Guillaume Lambert

Memory and Fitness Optimization of Bacteria under Fluctuating Environments

Bacteria prudently regulate their metabolic phenotypes by sensing the availability of specific nutrients, expressing the required genes for their metabolism, and repressing them after specific metabolites are depleted. It is unclear, however, how genetic networks maintain and transmit phenotypic states between generations under rapidly fluctuating environments. By subjecting bacteria to fluctuating carbon sources (glucose and lactose) using microfluidics, we discover two types of non-genetic memory in Escherichia coli and analyze their benefits. First, phenotypic memory conferred by transmission of stable intracellular lac proteins dramatically reduces lag phases under cyclical fluctuations with intermediate timescales (1–10 generations). Second, response memory, a hysteretic behavior in which gene expression persists after removal of its external inducer, enhances adaptation when environments fluctuate over short timescales (<1 generation). Using a mathematical model we analyze the benefits of memory across environmental fluctuation timescales. We show that memory mechanisms provide an important class of survival strategies in biology that improve long-term fitness under fluctuating environments. These results can be used to understand how organisms adapt to fluctuating levels of nutrients, antibiotics, and other environmental stresses.

Cell motility and drug gradients in the emergence of resistance to chemotherapy

Significance Ultimately, chemotherapy often fails because of the emergence of cancer cells resistant to the chemotherapy. We show that this emergence can be driven by the presence of chemotherapy drug gradients and motility of the cancer cells within the gradient. The emergence of resistance to chemotherapy by cancer cells, when combined with metastasis, is the primary driver of mortality in cancer and has proven to be refractory to many efforts. Theory and computer modeling suggest that the rate of emergence of resistance is driven by the strong selective pressure of mutagenic chemotherapy and enhanced by the motility of mutant cells in a chemotherapy gradient to areas of higher drug concentration and lower population competition. To test these models, we constructed a synthetic microecology which superposed a mutagenic doxorubicin gradient across a population of motile, metastatic breast cancer cells (MDA-MB-231). We observed the emergence of MDA-MB-231 cancer cells capable of proliferation at 200 nM doxorubicin in this complex microecology. Individual cell tracking showed both movement of the MDA-MB-231 cancer cells toward higher drug concentrations and proliferation of the cells at the highest doxorubicin concentrations within 72 h, showing the importance of both motility and drug gradients in the emergence of resistance.

Towards enabling femtosecond helicity-dependent spectroscopy with high-harmonic sources

Recent advances in high-harmonic generation gave rise to soft X-ray pulses with higher intensity, shorter duration and higher photon energy. One of the remaining shortages of this source is its restriction to linear polarization, since the yield of generation of elliptically polarized high harmonics has been low so far. We here show how this limitation is overcome by using a cross-polarized two-colour laser field. With this simple technique, we reach high degrees of ellipticity (up to 75%) with efficiencies similar to classically generated linearly polarized harmonics. To demonstrate these features and to prove the capacity of our source for applications, we measure the X-ray magnetic circular dichroism (XMCD) effect of nickel at the M2,3 absorption edge around 67 eV. There results open up the way towards femtosecond time-resolved experiments using high harmonics exploiting the powerful element-sensitive XMCD effect and resolving the ultrafast magnetization dynamics of individual components in complex materials.

A proposal for multi-tens of GW fully coherent femtosecond soft X-ray lasers

X-ray free-electron lasers1, 2 delivering up to 1 × 1013 coherent photons in femtosecond pulses are bringing about a revolution in X-ray science3, 4, 5. However, some plasma-based soft X-ray lasers6 are attractive because they spontaneously emit an even higher number of photons (1 × 1015), but these are emitted in incoherent and long (hundreds of picoseconds) pulses7 as a consequence of the amplification of stochastic incoherent self-emission. Previous experimental attempts to seed such amplifiers with coherent femtosecond soft X-rays resulted in as yet unexplained weak amplification of the seed and strong amplification of incoherent spontaneous emission8. Using a time-dependent Maxwell–Bloch model describing the amplification of both coherent and incoherent soft X-rays in plasma, we explain the observed inefficiency and propose a new amplification scheme based on the seeding of stretched high harmonics using a transposition of chirped pulse amplification to soft X-rays. This scheme is able to deliver 5 × 1014 fully coherent soft X-ray photons in 200 fs pulses and with a peak power of 20 GW.

Indirect excitation of ultrafast demagnetization.

Does the excitation of ultrafast magnetization require direct interaction between the photons of the optical pump pulse and the magnetic layer? Here, we demonstrate unambiguously that this is not the case. For this we have studied the magnetization dynamics of a ferromagnetic cobalt/palladium multilayer capped by an IR-opaque aluminum layer. Upon excitation with an intense femtosecond-short IR laser pulse, the film exhibits the classical ultrafast demagnetization phenomenon although only a negligible number of IR photons penetrate the aluminum layer. In comparison with an uncapped cobalt/palladium reference film, the initial demagnetization of the capped film occurs with a delayed onset and at a slower rate. Both observations are qualitatively in line with energy transport from the aluminum layer into the underlying magnetic film by the excited, hot electrons of the aluminum film. Our data thus confirm recent theoretical predictions.

Controlling the Cyanobacterial Clock by Synthetically Rewiring Metabolism

Circadian clocks are oscillatory systems that allow organisms to anticipate rhythmic changes in the environment. Several studies have shown that circadian clocks are connected to metabolism, but it is not generally clear whether metabolic signaling is one voice among many that influence the clock or whether metabolic cycling is the major clock synchronizer. To address this question in cyanobacteria, we used a synthetic biology approach to make normally autotrophic cells capable of growth on exogenous sugar. This allowed us to manipulate metabolism independently from light and dark. We found that feeding sugar to cultures blocked the clock-resetting effect of a dark pulse. Furthermore, in the absence of light, the clock efficiently synchronizes to metabolic cycles driven by rhythmic feeding. We conclude that metabolic activity, independent of its source, is the primary clock driver in cyanobacteria.

Ancient hot and cold genes and chemotherapy resistance emergence

Significance There are two broad components of information dynamics in cancer evolution. One involves permanent changes in which genes are subject to gain or loss-of-function substitutions. This is well established and the main focus of cancer research. The other component is the information in the human genome and preservation of that content. The cancer cell potentially has access to all of this and can upregulate or downregulate any number of strategies used for survival and proliferation during embryogenesis, development, and normal adaptation to environmental stresses. We suggest that nonsubstituted genes may be critical targets for chemotherapy; these nonmutated genes may be the most fundamental ones for preservation of cancer cell fitness, especially if their expression level changes. We use a microfabricated ecology with a doxorubicin gradient and population fragmentation to produce a strong Darwinian selective pressure that drives forward the rapid emergence of doxorubicin resistance in multiple myeloma (MM) cancer cells. RNA sequencing of the resistant cells was used to examine (i) emergence of genes with high de novo substitution densities (i.e., hot genes) and (ii) genes never substituted (i.e., cold genes). The set of cold genes, which were 21% of the genes sequenced, were further winnowed down by examining excess expression levels. Both the most highly substituted genes and the most highly expressed never-substituted genes were biased in age toward the most ancient of genes. This would support the model that cancer represents a revision back to ancient forms of life adapted to high fitness under extreme stress, and suggests that these ancient genes may be targets for cancer therapy.

The Goldilocks Principle and Antibiotic Resistance in Bacteria

We have designed and fabricated a microecology to mimic a naturally occurring bacterial culture, which includes the stress gradient, metapopulation, and cellular motility. In this microecology, we show that it is possible to fix the resistance to the mutagenic antibiotic Ciprofloxacin in wild-type Escherichia coli within 10 h. We found the evolution of resistance is further accelerated in microecology if bacteria have already acquired the phenotype of growth advantage at the stationary phase (GASP).

Bacteria and game theory: the rise and fall of cooperation in spatially heterogeneous environments

One of the predictions of game theory is that cooperative behaviours are vulnerable to exploitation by selfish individuals, but this result seemingly contradicts the survival of cooperation observed in nature. In this review, we will introduce game theoretical concepts that lead to this conclusion and show how the spatial competition dynamics between microorganisms can be used to model the survival and maintenance of cooperation. In particular, we focus on how Escherichia coli bacteria with a growth advantage in stationary phase (GASP) phenotype maintain a proliferative phenotype when faced with overcrowding to gain a fitness advantage over wild-type populations. We review recent experimental approaches studying the growth dynamics of competing GASP and wild-type strains of E. coli inside interconnected microfabricated habitats and use a game theoretical approach to analyse the observed inter-species interactions. We describe how the use of evolutionary game theory and the ideal free distribution accurately models the spatial distribution of cooperative and selfish individuals in spatially heterogeneous environments. Using bacteria as a model system of cooperative and selfish behaviours may lead to a better understanding of the competition dynamics of other organisms—including tumour–host interactions during cancer development and metastasis.

Physics of biofilms: the initial stages of biofilm formation and dynamics

One of the physiological responses of bacteria to external stress is to assemble into a biofilm. The formation of a biofilm greatly increases a bacterial populations resistance to a hostile environment by shielding cells, for example, from antibiotics. In this paper, we describe the conditions necessary for the emergence of biofilms in natural environments and relate them to the emergence of biofilm formation inside microfluidic devices. We show that competing species of Escherichia coli bacteria form biofilms to spatially segregate themselves in response to starvation stress, and use in situ methods to characterize the physical properties of the biofilms. Finally, we develop a microfluidic platform to study the inter-species interactions and show how biofilm-mediated genetic interactions can improve a species? resistance to external stress.