Day 26 thoughts.  Phagefinders. 

Planned:  EM visit, 1-3. 

Phage to take for EM:

Genevieve:  She HT 10-3 F1 lacy plate for EM analysis, Garden. 

How do rhodococcus top-agar plates look?

Did: 

Students prepared DNA from remaining phage samples, aliquoted samples for processing for electron-microscopy, archived samples, spent time measuring their phage electron-micrographs (for those students who had phage at this point), and wrote-up results regarding temperature differences and plaque morphologies. 

Today's materials:   

Pointers:  Regarding DNA preparation, it is almost mandatory to have a 65 C heating block...to heat the EDTA for making the STEP buffer. 

Today was a test to see if the phage lysis buffer could be used from the week before. 

Bill wondered ... and was curious about the possible point mutations that Chris's phage might have.  These 2 phages become excellent candidates for Graham to sequence...to determine if these are mutational or recombinant derived events. 

Bill: possibility that when we didn't get DNA,

short-contractile tails, not found frequently, perhaps these are a biased

Bill requested that Steve parafilm his plates. 

Steve needs to write up the results of his phage and how it has grown out.  Bill...suppose cells are infected with phage and make a product toxic to mycobacteria, bill says that based on size of phage, it is made in the center and tons of this lipid is made and diffuses out...or a protoein, or a carbohydrate...has an inhibitory effect.  Note that Steve's results indicate

You know when you do restriction digests, do a digest,....see if there is a similar BSTeII pattern to Steve's phage. 

PST I and EcoR1 as a good cutting enzyme.  recommended. 

Bill: applied and environmental micro paper regarding the phage diversity. 

Bill says that in the soil we worked with, we would never find tuberculosis.  But we would find lots of related bacteria or actinomyces.  A whole family of hi GC phages in this soil.  Indicit

Coronobacterium...we could take all the bacteria in genus, streptomyces, norcardia, coronobacterium, various mycobacteriaum, rhodococcus, and see if they could plaque on this...  [cross-species phage infection]. 

whole variety of ... most bacteria when out in the dirt do not get phage production.  This is a way to cause the bug to turn on.