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Abstract As air masses move within the troposphere, they transport a multitude of components including gases and particles such as pollen and microorganisms. These movements generate atmospheric highways that connect geographic areas at distant, local, and global scales that particles can ride depending on their aerodynamic properties and their reaction to environmental conditions. In this article we present an approach and an accompanying web application called tropolink for measuring the extent to which distant locations are potentially connected by air‐mass movement. This approach is based on the computation of trajectories of air masses with the HYSPLIT atmospheric transport and dispersion model, and on the computation of connection frequencies, called connectivities, in the purpose of building trajectory‐based geographical networks. It is illustrated for different spatial and temporal scales with three case studies related to plant epidemiology. The web application that we designed allows the user to easily perform intensive computation and mobilize massive archived gridded meteorological data to build weighted directed networks. The analysis of such networks allowed us for example, to describe the potential of invasion of a migratory pest beyond its actual distribution. Our approach could also be used to compute geographical networks generated by air‐mass movement for diverse application domains, for example, to assess long‐term risk of spread from persistent or recurrent sources of pollutants, including wildfire smoke.

Phospholamban (PLN) and Sarcolipin (SLN) are homologous membrane proteins that belong to the family of proteins that regulate the activity of the cardiac calcium pump (sarcoplasmic reticulum Ca2+-ATPase, SERCA). PLN and SLN share highly conserved leucine zipper motifs that control self-association; consequently, it has been proposed that both PLN and SLN assemble into stable pentamers in the membrane. In this study, we used molecular dynamics (MD) simulations and Western blot analysis to investigate the precise molecular architecture of the PLN and SLN oligomers. Analysis showed that the PLN pentamer is the predominant oligomer present in mouse ventricles and ventricle-like human iPSC-derived cardiomyocytes, in agreement with the MD simulations showing stable leucine zipper interactions across all protomer-protomer interfaces and MD replicates. Interestingly, we found that the PLN pentamer populates an asymmetric structure of the transmembrane region, which is likely an intrinsic feature of the oligomer in a lipid bilayer. The SLN pentamer is not favorably formed across MD replicates and species of origin; instead, SLN from human and mouse atria primarily populate coexisting dimeric and trimeric states. In contrast to previous studies, our findings indicate that the SLN pentamer is not the predominant oligomeric state populated in the membrane. We conclude that despite their structural homology, PLN and SLN adopt distinct oligomeric states in the membrane. We propose that the distinct oligomeric states populated by PLN and SLN may contribute to tissue-specific SERCA regulation via differences in protomer–oligomer exchange, oligomer–SERCA dynamics, and noise filtering during β-adrenergic stimulation in the heart.

Abstract Membrane proteins constitute a substantial fraction of the human proteome, thus representing a vast source of therapeutic drug targets. Indeed, newly devised technologies now allow targeting “undruggable” regions of membrane proteins to modulate protein function in the cell. Despite the advances in technology, the rapid translation of basic science discoveries into potential drug candidates targeting transmembrane protein domains remains challenging. We address this issue by harmonizing single molecule-based and ensemble-based atomistic simulations of ligand–membrane interactions with patient-derived induced pluripotent stem cell (iPSC)-based experiments to gain insights into drug delivery, cellular efficacy, and safety of molecules directed at membrane proteins. In this study, we interrogated the pharmacological activation of the cardiac Ca2+ pump (Sarcoplasmic reticulum Ca2+-ATPase, SERCA2a) in human iPSC-derived cardiac cells as a proof-of-concept model. The combined computational-experimental approach serves as a platform to explain the differences in the cell-based activity of candidates with similar functional profiles, thus streamlining the identification of drug-like candidates that directly target SERCA2a activation in human cardiac cells. Systematic cell-based studies further showed that a direct SERCA2a activator does not induce cardiotoxic pro-arrhythmogenic events in human cardiac cells, demonstrating that pharmacological stimulation of SERCA2a activity is a safe therapeutic approach targeting the heart. Overall, this novel multiscale platform encompasses organ-specific drug potency, efficacy, and safety, and opens new avenues to accelerate the bench-to-patient research aimed at designing effective therapies directed at membrane protein domains.

Sarcoplasmic reticulum Ca2+ pump (SERCA) is a critical component of the Ca2+ transport machinery in myocytes. There is clear evidence for regulation of SERCA activity by PLB, whose activity is modulated by phosphorylation of its N-terminal domain (residues 1–25), but there is less clear evidence for the role of this domain in PLB’s functional divergence. It is widely accepted that only sarcolipin (SLN), a protein that shares substantial homology with PLB, uncouples SERCA Ca2+ transport from ATP hydrolysis by inducing a structural change of its energy-transduction domain; yet, experimental evidence shows that the transmembrane domain of PLB (residues 26–52, PLB26–52) partially uncouples SERCA in vitro. These apparently conflicting mechanisms suggest that PLB’s uncoupling activity is encoded in its transmembrane domain, and that it is controlled by the N-terminal phosphorylation domain. To test this hypothesis, we performed molecular dynamics simulations (MDS) of the binary complex between PLB26–52 and SERCA. Comparison between PLB26–52 and wild-type PLB (PLBWT) showed no significant changes in the stability and orientation of the transmembrane helix, indicating that PLB26–52 forms a native-like complex with SERCA. MDS showed that PLB26–52 produces key intermolecular contacts and structural changes required for inhibition, in agreement with studies showing that PLB26–52 inhibits SERCA. However, deletion of the N-terminal phosphorylation domain facilitates an order-to-disorder shift in the energy-transduction domain associated with uncoupling of SERCA, albeit weaker than that induced by SLN. This mechanistic evidence reveals that the N-terminal phosphorylation domain of PLB is a primary contributor to the functional divergence among homologous SERCA regulators.

Absorption line spectroscopy offers one of the best opportunities to constrain the properties of galactic outflows and the environment of the circumgalactic medium. Extracting physical information from line profiles is difficult; however, for the physics governing the underlying radiation transfer is complicated and depends on many different parameters. Idealized analytical models are necessary to constrain the large parameter spaces efficiently, but are typically plagued by model degeneracy and systematic errors. Comparison tests with idealized numerical radiation transfer codes offer an excellent opportunity to confront both of these issues. In this paper, we present a detailed comparison between SALT, an analytical radiation transfer model for predicting UV spectra of galactic outflows, with the numerical radiation transfer software, RASCAS. Our analysis has led to upgrades to both models including an improved derivation of SALT and a customizable adaptive mesh refinement routine for RASCAS. We explore how well SALT, when paired with a Monte Carlo fitting procedure, can recover flow parameters from nonturbulent and turbulent flows. Overall we find that turbulence leads to biases in the recovery of kinematic parameters and the optical depth, but find that derived quantities (e.g., mass outflow rates, column density, etc.) are still well recovered. From the analysis, we estimate average uncertainties in our ability to measure metal flow rates spanning 0.65 (0.95) dex in M _⊙ yr ^−1 and uncertainties spanning 0.54 (0.94) dex in cm ^−2 for column densities at a resolution of 20 (100) km s ^−1 and signal-to-noise ratio = 10.

The search for novel therapeutic compounds remains an overwhelming task owing to the time-consuming and expensive nature of the drug development process and low success rates. Traditional methodologies that rely on the one drug-one target paradigm have proven insufficient for the treatment of multifactorial diseases, leading to a shift to multitarget approaches. In this emerging paradigm, molecules with off-target and promiscuous interactions may result in preferred therapies. In this study, we developed a general pipeline combining machine learning algorithms and a deep generator network to train a dual inhibitor classifier capable of identifying putative pharmacophoric traits. As a case study, we focused on dual inhibitors targeting DNA methyltransferase 1 (DNMT) and histone deacetylase 2 (HDAC2), two enzymes that play a central role in epigenetic regulation. We used this approach to identify dual inhibitors from a novel large natural product database in the public domain. We used docking and atomistic simulations as complementary approaches to establish the ligand-interaction profiles between the best hits and DNMT1/HDAC2. By using the combined ligand- and structure-based approaches, we discovered two promising novel scaffolds that can be used to simultaneously target both DNMT1 and HDAC2. We conclude that the flexibility and adaptability of the proposed pipeline has predictive capabilities of similar or derivative methods and is readily applicable to the discovery of small molecules targeting many other therapeutically relevant proteins.

This research has been conducted to develop the use of passive acoustic monitoring (PAM) in rivers, a surrogate method for bedload monitoring. PAM consists in measuring the underwater noise naturally generated by bedload particles when impacting the river bed. Monitored bedload acoustic signals depend on bedload characteristics (e.g., grain size distribution, fluxes) but are also affected by the environment in which the acoustic waves are propagated. This study focuses on the determination of propagation effects in rivers. An experimental approach has been conducted in several streams to estimate acoustic propagation laws in field conditions. It is found that acoustic waves are differently propagated according to their frequency. As reported in other studies, acoustic waves are affected by the existence of a cutoff frequency in the kilohertz region. This cutoff frequency is inversely proportional to the water depth: larger water depth enables a better propagation of the acoustic waves at low frequency. Above the cutoff frequency, attenuation coefficients are found to increase linearly with frequency. The power of bedload sounds is more attenuated at higher frequencies than at low frequencies, which means that, above the cutoff frequency, sounds of big particles are better propagated than sounds of small particles. Finally, it is observed that attenuation coefficients are variable within 2 orders of magnitude from one river to another. Attenuation coefficients are compared to several characteristics of the river (e.g., bed slope, surface grain size). It is found that acoustic waves are better propagated in rivers characterized by smaller bed slopes. Bed roughness and the presence of air bubbles in the water column are suspected to constrain the attenuation of acoustic wave in rivers.

The Olympic Mountains of Washington state (USA) represent the aerially exposed accretionary wedge of the Cascadia Subduction Zone and are thought to be in flux steady state, whereby the mass outflux (denudation) and influx (tectonic accretion) into the mountain range are balanced. We use a multi-method approach to investigate how temporal variations in the influx and outflux could affect previous interpretations of flux steady state. This includes the analysis of published and new thermochronometric ages for (U–Th) ∕ He dating of apatite and zircon (AHe and ZHe, respectively), fission-track dating of apatite and zircon (AFT and ZFT, respectively), 1-D thermo-kinematic modeling of thermochronometric data, and independent estimates of outflux and influx. In total, we present 61 new AHe, ZHe, AFT, and ZFT thermochronometric ages from 21 new samples. AHe ages are generally young ( 2 to −1 around 5–7 Ma. With the onset of Plio–Pleistocene glaciation, exhumation rates increased to values > 1 km Myr−1. This demonstrates that the material outflux varies through time, requiring a commensurate variation in influx to maintain flux steady state. Evaluation of the offshore and onshore sediment record shows that the material influx is also variable through time and that the amount of accreted sediment in the wedge is spatially variable. This qualitatively suggests that significant perturbations of steady state occur on shorter timescales (105–106 years), like those created by Plio–Pleistocene glaciation. Our quantitative assessment of influx and outflux indicates that the Olympic Mountains could be in flux steady state on long timescales (107 years).

In plants, the ancestral cyanobacterial triosephosphate isomerase (TPI) was replaced by a duplicated version of the cytosolic TPI. This isoform acquired a transit peptide for chloroplast localization and functions in the Calvin-Benson cycle. To gain insight into the reasons for this gene replacement in plants, we characterized the TPI from the photosynthetic bacteria Synechocystis (SyTPI). SyTPI presents typical TPI enzyme kinetics profiles and assembles as a homodimer composed of two subunits that arrange in a (β-α)8 fold. We found that oxidizing agents diamide (DA) and H2O2, as well as thiol-conjugating agents such as oxidized glutathione (GSSG) and methyl methanethiosulfonate (MMTS), do not inhibit the catalytic activity of SyTPI at concentrations required to inactivate plastidic and cytosolic TPIs from the plant model Arabidopsis thaliana (AtpdTPI and AtcTPI, respectively). The crystal structure of SyTPI revealed that each monomer contains three cysteines, C47, C127, and C176; however only the thiol group of C176 is solvent exposed. While AtcTPI and AtpdTPI are redox-regulated by chemical modifications of their accessible and reactive cysteines, we found that C176 of SyTPI is not sensitive to redox modification in vitro. Our data let us postulate that SyTPI was replaced by a eukaryotic TPI, because the latter contains redox-sensitive cysteines that may be subject to post-translational modifications required for modulating TPI's enzymatic activity.

La gouvernance territoriale est devenue un enjeu majeur et une question centrale pour la mise en œuvre des politiques publiques. Dans le cadre du programme de recherche en partenariat PSDR (programme de recherche pour et sur le développement régional), un collectif hybride composé de chercheurs, de professionnels du développement territorial et d'acteurs locaux s'est réuni au sein du projet Gouv.Innov. En s'appuyant sur plusieurs terrains d'étude, ce collectif a progressivement construit une définition de la gouvernance territoriale ainsi qu'une grille d'analyse qui sont apparues suffisamment robustes pour traiter la multiplicité des situations rencontrées sur le terrain. Un guide méthodologique a ensuite été co-construit pour la mise en œuvre de la gouvernance territoriale, visant surtout à faciliter l'apprentissage et à stimuler la réflexivité. Cet article présente les principaux résultats de ce projet de recherche en partenariat et les perspectives envisagées en insistant sur l'importance des apprentissages collectifs lors de la construction du guide. Nous concluons par une réflexion sur les modalités de mise en œuvre et l'intérêt d'une recherche en partenariat telle qu'elle a pu être menée dans le projet Gouv.Innov et des premières retombées concrètes.

The sodium-potassium ATPase (Na/K-ATPase, NKA) establishes ion gradients that facilitate many physiological functions including action potentials and secondary transport processes. NKA comprises a catalytic subunit (alpha) that interacts closely with an essential subunit (beta) and regulatory transmembrane micropeptides called FXYD proteins. In the heart, a key modulatory partner is the FXYD protein phospholemman (PLM, FXYD1), but the stoichiometry of the alpha-beta-PLM regulatory complex is unknown. Here, we used fluorescence lifetime imaging and spectroscopy to investigate the structure, stoichiometry, and affinity of the NKA-regulatory complex. We observed a concentration-dependent binding of the subunits of NKA-PLM regulatory complex, with avid association of the alpha subunit with the essential beta subunit as well as lower affinity alpha-alpha and alpha-PLM interactions. These data provide the first evidence that, in intact live cells, the regulatory complex is composed of two alpha subunits associated with two beta subunits, decorated with two PLM regulatory subunits. Docking and molecular dynamics (MD) simulations generated a structural model of the complex that is consistent with our experimental observations. We propose that alpha-alpha subunit interactions support conformational coupling of the catalytic subunits, which may enhance NKA turnover rate. These observations provide insight into the pathophysiology of heart failure, wherein low NKA expression may be insufficient to support formation of the complete regulatory complex with the stoichiometry (alpha-beta-PLM)2.