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

Link to this post \| posted 04 Sep, 2025 00:26
pia1@pitt.edu	debbie fixed! Thanks! Debbie.

Posted in: Bioinformatic Tools and Analyses → Genome length listed as unknown for phage PestoPenguin on PhagesDB

Link to this post \| posted 03 Sep, 2025 20:35
pia1@pitt.edu	Hi, Could someone please shed some light on why the genome length of phage PestoPenguin is listed as unknown on PhagesDB? The fasta file for this phage is available and when I click on Locally BLAST this genome, the header says ">Gorgonia phage PestoPenguin complete sequence, 60439 bp". Thanks! Ping

Posted in: Bioinformatic Tools and Analyses → Genome length listed as unknown for phage PestoPenguin on PhagesDB

Link to this post \| posted 06 Aug, 2025 16:18
pia1@pitt.edu	As a molecular biologist for more than 20 years, I'm completely new to TEM work. I'd really appreciate it if someone could share product information for: the "200–400 mesh carbon–formvar-coated copper grids"; the Pelco tab that holds the grid in position shown in this extremely helpful 2-minute video: https://www.youtube.com/watch?v=F0ZNUykXovk&t=41s Thank you in advance for any details, product numbers, vendors, or ordering sources you can share!

Link to this post | posted 06 Aug, 2025 16:18

pia1@pitt.edu

As a molecular biologist for more than 20 years, I'm completely new to TEM work. I'd really appreciate it if someone could share product information for:
the "200–400 mesh carbon–formvar-coated copper grids";
the Pelco tab that holds the grid in position shown in this extremely helpful 2-minute video: https://www.youtube.com/watch?v=F0ZNUykXovk&t=41s

Thank you in advance for any details, product numbers, vendors, or ordering sources you can share!

Posted in: Phage Discovery/Isolation → Ordering info for TEM work

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?

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