> Many bad studies require a lot of domain knowledge to understand why they're bad.
I went to grad school after some years practicing in the discipline. During those earlier years I neglected to introduce a Kozak sequence the first time constructing a protein expression cassette. These sequences, which are on the 5 prime region immediately adjacent to the protein open reading frame, are almost always required for decent translation of mRNA to protein in eukaryotes. And minor modifications to the Kozak sequence can have varying impact on protein expression. Since then this has always been top of my mind when doing such design.
So in grad school in a class we had various papers assigned to read and answer questions on. One peer-reviewed paper split a 5 prime untranslated region (an mRNA regulatory element) into two parts to determine which parts were most necessary for regulating expression of the protein. They placed these two parts directly adjacent to the protein open reading frame. And unfortunately, for the first half of the untranslated region, they neglected to keep the native Kozak sequence. Not unexpectedly, there was almost no protein expression from this. They concluded that the first half of the untranslated region was both necessary and sufficient for down regulation of expression.
I pointed out their fatal flaw and seriously impressed my professor who had only done a cursory reading of the paper before assigning it. I don't understand how this passed peer-review, but it did. I guess the reviewers didn't look at the mRNA sequence in detail. If they had, they would have noticed the altered Kozak site and would have required a further experiment with the native Kozak sequence.
The study was actually fine in basic design, the author just made an easy mistake, and no one caught it.
I went to grad school after some years practicing in the discipline. During those earlier years I neglected to introduce a Kozak sequence the first time constructing a protein expression cassette. These sequences, which are on the 5 prime region immediately adjacent to the protein open reading frame, are almost always required for decent translation of mRNA to protein in eukaryotes. And minor modifications to the Kozak sequence can have varying impact on protein expression. Since then this has always been top of my mind when doing such design.
So in grad school in a class we had various papers assigned to read and answer questions on. One peer-reviewed paper split a 5 prime untranslated region (an mRNA regulatory element) into two parts to determine which parts were most necessary for regulating expression of the protein. They placed these two parts directly adjacent to the protein open reading frame. And unfortunately, for the first half of the untranslated region, they neglected to keep the native Kozak sequence. Not unexpectedly, there was almost no protein expression from this. They concluded that the first half of the untranslated region was both necessary and sufficient for down regulation of expression.
I pointed out their fatal flaw and seriously impressed my professor who had only done a cursory reading of the paper before assigning it. I don't understand how this passed peer-review, but it did. I guess the reviewers didn't look at the mRNA sequence in detail. If they had, they would have noticed the altered Kozak site and would have required a further experiment with the native Kozak sequence.
The study was actually fine in basic design, the author just made an easy mistake, and no one caught it.