SEA-PHAGES | All posts created by pia1@pitt.edu

Link to this post \| posted 25 Jun, 2025 14:46
pia1@pitt.edu	Thanks for the quick response! Debbie. I'll move on to the next step with the homo-immunity test and will keep you posted with more data and most likely, more questions. Ping

Posted in: Lysogeny/Immunity → Liquid phage release assay

Link to this post \| posted 25 Jun, 2025 14:35
pia1@pitt.edu	Hello, My question is regarding the expected titer of phage in the supernatant of a liquid phage release assay from a potential lysogen. I'm trying to verify my potential G. terrae phage lysogens using liquid phage release assay. After 2 rounds of streak, I set up liquid culture for these potential lysogens for 3 days. I then collected and titrated the supernatant using spot test. The titers are at least 1x10^5 pfu/ml with clearing and plaque patterns consistent with the serial dilutions. I'm wondering if a titer of 1x10^5 pfu/ml is sufficient for me to conclude that I have a lysogen that is releasing phages, or if I should expect higher titers to draw that conclusion. Is there a recommended threshold of titer for this assay? Thanks! Ping

Link to this post | posted 25 Jun, 2025 14:35

pia1@pitt.edu

Hello,

My question is regarding the expected titer of phage in the supernatant of a liquid phage release assay from a potential lysogen.
I'm trying to verify my potential G. terrae phage lysogens using liquid phage release assay. After 2 rounds of streak, I set up liquid culture for these potential lysogens for 3 days. I then collected and titrated the supernatant using spot test. The titers are at least 1x10^5 pfu/ml with clearing and plaque patterns consistent with the serial dilutions. I'm wondering if a titer of 1x10^5 pfu/ml is sufficient for me to conclude that I have a lysogen that is releasing phages, or if I should expect higher titers to draw that conclusion. Is there a recommended threshold of titer for this assay?
Thanks!
Ping

Posted in: Lysogeny/Immunity → Liquid phage release assay

Link to this post \| posted 19 May, 2025 16:11
pia1@pitt.edu	scresawn pia1@pitt.edu pia1@pitt.edu Just wondering if anyone's experiencing issues with Phamerator. I've been getting the same "ERR_CONNECTION_TIMED_OUT" multiple times this morning. Please see attached for more details. Quick update, Phamerator is working now. We had a power outage this morning that knocked things offline temporarily. These services were down but are now back up and running: Phamerator.org, Notebook API, GenesDB.org. Thanks! Steve.

Link to this post | posted 19 May, 2025 16:11

pia1@pitt.edu

scresawn
pia1@pitt.edu
pia1@pitt.edu
Just wondering if anyone's experiencing issues with Phamerator. I've been getting the same "ERR_CONNECTION_TIMED_OUT" multiple times this morning. Please see attached for more details.
Quick update, Phamerator is working now.

We had a power outage this morning that knocked things offline temporarily. These services were down but are now back up and running: Phamerator.org, Notebook API, GenesDB.org.

Thanks! Steve.

Posted in: Phamerator → Phamerator down?

Link to this post \| posted 19 May, 2025 14:34
pia1@pitt.edu	pia1@pitt.edu Just wondering if anyone's experiencing issues with Phamerator. I've been getting the same "ERR_CONNECTION_TIMED_OUT" multiple times this morning. Please see attached for more details. Quick update, Phamerator is working now.

Posted in: Phamerator → Phamerator down?

Link to this post \| posted 19 May, 2025 12:10
pia1@pitt.edu	Just wondering if anyone's experiencing issues with Phamerator. I've been getting the same "ERR_CONNECTION_TIMED_OUT" multiple times this morning. Please see attached for more details. 23Kb

Posted in: Phamerator → Phamerator down?

Link to this post \| posted 19 Sep, 2024 20:09
pia1@pitt.edu	Thank you for fixing the Phamerator! Steve. You really saved my day

Posted in: Phamerator → Phamerator down?

Link to this post \| posted 19 Sep, 2024 16:39
pia1@pitt.edu	Phamerator is back online!

Posted in: Phamerator → Phamerator down?

Link to this post \| posted 18 Sep, 2024 18:47
pia1@pitt.edu	scresawn jrocheleau Just wondering if phamerator is currently down - I haven't been able to access it all morning. It says 'this site can't be reached.' Yes, it's currently down while we work through a hardware issue with the servers. Hi, we plan to teach Phamerator next week and would greatly appreciate it if you could provide an estimate of when Phamerator will be back online. This will help us determine whether we need to adjust our plans. Thank you!

Link to this post | posted 18 Sep, 2024 18:47

pia1@pitt.edu

scresawn
jrocheleau
Just wondering if phamerator is currently down - I haven't been able to access it all morning. It says 'this site can't be reached.'

Yes, it's currently down while we work through a hardware issue with the servers.

Hi, we plan to teach Phamerator next week and would greatly appreciate it if you could provide an estimate of when Phamerator will be back online. This will help us determine whether we need to adjust our plans. Thank you!

Posted in: Phamerator → Phamerator down?

Link to this post \| posted 22 May, 2024 15:30
pia1@pitt.edu	Both GeneMarkS and host trained GeneMark are back online through PhagesDB!

Posted in: PECAAN → GeneMarkS ?

Link to this post \| posted 21 May, 2024 17:30
pia1@pitt.edu	Hi, GeneMark is down on PhagesDB. So I tried to follow the instructions listed above to run GeneMarkS online. That didn't work for me. Please see attached for the error message I got. Has anyone got GeneMarkS to run today? Thanks! Ping 198Kb

Posted in: PECAAN → GeneMarkS ?

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