Browse Articles

Bouncing microdroplets on hydrophobic surfaces

Intuitively, slow droplets stick to a surface and faster droplets splash or bounce. However, recent work suggests that on nonwetting surfaces, whether microdroplets stick or bounce depends only on their size and fluid properties, but not on the incoming velocity. Here, we show using theory and experiments that even poorly wetting surfaces have a velocity-dependent criterion for bouncing of aqueous droplets, which is as high as 6 m/s for diameters of 30 to 50 μ m on hydrophobic surfaces such as Teflon. We quantify this criterion by analyzing the interplay of dissipation, surface adhesion, and incoming kinetic energy, and describe a wealth of associated phenomena, including air bubbles and satellite droplets. Our results on inertial microdroplets elucidate fundamental processes crucial to aerosol science and technology.

Collective behavior of “flexicles”

In recent years the functionality of synthetic active microparticles has edged even closer to that of their biological counterparts. However, we still lack the understanding needed to recreate at the microscale key features of autonomous behavior exhibited by microorganisms or swarms of macroscopic robots. In this study, we propose a model for a three-dimensional deformable cellular composite particle consisting of self-propelled rod-shaped colloids confined within a flexible vesicle—representing a superstructure we call a “flexicle” that couples particle deformation to the internal dynamics of the internal active components. Using molecular dynamics simulations, we investigate the collective behavior of dense systems composed of many flexicles. We show that individual flexicles exhibit shape changes upon collisions with other flexicles that lead to rearrangements of the internal active rods, which slows flexicle motion. This shape deformability gives rise to a diverse set of motility-induced phase separation phenomena and the spontaneous flow of flexicles reminiscent of the migration of cells in dense tissues. Our findings establish a foundation for designing responsive, cell-like active particles and developing strategies for controlling swarm migration and other autonomous swarm behaviors at cellular and colloidal scales.

12/15-lipoxygenase orchestrates murine wound healing via PPARγ-activating oxylipins acting holistically to dampen inflammation

12/15-lipoxygenase (12/15-LOX, Alox15 ) generates bioactive oxygenated lipids during inflammation, however its homeostatic role(s) in normal healing are unclear. Here, the role of 12/15-LOX in resolving skin wounds was elucidated, focusing on how its lipids act together in physiologically relevant amounts. In mice, wounding caused acute appearance of 12/15-LOX-expressing macrophages and stem cells, coupled to early generation of ~12 monohydroxy-oxylipins and enzymatically oxidized phospholipids (eoxPL). Alox15 deletion increased collagen deposition, stem cell/fibroblast proliferation, IL6/pSTAT3, pSMAD3, and interferon (IFN)-γ levels. Conversely, CD206 expression, F480+ cells, and MMP9 and MMP2 activities were reduced. Alox15 −/− skin was deficient in PPARγ/adiponectin activity. Furthermore, while pro-inflammatory genes were upregulated as normal during wounding, many including Il6, Il1b, ccl4, Cd14, Cd274, Clec4d, Clec4e, Csf3, Cxcl2, and miR-21 failed to revert to baseline during healing, indicating disruption of PPARγ’s anti-inflammatory brake on NLRP3/inflammasome and TGF-β signaling. Reconstituting Alox15 −/− wounds with a physiological mixture of Alox15 -derived primary oxylipins generated by healing wounds restored MMP and dampened collagen deposition. The oxylipin mixture activated the PPARγ response element in vitro, while in vivo, its coactivator, Helz2 , was significantly upregulated as well as several fatty acid and prostaglandin PPARγ ligands. Additional inflammatory and proliferative gene networks impacted by Alox15 −/− included Elf4, Cebpb , and Tcf3. In summary, 12/15-LOX generates abundant monohydroxy oxylipins that act together via PPARγ. The identification of multiple gene alterations reveals several targets for treating nonhealing wounds. Our studies demonstrate that 12/15-LOX oxylipins act in concert, dampening inflammation in vivo, revealing the need to consider lipid signaling holistically.

Mutations in the circadian cycle drive adaptive plasticity in cyanobacteria

Circadian clocks allow organisms to anticipate daily fluctuations in light and temperature, but how this anticipatory role promotes adaptation to different environments remains poorly understood. Here, we subjected the cyanobacterium Synechococcus elongatus PCC 7942 to a long-term evolution experiment under high light, high temperature, and elevated CO 2 levels. After 1,200 generations, we obtained a strain exhibiting a 600% increase in growth rate. Whole-genome sequencing revealed three mutations fixed in the evolved population, two of which were sufficient to recapitulate the fast-growing phenotype in the wild type. A mutation in the promoter of the shikimate kinase aroK led to its overexpression, while a mutation in the central circadian regulator sasA disrupted both the phase and amplitude of the circadian rhythm. Changes in circadian control led to widespread perturbations in the transcriptome and metabolome. These included major shifts in the Calvin–Benson–Bassham cycle and glycogen storage dynamics. While these changes increased fitness under the experimental conditions, they caused maladaptation when light or CO 2 levels were altered, revealing a trade-off between fitness and environmental flexibility. Our results demonstrate that mutations in circadian control can drive fast adaptation by modulating central metabolism, underscoring the circadian cycle as a cornerstone of cellular plasticity. Thus, targeting the circadian cycle could be key to engineering cyanobacterial strains optimized for carbon fixation and biomass production.

De novo design of protein binders to stabilize monomeric TDP-43 and inhibit its pathological aggregation

Pathological aggregation of transactive response DNA binding protein of 43 kDa (TDP-43), primarily driven by its low-complexity domain, is closely associated with various neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Despite the therapeutic potential of preventing TDP-43 aggregation, no effective small molecule or biomacromolecule therapeutics have been successfully developed so far. Here, we introduce a protein design strategy that yields de novo designed proteins capable of stabilizing the key amyloidogenic region of TDP-43 in its native helical conformation with nanomolar binding affinity. The binding mechanism was further characterized by the NMR and mutagenesis study. More importantly, we demonstrated that our designed protein binders efficiently reduced TDP-43 amyloid aggregation both in vitro and in cells. Our work provides a strategy for designing protein stabilizer of the native conformation of pathological proteins for preventing its amyloid aggregation, shedding light on the development of potential therapeutic approaches for ALS, FTLD, and other protein aggregation-associated diseases.

Loss of the ESX-5 secretion locus in <i>Mycobacterium tuberculosis</i> reshapes the mycomembrane and enhances ESX-1 substrate secretion

The ESX-5 secretion system, uniquely found in slow-growing mycobacteria, is predicted to secrete over 150 proteins across the inner membrane of Mycobacterium tuberculosis ( M.tb ). Although many of these substrates are believed to promote M.tb virulence, most remain poorly characterized. Here, we use a complete locus deletion strain of ESX-5 in M.tb to examine the molecular changes caused by a broad loss in ESX-5 secretory substrates. We confirmed the selective loss of PE/PPE proteins secreted by ESX-5 into both the culture filtrate (CF) and outer mycomembrane (OMM) fractions of the M.tb ∆esx5 mutant. In examining other ESX systems, we found that ESX-1 substrate levels were increased in both the CF and OMM fractions of the ∆esx5 mutant. Conversely, the ESX-3 locus was transcriptionally repressed upon ESX-5 deletion. We noted that the ∆esx5 mutant had altered morphology in the form of wrinkled distortions of the bacterial surface. Likewise, we identified increased susceptibility of the ∆esx5 mutant to a variety of large (molecular weight &gt;550 g/mol) antimicrobial compounds, suggesting that an intact ESX-5 system is required for M.tb to exclude such molecules. Our findings suggest that removing the ESX-5 system from M.tb fundamentally alters the properties of the mycobacterial OMM and impacts the expression and secretion activity of other ESX systems.

William S. Sly (1932–2025): A compassionate pioneer in biochemical genetics

William S. Sly, MD (1932–2025) was a biochemical geneticist who received his medical degree from Saint Louis University. He received additional training at the NIH with several members of the National Academy of Science and Nobel Prize winner Marshall Nirenberg. He is best known for discovering mucopolysaccharidosis type VII and developing a Food and Drug Administration-approved treatment for it. He served in several long-term leadership roles and won many accolades, including the Passano Foundation Award and induction into the National Academy of Sciences. Sly was equally well known as a kind and caring person who always made time for family, friends, colleagues, and patients. He is the personification of the caring and compassionate physician-scientist.

Procollagen IIA mediates positive feedback control of the mouse cardiogenic transcriptional network

Cardiogenesis relies on the integrated interplay between cardiac transcription factors and signaling pathways. Here, we uncover a role for type IIA procollagen (IIA), an extracellular matrix (ECM) protein encoded by an alternatively spliced Col2a1 transcript, encoding a N-terminal cysteine-rich domain, as a critical regulator in a cardiac gene regulatory feedback loop. The cysteine-rich domain of IIA protein was previously reported to interact with bone morphogenetic proteins (BMPs) and transforming growth factors-beta (TGFβ) in in vitro binding assays and acts as a BMP antagonist in amphibian embryo assays. We show that the Col2a1 gene in mice is activated in the developing heart by core cardiogenic factors (NKX2-5, GATA4, MEF2, and SRF) via cis-regulatory enhancer elements. IIA loss (ΔIIA) in mice results in depletion of Isl1- and Nkx2-5-expressing progenitors, causing outflow tract defects resembling disrupted BMP/TGFβ-SMAD signaling, alongside reduced nuclear pSMAD1/5/8 in cardiac tissues. Compound +/ΔIIA ; Smad4+/− mutants exhibit aggravated malformations. IIA enhances BMP-responsive reporter activity in cells in transactivation assays. We propose that IIA supports a positive functional role on SMAD4-dependent signaling, fine-tuning BMP/TGFβ signaling, thereby regulating GATA4 and NKX2-5 activity during second heart field progenitor specification. These findings position IIA procollagen as a key ECM component that integrates BMP/TGFβ signaling with cardiac transcription factors such as NKX2-5, revealing a feedback loop essential for cardiogenesis. Given its role in cardiac development, IIA emerges as a potential congenital heart disease risk factor.

Inverse stable isotope probing–metabolomics (InverSIP) identifies an iron acquisition system in a methane-oxidizing bacterial community

Methane is a potent greenhouse gas and a target for near-term climate change mitigation. In many natural ecosystems, methane is sequestered by microbial communities, yet little is known about how constituents of methane-oxidizing communities interact with each other and their environment. This lack of mechanistic understanding is a common issue for many important microbial communities, but it is difficult to draw links between available sequencing information and the metabolites that govern community interactions. Here, we develop and apply a technique called inverse stable isotope probing–metabolomics (InverSIP) to bridge the gap between metagenomic and metabolomic information and functionally characterize interactions in a complex methane-oxidizing community. Using InverSIP, we link a highly transcribed biosynthetic gene cluster in the community with its secondary metabolite product: methylocystabactin, a triscatecholate siderophore not previously observed in nature. We find that production of methylocystabactin is widespread among methanotrophic alphaproteobacteria and that it can be used by another methanotroph in the community that does not produce this siderophore itself. Functional assays reveal that methylocystabactin supports methanotroph growth and the activity of the methane-oxidizing enzyme soluble methane monooxygenase under conditions where bioavailable iron is limited, establishing an important molecular link between methane-oxidation and the insoluble iron found in many natural environments. These findings contribute to a molecular-level understanding of these environmentally important bacterial communities and establish InverSIP as a broadly applicable genomics-guided strategy for characterizing metabolites in microbial ecosystems.

Capturing the native structure of membrane proteins using vesicles

Membrane proteins play crucial roles in numerous biological processes and are important drug targets. However, structural studies of membrane proteins often rely on solubilization with detergents, which may not accurately reflect their native states in a cellular context. Additionally, identifying suitable detergents for individual membrane proteins can be a detailed and time-consuming process. Here, we developed a vesicle-based method that preserves the native lipid environment for subsequent structural and functional studies. Using the bacterial multidrug efflux transporter AcrB as an example, we isolated AcrB-containing vesicles and determined its cryo-EM structure with all protomers in a loose (L) state at 3.88 Å by incorporating our micrograph-based sorting strategy. Notably, compared to the L-state AcrB in liposomes and nanoparticles, the exterior transmembrane helices (TMs) in our map exhibited superior quality, featuring a continuous and clear representation of lα, which is positioned horizontally within the lipid bilayer. We further expanded our method by identifying endogenous membrane proteins, including F-ATPase and respiratory complexes, in vesicles generated using mitochondria from pig hearts. The high-resolution structure of respiratory complex III in vesicles revealed a shared subunit nine between two monomers. Briefly, our method presents a promising and straightforward approach for studying the structure and function of membrane proteins in their native environment, eliminating the need for detergent screening and protein purification.

Fatty acid 2-hydroxylase facilitates rotavirus uncoating and endosomal escape

Despite the clinical significance of many nonenveloped viruses, the molecular mechanisms of their internalization and membrane penetration are not well understood. Rotaviruses (RVs) are nonenveloped double-stranded RNA viruses and the leading cause of severe dehydrating diarrhea in infants and young children. We identified fatty acid 2-hydroxylase (encoded by FA2H ) in the fatty acid 2-hydroxylation pathway as a proviral gene that supports RV infection. Genetic ablation of FA2H interfered with an early step in RV entry for multiple human and animal strains. Intestinal epithelial cell–specific deletion of Fa2h limited RV replication and diarrhea incidence in vivo. Using transmission electron microscopy and immunofluorescence, we found that viral particles were trapped in early and late endosomes in FA2H knockout cells, preventing their further exit into the cytosol. The defect in RV infectivity could be partially restored by treatment of cells with long-chain 2-hydroxy ceramides or a calcium channel activator that promotes Ca 2+ efflux from endosomes. Both Junín virus, an arenavirus, and Shiga toxin, dependent on endosomal Ca 2+ transport, required FA2H for efficient entry. Together, this study highlights a role of fatty acid 2-hydroxylation in RV entry into host cells and implicates 2-hydroxy ceramides as potential key regulators of endosomal Ca 2+ levels, offering important insights for the development of host-directed therapies targeting fatty acid 2-hydroxylation to control microbial infections.

Upscaling behavioral interventions requires addressing selection bias

Nonlinear memory in cell-division dynamics across species

Regulation of cell growth and division is essential to achieve cell-size homeostasis. Recent advances in imaging technologies, such as “mother machines” for bacteria or yeast, have allowed long-term tracking of cell-size dynamics across many generations, and thus have brought major insights into the mechanisms underlying cell-size control. However, understanding the governing rules of cell growth and division within a quantitative dynamical-systems framework remains a major challenge. Here, we implement and apply a framework that makes it possible to infer stochastic-differential-equation models with Poisson noise directly from experimentally measured time series for cellular growth and division. To account for potential nonlinear memory effects, we parameterize the Poisson intensity of stochastic cell-division events in terms of both the cell’s current size and its ancestral history. By applying the algorithm to experimentally measured cell-size trajectories, we are able to quantitatively evaluate the linear one-step memory hypothesis underlying the popular “sizer,” “adder,” and “timer” models of cell homeostasis. For Escherichia coli and Bacillus subtilis bacteria, Schizosaccharomyces pombe yeast and Dictyostelium discoideum amoebae, we find that in many cases, the inferred stochastic models have a substantial nonlinear memory component. This suggests a need to reevaluate and generalize some of the currently prevailing linear-memory paradigms of cell homeostasis. More broadly, the underlying inference framework is directly applicable to identify quantitative models for stochastic jump processes in a wide range of scientific disciplines.

Manipulating anthracyclines for deeper tissue penetration and implications for glycolytic tissues

How drugs penetrate tissues is poorly understood yet important, since drugs that fail to reach their target will be ineffective. We followed the fate of anthracycline cancer drugs at high resolution by exploiting their intrinsic fluorescence. In a cell-based spheroid model, the soluble compound fluorescein penetrates the entire spheroid, unlike hydrophobic fluorescent lipids, which only enter the outermost cell layer. Anthracyclines have intermediate hydrophobicity. They enter the nucleus of a few outer cell layers at neutral pH, but penetrate the spheroids more deeply under acidic conditions, with a reduction in cell entry and cytotoxicity. The glycolytic conditions that prevail in the tumor microenvironment may thus limit cell entry and contribute to anthracycline drug resistance. We evaluated a library of anthracycline variants to determine the physicochemical properties related to tissue penetration depth. We find that this is determined by only three chemical properties: molar refractivity, topological polar surface area, and water solubility. Our findings suggest that modifications of anthracyclines may improve access and activity to deeply tissue-embedded targets such as pancreatic cancer.

Correction: Analysis of an engineered organoid model of pancreatic cancer identifies hypoxia as a contributing factor in determining transcriptional subtypes

<i>miR444b.2</i> –HsfA1– <i>AOC1</i> module mediates heat priming–enhanced blast resistance in rice

As global climate change exacerbates extreme heat events, the interplay between heat stress and blast disease resistance in rice remains poorly understood. In this study, through integrated transcriptome profiling and systematic phenotyping of mutants in several thermosensory pathways, we identified HsfA1 as a positive regulator of heat priming–enhanced blast resistance in rice. Systematic analysis of microRNA (miRNA) dynamics, bioinformatics prediction, and RNA pull-down experiments revealed that miR444b.2 , a temperature-responsive miRNA, directly suppresses the expression of HsfA1 by targeting the second exon of HsfA1 messenger RNA (mRNA). Genetic analyses demonstrated that heat stress–mediated suppression of miR444b.2 expression relieves the repression of HsfA1 , thereby enhancing blast resistance in rice. Furthermore, HsfA1 directly binds to the promoter of AOC1 , a key jasmonic acid (JA) biosynthesis gene, to activate its expression. Knockout of HsfA1 or AOC1 abolishes heat priming–enhanced JA accumulation and blast disease resistance, and the phenotypes are largely restored via AOC1 overexpression and MeJA treatment. Further identification of HsfA1 natural variants and generation of the HsfA1 uORF -edited lines with improved blast resistance offer potential strategies for breeding disease-resistant rice varieties. This study elucidates the miR444b.2 –HsfA1– AOC1 module that links thermal sensing to JA-mediated blast resistance, providing a molecular blueprint for engineering climate-resilient crops with concurrent biotic–abiotic stress tolerance.

Correction: Some new evidence using fractional integration about trends, breaks and persistence in polar amplification

Inflammation awakens dormant cancer cells by modulating the epithelial–mesenchymal phenotypic state

The awakening of dormant disseminated cancer cells appears to be responsible for the clinical relapses of patients whose primary tumors have been successfully cured months and even years earlier. In the present study, we demonstrate that dormant breast cancer cells lodged in the lungs reside in a highly mesenchymal, nonproliferative phenotypic state. The awakening of these cells is not triggered by a cancer cell-autonomous process. Instead, lung inflammation induced by the chemotherapeutic agent bleomycin effectively awakens dormant cancer cells, providing useful models for studying metastatic awakening. Mechanistically, the awakened cells shift from a highly mesenchymal to a quasi-mesenchymal phenotypic state in which they acquire tumorigenicity and proliferative ability. Once awakened, these cells can stably reside in this quasi-mesenchymal state and maintain their tumor-initiating ability, doing so without ongoing heterotypic signaling from the lung microenvironment. Epidermal growth factor receptor ligands released by the cells of the injured tissue microenvironment, including notably M2 type macrophages, promote dormant cancer cells to move toward this quasi-mesenchymal state, a transition that is critical for the awakening process. An understanding of the mechanisms of metastatic awakening may lead in the future to treatment strategies designed to prevent such awakening and resulting metastatic relapse.

Enhancing Mindfulness-Based Cognitive Therapy in a Virtual Reality: A Prospective Interventional Study

Resurfacing promotes antibacterial activity of a lipid A–binding nanobody

Nanobodies have been pursued as candidates for antimicrobial design due to their small size and versatile binding capacities, but direct antibacterial activity of a nanobody has yet to be described. Here, we employed a bacterial surface display platform to screen a synthetic library of nanobody variants for antimicrobial potential. We identified a candidate that binds the essential lipid A component of gram-negative lipopolysaccharide. Nonetheless, this nanobody required a weakened outer membrane to access its target and elicit its toxic activity. Borrowing from observations of innate immune proteins, we found that resurfacing nanobodies with positively charged residues enabled them to bind and perturb the gram-negative outer membrane, but this alone was not sufficient for toxic activity. However, when we resurface our lipid A-targeting nanobody, it gained the ability to disrupt the outer membrane and enact its antibacterial function against wild-type bacteria. This development of a dual-function nanobody that can reach and bind previously inaccessible gram-negative targets introduces a route for antimicrobial biologic advancement.