/
Today I learned about the existence of the dbpedia project. It essentially turns Wikipedia into a very large database, enabling the information within it to be searched in more specific ways than usual.

I found out about the project through this recent arXiv paper about computational fact checking. They used dbpedia to make a set of triples along the lines of "Cats are mammals." I suspect their project could be useful for more than just fact-checking claims of reptilian cats. Perhaps it could be mashed up with something like this timeline project to have a constantly-updated set of facts most likely to need verifying today.

Gotta have that Mechismo

/
Staphylococcus aureus alpha hemolysin. Not terribly relevant here but it looks nice. Structural view c/o Dcrjsr and Vincent Chen on Wikimedia Commons.
I found out about Mechismo today - it's a server-based tool for exploring the potential impacts of changes in protein sequences and structures. It will accept a list of potential variants of a protein (even just phosphorylation of a particular site, for example) and then return lists and networks of the potential impact. It's nicely presented and appears to be quite flexible. Here's my favorite part, though: unlike some other tools, it's not species-limited and looks like it should work with virtually any protein with an accession number. It will be worth trying out a bit more with some real data.

Here's the citation for the original paper (not quite sure how I missed it as it's been online since this past November, but it's hard to catch everything):
Betts, M. J. et al. Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions. Nucleic Acids Res. 43, e10– (2014).

Milk-borne viruses and toasty bacteria

/
Today I learned about two interesting items:

  • Human mammary tumor virus (HMTV) exists. There's a retrovirus in mice with the straightforward name of Mouse mammary tumor virus (MMTV) and, as the name implies, it's linked with mammary tumors in mice. Mother mice carrying the virus pass it to their pups through milk. HMTV is the human-specific equivalent of MMTV. That's about all I can say without venturing into the realm of contentious debate: we can't really say whether either virus directly causes breast cancer in humans. Even so, it tends to show up frequently in women who've had breast cancer and it's not the only type of retrovirus found in milk.
  • A paper from this past June (citation below) claims to have improved the heat tolerance of E. coli by expressing a heat shock protein from C. elegans in them. It's unusual to express C. elegans proteins in E. coli as they aren't even in the same domain of life (that being said, we regularly express viral proteins in our cells of choice in the lab and no one thinks twice about it). The authors claim that this heterologous expression allowed the experimental E. coli to grow at temps up to 50 degrees C and even briefly at 58 degrees. That's really hot - I've never been able to grow it above 42 degrees myself. I'm skeptical, not the least of which because there's some substantial speculation going on in this paper, but the results can't be that difficult to replicate, right?
Citation for that second item: Ezemaduka, A. N. et al. A small heat shock protein enables Escherichia coli to grow at a lethal temperature of 50°C conceivably by maintaining cell envelope integrity. J Bacteriol 196, 2004–2011 (2014).