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Questions Bioinformatics An Introduction

This document discusses bioinformatics techniques for identifying the enzymes that produce the antimalarial compound spruceanol in Peruvian Rosewood plants. It involves sequencing mRNA from plant tissues, converting the mRNA to cDNA using reverse transcription, performing RNA-seq to sequence the cDNA and quantify gene expression levels, identifying similar cytochrome P450 genes using sequence homology, and determining that gene C has the highest expression in leaves where spruceanol is found.

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Mariz Martinez
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96 views

Questions Bioinformatics An Introduction

This document discusses bioinformatics techniques for identifying the enzymes that produce the antimalarial compound spruceanol in Peruvian Rosewood plants. It involves sequencing mRNA from plant tissues, converting the mRNA to cDNA using reverse transcription, performing RNA-seq to sequence the cDNA and quantify gene expression levels, identifying similar cytochrome P450 genes using sequence homology, and determining that gene C has the highest expression in leaves where spruceanol is found.

Uploaded by

Mariz Martinez
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Bioinformatics: An introduction

Question 1: How do plants produce molecules like spruceanol?


✓ Enzymatic reactions
– Symbiosis with prokaryotes
– In the Calvin cycle of Photosynthesis
– Uptake from the soil

Question 2: The Peruvian Rosewood (Micrandra spruceana) plants are rare and not ideal for
cultivation. If we can identify the enzymes that produce spruceanol we can produce this antimalarial
compound in another species that can be efficiently cultivated.

What would you have to insert into the host species to produce spruceanol in large quantities so it
can be used as a drug?
✓ DNA
– Proteins
– RNA
– Enzymes

Question 3: How could you quantify the expression of Cytochrome P450 genes in different tissues?
✓ By measuring mRNA levels
– By quantifying relative abundance of amino acids
– By quantifying DNA copies
– By sorting protein lengths

Question 4: This means we need to determine the mRNA sequences as well as their relative
number of different mRNAs.

What method could we use to sequence the mRNA of the plant and quantify it at the same time?
✓ RNA-seq
– Southern blot
– RT-qPCR
– Whole genome sequencing

Question 5: In order to sequence the mRNA we need to convert it to DNA. What technique could
we use to convert the mRNA into DNA?
✓ Reverse transcription
– DNA synthesis
– Microarrays
– Quantitative PCR

Question 6: Which of these statements is true for cDNA?


✓ It contains no introns
– It needs to be spliced before translating into proteins
– It contains only exons
– It contains the introns

Question 7: The NGS workflow requires to reverse transcribe mRNA to cDNA. Which step would
not work with RNA?
✓ PCR
– Reverse transcription
– Binding to flow cell
– cDNA synthesis

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Question 8: Now we need to find the best organism to map the reads.
Have a look at the phylogenetic tree depicting different plants that were previously sequenced.

Which genome is best suited to map our sequence reads?

✓ Rubber tree (Hevea brasiliensis)


– Thale cress (Arabidopsis thaliana)
– Cassava (Manihot esculenta)
– Apple tree (Malus domestica)

Question 9: How could we use this known cytochrome P450 gene to identify other cytochrome
P450 genes in our Peruvian Rosewood (Micrandra spruceana) sequences?
✓ By searching for similar sequences
– By comparing the introns
– By finding all the sequences with the same length
– By identifying identical sequences

Question 10: Now let's have a look at the read counts for each of the four genes.

Which one of the following cytochrome P450 enzymes is the most likely candidate for catalyzing the
spruceanol biosynthesis?

Remember there is a lot of spruceanol in the leaves but not in the fruits.

✓C
–D
–B

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–A

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