The puzzling ecology of African Marantaceae forests.

Marantaceae forests are tropical rainforests characterized by a continuous understory layer of perennial giant herbs and a near absence of tree regeneration. Although widespread in West-Central Africa, Marantaceae forests have rarely been considered in the international literature. Yet, they pose key challenges and opportunities for theoretical ecology that transcend the borders of the continent. Specifically, we ask in this review whether open Marantaceae forests and dense closed-canopy forests can be considered as one of the few documented examples of alternative stable states in tropical forests. First, we introduce the different ecological factors that have been posited to drive Marantaceae forests (climate, soil, historical and recent anthropogenic pressures, herbivores) and develop the different hypotheses that have been suggested to explain how Marantaceae forests establish in relation with other vegetation types (understory invasion, early succession after disturbance, and intermediate successional stage). Then, we review the underlying ecological mechanisms that can explain the stability of Marantaceae forests in the long term (tree recruitment inhibition, promotion of and resilience to fire, adaptive reproduction, maintenance by megaherbivores). Although some uncertainties remain and call for further empirical and theoretical research, we found converging evidence that Marantaceae forests are associated with an ecological succession that has been deflected or arrested. If verified, Marantaceae forests may provide a useful model to understand critical transitions in forest ecosystems, which is of particular relevance to achieve sustainable forest management and mitigate global climate change.

Differences in enantiomeric diffusion can lead to selective chiral amplification.

A fundamental question associated with chirality is how mixtures containing equal amounts of interconverting enantiomers can spontaneously convert to systems enriched in only one of them. Enantiomers typically have similar chemical properties, but can exhibit distinct reactivity under specific conditions, and these differences can be used to bias the system's composition in favor of one enantiomer. Transport properties are also expected to differ for enantiomers in chiral solvents, but the role of such differences in chiral symmetry breaking has not been clarified yet. In this work, we develop a theoretical framework to show that asymmetry in diffusion properties can trigger a spontaneous and selective symmetry breaking in mixtures of enantiomers. We derive a generic evolution equation for the enantiomeric excess in a chiral solvent. This equation shows that the relative stability of homochiral domains is dictated by the difference of diffusion coefficients of the two enantiomers. Consequently, deracemization toward a specific enantiomeric excess can be achieved when this difference is large enough. These results hold significant implications for our understanding of chiral symmetry breaking.

N-representable one-electron reduced density matrix reconstruction with frozen core electrons.

Recent advances in quantum crystallography have shown that, beyond conventional charge density refinement, a one-electron reduced density matrix (1-RDM) satisfying N-representability conditions can be reconstructed using jointly experimental X-ray structure factors and directional Compton profiles (DCP) through semidefinite programming. So far, such reconstruction methods for 1-RDM, not constrained to idempotency, have been tested only on a toy model system (CO2). In this work, a new method is assessed on crystalline urea [CO(NH2)2] using static (0 K) and dynamic (50 K) artificial experimental data. An improved model, including symmetry constraints and frozen core-electron contribution, is introduced to better handle the increasing system complexity. Reconstructed 1-RDMs, deformation densities and DCP anisotropy are analysed, and it is demonstrated that the changes in the model significantly improve the reconstruction quality, even when there is insufficient information and data corruption. The robustness of the model and the strategy are thus shown to be well adapted to address the reconstruction problem from actual experimental scattering data.

Linking ABC transporters to the hallmarks of cancer.

Human ATP-binding cassette (ABC) transporters are ubiquitously expressed and transport a broad range of endogenous and xenobiotic substrates across extra- and intracellular membranes. Mutations in ABC genes cause 21 monogenic diseases, and polymorphisms in these genes are associated with susceptibility to complex diseases. ABC transporters also play a major role in drug bioavailability, and they mediate multidrug resistance in cancer. At least 13 ABC transporters were shown to be involved in drug resistance in vitro. In the past decade, efforts have been made to elucidate their roles in tumor biology. Herein, we explore their involvement in tumorigenesis, focusing on the hallmarks of cells as they make their way from normalcy to neoplastic growth states.

Identification of two novel heterodimeric ABC transporters in melanoma: ABCB5ß/B6 and ABCB5ß/B9.

ABCB5 is a member of the ABC transporter superfamily composed of 48 transporters, which have been extensively studied for their role in cancer multidrug resistance and, more recently, in tumorigenesis. ABCB5 has been identified as a marker of skin progenitor cells, melanoma, and limbal stem cells. It has also been associated with multidrug resistance in several cancers. The unique feature of ABCB5 is that it exists as both a full transporter (ABCB5FL) and a half transporter (ABCB5ß). Several studies have shown that the ABCB5ß homodimer does not confer multidrug resistance, in contrast to ABCB5FL. In this study, using three complementary techniques, (1) nanoluciferase-based bioluminescence resonance energy transfer, (2) coimmunoprecipitation, and (3) proximity ligation assay, we identified two novel heterodimers in melanoma: ABCB5ß/B6 and ABCB5ß/B9. Both heterodimers could be expressed in High-Five insect cells and ATPase assays revealed that both functional nucleotide-binding domains of homodimers and heterodimers are required for their basal ATPase activity. These results are an important step toward elucidating the functional role of ABCB5ß in melanocytes and melanoma.

The ß Isoform of Human ATP-Binding Cassette B5 Transporter, ABCB5ß, Localizes to the Endoplasmic Reticulum.

ABCB5ß is a member of the ABC transporter superfamily cloned from melanocytes. It has been reported as a marker of skin progenitor cells and melanoma stem cells. ABCB5ß has also been shown to exert an oncogenic activity and promote cancer metastasis. However, this protein remains poorly characterized. To elucidate its subcellular localization, we tested several anti-ABCB5 antibodies and prepared several tagged ABCB5ß cDNA constructs. We then used a combination of immunofluorescence and biochemical analyses to investigate the presence of ABCB5ß in different subcellular compartments of HeLa and MelJuSo cell lines. Treatment of the cells with the proteasome inhibitor MG132 showed that part of the population of newly synthesized ABCB5ß is degraded by the proteasome system. Interestingly, treatment with SAHA, a molecule that promotes chaperone-assisted folding, largely increased the expression of ABCB5ß. Nevertheless, the overall protein distribution in the cells remained similar to that of control conditions; the protein extensively colocalized with the endoplasmic reticulum marker calnexin. Taken together with cell surface biotinylation studies demonstrating that the protein does not reach the plasma membrane (even after SAHA treatment), the data indicate that ABCB5ß is a microsomal protein predominantly localized to the ER.

Probing the Allosteric Modulation of P-Glycoprotein: A Medicinal Chemistry Approach Toward the Identification of Noncompetitive P-Gp Inhibitors.

A medicinal chemistry approach combining in silico and in vitro methodologies was performed aiming at identifying and characterizing putative allosteric drug-binding sites (aDBSs) at the interface of the transmembrane- and nucleotide-binding domains (TMD-NBD) of P-glycoprotein. Two aDBSs were identified, one in TMD1/NBD1 and another one in TMD2/NBD2, by means of in silico fragment-based molecular dynamics and characterized in terms of size, polarity, and lining residues. From a small library of thioxanthone and flavanone derivatives, experimentally described to bind at the TMD-NBD interfaces, several compounds were identified to be able to decrease the verapamil-stimulated ATPase activity. An IC50 of 81 ± 6.6 µM is reported for a flavanone derivative in the ATPase assays, providing evidence for an allosteric efflux modulation in P-glycoprotein. Molecular docking and molecular dynamics gave additional insights on the binding mode on how flavanone derivatives may act as allosteric inhibitors.

Long-range communication between transmembrane- and nucleotide-binding domains does not depend on drug binding to mutant P-glycoprotein.

In this study, the impact of four P-gp mutations (G185V, G830V, F978A and ΔF335) on drug-binding and efflux-related signal-transmission mechanism was comprehensively evaluated in the presence of ligands within the drug-binding pocket (DBP), experimentally related with changes in their drug efflux profiles. The severe repacking of the transmembrane helices (TMH), induced by mutations and exacerbated by the presence of ligands, indicates that P-gp is sensitive to perturbations in the transmembrane region. Alterations on drug-binding were also observed as a consequence of the TMH repacking, but were not always correlated with alterations on ligands binding mode and/or binding affinity. Finally, and although all P-gp variants holo systems showed considerable changes in the intracellular coupling helices/nucleotide-binding domain (ICH-NBD) interactions, they seem to be primarily induced by the mutation itself rather than by the presence of ligands within the DBP. The data further suggest that the changes in drug efflux experimentally reported are mostly related with changes on drug specificity rather than effects on signal-transmission mechanism. We also hypothesize that an increase in the drug-binding affinity may also be related with the decreased drug efflux, while minor changes in binding affinities are possibly related with the increased drug efflux observed in transfected cells.Communicated by Ramaswamy H. Sarma.

Sclerotherapy of lower limb veins: Indications, contraindications and treatment strategies to prevent complications - A consensus document of the International Union of Phlebology-2023.

BACKGROUND: Sclerotherapy is a non-invasive procedure commonly used to treat superficial venous disease, vascular malformations and other ectatic vascular lesions. While extremely rare, sclerotherapy may be complicated by serious adverse events. OBJECTIVES: To categorise contraindications to sclerotherapy based on the available scientific evidence. METHODS: An international, multi-disciplinary panel of phlebologists reviewed the available scientific evidence and developed consensus where evidence was lacking or limited. RESULTS: Absolute Contraindications to sclerotherapy where the risk of harm would outweigh any benefits include known hypersensitivity to sclerosing agents; acute venous thromboembolism (VTE); severe neurological or cardiac adverse events complicating a previous sclerotherapy treatment; severe acute systemic illness or infection; and critical limb ischaemia. Relative Contraindications to sclerotherapy where the potential benefits of the proposed treatment would outweigh the risk of harm or the risks may be mitigated by other measures include pregnancy, postpartum and breastfeeding; hypercoagulable states with risk of VTE; risk of neurological adverse events; risk of cardiac adverse events and poorly controlled chronic systemic illness. Conditions and circumstances where Warnings and Precautions should be considered before proceeding with sclerotherapy include risk of cutaneous necrosis or cosmetic complications such as pigmentation and telangiectatic matting; intake of medications such as the oral contraceptive and other exogenous oestrogens, disulfiram and minocycline; and psychosocial factors and psychiatric comorbidities that may increase the risk of adverse events or compromise optimal treatment outcomes. CONCLUSIONS: Sclerotherapy can achieve safe clinical outcomes provided that (1) patient-related risk factors and in particular all material risks are (1a) adequately identified and the risk benefit ratio is clearly and openly discussed with treatment candidates within a reasonable timeframe prior to the actual procedure; (1b) when an individual is not a suitable candidate for the proposed intervention, conservative treatment options including the option of 'no intervention as a treatment option' are discussed; (1c) complex cases are referred for treatment in controlled and standardised settings and by practitioners with more expertise in the field; (1d) only suitable individuals with no absolute contraindications or those with relative contraindications where the benefits outweigh the risks are offered intervention; (1e) if proceeding with intervention, appropriate prophylactic measures and other risk-mitigating strategies are adopted and appropriate follow-up is organised; and (2) procedure-related risk factors are minimised by ensuring the treating physicians (2a) have adequate training in general phlebology with additional training in duplex ultrasound, procedural phlebology and in particular sclerotherapy; (2b) maintain their knowledge and competency over time and (2c) review and optimise their treatment strategies and techniques on a regular basis to keep up with the ongoing progress in medical technology and contemporary scientific evidence.

5-Fluoro-1,2,3-triazole motif in peptides and its electronic properties.

The 5-fluoro triazole amino acid scaffold prepared by halogen exchange has been incorporated into peptides. From the X-ray diffraction of the 5-fluoro triazole motif, the main observation was an important localization on one side of the negative potential surface. The fluorine atom reveals a cylindrical shape in its deformation electron density.

Spontaneous mirror symmetry breaking in reaction-diffusion systems: ambivalent role of the achiral precursor.

The behaviour of a Frank-like chemical network model featuring autocatalytic production of chiral enantiomers from achiral reactants is studied numerically in 1D and 2D systems using fluctuating initial conditions and accounting for diffusion processes. Our results reveal that the achiral substrate concentration can play an ambivalent role. It is shown that when the achiral reactant concentration is maintained constant and homogeneous in 1D systems, global homochirality is not systematically reached when the size of the system or the achiral reactant concentration are increased. However, with a fixed concentration gradient, coexisting homochiral domains of opposite handedness are no longer observed and homogeneous homochirality, i.e. the presence of a single stable homochiral domain, is recovered. In 2D systems, reaching global homochirality is just a matter of time. This time is dramatically increased when insufficient or excessive amount of achiral reactant is used. An optimal amount of achiral material is observed to maximise the enantiomer production rates.

Deciphering the roles of ABCB5 in normal and cancer cells.

ABCB5 encodes a full transporter (ABCB5FL) and a half transporter (ABCB5ß), which is unique in the ATP binding cassette (ABC) transporter superfamily. We discuss the roles of both isoforms in undifferentiated slow-cycling cells, multidrug resistance, and tumorigenesis, and their regulation pathways.

From molecular dynamics to quantum mechanics of misfolded proteins and amyloid-like macroaggregates applied to neurodegenerative diseases.

A misfolded protein compared with its native state lacks its biological function resulting in cell dysregulations and often death. Outdated hypotheses on protein folding must be revised: More realistic molecular models, focusing not only on classical molecular dynamics (MD) but also on ab initio quantum mechanics (QM) at the molecular orbitals (MOs) scale, which is not experimentally achievable, are presented to improve our understanding of the thermodynamics of the protein-protein interactions leading to misfolding and neurodegenerative diseases for future drug design. Protein misfolding is characterized by the formation of highly reactive beta-sheets oligomers leading to fibrillar macroscopic aggregates, which are studied with the models given herein that can be useful for the development of new immunotherapies against the Alzheimer's disease and prion, e.g. The example of the prion - an intrinsically disordered protein - is studied, but the models can be generalized to other misfolding diseases. The binding free energy and interactions in a complex of a misfolded prion with a native prion are first analyzed by MD and compared to a complex of two native conformers. A conversion of residues to toxic beta-sheets is observed in the optimized misfolded complex. Then, QM is used to compute, with a much better accuracy than that of MD, the binding free energy of the hydrophobic binding site, responsible of the aggregation, between the bound misfolded and native conformers in the misfolded complex. The latter quantity is significantly negative, so that aggregation is strong and fast. The frontier MOs from QM are used for docking to determine how the first repetitive beta-sheets building blocks of the nanofibrils can be assembled from initial cleaved complexes of the native and misfolded proteins. Successive aggregation of multiple monomers leads to an amyloid-like nanofibril that grows along a principal elongation direction, as also observed experimentally.

Spin-resolved atomic orbital model refinement for combined charge and spin density analysis: application to the YTiO3 perovskite.

A new crystallographic method is proposed in order to refine a spin-resolved atomic orbital model against X-ray and polarized neutron diffraction data. This atomic orbital model is applied to the YTiO3 perovskite crystal, where orbital ordering has previously been observed by several techniques: X-ray diffraction, polarized neutron diffraction and nuclear magnetic resonance. This method gives the radial extension, orientation and population of outer atomic orbitals for each atom. The interaction term between Ti3+, Y3+ cations and O2- ligands has been estimated. The refinement statistics obtained by means of the orbital method are compared with those obtained by the multipole model previously published.

Targeting tumor resistance mechanisms.

Cancer develops resistance to treatments through many mechanisms. Single-cell analyses reveal the intratumor heterogeneity and dynamic relationships between cancer cell subpopulations. These analyses also highlight that various mechanisms of resistance may coexist in a given tumor. Studies have unraveled how the microenvironment affects tumor response to treatments and how cancer cells may adapt to these treatments. Though challenging, individualized treatment based on the molecular characterization of the tumor should become the new standard of care. In the meantime, the success rate of clinical trials in oncology remains dramatically low. There is a need to do better and improve the predictability of preclinical models. This requires innovative changes in ex vivo models and the culture system currently being used. An innovative ligand design is also urgently needed. The limited arsenal of medicinal chemistry reactions and the biases of scaffold selection favor structurally similar compounds with linear shapes at the expense of disc and spherical shapes, which leave a large chemical shape space untouched. In this regard, venoms have received increasing interest as a wellspring for drug candidates. Overall, the characterization of tumor heterogeneity has contributed to advancing our understanding of the mechanisms that underlie cancer resistance to treatments. Targeting these mechanisms will require setting key milestones to significantly improve the translatability of preclinical studies to the clinic with the hope of increasing the success rate of clinical trials.

Alzheimer's disease: unraveling APOE4 binding to amyloid-beta peptide and lipids with molecular dynamics and quantum mechanics.

The apolipoprotein E (APOE) involved in lipid metabolism participates in the clearance and deposition of the amyloid-beta peptide of the Alzheimer's disease (AD). The isoform APOE4 with the ARG112 mutation is the main genetic risk for the late-onset AD. Herein, using both molecular dynamics and quantum mechanics, the binding mechanisms of APOE4 leading to the AD are unraveled and now available for drug design. The binding affinities of APOE4 compared to the normal APOE3 are computed for the four cases: the bare APOE, APOE bound to the amyloid-beta peptide, APOE bound to a lipid nanoparticle mimicking the lipid effects and APOE bound to both amyloid-beta peptide and lipid nanoparticle. When APOE4 is bound to the amyloid-beta peptide, its structure becomes misfolded. Its binding free energy is higher than that of APOE3 in complex with the amyloid-beta peptide. Salt bridges for the APOE correct folding are missing in APOE4, resulting in an increased deposition of the amyloid-beta peptide, compared to APOE3, which can lead to the AD. When both amyloid-beta peptide and lipid nanoparticle are bound to APOE4, there is a detrimental cooperativity between the two misfolding effects, and amyloid-beta peptide deposition is even more significant. Immunotherapies with anti-APOE4 antibodies are promising for drug design against APOE4, but only non-lipidated APOE4 can be targeted. Gene editing is an interesting research alternative, because the genes APOε4 and APOε3 differ by only one nucleotide.

Theoretical insights on helix repacking as the origin of P-glycoprotein promiscuity.

P-glycoprotein (P-gp, ABCB1) overexpression is, currently, one of the most important multidrug resistance (MDR) mechanisms in tumor cells. Thus, modulating drug efflux by P-gp has become one of the most promising approaches to overcome MDR in cancer. Yet, more insights on the molecular basis of drug specificity and efflux-related signal transmission mechanism between the transmembrane domains (TMDs) and the nucleotide binding domains (NBDs) are needed to develop molecules with higher selectivity and efficacy. Starting from a murine P-gp crystallographic structure at the inward-facing conformation (PDB ID: 4Q9H), we evaluated the structural quality of the herein generated human P-gp homology model. This initial human P-gp model, in the presence of the "linker" and inserted in a suitable lipid bilayer, was refined through molecular dynamics simulations and thoroughly validated. The best human P-gp model was further used to study the effect of four single-point mutations located at the TMDs, experimentally related with changes in substrate specificity and drug-stimulated ATPase activity. Remarkably, each P-gp mutation is able to induce transmembrane α-helices (TMHs) repacking, affecting the drug-binding pocket volume and the drug-binding sites properties (e.g. volume, shape and polarity) finally compromising drug binding at the substrate binding sites. Furthermore, intracellular coupling helices (ICH) also play an important role since changes in the TMHs rearrangement are shown to have an impact in residue interactions at the ICH-NBD interfaces, suggesting that identified TMHs repacking affect TMD-NBD contacts and interfere with signal transmission from the TMDs to the NBDs.

Inferring the one-electron reduced density matrix of molecular crystals from experimental data sets through semidefinite programming.

Constructing a quantum description of crystals from scattering experiments is of great significance to explain their macroscopic properties and to evaluate the pertinence of theoretical ab initio models. While reconstruction methods of the one-electron reduced density matrix have already been proposed, they are usually tied to strong assumptions that limit and may introduce bias in the model. The goal of this paper is to infer a one-electron reduced density matrix (1-RDM) with minimal assumptions. It has been found that the mathematical framework of semidefinite programming can achieve this goal. Additionally, it conveniently addresses the nontrivial constraints on the 1-RDM which were major hindrances for the existing models. The framework established in this work can be used as a reference to interpret experimental results. This method has been applied to the crystal of dry ice and provides very satisfactory results when compared with periodic ab initio calculations.

Spin resolved electron density study of YTiO3 in its ferromagnetic phase: signature of orbital ordering.

The present work reports on the charge and spin density modelling of YTiO3 in its ferromagnetic state (T C = 27 K). Accurate polarized neutron diffraction and high-resolution X-ray diffraction (XRD) experiments were carried out on a single crystal at the ORPHÉE reactor (LLB) and SPRING8 synchrotron source. The experimental data are modelled by the spin resolved pseudo-atomic multipolar model (Deutsch et al., 2012 ▸). The refinement strategy is discussed and the result of this electron density modelling is compared with that from XRD measured at 100 K and with density functional theory calculations. The results show that the spin and charge densities around the Ti atom have lobes directed away from the O atoms, confirming the filling of the t 2g orbitals of the Ti atom. The d xy orbital is less populated than d xz and d yz , which is a sign of a partial lift of degeneracy of the t 2g orbitals. This study confirms the orbital ordering at low temperature (20 K), which is already present in the paramagnetic state above the ferromagnetic transition (100 K).

Experimental and theoretical insights of functionalized hexavanadates on Na+/K+-ATPase activity; molecular interaction field, ab initio calculations and in vitro assays.

The influence of three functionalized hexavanadates (V6): Na2 [V6O13{(OCH2)3CCH3}2], [H2]2 [V6O13{(OCH2)3CCH2OCOCH2CH3}2] and [(C4H9)4N]2 [V6O13{(OCH2)3CCH2OOC(CH3)2-COOH}2 on Na+/K+-ATPase activity, was investigated in vitro. Including compounds already tested by Xu et al. (Journal of Inorganic Biochemistry 161 (2016) 27-36), all functionalized hexavanadates inhibit the activity of Na+/K+-ATPase in a dose-dependent manner but with different inhibitory potencies. Na2 [V6O13{(OCH2)3CCH3}2] was found to have the best inhibition properties - showing 50% inhibition IC50 = 5.50 × 10-5 M, while [(C4H9)4N]2 [V6O13{(OCH2)3CCH2OOC(CH3)2-COOH}2] showed the lowest inhibitory power, IC50 = 1.31 × 10-4 M. In order to understand the bioactivity of functionalized hexavanadates series, we have also used a combined theoretical approach: determination of electrostatic potential from ab initio theoretical calculations and computation of the molecular interaction field (MIF) surface.