Week7

=**Gene Expression**= November 10

Challanges for identifying funtionally important genetic variation: the promise of combining complementary research strategies Molecular Ecology (2005) 14, 3623-3642
 * Papers to discuss:**

Somatic mutation-mediated evolution of herbicide resistance in the nonindigenous invasive plant hydrilla (Hydrilla verticillata) by Michel et al. Molecular Ecology 13:3229-3237.

[| Hinfray et al.pdf] Brain and Gonadal Aromatase as Potential Targets of Endocrine Disrupting Chemicals in a Model Species, the Zebrafish (Danio rerio)

[|Sequence polymorphism can produce serious artefacts in real-time PCR assays: hard lessons from Pacific oysters.] BMC Genomics. 2008 May 20;9:234. 

[| Knudsen et al.pdf] Evaluation of the Branched-Chain DNA Assay for Measurement of RNA in Formalin-Fixed Tissues Journal of Molecular Diagnostics, Vol.10, No.2, March 2008

[|Website about use of zebrafish as a research model.]

[|Technology for creating zebrafish knockouts]

[|Learn more about endocrine disruptors]



[|QuantiGene® Reagent System] =QuantiGene® Reagent System=



QuantiGene assays bring the power of branched DNA (bDNA) technology to basic and pre-clinical research. The bDNA assay is a sandwich nucleic acid hybridization method that uses bDNA molecules to amplify signal from captured target RNA. bDNA technology forms the basis of the FDA-approved clinical diagnostic VERSANT 3.0 assays for HIV, HCV and HBV viral load, that are offered commercially by Siemens and have been in use for over a decade. Another advantage of bDNA assays is that RNA is measured directly from the sample source, without RNA purification or enzymatic manipulation, thereby avoiding inefficiencies and variability introduced by or errors inherent to these processes.
 * [reagent system#product_overview_3|Overview]
 * [reagent system#product_works_3|How it Works]
 * [reagent system#product_lit_3|Literature/Support]
 * [reagent system#catalog_listings|Catalog Listings]
 * Quantitatively measure gene expression with unparalleled accuracy and precision
 * RNA quantitation directly from cultured cell lysates or tissue homogenates
 * No RNA purification
 * No reverse transcription
 * No target amplification
 * Simple assay workflow
 * Widely used in biomarker discovery, secondary screening, microarray validation, quantification of RNAi knockdowns and predictive toxicology

Principle of QuantiGene Assay
Lyse cells to release mRNA in the presence of target probes. Target mRNA from lysed cells is captured by hybridization and transferred to the Capture Plate. || || Signal amplification is performed by hybridization of the bDNA Amplifier and Label Probe. || || Addition of chemiluminescence substrate yields a luminescent signal that is proportional to the amount of mRNA present in the sample. || ||
 * **Step 1**
 * **Step 2**
 * **Step 3**

[|Hydrilla in Washington]

Click on the presentation below for hydrilla info in Florida

**Other approaches for characterizing gene expression:**

 * [|NASBA]
 * [|DASL]
 * [|WTA]

[| Canales et al.pdf] Evaluation of DNA microarray results with quantitative gene expression platforms Nature Biotechnology Vol. 24, No. 9, September 2006
 * Additional Papers on the topic:**

Developmental expression of cytochrome P450 aromatase genes (CYP19a and CYP19b) in zebrafish fry (Danio rerio) Journal of Experimental Zoology 290:475-483.

An easy read about biomarkers and environmental health