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A baby boy is brought to the clinic suffering from impetigo (a bacterial skin infection).  Looking at his history he has had 7 bacterial ear infections, pink eye, has been hospitalized twice with bacterial pneumonia, and his parents report chronic diarrhea.  Suspecting an immunodeficiency, you have the lab sequence his genome and find the following mutations in the coding regions of genes encoding for 3 immune components.  
For each of these mutations say what the normal role of the immune component is including if it is on a certain type of cell or in fluids (6 points)  and what type of mutation was found in each of those genes (3 points NOTE: the whole gene is not shown, only the region with the mutation divided by codons).  Your group should decide which of these mutations is most likely to be playing a role in the boy’s problems and explain why you chose that mutation and not the other two (3 points).   
NADPH oxidase  Normal sequence   5′- ATT CGA  AAC- 3′
patient sequence    5′ ATT CAA AAC- 3′
C3                       Normal sequence 5′- TTT CGA ACG- 3′
patient sequence 5- TTT AGA ACG- 3′
MHCII                 Normal sequence 5′-ATC TAC TAA -3′
patient sequence 5′ ATC TAT  TAA- 3′
Is it safe for this patient to receive live-attenuated vaccines- why or why not (2 points)?  How about inactivated or subunit vaccines (2 points)?  Would vaccines benefit this patient, why or why not (2 points)? 
You also found a mutation in the promoter region for the gene for VDJ recombination.  Could a mutation in a promoter region lead to an immune problem, discuss why or why not (2 points).   Bonus: What immune cells require VDJ recombination, be specific, and could problems with VDJ cause your patients problems, be less severed, or more severe (2 points)?  

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