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Recent Activity
engstrom posted in AAA ATPase or RecA recombinase?
sklambet@ncsu.edu posted in DNA Master on M1 Mac
cdshaffer posted in Whole phage starterator reports
fbaliraine posted in Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?
Debbie Jacobs-Sera posted in Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?
All posts created by cellokiwi
Link to this post | posted 15 May, 2024 16:19 | |
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Hi Claire, I am having an issue where Aragorn is calling A BUNCH of tRNAs when I manually enter the FASTA and PECAAN is calling none of them. I went to put them in with the "Add a gene" button but it only lets me put in stop coordinates, not start. What am I missing? Thanks! |
Link to this post | posted 11 Jul, 2023 17:59 | |
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Hi Dan, I tried to do this and got the error attached in the screenshot. How do I fix this as DNA Master keeps giving me an "FTP Failure" error when I try to update or close it. DanRussell |
Link to this post | posted 17 Sep, 2022 19:15 | |
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What pH is perfect for these bugs? |
Link to this post | posted 13 Sep, 2022 12:52 | |
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So when you pass it, it goes back to yellow for a bit then turns orange again. We sadly don't have the resources to check 16S. Is there a resource for this through the program? The first time we saw it was in a lysogen so I just attributed it to wherever the genome had integrated itself messing with the color. Now, there has been zero change whatsoever. Same media, same CaCl2, same buffer, same incubator, same everything. One colleague suggested it is a carotenoid response to oxidative stress? Does that sound possible? Since we're using the same everything what would suddenly be stressing them out that wasn't before? In the picture the one on the left is a normal Arthrobacter culture and the one on the right is just starting to turn orange. They get darker than that. |
Link to this post | posted 12 Sep, 2022 16:19 | |
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Has anyone ever had experience with Arthrobacter turning orange rather than yellowish? We are pretty sure there is no contamination, but the culture is orange suddenly. |
Link to this post | posted 31 Mar, 2022 14:55 | |
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Debbie, Thank you SO much for the info. I feel much better for not being able to locate it since it is apparently a lot more complicated. Especially since it is a serine integrase. |
Link to this post | posted 29 Mar, 2022 20:01 | |
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Hello, I'm trying to find the attP of my temperate phage. I know it will be directly downstream of the integrase gene. However, how do we find the exact bp number? Is there a tool that will search for it? Is there a particular consensus I should be looking for? Thanks! |
Link to this post | posted 06 Oct, 2021 23:45 | |
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Hi, I was wondering if anyone knows of a good program/tool to construct circular diagrams of our genomes (given that they circularize almost immediately inside the host)? I'm wanting to relate gene expression data to location on the chromosome. Thanks in advance for your help! |
Link to this post | posted 13 Jan, 2020 21:01 | |
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Hello Hive Mind I'm hoping I can get some help with a one step growth curve. My students have tried two different protocols, one of which works successfully in another mycobacteriophage lab, and we have not been able to get a nice S-curve. There is a trend that we see every time, high titer initially that continues to drop. The earliest time point we have tried (other than 0 min which has no plaques) is 10 min and I honestly refuse to believe that they are completing a replication cycle that quickly… So why do we have essentially inverse data to what you would expect? Again, this is highly repeatable; we have tried many times. I'm attaching a representative graph of what we are seeing. Thanks for any and all help we can get! |
Link to this post | posted 15 Oct, 2019 15:00 | |
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We finally had success again by doing 2 things. We let the culture get older in the shaking flask before plating and we doubled the amount of bacteria (from 250 uL to 500uL) when we plated. I still don't know what to do about the fridge plates degrading. Letting them sit at room temp just makes this microbiologist get a nervous tick… lol. Good luck!UNHM |