SEA-PHAGES | All posts created by jdiaz

Link to this post \| posted 17 Sep, 2018 15:32
jdiaz	This year we've switched to Gordonia rubripertincta. Initial streak plates from the stock Debbie sent to us grew pink as expected, as did the subsequent P1FF and P2FF cultures. Plaque assay plates from direct isolation experiments also turned pink. This past week, however, they have failed to turn pink, and a new P1FF culture taken from the same pink P0FF streak plate as earlier grew as a tan/yellow solution after two days of growth in a shaker incubator. Incubations (including shaking) is always at 30C. I know the pink color accumulates over time, but I am trying to figure out why they are not turning pink now, when they did before. Aside from the usual things like testing new PYCa media, etc, I was wondering if anyone else has encountered a similar problem and can tell me a) should I be concerned, and b) ideas for what the problem might be, if any.

Link to this post | posted 17 Sep, 2018 15:32

This year we've switched to Gordonia rubripertincta. Initial streak plates from the stock Debbie sent to us grew pink as expected, as did the subsequent P1FF and P2FF cultures. Plaque assay plates from direct isolation experiments also turned pink. This past week, however, they have failed to turn pink, and a new P1FF culture taken from the same pink P0FF streak plate as earlier grew as a tan/yellow solution after two days of growth in a shaker incubator. Incubations (including shaking) is always at 30C.

I know the pink color accumulates over time, but I am trying to figure out why they are not turning pink now, when they did before. Aside from the usual things like testing new PYCa media, etc, I was wondering if anyone else has encountered a similar problem and can tell me a) should I be concerned, and b) ideas for what the problem might be, if any.

Posted in: Gordonia → G. rubri no longer turning pink in liquid or plates

Link to this post \| posted 17 Sep, 2018 15:27
jdiaz	I have been having similar issues with PYCa top agar, and was starting a new prep regimen this week - this info has been fantastic and super timely, thank you for asking, Nicole, and for all the great advice Karen, Dustin, and Debbie! Edited 17 Sep, 2018 15:27

Posted in: Phage Discovery/Isolation → Issues with getting PYCa top agar to solidify

Link to this post \| posted 12 Jun, 2018 02:30
jdiaz	I realized I forgot to add one clarification: the numbers next to the gene names in the synteny indicate the phage gp designation. In this example you can surmise that there is a gene between Holin and Lysin B which is not relevant to the three genes in question. I find this more straightforward than simply noting what's directly adjacent to the gene in question.

Posted in: Notes and Final Files → Suggested Format for Documenting Synteny

Link to this post \| posted 12 Jun, 2018 02:28
jdiaz	I had a chance at the annual Faculty Meeting to review a genome Claire Rinehart annotated and found he had a very elegant system for recording synteny arguments. I wanted to share that with the community with the minor modification of also adding three reference phages which demonstrate the synteny in question. Simpliphy gp 36 - called as Lysin B Synteny: Lysin A (33) - Holin (34) - Lysin B (36) (MadamMonkfish (E), NoSleep (E), Ukulele (E)) The letters next to the phage names are cluster designations. I find the format elegant and informative. If Welkin and the rest of the community find it useful, we can have it added to the Bioinformatics guide. Hope this is useful!

Link to this post | posted 12 Jun, 2018 02:28

jdiaz

I had a chance at the annual Faculty Meeting to review a genome Claire Rinehart annotated and found he had a very elegant system for recording synteny arguments. I wanted to share that with the community with the minor modification of also adding three reference phages which demonstrate the synteny in question.

Simpliphy gp 36 - called as Lysin B
Synteny: Lysin A (33) - Holin (34) - Lysin B (36) (MadamMonkfish (E), NoSleep (E), Ukulele (E))

The letters next to the phage names are cluster designations. I find the format elegant and informative. If Welkin and the rest of the community find it useful, we can have it added to the Bioinformatics guide.

Hope this is useful!

Posted in: Notes and Final Files → Suggested Format for Documenting Synteny

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