On error rates of Mutazyme

On a previous jocular post about the 'not for diagnostic purposes' tag on Mutazyme I mention the mutational rate of Mutazyme II. The exact mutations per kb per doubling is never mentioned in the manual, but can be extrapolated. (see also part III: Mutazyme and Manganese)

The heteroduplicity of error prone PCR plasmids

A mix of wt and

mutant...

In an error prone PCR the ep-aDNA is ligated onto a plasmid backbone and transformed. When assessing the diversity from a naïve plasmid pool, something odd is seen: some bases are mutated but not to saturation. This is often just dismissed or simply overlooked, but I suspect it is actually something interesting...

DNA gyrase for better yields

Transformation efficiency is a key part of library making... Which gets a bit tricky with large plasmids. A forgotten 90s paper would appear to have a solution, if it were not for a catch.

JW numbers in the Keio

Hirotada Mori is one of the top five names* in E. coli genomics as his group built the Keio and the ASKA collections. Yet the strains from the Keio and ASKA do not start with HM, but JW. Here is why...

Methodological sabotage of growth rates

Following the interest in a previous post about analysing growth curves in Matlab I would like to discuss issues in growth curves that can arise from the methodological/biological side of things. Fitting the data is perfect if the data is perfect, if not, looking at what is wrong by eye is warranted for future corrections.

Growth curves can be divided into phases (lag, exponential, stationary and death) and each has its pitfalls.

Wild about E. coli

Wild type E. coli is a funny concept, because there are actually multiple contestants for the title...

Cysteine racemase: an impossible enzyme?

Cysteine racemase is an enzyme (EC 5.1.1.10) that was characterised in lysates long ago, but have never been found since. Is it a real enzyme? Can the reaction happen well? The problem is that racemising via a carbanion intermediate something with a leaving group is not an easy feat.