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Publications (185)
A recent commentary raised concerns about aspects of the model and assumptions used in a previous study which demonstrated that selection can favor chromosomal alleles that confer higher plasmid donation rates. Here, the authors of that previous study respond to the concerns raised.
Changes in many dimensions of our lives have been accelerating, due notably to contemporary systemic crises and technological innovation. They invite us to rethink the ways we share information, learn and cooperate to face our personal, local and global challenges. The COVID-19 pandemic epitomizes the need to generate and nurture 'learning communit...
Evolution provides a creative fount of complex and subtle adaptations that often surprise the scientists who discover them. However, the creativity of evolution is not limited to the natural world: Artificial organisms evolving in computational environments have also elicited surprise and wonder from the researchers studying them. The process of ev...
We are witnessing a dramatic transformation in the way we do science. In recent years, significant flaws with existing scientific methods have come to light, including lack of transparency, insufficient involvement of stakeholders, disconnection from the public, and limited reproducibility of research findings. These concerns have sparked a global...
Natural selection is thought to shape the evolution of aging patterns, although how life-history trajectories orchestrate the inherently stochastic processes associated with aging is unclear. Tracking clonal growth-arrested Escherichia coli cohorts in an homogeneous environment at single-cell resolution, we demonstrate that the Gompertz law of expo...
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 deterio...
Despite advances in aging research, a multitude of aging models, and empirical evidence for diverse senescence patterns, understanding is lacking of the biological processes that shape senescence, both for simple and complex organisms. We show that for a isogenic Escherichia coli bacterial population senescence results from two stochastic processes...
Natural selection has long been hypothesised to shape ageing patterns, but whether and how ageing contributes to life-history evolution remains elusive. The complexity of various ageing-associated molecular mechanisms and their inherent stochasticity hinder reductionist approaches to the understanding of functional senescence, i.e. reduced fecundit...
In bacteria, cooperative genes encoding public good molecules are preferentially located on mobile genetic elements (MGEs), and horizontal transfer of MGEs favours the maintenance of public good cooperation. The rate of horizontal transfer itself can evolve in response to selective pressures acting on both MGEs and bacterial hosts: benefits and cos...
Le 4 avril 2018, François Taddei a remis aux ministres de l’Éducation nationale, de l’Enseignement supérieur et du Travail, un rapport intitulé "Un plan pour co-construire une société apprenante" visant à créer "un service public de la société apprenante". Cinq actions, qui regroupent 30 propositions détaillées, structurent ce plan. Les auteurs com...
Biological evolution provides a creative fount of complex and subtle adaptations, often surprising the scientists who discover them. However, because evolution is an algorithmic process that transcends the substrate in which it occurs, evolution's creativity is not limited to nature. Indeed, many researchers in the field of digital evolution have o...
Biological evolution provides a creative fount of complex and subtle adaptations, often surprising the scientists who discover them. However, because evolution is an algorithmic process that transcends the substrate in which it occurs, evolution's creativity is not limited to nature. Indeed, many researchers in the field of digital evolution have o...
Switching rate between cooperating and non-cooperating genotypes is a crucial social evolution factor, often neglected by game theory-inspired theoretical and experimental frameworks. We show that the evolution of alleles increasing the mutation or phenotypic switching rates toward cooperation is in itself a social dilemma. Although cooperative off...
Bacterial genes that confer crucial phenotypes, such as antibiotic resistance, can spread horizontally by residing on mobile genetic elements (MGEs). Although many mobile genes provide strong benefits to their hosts, the fitness consequences of the process of transfer itself are less clear. In previous studies, transfer has been interpreted as a pa...
Within-population strain dynamics during the transfer phase.
A: The change in frequency of the good donor strain D+ from t0 to t1, shown for s1, m, and s2 populations of the experiments presented in Fig 3, suggests that D+ strain fitness is frequency-dependent. Results are shown as means ± SEM (N ≥ 6). B: To confirm the existence of positive freque...
Selection coefficients for the K12 strain in competition with B.
Data are from the discrimination experiment, presented in Fig 2C. Data are available from FigShare at http://dx.doi.org/10.6084/m9.figshare.3199252.
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Synthetic bacterial strains to study the selection of donor ability.
The two competing strains differ in plasmid donor ability: D+ (red) bears FHR plasmid that confers high donor ability (indicated by pili), D− (white) does not bear FHR and can receive plasmids but not transfer them. D+C and D−C cells bear plasmid C that codes for resistance to the...
Parameters governing the selection of donor ability after strong initial dilution.
Simulations are the same as the ones described in Fig 4. In A, the change in D+ frequency from t0 to t2 is shown as a function of the proportion of C plasmids present in D+ strain before the selection phase (at t1), each point being the mean of 1,000 replicates. D+ c...
Selection coefficients for D+ strain in a population structured by strong dilution.
Data are from the simulations presented in Fig 4. Data are available from FigShare at http://dx.doi.org/10.6084/m9.figshare.3199252.
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Effect of the presence of parasitic plasmids on the selection of donor ability.
The change in D+ frequency from t0 to t2 is shown from simulation data (see Materials and Methods) as a function of the initial proportion of plasmids that are parasitic plasmids N. Results are shown for different values of C benefits on growth (with high C benefits, th...
Selection coefficient for the D+ strain in competition with D− in a structured population.
Data are from the structured population experiment, presented in Fig 3B. Data are available from FigShare at http://dx.doi.org/10.6084/m9.figshare.3199252.
(TIFF)
Effect of plasmid presence on the growth rate of E. coli strains used for discrimination experiments.
Growth rates were measured in 96-well plates in M9 medium at 37°C, similarly to the conditions of the competition experiment. The maximal growth rate for each strain (A) and plasmid cost derived from the effect on growth rate (B) were computed as m...
Plasmid dynamics during the transfer phase.
The change in frequency of D− cells bearing plasmid C-YFP (yellow) and plasmid C-GFP (green) is shown from t0 to t1 for s1, m, and s2 populations of the experiments presented in Fig 3. By design, C-GFP plasmids are initially present in D− only (see Materials and Methods) and decline in frequency as they a...
Dynamics of plasmid linkage to D+ strain with transfer and selection.
The metapopulation is the one described in Fig 6. Plasmid linkage to D+ is shown as a function of D+ donor ability and C plasmid benefit on growth (during the selection phase), for both plasmids at t1 (A), and for N plasmid at t2 (B). The linkage values in (A) are the same for C...
Schematic model details and analysis.
(DOCX)
Mobile genetic elements in bacteria are enriched in genes participating in social behaviors, suggesting an evolutionary link between gene mobility and social evolution. Cooperative behaviors, like the production of secreted public good molecules, are susceptible to the invasion of non-cooperative individuals, and their evolutionary maintenance requ...
Natural cooperative systems take many forms, ranging from one-dimensional cyanobacteria arrays to fractal-like biofilms. We use in silico experimental systems to study a previously overlooked factor in the evolution of cooperation, physical shape of the population. We compare the emergence and maintenance of cooperation in populations of digital or...
More and more researchers want to use games as a way of engaging the general public in their research; however game development takes time and requires significant programming knowledge. The goal of RedWire is to enable researchers to create games faster without starting from scratch each time. By encouraging re-mixing and mash-ups, we hope to prov...
Probing oriented bacterial cell growth on the nanoscale: A novel open-top micro-channel is developed to facilitate the AFM imaging of physically trapped but freely growing bacteria. The growth curves of individual Escherichia coli cells with nanometer resolution and their kinetic nano-mechanical properties are quantitatively measured.
Significance
Bacteria often cooperate through the production of public goods that change their environment. These processes can affect human health by increasing virulence or antibiotic resistance. Public good production is costly, making cooperation susceptible to invasion by nonproducing “cheater” individuals. Bacteria also readily share genes, e...
When cooperation has a direct cost and an indirect benefit, a selfish behavior is more likely to be selected for than an altruistic one. Kin and group selection do provide evolutionary explanations for the stability of cooperation in nature, but we still lack the full understanding of the genomic mechanisms that can prevent cheater invasion. In our...
Expression of P22 pid segregates asymmetrically between siblings and does not require integration of P22. Exponential phase cultures of LT2 were infected with P22 Δint Δpid::yfp (MOI = 0.1) and chased after 30 minutes with the virulent P22 H5 mutant (MOI = 20) to lyse cells not destined for non-lytic development of P22 Δint Δpid::yfp. Images A and...
Phage ES18 fails to activate the dgoT::MudK fusion in LT2K7. A plaque of phage ES18 grown on a lawn of LT2K7 fails to display LacZ activity (i.e. blue color) on LB X-Gal agar (left panel), while a similar experiment performed on green indicator agar (GI; right panel) confirms the actual infection of LT2K7.
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Author Summary
Viruses of bacteria, also referred to as (bacterio)phages, are the most abundant biological entity on earth and have a tremendous impact on the ecology of their hosts. It has traditionally been recognized that upon infection by a temperate phage the host cell is forced either to produce and release new virions during lytic developmen...
Pre-disposition clustered events detected by cellular growth rate. The lineage tree is same as Figure 3. The nodes where the two progenies emanating from two respective sister progenitor cells have a statistical significant difference at the end of the experiment in terms of growth rate are marked by a circle.
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Micro-colonies grown in the presence of streptomycin. Overnight culture is recovered in fresh medium for 2 hours then plated onto LB-agar with 3 µg/ml streptomycin. The images are taken 250 minutes after plating. The upper row is phase contrast image and the bottom is fluorescence image for the ibpAB promoter driven YFP expression. In these represe...
Streptomycin induced cell death characterized by Propidium Iodide (PI) staining. Cells were inoculated to agar pad with 4 ug/ml streptomycin and 10 ug/ml PI. The upper row shows the phase contrast snapshots of colony growth and the lower lane shows the red fluorescence signal from DNA intercalation of PI of depolarized cells. Note that grey-level s...
Correlation between progenitor sister cells fluorescence and progenies fluorescence intensity. The lineage tree corresponds to Video S3. Experimental condition is the same as Figure S11.
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Correlation between pipbAB promoter and prrna promoter activity. Overnight culture is diluted 200 fold in LB in 37°C for 2 hours. The exponential phase cell culture is then diluted into LB medium with or without streptomycin for another 2 hour. Cells are then plated on agar pad and quantified under fluorescence microscope. Red and blue dots indicat...
Cellular distance from micro-colony border. The distance between a single cell and the boarder of the micro-colony (BMC) is calculated as follows. Cells that are at the BMC are identified as boarder cells. The distance between boarder cells to BMC is zero. For the non-boarder cells, the distance of the cell to BMC is defined as the minimum distance...
Correlation between cellular growth rate and their geographic location. The cellular growth rate is found to be independent of the distance of the cell to the boarder of micro-colony. Four micro-colonies (Figures S11, S12, S13, S14) are quantified at the last images of the time-lapsed movies.
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Autocorrelation half-life determined by the linear model. The autocorrelation half-life (relative to the cellular doubling time) is calculated according to equation (4) for different values of and t.
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Time-lapse movie of micro-colony growth in microfluidics chamber with streptomycin induction at fourth generation.
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Location of dead cells in lineage tree. Dead cells and their common ancestors are high-lighted in red. The blue dashed line indicates the time of streptomycin induction. Dead cells are identified according to Figure 1B. The green dashed box indicates the sub-lineage shown in Figure 1C.
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Lineage structure randomization decreases SLCV. (A) The coefficient of measured variation of cellular fluorescence (data from the same lineage as in main text Figure 1, Figure 3) (B) 250 pairs of cells are chosen for switching their position in the lineage tree. Only cells that are born after stress induction are selected. Switch only happens betwe...
Correlation between progenitor sister cells fluorescence and progenies fluorescence intensity. The lineage tree corresponds to Figure 3 but with shorter time scale until 90 minutes after induction. When the significant event highlighted in red, the higher fluorescent progenitor sister gives rise to a sub-lineage with higher stress level. Otherwise...
Correlation between progenitor sister cells fluorescence and progenies fluorescence intensity. Experimental condition is the same as Figure S11.
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Correlation between progenitor sister cells fluorescence and progenies fluorescence intensity. Experimental condition is the same as Figure S11.
(PDF)
E. coli Population growth in presence of low streptomycin concentrations. Overnight culture is diluted 200 fold into fresh medium and agitated in 37°C for 2 hours. The culture is then diluted into medium with 0–4 µg/ml of streptomycin respectively. Further dilution is performed two hour afterwards to maintain low cell-density (OD<0.3) for measureme...
Flow cytometry quantification of single cell pibpAB driven fluorescence expression after streptomycin induction. For sample preparation see the legend of Figure S1. In each treatment, 1 ml of sample is taken every hour and kept on ice. Four hours after stress induction, all the samples are measured by flow-cytometry (Becton-Dickinson FACSAria) for...
Correlation between cell growth rate and fluorescence intensity. (A) Non-induced condition. The growth rate and fluorescence signal are measured two hours after inoculation into microfluidics device. (B) 60 minutes after stress induction. (C) 90 minutes after stress induction. Four micro-colonies are quantified in each condition.
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Stochastic modeling of IDCV and SLCV. The different colours of lines represent the same measures as in Figure 2, which are the mean value and the 99.8% confidence region of the mean (three fold of standard error) from 100 times of independent runs. (A) without stress induction; (B) with stress induction.
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Phenotypic correlations between non-induced cells and their stress induced progenies. (A) Fluorescence intensity. (B) Promoter activity, calculated as , where F is fluorescence intensity and k is cellular growth rate (C) Growth rate. All the values are normalized by the mean of respective micro-colony. Four micro-colonies are quantified.
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Co-induction of antibiotics and aTc. Exponential phase cells of strain harbouring both pterR and pibpAB driven fluorescence reporters are plated onto LB-agar pads containing ATC (25 ng/ml) with or without (A) Mitomycin (0.3 µg/ml) and (B) Nalidixic Acid (0.6 µg/ml). After 2–3 hours of colony growth, the fluorescence intensity is quantified under fl...
Time-lapse movie of micro-colony growth on 2D agar pad with 3 ug/ml streptomycin. The fluorescence signal is pibpAB driven YFP expression.
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Time-lapse movie of micro-colony growth in microfluidics chamber with streptomycin induction at fourth generation.
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Bacteria suffer various stresses in their unpredictable environment. In response, clonal populations may exhibit cell-to-cell variation, hypothetically to maximize their survival. The origins, propagation, and consequences of this variability remain poorly understood. Variability persists through cell division events, yet detailed lineage informati...
One of the tenets of the neodarwi- nian paradigm is the separation bet- ween selective pressure anf genera- tion of variability. Recent work on directed or adaptive mutage- nesis has challenged this view. The debate moved from the possibility of producing only useful mutations to the possible link betw<een envi- ronment and control of genetic varia...
Evolutionary adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung is limited by genetic variation, which depends on rates of horizontal gene transfer and mutation supply. Because each may increase following secondary infection or mutator emergence, we sought to ascertain the incidence of secondary infection and genetic variability in po...
An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News & Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.
E. coli MG1655 fails to induce any detectable proinflammatory response in vivo upon intestinal colonization of germ-free mice. Relative mRNA expression of CCL-20 and IL-12p40, two genes induced after binding of flagellin to its cognate receptor TLR5, in germ-free mice (GF, n = 7), conventional mice (Cv, n = 7) and in mice monocolonized with E. coli...
The ompB mutation of SG1 mutant improve growth in presence of bile salts. Representative growth curves in LB curves of ancestral (WT), one selected mutant of each phenotype (NM1, Mal−1 and SG1) and isogenic reconstructed strains supplemented with bile salts (0.5% wt/vol). Plates were incubated at 37°C under continuous orbital agitation in a plate r...
Motility Morphotypes on Soft Agar Plates
WT: large and smooth morphotype of the MG1655 strain. ΔfliC: pin point morphotype of an isogenic strain carrying a deletion in the fliC gene and therefore non-motile. ΔompR: large and smooth morphotype comparable to that of the WT strain. SG1: small and granular morphotype of a clone isolated 2 d after inocu...
The same diversification is observed in MyD88−/− and in WT mice. Evolution over time (in days) of new morphotypes CFU (mean +/− standard error of the mean) in the feces of mice inoculated with the E. coli MG1655 strain. No significant difference is observed between the WT mice (continuous lines) and MyD88−/− mice (dotted lines).
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The same proportion of flagellated bacteria is observed in different parts of the gut. A, B and C: images obtained by confocal microscopy of the same cecal area illustrating the homogenous repartition of flagellated bacteria: (A) propidium iodide (PI) staining, (B) Yfp expression from the pflic-yfp construct, (C) merge of PI, yfp and alexa647-phall...
Expression profile of E. coli genes known to respond to oxygen availability in aerated cultures, chemosat cultures and in mice caecum. Differences between the Ct of specified genes and the Ct of the endogenous reference gene (rpoD) in E. coli MG1655 populations growing in different conditions. A: aerated culture (10 ml of culture in 50 ml tubes, OD...
Primer sequences used for qRT-PCR. The table contains the sequence of all primers used for gene expression by semi quantitative RT-PCR.
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Selective advantage of envZ mutation decreases after day 3. Evolution over time (in days) of the ratio of envZ mutant to WT CFU in the feces of mice inoculated with MG1655 ptet-GFP ompBSG1-cat (containing the SG1 envZ mutation) and MG1655 ptet-RFP ompB-cat (containing the WT envZ allele) mixed at initial ratios of 1∶1 (diamonds), 1∶100 (squares), a...
SG1 mutant displays reduced expression of lamB. qRT-PCR on bacterial cultures demonstrate difference between the Ct of the lamB gene and the Ct of the endogenous reference gene (rpoD) in WT and SG1 strains.
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Radiative evolution in individual mice. Evolution over time (in days) of CFU morphotypes in the feces of 12 mouse inoculated with the E. coli MG1655 pfliC-yfp strain. The percentages of colony phenotypes in motility agar are indicated: large smooth (LS, similar to the ancestor), small granulous (SG) and totally non motile (NM). In 8 mouse, colonies...
Growth of the different mutants. Representative growth curves of the WT and isogenic mutants in 96 wells microplates, either in LB medium (A) or in M9 minimal medium containing glucose (B). 200 µl cultures were covered with oil to prevent evaporation, and were agitated for 1 minute before every reading. Experiments were realized with the plate read...