Friday, 6 January 2017

Top 5 useful facts about the MDS42 strain

MDS42, also known as the Blattner strain, is a strain made in 2006 by deleting 13% of the genome of E. coli K-12 MG1655. Unfortunately, as tools go, it rivals IKEA in cryptic instruction manuals.

Wednesday, 30 November 2016

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...

Thursday, 10 November 2016

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.

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...