Link to this post | posted 04 Jun, 2024 14:32

bgibb

Thanks for the replies here. Since my initial post, I emailed the editor handling my MRA to ask about this. Apparently, reviewers for MRA are given a template that includes a question about taxonomy and classification, which is why its coming up in the reviews. I submitted two MRAs this Spring, the first also had reviewer comments asking for classification, but the editor in that case left a note to ignore it. The editor of the second MRA did not leave such a note. However, in the email correspondence, he clarified why it was there and offered similar suggestions that Vic and Debbie made in the posts above for responding to the review request for phage classification info. A few years ago I attended a talk by one of the people on ICTV explaining the updated classification system for viruses (and phage). She showed a phylogenetic tree of phage that also included morphology. The two did not align and made a strong case for moving away from using morphology for classification purposes. I don't know enough about the specifics of ICTV classification system to say if its good or not, but its definitely not easy for us to use.

Link to this post | posted 30 May, 2024 14:03

bgibb

Hi Everyone, One of my MRAs describing phages Argan and Uzumaki just came back from review. One of the reviewers wants us to use ICTV guidelines to classify our phages. The International Committee on Taxonomy of Viruses (ICTV) revamped the process of viral classification, stripping away the use of phage morphology. As far as I can tell, the ICTV website does not provide a useful tool to help classify viruses. The Genbank entries for both phages offer some classification information. In this case, both of these phages have the following full lineage (Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; unclassified Caudoviricetes). This only takes me up through the Class level, and I feel stuck. Has anyone else had to do this? If so, do you have any tips for how I go further, or failing that, how I should respond to the reviewer's request? I have a feeling that this will become more common. Thanks, Bryan

Link to this post | posted 16 Sep, 2023 03:09
bgibb	Hi Tammy, We've started looking at holins, but not exhaustively. Its difficult to conclusively identify holins, but there are candidates located proximal to some of the endolysins in AZ, but not in others.

Link to this post | posted 07 Sep, 2023 20:04
bgibb	We're working to finish up a paper that describes these reference AZ phages and the subclusters breakdown for them, so no- not yet.

Link to this post | posted 03 Jun, 2023 14:32

bgibb

A working group of SEA faculty harmonized 33 AZ phages. These phages have had their start sites and functions checked and when necessary, corrected in genbank submissions. Although some of these phage were annotated a long time ago, the group re-annotated all the reference phage in an effort that we call harmonization. The following AZ phages were included in this process and should be used as reference when annotating new AZ phages. Adolin Adumb2043 Amyev Asa16 Cassia Crewmate DrManhattan DrSierra Elezi Emotion Eraser Janeemi JohnDoe Kaylissa KeAlii Lego Liebe Lizalica London Maureen Niobe ObiToo Phives Powerpuff Reedo Tbone Tuck Tweety19 VResidence VroomVroom Warda Yang YesChef Edited 10 Jun, 2024 13:10

Link to this post | posted 03 Jun, 2023 14:27
bgibb	All AZ phages found so far have a tail assembly chaperone with a programmed translational frameshift. The tail assembly chaperone is typically found in the left arm of the genome around gp14-16.

Link to this post | posted 03 Jun, 2023 14:19
bgibb	AZ phages contain a single endolysin gene, but the location within the genome and the pham for the endolysin gene is not consistent across the entire cluster. At least three patterns are observed within the cluster. Example include: Phives - Endolysin as gp1 Elezi - Endolysin in middle of genome, gp25 Powerpuff - Endolysin in right arm of genome, gp59 Edited 06 Jun, 2023 02:29

Link to this post | posted 06 May, 2022 03:06

bgibb

You're correct– I was looking at the instructor guide instead of the discovery guide. Thanks! viknesh bgibb There used to be three protocols for setting up TEM samples, but now there is only one 8.1c (parafilm drop method) in the Discovery guide and Instructor guide. Is there a reason that the other protocols were removed? I've had good luck with the pelco tab method. Bryan, I see all 3 protocols in the Discovery Guide - https://seaphagesphagediscoveryguide.helpdocsonline.com/8-0-toc

Link to this post | posted 05 May, 2022 17:19
bgibb	There used to be three protocols for setting up TEM samples, but now there is only one 8.1c (parafilm drop method) in the Discovery guide and Instructor guide. Is there a reason that the other protocols were removed? I've had good luck with the pelco tab method.