Saturday, 12 November 2016

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...

Saturday, 3 September 2016

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...

Tuesday, 23 August 2016

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.

Saturday, 20 August 2016

Wild about E. coli


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

Tuesday, 9 August 2016

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.


Friday, 27 May 2016

The witchcraft of knockouts

Making knockouts has a bad rep, but there seems to be a conspiracy afoot to make it feel like a mystic art.


Tuesday, 17 May 2016

Restriction cloning nostalgia

Today I was reminded of an invaluable table that was hung on the wall of every lab: the NEB buffer compatibility chart.

My favorite buffer is buffer 4.