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Plant Transcriptomics

In the Plant Transcriptomics Simulation, you will embark on a mission to identify the metabolic pathway that produces an antimalarial compound in a rare plant.

About This Simulation

In the Plant Transcriptomics Simulation, you will embark on a mission to identify the metabolic pathway that produces an antimalarial compound in a rare plant. You only have one plant specimen to extract the RNA and identify the enzymes that are needed to produce a novel antimalarial drug. You will use a method called RNA-seq to quantify the transcription of different genes. Will you be able to identify the enzymes and produce a novel drug that can save millions of people?

Find a novel antimalarial compound:

Your mission starts in the amazon rainforest. Local tribes people show you a plant that they use to cure malaria. Back in your lab a phytochemist identifies the antimalarial compound. You have to identify the enzymes responsible for the production of this potential drug.

Learn how molecular compounds are produced:

You will identify an enzymatic pathway that converts the precursor molecule into the antimalarial component. If you want to produce this compound at large quantities you need to to transform this enzymatic pathway into another organism. To do so, you need to identify the genes encoding the enzymes.

Extract the RNA:

All the information you need is contained within the composition of mRNA molecules in different plant tissues. If you want to learn how to extract mRNA from a sample you can perform the Guanidium thiocyanate-phenol-chloroform extraction method or ask the lab assistant to do it for you.

Learn about the structural difference of mRNA and DNA:

The key to the functions of mRNA and DNA is their structures. While the lab assistant is reverse transcribing your mRNA sample into cDNA you will be learning about the structure of these two amazing molecules.
Perform Next Generation Sequencing of your cDNA sample
You will sequence the cDNA of different plant tissues to determine the sequence and expression of the target enzymes. An animation will show you what is going on inside the flow cell and how millions of different sequences can be read in parallel.

Analyze your results using phylogenetic analysis and BLAST:

Like a detective you will need to analyze the huge amount of NGS reads and determine which enzyme is most likely involved in the biosynthesis of the antimalarial compound. You will learn how relatedness of DNA sequences can be used to identify unknown enzymes and learn the basics of sequence comparisons.

Screenshots

Collaborators

Learning Objectives

  • Learning about terpenoids and its benefit as an antimalarial drug
  • Understanding how Next Generation Sequencing technology can be used to screen candidate genes
  • Learning how to use BLAST and phylogenetic analysis gene annotation

Techniques

  • RNA extraction (optional)
  • Next Generation Sequencing: Cluster generation, Sequencing, Data analysis
  • Phylogenetic analysis
  • BLAST

Collaborator

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