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JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by debbie
Link to this post | posted 08 Dec, 2023 00:06 | |
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The immunity repressor in Feyre (gp 43) is interrupted by the insertion of the transposase. Preliminary testing shows that Feyre does not make a lysogen (and the immunity repressor is not working). |
Link to this post | posted 01 Dec, 2023 04:59 | |
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More papers about cluster K phages: Mycobacteriophage ZoeJ: A broad host-range close relative of mycobacteriophage TM4 https://pubmed.ncbi.nlm.nih.gov/30948168/ A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells https://pubmed.ncbi.nlm.nih.gov/17083467/ Mycobacteriophage TM4: genome structure and gene expression https://pubmed.ncbi.nlm.nih.gov/10645443/ Genome Sequences of Mycobacteriophages Amgine, Amohnition, Bella96, Cain, DarthP, Hammy, Krueger, LastHope, Peanam, PhelpsODU, Phrank, SirPhilip, Slimphazie, and Unicorn https://pubmed.ncbi.nlm.nih.gov/29217790/ Genome Sequences of Mycobacteriophages Findley, Hurricane, and TBond007. https://pubmed.ncbi.nlm.nih.gov/29122862/ Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557439/ |
Link to this post | posted 05 Oct, 2023 17:48 | |
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Hi all, I chatted with Graham about this and here's what i have gleaned from the conversation. Temperature and pH can affect how well the calcium goes into the solution. Maybe try a different source of peptone or yeast extract to see if it improves. best, debbie |
Link to this post | posted 05 Oct, 2023 15:16 | |
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Eric, Yep. Calcium does precipitate out of solution at high temps. You can omit Ca in the autoclaved recipe and then add it back as you use the agar. You can also play with the concentrations. What you can't do is omit calcium. Many phages need calcium for adsorption, infection and stability. Make sense? debbie |
Link to this post | posted 28 Sep, 2023 17:02 | |
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Hi Dane, In general, we keep one. But until the 'one' has been verified, meaning that the lysogen infection pattern 1) shows homoimmunity to the phage and 2)the phage is detected in the supernatant of the lysogen, more than 1 is advisable. The answer is also dependent on how the different streaks were obtained - from single colonies or out of a 'mesa', because having 4 different clones would be advisable depending on what you want to do. So what questions are you going to investigate with your newly made lysogens? Best, debbie |
Link to this post | posted 21 Aug, 2023 16:35 | |
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I agree with your student. I would not call it. From my collegue, Christian Gauthier, "It looks to have an extremely poor D-loop and a weird anticodon loop. Acceptor stem and pseudouridine stem/loop both look OK. If I were a gambling man, I’d speculate that there used to be a tRNA there, but it has undergone some mutational decay and is almost certainly defective. I wouldn’t be inclined to annotate it." Best, debbie |
Link to this post | posted 08 Aug, 2023 13:24 | |
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The immunity repressor (pham 99175) from cluster A is present in other cluster genomes along with their own cluster specific immunity repressor– specifically C1 (LittleE) , K (, and F1(DLane), CA (Phrankenstein), J(Courthouse), and K (SamScheppers). Graham described this “immunity theft” in Pope et al 2011 in PLoS One https://pubmed.ncbi.nlm.nih.gov/21298013/ From Rick Pollenz: Some of the cluster F1 (and the others Debbie mentioned) have TWO “immunity repressors”, one that is grouped to those mostly from cluster A (Pham 99175) and a second one that is specific to the cluster phage. These rogue one is typically found in a set of 2-3 reverse genes upstream of the integrase. The 2nd repressor is found downstream of the integrase in a 2nd set of reverse genes and groups to a different PHAM. Both sets of reverse genes are on during lysogeny and this is nicely illustrated in the RNA seq figure 4 for phage Fruitloop in the gp52 Wag paper (https://onlinelibrary.wiley.com/doi/10.1111/mmi.13946) where gp37 is the “rogue” hetroimmunity repressor and gp44 is the putative immunity repressor. |
Link to this post | posted 08 Aug, 2023 13:22 | |
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The immunity repressor (pham 99175) from cluster A is present in other cluster genomes along with their own cluster specific immunity repressor– specifically C1 (LittleE) , K (, and F1(DLane), CA (Phrankenstein), J(Courthouse), and K (SamScheppers). Graham described this “immunity theft” in Pope et al 2011 in PLoS One https://pubmed.ncbi.nlm.nih.gov/21298013/ From Rick Pollenz: Some of the cluster F1 (and the others Debbie mentioned) have TWO “immunity repressors”, one that is grouped to those mostly from cluster A (Pham 99175) and a second one that is specific to the cluster phage. These rogue one is typically found in a set of 2-3 reverse genes upstream of the integrase. The 2nd repressor is found downstream of the integrase in a 2nd set of reverse genes and groups to a different PHAM. Both sets of reverse genes are on during lysogeny and this is nicely illustrated in the RNA seq figure 4 for phage Fruitloop in the gp52 Wag paper (https://onlinelibrary.wiley.com/doi/10.1111/mmi.13946) where gp37 is the “rogue” hetroimmunity repressor and gp44 is the putative immunity repressor. |
Link to this post | posted 03 Aug, 2023 20:20 | |
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Hi Steve, Will you record? Thanks, debbie |
Link to this post | posted 31 Jul, 2023 19:31 | |
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The approved function list says you have to have a transposon to have a transposase. I don’t know the answer to that. I would ask that you looks as well as you can and if you don’t find something that looks like a transposon, just call the transposase and make note on your cover sheet. Another thing to consider is the types of transposons – papers will define the ends and that may help you find the transposon. |