Link to this post | posted 24 Oct, 2018 19:10

debbie

Hi all! Sometimes you may be looking for a reference genome and this might help. As of Sept., 2018 I am trying to clear the backlog of genomes and am attacking them cluster by cluster. Cluster B1s are on my list. As of today, October 24, 2018, I have QC'd 9 Cluster B1 phages to the best of my ability. I have cross-checked starts, respected Start-Associated-Sequences and addressed functions as well as I could. I will continue to bust through the list of whatever else is out there, but please use the following genomes as well scrutinized guides for your current/future Cluster B1 annotations: Altwerkus, Cannibal, Dione, Jillium, Keitherie, LuckyMarjie, Riggan, Spartan300, and Zelda. As I do more, I will add them to the list.

Link to this post | posted 21 Oct, 2018 13:18
debbie	Hi. Yes. Clustering is the same across the phylum. What strain are you using? I won't tell. debbie

Link to this post | posted 19 Oct, 2018 19:05
debbie	Claire, Good find! I would label it as Hypothetical Protein. Then I would write this note in the notes section of the DNA Master file and in the "Discovery Notes" of the phage page. We don't have an annotation field on the page page, so that is why I would put it there. debbie

Link to this post | posted 28 Sep, 2018 16:07
debbie	Terrific!

Link to this post | posted 18 Sep, 2018 20:58
debbie	The gene that has historically been called an RNAseE (gene 69 in Altwerkus) is a helix-turn-helix DNA binding protein.

Link to this post | posted 18 Sep, 2018 20:46
debbie	Maja is an Arthrobacter phage. Gene 27 has transmembranes identified. I do not know what the function is other than "membrane protein". Maja has 2 integrases - a serine and a tyrosine integrase. It also looks like it has most of the pieces of the lambda repressor system, though most are labeled as helix-turn-helix DNA binding proteins for now.

Link to this post | posted 17 Sep, 2018 15:55
debbie	Jason, The simplest explanation is one of the following: a. you have a non-pigmented mutant b. it is a contaminant (and no longer G. rubi) I would recommend going back to the frozen stock. debbie Edited 17 Sep, 2018 16:10

Link to this post | posted 14 Sep, 2018 14:14
debbie	I use the filtered sample. Evaluate this choice if the number of plaques is <10 in the spot. In this case, I MAY carefully consider picking from the spot. I would also change the volume that I plate from the enrichment. The second consideration is if the spot is contaminated. You may want to refilter or you may have to go back to the original sample and carefully filter. Good luck. debbie

Link to this post | posted 13 Sep, 2018 19:04

debbie

Nikki, Hi. I have no really data to share, but here is my experience. 1. How wet are the plates? sometimes if there is a lot of cold condensation on the surface of the plate, when you add top agar it stays a soup (or a slippery mess). You can avoid this by keeping your plates at room temperature (we do). There are no antibiotics in our PYCa plates, so no harm… 2. The hotter the top agar, the better. (I have no explanation for that, but I have less agar problems when my top agar is on the hot side of things.) 3. Yes, I think the room temperature, but more likely the humidity, plays a factor. I saw this most often when I was in classrooms and in a hurry to get the plates off the benches. I have not data to share to support that. Do you have students vent (i.e. crack them a bit) their plates when drying? I always vent my plates for a short time. It is unlikely that you have bunsen burners in the area, but having a bunsen burner burning in the background sometimes helps (may be totally unsafe in a student lab environment, so it is more important to stay safe). again, this works because the air is dryer.) All I've got for now. Good luck! debbie

Link to this post | posted 10 Sep, 2018 19:07

debbie

Denise, I knew I knew something about this but it took me a few prompts (thanks, Chris) to recall anything. It might be helpful to go to DMDB folder of the DNA Master application folder. there should be a GBS folder for each project. if you have no projects, you should not have any folders, so I am not sure that will fix anything. In July, I had the same problem. Here is what Jeffrey had me do to fix it. However, I couldn't fix and and sent him files. He eventually got it fixed, so I am not sure this will help. According to Jeffrey, the BLOB error means: That means the database tables are not synchronized; each table has multiple files, and premature closing of a program or other database failure can cause them to get out of sync. Close DNA Master Go to the program directory and open the Helper directory Run the dtutil32 program. This is an immensely useful program. Repeat steps below for any database errors. Click the “By Directory” button In the dialog, go to the DMDB directory and open the GenbankProjects.db file Click the Verify button Click the Rebuild button Note any reports that the verification or rebuild was not successful. If so, repeat steps 7 then 6 on the file. If there is corruption, they should rebuild without error, so no errors reported does not mean nothing is working. Repeat steps 4-8 for the GenBankAuthors and GenBankReferences files Restart DNA Master Those are the DB files for GenBank projects and are the most likely files with the out-of-sync entries. Me gain - So I tried this, like I said and couldn't make it work. since then, though, I have corrupted a file or 2. I sought out the GBsubmit folder and deleted the specific folder for a genome. When I did this, I corrupted an 'old' project, so i think it is still applicable to your problem… I know this isn't very helpful, but maybe in wiser hands than mine it will work… You are welcome to call. debbie Edited 10 Sep, 2018 19:10