The paper for today is:

Parks, J.M. et al. (2013). The Genetic Basis for Bacterial Mercury Methylation. Science, 339(6125), pp. 1332-1335. doi:10.1126/science.1230667.

(There is a tiny dog in this room and its constant yelpings and mewlings are making it quite hard to absorb this material.)

This is a quick little report about the genes used by mercury-methylating microbes to do their mercury-methylating work. The authors already knew about the corrinoid iron-sulfur protein (CFeSP) used to methylate metallic clusters on acetyl-CoA synthases, so they began to look for something similar in the genomes of mercury-methylating bacteria. They did find one within a Desulfovibrio desulfuricans genome along with a gene for a putatively associated ferredoxin. It's not just D. desulfuricans, either: the same pair of genes appears to be present in 51 other genome sequences, at least a few of which are known to be mercury-methylators. Beyond the bioinformatics, D. desulfuricans deletion mutants without these two genes appeared to grow normally yet had almost none of their usual Hg-methylating ability.

It is entirely possible that the two target genes in this study - referred to the authors as hgcA and hgcB - have some other functions. The genomes of some distantly related species do appear to contain hgcAB orthologs, including a set in the recently isolated Methanomassiliicoccus luminyensis, a commensal human gut-dwelling archaeon. It isn't clear why many of these species code for these enzymes or need anything like them at all. Studies of microbial metal metabolism look like another job for the "sequence everything that moves" approach.

Another Cytoscape quirk - when importing data, redundant pairs of interactions are usually - but not always - ignored. This is a problem when I actually want to see how many different sets of data produced the same interactions, so doing such a comparison may be a better job for Excel.

Cytoscape also has trouble importing VizMapper settings almost all the time. Sometimes importing the settings then saving and reloading the network irons out any bugs.

Edit: I figured out the problem with failure to recognize redundancy. Cytoscape ignores redundant entries if the interacting nodes are presented in the same order, so Node1 (pp) Node2 only gets added to the network once even if the data set includes it twice with different attributes, i.e. if Node1 (pp) Node2 from Data Set 1 and Node1 (pp) Node2 from Data Set 2 are both in the input file. If Node1 (pp) Node2 and Node2 (pp) Node1 are both in the input file, though, both interactions are retained despite just being the inverse of each other. A solution: import the attribute as an interaction type.

Argh, why is Google discontinuing Reader? Do people not use RSS feeds anymore? I know that the Big G really just wants to roll everything up into Google Plus Sign but they're hardly transparent about why they discontinue services like that. It's poor service (though not customer service, as evidenced by that internet adage along the lines of "if you're not paying anything, you're not the customer, you're the product).

An interesting note from a 2010 review of pathogenic E. coli by Croxen and Finlay in Nature Reviews Micro:

Intriguingly, EHEC can sense the hormones adrenaline and noradrenaline from host cells, as well as the quorum-sensing molecule auto-inducer 3 (AI-3) from gastrointestinal cells, to regulate motility and T3SS expression... Sensing of these molecules is required for virulence of EHEC in animal models and presents a new interaction that should be taken into account when considering pathogen–host interactions.

Some kind of a localization factor, perhaps, as adrenaline receptors are indeed present in the gastrointestinal tract.

It would be nice to actually accomplish something new in lab today but I'm spending an awful lot of time on small jobs like sending plasmid samples to labs in Austria and cleaning off plastic dishes so they can be sterilized (that job wouldn't even be necessary if said dishes didn't cost nearly $200 for a case of 60, but I guess lab materials are just obscenely expensive). There's also a bacterial pathogenesis exam tomorrow morning to study for. That material is generally fun to read, at least.

One hand washes the other.