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Recent Activity

All posts created by stpage

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

Link to this post \| posted 03 Mar, 2020 20:43
stpage	Yeah, that location in Mariokart is just AGGGCCG…. Yago84 did not call the frameshift but there is a aagggcct So maybe I should just follow that.

Posted in: Cluster DR Annotation Tips → Tail Assembly Chaperone

Link to this post \| posted 03 Mar, 2020 17:15
stpage	Thanks again, Erin. It makes more sense looking at the GenBank entry rather than Phamerator. I don't have that many Gs, but I'll try a mockup of the frameshift and see how it looks in Mariokart.

Posted in: Cluster DR Annotation Tips → Tail Assembly Chaperone