Restriction Digestion and Bacteria

Richard_Heath heath at mbcf.stjude.org
Sun Mar 12 14:12:14 EST 1995


In article <9503080913.aa16810 at etsuodt.etsu.edu>, betts at ORION.ETSU.EDU (GORDON BETTS) writes:
> Greetings,
> A microbiologist colleague has approached me about cooperating on a project
> he is giving a grad student concerning types of E. coli in a dairy herd.  My
> previous experience in cell culture has mostly centered around killing
> bacteria rather than trying to understand it so I am expanding my horizons
> again.
> His idea has to do with analyzing some samples he has in his freezer from 6
> years ago and comparing them with current E. coli populations at said dairy
> which now uses different antibiotics than in the past.  He wants to know if
> we can restriction digest genomic DNA to compare the E. coli.
> I suppose some specific questions are:
> 1) Is this project feasible?
> 2) Can simple restriction digestion of genomic DNA be used to compare
> different strains?
> 3) Would digestion of plasmids be a better approach?
> 4) What restriction enzymes would be best?
> 5) Instead must we use RFLP analysis to accomplish this project?
> Thanks,
> Gordon Betts
> Biology Dept.
> East Texas State University
> Commerce, TX 75429-3011
> 903/886-5369
> ============================================================================
> ======
> The Today show did a story on people that complain.  Don't you just hate
> stories like that?  They're such a waste of time.  And besides that, they're
> always....
> ============================================================================
> ======

You may also want to look into other methods, such as the use of REP
(repetitive extragenic palindromic) elements:  one ref I can give you is 

Dimri, G.P.  et al "Physical Mapping of Repetitive Extragenic Palindromic
Sequences in E. coli and Phylogentic Distribution among E. coli Strains and
other Enteric Bacteria"  J. Bacteriol, v174(14) pp4583-4593.

I have only come across these things from another angle, but they look as if
the can be of use in distinguishing strains.

Best Wishes,

Richard Heath



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