Plate <- “A12”

Adapt biosensor IDs in “Defining biosensor subsets”

BS_a <- “BS_AB045” BS_b <- “BS_AB046” BS_c <- “BS_AB047” BS_d <- “BS_AB048”

Cleaning up data

data <- data_raw %>%
  select (time, Well, BS, TF, Nar, Replicate, Abs1:Fluo2) %>%
  rename (OD = Abs1, FL_B = Fluo1, FL_T = Fluo2, Time = time)

data$Nar <- as.factor(data$Nar)
data$Replicate <- as.factor(data$Replicate)

med <- data %>%
  filter (BS == "EZ rich")

data <- data %>%
  mutate(ODc = OD - mean(med$OD), FL_Tc = FL_T - mean(med$FL_T), FL_Bc = FL_B - mean(med$FL_B)) %>%
  mutate (RFU_T = FL_T/OD, RFU_B = FL_B/OD, RFU_Tc = FL_Tc/ODc, RFU_Bc = FL_Bc/ODc)

nomed <- data %>%
  filter (BS != "EZ rich")

Basic plots

All data

Timepoint 30h seems a good timepoint for stationary phase analysis

Only medium

mean(med$OD)
## [1] 0.103435
mean(med$FL_T)
## [1] 46.66167
mean(med$FL_B)
## [1] 70.25167
grid.arrange(m2, m3, m1, m1 + ylim(0.095,0.15), nrow = 2)
## Warning: Removed 29 rows containing missing values (geom_point).

2 replicates (with and without naringenin) of medium start growing at around 30h. Bigger increase in OD, but no change in FL values.SAME TWO REPLICATES AS PLATE A11 (logical because same preculture plate P6)

Without medium

Defining biosensor subsets

control <- nomed %>%
  filter(BS == "Control")
BS_a <- nomed%>%
  filter(BS == "AB045")
BS_b <- nomed %>%
  filter(BS == "AB046")
BS_c <- nomed%>%
  filter(BS == "AB047")
BS_d <- nomed %>%
  filter(BS == "AB048")

Check per biosensor strain

Control

Seems that Nar has effect on growth (also in following graphs) - nicer spreading of results for the bottom measurements compared to the top (RFU_B vs RFU_T): larger dynamic range so trends better visible (for example horizontal trend for exp phase)

BS_a

BS_b

BS_c

BS_d

Summary

  • BS_a: Promoter is functional, unclear if repression/activation
  • BS_b: no clear repression/activation
  • BS_c: no clear repression/activation
  • BS_d: Repression can be observed