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.

Friday, 13 May 2016

Gene symbol poetry

A rather angry pathway.
"Regulatory protein for 2-phenylethylamine catabolism · two component sensor histidine kinase,essential for acid-tolerance · nikkomycin biosynthesis protein · galacturonide ABC transporter ATPase".
That is my first (and last) attempt at genetic constrained writing: the genes encoding those protein are feaR actS sanS togA, which is a rubbish sentence that makes somewhat sense.
Constrained writing () is an artistic challenge where one writes with a restricted dictionary, for example, there are no word with the letter e in the book Gadsby. Here I restricted my dictionary to words that are also gene symbols.