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The evolution of signaling and monitoring in plant–fungal networks
Experiments have shown that when one plant is attacked by a pathogen or herbivore, this can lead to other plants connected to the same mycorrhizal network up-regulating their defense mechanisms. It has been hypothesized that this represents signaling, with attacked plants producing a signal to warn other plants of impending harm. We examined the evolutionary plausibility of this and other hypotheses theoretically. We found that the evolution of plant signaling about an attack requires restrictive conditions, and so will rarely be evolutionarily stable. The problem is that signaling about an attack provides a benefit to competing neighbors, even if they are kin, and so reduces the relative fitness of signaling plants. Indeed, selection is often more likely to push plant behavior in the opposite direction—with plants signaling dishonestly about an attack that has not occurred, or suppressing a cue that they have been attacked. Instead, we show that there are two viable alternatives that could explain the empirical data: 1) the process of being attacked leads to a cue (information about the attack) which is too costly for the attacked plant to fully suppress; 2) mycorrhizal fungi monitor their host plants, detect when they are attacked, and then the fungi signal this information to warn other plants in their network. Our results suggest the empirical work that would be required to distinguish between these possibilities.
Molecular dynamics investigation of structural, thermal, and dynamic properties of maghemite through thermal cycling
We analyzed the thermal, structural, and dynamic properties of maghemite using classical molecular dynamics, focusing on bulk and nanoparticle systems. We explored their behavior when heated to high temperatures (above the melting point) and during cooling, as well as under thermal cycles ending at intermediate temperatures. Our findings show that in the bulk system, both the tetrahedral and octahedral iron sub-lattices undergo a phase transition prior to melting. Cooling the system from above this transition, or from above the melting point, leads to the formation of different metastable maghemite structures. In contrast, this sub-lattice transition is absent in nanoparticles, where melting occurs through an interface-mediated process. At temperatures just above the transition, nanoparticles adopt an ellipsoidal shape, which is retained during cooling. In addition, the specific heat of both bulk and nanoparticle systems at temperatures above the Debye temperature is evaluated and compared with the available experimental data. Overall, our results highlight the complex thermal behavior of maghemite across a range of temperatures, which remains insufficiently explored experimentally. Further experimental investigations could also provide valuable feedback for model refinements.
Identification of <i>ARHGEF11</i> (PDZ-RhoGEF) as an in vivo regulator of synapses and cognition
Given the influence of cognitive abilities on life outcomes, there is inherent value in identifying genes involved in controlling learning and memory. Further, cognitive dysfunction is a core feature of many neuropsychiatric disorders. Here, we use a combinatory in silico approach to identify human gene targets that will have an especially high likelihood of individually and directly impacting cognition. This broad and unbiased screen led to the specific identification of ARHGEF11 , which encodes PDZ-RhoGEF. PDZ-RhoGEF is a largely RhoA-specific activator that is highly enriched in dendritic spines, and recent work identified hyperexpression of PDZ-RhoGEF in the prefrontal cortex of bipolar disorder subjects, a disease characterized by an early emergence and persistence of broad scope cognitive dysfunction. Here, we characterize the effects of PDZ-RhoGEF on synaptic and behavioral phenotypes, and we identify molecular and biochemical mechanisms that control PDZ-RhoGEF’s expression, synaptic spatial localization, and enzymatic activity. Importantly, our identified direct regulators of PDZ-RhoGEF (miR-132 and DISC1) have themselves been repeatedly implicated in controlling cognitive phenotypes in humans, including those caused by several neuropsychiatric disorders. Taken together, our findings indicate that PDZ-RhoGEF is a key convergence point among multiple synaptic and cognition-relevant signaling cascades with potential translational significance.
Isovalent substitution-induced pseudodoping in ZrxTi1−xSe2 transition metal dichalcogenides
The crystal and electronic structure of ZrxTi1−xSe2 (0 &lt; x &lt; 1) compounds and their electrical resistivity have been studied in detail for the first time. A combination of soft x-ray spectroscopic methods (XPS, XAS, and ResPES) was used to investigate the electronic structure. The lattice parameters as a function of the metal concentration x obey Vegard’s law. It was shown that the substitution of Ti by Zr results in an increase in the Fermi energy, attributed to the lower binding energy of Zr 4d compared to Ti 3d in the ZrxTi1−xSe2 valence band. Given that the oxidation states of both Ti and Zr are +4, and the concentration of free charge carriers remains unchanged upon substitution, the observed effect is explained by a reduced density of electronic states near the Fermi level. The influence of temperature on the Ti 2p–3d and Zr 3p–4d ResPES spectra is interpreted in terms of pseudodoping occurring with the substitution of Ti by Zr.
Adenosine diphosphate stimulates VEGF-independent choroidal endothelial cell proliferation: A potential escape from anti-VEGF therapy
We hypothesized that a strategy employing tissue-specific endothelial cells (EC) might facilitate the identification of tissue- or organ-specific vascular functions of ubiquitous metabolites. An unbiased approach was employed to identify water-soluble small molecules with mitogenic activity on choroidal EC. We identified adenosine diphosphate (ADP) as a candidate, following biochemical purification from mouse EL4 lymphoma extracts. ADP stimulated the growth of bovine choroidal EC (BCEC) and other bovine or human eye-derived EC. ADP induced rapid phosphorylation of extracellular signal-regulated kinase in a dose- and time-dependent manner. ADP-induced BCEC proliferation could be blocked by pretreatment with specific antagonists of the purinergic receptor P2Y1 but not with a vascular endothelial growth factor (VEGF) inhibitor, indicating that the EC mitogenic effects of ADP are not mediated by stimulation of the VEGF pathway. Intravitreal administration of ADP expanded the neovascular area in a mouse model of choroidal neovascularization. Single-cell transcriptomics from human choroidal datasets show the expression of P2RY1, but not other ADP receptors, in EC with a pattern similar to VEGFR2. Although ADP has been reported to be a growth inhibitor for vascular EC, here we describe its growth-stimulating effects for BCEC and other eye-derived EC.
Preliminary evidence of immune infiltration and neutrophil degranulation in peripheral blood of non-obese OSA patients related to cognitive decline
Erratum: “Exciton and biexciton transient absorption spectra of CdSe quantum dots with varying diameters” [J. Chem. Phys. 160, 014708 (2024)]
Effective doses received by the gastrointestinal tract compartments of adults due to food intake in Egypt
Abstract 226Ra, 232Th, and 40K levels in various foods frequently consumed by Egyptians were determined using a gamma-ray spectrometer based on the germanium detector (HPGe). Activity concentrations of 226Ra, 232Th, and 40K were in the range of < 0.10 to 0.79 ± 0.07, < 0.09 to 0.42 ± 0.04, and < 1.96 to 89.73 ± 2.96 Bq/kg, respectively. The gastrointestinal tract (GIT) model was employed to estimate the effective doses received by the different parts of the adult’s gastrointestinal tract, i.e., stomach (ST), small intestine (SI), upper large intestine (ULI), and lower large intestine (LLI), due to the ingestion of the analyzed foods. This estimation was based on mathematical calculations of the energy absorbed by organs due to transformations of ingested radionuclides. The effective doses (μSv/y) received by each compartment were 8.86 (ST), 8.76 (SI), 66.90 (ULI), and 176.76 (LLI). The results do not exceed the safe thresholds set by global organizations UNSCEAR and WHO, 290 and 250–400 μSv/y, respectively. Therefore, radionuclide intakes due to investigated food consumption do not pose any significant radiological impact.
Slowly quenched, high pressure glassy B2O3 at DFT accuracy
Modeling inorganic glasses requires an accurate representation of interatomic interactions, large system sizes to allow for intermediate-range structural order, and slow quenching rates to eliminate kinetically trapped structural motifs. Neither first principles-based nor force field-based molecular dynamics (MD) simulations satisfy these three criteria unequivocally. Herein, we report the development of a machine learning potential (MLP) for a classic glass, B2O3, which meets these goals well. The MLP is trained on condensed phase configurations whose energies and forces on the atoms are obtained using periodic quantum density functional theory. Deep potential MD simulations based on this MLP accurately predict the equation of state and the densification of the glass with slower quenching from the melt. At ambient conditions, quenching rates larger than 1011 K/s are shown to lead to artifacts in the structure. Pressure-dependent x-ray and neutron structure factors from the simulations compare excellently with experimental data. High-pressure simulations of the glass show varied coordination geometries of boron and oxygen, which concur with experimental observations.
Argonaute2 modulates megakaryocyte development and sex-specific control of platelet protein expression and reactivity
Analysis of intramolecular modes of liquid water in two-dimensional spectroscopy: A classical hierarchical equations of motion approach
Two-dimensional (2D) vibrational spectroscopy is a powerful means of investigating the structure and dynamics of complex molecules in condensed phases. However, even in theory, analysis of 2D spectra resulting from complex inter- and intra-molecular motions using only molecular dynamics methods is not easy. This is because molecular motions comprise complex multiple modes and peaks broaden and overlap owing to various relaxation processes and inhomogeneous broadening. On the basis of an anharmonic multimode Brownian oscillator model with nonlinear system–bath coupling, we have developed an approach that simulates 2D spectra, taking into account arbitrary modes of intermolecular and intramolecular vibrations simultaneously. Although only two-mode quantum calculations are feasible with this model, owing to high computational costs, here we restrict ourselves to the classical case and perform three-mode calculations. We demonstrate the applicability of our method by calculating 2D correlation infrared spectra of water for symmetric stretching, antisymmetric stretching, and bending modes. The quantum effects of these results are deduced by comparing 2D quantum spectra previously obtained for two intramolecular modes with those obtained using our classical approach under the same physical conditions. The results show that the 2D spectra calculated by separating the stretching modes into symmetric and asymmetric modes provide better descriptions of peak profiles, such as the splitting of cross-peaks.
Evaluation of ampicillin plus ceftobiprole combination therapy in treating Enterococcus faecalis infective endocarditis and bloodstream infection
Multiple and transforming vibrational identities of atoms in amorphous solids
Identifying the diverse roles of disorderly packed atoms inside an amorphous solid has been a highly pursued but daunting task in glass physics. By analyzing the full-frequency vibrational modes of a model Cu50Zr50 glass, here, we classify the internal atoms into low-, subhigh-, and high-frequency ones that have different tendencies for rearrangements upon excitations. We find that low-frequency atoms are structurally unfavored and tend to aggregate. High-frequency atoms originating from compressed atomic pairs are also mechanically unstable. As yield approaches, shear-transformation rearrangements shift from low-frequency to high-frequency atoms. Subhigh-frequency atoms play the role of stable backbones. Given that atoms can have different identities, multiple identities are observed to overlap in space. Atoms with one vibrational identity often transform to another one, showing different preferences in transformation routes. Our results deepen the understanding of atomic structures for amorphous plasticity beyond the simplified picture of soft vs hard spots.
Triaxial behavior and microstructural insights of loose sandy soil stabilized with alkali activated slag
How to correct Ehrenfest nonadiabatic dynamics in open quantum systems: Ehrenfest plus random force (E + <i>σ</i>) dynamics
One key challenge in the study of nonadiabatic dynamics in open quantum systems is to balance computational efficiency and accuracy. Although Ehrenfest dynamics (ED) is computationally efficient and well-suited for large complex systems, ED often yields inaccurate results. To address these limitations, we improve the accuracy of the traditional ED by adding a random force (E + σ). In this work, the construction of random forces is considered in Markovian and non-Markovian scenarios, and we ensure the dynamics satisfy the detailed balance in both scenarios. By comparing our E + σ with existing methods such as the electronic friction model and surface hopping, we furthermore validate its reliability. In addition, the E + σ model still retains the high efficiency of ED and does not incur much additional computation. We believe that this method provides an alternative to accurately describe the mixed quantum–classical dynamics in open quantum systems, particularly for large complex systems.
Short-term airborne ultrasound induced cell death in tobacco cells and changed their wall components
Structural evolution of particle configurations: Zero-temperature phases under increasing confinement
In this study, we investigate the phase behavior and structural organization of colloidal particles in a two-dimensional (2D) system under isotropic harmonic confinement using overdamped Langevin dynamics simulations. We employ a modified mermaid potential, which introduces an additional short-distance term resulting in a null-force region, distinct from the conventional mermaid potential. This modification facilitates a richer exploration of self-assembled structures, revealing a variety of phases influenced by the interplay between confinement strength V0 and the interaction potential. Our analysis spans a wide range of parameters, resulting in a detailed phase diagram that captures transitions from dispersed clusters to well-ordered patterns, including square, triangular, rhomboidal, and mixed configurations, as the confinement strength increases. The findings underscore the intricate balance of forces governing the self-assembly of colloidal systems and offer valuable insights for future experimental realizations.
Insulator–metal transition in VO2 film on sapphire studied by broadband dielectric spectroscopy
Mixed atomistic–implicit quantum/classical approach to molecular nanoplasmonics
A multiscale quantum mechanical (QM)/classical approach is presented that is able to model the optical properties of complex nanostructures composed of a molecular system adsorbed on metal nanoparticles. The latter is described by a combined atomistic–continuum model, where the core is described using the implicit boundary element method (BEM) and the surface retains a fully atomistic picture and is treated employing the frequency-dependent fluctuating charge and fluctuating dipole (ωFQFμ) approach. The integrated QM/ωFQFμ-BEM model is numerically compared with state-of-the-art fully atomistic approaches, and the quality of the continuum/core partition is evaluated. The method is then extended to compute surface-enhanced Raman scattering within a time-dependent density functional theory framework.