DOI: 10.5061/dryad.m5576kb
title: Data from: Two stochastic processes shape diverse senescence patterns in a single-cell organism

description: 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.
description: Ranked cell growth
 RR
 code for Fig. S3Ranked cells
 growthRData for Fig.
 S3Basic bacteria cell
 data1This 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.csvDivision data of bacteria cellsFolder(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.csvLength data of indvidual cellsFolder(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.csvBootstrapping for Fig. 2C & DBuilds the data and bootstrapping (CI) for Fig. 2C & D and Fig. S5B. Builds dat1c, dat1D, and dat1cSbuildBacteriaData_bootstrap.rSome functions usedThese are some functions used in the main R code to analyze the data.bacteriaFunctions.rMain R codeThis 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.RR code for simulations Fig. 3 and Fig. S12, Fig. S13, Fig. S14R 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&Dest_age_at_death.rBuilds data and plots Fig. 3C & DThis R code builds and plots Fig. 3C & D, it loads hereweare.rdataplot_survivals.rData file for Fig. 3 C&DR data file for Fig. 3 C&Dhereweare.rdataProbability matrix of being in state i at age x for early daughtersProbability matrix of being in state i at age x for early daughtersP_i_at_x_gen1.txtProbability matrix of being in state i at age x for late daughtersProbability matrix of being in state i at age x for late daughtersP_i_at_x_gen2.txtProbability matrix of being in state i at age x for second gen late daughtersProbability matrix of being in state i at age x for second gen late daughtersP_i_at_x_gen3.txtState at death distribution Rdata file early daughtersThis data file includes the state at death distribution for early daughtersstate_at_death_gen1.RDataState at death distribution Rdata file late daughtersState at death distribution Rdata file late daughters with transmission of damage of 0.07state_at_death_gen2.RDataState at death distribution Rdata file late daughters 0% transmissionstate_at_death_gen2_0.RDataState at death distribution Rdata file late daughters 100% transmissionstate_at_death_gen2_1.RDataState at death distribution Rdata file late daughters 50% transmissionstate_at_death_gen2_05.RDataState at death distribution Rdata file late daughters 25% transmissionstate_at_death_gen2_025.RDataState at death distribution Rdata file second generation late daughters 7% transmissionstate_at_death_gen3.RDataState at death distribution Rdata file second gen late daughters 0% transmissionState at death distribution Rdata file second gen late daughters 0% transmissionstate_at_death_gen3_0.RDataState at death distribution Rdata file second gen late daughters 100% transmissionstate_at_death_gen3_1.RDataState at death distribution Rdata file second gen late daughters 50% transmissionstate_at_death_gen3_05.RDataState at death distribution Rdata file second gen late daughters 25% transmissionstate_at_death_gen3_025.RData