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GeneCalling: Transcript Profiling Coupled to a Gene Database Query

We describe the GeneCalling method for the discovery of differentially expressed genes, both known and novel, from any species including useful sequence information to determine the potential function of novel genes captured. The method relies on transcript visualization coupl ...

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Gene Expression Informatics

There are many methodologies for performing gene expression profiling on transcripts, and through their use scientists have been generating vast amounts of experimental data. Turning the raw experimental data into meaningful biological observation requires a number of proces ...

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Small Amplified RNA-SAGE

Serial analysis of gene expression (SAGE) is a powerful genome-wide analytic tool to determine expression profiles. Since its description in 1995 by Victor Velculescu et al.1, SAGE has been widely used. Recently, the efficiency of the method has been emphasized as a means to identify novel tran ...

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Standardized RT-PCR and the Standardized Expression Measurement Center

Standardized reverse transcriptase polymerase chain reaction (StaRT-PCR) is a modification of the competitive template (CT) RT method described by Gilliland et al. StaRT-PCR allows rapid, reproducible, standardized, quantitative measurement of data for many genes simultan ...

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Suppression Subtractive Hybridization

Suppression subtractive hybridization (SSH) is a widely used method for separating DNA molecules that distinguish two closely related DNA samples. Two of the main SSH applications are cDNA subtraction and genomic DNA subtraction. In fact, SSH is one of the most powerful and popular methods f ...

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Technical Considerations in Quantitating Gene Expression

Scientists routinely lecture and write about gene expression and the abundance of transcripts, but in reality, they extrapolate this information from a variety of measurements that different technologies may provide. Indeed, there are many reasons that applying different techno ...

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Quantitative and Discriminative Detection of Individual HIV-1 mRNA Subspecies by an RNase Mapping Assay

In addition to the Gag, Pol, and Env structural proteins, HIV-1 encodes at least six regulatory proteins: Tat, Rev, Nef, Vif, Vpr, and Vpu. All HIV-I proteins are encoded by overlapping reading frames and are expressed through the complex alternative splicing of a single precursor RNA leading to three m ...

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PCR Analysis for the Identification of Porcine Reproductive and Respiratory Syndrome Virus in Boar Semen

In 1987, a disease syndrome characterized by reproductive and respiratory symptoms in pigs was first described in the United States (1). Late-term abortions, increased numbers of stillborn and weak pigs, poor conception in breeding herds, along with respiratory distress and high morta ...

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PCR Diagnosis of the Bovine Immunodeficiency-Like Virus

The bovine immunodeficiency-like virus (BIV), also known as the bovine lentivirus or the bovine immunodeficiency virus, causes a persistent viral infection of cattle, and is found in cattle populations around the world (1,2). A closely related lentivirus, Jembrana disease virus, causes ...

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Measurement of TNF and iNOS mRNA Using cDNA-Equalized Reverse Transcriptase PCR

Since the polymerase chain reaction (PCR) for DNA amplification was first introduced in 1985 (1), the combination of reverse transcription with subsequent PCR amplification of the cDNA (RT-PCR) has been an increasingly utilized technique to analyze gene expression (2,3). In order for this ...

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Prenatal and Presymptomatic Diagnosis of Marfan Syndrome Using Fluorescence PCR and an Automated Sequencer

The Marfan syndrome (MFS) is an autosomal dominant heritable connective tissue disorder characterized by variable and pleiotropic manifestations primarily in the skeletal, ocular, and cardiovascular systems (1). Molecular defects in fibrillin-1, a 350 kDa glycoprotein, enco ...

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Detection of Rodent Parvoviruses by PCR

The rodent parvoviruses include mouse parvovirus (MPV), minute virus of mice (MVM), H-1 parvovirus (H-1), Kilham rat virus (KRV), rat parvovirus (RPV), and hamster parvovirus (HaPV). Recent reports suggest LuIII, an autonomous parvovirus of unknown host origin, may also belong to the rodent pa ...

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PCR Fingerprinting for Detection of Deleted or Amplified Sequences in Human Cancer

Genomic fingerprinting is one of several methods for screening human genome to identify genetic alterations in cancer cells. Arbitrarily primed polymerase chain reaction (AP-PCR) is a PCR-based genomic fingerprinting method (1). In AP-PCR, a single oligonucleotide is used to initia ...

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Detection of Transgene Integrants and Homologous Recombinants in Mice by Polymerase Chain Reaction

The use of genetically altered mice in research has increased exponentially since the production of the first transgenic mouse 15 yr ago. Within the past decade, the technique of targeted mutagenesis in mice has seen a similar rapid expansion in use, becoming a strategy widespread throughout a ...

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Detection and Isolation of Differentially Expressed Genes by PCR

The approx 3�109 basepairs that comprise a human genome are believed to contain at least 100,000 different genes (1). Many of these genes and the proteins that they encode have been isolated and identified, but the vast majority of these genes have yet to be characterized. A typical mammalian cell is bel ...

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Detection of Chlamydia trachomatis and Trichomonas vaginalis in the Vaginal Introitus, Posterior Vagina, and Endocervix by Polymerase Chain Reaction

Chlamydia trachomatis, an obligate intracellular bacterium, and Trichomonas vaginalis, a protozoan, are two of the most prevalent sexually transmitted pathogenic microorganisms worldwide. C. trachomatis is a major cause of pelvic inflammatory disease, occluded fallopian ...

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The Use of Flow Cytometry and RT-PCR in the Detection of Circulating PSA-Positive Cells in Prostate Cancer

Prostate cancer is the most common malignancy diagnosed in men in the Western hemisphere. Once early tumors are detected, prognosis is largely unpredictable, and clinicians are currently unable to inform the patient whether his tumour is likely to progress. New criteria to define the aggre ...

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Rapid Diagnosis of Pulmonary Tuberculosis Using Roche AMPLICOR™ Mycobacterium tuberculosis PCR Test

The rapid diagnosis of infectious diseases, particularly those because of their communicability present a public health problem, is the objective of the clinical microbiologist and the practicing physician. The need to attain this goal is exemplified by the resurgence of tuberculo ...

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PCR Detection of Toxoplasma gondii in Human Fetal Tissues

Primary acquisition of Toxoplasma gondii (T. gondii) in healthy male and female adults is usually an asymptomatic infection (toxoplasma infection) or results in a harmless disease (toxoplasmosis) with nonspecific symptoms including headache, myalgia, fatigue, or a flu-like cond ...

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Quantitative Measurement of mRNA Expression by Competitive RT-PCR

As a method of specific mRNA detection, the single most important advantage of RT-PCR is its sensitivity, because of the remarkable sensitivity of PCR. Isolation of polyA+ mRNA is unnecessary, and minute amounts of total RNA suffice. If random primers are used in the reverse transcription react ...

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