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Waema MW, Misinzo G, Kagira JM, Agola EL, Ngowi HA. DNA-Detection Based Diagnostics for Taenia solium Cysticercosis in Porcine. J Parasitol Res 2020; 2020:5706981. [PMID: 32395335 PMCID: PMC7199576 DOI: 10.1155/2020/5706981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 12/02/2019] [Indexed: 11/17/2022] Open
Abstract
Porcine cysticercosis is a neglected and underestimated disease caused by metacestode stage of the tapeworm, Taenia solium (T. solium). Pigs are the intermediate hosts of T. solium while human are the only known definitive host. The disease has an economic consequence because the affected farmers lose 50-100 percent of the value of pigs if they are infected. Lack of affordable, easy to use, sensitive, and specific molecular diagnostic tools for detection of infections at the farm level hinders the control of porcine cysticercosis in endemic areas. A number of DNA based diagnostic assays for the detection of T. solium infections in pigs have been developed and evaluated but none is applicable at low-resource areas where this disease is an endemic. This review focuses mainly on DNA based diagnostic methods, their sensitivity, specificity, and utilization at low-resource areas. We summarized data from 65 studies on the current DNA-detection based diagnostic techniques for T. solium cysticercosis in porcine, published in English between the years 2000-2018, identified through PubMed search engine. Of the different polymerase chain reaction (PCR) assays developed for identification of T. solium, the most sensitive (97-100%) and specific (100%) one is nested PCR. One study utilized loop-mediated isothermal amplification (LAMP) as a diagnostic tool for the detection of T. solium infections though its field use was never determined. Recombinase polymerase amplification (RPA) has been evaluated as a diagnostic tool for a variety of diseases, but has never been exploited for the diagnosis of cysticercosis/taeniasis. In conclusion, several molecular methods have been developed and evaluated in lab settings. However, there is need to validate these methods as a diagnostic tool to diagnose porcine cysticercosis in low-resource areas.
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Affiliation(s)
- Maxwell W. Waema
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Sokoine University of Agriculture, P.O Box 3297, Chuo Kikuu, Morogoro, Tanzania
| | - Gerald Misinzo
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Sokoine University of Agriculture, P.O Box 3297, Chuo Kikuu, Morogoro, Tanzania
| | - John M. Kagira
- Department of Animal Health and Production, Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000-00200, Nairobi, Kenya
| | - Eric L. Agola
- Centre of Biotechnology Research and Development, Kenya Medical Research Institute, P.O Box 3297, Nairobi, Kenya
| | - Helena A. Ngowi
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, P.O Box 3021, Chuo Kikuu, Morogoro, Tanzania
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da Silva SJR, Pardee K, Pena L. Loop-Mediated Isothermal Amplification (LAMP) for the Diagnosis of Zika Virus: A Review. Viruses 2019; 12:v12010019. [PMID: 31877989 PMCID: PMC7019470 DOI: 10.3390/v12010019] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 11/30/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
The recent outbreak of Zika virus (ZIKV) in the Americas and its devastating developmental and neurological manifestations has prompted the development of field-based diagnostics that are rapid, reliable, handheld, specific, sensitive, and inexpensive. The gold standard molecular method for lab-based diagnosis of ZIKV, from either patient samples or insect vectors, is reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The method, however, is costly and requires lab-based equipment and expertise, which severely limits its use as a point-of-care (POC) tool in resource-poor settings. Moreover, given the lack of antivirals or approved vaccines for ZIKV infection, a POC diagnostic test is urgently needed for the early detection of new outbreaks and to adequately manage patients. Loop-mediated isothermal amplification (LAMP) is a compelling alternative to RT-qPCR for ZIKV and other arboviruses. This low-cost molecular system can be freeze-dried for distribution and exhibits high specificity, sensitivity, and efficiency. A growing body of evidence suggests that LAMP assays can provide greater accessibility to much-needed diagnostics for ZIKV infections, especially in developing countries where the ZIKV is now endemic. This review summarizes the different LAMP methods that have been developed for the virus and summarizes their features, advantages, and limitations.
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Affiliation(s)
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada;
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhaes Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Brazil;
- Correspondence: ; Tel.: +55-81-2123-7849
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Ma YD, Li KH, Chen YH, Lee YM, Chou ST, Lai YY, Huang PC, Ma HP, Lee GB. A sample-to-answer, portable platform for rapid detection of pathogens with a smartphone interface. LAB ON A CHIP 2019; 19:3804-3814. [PMID: 31620745 DOI: 10.1039/c9lc00797k] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Emerging and re-emerging infectious diseases pose global threats to human health. Although several conventional diagnostic methods have been widely adopted in the clinic, the long turn-around times of "gold standard" culture-based techniques, as well as the limited sensitivity of lateral-flow strip assays, thwart medical progress. In this study, a smartphone-controlled, automated, and portable system was developed for rapid molecular diagnosis of pathogens (including viruses and bacteria) via the use of a colorimetric loop-mediated isothermal amplification (LAMP) approach on a passive, self-driven microfluidic device. The system was capable of 1) purifying viral or bacterial samples with specific affinity reagents that had been pre-conjugated to magnetic beads, 2) lysing pathogens at low temperatures, 3) executing isothermal nucleic acid amplification, and 4) quantifying the results of colorimetric assays for detection of pathogens with an integrated color sensor. The entire, 40 min analytical process was automatically performed with a novel punching-press mechanism that could be controlled and monitored by a smartphone. As a proof of concept, the influenza A (H1N1) virus and methicillin-resistant Staphylococcus aureus bacteria were used to characterize and optimize the device, and the limits of detection were experimentally found to be 3.2 × 10-3 hemagglutinating units (HAU) per reaction and 30 colony-forming units (CFU) per reaction, respectively; both such values represent high enough sensitivity for clinical adoption. Moreover, the colorimetric assay could be both qualitative and quantitative for detection of pathogens. This is the first instance of an easy-to-use, automated, and portable system for accurate and sensitive molecular diagnosis of either viruses or bacteria, and it is envisioned that this smartphone-controlled apparatus may serve as a platform for clinical, point-of-care pathogen detection, particularly in resource-limited settings.
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Affiliation(s)
- Yu-Dong Ma
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Kuang-Hsien Li
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Yi-Hong Chen
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Yung-Mao Lee
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Shang-Ta Chou
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Yue-Yuan Lai
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Po-Chiun Huang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Hsi-Pin Ma
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan. and Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, 30013 Taiwan and Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan
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Dávila-Ramos S, Castelán-Sánchez HG, Martínez-Ávila L, Sánchez-Carbente MDR, Peralta R, Hernández-Mendoza A, Dobson ADW, Gonzalez RA, Pastor N, Batista-García RA. A Review on Viral Metagenomics in Extreme Environments. Front Microbiol 2019; 10:2403. [PMID: 31749771 PMCID: PMC6842933 DOI: 10.3389/fmicb.2019.02403] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
Abstract
Viruses are the most abundant biological entities in the biosphere, and have the ability to infect Bacteria, Archaea, and Eukaryotes. The virome is estimated to be at least ten times more abundant than the microbiome with 107 viruses per milliliter and 109 viral particles per gram in marine waters and sediments or soils, respectively. Viruses represent a largely unexplored genetic diversity, having an important role in the genomic plasticity of their hosts. Moreover, they also play a significant role in the dynamics of microbial populations. In recent years, metagenomic approaches have gained increasing popularity in the study of environmental viromes, offering the possibility of extending our knowledge related to both virus diversity and their functional characterization. Extreme environments represent an interesting source of both microbiota and their virome due to their particular physicochemical conditions, such as very high or very low temperatures and >1 atm hydrostatic pressures, among others. Despite the fact that some progress has been made in our understanding of the ecology of the microbiota in these habitats, few metagenomic studies have described the viromes present in extreme ecosystems. Thus, limited advances have been made in our understanding of the virus community structure in extremophilic ecosystems, as well as in their biotechnological potential. In this review, we critically analyze recent progress in metagenomic based approaches to explore the viromes in extreme environments and we discuss the potential for new discoveries, as well as methodological challenges and perspectives.
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Affiliation(s)
- Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Hugo G. Castelán-Sánchez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Liliana Martínez-Ávila
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | | | - Raúl Peralta
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Ramón A. Gonzalez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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Heller RC, Chung S, Crissy K, Dumas K, Schuster D, Schoenfeld TW. Engineering of a thermostable viral polymerase using metagenome-derived diversity for highly sensitive and specific RT-PCR. Nucleic Acids Res 2019; 47:3619-3630. [PMID: 30767012 PMCID: PMC6468311 DOI: 10.1093/nar/gkz104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 12/02/2022] Open
Abstract
Reverse transcription is an essential initial step in the analysis of RNA for most PCR-based amplification and detection methods. Despite advancements in these technologies, efficient conversion of RNAs that form stable secondary structures and double-stranded RNA targets remains challenging as retroviral-derived reverse transcriptases are often not sufficiently thermostable to catalyze synthesis at temperatures high enough to completely relax these structures. Here we describe the engineering and improvement of a thermostable viral family A polymerase with inherent reverse transcriptase activity for use in RT-PCR. Using the 3173 PyroPhage polymerase, previously identified from hot spring metagenomic sampling, and additional thermostable orthologs as a source of natural diversity, we used gene shuffling for library generation and screened for novel variants that retain high thermostability and display elevated reverse transcriptase activity. We then created a fusion enzyme between a high-performing variant polymerase and the 5′→3′ nuclease domain of Taq DNA polymerase that provided compatibility with probe-based detection chemistries and enabled highly sensitive detection of structured RNA targets. This technology enables a flexible single-enzyme RT-PCR system that has several advantages compared with standard heat-labile reverse transcription methods.
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Affiliation(s)
- Ryan C Heller
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
| | - Suhman Chung
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
| | - Katarzyna Crissy
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
| | - Kyle Dumas
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
| | - David Schuster
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
| | - Thomas W Schoenfeld
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
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56
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Li G, Rabe KS, Nielsen J, Engqvist MKM. Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima. ACS Synth Biol 2019; 8:1411-1420. [PMID: 31117361 DOI: 10.1021/acssynbio.9b00099] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Enzymes that catalyze chemical reactions at high temperatures are used for industrial biocatalysis, applications in molecular biology, and as highly evolvable starting points for protein engineering. The optimal growth temperature (OGT) of organisms is commonly used to estimate the stability of enzymes encoded in their genomes, but the number of experimentally determined OGT values are limited, particularly for thermophilic organisms. Here, we report on the development of a machine learning model that can accurately predict OGT for bacteria, archaea, and microbial eukaryotes directly from their proteome-wide 2-mer amino acid composition. The trained model is made freely available for reuse. In a subsequent step we use OGT data in combination with amino acid composition of individual enzymes to develop a second machine learning model-for prediction of enzyme catalytic temperature optima ( Topt). The resulting model generates enzyme Topt estimates that are far superior to using OGT alone. Finally, we predict Topt for 6.5 million enzymes, covering 4447 enzyme classes, and make the resulting data set available to researchers. This work enables simple and rapid identification of enzymes that are potentially functional at extreme temperatures.
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Affiliation(s)
- Gang Li
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Kersten S Rabe
- Institute for Biological Interfaces 1 (IBG 1) , Karlsruhe Institute of Technology (KIT) , Group for Molecular Evolution, 76131 Karlsruhe , Germany
| | - Jens Nielsen
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
- Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , DK-2800 Kgs. Lyngby , Denmark
| | - Martin K M Engqvist
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
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57
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Leung V, Brooks M, Emerson S, Ali M, Filipe CDM. Ready-to-use thermally stable mastermix pills for molecular biology applications. Biotechnol Prog 2018; 35:e2764. [PMID: 30536873 DOI: 10.1002/btpr.2764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/14/2018] [Accepted: 12/06/2018] [Indexed: 11/12/2022]
Abstract
Rolling circle amplification (RCA), polymerase chain reaction (PCR), and loop-mediated isothermal amplification (LAMP), are powerful tools that can be used for gene manipulation, pathogen detection, and infectious disease diagnostics. However, these techniques require trained personnel, as the pipetting steps involved can lead to contamination and, consequently, erroneous results. Furthermore, many of the reagents used in molecular biology are thermally labile and must be kept within a cold-chain. In this article, we present a simple and cost-effective method that allows molecular biology reagents to be thermally stabilized into ready-to-use mastermixes via drying in pullulan and trehalose films. Our experimental results demonstrate that this method is capable of preserving the activity of RCA, PCR, LAMP, ligase, polynucleotide kinase, and Klenow fragment mastermixes for at least 3 months at ambient conditions. Thus, stabilizing reagents via drying in pullulan and trehalose film may allow for a drastic reduction in the number of pipetting steps and the elimination of the need for a cold chain. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2764, 2019.
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Affiliation(s)
- Vincent Leung
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Meredith Brooks
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Sophia Emerson
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Monsur Ali
- Biointerfaces Inst., McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Carlos D M Filipe
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
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58
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Gandasegui J, Fernández-Soto P, Dacal E, Rodríguez E, Saugar JM, Yepes E, Aznar-Ruiz-de-Alegría ML, Espasa M, Ninda A, Bocanegra C, Salvador F, Sulleiro E, Moreno M, Vicente B, López-Abán J, Muro A. Field and laboratory comparative evaluation of a LAMP assay for the diagnosis of urogenital schistosomiasis in Cubal, Central Angola. Trop Med Int Health 2018; 23:992-1001. [PMID: 29920859 DOI: 10.1111/tmi.13117] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To evaluate the performance of Rapid-Heat LAMPellet assay in field conditions for diagnosis of urogenital schistosomiasis in an endemic area in Cubal, Angola, and to assess the reproducibility in a reference laboratory. METHODS A total of 172 urine samples from school-age children were tested for microhaematuria, microscopic detection of Schistosoma haematobium eggs and LAMP for DNA detection. Urine samples were stored in a basic equipped laboratory. Field-LAMP tests were performed with and without prior DNA extraction from urine samples, and the results were read by turbidity and by colour change. When field procedures were finished, samples were sent to a reference laboratory to be reanalysed by LAMP. RESULTS A total of 83 of 172 (48.3%) were positive for microhaematuria, 87/172 (50.6%) were microscopy-positive for S. haematobium eggs detection, and 127/172 (73.8%) showed LAMP-positive results for detecting S. haematobium using purified DNA and 109/172 (63.4%) without prior DNA extraction. MacNemar's test showed a statistical significant relation between LAMP results and microscopy-detected S. haematobium infections and microhaematuria (P < 0.001 in both cases), respectively. When samples of purified DNA were reanalysed in a reference laboratory in Spain using the same LAMP methodology, the overall reproducibility achieved 72.1%. CONCLUSIONS The ease of use, simplicity and feasibility demonstrated by LAMP assay in field conditions together with the acceptable level of reproducibility achieved in a reference laboratory support the use of LAMP assay as an effective test for molecular diagnosis of urogenital schistosomiasis in endemic remote areas.
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Affiliation(s)
- Javier Gandasegui
- Infectious and Tropical Diseases Research Group (e-INTRO), Faculty of Pharmacy, Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), University of Salamanca, Salamanca, Spain
| | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Faculty of Pharmacy, Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), University of Salamanca, Salamanca, Spain
| | - Elena Dacal
- Department of Parasitology, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Esperanza Rodríguez
- Department of Parasitology, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - José María Saugar
- Department of Parasitology, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Edward Yepes
- Infectious and Tropical Diseases Research Group (e-INTRO), Faculty of Pharmacy, Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), University of Salamanca, Salamanca, Spain
| | | | - Mateu Espasa
- Microbiology Department, University Hospital Vall d'Hebron, PROSICS Barcelona, Barcelona, Spain
| | | | - Cristina Bocanegra
- Special Program for Infectious Diseases Vall d'Hebron-Drassanes, PROSICS Barcelona, Barcelona, Spain
| | - Fernando Salvador
- Infectious Diseases Department, Vall d'Hebron University Hospital, PROSICS Barcelona, Barcelona, Spain
| | - Elena Sulleiro
- Microbiology Department, University Hospital Vall d'Hebron, PROSICS Barcelona, Barcelona, Spain
| | | | - Belén Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Faculty of Pharmacy, Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), University of Salamanca, Salamanca, Spain
| | - Julio López-Abán
- Infectious and Tropical Diseases Research Group (e-INTRO), Faculty of Pharmacy, Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), University of Salamanca, Salamanca, Spain
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Faculty of Pharmacy, Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), University of Salamanca, Salamanca, Spain
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Hiltunen J, Liedert C, Hiltunen M, Huttunen OH, Hiitola-Keinänen J, Aikio S, Harjanne M, Kurkinen M, Hakalahti L, Lee LP. Roll-to-roll fabrication of integrated PDMS-paper microfluidics for nucleic acid amplification. LAB ON A CHIP 2018; 18:1552-1559. [PMID: 29708259 DOI: 10.1039/c8lc00269j] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Microfluidic-based integrated molecular diagnostic systems, which are automated, sensitive, specific, user-friendly, robust, rapid, easy-to-use, and portable, can revolutionize future medicine. Current research and development largely relies on polydimethylsiloxane (PDMS) to fabricate microfluidic devices. Since the transition from the proof-of-principle phase to clinical studies requires a vast number of integrated microfluidic devices, there is a need for a high-volume manufacturing method of silicone-based microfluidics. Here we present the first roll-to-roll (R2R) thermal imprinting method to fabricate integrated PDMS-paper microfluidics for molecular diagnostics, which allows production of tens of thousands of replicates in an hour. In order to validate the replicated molecular diagnostic platforms, on-chip amplification of viral ribonucleic acid (RNA) with loop-mediated isothermal amplification (LAMP) was demonstrated. These low-cost, rapid and accurate molecular diagnostic platforms will generate a wide range of applications in preventive personalized medicine, global healthcare, agriculture, food, environment, water monitoring, and global biosecurity.
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Affiliation(s)
- Jussi Hiltunen
- VTT-Technical Research Centre of Finland, Kaitoväylä 1, FIN-90590 Oulu, Finland.
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60
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Milligan JN, Shroff R, Garry DJ, Ellington AD. Evolution of a Thermophilic Strand-Displacing Polymerase Using High-Temperature Isothermal Compartmentalized Self-Replication. Biochemistry 2018; 57:4607-4619. [PMID: 29629759 DOI: 10.1021/acs.biochem.8b00200] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Strand-displacing polymerases are a crucial component of isothermal amplification (IA) reactions, where the lack of thermal cycling reduces equipment needs and improves the time to answer, especially for point-of-care applications. In order to improve the function of strand-displacing polymerases, we have developed an emulsion-based directed evolution scheme, high-temperature isothermal compartmentalized self-replication (HTI-CSR) that does not rely on thermal cycling. Starting from an algorithm-optimized shuffled library of exonuclease-deficient Family A polymerases from Geobacillus stearothermophilus (Bst LF) and Thermus aquaticus (Klentaq), we have applied HTI-CSR to generate a more thermostable strand-displacing polymerase variant that performs well in loop-mediated isothermal amplification and rolling circle amplification, even after thermal challenges of up to 95 °C that lead to better primer annealing. The new enzyme (v5.9) is also capable of a variety of new reactions, including isothermal hyperbranched rolling circle amplification. The HTI-CSR method should now prove useful for evolving additional beneficial phenotypes in strand-displacing polymerases.
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Affiliation(s)
- John N Milligan
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Raghav Shroff
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Daniel J Garry
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
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Knauf S, Lüert S, Šmajs D, Strouhal M, Chuma IS, Frischmann S, Bakheit M. Gene target selection for loop-mediated isothermal amplification for rapid discrimination of Treponema pallidum subspecies. PLoS Negl Trop Dis 2018; 12:e0006396. [PMID: 29649256 PMCID: PMC5978989 DOI: 10.1371/journal.pntd.0006396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 04/24/2018] [Accepted: 03/21/2018] [Indexed: 11/19/2022] Open
Abstract
We show proof of concept for gene targets (polA, tprL, and TP_0619) that can be used in loop-mediated isothermal amplification (LAMP) assays to rapidly differentiate infection with any of the three Treponema pallidum subspecies (pallidum (TPA), pertenue (TPE), and endemicum (TEN)) and which are known to infect humans and nonhuman primates (NHPs). Four TPA, six human, and two NHP TPE strains, as well as two human TEN strains were used to establish and validate the LAMP assays. All three LAMP assays were highly specific for the target DNA. Amplification was rapid (5-15 min) and within a range of 10E+6 to 10E+2 of target DNA molecules. Performance in NHP clinical samples was similar to the one seen in human TPE strains. The newly designed LAMP assays provide proof of concept for a diagnostic tool that enhances yaws clinical diagnosis. It is highly specific for the target DNA and does not require expensive laboratory equipment. Test results can potentially be interpreted with the naked eye, which makes it suitable for the use in remote clinical settings.
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Affiliation(s)
- Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz- Institute for Primate Research, Göttingen, Germany
| | - Simone Lüert
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz- Institute for Primate Research, Göttingen, Germany
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Idrissa S. Chuma
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz- Institute for Primate Research, Göttingen, Germany
- Sokoine University of Agriculture, Faculty of Veterinary Medicine, Morogoro, Tanzania
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Mauk MG, Song J, Liu C, Bau HH. Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests. BIOSENSORS 2018; 8:E17. [PMID: 29495424 PMCID: PMC5872065 DOI: 10.3390/bios8010017] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/29/2018] [Accepted: 02/09/2018] [Indexed: 01/10/2023]
Abstract
Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs) in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC) tests for resource-limited settings. Microfluidic cartridges ('chips') that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets) is demonstrated. Low-cost detection and added functionality (data analysis, control, communication) can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed.
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Affiliation(s)
- Michael G Mauk
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Jinzhao Song
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Changchun Liu
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Haim H Bau
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
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Wong YP, Othman S, Lau YL, Radu S, Chee HY. Loop-mediated isothermal amplification (LAMP): a versatile technique for detection of micro-organisms. J Appl Microbiol 2018; 124:626-643. [PMID: 29165905 PMCID: PMC7167136 DOI: 10.1111/jam.13647] [Citation(s) in RCA: 349] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/11/2022]
Abstract
Loop‐mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed primers to amplify targeted DNA strands. Following its first discovery by Notomi et al. (2000Nucleic Acids Res 28: E63), LAMP was further developed over the years which involved the combination of this technique with other molecular approaches, such as reverse transcription and multiplex amplification for the detection of infectious diseases caused by micro‐organisms in humans, livestock and plants. In this review, available types of LAMP techniques will be discussed together with their applications in detection of various micro‐organisms. Up to date, there are varieties of LAMP detection methods available including colorimetric and fluorescent detection, real‐time monitoring using turbidity metre and detection using lateral flow device which will also be highlighted in this review. Apart from that, commercialization of LAMP technique had also been reported such as lyophilized form of LAMP reagents kit and LAMP primer sets for detection of pathogenic micro‐organisms. On top of that, advantages and limitations of this molecular detection method are also described together with its future potential as a diagnostic method for infectious disease.
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Affiliation(s)
- Y-P Wong
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - S Othman
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Y-L Lau
- Department of Parasitology, Faculty of Medicine, Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, Kuala Lumpur, Malaysia
| | - S Radu
- Centre of Excellence for Food Safety Research (FOSREC), Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Malaysia
| | - H-Y Chee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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Song J, Liu C, Mauk MG, Peng J, Schoenfeld T, Bau HH. A Multifunctional Reactor with Dry-Stored Reagents for Enzymatic Amplification of Nucleic Acids. Anal Chem 2018; 90:1209-1216. [PMID: 29226671 PMCID: PMC6310013 DOI: 10.1021/acs.analchem.7b03834] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
To enable inexpensive molecular detection at the point-of-care and at home with minimal or no instrumentation, it is necessary to streamline unit operations and store reagents refrigeration-free. To address this need, a multifunctional enzymatic amplification reactor that combines solid-phase nucleic acid extraction, concentration, and purification; refrigeration-free storage of reagents with just-in-time release; and enzymatic amplification is designed, prototyped, and tested. A nucleic acid isolation membrane is placed at the reactor's inlet, and paraffin-encapsulated reagents are prestored within the reactor. When a sample mixed with chaotropic agents is filtered through the nucleic acid isolation membrane, the membrane binds nucleic acids from the sample. Importantly, the sample volume is decoupled from the reaction volume, enabling the use of relatively large sample volumes for high sensitivity. When the amplification reactor's temperature increases to its operating level, the paraffin encapsulating the reagents melts and moves out of the way. The reagents are hydrated, just-in-time, and the polymerase reaction proceeds. The amplification process can be monitored, in real-time. We demonstrate our reactors' ability to amplify both DNA and RNA targets using polymerase with both reverse-transcriptase and strand displacement activities to obtain sensitivities on-par with benchtop equipment and a shelf life exceeding 6 months.
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Affiliation(s)
- Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Changchun Liu
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael G. Mauk
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jing Peng
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Rapid and Simple Detection of Escherichia coli by Loop-Mediated Isothermal Amplification Assay in Urine Specimens. Avicenna J Med Biotechnol 2018; 10:269-272. [PMID: 30555663 PMCID: PMC6252025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND To improve urinary tract infection detection, we evaluated the specificity and sensitivity of Loop-mediated isothermal Amplification Method (LAMP) for detection of the Eschericia coli (E. coli) in urine samples, for the first time. METHODS Primers were designed to target the malB gene of Escherichia coli. LAMP assay was performed on urine specimens collected from patients with urinary tract infection symptoms. RESULTS As expected, LAMP was more specific and sensitive than direct microscopic tests. LAMP assay showed the best detection limit of DNA copies with 1.02 copies. CONCLUSION LAMP method offers several advantages in terms of sensitivity, rapidness and simplicity for detection of E. coli infection in urine samples. The LAMP method would be highly suitable for the early detection of the UTIs and also comfort quick diagnosis of UTI in clinical laboratories with limited equipment.
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DNA polymerases and biotechnological applications. Curr Opin Biotechnol 2017; 48:187-195. [PMID: 28618333 DOI: 10.1016/j.copbio.2017.04.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 04/17/2017] [Indexed: 01/04/2023]
Abstract
A multitude of biotechnological techniques used in basic research as well as in clinical diagnostics on an everyday basis depend on DNA polymerases and their intrinsic capability to replicate DNA strands with astoundingly high fidelity. Applications with fundamental importance to modern molecular biology, including the polymerase chain reaction and DNA sequencing, would not be feasible without the advances made in characterizing these enzymes over the course of the last 60 years. Nonetheless, the still growing application scope of DNA polymerases necessitates the identification of novel enzymes with tailor-made properties. In the recent past, DNA polymerases optimized for diverse PCR and sequencing applications as well as enzymes that accept a variety of unnatural substrates for the synthesis and reverse transcription of modified nucleic acids have been developed.
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Mauk M, Song J, Bau HH, Gross R, Bushman FD, Collman RG, Liu C. Miniaturized devices for point of care molecular detection of HIV. LAB ON A CHIP 2017; 17:382-394. [PMID: 28092381 PMCID: PMC5285266 DOI: 10.1039/c6lc01239f] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The HIV pandemic affects 36.7 million people worldwide, predominantly in resource-poor settings. Nucleic acid-based molecular detection of HIV plays a significant role in antiretroviral treatment monitoring for HIV patients, as well as diagnosis of HIV infection in infants. Currently available molecular diagnostic methods are complex, time-consuming and relatively expensive, thus limiting their use in resource-poor settings. Recent advances in microfluidics technology have made possible low-cost integrated miniaturized devices for molecular detection and quantification of HIV at the point of care. We review recent technical advances in molecular testing of HIV using microfluidic technology, with a focus on assays based on isothermal nucleic acid amplification. Microfluidic components for sample preparation, isothermal amplification and result detection are discussed and compared. We also discuss the challenges and future directions for developing an integrated "sample-to-result" microfluidic platform for HIV molecular detection.
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Affiliation(s)
- Michael Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Robert Gross
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Changchun Liu
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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Jevtuševskaja J, Krõlov K, Tulp I, Langel Ü. The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification. Expert Rev Mol Diagn 2017; 17:403-410. [PMID: 28092481 DOI: 10.1080/14737159.2017.1283218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assays Methods: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity. To quantify the inhibition, we employed quantitative loop-mediated isothermal amplification Results: The authors found that the presence of BSA, Mg 2+, and urea at physiologically relevant concentrations, as well as acidic or alkaline conditions did not affect the activity of any of the tested polymerases. However, addition of salt significantly affected the activity of the tested polymerases. CONCLUSION These findings may aid in the development of more sensitive, robust, cost effective isothermal amplification based molecular assays suitable for both point-of-care testing and on-site screening of pathogens directly from unprocessed urine which avoid the need for long and tedious DNA purification steps prior to amplification.
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Affiliation(s)
- Jekaterina Jevtuševskaja
- a Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu , Tatru , Estonia
| | - Katrin Krõlov
- a Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu , Tatru , Estonia
| | - Indrek Tulp
- b SelfD Technologie GmbH , Leipzig , Germany.,c University of Tartu, Institute of Chemistry , Tartu , Estonia
| | - Ülo Langel
- a Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu , Tatru , Estonia.,d Department of Neurochemistry , Stockholm University , Stockholm , Sweden
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Brumm PJ, Gowda K, Robb FT, Mead DA. The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. Front Microbiol 2016; 7:1979. [PMID: 28066333 PMCID: PMC5167688 DOI: 10.3389/fmicb.2016.01979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/25/2016] [Indexed: 11/13/2022] Open
Abstract
Here we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, Dictyoglomus turgidum, which is a Gram negative, strictly anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, 16 of which were cloned and expressed in our study. The GH5, GH10, and GH42 enzymes characterized in this study suggest that D. turgidum can utilize most plant-based polysaccharides except crystalline cellulose. The DNA polymerase I enzyme was also expressed and characterized. The pure enzyme showed improved amplification of long PCR targets compared to Taq polymerase. The genome contains a full complement of DNA modifying enzymes, and an unusually high copy number (4) of a new, ancestral family of polB type nucleotidyltransferases designated as MNT (minimal nucleotidyltransferases). Considering its optimal growth at 72°C, D. turgidum has an anomalously low G+C content of 39.9% that may account for the presence of reverse gyrase, usually associated with hyperthermophiles.
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Affiliation(s)
- Phillip J. Brumm
- C5-6 Technologies LLCFitchburg, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
| | - Krishne Gowda
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
- Lucigen CorporationMiddleton, WI, USA
| | - Frank T. Robb
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of MarylandBaltimore, MD, USA
| | - David A. Mead
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
- Varigen Biosciences CorporationMadison, WI, USA
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Kemleu S, Guelig D, Eboumbou Moukoko C, Essangui E, Diesburg S, Mouliom A, Melingui B, Manga J, Donkeu C, Epote A, Texier G, LaBarre P, Burton R, Ayong L. A Field-Tailored Reverse Transcription Loop-Mediated Isothermal Assay for High Sensitivity Detection of Plasmodium falciparum Infections. PLoS One 2016; 11:e0165506. [PMID: 27824866 PMCID: PMC5100904 DOI: 10.1371/journal.pone.0165506] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/13/2016] [Indexed: 11/19/2022] Open
Abstract
Highly sensitive and field deployable molecular diagnostic tools are critically needed for detecting submicroscopic, yet transmissible levels of malaria parasites prevalent in malaria endemic countries worldwide. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed and evaluated in comparison with thick blood smear microscopy, an antigen-based rapid diagnostic test (RDT), and an in-house RT-PCR targeting the same RT-LAMP transcript. The optimized assay detected Plasmodium falciparum infections in as little as 0.25ng of total parasite RNA, and exhibited a detection limit of 0.08 parasites/ μL when tested directly on infected whole blood lysates, or ~0.0008 parasites/ μL when using RNA extracts. Assay positivity was observed as early as eight minutes from initiation of the RT-LAMP and in most cases the reaction was complete before twenty minutes. Clinical evaluation of the assay on 132 suspected malaria cases resulted in a positivity rate of 90% for RT-LAMP using extracted RNA, and 85% when using whole blood lysates. The positivity rates were 70% for P. falciparum-specific RDT, 83% for RT-PCR, and 74% for thick blood smear microscopy (Mean parasite density = 36,986 parasites/ μL). Concordance rates between the developed RT-LAMP and comparator tests were greater than 75%, the lowest being with light microscopy (78%, McNemar's test: P = 0.0002), and the highest was with RT-PCR (87%, McNemar's test: P = 0.0523). Compared to reference RT-PCR, assay sensitivity was 90% for RT-LAMP on whole blood, and 96% for RT-LAMP using corresponding RNA extracts. Electricity-free heaters were further developed and evaluated in comparison with a battery-operated isothermal amplification machine for use with the developed test in resource-limited settings. Taken together, the data highlight the benefits of targeting high abundant RNA transcripts in molecular diagnosis, as well as the potential usefulness of the developed RT-LAMP-assay in malaria diagnosis in low to high parasite density settings.
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Affiliation(s)
- Sylvie Kemleu
- Malaria Research Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | - Dylan Guelig
- PATH, Seattle, Washington, United States of America
| | - Carole Eboumbou Moukoko
- Malaria Research Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon
- Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Douala, Cameroon
| | - Estelle Essangui
- Malaria Research Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon
- Faculty of Sciences, University of Douala, Douala, Cameroon
| | | | - Abas Mouliom
- Hematology Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | | | - Jeanne Manga
- Hematology Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | - Christiane Donkeu
- Malaria Research Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | - Annie Epote
- Hematology Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | - Gaëtan Texier
- Public Health & Epidemiology Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | - Paul LaBarre
- PATH, Seattle, Washington, United States of America
| | | | - Lawrence Ayong
- Malaria Research Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon
- * E-mail:
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Benzine JW, Brown KM, Agans KN, Godiska R, Mire CE, Gowda K, Converse B, Geisbert TW, Mead DA, Chander Y. Molecular Diagnostic Field Test for Point-of-Care Detection of Ebola Virus Directly From Blood. J Infect Dis 2016; 214:S234-S242. [PMID: 27638947 DOI: 10.1093/infdis/jiw330] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A molecular diagnostic method for robust detection of Ebola virus (EBOV) at the point of care (POC) directly from blood samples is described. This assay is based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) of the glycoprotein gene of EBOV. Complete reaction formulations were lyophilized in 0.2-mL polymerase chain reaction tubes. RT-LAMP reactions were performed on a battery-operated isothermal instrument. Limit of detection of this RT-LAMP assay was 2.8 × 102 plaque-forming units (PFU)/test and 1 × 103 PFU/test within 40 minutes for EBOV-Kikwit and EBOV-Makona, respectively. This assay was found to be specific for the detection of EBOV, as no nonspecific amplification was detected in blood samples spiked with closely related viruses and other pathogens. These results showed that this diagnostic test can be used at the point of care for rapid and specific detection of EBOV directly from blood with high sensitivity within 40 minutes.
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Affiliation(s)
| | | | - Krystle N Agans
- Department of Microbiology and Immunology Galveston National Laboratory, University of Texas Medical Branch at Galveston
| | | | - Chad E Mire
- Department of Microbiology and Immunology Galveston National Laboratory, University of Texas Medical Branch at Galveston
| | | | | | - Thomas W Geisbert
- Department of Microbiology and Immunology Galveston National Laboratory, University of Texas Medical Branch at Galveston
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Safavieh M, Kanakasabapathy MK, Tarlan F, Ahmed MU, Zourob M, Asghar W, Shafiee H. Emerging Loop-Mediated Isothermal Amplification-Based Microchip and Microdevice Technologies for Nucleic Acid Detection. ACS Biomater Sci Eng 2016; 2:278-294. [PMID: 28503658 PMCID: PMC5425166 DOI: 10.1021/acsbiomaterials.5b00449] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rapid, sensitive, and selective pathogen detection is of paramount importance in infectious disease diagnosis and treatment monitoring. Currently available diagnostic assays based on polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) are time-consuming, complex, and relatively expensive, thus limiting their utility in resource-limited settings. Loop-mediated isothermal amplification (LAMP) technique has been used extensively in the development of rapid and sensitive diagnostic assays for pathogen detection and nucleic acid analysis and hold great promise for revolutionizing point-of-care molecular diagnostics. Here, we review novel LAMP-based lab-on-a-chip (LOC) diagnostic assays developed for pathogen detection over the past several years. We review various LOC platforms based on their design strategies for pathogen detection and discuss LAMP-based platforms still in development and already in the commercial pipeline. This review is intended as a guide to the use of LAMP techniques in LOC platforms for molecular diagnostics and genomic amplifications.
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Affiliation(s)
- Mohammadali Safavieh
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Manoj K. Kanakasabapathy
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Farhang Tarlan
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Minhaz U. Ahmed
- Biosensors and Biotechnology Laboratory, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, Negara Brunei Darussalam
| | - Mohammed Zourob
- Department of Chemistry, College of Science, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia
| | - Waseem Asghar
- Department of Computer Engineering & Electrical Engineering and Computer Science, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431, United States
| | - Hadi Shafiee
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
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The Novel Multiple Inner Primers-Loop-Mediated Isothermal Amplification (MIP-LAMP) for Rapid Detection and Differentiation of Listeria monocytogenes. Molecules 2015; 20:21515-31. [PMID: 26633345 PMCID: PMC6332088 DOI: 10.3390/molecules201219787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/16/2015] [Accepted: 11/16/2015] [Indexed: 12/19/2022] Open
Abstract
Here, a novel model of loop-mediated isothermal amplification (LAMP), termed multiple inner primers-LAMP (MIP-LAMP), was devised and successfully applied to detect Listeria monocytogenes. A set of 10 specific MIP-LAMP primers, which recognized 14 different regions of target gene, was designed to target a sequence in the hlyA gene. The MIP-LAMP assay efficiently amplified the target element within 35 min at 63 °C and was evaluated for sensitivity and specificity. The templates were specially amplified in the presence of the genomic DNA from L. monocytogenes. The limit of detection (LoD) of MIP-LAMP assay was 62.5 fg/reaction using purified L. monocytogenes DNA. The LoD for DNA isolated from serial dilutions of L. monocytogenes cells in buffer and in milk corresponded to 2.4 CFU and 24 CFU, respectively. The amplified products were analyzed by real-time monitoring of changes in turbidity, and visualized by adding Loop Fluorescent Detection Reagent (FD), or as a ladder-like banding pattern on gel electrophoresis. A total of 48 pork samples were investigated for L. monocytogenes by the novel MIP-LAMP method, and the diagnostic accuracy was shown to be 100% when compared to the culture-biotechnical method. In conclusion, the MIP-LAMP methodology was demonstrated to be a reliable, sensitive and specific tool for rapid detection of L. monocytogenes strains.
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Shi C, Shen X, Niu S, Ma C. Innate Reverse Transcriptase Activity of DNA Polymerase for Isothermal RNA Direct Detection. J Am Chem Soc 2015; 137:13804-6. [PMID: 26474356 DOI: 10.1021/jacs.5b08144] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA detection has become one of the most robust parts in molecular biology, medical diagnostics and drug discovery. Conventional RNA detection methods involve an extra reverse transcription step, which limits their further application for RNA rapid detection. We herein report a novel finding that Bst and Klenow DNA polymerases possess innate reverse transcriptase activities, so that the reverse transcription step and next amplification reaction can be combined to one step in isothermal RNA detection. We have demonstrated that Bst and Klenow DNA polymerases could be successfully used to reverse transcribe RNA within 125-nt length by real time RT-PCR and polyacrylamide gel electrophoresis (PAGE). Our findings will spur the development of a myriad of simple and easy to use RNA detection technologies for isothermal RNA direct detection. This will just meet the future needs of bioanalysis and clinical diagnosis to RNA rapid detection in POC settings and inspection and quarantine.
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Affiliation(s)
- Chao Shi
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao 266042, PR China
| | - Xiaotong Shen
- Shandong Provincial Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao 266042, PR China
| | - Shuyan Niu
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao 266042, PR China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao 266042, PR China
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76
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Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification. MICROARRAYS 2015; 4:474-89. [PMID: 27600235 PMCID: PMC4996405 DOI: 10.3390/microarrays4040474] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 10/02/2015] [Accepted: 10/10/2015] [Indexed: 02/06/2023]
Abstract
Microfluidic components and systems for rapid (<60 min), low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs) are described. A microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane”) to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD) better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.
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77
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Damhorst GL, Duarte-Guevara C, Chen W, Ghonge T, Cunningham BT, Bashir R. Smartphone-Imaged HIV-1 Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) on a Chip from Whole Blood. ENGINEERING (BEIJING, CHINA) 2015; 1:324-335. [PMID: 26705482 PMCID: PMC4687746 DOI: 10.15302/j-eng-2015072] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Viral load measurements are an essential tool for the long-term clinical care of hum an immunodeficiency virus (HIV)-positive individuals. The gold standards in viral load instrumentation, however, are still too limited by their size, cost, and sophisticated operation for these measurements to be ubiquitous in remote settings with poor healthcare infrastructure, including parts of the world that are disproportionately affected by HIV infection. The challenge of developing a point-of-care platform capable of making viral load more accessible has been frequently approached but no solution has yet emerged that meets the practical requirements of low cost, portability, and ease-of-use. In this paper, we perform reverse-transcription loop-mediated isothermal amplification (RT-LAMP) on minimally processed HIV-spiked whole blood samples with a microfluidic and silicon microchip platform, and perform fluorescence measurements with a consumer smartphone. Our integrated assay shows amplification from as few as three viruses in a ~ 60 nL RT-LAMP droplet, corresponding to a whole blood concentration of 670 viruses per µL of whole blood. The technology contains greater power in a digital RT-LAMP approach that could be scaled up for the determination of viral load from a finger prick of blood in the clinical care of HIV-positive individuals. We demonstrate that all aspects of this viral load approach, from a drop of blood to imaging the RT-LAMP reaction, are compatible with lab-on-a-chip components and mobile instrumentation.
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Affiliation(s)
- Gregory L. Damhorst
- Department of Bioengineering, The University of Illinois at
Urbana-Champaign, Urbana, IL 61801, USA
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Carlos Duarte-Guevara
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, The
University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Weili Chen
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, The
University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tanmay Ghonge
- Department of Bioengineering, The University of Illinois at
Urbana-Champaign, Urbana, IL 61801, USA
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brian T. Cunningham
- Department of Bioengineering, The University of Illinois at
Urbana-Champaign, Urbana, IL 61801, USA
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, The
University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rashid Bashir
- Department of Bioengineering, The University of Illinois at
Urbana-Champaign, Urbana, IL 61801, USA
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, The
University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence author.
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78
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Oscorbin IP, Boyarskikh UA, Filipenko ML. Large Fragment of DNA Polymerase I from Geobacillus sp. 777: Cloning and Comparison with DNA Polymerases I in Practical Applications. Mol Biotechnol 2015; 57:947-59. [DOI: 10.1007/s12033-015-9886-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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79
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Gao G, Smith DI. Mate-Pair Sequencing as a Powerful Clinical Tool for the Characterization of Cancers with a DNA Viral Etiology. Viruses 2015; 7:4507-28. [PMID: 26262638 PMCID: PMC4576192 DOI: 10.3390/v7082831] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/16/2015] [Accepted: 07/29/2015] [Indexed: 01/18/2023] Open
Abstract
DNA viruses are known to be associated with a variety of different cancers. Human papillomaviruses (HPV) are a family of viruses and several of its sub-types are classified as high-risk HPVs as they are found to be associated with the development of a number of different cancers. Almost all cervical cancers appear to be driven by HPV infection and HPV is also found in most cancers of the anus and at least half the cancers of the vulva, penis and vagina, and increasingly found in one sub-type of head and neck cancers namely oropharyngeal squamous cell carcinoma. Our understanding of HPVs role in cancer development comes from extensive studies done on cervical cancer and it has just been assumed that HPV plays an identical role in the development of all other cancers arising in the presence of HPV sequences, although this has not been proven. Most invasive cervical cancers have the HPV genome integrated into one or more sites within the human genome. One powerful tool to examine all the sites of HPV integration in a cancer but that also provides a comprehensive view of genomic alterations in that cancer is the use of next generation sequencing of mate-pair libraries produced from the DNA isolated. We will describe how this powerful technology can provide important information about the genomic organization within an individual cancer genome, and how this has demonstrated that HPVs role in oropharyngeal squamous cell carcinoma is distinct from that in cervical cancer. We will also describe why the sequencing of mate-pair libraries could be a powerful clinical tool for the management of patients with a DNA viral etiology and how this could quickly transform the care of these patients.
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Affiliation(s)
- Ge Gao
- Division of Experimental Pathology, Mayo Clinic, Rochester, MN 55905, USA.
| | - David I Smith
- Division of Experimental Pathology, Mayo Clinic, Rochester, MN 55905, USA.
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80
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Kubota R, Jenkins DM. Real-time duplex applications of loop-mediated AMPlification (LAMP) by assimilating probes. Int J Mol Sci 2015; 16:4786-99. [PMID: 25741765 PMCID: PMC4394449 DOI: 10.3390/ijms16034786] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/27/2015] [Accepted: 01/28/2015] [Indexed: 12/15/2022] Open
Abstract
Isothermal nucleic-acid amplification methods such as Loop-Mediated isothermal AMPlification (LAMP) are increasingly appealing alternatives to PCR for use in portable diagnostic system due to the low cost, weight, and power requirements of the instrumentation. As such, interest in developing new probes and other functionality based on the LAMP reaction has been intense. Here, we report on the development of duplexed LAMP assays for pathogen detection using spectrally unique Assimilating Probes. As proof of principle, we used a reaction for Salmonella enterica as a model coupled with a reaction for λ-phage DNA as an internal control, as well as a duplexed assay to sub-type specific quarantine strains of the bacterial wilt pathogen Ralstonia solanacearum. Detection limits for bacterial DNA analyzed in individual reactions was less than 100 genomic equivalents in all cases, and increased by one to two orders of magnitude when reactions were coupled in duplexed formats. Even so, due to the more robust activity of newly available strand-displacing polymerases, the duplexed assays reported here were more powerful than analogous individual reactions reported only a few years ago, and represent a significant advance for incorporation of internal controls to validate assay results in the field.
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Affiliation(s)
- Ryo Kubota
- Diagenetix, Inc., Honolulu, HI 96822, USA.
- Department of Molecular Biosciences and Bioengineering, University of Hawai'.i, Mānoa, 1955 East-West Road, Honolulu, HI 96822, USA.
| | - Daniel M Jenkins
- Department of Molecular Biosciences and Bioengineering, University of Hawai'.i, Mānoa, 1955 East-West Road, Honolulu, HI 96822, USA.
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81
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Niessen L. Current state and future perspectives of loop-mediated isothermal amplification (LAMP)-based diagnosis of filamentous fungi and yeasts. Appl Microbiol Biotechnol 2014; 99:553-74. [PMID: 25492418 DOI: 10.1007/s00253-014-6196-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 11/30/2022]
Abstract
Loop-mediated isothermal amplification is a rather novel method of enzymatic deoxyribonucleic acid amplification which can be applied for the diagnosis of viruses, bacteria, and fungi. Although firmly established in viral and bacterial diagnosis, the technology has only recently been applied to a noteworthy number of species in the filamentous fungi and yeasts. The current review gives an overview of the literature so far published on the topic by discussing the different groups of fungal organisms to which the method has been applied. Moreover, the method is described in detail as well as the different possibilities available for signal detection and quantification and sample preparation. Future perspective of loop-mediated isothermal amplification-based assays is discussed in the light of applicability for fungal diagnostics.
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Affiliation(s)
- Ludwig Niessen
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Gregor-Mendel-Straße 4, 85354, Freising, Germany,
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82
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Gardner AF, Kelman Z. DNA polymerases in biotechnology. Front Microbiol 2014; 5:659. [PMID: 25520711 PMCID: PMC4249456 DOI: 10.3389/fmicb.2014.00659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/13/2014] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Zvi Kelman
- National Institute of Standards and Technology Gaithersburg, MD, USA ; Institute for Bioscience and Biotechnology Research Rockville, MD, USA
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