Publications by authors named "Stanislas Leibler"

In view of changing climatic conditions and disappearing natural resources such as fertile soil and water, exploring alternatives to today's industrial monocrop farming becomes essential. One promising farming practice is intercropping (IC), in which two or more crop species are grown together. Many experiments have shown that, under certain circumstances, IC can decrease soil erosion and fertilizer use, improve soil health and land management, while preserving crop production levels.

View Article and Find Full Text PDF

Genetic assimilation is the process by which a phenotype that is initially induced by an environmental stimulus becomes stably inherited in the absence of the stimulus after a few generations of selection. While the concept has attracted much debate after being introduced by C. H.

View Article and Find Full Text PDF

SignificanceEvolution through natural selection is an overwhelmingly complex process, and it is not surprising that theoretical approaches are strongly simplifying it. For instance, population genetics considers mainly dynamics of gene allele frequencies. Here, we develop a complementary approach to evolutionary dynamics based on three elements-organism reproduction, variations, and selection-that are essential for any evolutionary theory.

View Article and Find Full Text PDF

Isogenic populations often display remarkable levels of phenotypic diversity even in constant, homogeneous environments. Such diversity results from differences between individuals ("nongenetic individuality") as well as changes during individuals' lifetimes ("changeability"). Yet, studies that capture and quantify both sources of diversity are scarce.

View Article and Find Full Text PDF

Analysis of single-cell measurements of bacterial growth and division often relied on testing preconceived models of cell size control mechanisms. Such an approach could limit the scope of data analysis and prevent us from uncovering new information. Here, we take an "agnostic" approach by applying regression methods to multiple simultaneously measured cellular variables, which allow us to infer dependencies among those variables from their apparent correlations.

View Article and Find Full Text PDF

Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular functions are carried out not by long, isolated proteins, but rather by multiprotein complexes.

View Article and Find Full Text PDF

The dynamics of ecological change following a major perturbation, known as succession, are influenced by random processes. Direct quantitation of the degree of contingency in succession requires chronological study of replicate ecosystems. We previously found that population dynamics in carefully controlled, replicated synthetic microbial ecosystems were strongly deterministic over several months.

View Article and Find Full Text PDF

Biological organisms exhibit diverse strategies for adapting to varying environments. For example, a population of organisms may express the same phenotype in all environments ("unvarying strategy") or follow environmental cues and express alternative phenotypes to match the environment ("tracking strategy"), or diversify into coexisting phenotypes to cope with environmental uncertainty ("bet-hedging strategy"). We introduce a general framework for studying how organisms respond to environmental variations, which models an adaptation strategy by an abstract mapping from environmental cues to phenotypic traits.

View Article and Find Full Text PDF

Phenotypic plasticity refers to the capacity of the same organisms to exhibit different characteristics under varied environmental conditions. A plastic developmental program allows organisms to sense environmental cues in early stages of life and express phenotypes that are better fitted to environments encountered later in life. This is often considered an adaptive strategy for living in varying environments as long as the plastic response is sufficiently fast, is accurate, and is not too costly.

View Article and Find Full Text PDF

The abundance of available static protein structural data makes the more effective analysis and interpretation of this data a valuable tool to supplement the experimental study of protein mechanics. Structural displacements can be difficult to analyze and interpret. Previously, we showed that strains provide a more natural and interpretable representation of protein deformations, revealing mechanical coupling between spatially distinct sites of allosteric proteins.

View Article and Find Full Text PDF

Biological organisms have to cope with stochastic variations in both the external environment and the internal population dynamics. Theoretical studies and laboratory experiments suggest that population diversification could be an effective bet-hedging strategy for adaptation to varying environments. Here we show that bet hedging can also be effective against demographic fluctuations that pose a trade-off between growth and survival for populations even in a constant environment.

View Article and Find Full Text PDF

In many proteins, especially allosteric proteins that communicate regulatory states from allosteric to active sites, structural deformations are functionally important. To understand these deformations, dynamical experiments are ideal but challenging. Using static structural information, although more limited than dynamical analysis, is much more accessible.

View Article and Find Full Text PDF

Organisms can adapt to a randomly varying environment by creating phenotypic diversity in their population, a phenomenon often referred to as "bet hedging." The favorable level of phenotypic diversity depends on the statistics of environmental variations over timescales of many generations. Could organisms gather such long-term environmental information to adjust their phenotypic diversity? We show that this process can be achieved through a simple and general learning mechanism based on a transgenerational feedback: The phenotype of the parent is progressively reinforced in the distribution of phenotypes among the offspring.

View Article and Find Full Text PDF

Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed "sectors". The method applies spectral analysis to a matrix obtained by combining correlation information with sequence conservation. It has been asserted that the protein sectors identified by SCA are functionally significant, with different sectors controlling different biochemical properties of the protein.

View Article and Find Full Text PDF

Self-assembly materials are traditionally designed so that molecular or mesoscale components form a single kind of large structure. Here, we propose a scheme to create "multifarious assembly mixtures," which self-assemble many different large structures from a set of shared components. We show that the number of multifarious structures stored in the solution of components increases rapidly with the number of different types of components.

View Article and Find Full Text PDF

The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. However, although evolution by natural selection requires new heritable traits to be produced and transmitted, it does not prescribe, per se, the mechanisms by which this is operated. The mechanisms of inheritance are not, however, unconstrained, because they are themselves subject to natural selection.

View Article and Find Full Text PDF

The dynamical evolution of complex systems is often intrinsically stochastic and subject to external random forces. In order to study the resulting variability in dynamics, it is essential to make measurements on replicate systems and to separate arbitrary variation of the average dynamics of these replicates from fluctuations around the average dynamics. Here we do so for population time-series data from replicate ecosystems sharing a common average dynamics or common trend.

View Article and Find Full Text PDF

Systematic studies of phenotypic diversity--required for understanding evolution--lag behind investigations of genetic diversity. Here we develop a quantitative approach to studying behavioral diversity, which we apply to swimming of the ciliate Tetrahymena. We measure the full-lifetime behavior of hundreds of individual organisms at high temporal resolution, over several generations and in diverse nutrient conditions.

View Article and Find Full Text PDF

Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to infrequently dividing or nondividing "persisters." Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH).

View Article and Find Full Text PDF

Proofreading mechanisms increase specificity in biochemical reactions by allowing for the dissociation of intermediate complexes. These mechanisms disrupt and reset the reaction to undo errors at the cost of increased time of reaction and free energy expenditure. Here, we draw an analogy between proofreading and microtubule growth which share some of the features described above.

View Article and Find Full Text PDF

Contingency, the persistent influence of past random events, pervades biology. To what extent, then, is each course of ecological or evolutionary dynamics unique, and to what extent are these dynamics subject to a common statistical structure? Addressing this question requires replicate measurements to search for emergent statistical laws. We establish a readily replicated microbial closed ecosystem (CES), sustaining its three species for years.

View Article and Find Full Text PDF

To understand dynamic developmental processes, living tissues have to be imaged frequently and for extended periods of time. Root development is extensively studied at cellular resolution to understand basic mechanisms underlying pattern formation and maintenance in plants. Unfortunately, ensuring continuous specimen access, while preserving physiological conditions and preventing photo-damage, poses major barriers to measurements of cellular dynamics in growing organs such as plant roots.

View Article and Find Full Text PDF

Allosteric coupling between protein domains is fundamental to many cellular processes. For example, Hsp70 molecular chaperones use ATP binding by their actin-like N-terminal ATPase domain to control substrate interactions in their C-terminal substrate-binding domain, a reaction that is critical for protein folding in cells. Here, we generalize the statistical coupling analysis to simultaneously evaluate co-evolution between protein residues and functional divergence between sequences in protein sub-families.

View Article and Find Full Text PDF

Measurements of population dynamics are ubiquitous in experiments with microorganisms. Studies with microbes elucidating adaptation, selection, and competition rely on measurements of changing populations in time. Despite this importance, quantitative methods for measuring population dynamics microscopically, with high time resolution, across many replicates remain limited.

View Article and Find Full Text PDF

A fundamental problem in biology is understanding the evolutionary emergence and maintenance of altruistic behaviors. A well-recognized conceptual insight is provided by a general mathematical relation, Hamilton's rule. This rule can in principle be invoked to explain natural examples of cooperation, but measuring the variables that it involves is a particularly challenging problem and controlling these variables experimentally an even more daunting task.

View Article and Find Full Text PDF