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All posts created by c.sunnen

| posted 13 Sep, 2018 18:52
Hi all!
This is the first year we're working with M. foliorum, so we've switched to PYCa from 7H9. We've had issues with TA solidifying in the past, and the solution was to increase our agar concentration. But I'm wondering if there is any further insight/ideas as to what's happening in this particular case.

We make individual bottles (~100-200mL) 1x TA and keep them in a water bath at 60deg, so that each pair of students has their own bottle. All bottles are aliquoted from the same stock, right out of the autoclave. Students are instructed to take their bottles out and wait until they can safely handle them (not to hot to pick up), before plating. This is usually on the order of 5-10min.

Some of my students are having success plating, and others can't get their TA to solidify; even when left out for 2+ hours! In one case, I had a student plate 12 plates total; her first one never solidified, but the other 11 did within about 10-15min). Also, it seems to really only a be a problem with our morning class (but not our afternoon class). It's very strange.

I wonder how important temperature is in this process? Is it possible that if it's too hot, it simply will never solidify? Or is it possible that the plates can be too hot/cold/moist/dry? Any insight is appreciated!

Thanks hive mind!
Posted in: Phage Discovery/IsolationIssues with getting PYCa top agar to solidify
| posted 10 Jul, 2018 21:15
Hi. I'd like to ask for a bit of clarification here. I'm QCing MilleniumForce (another F1), and I've got 2 genes that both match to HTH DNA binding domains and immunity repressor when BLASTed. Both have pretty convincing HHPred data. Both are in the reverse direction. So my question is more about synteny. Which one is it? My options are (stop=34769) upstream and adjacent to Cro and antirepressor (both fwd), or further upstream than that by a few genes (stop=31573). I'm assuming it's the one directly adjacent to Cro?

Thanks!
Nikki
Posted in: Functional AnnotationImmunity repressors in Cluster F
| posted 11 Jun, 2018 14:12
Okay! I'm QCing an F cluster (QuickMath) that calls a transposase. According to the approved functions list, there must be a tranposon. I don't know how to begin to check for this.

Thanks!
Posted in: Functional Annotationtransposase in F cluster?
| posted 21 May, 2018 13:54
I'm posting here because it seems logical to me to keep this MPME question within this thread. In the F1, NormanBulbieJr, we have a sequence that is only one amino acid different from the MPME1 in BPs_58. For now, I'm calling it MPME1, but perhaps it's a new one? Results below are from phagesdb:

>BPs_58, function unknown, 123
Length = 123

Score = 270 bits (690), Expect = 5e-73
Identities = 122/123 (99%), Positives = 122/123 (99%)

Query: 1 MFPITDTRREMTTMPTTEHESDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS 60
MFPITDTRREMTTMPTTEH SDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS
Sbjct: 1 MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS 60

Query: 61 TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDMLVVFDYDTSPNKAQADTADD 120
TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDMLVVFDYDTSPNKAQADTADD
Sbjct: 61 TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDMLVVFDYDTSPNKAQADTADD 120

Query: 121 DPR 123
DPR
Sbjct: 121 DPR 123
Posted in: Cluster F Annotation TipsMPMEs--which one?
| posted 10 May, 2018 18:21
Hey Greg,

I found your question while I was looking for something else, but I might be helpful. We do something similar with our students, in that they maintain an electronic (GoogleDocs) annotation notebook. So for every gene they annotate in DNAMaster, they also have a more complete entry with screenshots in our shared GoogleDrive folder. So we have all the HHPred screenshots (whether it supported a function or not). It's not the complete report, but it does show the alignment/top hits and their e-values, etc.

Sorry you didn't get any suggestions earlier!
Nikki
Posted in: DNA MasterHHPred Question - Concern
| posted 17 Jan, 2018 15:25
Close up of the table that appears upon opening, that lists the errors. Note that clicking the "download from FTP site" also doesn't fix the problem.
Posted in: DNA MasterError messages upon startup
| posted 17 Jan, 2018 15:25
The second is attached here. I can't remember when exactly it appears, but shortly after closing out the first. I think it pops up when you try to open a file. Note that it will let you proceed… but then it craps out and fails.
Posted in: DNA MasterError messages upon startup
| posted 17 Jan, 2018 15:24
Hello hive-mind!
We are having issues with DNA Master upon start-up. This is only happening to our 2 new instructors that have recently downloaded and installed DNA Master (back in December, I think). One is running it on a PC, the other in the Wine bottle on a Mac. I've included the screenshots below from the PC. It appears as though the program is actually missing pieces (like it installed incorrectly), but uninstalling and re-downloading/re-installing is not fixing the errors. Please help! Those of us that had DNA Master installed previously are not encountering these errors. I'm concerned that our students will also encounter this issue…
(Please note that I also posted this in the "Annotation" forum about a week ago, but haven't received any responses yet. I figured this was a more appropriate place to post my question).

Thanks! Additional images of the errors in subsequent messages. Attached is the first error message to appear upon startup.
Posted in: DNA MasterError messages upon startup
| posted 11 Jan, 2018 21:51
Close up of the table that appears upon opening, that lists the errors. Note that clicking the "download from FTP site" also doesn't fix the problem.
Posted in: DNA MasterDNA Master errors
| posted 11 Jan, 2018 21:50
First error message, encountered upon opening DNA Master is found above. The second is attached here. I can't remember when exactly it appears, but shortly after closing out the first.
Posted in: DNA MasterDNA Master errors