtPCR) is widely used as a research and diagnostic tool. Notwithstanding its many powerful features, the method is limited in the degree of multiplexing to about 6 due to spectral overlap of the available fluorophores. A new method is presented that allows quantitative amplification detection at higher multiplexing by the integration of amplification in solution and monitoring via hybridization to a microarray in real-time. This method does not require any manipulation of the PCR product and runs in a single closed chamber. Employing labeled primers, one of the main challenges is to measure surface signals against a high fluorescence background from solution. A compact, confocal scanner is employed, based on miniaturized optics from DVD technology and combined with a flat thermocycler for simultaneous scanning and heating. The feasibility of this method is demonstrated in singleplex with an analytical sensitivity comparable to routine qrtPCR.
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Affiliation(s)
- Anke Pierik
- Philips Research, High Tech Campus 11, 5656 AE Eindhoven, The Netherlands.
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Delport F, Pollet J, Janssen K, Verbruggen B, Knez K, Spasic D, Lammertyn J. Real-time monitoring of DNA hybridization and melting processes using a fiber optic sensor. NANOTECHNOLOGY 2012; 23:065503. [PMID: 22248883 DOI: 10.1088/0957-4484/23/6/065503] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this paper a fiber optic surface plasmon resonance (FO-SPR) sensor was used to analyze the melting process of DNA linked to silica nanoparticles. Real-time monitoring of a DNA melting process has rarely been studied using surface plasmon resonance (SPR), since most commercial SPR setups do not allow for dynamic and accurate temperature control above 50 °C. The FO-SPR sensor platform, with silica nanobead signal amplification, allows sensing inside a standard PCR thermocycler, which makes high resolution DNA melting curve analysis possible. This innovative combination was used to characterize the hybridization and melting events between DNA immobilized on the sensor surface and DNA probes on silica nanoparticles. At optimized hybridization conditions complementary DNA strands of different lengths could be distinguished. While the real-time FO-SPR analysis of DNA hybridization did not result in significant variances, the analysis of DNA melting determined the exact length of overlap and the matching Gibbs energy.
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Affiliation(s)
- Filip Delport
- Department of Biosystems, Division Mechatronics, Biostatistics and Sensors, KULeuven, Leuven, Belgium
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Linko V, Leppiniemi J, Shen B, Niskanen E, Hytönen VP, Toppari JJ. Growth of immobilized DNA by polymerase: bridging nanoelectrodes with individual dsDNA molecules. NANOSCALE 2011; 3:3788-3792. [PMID: 21811739 DOI: 10.1039/c1nr10518c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present a method for controlled connection of gold electrodes with dsDNA molecules (locally on a chip) by utilizing polymerase to elongate single-stranded DNA primers attached to the electrodes. Thiol-modified oligonucleotides are directed and immobilized to nanoscale electrodes by means of dielectrophoretic trapping, and extended in a procedure mimicking PCR, finally forming a complete dsDNA molecule bridging the gap between the electrodes. The technique opens up opportunities for building from the bottom-up, for detection and sensing applications, and also for molecular electronics.
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Affiliation(s)
- Veikko Linko
- Nanoscience Center, Department of Physics, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland.
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Kim ES, Hong BJ, Park CW, Kim Y, Park JW, Choi KY. Effects of lateral spacing on enzymatic on-chip DNA polymerization. Biosens Bioelectron 2010; 26:2566-73. [PMID: 21146395 DOI: 10.1016/j.bios.2010.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 10/15/2010] [Accepted: 11/09/2010] [Indexed: 02/01/2023]
Abstract
Enzymatic on-chip DNA polymerization can be utilized to elongate surface-bound primers with DNA polymerase and to enhance the signal in the detection of target DNAs on the solid support. In order to investigate the steric effect of the enzymatic reaction on the solid support, we compared the efficiency of on-chip DNA polymerization on a high-density surface with that on a spacing-controlled surface. The spacing-controlled, 9-acid dendron-coated surface exhibited approximately 8-fold higher efficiency of on-chip DNA polymerization compared with the high-density surface. The increase in fluorescence intensity during the on-chip DNA polymerization could be fit to an exponential equation, and the saturation level of the 9-acid dendron slide was 7 times higher than that of the high-density slide. The on-chip DNA polymerization was employed to measure the transcription level of nine genes related to epithelial-to-mesenchymal transition in hepatocellular carcinoma cells. Compared to the high-density surface, the dendron-coated surface exhibited a lower detection limit in the on-chip DNA polymerization and higher correlation with transcription levels as determined by quantitative real-time PCR. Our results suggest that control of the lateral spacing of DNA strands on the solid support should significantly enhance the accessibility of DNA polymerase and the efficiency of the on-chip DNA polymerization.
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Affiliation(s)
- Eung-Sam Kim
- School of Interdisciplinary Bioscience and Bioengineering, National Core Research Center for Systems Bio-Dynamics, Pohang University of Science and Technology, San 31 Hyoja-dong, Pohang 790-784, South Korea
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Drobyshev AL, Nasedkina TV, Zakharova NV. The role of DNA diffusion in solid phase polymerase chain reaction with gel-immobilized primers in planar and capillary microarray format. BIOMICROFLUIDICS 2009; 3:44112. [PMID: 20216974 PMCID: PMC2835292 DOI: 10.1063/1.3271461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Accepted: 11/13/2009] [Indexed: 05/11/2023]
Abstract
The solid phase polymerase chain reaction (PCR) on a gel-based microarray system was studied under various durations of individual stages of the PCR cycle and spatial restriction of the reaction volume. Combining the experimental study with numerical modeling, we demonstrated that the diffusion of the PCR product in and out of a microarray element during the annealing and melting stages, respectively, is the main factor responsible for distinctive features of the studied type of PCR. The restriction of reaction volume leads to faster PCR signal growth. Particularly, the capillary array, whereby gel-based microarray elements are located on a glass bar inserted into capillary chamber, was found to be a suitable format for the development of the platform.
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Tiemann-Boege I, Curtis C, Shinde DN, Goodman DB, Tavaré S, Arnheim N. Product length, dye choice, and detection chemistry in the bead-emulsion amplification of millions of single DNA molecules in parallel. Anal Chem 2009; 81:5770-6. [PMID: 19601653 DOI: 10.1021/ac900633y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The amplification of millions of single molecules in parallel can be performed on microscopic magnetic beads that are contained in aqueous compartments of an oil-buffer emulsion. These bead-emulsion amplification (BEA) reactions result in beads that are covered by almost-identical copies derived from a single template. The post-amplification analysis is performed using different fluorophore-labeled probes. We have identified BEA reaction conditions that efficiently produce longer amplicons of up to 450 base pairs. These conditions include the use of a Titanium Taq amplification system. Second, we explored alternate fluorophores coupled to probes for post-PCR DNA analysis. We demonstrate that four different Alexa fluorophores can be used simultaneously with extremely low crosstalk. Finally, we developed an allele-specific extension chemistry that is based on Alexa dyes to query individual nucleotides of the amplified material that is both highly efficient and specific.
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11
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Helicase dependent OnChip-amplification and its use in multiplex pathogen detection. Clin Chim Acta 2009; 403:244-8. [DOI: 10.1016/j.cca.2009.03.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 02/25/2009] [Accepted: 03/10/2009] [Indexed: 11/18/2022]
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12
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Brose C, Schmitt D, von Briesen H, Reimann M. Directed differentiation of pancreatic stem cells by soluble and immobilised signalling factors. Ann Anat 2009; 191:83-93. [DOI: 10.1016/j.aanat.2008.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 07/18/2008] [Accepted: 09/03/2008] [Indexed: 12/17/2022]
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13
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Wang Z, Wang C, Yin J, Li T, Song M, Lu M, Wang H. Focusing and stabilization of bis-intercalating dye-DNA complexes for high-sensitive CE-LIF DNA analysis. Electrophoresis 2008; 29:4454-62. [DOI: 10.1002/elps.200800230] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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von Nickisch-Rosenegk M, Marschan X, Andresen D, Bier FF. Reverse transcription-polymerase chain reaction on a microarray: the integrating concept of "active arrays". Anal Bioanal Chem 2008; 391:1671-8. [PMID: 18506429 DOI: 10.1007/s00216-008-2154-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Accepted: 04/21/2008] [Indexed: 11/29/2022]
Abstract
In this report we describe the proof of principle of a reverse transcription polymerase chain reaction (RT-PCR) but on-chip, with immobilized specific primers using a transcriptome of mouse-muscle fibroblasts for detection of muscle-specific expression products of these cells. The isolated total mRNA was directly incubated on an array of immobilized and solubilized specific primers, which allow the amplification of certain muscle-specific RNAs via its immobilized cDNAs. In contrast to others, the immobilized cDNA-products were directly synthesized on the chip by applying covalently bound specific primers. The products were detected by the incorporated and fluorophore-modified specific primers of the subsequently synthezised second strand. In addition, this second-strand served as a further template (like the basically used mRNA) in the subsequent solid-phase-PCR to amplify first-strand cDNA copies at the remaining immobilized specific primer-probes. This is the intrinsic factor of the amplification of certain signals of this application. The specific cDNA templates of genes coding for subunits of the mouse muscle acetylcholine receptor (Chrna1, Chrnb1, Chrnd) and the genes coding for myogenin (Myog), muscle creatine kinase (Ckmm), and ATPase (Atp2a2) were amplified on a biochip by RT-PCR directly from freshly isolated mRNA. The resulting procedure allows the detection of mRNA sequences from less than 5 pg of total RNA preparations.
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Affiliation(s)
- Markus von Nickisch-Rosenegk
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam, Department Nanobiotechnology and Nanomedicine, Am Mühlenberg 13, 14476, Potsdam-Golm, Germany.
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Abstract
Microarray technology provides new analytical devices that allow the parallel and simultaneous detection of several thousands of probes within one sample. Microarrays, sometimes called DNA chips, are widely used in gene-expression analysis, genotyping of individuals, analysis of point mutations and single nucleotide polymorphisms (SNP) as well as other genomic or transcriptomic variations. In this chapter we give a survey of common microarray manufacturing, the selection of support material, immobilisation and hybridisation and the detection with labelled complementary strands. However, DNA arrays may also serve as the basis for more complex analysis based on the action of enzymes on the immobilized templates. This property gives DNA microarrays the potential for being the template for whole PCR and transcription experiments with high parallelism, as will be discussed in the last section of this chapter.
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McCarthy EL, Bickerstaff LE, da Cunha MP, Millard PJ. Nucleic acid sensing by regenerable surface-associated isothermal rolling circle amplification. Biosens Bioelectron 2007; 22:1236-44. [PMID: 16797962 DOI: 10.1016/j.bios.2006.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 04/27/2006] [Accepted: 05/02/2006] [Indexed: 10/24/2022]
Abstract
A novel method for regenerating biosensors has been developed in which the highly specific detection of nucleic acid sequences is carried out using molecular padlock probe (MPP) technology and surface-associated rolling circle amplification (RCA). This technique has a low occurrence of false positive results when compared to polymerase chain reaction, and is an isothermal reaction, which is advantageous in systems requiring low power consumption such as remote field sensing applications. Gold-sputtered 96-well polystyrene microplates and a fluorescent label were used to explore the detection limits of the surface-associated RCA technique, specificity for different MPP, conditions for regeneration of the biomolecular sensing surface, and reproducibility of measurements on regenerated surfaces. The technique was used to create highly selective biomolecular surfaces capable of discriminating between DNA oligonucleotides with sequences identical to RNA from infectious salmon anemia (ISA) and infectious hematopoietic necrosis (IHN) virus. As little as 0.6 fmol of circularized MPP was detectable with this fluorimetric assay. The sensing layers could be reused for at least four cycles of amplification using thermal denaturation, with less than 33% decrease in RCA response over time. Because the nucleic acid product of the test is attached to a surface during amplification, the technique is directly applicable to a variety of existing sensing platforms, including acoustic wave and optical devices.
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Affiliation(s)
- Erik L McCarthy
- Department of Chemical and Biological Engineering/LASST, 245 ESRB-Barrows, University of Maine, Orono, ME 04469, USA
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Gilbride KA, Lee DY, Beaudette LA. Molecular techniques in wastewater: Understanding microbial communities, detecting pathogens, and real-time process control. J Microbiol Methods 2006; 66:1-20. [PMID: 16635533 DOI: 10.1016/j.mimet.2006.02.016] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 01/30/2006] [Accepted: 02/28/2006] [Indexed: 10/24/2022]
Abstract
Traditionally, the detection of pathogens in water, wastewater, and other environmental samples is restricted by the ability to culture such organisms from complex environmental samples. During the last decade the use of molecular methods have supplied the means for examining microbial diversity and detecting specific organisms without the need for cultivation. The application of molecular techniques to the study of natural and engineered environmental systems has increased our insight into the vast diversity and interaction of microorganisms present in complex environments. In this paper, we will review the current and emerging molecular approaches for characterizing microbial community composition and structure in wastewater processes. Recent studies show that advances in microarray assays are increasing our capability of detecting hundreds and even thousands of DNA sequences simultaneously and rapidly. With the current progress in microfluidics and optoelectronics, the ability to automate a detection/identification system is now being realized. The status of such a system for wastewater monitoring is discussed.
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Affiliation(s)
- K A Gilbride
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St. Toronto, ON, Canada M4B 2K3.
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Steffen J, von Nickisch-Rosenegk M, Bier FF. In vitro transcription of a whole gene on a surface-coupled template. LAB ON A CHIP 2005; 5:665-8. [PMID: 15915259 DOI: 10.1039/b501091h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
An artificial gene was constructed combining the T7 promoter and terminator with the EGFP-gene from the plasmid pEGFP. The functionality of the construct was shown by in vitro translation. The gene-construct was immobilised on a planar glass surface. The transcription was performed on the immobilised gene and mRNA was determined by RT-PCR. Multiple use of the immobilised gene was demonstrated.
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Affiliation(s)
- Jenny Steffen
- Fraunhofer Institute for Biomedical Engineering, Dept. Molecular Bioanalytics and Bioelectronics, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.
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