TemperateMOI

This repo contains two small projects.

1 ) MOI:

• Determines if temperate phages can entrap spores & explores the relationship with MOI

2. PlvGe (Plaques vs. Germination):

• Compares the ratios of plaques vs. the number of countable germinated spores from the same mixture.

MOI

Code:

• 202511133_1301_moicleaning.Rmd normalization of all plaque count MOI data of lytic vs. wt phi3t across trials

• 20251113_1215_allMOIS.Rmd plotting regression relationship between MOI & phage lifestyle (lytic, wt phi3t)

• 20251113_1444_PilotFig.Rmd PFU comparison across MOI of 1 for lytic and wt phi3t -- (note that MOI is listed as 0 in dataset because it is in logform. MOI log = 0 is MOI =1)

data/:

• .csv files of plaque counts of phi3t lytic and WT across multiple MOIs and dilutions
• data from is repeated iterations (different mois) between 08/2025-11/2025.
• briefly: d6 was treated with equivalent mois of lytic and wt phi3t, allowed to incubate overnight, treated with heat to isolate spores, and counted.

archive/ folder

• can be safely ignored (it includes reference code that was used to inform SporeMOI and/or old code drafts)

PlvGe (Plaques vs. Germinated Spores)

PlvGe_data/

• plaque and germinated spore counts from both spbeta and phi3t (lytic & wt phenotypes) at various MOIs (mostly 1)

• note that spore counts and plaques are paired (i.e. came from the same samples but were plated differently to count either # of entrapped virospores or # of uninfected germinating spores)

• datasets with _nocount at the end are the same as the datasets lacking the _nocount suffix, just have had all 0 data removed for easier datacleaning -- the ones with zero counts are kept only for posterity/reference

• most data is from 08-09 2025 pilot to see if entrapment was even possible in temperate phage, but later, 20251113_1204_MOI6_4 was added (from spore MOI) since methods were equivalent & plaque/spore count is known.

Code:

• 20250924_LyticVsWt_Collated.Rmd combines all data/ and analysis related to plaque count vs. germinated count
• Important to note what the three types of treatments referenced in this dataset mean:

1. Lytic infection: d6 cells exposed to the dSrof lytic mutant, incubated ON and isolated for spores.

2. WT infection: d6 cells exposed to WT temperate phage, incubated ON and isolated for spores.

3. Prophage (lysogen) infection: d6 cells with integrated prophage (so all cells already carry the temperate phage prior to the experiment, and are therefore 100% pre-infected with the WT strain)

• 20250919_sporevveglawns.Rmd looks at the difference between countable plaques of phi3T lysogens when plated on vegetative d6 lawns vs. spore d6 lawns.

archive_PlvGe

• original drafts of the code that resulted in 20250924_LyticVsWt_Collated.Rmd
• was initally in multiple parts/analysis, so LyticVsWt_Collated combines these efforts
• can be safely ignored and may be nonfunctional, but are kept for posterity/reference