In silico evolution of diauxic growth

The glucose effect is a well known phenomenon whereby cells, when presented with two different nutrients, show a diauxic growth pattern, i.e. an episode of exponential growth followed by a lag phase of reduced growth followed by a second phase of exponential growth. Diauxic growth is usually thought of as a an adaptation to maximise biomass production in an environment offering two or more carbon sources. While diauxic growth has been studied widely both experimentally and theoretically, the hypothesis that diauxic growth is a strategy to increase overall growth has remained an unconfirmed conjecture. Here, we present a minimal mathematical model of a bacterial nutrient uptake system and metabolism. We subject this model to artificial evolution to test under which conditions diauxic growth evolves. As a result, we find that, indeed, sequential uptake of nutrients emerges if there is competition for nutrients and the metabolism/uptake system is capacity limited. However, we also find that diauxic growth is a secondary effect of this system and that the speed-up of nutrient uptake is a much larger effect. Notably, this speed-up of nutrient uptake coincides with an overall reduction of efficiency. Our two main conclusions are: (i) Cells competing for the same nutrients evolve rapid but inefficient growth dynamics. (ii) In the deterministic models we use here no substantial lag-phase evolves. This suggests that the lag-phase is a consequence of stochastic gene expression

Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy

Development of single-molecule localization microscopy techniques has allowed nanometre scale localization accuracy inside cells, permitting the resolution of ultra-fine cell structure and the elucidation of crucial molecular mechanisms. Application of these methodologies to understanding processes underlying DNA replication and repair has been limited to defined in vitro biochemical analysis and prokaryotic cells. In order to expand these techniques to eukaryotic systems, we have further developed a photo-activated localization microscopy-based method to directly visualize DNA-associated proteins in unfixed eukaryotic cells. We demonstrate that motion blurring of fluorescence due to protein diffusivity can be used to selectively image the DNA-bound population of proteins. We designed and tested a simple methodology and show that it can be used to detect changes in DNA binding of a replicative helicase subunit, Mcm4, and the replication sliding clamp, PCNA, between different stages of the cell cycle and between distinct genetic backgrounds

Structure and lithium transport pathways in Li₂FeSiO₄ cathodes for lithium batteries

The importance of exploring new low-cost and safe cathodes for large-scale lithium batteries has led to increasing interest in Li(2)FeSiO(4). The structure of Li(2)FeSiO(4) undergoes significant change on cycling, from the as-prepared γ(s) form to an inverse β(II) polymorph; therefore it is important to establish the structure of the cycled material. In γ(s) half the LiO(4), FeO(4), and SiO(4) tetrahedra point in opposite directions in an ordered manner and exhibit extensive edge sharing. Transformation to the inverse β(II) polymorph on cycling involves inversion of half the SiO(4), FeO(4), and LiO(4) tetrahedra, such that they all now point in the same direction, eliminating edge sharing between cation sites and flattening the oxygen layers. As a result of the structural changes, Li(+) transport paths and corresponding Li-Li separations in the cycled structure are quite different from the as-prepared material, as revealed here by computer modeling, and involve distinct zigzag paths between both Li sites and through intervening unoccupied octahedral sites that share faces with the LiO(4) tetrahedra

Charge-tunnelling and self-trapping: common origins for blinking, grey-state emission and photoluminescence enhancement in semiconductor quantum dots

Understanding instabilities in the photoluminescence (PL) from light emitting materials is crucial to optimizing their performance for different applications. Semiconductor quantum dots (QDs) offer bright, size tunable emission, properties that are now being exploited in a broad range of developing technologies from displays and solar cells to biomaging and optical storage. However, instabilities such as photoluminescence intermittency, enhancement and bleaching of emission in these materials can be detrimental to their utility. Here, we report dielectric dependent blinking, intensity-“spikes” and low-level, “grey”-state emission, as well as PL enhancement in ZnS capped CdSe QDs; observations that we found consistent with a charge-tunnelling and self-trapping (CTST) description of exciton-dynamics on the QD–host system. In particular, modulation of PL in grey-states and PL enhancement are found to have a common origin in the equilibrium between exciton charge carrier core and surface-states within the CTST framework. Parameterized in terms of size and electrostatic properties of the QD and its nanoenvironment, the CTST offers predictive insight into exciton-dynamics in these nanomaterials

The lag-phase during diauxic growth is a trade-off between fast adaptation and high growth rate

Bi-phasic or diauxic growth is often observed when microbes are grown in a chemically defined medium containing two sugars (for example glucose and lactose). Typically, the two growth stages are separated by an often lengthy phase of arrested growth, the so-called lag-phase. Diauxic growth is usually interpreted as an adaptation to maximise population growth in multi-nutrient environments. However, the lag-phase implies a substantial loss of growth during the switch-over. It therefore remains unexplained why the lag-phase is adaptive. Here we show by means of a stochastic simulation model based on the bacterial PTS system that it is not possible to shorten the lag-phase without incurring a permanent growth-penalty. Mechanistically, this is due to the inherent and well established limitations of biological sensors to operate efficiently at a given resource cost. Hence, there is a trade-off between lost growth during the diauxic switch and the long-term growth potential of the cell. Using simulated evolution we predict that the lag-phase will evolve depending on the distribution of conditions experienced during adaptation. In environments where switching is less frequently required, the lag-phase will evolve to be longer whereas, in frequently changing environments, the lag-phase will evolve to be shorter

Understanding voltage decay in lithium-excess layered cathode materials through oxygen-centred structural arrangement

Lithium-excess 3d-transition-metal layered oxides (Li1+xNiyCozMn1-x-y-zO2, > 250 mAh g(-1)) suffer from severe voltage decay upon cycling, which decreases energy density and hinders further research and development. Nevertheless, the lack of understanding on chemical and structural uniqueness of the material prevents the interpretation of internal degradation chemistry. Here, we discover a fundamental reason of the voltage decay phenomenon by comparing ordered and cation-disordered materials with a combination of X-ray absorption spectroscopy and transmission electron microscopy studies. The cation arrangement determines the transition metal-oxygen covalency and structural reversibility related to voltage decay. The identification of structural arrangement with de-lithiated oxygen-centred octahedron and interactions between octahedrons affecting the oxygen stability and transition metal mobility of layered oxide provides the insight into the degradation chemistry of cathode materials and a way to develop high-energy density electrodes

Le compartiment sauvage de la carotte en France : des ressources génétiques importantes et pourtant méconnues

La France est considérée comme centre secondaire de diversification de la carotte, du fait de l’activité importante de sélection (par des maraîchers ou semenciers), ce qui justifie les actions de conservation et connaissance des variétés anciennes menées par le réseau de ressources génétiques « Carotte et autres Daucus ». Par contre, le compartiment sauvage est méconnu et sous-exploité, alors qu’il s’agit d’une espèce pour laquelle de nombreuses populations existent sur le territoire français, avec une situation très contrastée. Si la carotte sauvage D. carota spp carota n’est pas en danger, d’autres sous espèces sont protégées (ssp gadecaei) ou menacées du fait de la dégradation de leur milieux naturels notamment en zone littorale ou de possibles introgressions avec la sous-espèce carota. Le travail présenté porte donc sur : i/ la sauvegarde et la mise à disposition des ressources génétiques sauvages, à travers l’inventaire de populations in situ et la constitution de collections ex-situ ; ii/ l’approfondissement de la connaissance et de l’identification taxonomique des sous-espèces sauvages ; iii/ la connaissance de la diversité au sein du compartiment sauvage (marqueurs SSR et données écologiques) ; et iv/ l’évaluation des ressources génétiques sauvages de carotte pour permettre leur exploitation (fertilité, croisements avec le compartiment cultivé, tolérance à différents bioagresseurs). Ce programme fait l’objet du soutien d’un contrat de branche du ministère de l’agriculture et implique les membres du réseau « Carotte et autres Daucus ».

Structural characterization of the Ta-rich part of the Ta–Al system

The Ta-rich part of the Ta-Al system has been investigated. On the one hand, the accommodation of the non-stoichiometry in the σ phase has been studied by Rietveld refinement of X-ray powder data obtained from different samples on both sides of the ideal composition (Ta2Al, P42/mnm, tP30). On the other hand, the structure of the β phase has been determined ab initio from powder synchrotron data (analyzed composition Ta50.7Al49.3, refined composition Ta52.6(5)Al47.4(5) (Ta45.2(4)Al40.8(4)), stoichiometric composition Ta48Al38, mP86, P21/c, a = 9.8707(1)Å, b = 9.8766(1)Å, c = 16.3539(2), β = 116.478(1), RB = 2.6%). This phase is shown to be closely related to the group of the topologically close packed phases. In addition, phase relations have been accurately determined in the Ta-rich end of the system