Link to this post | posted 08 Jul, 2017 20:08
lhughes	Thanks for the link, Steve.

Link to this post | posted 07 Jul, 2017 21:03
lhughes	Welkin Pope Yep, we can add officially. give me a phage name and gene number. Aaronocolus_57 I already put it down on the "pending" section of the working list. Will we go with written out "deoxynucleoside monophosphate kinase" or "dNMP kinase"?

Link to this post | posted 03 Jul, 2017 21:50

lhughes

Hi Joyce: At UNT we currently prepare spore suspensions by the following procedure: Spore Harvest Note: Prior to use, all solutions and apparati should be sterilized by autoclaving. 1. Pipet 6-8ml dH2O to a well-sporulating plate (2-3ml for slant cultures). 2. Scrape of growth with a sterile loop to release spores. 3. Collect solution off the top of the plate using a pipet and transfer all liquid into a sterile 15 conical tube. 4. Mix vigorously on a vortex mixer for 1-2 minutes. 5. Filter by vacuum through fiberglass wool to remove mycelial fragments. 6. Centrifuge at 1800 x g for 10 minutes in a Sorvall H1000B rotor (3000 RPM using the Sorvall centrifuge in the HHMI lab) 7. Carefully pour off the supernatant (leave about .5ml or last few drops in) 8. Add 1ml dH2O and mix well. 9. Transfer the mixture to a screw-top vial containing 0.5ml of 80% (w/v) glycerol to achieve a final concentration of 20% glycerol. 10. Store in the freezer at -20 degree celsius. Steve Caruso at UMBC has a slightly different protocol (maybe he can post his as well). On your second question, we use only spread plates for our lawns (the Streptomyces Phage Discovery Guide shouldn't say top agar anywhere - unless I missed an edit somewhere) with good success. We also work from liquid cultures for the spread plates (there are other protocols out there that use spores and top agar, but most require a spore germination step that takes a lot more time). I am assuming that you are planning to use S. griseus (each species has their own quirks). Hope this helps, Lee

Link to this post | posted 01 Jul, 2017 21:17
lhughes	A lot of the BD1 Streptomyces phages have a "dNMP kinase" that isn't on the official list. HHPRED matches are written as "deoxynucleoside monophosphate kinase" so I thought written out might be better? Can we add officially?

Link to this post | posted 01 Jul, 2017 20:56
lhughes	The official list has RuvC resolvase, but all my HHPRED hits for some of our genes are hitting Holliday Junction Resolvase (which I am assuming, hopefully correctly, is really the same thing by a different name). None of the hits use the RuvC resolvase term. Should I stick with RuvC resolvase or would it be better to start using Holliday junction resolvase? Lee

Link to this post | posted 20 May, 2017 16:29
lhughes	The function "DNA-binding ferritin-like protein" is in Streptomyces phage Jay2Jay (BE1), but isn't on the approved list. Should we keep this in the other BE1 with the same gene call or have it removed from Jay2Jay? Thanks, Lee

Link to this post | posted 11 Mar, 2017 03:12
lhughes	Katie: I usually see phage on the site immediately after adding (though the information on the genes takes some time to update). I looked and don't see Warpy on the list at all. Do you have admin rights? I'm just guessing, but that could be an issue. Claire at WKU would be the ultimate source of information to clear up this question. Lee

Link to this post | posted 19 Feb, 2017 20:55
lhughes	I am pretty sure that this is simply due to two independent autoannotations differing in some calls. If you have a class of students each run the autoannotation independently, you will find cases of this where the calls are slightly different in some cases. Lee

Link to this post | posted 03 Feb, 2017 20:41
lhughes	Thanks for the information. I'll think about what I need and determine the best solution to use. Lee

Link to this post | posted 03 Feb, 2017 03:52
lhughes	Bump - Checking to see if anyone can answer my question about getting cluster information into a PhamDB database (see previous post). Thanks, Lee