Fabrication of 3D continuous-flow reverse-transcription polymerase chain reaction microdevice integrated with on-chip fluorescence detection for semi-quantitative assessment of gene expression.

We fabricate a three-dimensional (3D) microdevice operated with minimal peripheral accessories, including a portable pump for semi-automated sample delivery and a single heater for temperature control, for performing reverse transcription polymerase chain reaction (RT-PCR) integrated with a downstream fluorescence detection module for semi-quantitative assessment of gene expression. The microdevice was fabricated by wrapping a polytetrafluoroethylene (PTFE) tube around a pre-designed polycarbonate mold to create a seamless microchannel for both the reverse transcription (RT) of RNA and the amplification of complementary DNA. In addition, a silicone tube, which underwent a two-step surface modification mediated by polyethyleneimine and glutaraldehyde coating, was connected at the outlet to capture amplicons downstream of the PTFE tube for on-site fluorescence detection. This fabrication method enabled continuous-flow RT-PCR (CF RT-PCR) using the 3D CF RT-PCR microdevice as a reactor, a single heater for the temperature control of both RT and PCR processes, and a disposable plastic syringe for semi-automated sample delivery. The microdevice was successfully implemented for the identification of the ß-actin gene, a constitutively expressed gene in all cells, and the sphingosine-1-phosphate lyase 1 gene, a potential pharmacological target gene in the diagnosis of cancer, diabetes, and atherosclerosis. This portable integrated microdevice offers a potential approach towards preliminary studies of gene expression and identification of RNA viruses.

RT-PCR and real-time RT-PCR methods for the detection of potato virus Y in potato leaves and tubers.

Potato virus Y (PVY) is a major threat to potato crops around the world. It is an RNA virus of the family Potyviridae, exhibiting many different strains that cause a range of symptoms in potato. ELISA detection of viral proteins has traditionally been used to quantify virus incidence in a crop or seed lot. ELISA, however, cannot reliably detect the virus directly in dormant tubers, requiring several weeks of sprouting tubers to produce detectable levels of virus. Nor can ELISA fully discriminate between the wide range of strains of the virus. Several techniques for directly detecting the viral RNA have been developed which allow rapid detection of PVY in leaf or tuber tissue, and that can be used to easily distinguish between different strains of the virus. Described in this chapter are several protocols for the extraction of RNA from leaf and tuber tissues, and three detection methods based upon reverse-transcription-PCR (RT-PCR). First described is a traditional two-step protocol with separate reverse transcription of viral RNA into cDNA, then PCR to amplify the viral cDNA fragment. Second described is a one-step RT-PCR protocol combining the cDNA production and PCR in one tube and one step, which greatly reduces material and labor costs for PVY detection. The third protocol is a real-time RT-PCR procedure which not only saves on labor but also allows for more precise quantification of PVY titre. The three protocols are described in detail, and accompanied with a discussion of their relative advantages, costs, and possibilities for cost-saving modifications. While these techniques have primarily been developed for large-scale screening of many samples for determining viral incidence in commercial fields or seed lots, they are also amenable to use in smaller-scale research applications.

American ginseng (Panax quinquefolius) administration does not affect performance of the Roche COBAS Ampliprep/Taqman HIV-1 RNA assay.

BACKGROUND: Previous data indicate that purified components of ginseng can inhibit HIV reverse transcriptase in vitro, suggesting that ginseng components in plasma may interfere with HIV-1 RNA detection assays. METHODS: Pre- and post-dose plasma from three volunteers dosed with 3000 mg American ginseng was spiked with HIV and analyzed by the Roche COBAS Ampliprep/Taqman v2.0 HIV-1 RNA assay. RESULTS: Presence of American ginseng had no significant effect on measured HIV-1 RNA concentration. Variation within pre- and post-dose plasma pair was insignificant and within assay performance limits. CONCLUSION: Plasma from subjects dosed with 3000 mg American ginseng does not interfere with the Roche COBAS Ampliprep/Taqman v2.0 HIV-1 RNA assay. This implies that in vitro inhibition of HIV reverse transcriptase by American ginseng components is unlikely to be clinically relevant.

A rapid detection method for the ryanodine receptor 1 (C7360G) mutation in Quarter Horses.

BACKGROUND: Anesthetic-induced malignant hyperthermia has been documented in Quarter Horses and is caused by a single-point mutation in the ryanodine receptor 1 gene at nucleotide C7360G generating a R2454G amino acid substitution. An accurate, faster molecular test that is less prone to contamination would facilitate screening for the mutation in horses intended for breeding, in those undergoing surgical procedures, and in those with clinical signs compatible with malignant hyperthermia. OBJECTIVE: To report a rapid and accurate method for the detection of the ryanodine receptor 1 C7360G mutation. ANIMALS: Eleven diseased, 10 healthy, and 225 randomly selected Quarter Horses. METHODS: This study included horses with the ryanodine receptor 1 C7360G mutation as detected by gene sequencing. Available genomic and complementary DNA extracted from whole blood, hair or skeletal muscle was used for genetic analysis. Real-time polymerase chain reaction (RT-PCR) melting curve analysis was performed by equine specific primers and 2 hybridization probes (sensor and anchor probes) that contain the site of the mutation. Results from this method were blinded and compared with nucleic acid sequencing for validation. RESULTS: A rapid genotyping assay with fluorescence resonance energy transfer probes and melting curve analysis was accurate (100% agreement, K= 1) for identification of affected horses. The prevalence of the mutation in a random population of Quarter Horses was 1.3%. CONCLUSIONS AND CLINICAL IMPORTANCE: Malignant hyperthermia in Quarter Horses can be rapidly and accurately detected by RT-PCR melting curve genotyping with hybridization probes.

Simultaneous detection and identification of four pome fruit viruses by one-tube pentaplex RT-PCR.

A pentaplex reverse-transcription polymerase chain reaction (Pentaplex RT-PCR) in a single tube was developed for the simultaneous detection of the pome fruit viruses: Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV), Apple chlorotic leaf spot virus (ACLSV) and Apple mosaic virus (ApMV). This is the first report of the simultaneous detection of all four viruses and host mRNA as an internal specific control. Pentaplex RT-PCR was applied successfully throughout the year, using different plant organs (leaves or dormant buds). The sensitivity of detection by monoplex- and pentaplex RT-PCR assays was comparable. Different combinations of mixed infections of viruses were identified in samples of infected apple and pear trees from different geographical regions. The pentaplex RT-PCR assay developed was sensitive, simple, rapid, and reliable for simultaneous detection of the four viruses in extracts of leaves or dormant buds.

The use of GAP-43 mRNA quantification in high throughput screening of putative neuroprotective agents in dorsal root ganglion cultures.

Large scale screening for neuroprotective drugs for peripheral neuropathies requires development of a high throughput system that is reliable and reproducible. Currently most accurate outcome measures of axonal degeneration are based on time-consuming, laborious measurement of morphological changes in neurites. In order to improve on the scalability of the screening procedure we developed a real-time RT-PCR based method of gene expression that correlates very well with morphological measures of neuritic degeneration. We examined the changes in GAP-43 expression in primary dorsal root ganglion (DRG) neurons in vitro with exposure to a zalcitabine (ddC), an antiretroviral drug that causes neuropathy in human immunodeficiency virus (HIV)-infected individuals, with and without FK506, an immunophilin ligand with neuroprotective and neuroregenerative properties. Similar to morphological measures of neuritic degeneration, in ddC-treated cultures there was a reduction in the expression of GAP-43 mRNA. This was prevented, in a dose-dependent manner, by co-administration of FK506. This assay, performed in a 96-well format, can easily be scaled for high throughput screening (HTS) using robotic systems.

Single cell RT-PCR analysis of tyrosine kinase receptor expression in adult rat retinal ganglion cells isolated by retinal sandwiching.

We describe a protocol for analysis of gene expression in single, acutely dissociated adult rat retinal ganglion cells using RT-PCR. Retrograde tracing of retinal ganglion cells from the superior colliculi was conducted using Fluorogold. Retinas were dissected and ganglion cells isolated using retinal layer separation (sandwiching). Single, fluorescently labelled retinal ganglion cells were aspirated using a micropipette and used for PCR. Two PCR protocols are described where single cell cDNA was analysed for TrkB and GAPDH or TrkB, TrkC, Ret, Met, ErbB2 and Beta-actin by multiplex-PCR. All five tyrosine kinase receptors were amplified from single retinal ganglion cells. The method will prove useful for the molecular characterization of adult retinal ganglion cells.

Genotyping on a complementary metal oxide semiconductor silicon polymerase chain reaction chip with integrated DNA microarray.

A novel method for the fast identification of genetic material utilizing a micro-DNA amplification and analysis device (micro-DAAD) consisting of multiple PCR microreactors with integrated DNA microarrays was developed. The device was fabricated in Si-technology and used for the genotyping of Chinese medicinal plants on the basis of differences in the noncoding region of the 5S-rRNA gene. Successful amplification of the genetic material and the consecutive analysis of the fluorescent-labeled amplicons in the micro-DAAD by the integrated oligonucleotide probes were demonstrated. Parallel analysis was performed by loading the four PCR reactors of the micro-DAAD with different samples of 3-microL volume. Temperature sensors and heating elements of the micro-DAAD enable precise temperature control and fast cycling, allowing the rapid completion of a combined amplification and analysis (hybridization) experiment.