University of Évry Val d'Essonne

Ouldali H., Sarthak K., Ensslen T., Piguet F., Manivet P., Pelta J., Behrends J.C., Aksimentiev A., Oukhaled A.

Efforts to sequence single protein molecules in nanopores1–5 have been hampered by the lack of techniques with sufficient sensitivity to discern the subtle molecular differences among all twenty amino acids. Here we report ionic current detection of all twenty proteinogenic amino acids in an aerolysin nanopore with the help of a short polycationic carrier. Application of molecular dynamics simulations revealed that the aerolysin nanopore has a built-in single-molecule trap that fully confines a polycationic carrier-bound amino acid inside the sensing region of the aerolysin. This structural feature means that each amino acid spends sufficient time in the pore for sensitive measurement of the excluded volume of the amino acid. We show that distinct current blockades in wild-type aerolysin can be used to identify 13 of the 20 natural amino acids. Furthermore, we show that chemical modifications, instrumentation advances and nanopore engineering offer a route toward identification of the remaining seven amino acids. These findings may pave the way to nanopore protein sequencing. Individual amino acids fused to a highly charged heptapeptide are discriminated in an aerolysin nanopore.

Gautreau G., Bazin A., Gachet M., Planel R., Burlot L., Dubois M., Perrin A., Médigue C., Calteau A., Cruveiller S., Matias C., Ambroise C., Rocha E.P., Vallenet D.

The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species. These methods usually lack multivariate statistical models to infer the partitions and the optimal number of classes and don’t account for genome organization. We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. Our method, named PPanGGOLiN, partitions nodes using an Expectation-Maximization algorithm based on multivariate Bernoulli Mixture Model coupled with a Markov Random Field. This approach takes into account the topology of the graph and the presence/absence of genes in pangenomes to classify gene families into persistent, cloud, and one or several shell partitions. By analyzing the partitioned pangenome graphs of isolate genomes from 439 species and metagenome-assembled genomes from 78 species, we demonstrate that our method is effective in estimating the persistent genome. Interestingly, it shows that the shell genome is a key element to understand genome dynamics, presumably because it reflects how genes present at intermediate frequencies drive adaptation of species, and its proportion in genomes is independent of genome size. The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative genomics. The software is freely available at https://github.com/labgem/PPanGGOLiN.

Patra S., Germann M., Karr J.-., Haidar M., Hilico L., Korobov V.I., Cozijn F.M., Eikema K.S., Ubachs W., Koelemeij J.C.

A very precise ratio The value of the ratio of the masses of the proton and the electron has a bearing on the values of other physical constants. This ratio is known to a very high precision. Patra et al. improved this precision even further by measuring particular frequencies in the rovibrational spectrum of the hydrogen deuteride molecular ion (HD + ) (see the Perspective by Hori). To reach this high precision, the researchers placed the HD + molecules in an ion trap and surrounded them by beryllium ions. The cold beryllium ions then helped cool the HD + molecules, making the HD + spectral lines narrow enough that the proton-electron mass ratio could be extracted by comparison with theoretical predictions. Science , this issue p. 1238 ; see also p. 1160

Lallemand T., Leduc M., Landès C., Rizzon C., Lerat E.

Gene duplication is an important evolutionary mechanism allowing to provide new genetic material and thus opportunities to acquire new gene functions for an organism, with major implications such as speciation events. Various processes are known to allow a gene to be duplicated and different models explain how duplicated genes can be maintained in genomes. Due to their particular importance, the identification of duplicated genes is essential when studying genome evolution but it can still be a challenge due to the various fates duplicated genes can encounter. In this review, we first describe the evolutionary processes allowing the formation of duplicated genes but also describe the various bioinformatic approaches that can be used to identify them in genome sequences. Indeed, these bioinformatic approaches differ according to the underlying duplication mechanism. Hence, understanding the specificity of the duplicated genes of interest is a great asset for tool selection and should be taken into account when exploring a biological question.

Gordon S.P., Contreras-Moreira B., Levy J.J., Djamei A., Czedik-Eysenberg A., Tartaglio V.S., Session A., Martin J., Cartwright A., Katz A., Singan V.R., Goltsman E., Barry K., Dinh-Thi V.H., Chalhoub B., et. al.

Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution. Existing plant pan-genomic studies usually report considerable intraspecific whole gene presence-absence variation. Here, the authors use pan-genomic approach to reveal gradual polyploid genome evolution by analyzing of Brachypodium hybridum and its diploid progenitors.

Tuladhar A., Dewan S., Pezzotti S., Brigiano F.S., Creazzo F., Gaigeot M., Borguet E.

The structure and ultrafast dynamics of the electric double layer (EDL) are central to chemical reactivity and physical properties at solid/aqueous interfaces. While the Gouy-Chapman-Stern model is widely used to describe EDLs, it is solely based on the macroscopic electrostatic attraction of electrolytes for the charged surfaces. Structure and dynamics in the Stern layer are, however, more complex because of competing effects due to the localized surface charge distribution, surface-solvent-ion correlations, and the interfacial hydrogen bonding environment. Here, we report combined time-resolved vibrational sum frequency generation (TR-vSFG) spectroscopy with ab initio DFT-based molecular dynamics simulations (AIMD/DFT-MD) to get direct access to the molecular-level understanding of how ions change the structure and dynamics of the EDL. We show that innersphere adsorbed ions tune the hydrophobicity of the silica-aqueous interface by shifting the structural makeup in the Stern layer from dominant water-surface interactions to water-water interactions. This drives an initially inhomogeneous interfacial water coordination landscape observed at the neat interface toward a homogeneous, highly interconnected in-plane 2D hydrogen bonding (2D-HB) network at the ionic interface, reminiscent of the canonical, hydrophobic air-water interface. This ion-induced transformation results in a characteristic decrease of the vibrational lifetime (T1) of excited interfacial O-H stretching modes from T1 ∼ 600 fs to T1 ∼ 250 fs. Hence, we propose that the T1 determined by TR-vSFG in combination with DFT-MD simulations can be widely used for a quantitative spectroscopic probe of the ion kosmotropic/chaotropic effect at aqueous interfaces as well as of the ion-induced surface hydrophobicity.

Kettani M., Bandelier P.

This paper examines the cost competitiveness of an extra-large-scale (275,000 m3/d) solar-powered desalination, taking as a case study the Chtouka Ait Baha plant in Morocco. It assesses the conditions at which solar Photovoltaics (PV) and Concentrated Solar Power (CSP) would be competitive with a grid (mainly fossil) driven desalination plant for the reference year and by 2030. The paper considers also a scenario where battery storage complements PV power generation. To conduct the analysis, a simple model of water cost calculation is built. Second, the cost related to energy consumption is calculated for different power supply options to evaluate the impact of energy provision cost on the final cost of water. The first main result of this paper is that desalinated water can be obtained at an acceptable cost of around 1 $/m3. The second one is that PV without storage remains the cheapest power supply option today and by 2030. Storage based solution appears less competitive today but can be more attractive in a framework of increasing electricity grid prices and higher flexibility requirements in the future. The paper gives recommendations regarding the implication of different technology choices in the framework of the future Moroccan energy system.

Bakels S., Gaigeot M., Rijs A.M.

Gas-phase, double resonance IR spectroscopy has proven to be an excellent approach to obtain structural information on peptides ranging from single amino acids to large peptides and peptide clusters. In this review, we discuss the state-of-the-art of infrared action spectroscopy of peptides in the far-IR and THz regime. An introduction to the field of far-IR spectroscopy is given, thereby highlighting the opportunities that are provided for gas-phase research on neutral peptides. Current experimental methods, including spectroscopic schemes, have been reviewed. Structural information from the experimental far-IR spectra can be obtained with the help of suitable theoretical approaches such as dynamical DFT techniques and the recently developed Graph Theory. The aim of this review is to underline how the synergy between far-IR spectroscopy and theory can provide an unprecedented picture of the structure of neutral biomolecules in the gas phase. The far-IR signatures of the discussed studies are summarized in a far-IR map, in order to gain insight into the origin of the far-IR localized and delocalized motions present in peptides and where they can be found in the electromagnetic spectrum.

Karr J., Marchand D., Voutier E.

The proton charge radius has been measured since the 1950s using elastic electron–proton scattering and ordinary hydrogen atomic spectroscopy. In 2010, a highly precise measurement of the proton charge radius using, for the first time, muonic hydrogen spectroscopy unexpectedly led to controversy, as the value disagreed with the previously accepted one. Since then, atomic and nuclear physicists have been trying to understand this discrepancy by checking theories, questioning experimental methods and performing new experiments. Recently, two measurements from electron scattering and ordinary hydrogen spectroscopy were found to agree with the results from muonic atom spectroscopy. Is the ‘proton-radius puzzle’ now resolved? In this Review, we scrutinize the experimental studies of the proton radius to gain insight on this issue. We provide a brief history of the proton before describing the techniques used to measure its radius and the current status of the field. We assess the precision and reliability of available experimental data, with particular focus on the most recent results. Finally, we discuss the forthcoming new generation of refined experiments and theoretical calculations that aim to definitely end the debate on the proton size. The charge radius of the proton is controversial because measurements by different methods disagree. Recent results indicate that these measurements might be reconciled. In this Review, we discuss the experimental techniques used to measure the proton radius and describe the current status of the field as well as forthcoming experiments.

Conti Nibali V., Pezzotti S., Sebastiani F., Galimberti D.R., Schwaab G., Heyden M., Gaigeot M.-., Havenith M.

Water, being the universal solvent, acts as a competing agent in fundamental processes, such as folding, aggregation or biomolecular recognition. A molecular understanding of hydrophobic hydration is of central importance to understanding the subtle free energy differences, which dictate function. Ab initio and classical molecular dynamics simulations yield two distinct hydration water populations in the hydration shell of solvated tert-butanol noted as HB-wrap and HB-hydration2bulk. The experimentally observed hydration water spectrum can be dissected into two modes, centered at 164 and 195 cm-1. By comparison to the simulations, these two bands are attributed to the HB-wrap and HB-hydration2bulk populations, respectively. We derive a quantitative correlation between the population in each of these two local water coordination motifs and the temperature dependence of the solvation entropy. The crossover from entropy to enthalpy dominated solvation at elevated temperatures, as predicted by theory and observed experimentally, can be rationalized in terms of the distinct temperature stability and thermodynamic signatures of HB-wrap and HB-hydration2bulk.