Chapter 3 Flashcards
Describe NE327 and NE201KT7 and their resistance genes
Both from nebraska transposon library, based on USA300 (CA-MRSA), cured from plasmids. Both initially with phi2 + phi3 prophage. NE327 has ermB gene knocking out phi3 integrase. NE201KT7 is a modified NE201 with kanamycin resistance marker knocking out phi2 integrase, and tetK resistance on plasmid PT181.
How do you know there’s no baseline transfer?
No transfer detected when growing these strains without exogenous phage and with CaCl2, suggests prophage can’t help. No tra genes for conjugation. DNAse doesn’t affect transfer, ruling out transformation.
How do you know the prophage aren’t responsible for transfer?
No transfer without the exogenous phage. Phi2 and phi3 integrase knocked out, but lysogenic immunity still present, so would all have to happen during a single burst. However, 80alpha is reported as helper phage, so might boost phi2 and phi3. But these would then mix with 80alpha transducing phage so not really distinguishable, same population in model.
How do you know that your DRP are not all lysogenic?
Exceedingly unlikely that the DRP would just so happen to be the only bacteria in the entire coculture to have become lysogenic (even if did, would suggest they all then automatically became DRP, so would be an even more worrying finding). And any other DRP then would appear then immediately be killed off by phage
What are the length of ermB and tetK?
ermB 700, tetK 1400
Why use DIC and not AIC?
AIC relies on a maximum likelihood estimate, whilst DIC takes into account the deviance of likelihood across model fits. Assumption that posterior is approximately normal though
Why did you not attempt to measure your parameters experimentally?
In theory possible, but would have required other experiments, and in the end would still have to disentangle them (adsorption rate, burst size, latent period…). Approach here made use of priors when possible (for latent period and burst size), and allowed us to simultaneously fit all models with their different interactions. Eg link between phage burst size and bacterial growth by definition would suggest that burst size measured at one time may not represent burst size across the board.
