Despite advances in aging research, a multitude of aging models, and empirical evidence for diverse senescence patterns, understanding of the biological processes that shape senescence is lacking. We show that senescence of an isogenic Escherichia coli bacterial population results from two stochastic processes. The first process is a random deterioration process within the cell, such as generated by random accumulation of damage. This primary process leads to an exponential increase in mortality early in life followed by a late age mortality plateau. The second process relates to the stochastic asymmetric transmission at cell fission of an unknown factor that influences mortality. This secondary process explains the difference between the classical mortality plateaus detected for young mothers’ offspring and the near nonsenescence of old mothers’ offspring as well as the lack of a mother–offspring correlation in age at death. We observed that lifespan is predominantly determined by underlying stochastic stage dynamics. Surprisingly, our findings support models developed for metazoans that base their arguments on stage‐specific actions of alleles to understand the evolution of senescence. We call for exploration of similar stochastic influences that shape aging patterns beyond simple organisms.
Ranked cell growth R
R code for Fig. S3
Ranked cells growthR
Data for Fig. S3
Basic bacteria cell data1
This data file contains information on 1)Folder (image frame), 2)Slicenumber (side channel number within image frame), 3)Death first cell (age at death of the bottom most mother cell, i.e. early daughter cell), 4)death second cell (age at death of the late daughter cell), 5)death third cell (age at death second generation late daughter cell), 6)average div.1 (average divisions mother, should not be used), 7)average div.2 (average divisions late daughters, should not be used), 8)average div.3 (average divisions second generation late daughters, should not be used).
data.1.csv
Division data of bacteria cells
Folder(Image frame) SliceNum (Side channel number) CellNum (order of cells in the dead end side channel, mother/early daughter=1, etc.) Death (age at death) AverDiv (average number of divisions) Div1...DIV1195 (was there a division at the 1...to 1195th 4 min interval).
div2.1.csv
Length data of indvidual cells
Folder(Image frame) SliceNum (Side channel number) CellNum (order of cells in the dead end side channel, mother/early daughter=1, etc.) Death (age at death) AverDiv (average number of divisions) size1...size1195 (size at the 1...to 1195th 4 min interval).
leng3.1.csv
Bootstrapping for Fig. 2C & D
Builds the data and bootstrapping (CI) for Fig. 2C & D and Fig. S5B. Builds dat1c, dat1D, and dat1cS
buildBacteriaData_bootstrap.r
Some functions used
These are some functions used in the main R code to analyze the data.
bacteriaFunctions.r
Main R code
This code generates Fig. 2 (for Fig. 2C&D) you need to run the bootstrapping, Fig. S9, S10, S6, S7, S5, S4, and S8. It also generates some new data frames.
R code basic stats.R
R code for simulations Fig. 3 and Fig. S12, Fig. S13, Fig. S14
R code for simulations Fig. 3 and Fig. S12, Fig. S13, Fig. S14. You also need to run extra R code plot_survivals for Fig. 3C&D
est_age_at_death.r
Builds data and plots Fig. 3C & D
This R code builds and plots Fig. 3C & D, it loads hereweare.rdata
plot_survivals.r
Data file for Fig. 3 C&D
R data file for Fig. 3 C&D
hereweare.rdata
Probability matrix of being in state i at age x for early daughters
Probability matrix of being in state i at age x for early daughters
P_i_at_x_gen1.txt
Probability matrix of being in state i at age x for late daughters
Probability matrix of being in state i at age x for late daughters
P_i_at_x_gen2.txt
Probability matrix of being in state i at age x for second gen late daughters
Probability matrix of being in state i at age x for second gen late daughters
P_i_at_x_gen3.txt
State at death distribution Rdata file early daughters
This data file includes the state at death distribution for early daughters
state_at_death_gen1.RData
State at death distribution Rdata file late daughters
State at death distribution Rdata file late daughters with transmission of damage of 0.07
state_at_death_gen2.RData
State at death distribution Rdata file late daughters 0% transmission
state_at_death_gen2_0.RData
State at death distribution Rdata file late daughters 100% transmission
state_at_death_gen2_1.RData
State at death distribution Rdata file late daughters 50% transmission
state_at_death_gen2_05.RData
State at death distribution Rdata file late daughters 25% transmission
state_at_death_gen2_025.RData
State at death distribution Rdata file second generation late daughters 7% transmission
state_at_death_gen3.RData
State at death distribution Rdata file second gen late daughters 0% transmission
State at death distribution Rdata file second gen late daughters 0% transmission
state_at_death_gen3_0.RData
State at death distribution Rdata file second gen late daughters 100% transmission
state_at_death_gen3_1.RData
State at death distribution Rdata file second gen late daughters 50% transmission
state_at_death_gen3_05.RData
State at death distribution Rdata file second gen late daughters 25% transmission
state_at_death_gen3_025.RData