Browse Articles

Impact of Mg ²⁺ and pH on amorphous calcium carbonate nanoparticle formation: Implications for biomineralization and ocean acidification

Crystallization by amorphous calcium carbonate (ACC) particle attachment (CPA) is a prevalent biomineralization mechanism among calcifying organisms. A narrow, controlled size distribution of ACC nanoparticles is essential for macroscopic crystal formation via CPA. Using in situ synchrotron small-angle X-ray scattering, we demonstrate that synthetic magnesium-stabilized ACC (Mg-ACC) nanoparticles form with an exceptionally narrow size distribution near the spinodal line during liquid–liquid phase separation. We monitored ACC formation kinetics at pH 8.4 to 8.9 and Mg 2 + contents of 50 to 80%, observing a 2-order magnitude rise in nucleation kinetics for a 0.1 pH increase and a 6-order magnitude rise for a 10% Mg 2 + decrease. Within the binodal region, faster nucleation kinetics result in more monodisperse particles, narrowing the particle size distribution by factors of 2 for a pH increase of merely 0.1 and by a factor of 3 for a 10% Mg 2 + decrease. While the influence of Mg 2 + on calcite biomineralization is well studied, its effect on Mg-ACC formation and particle size distribution-an essential parameter in CPA-based biomineralization pathways-remained unexplored. These findings highlight the delicate interplay of pH and Mg 2 + in controlling the kinetics and thermodynamics of Mg-ACC formation, significantly impacting particle size distribution.

Architecture of <i>Pseudomonas aeruginosa</i> glutamyl-tRNA synthetase defines a subfamily of dimeric class Ib aminoacyl-tRNA synthetases

The aminoacyl-tRNA synthetases (AaRSs) are an ancient family of structurally diverse enzymes that are divided into two major classes. The functionalities of most AaRSs are inextricably linked to their oligomeric states. While GluRSs were previously classified as monomers, the current investigation reveals that the form expressed in Pseudomonas aeruginosa is a rotationally pseudosymmetrical homodimer featuring intersubunit tRNA binding sites. Both subunits display a highly bent, “pipe strap” conformation, with the anticodon binding domain directed toward the active site. The tRNA binding sites are similar in shape to those of the monomeric GluRSs, but are formed through an approximately 180-degree rotation of the anticodon binding domains and dimerization via the anticodon and D-arm binding domains. As a result, each anticodon binding domain is poised to recognize the anticodon loop of a tRNA bound to the adjacent protomer. Additionally, the anticodon binding domain has an α-helical C -terminal extension containing a conserved lysine-rich consensus motif positioned near the predicted location of the acceptor arm, suggesting dual functions in tRNA recognition. The unique architecture of Pa GluRS broadens the structural diversity of the GluRS family, and member synthetases of all bacterial AaRS subclasses have now been identified that exhibit oligomerization.

Linked nitrogen and carbon dynamics reveal distinct pools and patterns in a deep, weathered bedrock rhizosphere

Nitrogen is one of the most limiting nutrients to forest productivity worldwide. Recently, it has been established that diverse ecosystems source a substantial fraction of their water from weathered bedrock, leading to questions about whether root-driven nitrogen cycling extends into weathered bedrock as well. In this study, we specifically examined nitrogen dynamics using specialized instrumentation distributed across a 16 m weathered bedrock vadose zone (WBVZ) underlying an old growth forest in northern California where the rhizosphere—composed of plant roots and their associated microbiome—extends meters into rock. We documented total dissolved nitrogen (TDN), dissolved organic carbon (DOC), inorganic nitrogen (ammonium and nitrate), and CO 2 and O 2 gases every 1.5 m to 16 m depth for 2 y. We found that TDN concentrations increased with depth, were an order of magnitude greater at 15 m than in the upper 30 cm, and that the majority of TDN throughout the weathered bedrock vadose zone was organic. We also found that TDN concentrations are influenced by depth, season, and interannual precipitation patterns. Carbon isotope composition of the DOC suggests that dissolved organic matter in the WBVZ is primarily derived from plant sources, and not the nitrogen-rich bedrock. We conclude that nitrogen dynamics in the WBVZ may be driven, in part, by an active rhizosphere, meters below the base of soil, and we argue that weathered bedrock horizons may play a key role in C-N cycling in ecosystems with deep-rooted plants.

Inheritance of extraordinary metabolic activity from parental bacteria individuals

Many phenotypic traits, such as fermentation activity, have been shown to be instable due to stochastic gene expression and environmental influence. While previous studies only have obtained understanding at the level of the microbial community, the fate of extraordinary traits of an individual through generations of reproduction has yet to be adequately investigated. This work uses the lactic acid bacteri Lactiplantibacillus plantarum as a research model to study the activity inheritance between parental generations and filial generations. An integrated single-cell manipulation strategy is established, including fluorescent screening using an extracellular pH probe and a microwell array, micropicking using a micropipette, and amplifying an individual bacterium via single-cell culture. Consequently, it is found that daughter bacteria can well inherit the strong acid-producing activity from their parental bacterial individuals, although as the reproduction proceeds over 30 generations, the offspring gradually regresses to the mediocre, thus setting a caveat for the limiting generations for desired inheritance. This is likely due to the deterioration of the cell living environment. This work illustrates the inheritable features of bacterial metabolic traits at the level of individual bacteria and is therefore fundamentally insightful for biotechnological applications like bioenergy production that require consistent or at least predictable metabolic performance.

Structure of the human TWIK-2 potassium channel and its inhibition by pimozide

The potassium channel TWIK-2 is crucial for ATP-induced activation of the NLRP3 inflammasome in macrophages. The channel is a member of the two-pore domain potassium (K2P) channel superfamily and an emerging therapeutic target to mitigate severe inflammatory injury involving NLRP3 activation. We report the cryo-EM structure of human TWIK-2. In comparison to other K2P channels, the structure reveals an unusual “up” conformation of Tyr111 in the selectivity filter and a resulting SF1-P1 pocket behind the filter. Density for acyl chains is present in fenestrations within the transmembrane region that connects the central cavity of the pore to the lipid membrane. Despite its importance as a drug target, limited pharmacological tools are available for TWIK-2. A previous study suggested that the FDA-approved small molecule pimozide might inhibit TWIK-2. Using a reconstituted system, we show that pimozide directly inhibits the channel and we determine a cryo-EM structure of a complex with the drug. Pimozide displaces the acyl chains within the fenestrations and binds below the selectivity filter where it would impede ion permeation. The drug may access its binding site by lateral diffusion in the membrane, suggesting that other hydrophobic small molecules could have utility for inhibiting TWIK-2. The work defines the structure of TWIK-2 and provides a structural foundation for development of more specific inhibitors with potential utility as anti-inflammatory drugs.

Nonequilibrium relaxation exponentially delays the onset of quantum diffusion

Predicting the exact many-body quantum dynamics of polarons in materials with strong carrier–phonon interactions presents a fundamental challenge, often necessitating one to adopt approximations that sacrifice the ability to predict the transition from nonequilibrium relaxation to thermodynamic equilibrium. Here, we exploit a recent breakthrough that generalizes the concept of memory beyond its conventional temporal meaning to also encompass space. Specifically, we leverage our finding that the dynamics of observables in systems with local couplings satisfy Green’s functions with kernels that are local in time and space. This enables us to employ the dynamics of small lattices over short times to predict the dynamics of thermodynamically large lattices over arbitrarily long timescales while circumventing the deleterious impacts of finite-size effects. We thus interrogate the exact nonequilibrium formation and migration of polarons in one- (1D) and two-dimensional (2D) systems, revealing that their motion approaches diffusive transport only asymptotically in time and system size. We also compare transport in 1D and 2D systems to investigate the effect of dimension in polaron migration physics, illustrating how energy variations can cause localization—a phenomenon observable via current microscopy experiments.

Social dominance in rats is a determinant of susceptibility to stress

Establishing a dominance hierarchy in social organisms is important for access to resources. Stress has been proposed as a major factor influencing an animal’s likely position in a social hierarchy. Although individual differences in vulnerability to stress are increasingly recognized, how social hierarchy affects vulnerability remains relatively understudied. Here, we examined how the social dominance status of adult male Sprague-Dawley rats influences their response to stress in interactions with a familiar animal living in the same cage, and separately when confronting an unfamiliar rat of uncertain dominance status from another cage, using the tube test. Having determined the relatively stable within-cage social dominance status of animals, half were subjected to a single episode of 2-h immobilization stress. Cagemates, both control and stressed rats, again faced one another 1 d and 10 d after stress. First, the predetermined hierarchical rank among familiar cagemates was relatively unaffected by stress. However, second, the same stress had a differential impact in competitions between unfamiliar rats. Socially dominant control rats continued to win competitions but subordinate control rats, that had previously lost, sometimes started to win against previously dominant rats that had been stressed. Strikingly, subordinate stressed rats displayed consistent submissive-like behavior and they alone showed differential effects on dendritic spine density in the amygdala. Thus, an individual’s social rank can influence its response to stress, an effect that is detectable in interactions with unfamiliar animals. These findings provide an additional dimension to animal models of stress used for exploring facets of social anxiety and withdrawal in stress-related psychiatric disorders.

Correction to Supporting Information for Jensen et al., Bcl2L13 is a ceramide synthase inhibitor in glioblastoma

Blocking C-terminal processing of KRAS4b via a direct covalent attack on the CaaX-box cysteine

RAS is the most frequently mutated oncogene in cancer. RAS proteins show high sequence similarities in their G-domains but are significantly different in their C-terminal hypervariable regions (HVR). These regions interact with the cell membrane via lipid anchors that result from posttranslational modifications (PTM) of cysteine residues. KRAS4b is unique as it has only one cysteine that undergoes PTM, C185. Small molecule covalent modification of C185 would block any form of prenylation and subsequently inhibit attachment of KRAS4b to the cell membrane, blocking its biological activity. We translated this concept to the discovery and development of disulfide tethering screen hits into irreversible covalent modifiers of C185. These compounds inhibited proliferation of KRAS4b-driven mouse embryonic fibroblasts, but not cells driven by N-myristoylated KRAS4b that harbor a C185S mutation and are not dependent on C185 prenylation. Top–down proteomics was used to confirm target engagement in cells. These compounds bind in a pocket formed when the HVR folds back between helix 3 and 4 in the G-domain (HVR-α3-α4). This interaction can happen in the absence of small molecules as predicted by molecular dynamics simulations and is stabilized in the presence of C185 binders as confirmed by small-angle X-ray scattering and solution NMR. NOESY-HSQC, an NMR approach that measures internuclear distances of 6 Å or less, and structure analysis identified the critical residues and interactions that define the HVR-α3-α4 pocket. Further development of compounds that bind to this pocket could be the basis of a new approach to targeting KRAS cancers.

The developmental factor TBX3 engages with the Wnt/β-catenin transcriptional complex in colorectal cancer to regulate metastasis genes

Wnt signaling orchestrates gene expression in a plethora of processes during development and adult cell homeostasis via the action of nuclear β-catenin. Yet, little is known about how β-catenin generates context-specific transcriptional outcomes. Understanding this will reveal how aberrant Wnt/β-catenin signaling causes neoplasia specifically of the colorectal epithelium. We have previously identified the transcription factor TBX3 as a tissue-specific component of the Wnt/β-catenin nuclear complex during mouse forelimb development. In this study, we show that TBX3 is functionally active in human colorectal cancer (CRC). Here, genome-wide binding and transcriptomics analyses reveal that TBX3 regulates cancer metastasis genes in cooperation with Wnt/β-catenin. Proteomics proximity labeling performed across Wnt pathway activation shows that TBX3 engages with several transcription factors and chromatin remodeling complexes found at Wnt responsive elements (WRE). Protein sequence and structure analysis of TBX3 revealed short motifs, including an exposed Asn-Pro-Phe (NPF), that mediate these interactions. Deletion of these motifs abrogates TBX3’s proximity to its protein partners and its ability to enhance the Wnt-dependent transcription. TBX3 emerges as a key modulator of the oncogenic activity of Wnt/β-catenin in CRC, and its mechanism of action exposes protein-interaction surfaces as putative druggable targets.

Thioredoxin-1 inhibits NLRP3-mediated pyroptosis by regulating TXNIP in models of Alzheimer’s disease

Derivational morphology reveals analogical generalization in large language models

What mechanisms underlie linguistic generalization in large language models (LLMs)? This question has attracted considerable attention, with most studies analyzing the extent to which the language skills of LLMs resemble rules. As of yet, it is not known whether linguistic generalization in LLMs could equally well be explained as the result of analogy. A key shortcoming of prior research is its focus on regular linguistic phenomena, for which rule-based and analogical approaches make the same predictions. Here, we instead examine derivational morphology, specifically English adjective nominalization, which displays notable variability. We introduce a method for investigating linguistic generalization in LLMs: Focusing on GPT-J, we fit cognitive models that instantiate rule-based and analogical learning to the LLM training data and compare their predictions on a set of nonce adjectives with those of the LLM, allowing us to draw direct conclusions regarding underlying mechanisms. As expected, rule-based and analogical models explain the predictions of GPT-J equally well for adjectives with regular nominalization patterns. However, for adjectives with variable nominalization patterns, the analogical model provides a much better match. Furthermore, GPT-J’s behavior is sensitive to the individual word frequencies, even for regular forms, a behavior that is consistent with an analogical account but not a rule-based one. These findings refute the hypothesis that GPT-J’s linguistic generalization on adjective nominalization involves rules, suggesting analogy as the underlying mechanism. Overall, our study suggests that analogical processes play a bigger role in the linguistic generalization of LLMs than previously thought.

Development and validation of a risk model for effective immune and stromal related signature predicting prognosis of patients with ovarian cancer

Durably reducing partisan animosity through multiple scalable treatments

Recent research has identified several effective strategies for reducing Americans’ animosity toward supporters of opposing political parties. However, whether these strategies can durably reduce partisan animosity in a scalable manner and in everyday life remains unclear. We bridge the gap between prior research and useful application by assessing whether exposure to multiple, scalable treatments that portray inparty and outparty members interacting positively, receiving accurate information about one another’s views, and learning about cross-party similarities can a) durably shift partisans’ sentiments and b) influence partisans’ sentiments toward specific, personally known others encountered in everyday life—not only general, hypothetical, or one-off rival partisans. In a longitudinal survey experiment, we find that exposure to three brief, scalable treatments over a week reduces partisan animosity, with effects persisting for at least a month. Moreover, the treatments durably ameliorate animosity toward both general outparty members and a personally known outparty member, specified prior to the treatments. These findings suggest promising avenues for redressing social divisions in real-world contexts.

Innovative fast and low-cost method for the detection of living bacteria based on trajectory

Abstract Detection of pathogens is a major concern in many fields like medicine, pharmaceuticals, or agri-food. Most conventional detection methods require skilled staff and specific laboratory equipment for sample collection and analysis or are specific to a given pathogen. Thus, they cannot be easily integrated into a portable device. In addition, the time-to-response, including the sample collection, possible transport to the measurement equipment, and analysis, is often quite long, making real-time screening of a large number of samples impossible. This paper presents a new approach that better fulfills industry needs in terms of integrated real-time wide screening of a large number of samples. It combines optical imaging, object detection and tracking, and machine-learning-based classification. Three of the most common bacteria are selected for this study. For all of them, living bacteria are distinguished from inert and inorganic objects (1 μm latex beads) based on their trajectory, with a high degree of confidence. Discrimination between living and dead bacteria of the same species is also achieved. Finally, the method successfully detects abnormal concentrations of a given bacterium compared to a standard baseline solution. Although there is still room for improvement, these results provide a proof of concept for this technology, which has strong application potential in infection spread prevention.

Unbiased mechanical cloaks

The distinction between “reinforcement” and “cloaking” has been overlooked in optimization-based design of devices intended to conceal a defect in an elastic medium. In the former, a so-called “cloak” is severely biased toward one or a few specific elastic disturbances, whereas in the latter, an “unbiased cloak” is effective under any elastic disturbance. We propose a two-stage approach for optimization-based design of elastostatic cloaks that targets true, unbiased cloaks. First, we perform load-case optimization to find a finite set of worst-case design loads. Then we perform topology optimization of the cloak microstructure under these worst-case loads using a judicious choice of the objective function, formulated in terms of energy mismatch. Although a small subset of the infinite load cases that the cloak must handle, these highly nonintuitive, worst-case loads lead to designs that approach perfect and unbiased elastostatic cloaking. In demonstration, we consider elastic media composed of spinodal architected materials, which provides an ideal testbed for exploring elastostatic cloaks in media with varying anisotropy and porosity, without sacrificing manufacturability. To numerically verify the universal nature of our cloaks, we compare the elastic response of the medium containing the cloaked defect to that of the undisturbed medium under many random load cases not considered during design. By using digital light processing additive manufacturing to realize the elastic media containing cloaked defects and analyzing their response experimentally using compression testing with digital image correlation, this study provides a physical demonstration of elastostatic cloaking of a three-dimensional defect in a three-dimensional medium.

Microscopic anthropogenic waste ingestion by small terrestrial European passerines: evidence from finch and tit families

Abstract Microscopic anthropogenic waste (MAW) has become a major environmental concern worldwide. Our study aimed to assess the accumulation of MAW in the gastrointestinal tracts of nine common European passerine species from finch (Fringillidae) and tit (Paridae) families, and evaluate their suitability for environmental monitoring. We searched for MAW in the birds’ stomachs and intestines and identified suspected particles using Raman microspectroscopy. In total, we found 57 MAW particles in 31 out of 149 analyzed individuals, 7 of which were microplastics (polyethylene, polyethylene terephthalate, polystyrene), 1 was identified as carbon nanotube, while 49 were cellulosic-based (cotton, cellulose, rayon, viscose). The generalized linear mixed models identified bird family and time in season as significant predictors of MAW ingestion. Finches ingested more MAW than tits, and higher ingestion rates were observed during the non-breeding period. Other predictors, including bird sex, age, gastrointestinal tract section, and site, showed varying but non-significant effects. As predicted, the studied species exhibited a lower ingestion rate of MAW compared to terrestrial birds studied so far, possibly due to their diet and feeding behavior. Given that these species are prey for many avian and non-avian predators, they may contribute to the transfer of MAW to higher trophic levels.

Acute chromatin decompaction stiffens the nucleus as revealed by nanopillar-induced nuclear deformation in cells

Chromatin architecture is critical in determining nuclear mechanics. Most studies focus on the mechanical rigidity conferred by chromatin condensation from densely packed heterochromatin, but less is known on how transient chromatin decompaction impinge on nucleus stiffness. Here, we used an array of vertically aligned nanopillars to study nuclear deformability in situ after chromatin decompaction in cells. The nucleus significantly stiffened within 4 h of chromatin decompaction but softened at longer timescales. This acute stiffening of the nucleus was underpinned predominantly by an increase in nucleus volume and nuclear import, and partially by enhanced lamin protein recruitment to the periphery. The coupling between nucleus stiffening and acute chromatin decompaction was observed in low malignancy cancer cell lines (e.g. MCF7, PEO1, A549) but weakened in highly malignant counterparts (e.g. MDA-MB-231, HEYA8, HT1080) due to the capacity to efficiently compact heterochromatin into foci that sustains nucleus deformability required for confined migration. Our work signals how rapid chromatin remodeling is a physiologically relevant pathway to modulate nucleus mechanics and cell migration behavior.

DRP2 promotes EMT and serves as a potential therapeutic target for LUAD treatment

Directional water navigation and reallocation in <i>Tillandsia capitata</i>

Liquid manipulation is ubiquitous in nature and engineering, enabling controllable and efficient liquid delivery. Conventional understanding of liquid manipulation relies on inhomogeneous chemical modifications or single-scale structure design. Here, we present how water is directionally navigated and spontaneously reallocated at high efficiency via the cross-scale topology on Tillandsia capitata leaves. These leaves feature transversely curved lanceolate macrostructures decorated by a layer of microtrichomes with varied morphologies. The macrostructure creates a lanceolate effect in the transport direction for fundamental navigation. At the same time, the microtrichomes serve dual functions: constructing a self-wetting superhydrophilic surface to facilitate the water transport speed and implementing water spreading in the opposite direction for autonomous reallocation. We explain the multiscale transport behavior through theoretic analysis and finite element simulations. Our findings demonstrate how cross-scale topographies jointly function in efficient autonomous fluid manipulation, with potential applications such as droplet driving, fog harvesting, and seawater desalination, offering pathways for improving liquid processing efficiency and reducing energy consumption.