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Edgü G, Freund LJ, Hartje S, Tacke E, Hofferbert HR, Twyman RM, Noll GA, Muth J, Prüfer D. Fast, Precise, and Reliable Multiplex Detection of Potato Viruses by Loop-Mediated Isothermal Amplification. Int J Mol Sci 2020; 21:ijms21228741. [PMID: 33228234 PMCID: PMC7699554 DOI: 10.3390/ijms21228741] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/04/2022] Open
Abstract
Potato is an important staple food crop in both developed and developing countries. However, potato plants are susceptible to several economically important viruses that reduce yields by up to 50% and affect tuber quality. One of the major threats is corky ringspot, which is a tuber necrosis caused by tobacco rattle virus (TRV). The appearance of corky ringspot symptoms on tubers prior to commercialization results in ≈ 45% of the tubers being downgraded in quality and value, while ≈ 55% are declared unsaleable. To improve current disease management practices, we have developed simple diagnostic methods for the reliable detection of TRV without RNA purification, involving minimalized sample handling (mini), subsequent improved colorimetric loop-mediated isothermal amplification (LAMP), and final verification by lateral-flow dipstick (LFD) analysis. Having optimized the mini-LAMP-LFD approach for the sensitive and specific detection of TRV, we confirmed the reliability and robustness of this approach by the simultaneous detection of TRV and other harmful viruses in duplex LAMP reactions. Therefore, our new approach offers breeders, producers, and farmers an inexpensive and efficient new platform for disease management in potato breeding and cultivation.
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Affiliation(s)
- Güven Edgü
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Lena Julie Freund
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Stefanie Hartje
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Eckhard Tacke
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Hans-Reinhard Hofferbert
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Richard M. Twyman
- Twyman Research Management Ltd., P.O. Box 493, Scarborough YO11 9FJ, UK;
| | - Gundula A. Noll
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany;
| | - Jost Muth
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Dirk Prüfer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany;
- Correspondence: ; Tel.: +49-251-8322302
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Weidmann M, Faye O, Faye O, Abd El Wahed A, Patel P, Batejat C, Manugerra JC, Adjami A, Niedrig M, Hufert FT, Sall AA. Development of Mobile Laboratory for Viral Hemorrhagic Fever Detection in Africa. J Infect Dis 2019; 218:1622-1630. [PMID: 29917112 PMCID: PMC6173574 DOI: 10.1093/infdis/jiy362] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/12/2018] [Indexed: 11/22/2022] Open
Abstract
Background A mobile laboratory transportable on commercial flights was developed to enable local response to viral hemorrhagic fever outbreaks. Methods The development progressed from use of mobile real-time reverse-transcription polymerase chain reaction to mobile real-time recombinase polymerase amplification. In this study, we describe various stages of the mobile laboratory development. Results A brief overview of mobile laboratory deployments, which culminated in the first on-site detection of Ebola virus disease (EVD) in March 2014, and their successful use in a campaign to roll back EVD cases in Conakry in the West Africa Ebola virus outbreak are described. Conclusions The developed mobile laboratory successfully enabled local teams to perform rapid disgnostic testing for viral hemorrhagic fever.
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Affiliation(s)
- Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Scotland, United Kingdom
- Correspondence: M. Weidmann, Dr. rer. nat., University of Stirling, Institute of Aquaculture, Stirling FK9 4LA, Scotland, United Kingdom ()
| | - Ousmane Faye
- Arbovirus Unit, Pasteur Institute, Dakar, Senegal
| | - Oumar Faye
- Arbovirus Unit, Pasteur Institute, Dakar, Senegal
| | - Ahmed Abd El Wahed
- Unit of Infection Models, German Primate Center, Goettingen, Germany
- Division of Microbiology and Animal Hygiene, University of Goettingen, Germany
| | | | - Christophe Batejat
- Laboratory for Urgent Response to Biological Threats (CIBU), Environment and Infectious Risks Unit, Institut Pasteur, Paris, France
| | - Jean Claude Manugerra
- Laboratory for Urgent Response to Biological Threats (CIBU), Environment and Infectious Risks Unit, Institut Pasteur, Paris, France
| | - Aimee Adjami
- Multi Disease Surveillance Centre WHO, Ougadougou, Burkina Faso
| | | | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane (and Member of the Faculty of Environment and Natural Sciences of B-TU Senftenberg site), Senftenberg, Brandenburg, Germany
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Abstract
The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics. Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica. Sequencing was performed using a MK1B MinION sequencer from Oxford Nanopore Technologies (ONT; Oxford, United Kingdom) that was equipped with software to operate without internet connectivity. One-direction (1D) genomic libraries were prepared using portable field techniques on DNA isolated from desiccated microbial mats. By adequately insulating the sequencer and laptop, it was possible to run the sequencing protocol for up to 2½ h under arduous conditions.
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Affiliation(s)
- Sarah S. Johnson
- Department of Biology, Georgetown University, Washington, DC 20057, USA
- Science, Technology, and International Affairs Program, Georgetown University, Washington, DC 20057, USA
| | - Elena Zaikova
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - David S. Goerlitz
- Georgetown University Medical Center, Washington, DC 20057, USA; and
| | - Yu Bai
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Scott W. Tighe
- Advanced Genomics Lab, University of Vermont Cancer Center, Burlington, Vermont 05405, USA
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Zhao Y, Monroy GL, You S, Shelton RL, Nolan RM, Tu H, Chaney EJ, Boppart SA. Rapid diagnosis and differentiation of microbial pathogens in otitis media with a combined Raman spectroscopy and low-coherence interferometry probe: toward in vivo implementation. J Biomed Opt 2016; 21:107005. [PMID: 27802456 PMCID: PMC5997004 DOI: 10.1117/1.jbo.21.10.107005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/07/2016] [Indexed: 05/03/2023]
Abstract
We investigate and demonstrate the feasibility of using a combined Raman scattering (RS) spectroscopy and low-coherence interferometry (LCI) probe to differentiate microbial pathogens and improve our diagnostic ability of ear infections [otitis media (OM)]. While the RS probe provides noninvasive molecular information to identify and differentiate infectious microorganisms, the LCI probe helps to identify depth-resolved structural information as well as to guide and monitor positioning of the Raman spectroscopy beam for relatively longer signal acquisition times. A series of phantom studies, including the use of human middle ear effusion samples, were performed to mimic the conditions of in vivo investigations. These were also conducted to validate the feasibility of using this combined RS/LCI probe for point-of-care diagnosis of the infectious pathogen(s) in OM patients. This work establishes important parameters for future in vivo investigations of fast and accurate determination and diagnosis of infectious microorganisms in OM patients, potentially improving the efficacy and outcome of OM treatments, and importantly reducing the misuse of antibiotics in the presence of viral infections.
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Affiliation(s)
- Youbo Zhao
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Guillermo L. Monroy
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
- University of Illinois at Urbana–Champaign, Department of Bioengineering, 1304 West Springfield Avenue, Urbana, Illinois 61801, United States
| | - Sixian You
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
- University of Illinois at Urbana–Champaign, Department of Bioengineering, 1304 West Springfield Avenue, Urbana, Illinois 61801, United States
| | - Ryan L. Shelton
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ryan M. Nolan
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Haohua Tu
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Eric J. Chaney
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Stephen A. Boppart
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
- University of Illinois at Urbana–Champaign, Department of Bioengineering, 1304 West Springfield Avenue, Urbana, Illinois 61801, United States
- University of Illinois at Urbana–Champaign, Department of Electrical and Computer Engineering, 306 North Wright Street, Urbana, Illinois 61801, United States
- University of Illinois at Urbana–Champaign, Department of Internal Medicine, 506 South Mathews Avenue, Urbana, Illinois 61801, United States
- Address all correspondence to: Stephen A. Boppart, E-mail:
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Nguyen TPO, Tran BM, Lee NY. Thermally robust and biomolecule-friendly room-temperature bonding for the fabrication of elastomer-plastic hybrid microdevices. Lab Chip 2016; 16:3251-3259. [PMID: 27412355 DOI: 10.1039/c6lc00751a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Here, we introduce a simple and fast method for bonding a poly(dimethylsiloxane) (PDMS) silicone elastomer to different plastics. In this technique, surface modification and subsequent bonding processes are performed at room temperature. Furthermore, only one chemical is needed, and no surface oxidation step is necessary prior to bonding. This bonding method is particularly suitable for encapsulating biomolecules that are sensitive to external stimuli, such as heat or plasma treatment, and for embedding fracturable materials prior to the bonding step. Microchannel-fabricated PDMS was first oxidized by plasma treatment and reacted with aminosilane by forming strong siloxane bonds (Si-O-Si) at room temperature. Without the surface oxidation of the amine-terminated PDMS and plastic, the two heterogeneous substrates were brought into intimate physical contact and left at room temperature. Subsequently, aminolysis occurred, leading to the generation of a permanent seal via the formation of robust urethane bonds after only 5 min of assembling. Using this method, large-area (10 × 10 cm) bonding was successfully realized. The surface was characterized by contact angle measurements and X-ray photoelectron spectroscopy (XPS) analyses, and the bonding strength was analyzed by performing peel, delamination, leak, and burst tests. The bond strength of the PDMS-polycarbonate (PC) assembly was approximately 409 ± 6.6 kPa, and the assembly withstood the injection of a tremendous amount of liquid with the per-minute injection volume exceeding 2000 times its total internal volume. The thermal stability of the bonded microdevice was confirmed by performing a chamber-type multiplex polymerase chain reaction (PCR) of two major foodborne pathogens - Escherichia coli O157:H7 and Salmonella typhimurium - and assessing the possibility for on-site direct detection of PCR amplicons. This bonding method demonstrated high potential for the stable construction of closed microfluidic systems socketed with biomolecule-immobilized surfaces such as DNA, antibody, enzyme, peptide, and protein microarrays.
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Affiliation(s)
- T P O Nguyen
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 461-701, Korea.
| | - B M Tran
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 461-701, Korea.
| | - N Y Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 461-701, Korea. and Gachon Medical Research Institute, Gil Medical Center, Inchon 405-760, Korea
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6
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Redko I. [NEW APPROACHES TO THE EARLY DIAGNOSIS OF INTRAUTERINE VIRAL INFECTIONS IN NEWBORNS]. Georgian Med News 2015:12-15. [PMID: 26656544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The importance of intrauterine viral infections in newborns pathology remain incompletely understood, as there is the problem of early verification of the etiologic pathogen. The aim of the study was to develop diagnostic criteria for intrauterine viral infections by introducing rapid diagnostic methods, the study of perinatal factors, medical history, clinical course and laboratory data. Clinical and laboratory examination 834 mothers and their newborn patients with suspected intrauterine infection. We observed 224 children with verified intrauterine viral infection. Studied the history of perinatal risk factors, clinical features and laboratory data. Studies have shown that the predominant form of mixed infections (85.7%). On the basis of statistical methods developed diagnostic criteria and algorithm of differential diagnosis of all possible variants of infection. Testing diagnostic algorithm has shown high reliability of diagnostic criteria, which allows recommend them for clinical use.
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Affiliation(s)
- I Redko
- Zaporozhye Medical Academy of Post-Graduated Education, Ukraine
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7
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Mascher M, Wu S, Amand PS, Stein N, Poland J. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 2013; 8:e76925. [PMID: 24098570 PMCID: PMC3789676 DOI: 10.1371/journal.pone.0076925] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/04/2013] [Indexed: 12/17/2022] Open
Abstract
The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL) population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new sequencing technologies, analysis tools and genomic resources develop.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Shuangye Wu
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
| | - Paul St. Amand
- United States Department of Agriculture, Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, United States of America
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Jesse Poland
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
- United States Department of Agriculture, Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, United States of America
- * E-mail:
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8
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Mascher M, Wu S, Amand PS, Stein N, Poland J. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 2013; 8:e76925. [PMID: 24098570 DOI: 10.1371/journal.pone.076925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/04/2013] [Indexed: 05/27/2023] Open
Abstract
The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL) population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new sequencing technologies, analysis tools and genomic resources develop.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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Govindarajan AV, Ramachandran S, Vigil GD, Yager P, Böhringer KF. A low cost point-of-care viscous sample preparation device for molecular diagnosis in the developing world; an example of microfluidic origami. Lab Chip 2012; 12:174-181. [PMID: 22068336 DOI: 10.1039/c1lc20622b] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The lab-on-a-chip concept has led to several point-of-care (POC) diagnostic microfluidic platforms. However, few of these can process raw samples for molecular diagnosis and fewer yet are suited for use in a resource-limited setting without permanent electrical infrastructure. We present here a very low cost paper microfluidic device for POC extraction of bacterial DNA from raw viscous samples--a challenge for conventional microfluidic platforms. This is an example of "microfluidic origami" in that the system is activated by folding; demonstrated here is room temperature cell lysis and DNA extraction from pig mucin (simulating sputum) spiked with E. coli without the use of external power. The microfluidic origami device features dry reagent storage and rehydration of the lysis buffer. We demonstrate DNA extraction from samples with a bacterial load as low as 33 CFU ml(-1). Extraction times, starting from the raw sample, have been optimized to about 1.5 h without the use of external power, or to within 1 h using an oven or a heater block. The fabrication of this paper microfluidic device can be translated into high volume production in the developing world without the need for a semiconductor clean room or a microfabrication facility. The sample preparation can be performed with the addition of just the sample, water, ethanol and elute buffer to the device, thus reducing chemical hazards during transport and handling.
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Affiliation(s)
- A V Govindarajan
- University of Washington, Electrical Engineering, Campus Box 352500, Seattle, WA 98195, USA
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Esen N, Ozkütük A, Coban H, Atlas E. [Three step MIRU-VNTR for routine mycobacteriology laboratory practice]. MIKROBIYOL BUL 2010; 44:375-383. [PMID: 21063987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Several methods are available for the molecular typing of Mycobacterium tuberculosis complex isolates. The results of the recent research demonstrated that Mycobacterial Interspersed Repetitive Unit (MIRU)-Variable Number Tandem Repeats (VNTR) method has high discriminatory power and reproducibility, is easy to perform, and available for multi-center studies and automation. However, there is insufficient data about the MIRU-VNTR profiles in Turkey. The aim of this study was to determine the most appropriate MIRU-VNTR combinations to distinguish cross contaminations and nosocomial infections in routine mycobacteriology laboratory practice. Following molecular typing of 152 clinical isolates which were consecutively isolated from different patients in two years period (August 2004-July 2006) in our laboratory, a retrospective analysis of MIRU-VNTR data of 12 loci primers was performed by an "in-house" computer based programme. The programme was prepared by using Microsoft QuickBASIC programming language and all of the data were calculated by the help of this programme. The best combinations to differentiate the clusters and to identify the unique isolates were determined out of 4095 possible results of 12 different primer pairs. According to our 152 MIRU-VNTR results, to determine cross contaminations and nosocomial infections in routine mycobacteriology laboratory practice, we recommend to use primers 26, 40, 16, 10 and 23 in the first step; primers 31, 27, 20 and 2 in the second step, and primers 4, 24 and 39 in the third step. The created software is user friendly, fast and meets the requirements of routine clinical mycobacteriology laboratories. Besides its discriminatory power, the speed and cost-effectiveness of a typing method is also considerable. According to the results of this study it was suggested that for more rapid and economic molecular typing of M.tuberculosis and related epidemiological investigations, MIRU-VNTR should be performed in a stepwise manner.
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Affiliation(s)
- Nuran Esen
- Dokuz Eylül Üniversitesi Tıp Fakültesi, Tıbbi Mikrobiyoloji Anabilim Dalı, İzmir, Türkiye.
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