Question

(12 pts) Imagine that you are part of an international medical team. You are investigating a strange virus that has broken out in the US. You have samples of the virus from January when it was first detected and samples taken from patients in May. The virus uses a specific protein to attach to a receptor on lung cells and infect the people. You notice the that the attachment protein in the January samples has a different amino acid sequence than the attachment protein in the May samples. In the 20th position of the primary structure the January sample has serine. In the May sample serine has been replaced by alanine. Early in the outbreak doctors were giving a medicine to people that seemed to decrease the duration of the disease. The same medicine is not working in May. The medicine blocks the attachment protein so it cannot adhere to the lung cell.

1. (2pts) Propose a logical, hypothesis, supported by the evidence provided that states this virus will mutate if exposed to the medicine. Use a major biological theory to help explain you hypothesis. Is this an example of inductive or deductive reasoning? Explain

2. (4pts) Describe a controlled experiment to test your hypothesis. You must Include the number of subjects, and the type of statistic you would use to compare the groups as well as:

   i. Control and experimental variable.
   ii. Independent and dependent variable

3. If the p value for a t-test between the control and experimental group = 0.03 what would you conclude about the experiment. Explain.

4. (2pts) How could exposure to a medicine create a resistant virus? Use a specific theory to support your ideas and describe a step by step process that could result in a resistant virus.

5. (2pts) Provide a logical, chemistry based explanation, the describes potential changes at the molecular level, for why the substitution of alanine for serine in the viral attachment protein could change the effectiveness of the medicine.

6. (2 pts) Which level/s of protein structure does the substitution of alanine for serine affect? Explain

Answer 1

• Hypothesis - This Medicine leads to the mutation in the viral protein's receptor binding site, leading to its inefficiency.

This hypothesis is based on inductive reasoning as the observations obtained from the clinical data in both the months lead to the generalizations that form the basis of the paradigm.

• Controlled experiment

A study population of the patients who received the medicine for viral disease is created, considering both the time-points of January and May, when they took the medicine.

After all the groups and the time durations are determined, medicine effectiveness is checked by collecting the serum samples from the patients and controls. Mass spectrometry based assay is conducted to know the modification that has happened on the viral protein amino acid residue (i.e. Serine to glycine conversion), in both January and May samples. Then for checking the drug-binding, FRET- based assay can be employed.

i) Control variables are individuals who received some placebo medicine instead of the original one ( to exempt the variations caused due to the other biochemical factors present in a person's body)

Experimental variables are patients who receive the medicine due to the viral infection in both the time points.

ii) Independent variable is the medicine given to the patient as it will not be altered by the patient.

Dependent variable: Receptor-binding amino acid residue in the viral protein.

P > 0.05 is the probability that the hypothesis is true. As in this case, it is found to be 0.03, the observations seem to be significant. So, It can be concluded that the medicine is capable of altering the viral protein structure based on this statistics value.

• This phenomenon is known as 'antigenic shift' whereby a medicine cause change in the antigenic structure of a virus. It happens either when the medicine is given in sub-optimal doses or for a longer period of time. As this particular mutation in the amino acid residue provided survival advantage to the virus, it got selected.