SEA-PHAGES | All posts created by nic.vega

Link to this post \| posted yesterday, 19:24
nic.vega	We're having a go at library prep, but the core here apparently isn't sure where to start for non-mammalian DNA. Does anyone have settings for Covaris (E220) (we're sequencing on iSeq 2x150, shooting for fragments ~400 bp)? From restriction gels, I think our genomes are all around average size for globi phage (~40-50 kb).

Posted in: Sequencing, Assembling, and Finishing Genomes → Covaris fragmentation

Link to this post \| posted 26 Oct, 2024 14:52
nic.vega	If your students are still struggling with webbed plates, particularly for low-yield or small plaque phage, we've had good luck (1) increasing the incubation time of bacteria + phage before making plaque plates to allow a lysis cycle (I'm using 1h instead of 15 minutes with globi as host, your timing may vary) and (2) dropping the top agar concentration in PYCa to 0.2-0.3% by diluting with phage buffer - this also provides 2.5-5% glycerol, which can help increase plaque size (Santos, Sílvio B., Carla M. Carvalho, Sanna Sillankorva, Ana Nicolau, Eugénio C. Ferreira, and Joana Azeredo. 2009. “The Use of Antibiotics to Improve Phage Detection and Enumeration by the Double-Layer Agar Technique.” BMC Microbiology 9 (1): 148. https://doi.org/10.1186/1471-2180-9-148.) 73Kb

Link to this post | posted 26 Oct, 2024 14:52

nic.vega

If your students are still struggling with webbed plates, particularly for low-yield or small plaque phage, we've had good luck (1) increasing the incubation time of bacteria + phage before making plaque plates to allow a lysis cycle (I'm using 1h instead of 15 minutes with globi as host, your timing may vary) and (2) dropping the top agar concentration in PYCa to 0.2-0.3% *by diluting with phage buffer* - this also provides 2.5-5% glycerol, which can help increase plaque size (Santos, Sílvio B., Carla M. Carvalho, Sanna Sillankorva, Ana Nicolau, Eugénio C. Ferreira, and Joana Azeredo. 2009. “The Use of Antibiotics to Improve Phage Detection and Enumeration by the Double-Layer Agar Technique.” BMC Microbiology 9 (1): 148. https://doi.org/10.1186/1471-2180-9-148.)

Posted in: Phage Discovery/Isolation → Webbed plate hack for low-titer stocks and small plaques

Link to this post \| posted 26 Oct, 2024 14:35
nic.vega	A few newer papers (and one old one) that may be of interest: Gallet, Romain, Sherin Kannoly, and Ing-Nang Wang. 2011. “Effects of Bacteriophage Traits on Plaque Formation.” BMC Microbiology 11 (1): 181. https://doi.org/10.1186/1471-2180-11-181. Germida, James J., and L. E. Casida. 1981. “Isolation of Arthrobacter Bacteriophage from Soil.” Applied and Environmental Microbiology 41 (6): 1389–93. Keen, Eric C. 2015. “A Century of Phage Research: Bacteriophages and the Shaping of Modern Biology.” BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology 37 (1): 6–9. https://doi.org/10.1002/bies.201400152. Zrelovs, Nikita, Andris Dislers, and Andris Kazaks. 2021. “Motley Crew: Overview of the Currently Available Phage Diversity.” Frontiers in Microbiology 11 (January). https://doi.org/10.3389/fmicb.2020.579452.

Link to this post | posted 26 Oct, 2024 14:35

nic.vega

A few newer papers (and one old one) that may be of interest:

Gallet, Romain, Sherin Kannoly, and Ing-Nang Wang. 2011. “Effects of Bacteriophage Traits on Plaque Formation.” BMC Microbiology 11 (1): 181. https://doi.org/10.1186/1471-2180-11-181.

Germida, James J., and L. E. Casida. 1981. “Isolation of Arthrobacter Bacteriophage from Soil.” Applied and Environmental Microbiology 41 (6): 1389–93.

Keen, Eric C. 2015. “A Century of Phage Research: Bacteriophages and the Shaping of Modern Biology.” BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology 37 (1): 6–9. https://doi.org/10.1002/bies.201400152.

Zrelovs, Nikita, Andris Dislers, and Andris Kazaks. 2021. “Motley Crew: Overview of the Currently Available Phage Diversity.” Frontiers in Microbiology 11 (January). https://doi.org/10.3389/fmicb.2020.579452.

Posted in: Papers → Introductory Phage Papers

Link to this post \| posted 11 Oct, 2024 13:40
nic.vega	Did you change batches of media around the time plating started to fail? In particular, if the Mg/Ca levels are off in the PYCa, that can significantly affect phage sorption & plating efficiency.

Posted in: Arthrobacter → Arthrobacter vanishing plaques

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