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Dr.T.V.Rao MD
Genotyping Methods
Genetic methods generally seek to detect polymorphisim at the level of nucleic acid Genotypes are more specific, more easily quantified and standardized among the different organisms
Basic requirement
The genome is unique in each individual Ultimate discriminatory step would be to sequence the entire genome of every organism, but not practical or economical
What is Practicable
Several methods in detecting nuclei acid polymorphisim in a chosen genetic marker are commonly used to target the genome or organism.
Restriction Endonuleases
It was discovered that a type of bacterial enzyme was found to have the ability to cut DNA in a test tube. These restriction endonulease, so named because they cut double stranded DNA at restricted sites, were discovered as a natural part of the bacterial machinery.
Restriction endonulease EcoRI cuts doublestranded DNA and generates sticky ends.
Genetic markers are nucleotide sequences within the genome that are polymorphic (with differences) between strains of the same organisms
Choice of Markers
Markers depend on Type of study, Recent outbreak Rapid evolving markers. Markers related to evolution of organism over years require more stable markers
Kary Mullis shared the 1993 Nobel Prize in Chemistry with Michael Smith. Mullis received the prize for his development of the Polymerase Chain Reaction (PCR)
A process first described by Kjell Kleppe and 1968 Nobel laureate H. Gobind Khorana that allows the amplification of specific DNA sequences. The improvements provided by Mullis have made PCR a central technique in biochemistry and molecular biology
Almost all PCR applications employ a heat-stable DNA polymerase, such as Taq polymerase, an enzyme originally isolated from the bacterium Thermus aquaticus.
This DNA polymerase enzymatically assembles a new DNA strand from DNA building blocks, the nucleotides, by using single-stranded DNA as a template and DNA Oligonucleotide (also called DNA primers), which are required for initiation of DNA synthesis.
Molecular detection has mostly come to the clinical microbiology laboratory in the form of PCR technology, initially involving single round or nested procedures with detection by gel electrophoresis.
Polymerase chain reaction (PCR) techniques have led the way into this new era by allowing rapid detection of microorganisms that were previously difficult or impossible to detect by traditional microbiological methods.
With the advent of multiplex PCR, realtime PCR and improvements in efficiency through automation, the costs of molecular methods are decreasing such that the role of molecular methods will further increase.
Molecular methods have now progressed beyond identification to detect antimicrobial resistance genes and provide public health information such as strain characterisation by genotyping.
Nucleic acid-based tests used in diagnosing infectious diseases use standard methods for isolating nucleic acids from organisms and clinical material and restriction endonulease enzymes, gel electrophoresis, and nucleic acid hybridization techniques to analyze DNA or RNA
Fairly recently, a new method of PCR quantification has been invented. This is called real-time PCR because it allows the scientist to actually view the increase in the amount of DNA as it is amplified.
The Real Time assays are proving to better technologies 1 Rapid 2 Quantitative measurement 3 Lower contamination rate 4 Higher sensitivity 5 Higher specificity 6 Easy standardization Now a new gold standard for rapid diagnosis of virus infection in the acute phase samples.
RT - PCR
Proving to be Accurate Precise Easy to perform RT PCR technologies are easy to transfer research Laboratory protocols to Diagnostic Laboratories
OVERVIEW of RT - PCR
tissue
extract RNA
All real time PCR systems rely upon the detection and quantization of fluorescent reporter, the signal of which increases in direct proportion of the amount of PCR product in a reaction.
The simplest and economical format the reporter is the double strand DNA specific dye SYBR Green Called as Molecular Probe.
Limitations of SYBERGreen
Advantages
Inexpensive Easy to Use Sensitive
Disadvantages
SYBR green will bind to any double stranded DNA in a reaction, may result in an overestimation of the target concentration
Two most popular alternatives to SYBR green are TaqMan and Molecular Beacons. Both technologies depend on hybridization probes relying on fluorescence resonance energy transfer.( FRET) and quantization
TaqMAN
TaqMAN Sequencing
TaqMAN probes
Documentation of Amplification
The light emitted from the dye in the excited state is received by a computer and shown on a graph display, such as this, showing PCR cycles on the Xaxis and a logarithmic indication of intensity on the Y-axis.
Molecular Beacons
Molecular Beacons Uses FRET Fluorescence Resonance Energy Transfer Uses two sequence specific Oligonucleotide labelled with fluorescent dyes
Molecular beacons are designed to adopt a hairpin structure while free in solution, brining the fluorescent dye and quencher in close proximity. When a molecular beacon hybridizes to a target the fluorescent dye emits light upon irradiation, and rebind to target in every cycle for signal measurement.
LAMP
Amplification and detection of gene can be completed in a single step, by incubating the mixture of samples, primers DNA polymerase with strand displacement activity and substrates at a constant temperature of 630c.
LAMP
Compared with PCR, and real time PCR, the LAMP has advantages of reaction simplicity and detection sensitivity. The higher sensitivity and specificity of LAMP reaction is attributed to continuous amplification under isothermal condition employing six primers recognizing eight distinct regions of the target.
Advantages of LAMP
LAMP functions on isothermal amplification. LAMP does not require any thermal cycler and thus cane be performed even with water bath/heating block LAMP method do not require sophisticated temperature control devices Cost effective
In LAMP both amplification and detection occur simultaneously during the exponential phase without going through the plateau phase where the non spurious amplification leads to lower sensitivity and false positivity.
A one step single tube real time accelerated reverse transcription loop mediated isothermal amplification (RT-LAMP) assays for rapid detection of some recently emerged viral pathogen eg West Nile, SARS, Dengue, Japanese encephalitis Chikungunya Norwalk, H5N1 highly pathogenic avian influenza., and CMV,HPV,VZV
Multiplex PCR
TaqMan probes and Molecular beacons allow multiple DNA species to be measured in the same sample ( Multiplex PCR) since fluorescent dyes with different emission spectra may be attached to different probes
Multiplex real time quantitative RT-PCR assays have been developed for simultaneous detection identification and quantification of HBV, HCV and HIV-! In plasma and Serum samples.
Molecular beacons are short segments of single-stranded DNA (Figure 1). The sequence of each molecular beacon must be customized to detect the PCR product of interest.
Molecular methods are necessary if the traditional methods provide poor results
Microscopy gives false positive results - T.vaginalis, N.gonorrhoeae Intracellular pathogens viruses, M.genitalium Low sensitivity Chlamydia sp.,Neisseria sp. Seropositivity is common Chlamydia sp. Subtyping is mandatory HSV, HPV, HCV Microbial growth is slow M. tuberculosis
Directly
Sybr green Quality of primers critical
Indirectly
In addition to primers, add a fluorescently labeled hybridization probe Many different approaches to this, see Bustin
Importance of controls
Positive control
checks that reagents and primers work especially importance if trying to show absence of expression of a gene
Standards
Same copy number in all cells Expressed in all cells Medium copy number advantageous
Reasonably large introns No pseudo gene No alternate splicing in region you want to PCR
Quantitation of gene expression Pathogen detection Viral quantitation Array verification Drug therapy efficacy DNA damage measurement Quality control and assay validation Genotyping
QC & QA
Quality control & assurance
DNA preparation
No alternative
Laboratory Thermocycler Detection Documentation
Mixing site
Amplification
Clean room
R&D
(Research and development)
Stock solutions
The QIAGEN One Step RT-PCR Kit is designed for easy and sensitive one-step RT-PCR using any RNA template. A unique enzyme combination and specially developed reaction buffer ensure efficient reverse transcription and PCR in one tube.
RobusT RT-PCR Kits perform cDNA synthesis and PCR amplification of cDNA successively in a single tube during a continuous thermal cycling
Advantages
Molecular methods
High sensitivity and specificity Detects pathogen, not immune response Quick results High transport toleration
To perform PCR for the repetitive detection of a specific sequence, three distinct laboratory areas are required. The specific technical operations, reagents ,and personnel considerations
PCR contamination be considered as a form of infection. If standard sterile techniques that would be applied to tissue culture or microbiological manipulations are applied to PCR, then the risk of contamination will be greatly reduced. Above all else, common sense should prevail.
Avoiding contamination
The single most important source of PCR product contamination is the generation of aerosols of PCR amplicons that is associated with the post-PCR analysis. Methods for eliminating this aerosol range from physical design of laboratories and use of specific pipettes to chemical and enzymatic approaches. The choice of method is often dependent on the frequency of amplification of a target amplicon and the relative amounts and concentrations of the amplicons created by the PCR.