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Siqueira JF, Sakamoto M, Rosado AS. Microbial Community Profiling Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE). Methods Mol Biol 2023; 2588:91-104. [PMID: 36418684 DOI: 10.1007/978-1-0716-2780-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In their natural environments, microorganisms usually live in organized communities. Profiling analysis of microbial communities has recently assumed special relevance as it allows a thorough understanding of the diversity of the microbiota, its behavior over time, and the establishment of patterns associated with health and disease. The application of molecular biology approaches holds the advantage of including culture-difficult and as-yet-uncultivated phylotypes in the profiles, providing a more comprehensive picture of the microbial community. This chapter focuses on two particular techniques, namely terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE), both of which have been widely used in environmental studies and have been recently successfully used by the authors in the study of the oral microbial communities associated with conditions of health and disease.
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Affiliation(s)
- José F Siqueira
- Department of Endodontics and Molecular Microbiology Laboratory, Iguaçu University, Rio de Janeiro, Brazil.
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama, Japan
| | - Alexandre S Rosado
- Institute of Microbiology Prof. Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Siqueira JF, Sakamoto M, Rosado AS. Microbial Community Profiling Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE). Methods Mol Biol 2018; 1537:139-152. [PMID: 27924592 DOI: 10.1007/978-1-4939-6685-1_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
In their natural environments, microorganisms usually live in organized communities. Profiling analysis of microbial communities has recently assumed special relevance as it allows a thorough understanding of the diversity of the microbiota, its behavior over time, and the establishment of patterns associated with health and disease. The application of molecular biology approaches holds the advantage of including culture-difficult and as-yet-uncultivated phylotypes in the profiles, providing a more comprehensive picture of the microbial community. This chapter focuses on two particular techniques, namely, terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE), both of which have been widely used in environmental studies and have been successfully used by the authors in the study of the oral microbial communities associated with conditions of health and disease.
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Affiliation(s)
- José F Siqueira
- Molecular Microbiology Laboratory, Department of Endodontics, Estácio de Sá University, Rio de Janeiro, Brazil.
- Faculty of Dentistry, Estácio de Sá University, Av. Alfredo Baltazar da Silveira, 580/cobertura, Recreio, Rio de Janeiro, RJ, 22790-710, Brazil.
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama, Japan
| | - Alexandre S Rosado
- Institute of Microbiology Prof. Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Rodríguez F, Cai D, Teng Y, Spooner D. Asymmetric single-strand conformation polymorphism: an accurate and cost-effective method to amplify and sequence allelic variants. AMERICAN JOURNAL OF BOTANY 2011; 98:1061-1067. [PMID: 21730333 DOI: 10.3732/ajb.1000251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY An efficient alternative strategy to conventional cloning was needed to generate high-quality DNA sequences from a variety of nuclear orthologs for phylogenetic studies. This method would facilitate studies and minimize technical problems typically encountered in cloning methodologies. METHODS We tested a variety of single-strand conformation polymorphism (SSCP) protocols including purified and unpurified symmetric and asymmetric PCR, loading buffers, and electrophoresis conditions (buffers, matrix, running time, temperature). Results obtained from direct SSCP band sequencing were compared to those obtained from cloning. KEY RESULTS Our optimized protocol uses asymmetric PCR, with the majority of the samples run in polyacrylamide gel electrophoresis (PAGE). It consistently separated PCR products from 450 to 1200 bp. CONCLUSIONS Asymmetric PCR single-strand conformation polymorphism is an efficient alternative technique for isolating allelic variants of highly heterozygous individuals, with its greatest applications in sequencing allopolyploids. It eliminates two common problems encountered in cloning: PCR recombination and heteroduplex fixation. In addition, our protocol greatly lowers costs and time associated with procedures.
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Affiliation(s)
- Flor Rodríguez
- USDA, Agricultural Research Service, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706-1590, USA
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Jones KL, Mikulski CM, Barnhorst A, Doucette GJ. Comparative analysis of bacterioplankton assemblages from Karenia brevis bloom and nonbloom water on the west Florida shelf (Gulf of Mexico, USA) using 16S rRNA gene clone libraries. FEMS Microbiol Ecol 2010; 73:468-85. [PMID: 20618855 DOI: 10.1111/j.1574-6941.2010.00914.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The brevetoxin-producing dinoflagellate, Karenia brevis, forms nearly annual blooms off the Florida west coast, severely impacting the region's ecology and economy. Bacteria are often cited as either promoting or interfering with the development of algal blooms, and thus a detailed study of the bacterioplankton assemblages associated with K. brevis was undertaken. We developed sixteen 16S rRNA gene clone libraries from K. brevis bloom and adjacent nonbloom water to determine the bacterial groups present and assess the influence of K. brevis cell number and/or depth on bacterioplankton community composition. Most notably, bacterial groups such as Rhodobacterales (Alphaproteobacteria) and Cytophagales/Sphingobacteriales (Bacteroidetes), reported previously to be associated with other harmful algal species, were often abundant in the presence of K. brevis. Cyanobacteria frequently dominated surface samples containing no detectable K. brevis, consistent with earlier work suggesting that these photosynthetic organisms may be important in promoting the proliferation of these blooms by conditioning the water. Moreover, differences in the abundance/diversity of traditionally more rare and often undocumented phylogenetic groups (e.g. Betaproteobacteria, Deltaproteobacteria, Chloroflexus, Firmicutes) were apparent in bloom vs. nonbloom water. This is the first study to document the association of these phylogenetic groups with natural K. brevis populations and suggests a potential role for these microorganisms in K. brevis bloom dynamics.
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Affiliation(s)
- Kelly L Jones
- Marine Biotoxins Program, NOAA/National Ocean Service, Charleston, SC 29412, USA
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Siqueira JF, Sakamoto M, Rosado AS. Microbial community profiling using terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Methods Mol Biol 2010; 666:71-85. [PMID: 20717779 DOI: 10.1007/978-1-60761-820-1_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In their natural environments, microorganisms usually live in organized communities. Profiling analysis of microbial communities has recently assumed special relevance as it allows a thorough understanding of the diversity of the microbiota, its behavior over time, and the establishment of patterns associated with health and disease. The application of molecular biology approaches holds the advantage of including culture-difficult and as-yet-uncultivated phylotypes in the profiles, providing a more comprehensive picture of the microbial community. This chapter focuses on two particular techniques: the terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE), both of which have been widely used in environmental studies and have been recently successfully used by the authors in the study of the oral microbial communities associated with conditions of health and disease.
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Affiliation(s)
- José F Siqueira
- Molecular Microbiology Laboratory, Department of Endodontics, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, RJ, Brazil
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Abstract
Molecular approaches are providing new insights into the genetic diversity of schistosomes and their intermediate snail hosts. For instance, molecular tools based on the polymerase chain reaction are being developed for the diagnosis of schistosomiasis and the detection of prepatent schistosome infections in snails at transmission sites. Robust phylogenies of the different species of Schistosoma, Bulinus and Biomphalaria have been determined and novel methods are available to identify the different and cryptic taxa involved. Microsatellite analyses and mitochondrial DNA sequencing methods have been developed and are contributing to a better understanding of the genetic structure of both schistosome and snail populations. New sampling procedures to capture DNA of eggs and larval stages of schistosomes in field situations are facilitating more detailed and ethically advantageous studies on parasite heterogeneity. Knowledge of the genetic diversity of schistosome and snail populations adds a further dimension to the monitoring and surveillance of disease, and the implementation of new molecular-based approaches will be of increasing importance in helping to assess the impact of schistosomiasis control strategies.
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Jex AR, Smith HV, Monis PT, Campbell BE, Gasser RB. Cryptosporidium--biotechnological advances in the detection, diagnosis and analysis of genetic variation. Biotechnol Adv 2008; 26:304-17. [PMID: 18430539 DOI: 10.1016/j.biotechadv.2008.02.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Revised: 01/29/2008] [Accepted: 02/14/2008] [Indexed: 11/19/2022]
Abstract
Cryptosporidiosis is predominantly a gastrointestinal disease of humans and other animals, caused by various species of protozoan parasites representing the genus Cryptosporidium. This disease, transmitted mainly via the faecal-oral route (in water or food), is of major socioeconomic importance worldwide. The diagnosis and genetic characterization of the different species and population variants (usually recognised as "genotypes" or "subgenotypes") of Cryptosporidium is central to the prevention, surveillance and control of cryptosporidiosis, particularly given that there is presently no broadly applicable treatment regimen for this disease. Although traditional phenotypic techniques have had major limitations in the specific diagnosis of cryptosporidiosis, there have been major advances in the development of molecular analytical and diagnostic tools. This article provides a concise account of Cryptosporidium and cryptosporidiosis, and focuses mainly on recent advances in nucleic acid-based approaches for the diagnosis of cryptosporidiosis and analysis of genetic variation within and among species of Cryptosporidium. These advances represent a significant step toward an improved understanding of the epidemiology as well as the prevention and control of cryptosporidiosis.
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Affiliation(s)
- A R Jex
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia.
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Traub RJ, Monis PT, Robertson ID. Molecular epidemiology: A multidisciplinary approach to understanding parasitic zoonoses. Int J Parasitol 2005; 35:1295-307. [PMID: 16143334 DOI: 10.1016/j.ijpara.2005.06.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 06/21/2005] [Accepted: 06/23/2005] [Indexed: 10/25/2022]
Abstract
Sound application of molecular epidemiological principles requires working knowledge of both molecular biological and epidemiological methods. Molecular tools have become an increasingly important part of studying the epidemiology of infectious agents. Molecular tools have allowed the aetiological agent within a population to be diagnosed with a greater degree of efficiency and accuracy than conventional diagnostic tools. They have increased the understanding of the pathogenicity, virulence, and host-parasite relationships of the aetiological agent, provided information on the genetic structure and taxonomy of the parasite and allowed the zoonotic potential of previously unidentified agents to be determined. This review describes the concept of epidemiology and proper study design, describes the array of currently available molecular biological tools and provides examples of studies that have integrated both disciplines to successfully unravel zoonotic relationships that would otherwise be impossible utilising conventional diagnostic tools. The current limitations of applying these tools, including cautions that need to be addressed during their application are also discussed.
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Affiliation(s)
- R J Traub
- WHO Collaborating Centre for the Molecular Epidemiology of Parasitic Infections, School of Veterinary and Biomedical Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia.
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Savan R, Kono T, Itami T, Sakai M. Loop-mediated isothermal amplification: an emerging technology for detection of fish and shellfish pathogens. JOURNAL OF FISH DISEASES 2005; 28:573-81. [PMID: 16302951 PMCID: PMC7197467 DOI: 10.1111/j.1365-2761.2005.00670.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Fish and shellfish diseases are a constant threat to the sustainability and economic viability of aquaculture. Early diagnosis plays a vital role in management of fish and shellfish diseases. Traditionally, various biochemical and serological tests have been used for fish disease diagnosis. However, the time and expertise required for such diagnoses makes it difficult for aquaculturists to easily adopt them under production conditions. Polymerase chain reaction and probe-based nucleic acid detection have become increasingly popular in fish and shellfish diagnostics. Recently, a novel technique called loop-mediated isothermal amplification (LAMP) has been developed, which is highly sensitive and rapid. LAMP has been used for the detection of bacterial, viral, fungal and parasitic diseases in both animal and plants. In aquaculture, LAMP-based detection of pathogens like Edwardsiella tarda, E. ictaluri, Nocardia seriolae, Tetracapsuloides bryosalmonae, white spot syndrome virus and infectious haematopoietic necrosis virus have been reported. In this review, the application of LAMP for the detection of aquaculture-associated pathogens is discussed.
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Affiliation(s)
- R Savan
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - T Kono
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - T Itami
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - M Sakai
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
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Siqueira JF, Rôças IN. Exploiting Molecular Methods to Explore Endodontic Infections: Part 1—Current Molecular Technologies for Microbiological Diagnosis. J Endod 2005; 31:411-23. [PMID: 15917679 DOI: 10.1097/01.don.0000157989.44949.26] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Endodontic infections have been traditionally studied by culture-dependent methods. However, as with other areas of clinical microbiology, culture-based investigations are plagued by significant problems, including the probable involvement of viable but uncultivable micro-organisms with disease causation and inaccurate microbial identification. Innumerous molecular technologies have been used for microbiological diagnosis in clinical microbiology, but only recently some of these techniques have been applied in endodontic microbiology research. This paper intended to review the main molecular methods that have been used or have the potential to be used in the study of endodontic infections. Moreover, advantages and limitations of current molecular techniques when compared to conventional methods for microbial identification are also discussed.
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Affiliation(s)
- J F Siqueira
- Department of Endodontics, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil.
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Siqueira JF, Rôças IN, Rosado AS. Investigation of bacterial communities associated with asymptomatic and symptomatic endodontic infections by denaturing gradient gel electrophoresis fingerprinting approach. ACTA ACUST UNITED AC 2004; 19:363-70. [PMID: 15491461 DOI: 10.1111/j.1399-302x.2004.00170.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The purpose of the present study was to investigate the bacterial communities associated with asymptomatic and symptomatic endodontic infections and to compare denaturing gradient gel electrophoresis (DGGE) fingerprinting patterns of these two clinical conditions. The root canal microbiota of teeth associated with asymptomatic or symptomatic periradicular lesions was profiled by the PCR-DGGE method and then compared, taking into consideration the banding patterns. Bacteria were present in all examined cases. Comparative analysis of the two clinical conditions revealed bands that were common to both symptomatic and asymptomatic cases, but most DGGE bands appeared to be unique for each clinical condition. No single band occurred in all profiles. The mean number of bands detected in the 16S rDNA community profiles were 12.1 +/- 9.4 (range 2-29) for symptomatic samples and 6.7 +/- 2.7 (range 2-11) for asymptomatic ones. Clustering methods and principal component analysis of DGGE banding pattern placed the samples according to the presence or absence of symptoms. Four intense bands that were excised from the gel and sequenced showed similarities to species of the Campylobacter genus (found in 5/12 asymptomatic and in 3/11 symptomatic cases), Fusobacterium genus (4/11 symptomatic cases), Acinetobacter genus (5/12 asymptomatic cases), and Enterobacteriaceae family (11/12 asymptomatic and 2/11 symptomatic cases). The profiles of the predominant bacterial community appeared to be unique for each individual. These findings confirm that endodontic infections are polymicrobial and showed that there are significant differences in the predominant bacterial composition between asymptomatic and symptomatic cases.
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Affiliation(s)
- J F Siqueira
- Department of Endodontics, Estácio de Sá University, Rio de Janeiro, RJ, Brazil.
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Abstract
Molecular techniques are increasingly being used to study the ecology of a variety of organisms. These techniques represent important tools for the study of the systematics, population genetics, biogeography and ecology of parasites. Here, we review the techniques that have been employed to study the ecology and systematics of parasites (including bacteria and viruses). Particular emphasis is placed on the techniques of isoenzyme electrophoresis, in situ hybridisation and nucleic acid amplification to characterise parasite/microbial communities. The application of these techniques will be exemplified using ticks, bacterial endosymbionts and parasitic protozoa.
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Affiliation(s)
- Paul T Monis
- Microbiology Unit, Australian Water Quality Centre, Private Mail Bag 3, South Australia 5108, Salisbury, Australia.
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Gasser RB, Newton SE. Genomic and genetic research on bursate nematodes: significance, implications and prospects. Int J Parasitol 2000; 30:509-34. [PMID: 10731573 DOI: 10.1016/s0020-7519(00)00021-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular genetic research on parasitic nematodes (order Strongylida) is of major significance for many fundamental and applied areas of medical and veterinary parasitology. The advent of gene technology has led to some progress for this group of nematodes, particularly in studying parasite systematics, drug resistance and population genetics, and in the development of diagnostic assays and the characterisation of potential vaccine and drug targets. This paper gives an account of the molecular biology and genetics of strongylid nematodes, mainly of veterinary socio-economic importance, indicates the implications of such research and gives a perspective on genome research for this important parasite group, in light of recent technological advances and knowledge of the genomes of other metazoan organisms.
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Affiliation(s)
- R B Gasser
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria, Australia.
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Abstract
This review consists of 11 papers presented at the Consensus Conference on Cryptosporidium in Water (Parasitology Stream), held in Melbourne, Australia, from 5 to 6th October 1998. The conference was sponsored by the Water Services Association of Australia, the Australian Water and Wastewater Association, and the Collaborative Research Centre for Water Quality and Treatment. The papers summarise the advantages and disadvantages of various contemporary technologies applicable to parasite propagation and biochemical/molecular characterisation. Studies have detected distinct genetic differences between clinical isolates from humans and animals, and it is hoped that comprehensive documentation studies will facilitate the identification of environmental isolates in the not too distant future.
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Affiliation(s)
- R B Gasser
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
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Monis PT, Andrews RH. Molecular epidemiology: assumptions and limitations of commonly applied methods. Int J Parasitol 1998; 28:981-7. [PMID: 9673876 DOI: 10.1016/s0020-7519(98)00042-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An understanding of the epidemiology of a disease (i.e. its aetiology, transmission patterns) is crucial for the development and implementation of effective management practices. This requires sound epidemiological data. It is therefore important that scientists understand the assumptions and limitations of the methods used to gather such data. The aim of this paper is to discuss some of the assumptions and limitations of PCR-based methods used in studies of epidemiology. Since its development, PCR has had a major impact in the biological sciences. The ability to selectively amplify a specific region of the genome from a small amount of DNA makes this technique particularly useful as a diagnostic tool. A variety of PCR-based methods are available which can be used to identify strains and species of parasites. Some of these methods, such as random amplification of polymorphic DNA, have intrinsic properties which can limit their application. Other methods, such as PCR-restriction fragment length polymorphism, require the availability of a sound taxonomic or genetic framework for the development of any diagnostic system for a particular organism. The problems encountered developing diagnostic probes in the absence of such a framework will be discussed using Giardia intestinalis as an example.
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Affiliation(s)
- P T Monis
- Department of Microbiology and Immunology, University of Adelaide, Australia.
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