Wild animals carry all sorts of viruses. Not only do these viruses harm animals, they can also spread widely between animal populations and can sometimes affect human health too. Viruses that we know affect humans, such as rabies, HIV and influenza, all originated in animals.

DNA and Drug-resistance

This activity has two parts:

Extracting DNA from strawberries

Sequencing genetic material from hosts and from their infecting viruses is a very widespread technique in studying the biology of viral infections. Although viral sequencing is not readily available in schools, the techniques for extracting DNA from living materials are easy to do. In this example strawberries are used to give a blood-red mixture from which the DNA is extracted.  If strawberries are not available dried peas are an excellent source of DNA. You can use this procedure from the University of Utah which uses peas ( http://learn.genetics.utah.edu/content/labs/extraction/howto/), and meat tenderiser which acts as an enzyme. If you can't find meat tenderiser then you can try pineapple juice.

Materials required

Safety glasses
Strawberries
Salt
Pestle and mortar
Tea strainers


Teaspoons
Tablespoons
Beakers (50 cm3)
Washing-up liquid
Ethanol (this needs to be ice cold) (Highly flammable, Harmful see CLEAPSS Hazcard 40A)
Test-tubes (15 cm3)
Test-tube racks

Follow the procedure on the students' sheet.

Safety: Wear eye protection. A risk assessment must be done for the practical activity.

HIV drug resistance online activity

Introduce the students to the on-line activity explaining to them what they should do.

Instructions can be found on the students' sheet.

The link to the online activity is at:

http://www.zoo.ox.ac.uk/royalsociety350/summer_science/emerging_infections/

In this on-line activity students pick a patient identity (Patient ID) from a list and must then choose an appropriate set of medicines based upon a sequence from that patient's virus.

They receive a nucleotide sequence and must use the triplet code to complete the amino acid sequence associated with their patient's nucleotide sequence. When they have correctly completed this they are shown two viral sequences, one with two drug resistance mutations and one with none. They then pick a set of drugs to prescribe to the patient.

Changes in the amount of virus in the patient's blood once they start treatment are then displayed. If the student chooses the correct drug combination the virus falls to undetectable levels. If they choose the wrong drug combination the fall in the amount of virus is only temporary.

www.avert.org/treatment.htm is an excellent online resource describing details about therapies for HIV infection.

Answers

  • 1. Just a single mutation from a TAT triplet to a TAG triplet.
  • 2. The 181 cys mutation gives resistance to Nevirapine.
  • 3. Combination therapy is used to slow or prevent the development of drug resistance.
  • 4. Zidovudine, Tenofovir and Kaletra is a drug combination that does not contain the two drugs Lamivudine and Nevirapine to which the 184 val and 181 cys mutations give resistance.

Curriculum links

Organisms and health 5b: Variation within species can lead to evolutionary changes, and similarities and differences between species can be measured and classified.
5c: The way in which organisms function are related to the genes in their cells.
5e: Human health is affected by a range of environmental and inherited factors, by the use and misuse of drugs and by medical treatments.

Applicable examination units

Exam Board Unit

Edexcel: GCSE science

B1: Variation

Topic 2: Genes

WJEC: GCSE Science

B2: Genes and variety

Variation

Northern Ireland Curriculum: GCSE Single Award Science

2: Human activity and health

2.5 ... recognise that disease can be caused by microbes, including bacteria, viruses, fungi.

Northern Ireland Curriculum: GCSE Double Award Science

3.1 Living organisms and life processes

Defence: 3.1.18 Disease can be caused by viruses.

Northern Ireland Curriculum: GCSE Biology

3.4 Microbiology

3.4.3 The harmful role of viruses, bacteria, and fungi


 

Science for you to try

DNA and drug resistance

A team from the University of Oxford investigate how viruses transfer from animals to humans. Many viruses change their genetic code and this allows them to adapt to new environments and hosts. By studying changes in DNA we can understand how these 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

Download a pdf of the instructions here.

strawberriesYou 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 the cell nuclei. Cell membranes are made up of a fatty lipid bilayer which can be broken down using a detergent, such as 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.

virus 1 200px

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.

virus 2 200px

 

 

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.

Download a pdf of the instructions here.

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 type of HIV that carries drug resistance mutations. The doctor can then decide which type of drug to give the patient.

This HIV drug resistance activity uses real HIV sequences to illustrate the use of genetic sequences in making treatment decisions.

Using the website below, you will be looking at different patients' genetic sequences and prescribing a set of drugs to treat the virus. First you will have to work out whether your patient has a wild type or drug resistant sequence, and then you have to prescribe the right set of drugs.

Go to: www.zoo.ox.ac.uk/royalsociety350/summer_science/emerging_infections/

You will need to read the instructions below to use this site.

DNA_3001. Choose a patient ID number.

2. You will receive a nucleotide sequence (the DNA code is made from four types of nucleotides: A, C, G and T). From the list below the sequence select the  correct triplet code to complete the amino acid sequence (combinations of 3 nucleotides code for amino acids). 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?
  4. What drug combination could be used in the presence of resistance mutations at positions 181 and 184?