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Nanoscale self-assembly and water retention properties of silk fibroin–riboflavin hydrogel

Silk-fibroin hydrogels have gained considerable attention in recent years for their versatile biomedical applications. The physical properties of a complex hydrogel, comprising silk fibroin and riboflavin, surpass those of the silk fibroin-hydrogel without additives. This study investigates silk fibroin–riboflavin (silk–RIB) hydrogel at the atomistic level to uncover molecular structures and chemical characteristics specific to silk fibroin and riboflavin molecules in an aqueous medium. The interplay between hydrophilic riboflavin and hydrophobic silk fibroin polymers facilitates the formation of solubilized silk fiber, which subsequently evolves into a nano-scale hydrogel over time. Eventually, the interlinked RIB stacks form a scaffold that not only accommodates silk fibroin aggregates but also encloses water pockets, preserving the moisture level and enhancing the thermal conductivity of the hydrogel. To explore water retention properties and the role of ions, two sets of simulations of semi-hydrated hydrogel in the presence and absence of ions are conducted. The presence of ions significantly influences the dynamics of RIB and silk fibroin. Favorable interactions with the ions impede the unrestricted diffusion of these larger molecules, potentially leading to a stable structure capable of retaining water for a prolonged duration. The complete removal of water results in further shrinkage of the anhydrous silk–RIB hydrogel or xerogel (XG), yet its porosity and structural integrity remain intact. These findings offer valuable insights into the behavior of silk fibroin hydrogel and XG, paving the way for materials engineering in aqueous environments to develop biomedical devices with customized functional properties.

CryoEM structure of an MHC-I/TAPBPR peptide-bound intermediate reveals the mechanism of antigen proofreading

Class I major histocompatibility complex (MHC-I) proteins play a pivotal role in adaptive immunity by displaying epitopic peptides to CD8+ T cells. The chaperones tapasin and TAPBPR promote the selection of immunogenic antigens from a large pool of intracellular peptides. Interactions of chaperoned MHC-I molecules with incoming peptides are transient in nature, and as a result, the precise antigen proofreading mechanism remains elusive. Here, we leverage a high-fidelity TAPBPR variant and conformationally stabilized MHC-I, to determine the solution structure of the human antigen editing complex bound to a peptide decoy by cryogenic electron microscopy (cryo-EM) at an average resolution of 3.0 Å. Antigen proofreading is mediated by transient interactions formed between the nascent peptide binding groove with the P2/P3 peptide anchors, where conserved MHC-I residues stabilize incoming peptides through backbone-focused contacts. Finally, using our high-fidelity chaperone, we demonstrate robust peptide exchange on the cell surface across multiple clinically relevant human MHC-I allomorphs. Our work has important ramifications for understanding the selection of immunogenic epitopes for T cell screening and vaccine design applications.

Preventing Site-Specific Calpain Proteolysis of Junctophilin-2 Protects Against Stress-Induced Excitation-Contraction Uncoupling and Heart Failure Development

BACKGROUND: Excitation-contraction (E-C) coupling processes become disrupted in heart failure (HF), resulting in abnormal Ca 2+ homeostasis, maladaptive structural and transcriptional remodeling, and cardiac dysfunction. Junctophilin-2 (JP2) is an essential component of the E-C coupling apparatus but becomes site-specifically cleaved by calpain, leading to disruption of E-C coupling, plasmalemmal transverse tubule degeneration, abnormal Ca 2+ homeostasis, and HF. However, it is not clear whether preventing site-specific calpain cleavage of JP2 is sufficient to protect the heart against stress-induced pathological cardiac remodeling in vivo. METHODS: Calpain-resistant JP2 knock-in mice (JP2 CR ) were generated by deleting the primary JP2 calpain cleavage site. Stress-dependent JP2 cleavage was assessed through in vitro cleavage assays and in isolated cardiomyocytes treated with 1 μmol/L isoproterenol by immunofluorescence. Cardiac outcomes were assessed in wild-type and JP2 CR mice 5 weeks after transverse aortic constriction compared with sham surgery using echocardiography, histology, and RNA-sequencing methods. E-C coupling efficiency was measured by in situ confocal microscopy. E-C coupling proteins were evaluated by calpain assays and Western blotting. The effectiveness of adeno-associated virus gene therapy with JP2 CR , JP2, or green fluorescent protein to slow HF progression was evaluated in mice with established cardiac dysfunction. RESULTS: JP2 proteolysis by calpain and in response to transverse aortic constriction and isoproterenol was blocked in JP2 CR cardiomyocytes. JP2 CR hearts are more resistant to pressure-overload stress, having significantly improved Ca 2+ homeostasis and transverse tubule organization with significantly attenuated cardiac dysfunction, hypertrophy, lung edema, fibrosis, and gene expression changes relative to wild-type mice. JP2 CR preserves the integrity of calpain-sensitive E-C coupling–related proteins, including ryanodine receptor 2, Ca V 1.2, and sarcoplasmic reticulum calcium ATPase 2a, by attenuating transverse aortic constriction–induced increases in calpain activity. Furthermore, JP2 CR gene therapy after the onset of cardiac dysfunction was found to be effective at slowing the progression of HF and superior to wild-type JP2. CONCLUSIONS: The data presented here demonstrate that preserving JP2-dependent E-C coupling by prohibiting the site-specific calpain cleavage of JP2 offers multifaceted beneficial effects, conferring cardiac protection against stress-induced proteolysis, hypertrophy, and HF. Our data also indicate that specifically targeting the primary calpain cleavage site of JP2 by gene therapy approaches holds great therapeutic potential as a novel precision medicine for treating HF.

Open-boundary molecular dynamics of ultrasound using supramolecular water models

Ultrasound can be used to manipulate protein function and activity, as well as for targeted drug delivery, making it a powerful diagnostic and therapeutic modality with wide applications in sonochemistry, nanotechnology, and engineering. However, a general particle-based approach to ultrasound modeling remains challenging due to the significant disparity between characteristic time scales governing ultrasound propagation. In this study, we use open-boundary molecular dynamics to simulate ultrasound waves in liquid water under ambient conditions by employing supramolecular water models, i.e., the Martini 3, dissipative particle dynamics, and many-body dissipative particle dynamics models. We demonstrate that our approach successfully reproduces the solution of the traveling wave equation and captures the velocity dispersion characteristic of high-frequency ultrasound waves.

Nonapoptotic role of EGL-1 in exopher production and neuronal health in <i>Caenorhabditis elegans</i>

While traditionally studied for their proapoptotic functions in activating the caspase, research suggests BH3-only proteins also have other roles such as mitochondrial dynamics regulation. Here, we find that EGL-1, the BH3-only protein in Caenorhabditis elegans , promotes the cell-autonomous production of exophers in adult neurons. Exophers are large, micron-scale vesicles that are ejected from the cell and contain cellular components such as mitochondria. EGL-1 facilitates exopher production potentially through regulation of mitochondrial dynamics. Moreover, an endogenous, low level of EGL-1 expression appears to benefit dendritic health. Our findings provide insights into the role of neuronal BH3-only protein in mitochondrial dynamics, downstream exopher production, and ultimately neuronal health.

Efficacy and Safety of Finerenone in Patients With Primary Aldosteronism: A Pilot Randomized Controlled Trial

Retractions caused by honest mistakes are extremely stressful, say researchers

Multidimensional quantum dynamics with explicitly correlated Gaussian wave packets using Rothe’s method

In a previous publication [S. E. Schrader et al., J. Chem. Phys. 161, 044105 (2024)], it has been shown that Rothe’s method can be used to solve the time-dependent Schrödinger equation for the hydrogen atom in a strong laser field using time-dependent Gaussian wave packets. Here, we generalize these results, showing that Rothe’s method can propagate arbitrary numbers of thawed, complex-valued, Explicitly Correlated Gaussian (ECGs) functions with dense correlation matrices for systems with varying dimensionality. We consider the multidimensional Hénon–Heiles potential and show that the dynamics can be quantitatively reproduced using only 30 Gaussians in 2D and that accurate spectra can be obtained using 20 Gaussians in 2D and 30–40 Gaussians in 3D and 4D. Therefore, the relevant multidimensional dynamics can be described at high quality using only a small number of ECGs that give a very compact representation of the wave function. This efficient representation, along with the demonstrated ability of Rothe’s method to propagate Gaussian wave packets in strong fields and ECGs in complex potentials, paves the way for accurate molecular dynamics calculations beyond the Born–Oppenheimer approximation in strong fields.

Device-Measured 24-Hour Movement Behaviors and Blood Pressure: A 6-Part Compositional Individual Participant Data Analysis in the ProPASS Consortium

BACKGROUND: Blood pressure (BP)–lowering effects of structured exercise are well-established. Effects of 24-hour movement behaviors captured in free-living settings have received less attention. This cross-sectional study investigated associations between a 24-hour behavior composition comprising 6 parts (sleeping, sedentary behavior, standing, slow walking, fast walking, and combined exercise-like activity [eg, running and cycling]) and systolic BP (SBP) and diastolic BP (DBP). METHODS: Data from thigh-worn accelerometers and BP measurements were collected from 6 cohorts in the Prospective Physical Activity, Sitting and Sleep consortium (ProPASS) (n=14 761; mean±SD, 54.2±9.6 years). Individual participant analysis using compositional data analysis was conducted with adjustments for relevant harmonized covariates. Based on the average sample composition, reallocation plots examined estimated BP reductions through behavioral replacement; the theoretical benefits of optimal (ie, clinically meaningful improvement in SBP [2 mm Hg] or DBP [1 mm Hg]) and minimal (ie, 5-minute reallocation) behavioral replacements were identified. RESULTS: The average 24-hour composition consisted of sleeping (7.13±1.19 hours), sedentary behavior (10.7±1.9 hours), standing (3.2±1.1 hours), slow walking (1.6±0.6 hours), fast walking (1.1±0.5 hours), and exercise-like activity (16.0±16.3 minutes). More time spent exercising or sleeping, relative to other behaviors, was associated with lower BP. An additional 5 minutes of exercise-like activity was associated with estimated reductions of –0.68 mm Hg (95% CI, –0.15, –1.21) SBP and –0.54 mm Hg (95% CI, –0.19, 0.89) DBP. Clinically meaningful improvements in SBP and DBP were estimated after 20 to 27 minutes and 10 to 15 minutes of reallocation of time in other behaviors into additional exercise. Although more time spent being sedentary was adversely associated with SBP and DBP, there was minimal impact of standing or walking. CONCLUSIONS: Study findings reiterate the importance of exercise for BP control, suggesting that small additional amounts of exercise are associated with lower BP in a free-living setting.

AI-powered contract automation helps research managers level up

Toward mitigating the impact of non-bulk defects on describing water structure in salt aqueous solutions: Characterizing solution density with a network-based structural indicator

Structural indicators, also known as structural descriptors, including order parameters, have been proposed to quantify the structural properties of water to account for its anomalous behaviors. However, these indicators, mainly designed for bulk water, are not naturally transferrable to the vicinity of ions due to disruptions in the immediate neighboring space and a resulting loss of feature completeness. To address these non-bulk defects, we introduced a structural indicator that draws on the concept of clique number from graph theory and the criterion in agglomerative clustering, denoted as the average cluster number. This structural indicator aims to discern intrinsic structural characteristics within the water molecules regardless of the ions occupying the neighboring space, without requiring additional corrections. From molecular dynamics simulation results for neat water and salt aqueous solutions utilizing the TIP4P/2005 water model and the Madrid-2019 force field, we characterized the variations in densities with temperature using this network-based indicator, thereby demonstrating its practical utility. The findings suggest that at lower temperatures, the addition of ions disrupts the intrinsic structure of water molecules, with this effect diminishing as the temperature rises. Cations with larger charge density tend to induce stronger disruptions. This study highlights the importance of mitigating the impact of non-bulk defects before applying the indicators to analyze water’s intrinsic structural properties in solutions. By doing so, the relationship between changes in water structure and solution behaviors can be more accurately assessed.

Multiplicity of type 6 secretion system toxins limits the evolution of resistance

The bacterial type 6 secretion system (T6SS) is a toxin-injecting nanoweapon that mediates competition in plant- and animal-associated microbial communities. Bacteria can evolve de novo resistance against T6SS attacks, but resistance is far from universal in natural communities, suggesting key features of T6SS weaponry may act to limit its evolution. Here, we combine ecoevolutionary modeling and experimental evolution to examine how toxin type and multiplicity in Acinetobacter baylyi attackers shape resistance evolution in susceptible Escherichia coli competitors. In both our models and experiments, we find that combinations of multiple distinct toxins limit resistance evolution by creating genetic bottlenecks, driving resistant lineages extinct before they can reach high frequency. We also show that, paradoxically, single-toxin attackers can drive the evolution of cross-resistance, protecting bacteria against unfamiliar toxin combinations, even though such evolutionary pathways were inaccessible against multitoxin attackers. Our findings indicate that, comparable to antimicrobial and anticancer combination therapies, multitoxin T6SS arsenals function to limit resistance evolution in competing microbes. This helps us to understand why T6SSs remain widespread and effective weapons in microbial communities, and why many T6SS-armed bacteria encode functionally diverse anticompetitor toxins.

Swinging Pendulum Between Risks and Benefits of Antiplatelet Agents: A Call for Consistency in the Interpretation of Evidence and Guideline Recommendations

Thermodynamics of nucleosome breathing and positioning

Nucleosomes are fundamental units of chromatin in which a length of genomic DNA is wrapped around a histone octamer spool in a left-handed superhelix. Large-scale nucleosome maps show a wide distribution of DNA wrapping lengths, which in some cases are tens of base pairs (bp) shorter than the 147 bp canonical wrapping length observed in nucleosome crystal structures. Here, we develop a thermodynamic model that assumes a constant free energy cost of unwrapping a nucleosomal bp. Our model also incorporates linker DNA—short DNA segments between neighboring nucleosomes imposed by the folding of nucleosome arrays into chromatin fibers and other higher-order chromatin structures. We use this model to study nucleosome positioning and occupancy in the presence of nucleosome “breathing”—partial unwrapping and rewrapping of nucleosomal DNA due to interactions with the neighboring particles. We find that, as the unwrapping cost per bp and the chemical potential are varied, the nucleosome arrays are characterized by three distinct states, with low, intermediate, and high densities. The transition between the latter two states proceeds through an equiprobable state in which all nucleosome wrapping lengths are equally likely. We study the equiprobable state theoretically using a mean-field approach, obtaining an excellent agreement with numerical simulations. Finally, we use our model to reproduce S. cerevisiae nucleosome occupancy profiles observed in the vicinity of transcription start sites, as well as genome-wide distributions of nucleosome wrapping lengths. Overall, our results highlight the key role of partial nucleosome unwrapping in shaping the genome-wide patterns of nucleosome positioning and occupancy.

Structural basis for TIR domain–mediated innate immune signaling by Toll-like receptor adaptors TRIF and TRAM

Innate immunity relies on Toll-like receptors (TLRs) to detect pathogen-associated molecular patterns. The TIR (Toll/interleukin-1 receptor) domain-containing TLR adaptors TRIF (TIR domain–containing adaptor-inducing interferon-β) and TRAM (TRIF-related adaptor molecule) are essential for MyD88-independent TLR signaling. However, the structural basis of TRIF and TRAM TIR domain–based signaling remains unclear. Here, we present cryo-EM structures of filaments formed by TRIF and TRAM TIR domains at resolutions of 3.3 Å and 5.6 Å, respectively. Both structures reveal two-stranded parallel helical arrangements. Functional studies underscore the importance of intrastrand interactions, mediated by the BB-loop, and interstrand interactions in TLR4-mediated signaling. We also report the crystal structure of the monomeric TRAM TIR domain bearing the BB loop mutation C117H, which reveals conformational differences consistent with its inactivity. Our findings suggest a unified signaling mechanism by the TIR domains of the four signaling TLR adaptors MyD88, MAL, TRIF, and TRAM and reveal potential therapeutic targets for immunity-related disorders.

Letter by Chen et al Regarding Article, “Piezo1-Mediated Neurogenic Inflammatory Cascade Exacerbates Ventricular Remodeling After Myocardial Infarction”

A partition function estimator

We propose an estimator that allows us to calculate the value of a simple system’s partition function using finite sampling. The core idea is to neglect the contribution from high energy microstates, which are difficult to be sampled properly, and then calculate a volume correction term to compensate for this. As a proof of concept, the estimator is applied to calculate the partition function for several model systems, ranging from a simple harmonic oscillator to a Lennard-Jones fluid with hundreds of particles. Our results agree well with the numerically exact solutions or reference data, demonstrating that efficiently estimating partition functions for the studied example cases is possible and computationally affordable.

Anti-CTLA-4 generates greater memory response than anti-PD-1 via TCF-1

The effects of T cell differentiation arising from immune checkpoint inhibition targeting cytotoxic T lymphocyte–associated antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1) on the immunological memory response remain unclear. Our investigation into the effects of anti-CTLA-4 and anti-PD-1 on memory T cell formation in mice reveals that memory T cells generated by anti-CTLA-4 exhibit greater expansion, cytokine production, and antitumor activity than those from anti-PD-1. Notably, anti-CTLA-4 preserves more T cell factor-1 (TCF-1)+ T cells during priming, while anti-PD-1 leads to more thymocyte selection-associated high mobility group box (TOX)+ T cells. Experiments using conditional Tcf7 - or Tox -knockout mice highlight that TCF-1 is essential for the memory response generated by anti-CTLA-4, whereas TOX deletion alone in T cells has no effect on the response to anti-PD-1. Deepening our understanding of how checkpoint inhibition affects memory response is crucial for advancing our understanding of the enduring impacts of these immunotherapies on the immune system.

Exercise Training in Patients With Hypertrophic Cardiomyopathy Without Left Ventricular Outflow Tract Obstruction: A Randomized Clinical Trial

BACKGROUND: Patients with hypertrophic cardiomyopathy without left ventricular outflow tract obstruction commonly experience reduced exercise capacity. Physical training improves exercise capacity in these patients, but whether the underlying effects of exercise are a result of central hemodynamic or peripheral improvement is unclear. This study assessed whether exercise training reduces left ventricular filling pressure measured during exercise in patients with hypertrophic cardiomyopathy without left ventricular outflow tract obstruction. METHODS: Between March 2019 and June 2022, patients with hypertrophic cardiomyopathy without left ventricular outflow tract obstruction were randomly assigned (1:1) to a 12-week (3 h/wk) supervised, moderate-intensity exercise training program or continued usual activity. The primary outcome was the change in invasively measured pulmonary capillary wedge pressure during mild exercise (25 W) from baseline to week 12. Pressure tracings were analyzed offline by a blinded investigator. Secondary outcomes included changes in peak oxygen consumption, cardiac index, quality of life, echocardiographic indices of diastolic function, and natriuretic peptides. RESULTS: Of 59 patients randomized (mean age, 58.1 [12.2] years; 27% women), 51 (86%) completed all follow-up assessments. At week 12, the change in 25-W pulmonary capillary wedge pressure was –2.8 (6.8) mm Hg in the exercise group, compared with +1.2 (4.9) mm Hg in the usual-activity group (between-group difference, 4.0 mm Hg [95% CI, 0.7–7.3]; P =0.018). Peak oxygen consumption improved by +1.8 (2.0) mL·kg⁻¹·min⁻¹ in the exercise group versus –0.3 (3.1) mL·kg⁻¹·min⁻¹ in the usual-activity group ( P =0.005). Exercise training improved the ventilatory efficiency (V E /VCO 2 ) slope compared with usual activity (between-group difference, 2.0 [95% CI, 0.6–3.5]; P =0.006). Peak cardiac index improved by +0.38 (1.38) L·min⁻¹·m⁻² in exercise versus –0.85 (1.20) L·min⁻¹·m⁻² in the usual-activity group ( P =0.002). Change in overall Kansas City Cardiomyopathy Questionnaire score was similar between groups. However, the change in physical limitation scores (+8.4 [12.0] points in exercise versus +0.7 [6.8] points in usual-activity group; P =0.034) and quality-of-life scores (+8.7 [18.0] points in exercise versus 0.7 [4.0] points in usual-activity group; P =0.01) differed significantly. There were no significant changes in diastolic function assessed by echocardiography or in natriuretic peptides. CONCLUSIONS: In patients with hypertrophic cardiomyopathy without left ventricular outflow tract obstruction, a 12-week moderate-intensity exercise training program resulted in reduced left ventricular filling pressures at mild exertion and improved exercise performance. REGISTRATION: URL: https://www.clinicaltrials.gov ; Unique identifier: NCT03537183.

Electric dipole moment of excited octupolar molecules: Potential qubit implementation

The first excited state of conjugated donor–acceptor molecules of C3 symmetry (octupolar molecules) is doubly degenerate. Such a doublet is known to be isomorphic to a spin 1/2. It is shown that a large electric dipole moment is associated with this spin. Since the mean value of the electric dipole moment of an octupolar molecule is a measure of the symmetry breaking charge transfer, a dimensionless dipole moment called the dissymmetry vector is introduced. The dissymmetry vector operator is constructed. A linear tensor connection between this operator and the Pauli matrices is found. The tensor character is due to the two-dimensionality of the dipole moment. The dipole moment can rotate freely in the plane of the molecule as long as the C3 symmetry is maintained. The rotation is associated only with the rearrangement of the electronic subsystem of the molecule and does not affect the spatial position of the nuclei. This opens up the possibility of changing the dipole moment state on a subpicosecond time scale. The Jahn–Teller effect on the dissymmetry vector is considered in detail. It is shown that the dissymmetry vector can be controlled using electric fields in the same way as three-dimensional spin if both static and alternating electric fields are in the plane of the molecule. The conducted studies indicate that the dipole moment of excited octupolar molecules is a promising candidate for the physical implementation of a qubit.