Science for you to try - Emerging infections: viruses that come in from the wild
DNA and Drug resistance
The team from the University of Oxford research how ‘wild viruses’ cross the species barrier to transform into emerging infections in humans. Many viruses change their genetic code and this allows them to adapt to new environments and hosts, and so by studying these changes in DNA we can understand how these wild viruses become a threat to humans.
So what does a DNA strand look like, and how do viruses pose a challenge to the use of drugs to treat them? Try these two activities to find out:
Procedure - Extracting DNA from strawberries
You will need:
- Strawberries
- Salt
- Pestle and mortar
- Tea strainers
- Teaspoons
- Tablespoons
- Beakers (50 cm3)
- Washing-up liquid
- Ethanol (this needs to be ice cold)
- Test-tubes (15 cm3)
- Test-tube racks
Safety: Wear safety glasses.
Strawberry DNA is contained in the nucleus of the strawberry cells, so to extract the DNA we will need to break down the membranes of the cells and nuclei. These membranes are made up of a fatty lipid bilayer which can be broken down using a detergent. In this activity we will be using washing-up liquid.
1. Take two medium sized strawberries and crush them with a pinch of salt in a pestle and mortar.
2. Add a few tablespoons of water and pound some more. You want lumpy red water. Strain off the lumps through a tea strainer, saving the liquid in a beaker.
3. Add about one teaspoon of washing-up liquid. Then stir gently. You do not want froth. Leave to stand for 10 minutes.
4. Put about 4 cm3 of strawberry mixture into a 15 cm3 test-tube.
5. Tilt your strawberry-red test-tube and then gently pour ice-cold ethanol into the tube down the side to form a separate layer on the top of the strawberry mixture. You need equal quantities of alcohol and strawberry mixture.
6. Stand the test-tube in a rack and watch while white strands of DNA rise into the alcohol layer from the strawberry mixture.
Procedure - HIV drug resistance
In this online activity, developed by the Emerging Infections exhibit team from the University of Oxford, you will have to sequence DNA and prescribe the appropriate drug.
Sequencing a virus that has infected someone can give a lot of useful information. For example, when prescribing drugs to someone infected with HIV it is very useful to know if they are infected with a strain of HIV that carries drug resistance mutations. This HIV drug resistance activity uses real HIV sequences to illustrate the use of this type of information in making treatment decisions.
Using the website below, you will be looking at different patients' nucleotide sequences and prescribing a set of drugs to treat the virus, but you will have to work out whether your patient has a wild type or drug resistant sequence to prescribe the right set of drugs.
www.zoo.ox.ac.uk/royalsociety350/summer_science/emerging_infections/
You will need to read the instructions below to use this site.
1. Choose a patient ID number.
2. You will receive a nucleotide sequence. From the list below the sequence select the correct triplet code to complete the amino acid sequence. Click on the code and drag it to the correct position in the sequence.
For example, if you were looking for the amino acid coded for by TGT, go to 'T' in the 1st position (top row), then read across to find ‘G’ in the 2nd position (fourth column), then look down the column to find the final third position to complete the sequence TGT. You are told that the amino acid is Cysteine. Drag and drop this into position. If it’s correct then it will go green, incorrect and it will turn red.
Continue filling in the blanks until you have a full, correctly placed, sequence of amino acids.
3. When you have correctly completed this you will see two viral sequences, one with two drug resistance mutations and one with none (the 'wild type' sequence). Decide which type of nucleotide sequence yours is.
4. Pick a set of drugs to prescribe to the patient, and watch what happens on the graph.
What's next?
Want to do more? Then have a look at the questions below. You can use the sequencing activity website to help you find the answers.
- 1. What is the smallest number of nucleotide changes necessary to make a mutation from tyrosine to cysteine?
- 2. A mutation from tyrosine to cysteine at position 181 in HIV gives resistance to which drug?
- 3. Combination therapy uses several drugs at the same time. Why do you think this is used?
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4. What drug combination could be used in the presence of resistance mutations at positions 181 and 184?
Teacher's Instructions
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