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Recent Activity

All posts created by stpage

Link to this post \| posted 14 Mar, 2022 14:25
stpage	Hi, we had this discussion when we annotated MarioKart a little over a year ago. I am not sure that there is not a frameshift but just felt like there wasn't enough evidence to call it. Nhagos and Sours have 4 Gs around the end of gene 21 that is the region identified as the slippery sequence. Does yours have Pham 113375 or 115039? It might be worth tracking it by Pham rather than by cluster.

Posted in: Frameshifts and Introns → Frameshift in DR phages?

Link to this post \| posted 15 Nov, 2021 17:17
stpage	fogartym1 Thanks Vic! We will try it out and report back on how it goes. Marie Hi, did you ever have any luck with this? I have a student who has apparently lost their phage that they isolated a couple of weeks ago. We'd like to take his old plaques and PB and amplify them back up. Thanks.

Posted in: Phage Discovery/Isolation → Protocol to grow phage in culture?

Link to this post \| posted 27 Oct, 2021 23:34
stpage	Thanks, Vic. That is helpful. We were losing some DNA and weren't sure if we were getting capsid denaturation from the proteinase K. Different protocols seem to have wildly different proteinase K conditions.

Posted in: Phage Discovery/Isolation → Capsid denaturation

Link to this post \| posted 27 Oct, 2021 19:27
stpage	Hi, the phage discovery has RNase/DNase/ProteinaseK treatment followed by CleanupResin (guanidinium thiocyanate) to denature the capsid. Some protocols seem to use proteinaseK to denature the capsid. (https://www.mdpi.com/2409-9279/1/3/27/pdf-vor) and some seem intermediate (https://pubmed.ncbi.nlm.nih.gov/29417429/). Is it very phage dependent? With new hosts do we need to optimize the proteinaseK treatment??

Link to this post | posted 27 Oct, 2021 19:27

stpage

Hi, the phage discovery has RNase/DNase/ProteinaseK treatment followed by CleanupResin (guanidinium thiocyanate) to denature the capsid.
Some protocols seem to use proteinaseK to denature the capsid. (https://www.mdpi.com/2409-9279/1/3/27/pdf-vor)
and some seem intermediate (https://pubmed.ncbi.nlm.nih.gov/29417429/).

Is it very phage dependent? With new hosts do we need to optimize the proteinaseK treatment??

Posted in: Phage Discovery/Isolation → Capsid denaturation

Link to this post \| posted 26 Feb, 2021 18:57
stpage	There are 6 B1 phages in phagesdb calling the holin.

Posted in: Cluster B Annotation Tips → Holin

Link to this post \| posted 26 Feb, 2021 18:57
stpage	There are 6 B1 phages in phagesdb calling the holin.

Posted in: Cluster B Annotation Tips → Holin

Link to this post \| posted 19 Feb, 2021 19:16
stpage	stpage Thanks, Chris. That was pretty peppy response for a Friday afternoon….@! FIrefox worked, thanks.

Posted in: DNA Master → DNA master server down?

Link to this post \| posted 19 Feb, 2021 19:12
stpage	Thanks, Chris. That was pretty peppy response for a Friday afternoon….@!

Posted in: DNA Master → DNA master server down?

Link to this post \| posted 19 Feb, 2021 17:30
stpage	Is the DNA master server ftp://cobamide2.bio.pitt.edu/DNAMas/dna%20master.exe having trouble this week or is it us? Shallee

Posted in: DNA Master → DNA master server down?

Link to this post \| posted 09 Mar, 2020 20:24
stpage	Pham95856 still has a range of functions listed: Within that pham, there are functional annotations for RNAseE, sigma factor, DNase, endoribonuclease and just helix-turn-helix DNA binding domain protein. I know some B cluster in that pham were changed from RNAseE to helix-turn-helix DNA binding domain protein. Is that the best choice for our DR cluster.

Posted in: Functional Annotation → ribonuclease function