Diet in the Sardinian Bronze Age: models, collagen isotopic data, issues and perspectives

Traditional reconstructions depict Sardinian Bronze Age economy as a mixed one characterized by a remarkable importance of pastoralism, opposed to a more ‘agricultural’ Neolithic. The first few isotopic data, though not unambiguously, seem to indicate quite the opposite compared with earlier times, reflecting possibly a higher dependence on vegetal foods, with possible marginal contributions of aquatic foods and/or C4 plants at one coastal site. However, the importance of ecosystem-wide shifts in interpreting collagen data for comparative purposes is underlined, with specific examples from Sardinia, and so is the rarity of collections including faunal and botanical specimens alongside humans, which would help establish a local isotopic baseline. Efforts to discriminate animal vs. vegetal contributions in Bronze Age diets that are fully based on C3 ecosystems, therefore, remain tentative. Isotopic research in progress on Sardinian diet and climate from the Copper Age up to the Nuragic Late Bronze (2800-1100 BC) is expected to provide a better grasp on temporal and geographic variation.Les reconstitutions alimentaires traditionnelles dépeignent l’économie de l’âge du Bronze en Sardaigne comme une économie mixte caractérisée par une grande importance de l’élevage des moutons, juxtaposée à une période néolithique plus agricole. Les premières données isotopiques, bien que peu nombreuses encore, semblent, d’une façon ambigüe, plutôt indiquer le contraire lorsqu’on les compare aux données des périodes précédentes. Elles montrent une plus grande dépendance des aliments végétaux avec peut-être la contribution marginale d’aliments aquatiques et/ou des plantes issues du milieu côtier. Afin de palier le manque d’études sur les restes fauniques et botaniques et dans le but de réaliser des comparaisons à l’échelle de la Sardaigne, une analyse détaillée des données isotopiques des collagènes a été réalisée pour cerner l’importance de modifications isotopiques de l’écosystème tout entier. Une recherche en cours sur la diète et sur le climat dans la Sardaigne à partir du Néolithique jusqu’à l’âge du Fer (4700-500 avant J.C.) devrait permettre une meilleure interprétation de la variabilité isotopique d’un point de vue chronologique et géographique

Harnessing gene expression to identify the genetic basis of drug resistance

The advent of cost-effective genotyping and sequencing methods have recently made it possible to ask questions that address the genetic basis of phenotypic diversity and how natural variants interact with the environment. We developed Camelot (CAusal Modelling with Expression Linkage for cOmplex Traits), a statistical method that integrates genotype, gene expression and phenotype data to automatically build models that both predict complex quantitative phenotypes and identify genes that actively influence these traits. Camelot integrates genotype and gene expression data, both generated under a reference condition, to predict the response to entirely different conditions. We systematically applied our algorithm to data generated from a collection of yeast segregants, using genotype and gene expression data generated under drug-free conditions to predict the response to 94 drugs and experimentally confirmed 14 novel gene–drug interactions. Our approach is robust, applicable to other phenotypes and species, and has potential for applications in personalized medicine, for example, in predicting how an individual will respond to a previously unseen drug

Dramatic differences in carbon dioxide adsorption and initial steps of reduction between silver and copper

Converting carbon dioxide (CO_2) into liquid fuels and synthesis gas is a world-wide priority. But there is no experimental information on the initial atomic level events for CO_2 electroreduction on the metal catalysts to provide the basis for developing improved catalysts. Here we combine ambient pressure X-ray photoelectron spectroscopy with quantum mechanics to examine the processes as Ag is exposed to CO_2 both alone and in the presence of H_2O at 298 K. We find that CO_2 reacts with surface O on Ag to form a chemisorbed species (O = CO_2^(δ−)). Adding H_2O and CO_2 then leads to up to four water attaching on O = CO_2^(δ−) and two water attaching on chemisorbed (b-)CO_2. On Ag we find a much more favorable mechanism involving the O = CO_2^(δ−) compared to that involving b-CO_2 on Cu. Each metal surface modifies the gas-catalyst interactions, providing a basis for tuning CO_2 adsorption behavior to facilitate selective product formations

Subsurface oxide plays a critical role in CO_2 activation by Cu(111) surfaces to form chemisorbed CO_2 , the first step in reduction of CO_2

A national priority is to convert CO_2 into high-value chemical products such as liquid fuels. Because current electrocatalysts are not adequate, we aim to discover new catalysts by obtaining a detailed understanding of the initial steps of CO_2 electroreduction on copper surfaces, the best current catalysts. Using ambient pressure X-ray photoelectron spectroscopy interpreted with quantum mechanical prediction of the structures and free energies, we show that the presence of a thin suboxide structure below the copper surface is essential to bind the CO_2 in the physisorbed configuration at 298 K, and we show that this suboxide is essential for converting to the chemisorbed CO_2 in the presence of water as the first step toward CO_2 reduction products such as formate and CO. This optimum suboxide leads to both neutral and charged Cu surface sites, providing fresh insights into how to design improved carbon dioxide reduction catalysts

Synergy between Silver-Copper Surface Alloy Composition and Carbon Dioxide Adsorption and Activation

Bimetallic electrocatalysts provide a promising strategy for improving performance, especially in the enhancement of selectivity of CO₂ reduction reactions. However, the first step of CO₂ activation on bimetallic materials remains obscure. Considering bimetallic silver–copper (AgCu) as an example, we coupled ambient pressure X-ray photoelectron spectroscopy (APXPS) and quantum mechanics (QM) to examine CO₂ adsorption and activation on AgCu exposed to CO₂ with and without H₂O at 298 K. The interplay between adsorbed species and the surface alloy composition of Cu and Ag is studied in atomic details. The APXPS experiment and density functional theory (DFT) calculations indicate that the clean sample has a Ag-rich surface layer. Upon adsorption of CO₂ and surface O, we found that it is thermodynamically more favorable to induce subsurface Cu atoms substitution for some surface Ag atoms, modifying the stability and activation of CO₂-related chemisorbed species. We further characterized this substitution effect by correlating the new adsorption species with the observed binding energy (BE) shift and intensity change in APXPS

Initial steps in forming the electrode electrolyte interface: H_2O adsorption and complex formation on the Ag(111) surface from combining Quantum Mechanics calculations and X-ray Photoelectron Spectroscopy

The interaction of water with metal surfaces is at the heart of electrocatalysis. But there remain enormous uncertainties about the atomistic interactions at the electrode–electrolyte interface (EEI). As the first step toward an understanding of the EEI, we report here the details of the initial steps of H_2O adsorption and complex formation on a Ag(111) surface, based on coupling quantum mechanics (QM) and ambient-pressure X-ray photoelectron spectroscopy (APXPS) experiments. We find a close and direct comparison between simulation and experiment, validated under various isotherm and isobar conditions. We identify five observable oxygen-containing species whose concentrations depend sensitively on temperature and pressure: chemisorbed O* and OH*, H_2O* stabilized by hydrogen bond interactions with OH* or O*, and multilayer H_2O*. We identify the species experimentally by their O 1s core-level shift that we calculate with QM along with the structures and free energies as a function of temperature and pressure. This leads to a chemical reaction network (CRN) that we use to predict the time evolution of their concentrations over a wide range of temperature (298–798 K) and pressure conditions (10^(–6)–1 Torr), which agree well with the populations determined from APXPS. This multistep simulation CRN protocol should be useful for other heterogeneous catalytic systems

Initial steps in forming the electrode electrolyte interface: H_2O adsorption and complex formation on the Ag(111) surface from combining Quantum Mechanics calculations and X-ray Photoelectron Spectroscopy

The interaction of water with metal surfaces is at the heart of electrocatalysis. But there remain enormous uncertainties about the atomistic interactions at the electrode–electrolyte interface (EEI). As the first step toward an understanding of the EEI, we report here the details of the initial steps of H_2O adsorption and complex formation on a Ag(111) surface, based on coupling quantum mechanics (QM) and ambient-pressure X-ray photoelectron spectroscopy (APXPS) experiments. We find a close and direct comparison between simulation and experiment, validated under various isotherm and isobar conditions. We identify five observable oxygen-containing species whose concentrations depend sensitively on temperature and pressure: chemisorbed O* and OH*, H_2O* stabilized by hydrogen bond interactions with OH* or O*, and multilayer H_2O*. We identify the species experimentally by their O 1s core-level shift that we calculate with QM along with the structures and free energies as a function of temperature and pressure. This leads to a chemical reaction network (CRN) that we use to predict the time evolution of their concentrations over a wide range of temperature (298–798 K) and pressure conditions (10^(–6)–1 Torr), which agree well with the populations determined from APXPS. This multistep simulation CRN protocol should be useful for other heterogeneous catalytic systems

Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut

The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta) genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an α-xylosidase, a β-glucosidase, and two α-L-arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins

A β-mannanase with a lysozyme-like fold and a novel molecular catalytic mechanism

The enzymatic cleavage of β-1,4-mannans is achieved by endo-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β- Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that β- mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure. A representative GH family 134 endo-β-1,4-mannanase from a Streptomyces sp. displays a fold closely related to that of hen egg white lysozyme but acts with inversion of stereochemistry. A Michaelis complex with mannopentaose, and a product complex with mannotriose, reveal ligands with pyranose rings distorted in an unusual inverted chair conformation. Ab initio quantum mechanics/molecular mechanics metadynamics quantified the energetically accessible ring conformations and provided evidence in support of a 1C4 → 3H4 ‡ → 3S1 conformational itinerary along the reaction coordinate. This work, in concert with that on GH family 124 cellulases, reveals how the lysozyme fold can be co-opted to catalyze the hydrolysis of different polysaccharides in a mechanistically distinct manner