instances =?

Instances = occurrences or manifestations

Each appearance of these naturally occuring codons on the DNA strand would be replaced by with a researcher written codon.

the researchers describe how they replaced instances of a codon -- a DNA "word" of three nucleotide letters -- in 32 strains of E. coli, and then coaxed those partially-edited strains along an evolutionary path toward a single cell line in which all 314 instances of the codon had been replaced.

Good point. This is a difficult passage for a non-geneticist.

Each DNA strand has more then one type of codon. Codon being a consecutive three letter word. The letters to a DNA are A, C, G, and T. The codon they might have replaced might be any combination of CAT in the given DNA strand. Another codon would be ACT, etc....

A codon might mean a defined and designated set of 3 letters AKA a specific codon rather then more then one type of codons.

I think I understand this now. I hope I can get what's in my head across in a clear enough fashion.

Quote:

the researchers describe how they replaced instances of a codon -- a DNA "word" of three nucleotide letters -- in 32 strains of E. coli, and then coaxed those partially-edited strains along an evolutionary path toward a single cell line in which all 314 instances of the codon had been replaced.

The scientists in the beginning of the experiment DID NOT physically replace ALL codons in the strand. **In this case, instances refer to the number of times the scientists could in fact find and replace the natural codon with their designed codon. I'm thinking that it may be too difficult to replace all of the designated codons in the first phase.**

Their goal is to replace all 314 designated codons. I believe they do this via forcing the DNA strand to reproduce itself as described in the following passage:
then coaxed those partially-edited strains** along an evolutionary path

I guess each subsequent generation, the naturally designated codon will disappear and their introduced/designed codon will become more dominant in replacing the codon they want removed.

Good point. This is a difficult passage for a non-geneticist.


I guess each subsequent generation, the naturally designated codon will disappear and their introduced/designed codon will become more dominant in replacing the codon they want removed.

Eager to share their enabling technology, the team published their results as CAGE reached the semifinal round. Results suggested that the final four strains were healthy, even as the team assembled four groups of 80 engineered alterations into stretches of the chromosome surpassing 1 million DNA base pairs. "We encountered a great deal of skepticism early on that we could make so many changes and preserve the health of these cells," Carr said. "But that's what we've seen."

The context has "all 314 instances of the codon." If it has been written as "all 314 instances of the codons," it will be understood easily.

oristarA wrote:

The context has "all 314 instances of the codon." If it has been written as "all 314 instances of the codons," it will be understood easily.

It would be misundersood easily! The writing is well done. You are being directed to focus on the fact that they are talking about 314 instances [identical examples] of one particular codon. An instance is a singular thing. The use of the singular emphasises the fact that they are replacing the same thing each time.

"...they replaced instances of a codon [the same codon] -- a [note singular] DNA "word" of three nucleotide letters -- in 32 strains of E. coli, and then coaxed those partially-edited strains along an evolutionary path toward a single cell line in which all 314 instances of the codon [same codon] had been replaced".

It's like replacing every instance of the letter 'a' in "Mary had a little lamb" and getting "Mory hod o little lomb". You replace each 'a' but leave the other letters alone.