Link to this post | posted 11 Aug, 2025 12:55
stpage	Hi, has anyone done kinetics assays on the phage replication using chloroform? We got some discrepant results…..

Link to this post | posted 22 Jul, 2025 13:12
stpage	Contracted tail 533Kb

Link to this post | posted 22 Jul, 2025 13:11
stpage	Hi, I have some fun TEM pictures, one typical, one with the tail contracted and one with the tail protein (like the gp18 of T4) that is unwinding off of the center stalk? (or maybe contracted with a long fiber of schmutz behind it) Edited 22 Jul, 2025 13:13 501Kb

Link to this post | posted 12 Jun, 2025 18:15

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I think I would say in general that the pleskstrin-homology domains closely share a structure, but do not closely share sequence similarity *nor function*. So, not super useful annotation anyway. See: Mark A. Lemmon, Chapter 136 - Pleckstrin Homology (PH) Domains, Editor(s): Ralph A. Bradshaw, Edward A. Dennis, Handbook of Cell Signaling (Second Edition), Academic Press, 2010, Pages 1093-1101, ISBN 9780123741455, https://doi.org/10.1016/B978-0-12-374145-5.00136-4. (https://www.sciencedirect.com/science/article/pii/B9780123741455001364)

Link to this post | posted 20 May, 2025 18:36
stpage	I ran alpha fold and HHPRED and am not super-convinced. It's only a beta-alpha-beta so pretty small compared to the other structures. But, the closest match in both HHPRED and alphafold is to a bacterial PH domain. So, certainly PH-domain-like. See attachment. 1.45Mb

Link to this post | posted 04 Apr, 2025 08:51

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mthomas There are several putative SAM-degrading enzymes in HollowPurple (e.g., SAM lyase –gp#120 w/ stop codon at 62,755 – evidence is based on HHpred hits; see the entry in PECAAN). If real, these are probably a counter-defense against the bacterial restriction-modification system. (see https://doi.org/10.7554/eLife.61818). There are no SAM-degrading enzymes in other phages in seaphages.org. Thoughts on including this? Can you post the HHPRED coverage and percent identity? What do you get when you do an amino acid sequence alignment against the SAM lyase from T3?

Link to this post | posted 03 Apr, 2025 16:38
stpage	Hi, here is a student tutorial I wrote for the Genome Education partnership. If you have any questions or suggestions, drop me an email! 1.33Mb

Link to this post | posted 03 Mar, 2025 19:41
stpage	Hi is there a standard protocol for reviving phage from -80 stocks? Well, I assume there is. What I mean is, what do y'all recommend?

Link to this post | posted 22 Jan, 2025 20:42
stpage	Our A.glob lawns are often like that but we have been using top agar from early in last semester. We'll give that a try. Thanks, Vic!

Link to this post | posted 22 Jan, 2025 19:10

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So, we have had a lot of trouble amplifying, with great spot tests and poor plaque assays (a lot of killing at high concentration but no nice plaques at any concentration). I suspect lysis from without. So, after checking to make sure that we are plating from a single colony of the correct host, what would be the next step? Some spot test plate pictures attached. Edited 22 Jan, 2025 19:11 2.41Mb 2.44Mb