Link to this post | posted 14 Sep, 2018 13:41
c.sunnen	Karen, Thanks! This was another of my suspicions; if there was something different about those bottles that got aliquotted first, vs. those that got aliquotted last. The speed of responses has been exceptional, all! I'll let you know how we fair next week with fresh agar, warm plates, and venting while solidifying! Nikki

Link to this post | posted 14 Sep, 2018 12:53

c.sunnen

Thank-you both! These are the kinds of things I'd suspected (and could explain why the morning class is having issues, but the afternoon class is not; plates are generally already pulled out and sitting at room temp for the afternoon class, but not the morning). Interesting side note: We took a couple bottles of TA out of the water bath and let them sit out at room temp. Many hours later, they are still liquid. So I think a new batch of TA is in order anyway! But we'll be sure to use room temp plates, and we'll keep the water bath at 60deg (relatively hot!). Thanks again! Nikki

Link to this post | posted 13 Sep, 2018 18:52

c.sunnen

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!

Link to this post | posted 10 Jul, 2018 21:15

c.sunnen

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

Link to this post | posted 11 Jun, 2018 14:12
c.sunnen	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!

Link to this post | posted 21 May, 2018 13:54

c.sunnen

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

Link to this post | posted 10 May, 2018 18:21

c.sunnen

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

Link to this post | posted 17 Jan, 2018 15:25
c.sunnen	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. 41Kb

Link to this post | posted 17 Jan, 2018 15:25
c.sunnen	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. 142Kb

Link to this post | posted 17 Jan, 2018 15:24

c.sunnen

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. 143Kb