Link to this post | posted 28 Oct, 2018 14:40

debbie

Rick, Hi. You can find out which clusters of actinobacteriophages are predicted to be temperate by checking the cluster list. http://phagesdb.org/clusters/ There can always be exceptions, but the clues will be present in the genomes. My student researchers have been looking for lysogens by microbacterium phages for a while now. To date, we have one. It appears Zeta1847 forms lysogens. It is a M. paraoxydans phage. debbie Edited 28 Oct, 2018 14:41

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