Link to this post | posted 14 Nov, 2025 19:13

debbie

Beth, Hmm. If you original colony was surrounded by phage, you may be picking up exogenous phage. So streak it 3 times on agar. Then grow a culture and plate. Is the background filled with plaques? You can perform a streak of that bacteria on a plate of wild type bacteria, but use the culture to make your lysogen plate for testing. If that is what you have done, then your lysogen is very leaky…. You may never get a culture grown, but if you do and you plate, and it is a webbed looking plate. sometimes the spot titers will still show up, even in the mess. Have you tried to grow up the lysogen using a phage seeded plate (instead of cultures the cells from a spot). if so, do you have %lysogeny numbers? Just all something to think about. debbie

Link to this post | posted 14 Nov, 2025 18:27
debbie	Hi Beth, Have you colony purified the lysogen? You want to remove exogenous phage from the bacteria that you are growing in a liquid culture. If you are starting from a plate seeded (or loaded) with phage, you will get lots of killing in a liquid culture. Best, debbie

Link to this post | posted 08 Nov, 2025 03:38
debbie	Ping, I would not do that. The lysogen could technically (though unlikely) be to the other phage. It would be helpful to have a pcr designed to show integration….. I would recommend testing other DC1 phages on the lysogen. debbie

Link to this post | posted 07 Nov, 2025 22:21
debbie	Ping, My best suggestion is to plate for single plaques, and pick a plaque that represents the majority of phenotypes THAT IS WELL ISOLATED FROM OTHERS PLAQUES and make a new stock. You can PCR to confirm, but not rule out contamination. When purifying, pick early. I hope that makes sense. best, debbie

Link to this post | posted 07 Nov, 2025 18:47

debbie

Hi Ping, You have a seqeunce right? And you have identified the repressor. You can compare it to other DC1 phage sequences. And you have other DC1 phages in your U of Pittsburgh collection. Test those! Consider compiling the data of DC1 phages, their infections patterns and their genomic comparisons (especially of the repressor sequence). And note that the simplest answer may be the best one - is your lysate pure? And I agree with Vic - grids of dilutions presented in a comparative way (when you repeat) will produce publication quality pictures. debbie

Link to this post | posted 07 Nov, 2025 15:50

debbie

If both phages have the same repressor, then a lysogen of one should not be infected by the other phage. We have examples where the phages of the same cluster do infect a lysogen, but their repressor is broken/absent. We also have examples where a phage can carry 2 different repressors (why not, right?) and keep keep out phages of a different cluster. in order for a phage to maintain lysogeny, a repressor can be essential. Papers include Cell, 2023. Other papers of D29. A paper about phage Tweety…. Lots of examples. debbie

Link to this post | posted 31 Oct, 2025 13:09
debbie	Thanks Rick! Christine - I would follow Rick's advice! debbie

Link to this post | posted 30 Oct, 2025 01:56
debbie	Hi Haley and Christine, I don't believe that there is enough evidence to calla function for this protein. Be sue to document this call when submitting it. Include this post in your cover sheet. Thanks, debbie

Link to this post | posted 22 Oct, 2025 15:00
debbie	Nope! But provide that here and I will add that to the function list, so others can pick the best model number. Would that work? Also provide me with the list of genes that you have called. I can add them as examples too. Thanks, debbie

Link to this post | posted 22 Oct, 2025 14:51
debbie	Hi Peter, We are going to cautiously weigh in on what to name the various structures of siphoviruses. The data is coming to us fast and furious, and not all crystallographers are using the same nomenclature. I have added the features (as you have identified)to the Approved Function List that I think we can call with a modicum of confidence. Let me know if my list works! Thanks, debbie