Day 9 thoughts.  Phagefinders. 

Planned:  Assign a lab manager today.  11:30, journalism group will photograph us for publication.  Could count phages in a plaque, backtrack how many phages can be found in a single plaque.  Bill in

3) Trip to library, to get the science news article.  Since we have new virus, we should pick from a plate, and mark our old samples.  (reserve)

4) Time to work on paragraphs.

6) Spend some time on the hatfull websites.  (didn't yesterday)

2) Dilution plate BXZ1.  (reserve)

4) Prep of a M. smeg culture from a single colony.  (didn't yesterday)

Did: 

Bill came in at 10 AM when the photography crew arrived, and then spoke with the students for awhile. 

http://www.pitt.edu/~gfh/ is the homepage of the Hatfull Lab, we discussed this website today. 

PittCHronicle, Newspaper of the University of Pittsburgh May 12, 2003 profiled Hatfull research. 

We counted our D29 plaques today, even though they had only grown for 1 day. 

D29 phage plaques counts:

Student:            # plaques on -6 plate        Old/New Smeg.   Partner

Stephen            51                                    old                    Kristen

Kristen              44                                    new                  Stephen

Lazlo                61                                    new                  Chris

Chris                49                                    old                    Lazlo

Amanda            48                                    new                  Blake

therefore, no real trend or conclusion with respect to age of the M. smegmatis and the number of plaques formed, even though the older smeg was more than a week old and had remained at room temperature and become "chunky and swirly".  The newer smeg had propagated from that same sample. 

Our discussion today also included the ethics of who gets to name a phage, or have possession of the sample, if more than one student has worked with the phage and if the soil sample was collected as a group.  I've found this to be an interesting and relevant topic for discussion because it could become an issue between the students if something interesting is discovered.  It's fun to be light-hearted about this topic yet also reference some of the interactions that scientists might be faced with during a research endeavor. 

Today's materials:   

Pointers:

Bill's comments: let plates where we don't see anything incubate for a week.  Bill looked at individual students lawns, even though it had only been 1 day...Bill commented on the plating technique, appreciating good lawn.  Bill wanted all students to count their -6 plates today, use ethanol to erase the markings, mark the side of plate, don't erase where your marks are, and see tomorrow if their are new plaques that were not counted today.  Can't do the -5.  Bill recommends that we harvest from Lacy plates tomorrow, using our -4. 

Bill question: how long will you guys

Since we did dilutions of our single plaques yesterday, Bill recommended that we count on plates today where is 20-200 on our dilutions, Let incubate and count these.  Bill has a seminar at 10; he will be in at 11 and wants to look at plates and will talk tomorrow. 

Marissa Pedulla, first author of the cell paper, is an olympic judo contender.  She is going to be the head coach for US olympic coach at Pittsburg.  ...another BXZ1 phage has been gotten in pittsburg, it is one of only 2 phages found to date that could be used as a generalized transducing phage, a useful tool in bacterial genetics.  is a very big phage...when compare bxz1 to other phages...will see these are much smaller, because genome of bxz1 is about 180 kb, while most mycobacterial phage are in range of 80 kb, is about half the size.  more dna must be fit.  corndog...this was found right outside university of pitt, in dirt, they found 2 phages from allantown closely like bxb1 in resemblance...4 x size from D29, intense center and halo..genomically similar, but still different.  never found same phage twice, are lots of phages to be found.  this weekend, if at interesting places, since are experts, just keep getting samples.  keep records of where isolating phages from.  plan is at 1110 tomorrow, wants to see everyones plates, numbers that you count, recount plates, tomorrow use red markers if additional plaques...and we will talk then. 

Phage are not readily called virus, although I have been tempted.  An MD that teaches infectious disease at Einstein gave me this rational: viruses are animal pathogens, and are not really able to subsist in the environment.  However, phages are able to persist in the environment.  Recognize that a little bit of phage on the countertop today will probably be there tomorrow!