Dr. Verybad has discovered a new neurodegenerative disease (Verybad disease, VBD

Question

Dr. Verybad has discovered a new neurodegenerative disease (Verybad disease, VBD). The disease starts as headaches and muscle weakness and progresses to cognitive impairment, loss of muscle control, and death. The cause of the disease is currently unknown and there is no treatment. Dr. Verybad has a hypothesis that this is the result of a mutation in a gene located on the X chromosome called Dont Touch This gene 1 (Dtt1). Dr. Verybad wants to sequence the gene to determine if there is a mutation in Dtt1 responsible for the pathogenesis of VBD.

1-If there is a mutation in the sequence approximately 250 base-pairs upstream of the transcription start sight, what might this mutation be affecting? Propose 1 experiment to investigate this possibility. Explain the protocol, controls, and expected results.

2-If there is a mutation that falls within an intron close to an exon junction, what might this mutation be affecting? Propose 1 experiment to investigate this possibility. Explain the protocol, controls, and expected results.

Explanation / Answer

1. if the mutation is before the transcription site, then problem must be in initiating the transcription of the DNA sequence. The transcription factors and enzymes might not be able to bind, resulting in no formation of mRNA and then subsequent protein.

Control for this experiment would be a normal cell. We will take its mRNA transcript and compare with that of the defected cell.

Protocol- extract complete mRNA from normal and defected cells and compare their sequence (first we can do PCR for amplification and then BLAST or any other BIOINFORMATICS software to compare the sequence.

2. If the mutation is within the gene, then transcription might hault resulted in truncated protein.

Here we can take use of knowledge of proteomics. we can compare the proteins from a normal and defected cell.

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