Ancient genomics sheds light on past plagues

This caught my eye as I had just talked a bit about Yersinia pestis in class about 1-2 weeks ago. This species is generally assigned as the causative agent of the plague that wiped out 1/3 of Europe in the mid1300's. Researchers obtained DNA from Black Plague victims from the 1300's and were able to pull out and sequence the genome of the bacterium that caused it. Their initial questions were 1) was Y. pestis actually the cause and 2) if so, how did this strain relate to today's strains?

When they compared the genome to modern Y. pestis, they found that 1) it was indeed Y. pestis, and 2) there is little change between the ancient strain and the current strain suggesting that it wasn't necessarily a abnormally virulent strain.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10549.html

A few posts ago I noted the use of genomics to track modern epidemics. This study adds a unique component by analyzing ancient genomes. Took a peek at the methods - they had to enrich the DNA by using modern Y. pestis fragments to pull out the ancient bacterial DNA, otherwise it's a needle in a haystack! 

Megavirus chilensis takes current award for biggest virus

From Oct 10, 2011 issue of PNAS

http://www.pnas.org/content/early/2011/10/04/1110889108.abstract

isolated from the sea near Chile, somewhat related to the prior record-holder Mimivirus, contains 1120 protein-coding genes, 1.26 Mbp of DNA, and size of ~0.2-0.3 uM

(image from geekosystem.com)

next generation sequencing strikes again

A while back I noted a "proof-of-concept" study where researchers took a problematic strain of E. coli from an outbreak, pumped out the genomic sequence and analysis in a few days and were able to make great strides in understanding the nature of why this particular strain was a problem.

The same research group have now applied that to Klebsiella pneumoniae Oxa-48 - a bacterial strain responsible for hospital infections in the Netherlands. This really seems to support the importance of DNA technology advances and how genomic level information will be used in the future.

Got them "antimicrobials in my boots" blues

Bought a pair of hiking boots today and noticed that they had "Microbe Shield" on them. I couldn't resist - I had to find out what they were doing that made it antimicrobial. Obviously with something like a boot you don't exactly impregnate it with ampicillin. Here's what I found out about that

The companie's name is Aegis. They've synthesized an interesting molecule that has 3 main components. The first part of the molecule is bound to the material. The second part of the molecule is positively charged and therefore attracts the negatively charged bacteria to it (quiz - what makes the bacterial wall negatively charged?). The third part of the molecule is rigid and "stabs" the cell. The molecule doesn't get consumed in the interaction therefore it can act for a long time.

They have an interesting interactive about the mode of action of the molecule at:

http://www.microbeshield.com/index.php?option=com_content&view=article&id=31&Itemid=3

update 3/15/13 - looks like the business has been restructured

http://www.microban.com/americas/english

the tech video can now be found at http://www.youtube.com/watch?v=UmQy0AunWGo

slime molds as models

http://www.nytimes.com/2011/10/04/science/04slime.html?_r=1&ref=science

neat stuff about a great group of eukaryotic microbes.

Here's a link to the map experiment that is referred to in here. 

http://www.wired.com/wiredscience/2011/05/slime-mold-iberia/