Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement

International audience

A comparative study between microsatellite and allozyme markers was conducted on natural populations of resident brown trout (Salmo trutta) sampled over a reduced geographical scale and on hatchery strains. The higher level of polymorphism observed at microsatellite loci resulted in higher power of statistical tests for differentiation among population samples and for genotypic linkage disequilibrium. Genetic distances of Cavalli-Sforza and Edwards were on average two times larger for microsatellites than for allozymes but multilocus FST estimates computed over the entire set of populations were not significantly different for both categories of markers. Assignment tests of individual fish to the set of sampled populations demonstrated a much higher efficiency of microsatellites compared to allozymes. Pairwise multilocus FST estimates were significantly correlated to waterway distances and there was a significant tendency for the incorrectly classified individuals to be assigned to one of the nearest populations, indicating that isolation-by-distance acted significantly on brown trout populations. This increase of differentiation with distance was higher for allozymes than for microsatellites. Traditional measures of genetic differentiation (Cavalli-Sforza and Edwards' chord distance and FST) were compared for microsatellites to recently proposed statistics taking into account allele size differences (Goldstein's distance and PST). Using Goldstein's distance for neighbour-joining analysis did not improve the tree structure resolution. Multilocus estimates of PST and FST were not significantly different when computed over the entire set of populations but no significant correlation was detected between matrices of pairwise multilocus PST estimates and waterway distances.

Silica is the most abundant metal oxide and the main component of the Earth's crust. Its behavior in contact with water plays a critical role in a variety of geochemical and environmental processes. Despite its key role, the details of the aqueous silica interface at the microscopic molecular level are still elusive. Here we provide such a detailed understanding of the molecular behavior of the silica-water interface, using density functional theory based molecular dynamics (DFTMD) simulations, where a consistent treatment of the electronic structure of solvent and surface is provided. We have calculated the acidity of the silanol groups at the interface directly from the DFTMD simulations, without any fitting of parameters to the experimental data. We find two types of silanol groups at the surface of quartz: out-of-plane silanols with a strong acidic character (pKa = 5.6), which consequently results in the formation of strong and short hydrogen bonds with water molecules at the interface, and in-plane silanols with a pKa of 8.5, forming weak hydrogen bonds with the interfacial water molecules. Our estimate of the quartz point of zero charge (1.0) is found in good agreement with the experimental value of 1.9. We have also shown how the silanols orientation and their hydrogen bond properties are responsible for an amphoteric behavior of the surface. A detailed analysis has identified two species of adsorbed water molecules at the solid-liquid interface, which using the language of vibrational spectroscopy can be identified as "liquid-like" and "ice-like" water or, in other words, water molecules forming respectively weak and strong H-bonds with the oxide surface. These two populations of water are in turn responsible for two distinct peaks in the infrared spectrum of interfacial water and thus provide a molecular explanation of the experimental sum frequency generation spectrum recorded in the literature. In the specific case of quartz, we show that the liquid-/ice-like behavior is the result of the silanol groups ability to donate or accept hydrogen bonds with different strengths, which consequently modulates the vibrational properties of the adsorbed water layer.

This study compares the properties of dominant markers, such as amplified fragment length polymorphisms (AFLPs), with those of codominant multiallelic markers, such as microsatellites, in reconstructing parentage. These two types of markers were used to search for both parents of an individual without prior knowledge of their relationships, by calculating likelihood ratios based on genotypic data, including mistyping. Experimental data on 89 oak trees genotyped for six microsatellite markers and 159 polymorphic AFLP loci were used as a starting point for simulations and tests. Both sets of markers produced high exclusion probabilities, and among dominant markers those with dominant allele frequencies in the range 0.1-0.4 were more informative. Such codominant and dominant markers can be used to construct powerful statistical tests to decide whether a genotyped individual (or two individuals) can be considered as the true parent (or parent pair). Gene flow from outside the study stand (GFO), inferred from parentage analysis with microsatellites, overestimated the true GFO, whereas with AFLPs it was underestimated. As expected, dominant markers are less efficient than codominant markers for achieving this, but can still be used with good confidence, especially when loci are deliberately selected according to their allele frequencies.

There are still unmet needs in finding new technologies for biomedical diagnostic and industrial applications. A technology allowing the analysis of size and sequence of short peptide molecules of only few molecular copies is still challenging. The fast, low-cost and label-free single-molecule nanopore technology could be an alternative for addressing these critical issues. Here, we demonstrate that the wild-type aerolysin nanopore enables the size-discrimination of several short uniformly charged homopeptides, mixed in solution, with a single amino acid resolution. Our system is very sensitive, allowing detecting and characterizing a few dozens of peptide impurities in a high purity commercial peptide sample, while conventional analysis techniques fail to do so.

The past decades have seen density functional theory (DFT) evolve from a rising star in computational quantum chemistry to one of its major players. This Theme Issue, which comes half a century after the publication of the Hohenberg-Kohn theorems that laid the foundations of modern DFT, reviews progress and challenges in present-day DFT research. Rather than trying to be comprehensive, this Theme Issue attempts to give a flavour of selected aspects of DFT.

Paper aging and conservation are matters of concern to those responsible for archives and library collections. Wood-derived fibers are mainly composed of cellulose, hemicelluloses, and lignin, but paper composition can also include additives, such as starch, minerals, and synthetic polymers. Therefore, paper is a multi-component material, and because of its complex and varied nature, research findings in paper chemistry can be difficult to interpret. Deterioration of paper is caused by many factors such as acid hydrolysis, oxidative agents, light, air pollution, or the presence of microorganisms. The origin of the cellulosic material, as well as pulping and papermaking procedures, additives, and storage conditions play a crucial role. The chemical changes occurring within paper thus involve multi-parameter processes. The purpose of this review, which mainly focuses on the most recent decade, is to provide a description of the more important changes produced by aging and an update of the new tools available for the study of paper deterioration and its conservation.

Protein export is an essential mechanism in living cells and exported proteins are usually translocated through a protein-conducting channel in an unfolded state. Here we analyze, by electrical detection, the entry and transport of unfolded proteins, at the single molecule level, with different stabilities through an aerolysin pore, as a function of the applied voltage and protein concentration. The frequency of ionic current blockades varies exponentially as a function of the applied voltage and linearly as a function of protein concentration. The transport time of unfolded proteins decreases exponentially when the applied voltage increases. We prove that the ionic current blockade duration of a double-sized protein is longer than that assessed for a single protein supporting the transport phenomenon. Our results fit with the theory of confined polyelectrolyte and with some experimental results about DNA or synthetic polyelectrolyte translocation through protein channels as a function of applied voltage. We discuss the potential of the aerolysin nanopore as a tool for protein folding studies as it has already been done for α-hemolysin.

The slow kinetics of the electrochemical oxygen reduction reaction (ORR) is a crucial bottleneck in the development of microbial fuel cells (MFCs). This article firstly gives an overview of the particular constraints imposed on ORR by MFC operating conditions: neutral pH, slow oxygen mass transfer, sensitivity to reactive oxygen species, fouling and biofouling. A review of the literature is then proposed to assess how microbial catalysis could afford suitable solutions. Actually, microbial catalysis of ORR occurs spontaneously on the surface of metallic materials and is an effective motor of microbial corrosion. In this framework, several mechanisms have been proposed, which are reviewed in the second part of the article. The last part describes the efforts made in the domain of MFCs to determine the microbial ecology of electroactive biofilms and define efficient protocols for the formation of microbial oxygen-reducing cathodes. Although no clear mechanism has been established yet, several promising solutions have been recently proposed.

Apis mellifera is composed of three evolutionary branches including mainly African (branch A), western and northern European (branch M), and southeastern European (branch C) populations. The existence of morphological clines extending from the equator to the Polar Circle through Morocco and Spain raised the hypothesis that the branch M originated in Africa. Mitochondrial DNA analysis revealed that branches A and M were characterized by highly diverged lineages implying very remote links between both branches. It also revealed that mtDNA haplotypes from lineages A coexisted with haplotypes M in the Iberian Peninsula and formed a south-north frequency cline, suggesting that this area could be a secondary contact zone between the two branches. By analyzing 11 populations sampled along a France-Spain/Portugal-Morocco-Guinea transect at 8 microsatellite loci and the DraI RFLP of the COI-COII mtDNA marker, we show that Iberian populations do not present any trace of "africanization" and are very similar to French populations when considering microsatellite markers. Therefore, the Iberian Peninsula is not a transition area. The higher haplotype A variability observed in Spanish and Portuguese samples compared to that found in Africa is explained by a higher mutation rate and multiple and recent introductions. Selection appears to be the best explanation to the morphological and allozymic clines and to the diffusion and maintenance of African haplotypes in Spain and Portugal.

We report experimentally the dynamic properties of the entry and transport of unfolded and native proteins through a solid-state nanopore as a function of applied voltage, and we discuss the experimental data obtained as compared to theory. We show an exponential increase in the event frequency of current blockades and an exponential decrease in transport times as a function of the electric driving force. The normalized current blockage ratio remains constant or decreases for folded or unfolded proteins, respectively, as a function of the transmembrane potential. The unfolded protein is stretched under the electric driving force. The dwell time of native compact proteins in the pore is almost 1 order of magnitude longer than that of unfolded proteins, and the event frequency for both protein conformations is low. We discuss the possible phenomena hindering the transport of proteins through the pores, which could explain these anomalous dynamics, in particular, electro-osmotic counterflow and protein adsorption on the nanopore wall.

The study of chemo-mechanical stress taking place in the electrodes of a battery during cycling is of paramount importance to extend the lifetime of the device. This aspect is particularly relevant for all-solid-state batteries where the stress can be transmitted across the device due to the stiff nature of the solid electrolyte. However, stress monitoring generally relies on sensors located outside of the battery, therefore providing information only at device level and failing to detect local changes. Here, we report a method to investigate the chemo-mechanical stress occurring at both positive and negative electrodes and at the electrode/electrolyte interface during battery operation. To such effect, optical fiber Bragg grating sensors were embedded inside coin and Swagelok cells containing either liquid or solid-state electrolyte. The optical signal was monitored during battery cycling, further translated into stress and correlated with the voltage profile. This work proposes an operando technique for stress monitoring with potential use in cell diagnosis and battery design.

Proteins subjected to an electric field and forced to pass through a nanopore induce blockades of ionic current that depend on the protein and nanopore characteristics and interactions between them. Recent advances in the analysis of these blockades have highlighted a variety of phenomena that can be used to study protein translocation and protein folding, to probe single-molecule catalytic reactions in order to obtain kinetic and thermodynamic information, and to detect protein-antibody complexes, proteins with DNA and RNA aptamers, and protein-pore interactions. Nanopore design is now well controlled, allowing the development of future biotechnologies and medicine applications.

The organization of water at the interface with silica and alumina oxides is analysed using density functional theory-based molecular dynamics simulation (DFT-MD). The interfacial hydrogen bonding is investigated in detail and related to the chemistry of the oxide surfaces by computing the surface charge density and acidity. We find that water molecules hydrogen-bonded to the surface have different orientations depending on the strength of the hydrogen bonds and use this observation to explain the features in the surface vibrational spectra measured by sum frequency generation spectroscopy. In particular, 'ice-like' and 'liquid-like' features in these spectra are interpreted as the result of hydrogen bonds of different strengths between surface silanols/aluminols and water.

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.

Most proteins comprise one or several domains. New domain architectures can be created by combining previously existing domains. The elementary events that create new domain architectures may be categorized into three classes, namely domain(s) insertion or deletion (indel), exchange and repetition. Using 'DomainTeam', a tool dedicated to the search for microsyntenies of domains, we quantified the relative contribution of these events. This tool allowed us to collect homologous bacterial genes encoding proteins that have obviously evolved by modular assembly of domains. We show that indels are the most frequent elementary events and that they occur in most cases at either the N- or C-terminus of the proteins. As revealed by the genomic neighbourhood/context of the corresponding genes, we show that a substantial number of these terminal indels are the consequence of gene fusions/fissions. We provide evidence showing that the contribution of gene fusion/fission to the evolution of multi-domain bacterial proteins is lower-bounded by 27% and upper-bounded by 64%. We conclude that gene fusion/fission is a major contributor to the evolution of multi-domain bacterial proteins.

Brassinosteroids (BRs) are steroid hormones that coordinate fundamental developmental programs in plants. In this study we show that in addition to the well established roles of BRs in regulating cell elongation and cell division events, BRs also govern cell fate decisions during stomata development in Arabidopsis thaliana. In wild-type A. thaliana, stomatal distribution follows the one-cell spacing rule; that is, adjacent stomata are spaced by at least one intervening pavement cell. This rule is interrupted in BR-deficient and BR signaling-deficient A. thaliana mutants, resulting in clustered stomata. We demonstrate that BIN2 and its homologues, GSK3/Shaggy-like kinases involved in BR signaling, can phosphorylate the MAPK kinases MKK4 and MKK5, which are members of the MAPK module YODA-MKK4/5-MPK3/6 that controls stomata development and patterning. BIN2 phosphorylates a GSK3/Shaggy-like kinase recognition motif in MKK4, which reduces MKK4 activity against its substrate MPK6 in vitro. In vivo we show that MKK4 and MKK5 act downstream of BR signaling because their overexpression rescued stomata patterning defects in BR-deficient plants. A model is proposed in which GSK3-mediated phosphorylation of MKK4 and MKK5 enables for a dynamic integration of endogenous or environmental cues signaled by BRs into cell fate decisions governed by the YODA-MKK4/5-MPK3/6 module.

Theoretical spectroscopy is mandatory for a precise understanding and assignment of experimental spectra recorded at finite temperature. We review here room temperature DFT-based molecular dynamics simulations for the purpose of interpreting finite temperature infrared spectra of peptides of increasing size and complexity, in terms of temperature-dependent conformational dynamics and flexibility, and vibrational anharmonicities (potential energy surface anharmonicities, vibrational mode couplings and dipole anharmonicities). We take examples from our research projects in order to illustrate the main key-points and strengths of dynamical spectra modeling in that context. The calculations are presented in relation to room temperature gas phase IR-MPD experiments and room temperature liquid phase IR absorption experiments. These illustrations of floppy polypeptides have been chosen in order to convey the following ideas: temperature-dependent spectra modeling is pivotal for a precise understanding of gas phase spectra recorded at room temperature, including conformational dynamics and vibrational anharmonicities; harmonic spectroscopy (as commonly performed in the literature) can be misleading and even erroneous for a proper interpretation of spectra recorded at finite temperature; taking into account vibrational anharmonicities is pivotal for a proper interplay between theory and experiments; amide I-III bands are not necessarily the most relevant fingerprints for unraveling the local structures of peptides and more complex systems; liquid phase simulations have unraveled relationships between the zwitterionic properties of the peptide bonds and infrared signatures. The review presents a state-of-the-art account of the domain and offers perspectives and new developments for future still more challenging applications.

Interfaces between water and silicates are ubiquitous and relevant for, among others, geochemistry, atmospheric chemistry, and chromatography. The molecular-level details of water organization at silica surfaces are important for a fundamental understanding of this interface. While silica is hydrophilic, weakly hydrogen-bonded OH groups have been identified at the surface of silica, characterized by a high O-H stretch vibrational frequency. Here, through a combination of experimental and theoretical surface-selective vibrational spectroscopy, we demonstrate that these OH groups originate from very weakly hydrogen-bonded water molecules at the nominally hydrophilic silica interface. The properties of these OH groups are very similar to those typically observed at hydrophobic surfaces. Molecular dynamics simulations illustrate that these weakly hydrogen-bonded water OH groups are pointing with their hydrogen atom toward local hydrophobic sites consisting of oxygen bridges of the silica. An increased density of these molecular hydrophobic sites, evident from an increase in weakly hydrogen-bonded water OH groups, correlates with an increased macroscopic contact angle.

Deficiency of the dysferlin protein presents as two major clinical phenotypes: limb-girdle muscular dystrophy type 2B and Miyoshi myopathy. Dysferlin is known to participate in membrane repair, providing a potential hypothesis to the underlying pathophysiology of these diseases. The size of the dysferlin cDNA prevents its direct incorporation into an adeno-associated virus (AAV) vector for therapeutic gene transfer into muscle. To bypass this limitation, we split the dysferlin cDNA at the exon 28/29 junction and cloned it into two independent AAV vectors carrying the appropriate splicing sequences. Intramuscular injection of the corresponding vectors into a dysferlin-deficient mouse model led to the expression of full-length dysferlin for at least 1 year. Importantly, systemic injection in the tail vein of the two vectors led to a widespread although weak expression of the full-length protein. Injections were associated with an improvement of the histological aspect of the muscle, a reduction in the number of necrotic fibers, restoration of membrane repair capacity and a global improvement in locomotor activity. Altogether, these data support the use of such a strategy for the treatment of dysferlin deficiency.