SEA-PHAGES | All posts created by SBS

Link to this post \| posted 07 Mar, 2023 16:49
SBS_UNL	tperezmo Hello all, I checked previous conversations for RBS but they don't match the error we receive. 2 of our students are unable to visualize the RBS table with the Z values included. We have done the following with no result: uninstall and reinstall, update DNA Master to latest version successfully. Neither brings up the RBS table with all the required information. Other PCs were able to see the RBS table after the DNA Master update. Hope you are able to help us! Thank you Tiara good morning. Just a suggestion…One of my students had a similar issue after re-installing the program on her laptop (she had a working program; her OS system crashed but then 'worked' after re-booting). We looked at the DNA Master preferences and some of settings were correct but some had changed! Perhaps reviewing yours might reveal some quirky changes that might need to be re-set? Cathy Chia Univ. Nebraska-Lincoln Edited 07 Mar, 2023 20:59

Link to this post | posted 07 Mar, 2023 16:49

tperezmo
Hello all,

I checked previous conversations for RBS but they don't match the error we receive. 2 of our students are unable to visualize the RBS table with the Z values included. We have done the following with no result: uninstall and reinstall, update DNA Master to latest version successfully. Neither brings up the RBS table with all the required information. Other PCs were able to see the RBS table after the DNA Master update.
Hope you are able to help us!
Thank you

Tiara

good morning. Just a suggestion…One of my students had a similar issue after re-installing the program on her laptop (she had a working program; her OS system crashed but then 'worked' after re-booting). We looked at the DNA Master preferences and some of settings were correct but some had changed! Perhaps reviewing yours might reveal some quirky changes that might need to be re-set?
Cathy Chia
Univ. Nebraska-Lincoln

Edited 07 Mar, 2023 20:59

Posted in: DNA Master → RBS table in PC

Link to this post \| posted 25 Jan, 2022 00:52
SBS_UNL	sahas Hi I was wondering if anyone can recommend a place/lab to send our samples for electron microscopy? We haven't been successful in finding a resource yet. Any help will be highly appreciated. Thanks Sangha Our Core Microscopy Facility has done TEM for the phage course here at the Univ. Nebraska-Lincoln, and neighboring schools (Nebraska Wesleyan also in Lincoln, and Doane Univ. in nearby Crete), so has lots of experience with phage samples. Here is the web site: https://biotech.unl.edu/microscopy with contact info and fees. I don't know how busy the TEM is, but if you find the rates work for your budget, you can check with the Director about their schedule. Cathy Chia UNL

Link to this post | posted 25 Jan, 2022 00:52

SBS_UNL

sahas
Hi
I was wondering if anyone can recommend a place/lab to send our samples for electron microscopy? We haven't been successful in finding a resource yet.
Any help will be highly appreciated.
Thanks
Sangha

Our Core Microscopy Facility has done TEM for the phage course here at the Univ. Nebraska-Lincoln, and neighboring schools (Nebraska Wesleyan also in Lincoln, and Doane Univ. in nearby Crete), so has lots of experience with phage samples. Here is the web site: https://biotech.unl.edu/microscopy with contact info and fees. I don't know how busy the TEM is, but if you find the rates work for your budget, you can check with the Director about their schedule.
Cathy Chia
UNL

Posted in: General Message Board → Electron Microscopy

Link to this post \| posted 17 Apr, 2021 16:49
SBS_UNL	cdshaffer OK just an update. The most recent version of the database (403) vine_74 is back to pham 58246. It still appears as pham 57934 on phagesdb so the phagesdb links are out of date and will not work but the first link above will, at some point phagesdb will update and should then report vine_74 is back in pham 58426. Thank you for the followup.

Posted in: Starterator → Pham not found in Starterator

Link to this post \| posted 14 Apr, 2021 20:41
SBS_UNL	We are annotating Vine. The pham for gene 74 (start 47825) was 58426 when initially phamerated. It is now pham 57943 (7 members), but a starterator report was not available yesterday, and unavailable today. Version 402 shows for phagesdb and starterator, and phamerator.org. Any insights will be appreciated. Thank you.

Posted in: Starterator → Pham not found in Starterator

Link to this post \| posted 27 Feb, 2019 00:07
SBS_UNL	Debbie Jacobs-Sera Cathy, The owner of the file got hacked which is where that google sheet resided. I just learned of this today, so I am going to need some time to see if this attached list matches what was posted. In the meantime, here is the list I have. Thank you for the info and spreadsheet. Cathy

Posted in: Phage Discovery/Isolation → Cluster Specific Primers

Link to this post \| posted 26 Feb, 2019 20:49
SBS_UNL	Hello, Students last spring used the PCR protocol dated 11-14-17 (found in Protocols of phagesdb), and we accessed the Hatfull primers (link to Google sheets) when ordering primers. I am now getting a message that the page has been deleted. Is there a new link for the primers or ? I would like to use this exercise again this semester – it worked well to reinforce agarose gel electrophoresis as well as for understanding PCR. Cathy Chia Univ. Nebraska-Lincoln Edited 26 Feb, 2019 20:52

Link to this post | posted 26 Feb, 2019 20:49

SBS_UNL

Hello,
Students last spring used the PCR protocol dated 11-14-17 (found in Protocols of phagesdb), and we accessed the Hatfull primers (link to Google sheets) when ordering primers. I am now getting a message that the page has been deleted. Is there a new link for the primers or ?

I would like to use this exercise again this semester – it worked well to reinforce agarose gel electrophoresis as well as for understanding PCR.

Cathy Chia
Univ. Nebraska-Lincoln

Edited 26 Feb, 2019 20:52

Posted in: Phage Discovery/Isolation → Cluster Specific Primers

Link to this post \| posted 07 Nov, 2016 15:00
SBS_UNL	My query is somewhat related to DNA extraction/recovery. Using the Wizard kit (kit is newly purchased; and we are following carefully protocol 9.1) we are getting meager yields of DNA for our lysates (titers = or > 10^9 pfu/mL; DNA averaging 20 to 25 ng/µL). At first I thought our lysates were 'old', but even extracting immediately after collecting lysates (a spot plate titer indicated a high titer for the fresh lysate) did not boost the yield. I will concentrate the recent lysates, and have the students extract the concentrate. Are we overlooking something? Any suggestions to increase the recovery of DNA? Cathy Chia at Univ Nebraska-Lincoln (Cohort 9) Viknesh Sivanathan Hi Rodney, I can't say I've seen this, and have not yet heard from anyone with this problem. Perhaps someone who has will chime in. In the meanwhile, would you share a gel where you see the degradation only in the presence of restriction enzyme buffer? I assume the buffer isn't contaminated with DNAse, and that you are using brand new buffer when you used the new enzymes? Vic

Link to this post | posted 07 Nov, 2016 15:00

SBS_UNL

My query is somewhat related to DNA extraction/recovery. Using the Wizard kit (kit is newly purchased; and we are following carefully protocol 9.1) we are getting meager yields of DNA for our lysates (titers = or > 10^9 pfu/mL; DNA averaging 20 to 25 ng/µL). At first I thought our lysates were 'old', but even extracting immediately after collecting lysates (a spot plate titer indicated a high titer for the fresh lysate) did not boost the yield. I will concentrate the recent lysates, and have the students extract the concentrate. Are we overlooking something? Any suggestions to increase the recovery of DNA?
Cathy Chia at Univ Nebraska-Lincoln (Cohort 9)

Viknesh Sivanathan
Hi Rodney,

I can't say I've seen this, and have not yet heard from anyone with this problem. Perhaps someone who has will chime in.
In the meanwhile, would you share a gel where you see the degradation only in the presence of restriction enzyme buffer? I assume the buffer isn't contaminated with DNAse, and that you are using brand new buffer when you used the new enzymes?

Vic

Posted in: Phage Discovery/Isolation → Yield and degradation of DNA isolated by new protocol

Recent Activity

All posts created by SBS_UNL