a group of forensic scientists were studying the corps of Kim Jong Nam. During t

Question

a group of forensic scientists were studying the corps of Kim Jong Nam. During the investigation, the corps drew a single, deep breath due to contraction of the diaphragm . The group was startled, and immediately started to try and determine the cause of the deep inhalation. They found that cholera toxin was present is cell bodies of the phrenic nerve (which innervates the diaphragm).What technique could the group use to determine if cholera toxin caused changes to gene expression in addition to its non-genomic effects. . Briefly describe the technique.

Explanation / Answer

The polymerase chain reaction is a technique that employs two short, specific DNA oligonucleotides (primers) and the enzyme DNA polymerase to synthesize multiple copies of DNA in the portion of the bacterial gnome that is flanked by the two primers. In the PCR for cholera toxin, the specific primers detect only the gene encoding the A subunit of cholera toxin (ctxA). The amplified DNA from ctxA is detected as a 564-bp band in an agarose gel. This PCR test is a colony confirmation test.

In this technique, the number of reads aligning to each genomic position on each strand is calculated. Each genomic position is annotated based on its location within the sense or antisense strand of ORFs, rRNA, tRNA, or regRNA or in an intergenic region. Positions are the antisense strand of one gene overlapped the sense strand of another are annotated as sense. The total number of reads aligning to each category and to each annotated gene is calculated. Putative transcription units (PTUs) are identified as stretches of 50–450 consecutive positions with read coverage > 20 that did not overlap annotated genes. Overlapping PTUs from biological replicates are resolved to give the final list of unique PTUs.

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