Newcastle University Drylab/2 June 2008

Mark
Today began implementing the exercises set in the Java tutorial into my EA. I created two classes called Node and Promoter, where I created a number of promoter objects to be associated with each node. This has now replaced the double arrays that I started off with in my program. Each promoter object has a name prefixes with P, followed by a number (from count). I have defined 14 different promoters, and for each node 5 of these ate selected randomly and input into a subArray which is then added to the Promoter array in the Promoter class. This is carried out for each node in the three layers in the network, the input/hidden/ and output layers. A double threshold value has also been stated, which in this case has been set to ten. Only when the promoter threshold values in the five promoters add up to ten will the fitness be accepted. Untill this point the EA will mutate the network. This mutate method is what I will begin writing tonight and tomorrow.

Have also spent some time today investigating the LisRK and agr two component systems in Listeria monocytogenes. Delved deep into the literature and also carried out a number of Bioinformatics analyses using UniProt, pfam (although it was down for most of the day), Kegg and Blast. The conclusions that I have drawn from this are that the LisRK system is very unique (in terms of identity), but we would be sensing the unknown, as an A-I has not yet been identified for this organism. In the arg system, I have discovered that again there is only 100% identity for the agrC sensor kinase, but similarity is quite high for one other Listeria species. These findings need to be discussed in full in the meeting on thursday before going any further with this organism. The findings in terms of papers and Blast results are shown below for Listeris monocytogenes:

This evening continuing in the same vein with Staphylococcus aureus.

Megan
Protein analysis using bioinformatic tools on the vnc operon. Firstly I found the EMBL record of the genomic region that contains the vnc system. This contains the vncS, vncR, coding region for the peptide that is sensed. These are parts that I alreaady knew would be involved in the two component system. There are also a number of hypothetical proteins, conserved regions and transporters. Fisrtly the 3 aforementioned parts will be analysed then I will move on to assess the other proteins, their role and whether they are required within the system to be used.

This analysis highlights inforamtion on the proteins that we were expecting to use. However I have not uncovered the repressor that is thought to be present. The case may be that this is not contained in this section of the genome. Further work is required to try to find this as it would be a problem if we are unable to use this two-component system.

Attempted to start the Java exercise that has been set by Morgan for my individual project. Didn't go very well, ended up a big java mess, very confusing to get my head round- probably should have tackled this during the daytime when Morgan was around.