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Polymerase Chain Reaction

Polymerase chain reaction (PCR) is a powerful technology that amplifies specific DNA sequences exponentially, enabling researchers to study and analyze genetic material with unprecedented precision.
This revolutionary technique involves the cyclical replication of DNA fragments, driven by a heat-stable DNA polymerase enzyme.
PCR has transformed fields such as molecular biology, genetics, diagnostics, and forensics, allowing for highly sensitive and specific detection of genetic targets.
With its ability to generate millions of copies from a single DNA molecule, PCR has become an indispensable tool for a wide range of applications, from disease diagnostics to evolutionary studies.
The simplicity, speed, and versatility of PCR have made it a foundational technique in modern biomedical research and clinical practice.

Most cited protocols related to «Polymerase Chain Reaction»

A main limitation of efficiency calibrated method and ΔΔCt method is that only one set of cDNA samples are employed to determine the amplification efficiency. It was assumed that the same amplification efficiency could be applied to other cDNA samples as long as the primers and amplification conditions are the same. However, amplification efficiency not only depends on the primer characteristics, but also varies among different cDNA samples. Using a standard curve for only one set of tested samples to derive the amplification efficiency might overlook the error introduced by sample differences. In our experimental design, we have performed standard curve experiments with four concentrations of three replicates for all samples and genes involved. The ΔΔCt will derive from the standard curves only, and the data quality is examined for each gene and sample combination. The analysis of two samples is presented in the paper as an example. A minimal of PCRs of two replicates in three concentrations will be required for each sample. Even though more effort is required, the data is more reliable out of stringent data quality control and data analysis based on statistical models.
The output dataset included Ct number, gene name, sample name, concentration and replicate. We used Microsoft® Excel to open the exported Ct file from an ABI 7000 sequence analysis system and then to transform data into a tab delimited text file for SAS processing. The sample data set is shown in Table 1.
All programs were developed with SAS 9.1 (SAS Institute).
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Publication 2006
DNA, Complementary DNA Replication Genes Oligonucleotide Primers Polymerase Chain Reaction
HaploGrep 2 is a web application that communicates through a REST API with the web server. Thus, all computation intensive tasks are executed directly on the server. The haplogroup classification itself is based on pre-calculated phylogenetic weights that correspond to the occurrence per position in Phylotree and reflecting the mutational stability of a variant. In the updated classification algorithm, the weights are now scaled from 1 to 10 in a non-linear way (see Supplementary Table S1). Thus, the rare occurrences of variants in Phylotree will no longer influence the classification toward those haplogroups as much as in the previous version. Once the data is imported, the haplogroup classification is started automatically. Optimizations within the code led to a 20-fold speed-up compared to HaploGrep 1. By storing only the 50 highest ranked haplogroups per sample the memory consumption could be reduced significantly.
Furthermore, new dissimilarity metrics for the mtDNA haplogroup classification were introduced. In addition to the already implemented Kulczynski distance (1 (link)), the Jaccard index, the Hamming distance and the Kimura 2-parameter distance were included (24 ) (see Supplementary Table S2 and 3 for performance comparison). Further major improvements included a check for artificial recombination (25 (link)) and a check for systematic artefacts and for rare or potential phantom mutations (26 (link)). For detecting artificial recombination, we apply two different strategies: the first strategy, proposed by Kong et al. (27 (link)), counts the remaining variants that were not assigned to the resulting best haplogroup, and tests whether these variants could be assigned to another haplogroup. For this step, mutational hotspots are excluded (e.g. 315.1C or 16519). The second recombination strategy assumes prior knowledge about the specific placement of the fragments of the polymerase chain reaction products (amplicons). With this information in hand, a check comparing the profiles relative to the fragment ranges can be executed. The user-defined fragments are generated, and the profiles split accordingly. If the distance of both haplogroup fragments exceeds five phylogenetic nodes, the sample is listed as potentially contaminated.
Publication 2016
DNA, Mitochondrial Memory Mutation Polymerase Chain Reaction Recombination, Genetic
The ongoing rapid cost reduction of Illumina paired-end sequencing has resulted in the increasingly common use of this technology for a wide range of genomic studies, and the volume of such data is growing exponentially. Generating high-quality variant calls from raw sequence data requires numerous data processing steps using multiple tools in complex pipelines. Typically, the first step in this analysis is the alignment of the sequence data to a reference genome, followed by the removal of duplicate read-pairs that arise as artifacts either during polymerase chain reaction amplification or sequencing. This is an important pipeline step, as failure to remove duplicate measurements can result in biased downstream analyses.
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Publication 2014
Genome Polymerase Chain Reaction Sequence Alignment
Four lower respiratory tract samples, including bronchoalveolar-lavage fluid, were collected from patients with pneumonia of unknown cause who were identified in Wuhan on December 21, 2019, or later and who had been present at the Huanan Seafood Market close to the time of their clinical presentation. Seven bronchoalveolar-lavage fluid specimens were collected from patients in Beijing hospitals with pneumonia of known cause to serve as control samples. Extraction of nucleic acids from clinical samples (including uninfected cultures that served as negative controls) was performed with a High Pure Viral Nucleic Acid Kit, as described by the manufacturer (Roche). Extracted nucleic acid samples were tested for viruses and bacteria by polymerase chain reaction (PCR), using the RespiFinderSmart22kit (PathoFinder BV) and the LightCycler 480 real-time PCR system, in accordance with manufacturer instructions.12 (link) Samples were analyzed for 22 pathogens (18 viruses and 4 bacteria) as detailed in the Supplementary Appendix. In addition, unbiased, high-throughput sequencing, described previously,13 (link) was used to discover microbial sequences not identifiable by the means described above. A real-time reverse transcription PCR (RT-PCR) assay was used to detect viral RNA by targeting a consensus RdRp region of pan β-CoV, as described in the Supplementary Appendix.
Publication 2020
Bacteria Biological Assay Bronchoalveolar Lavage Fluid Nucleic Acids Pathogenicity Patients Pneumonia Polymerase Chain Reaction Real-Time Polymerase Chain Reaction Respiratory System Reverse Transcription RNA, Viral Seafood Virus
Fifty to 100 ml of clonal culture were filtered onto 25 mm, 5 μm pore size, polycarbonate membrane filters (Millipore) for DNA extraction using either the DNeasy Plant Mini Kit (Qiagen) or the Easy-DNA Kit (Invitrogen), following manufacturer instructions. The internal transcribed spacer sequence 1 (ITS1) was polymerase chain reaction (PCR)-amplified with primers 1645F and Dit5.8sR as described in [30 ]. Products from six amplification reactions were pooled and purified in one of two ways. The pooled PCR product was either directly purified using the High Pure PCR Product Purification Kit (Roche Applied Science) or electrophoresed in 1% agarose gels and bands of the appropriate size were excised and extracted from the agarose with the QIAquick Gel Extraction Kit (Qiagen). The resulting fragments were sequenced using primers 1645F and Dit5.8sR with the DYEnamic ET Terminator Cycle Sequencing Kit (GE Healthcare Bio-sciences Corp., New Jersey) and analyzed on a MegaBACE 1000 automated sequencer (GE Healthcare Biosciences Corp., New Jersey). Sequences were assigned to a population by aligning them to two type-sequences [Genbank: DQ329268] (population 1; ITS1-1) and [Genbank: DQ329270] (population 2; ITS1-2). Genbank accession numbers for ITS1 sequences from our study are [Genbank: GQ370472-GQ370503].
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Publication 2010
Clone Cells Oligonucleotide Primers Plants polycarbonate Polymerase Chain Reaction Sepharose Tissue, Membrane

Most recents protocols related to «Polymerase Chain Reaction»

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Example 4

Syphilis is an STI that can cause long-term complications if not treated correctly. Symptoms in adults are divided into stages. These stages are primary, secondary, latent, and late syphilis. In pregnant women, having syphilis can lead to giving birth to a low birth weight baby. It can also lead to delivering the baby too early or stillborn (CDC fact sheet, 2015).

Although T. pallidum cannot be grown in culture, there are many tests for the direct and indirect diagnosis of syphilis. Still, there is no single optimal test. Direct diagnostic methods include the detection of T. pallidum by microscopic examination of fluid or smears from lesions, histological examination of tissues or nucleic acid amplification methods such as polymerase chain reaction (PCR). Indirect diagnosis is based on serological tests for the detection of antibodies (Ratnam S, Can J Infect Dis Med Microbiol 2005). Treatment includes a single dose of intramuscular administration of penicillin (2.4 Million units).

In some embodiments, the disclosed device can be used to detect syphilis infections from menstrual blood or cervicovaginal fluids.

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Patent 2024
Adult Antibodies BLOOD Childbirth Diagnosis Globus Pallidus Infant Infection Medical Devices Menstruation Microscopy Nucleic Acid Amplification Techniques Penicillins Polymerase Chain Reaction Pregnant Women Syphilis Syphilis, tertiary Tests, Serologic Tissues

Example 56

Escherichia coli Nissle 1917 (E. coli Nissle) and engineered derivatives test positive for a low level presence of phage 3 in a validated bacteriophage plaque assay. Bacteriophage plaque assays were conducted to determine presence and levels of bacteriophage. In brief, supernatants from cultures of test bacteria that were grown overnight were mixed with a phage-sensitive indicator strain and plated in soft agar to detect the formation of plaques, indicative of the presence of bacteriophage. Polymerase chain reaction (PCR) primers were designed to detect the three different endogenous prophages identified in the bioinformatics analyses, and were used to assess plaques for the presence of phage-specific DNA.

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Patent 2024
Agar Bacteria Bacteriophage Plaque Assay Bacteriophages derivatives Escherichia coli Oligonucleotide Primers Polymerase Chain Reaction Prophages Senile Plaques Strains
The samples were received in ethylenediaminetetraacetate (EDTA) tubes. According to the manufacturer’s instructions, DNA was extracted using the GeneJET Whole Blood Genomic DNA Purification Mini Kit (Thermofisher, Paisley, United Kingdom). The purified DNA was assessed for quality and quantity using NanoDrop 200 spectrophotometer (Thermofisher, Paisley, United Kingdom). Using standard polymerase chain reaction (PCR) techniques, a primer was used to capture the single nucleotide variant corresponding to the UCP2−866 G/A polymorphism (rs659366). In brief, 50 ng of DNA template was mixed with 0.5 µM of each of forward (5’ CAC GCT GCT TCT GCC AGG AC 3’) and reverse (5’ AGG CGT CAG GAG ATG GAC CG 3’) primers in a volume of 12.5 µL of sterile water. To make a total volume of 25 L, the mixture was mixed with an equal volume (12.5 µL) of the 2X PCR master mix (Phusion Green Host Start II High-Fidelity PCR Master Mix) (Thermo Fisher Scientific, Paisley, UK). The following thermal profile was used for the PCR amplification: Initial denaturation at 95°C for 4 minutes, then 35 cycles of denaturation at 94°C for 30 seconds, annealing at 58°C for 30 seconds, and elongation at 72°C for 30 seconds, followed by a 10-minute final extension step at 72°C. PCR products were digested by Mlu I restriction enzyme (NEB, Ipswich, MA, USA) and separated on 2% agarose gel electrophoresis. Due to the lack of a Mlu I site, the (−866)A/A genotype was identified by a single 363 bp fragment, whereas the wild-type (−866)G/G genotype was digested into 295 bp and 68 bp fragments.12 (link),14 (link)
Publication 2023
BLOOD DNA Restriction Enzymes Electrophoresis, Agar Gel Genetic Polymorphism Genome Genotype Neoplasm Metastasis Nucleotides Oligonucleotide Primers Polymerase Chain Reaction Sterility, Reproductive
Figure 1 shows a directed acyclic graph (DAG) of factors associated with pregnancy and dengue severity. Analysis was restricted to women of their reproductive age and defined by an age range of 15 to 49 years [15 ]. At each municipality clinic, women presenting with febrile illness characteristic of dengue fever were further tested for dengue antigens. An individual was defined as having dengue if she had a clinical diagnosis of DF and there was laboratory-confirmed evidence of non-structural protein (NS1) of DENV or a positive immunoglobulin M (IgM). DENV serotypes were determined based on polymerase chain reaction RT-qPCR results [16 ]. An individual with confirmed dengue had either DENV-1, DENV-2, DENV-3, or DENV-4 serotype. An individual with dengue was reported as having non-severe dengue, severe dengue, dengue without warning signs, dengue with warning signs, or ‘other’. Individuals with no dengue classification or ‘other’ classification were excluded from the analysis. The World Health Organization’s revised 2009 classification of DF emphasizes the inclusion of warning signs as a diagnostic criterion for probable and potentially severe dengue [17 (link)]. However, this classification requires laboratory-confirmed results to prevent inflation of the number of severe dengue cases. Because our dataset contained both clinical and laboratory-confirmed diagnoses, severe dengue was defined as individuals with severe dengue or having dengue with warning signs, while non-severe dengue was defined as individuals ‘having non-severe dengue or dengue without warning signs’. A woman was identified as pregnant or not pregnant based on pregnancy status classification retrieved from the dataset. Region was categorized as Center, Center West, Northeast, Northwest, and Southeast. Classification of the region has been defined elsewhere [18 (link)]. Hypertension and Diabetes were binary variables with ‘1’ indicating the presence of disease and ‘0’ indicating the absence of disease.

A directed acyclic graph of factors associated with pregnancy and dengue severity

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Publication 2023
A-factor (Streptomyces) Antigens Dengue Fever Diabetes Mellitus Diagnosis factor A Fever High Blood Pressures Immunoglobulin M Polymerase Chain Reaction Pregnancy Proteins Reproduction Severe Dengue Woman
The GSE59867 dataset, based on the GPL6244 platform, was published by Maciejak et al. [25 (link)] and was used as the independent external validation set, including 111 patients with AMI at admission and 46 patients with stable coronary artery disease. The “limma” package was used to normalize the gene expression profiles [26 (link)].
Whole blood samples were collected from five AMI patients and five normal patients for real-time quantitative polymerase chain reaction (qPCR) to confirm the results. The study was approved by the Ethics Committee of Jiangxi Provincial People’s Hospital, and all patients signed informed consent forms. All patient samples were processed to isolate peripheral blood mononuclear cells immediately after collection and stored at −80°C before RNA extraction. After the samples were pretreated, RNA was extracted using TRIzol reagent (Invitrogen), and qPCR was performed. Total RNA was reverse transcribed into complementary DNA by a qPCR real-time kit (Invitrogen) following the manufacturer’s instructions. Relative gene expression was analyzed by the 2−ΔΔCT method with normalization to ACTB (internal reference gene). All primers used in this study are shown in Table 1. Data are presented as the mean ± standard deviation. GraphPad Prism 8 software (GraphPad Software, CA) and R software were used for statistical analyses. Analysis of variance or a t test was used for statistical comparisons. P < 0.05 was considered significant.
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Publication 2023
BLOOD Coronary Artery Disease DNA, Complementary Ethics Committees, Clinical Gene Expression Genes Oligonucleotide Primers Patients PBMC Peripheral Blood Mononuclear Cells Polymerase Chain Reaction prisma Real-Time Polymerase Chain Reaction trizol

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More about "Polymerase Chain Reaction"

Polymerase Chain Reaction (PCR) is a revolutionary DNA amplification technique that has transformed numerous fields, including molecular biology, genetics, diagnostics, and forensics.
This powerful tool, also known as qPCR, RT-PCR, and digital PCR, exponentially replicates specific DNA sequences, enabling researchers to study and analyze genetic material with unprecedented precision.
PCR involves the cyclical replication of DNA fragments, driven by a heat-stable DNA polymerase enzyme, such as Taq polymerase.
This process allows for the generation of millions of copies from a single DNA molecule, making it an indispensable technique for a wide range of applications.
PCR has become a foundational technique in modern biomedical research and clinical practice, with its simplicity, speed, and versatility.
It is commonly used in conjunction with other molecular biology tools, such as TRIzol reagent for RNA extraction, the RNeasy Mini Kit for purifying RNA, the QIAamp DNA Mini Kit for DNA extraction, and the MiSeq platform for high-throughput sequencing.
Reverse transcription PCR (RT-PCR) is a variant of PCR that allows for the detection and quantification of RNA by first converting it into complementary DNA (cDNA) using enzymes like the High-Capacity cDNA Reverse Transcription Kit or the PrimeScript RT reagent kit.
Additionally, the QIAamp DNA Blood Mini Kit and the DNeasy Blood and Tissue Kit are widely used for DNA extraction from various biological samples.
With the power of PCR, researchers can now explore a wide range of applications, from disease diagnostics and genetic profiling to evolutionary studies and forensic investigations.
The ongoing advancements in PCR technology, such as the development of digital PCR, continue to push the boundaries of what is possible in the field of molecular biology and beyond.