Browse Articles

Collective bacterial condensation is fundamentally constrained by the emergence of active turbulence

Collective bacterial condensation arises from positive feedback between the ability of bacteria to generate chemical gradients in their environment and their chemotactic ability to follow those gradients. This feedback drives the spontaneous formation of local cell accumulations, characterized by sharp cell-density gradients, even in the absence of physical boundaries. By following the dynamics of bacterial condensation in uniform acidic environments, we show that condensation is critically constrained by the spontaneous emergence of correlated bacterial swimming and the associated active turbulence. These collective behaviors generate vortex-like cell motion with a pronounced radial component directed down the cell-density gradient. This, in turn, induces local fluid motion that broadens the condensate and expels nonchemotactic bacteria. When condensates are strongly confined in thin layers, the radial component of fluid motion diminishes and condensation is enhanced. Moreover, in porous environments, correlated bacterial motion is strongly suppressed, allowing spontaneous condensation to progress even further until it reaches the limits imposed by the nonlocal nature of bacterial chemotaxis. Overall, these findings highlight the fundamental interplay between self-generated bacterial condensation and correlated swimming.

Explainable VGG16 transfer learning with SHAP and grad-CAM for wax moth pest and infestation detection in honeybee apiaries using imaging data

A cyanide-free route towards the electrosynthesis of nitriles

Sleep deprivation exhibits an age-dependent effect on infraslow global brain activity

Infraslow (<0.1 Hz) global brain activity, quantified by the global mean blood-oxygenation-level-dependent (gBOLD) signal in resting-state functional magnetic resonance imaging (fMRI), is elevated during sleep and coupled to cerebrospinal fluid (CSF) dynamics, a key pathway for the brain waste clearance implicated in neurodegenerative disorders such as Alzheimer’s disease. However, the effect of sleep deprivation on gBOLD activity and its interaction with aging remain poorly understood. Using a rigorously controlled in-laboratory total sleep deprivation (TSD) protocol, we demonstrate that TSD significantly increases both the gBOLD signal amplitude and its coupling with CSF flow, suggesting a compensatory mechanism that may enhance glymphatic clearance following acute sleep loss. Notably, these TSD-induced enhancements exhibit robust age dependency, with markedly attenuated responses in midlife adults (40 to 50 y). The absence of this compensatory mechanism in midlife may exacerbate age-related impairments in neurotoxic clearance and increase dementia susceptibility, thereby offering mechanistic insights into the nexus between sleep disruption, aging, and neurodegeneration.

Multi-ancestry genome-wide association study in all of Us for primary open-angle glaucoma

Abstract This study aims to identify new genetic loci associated with primary open-angle glaucoma (POAG) and explore shared genetic risk factors across African, European, and Admixed American/Latino populations. Genome-wide Association Study (GWAS) utilizing data from the All of Us Research Program. The study included 374,254 participants, with 4,305 individuals diagnosed with POAG and 369,949 controls. Participants were categorized by ancestry: European, African, and Admixed American/Latino. We used short-read sequencing data and applied strict quality control measures (MAF > 0.01, INFO > 0.8). GWAS were conducted for each ancestry group using a logistic mixed model, adjusting for age, sex, and the top 11 principal components. A fixed-effect meta-analysis combined the results across ancestries. Genome-wide significance was set at p  < 5 × 10 − 8 . The primary outcome measures were the identification of genetic loci associated with POAG, and the analysis of transcription factors linked to these loci in relevant tissues. In the European cohort, we identified four novel loci associated with POAG, linked to the TUT4 , RYK , MOXD1 , and UBAP2 genes, as well as the previously known TMCO1 locus. In the African cohort, we found five new loci, including TSPAN17 , SLC16A7 , LOC100506869 , LINC02388 , and LOC107984606 . For the Admixed American/Latino cohort, we identified GATA5 , FAM135B , and LINC00871 genes as novel loci. Our analysis identified three novel loci in individuals of European ancestry, mapped to the genes TUT4 , RYK , and MOXD1 . We identified 56 genome-wide significant variants, including six putative novel loci, and found that most ancestry-specific signals replicated in the cross-ancestry meta-analysis, with the exception of several attenuated associations in the smaller Admixed American/Latino cohort. These findings indicate that the genetic determinants contributing to POAG may differ across populations, underscoring the importance of accounting for population-specific genetic architectures in the study of complex traits. Given the substantial variation in POAG prevalence among ancestries, it is plausible that certain genetic variants exert ancestry-specific effects. Consequently, conducting ancestry-stratified GWAS is essential for elucidating these unique genetic contributions. 

Phosphoregulation of the novel hemi-arrestin MAPK scaffold Sms1 prevents untimely mating

Abstract Mitogen-activated protein kinases (MAPK) are ancestral kinases that form essential signalling cascades. However, scaffolds that recruit kinases to subcellular locations and promote signal transduction have only been described in a few species. Notably, no scaffold was thought necessary for the MAPK cascade promoting sexual differentiation in fission yeast. Here, we identify the hemi-arrestin protein Sms1 as a novel scaffold of this MAPK cascade. Interactions with PIP2 and the pheromone receptor–coupled Gα subunit target Sms1 to plasma membrane patches, where it assembles the active cascade by binding each MAP kinase. These interactions are essential for signal transduction and local signal interpretation for polarised growth. Phosphorylation, including by the MAPK itself, antagonises Sms1 membrane translocation, establishing a negative feedback that underlies polarity patch turnover and prevents untimely mating attempts. Thus, Sms1 is a MAPK scaffold with canonical functions despite its distinct structural fold, highlighting convergent evolution of MAPK scaffolds across eukaryotes.

Electron localization in noncompact covalent bonds captured by the r ² SCAN+ <i>V</i> approach

In density functional theory, the SCAN (Strongly Constrained and Appropriately Normed) and r 2 SCAN (regularized–restored SCAN) functionals significantly improve over GGA (Generalized Gradient Approximation) functionals such as PBE (Perdew–Burke–Ernzerhof) in predicting electronic, magnetic, and structural properties across various materials, including transition-metal compounds. However, there remain puzzling cases where SCAN/r 2 SCAN underperform, such as in calculating the band structure of graphene, the magnetic moment of Fe, the potential energy curve of the Cr 2 molecule, and the bond length of VO 2 . This research identifies a common characteristic among these challenging materials: noncompact covalent bonding through s-s , p-p , or d-d electron hybridization. While SCAN/r 2 SCAN excel at capturing electron localization at local atomic sites, they struggle to accurately describe electron localization in noncompact covalent bonds, resulting in a biased improvement. To address this issue, we propose the r 2 SCAN+ V approach as a practical modification that improves accuracy across all the tested materials. The parameter V is 4 eV for metallic Fe, but substantially lower for the other cases. Our findings provide valuable insights for the future development of advanced functionals.

Projecting groundwater flood risk in a lowland karst system under future climates

Hygroscopicity-driven spontaneous sustainable direct lithium extraction

The quasi-liquid layer thickness controls clathrate hydrates’ growth rate

Clathrate hydrates are fascinating materials that offer many attractive benefits for carbon sequestration, water desalination, intermittent natural gas storage, chemical separations, and other applications. However, their slow growth kinetics prevents the cost-effective realization of hydrate-based technologies. To overcome this challenge, chemical additives have been identified to control hydrates’ growth rate. Among others, the surfactant sodium dodecyl sulfate (SDS) and the amino acid L-tryptophan (TRP) are both effective at low concentrations. While SDS is widely available but raises environmental concerns, TRP is environmentally benign. Although both SDS and TRP are interfacially active, the molecular mechanism responsible for their ability to enhance hydrate growth is not known, nor is the reason why these compounds are effective at low concentrations. It is demonstrated here that both SDS and TRP, when adsorbed, affect the thickness of the quasi-liquid layer (QLL) at the hydrate–water interface, which, in turn, promotes the adsorption of CO 2 from the liquid phase to the growing hydrate. The QLL amplifies the effect to mesoscopic length scales, explaining why small amounts of these surface-active compounds enhance hydrate growth rate.

Optimization of diffractive optical elements for automotive adaptive front-lighting systems: compliance with ECE-R123

Endothelial C-type natriuretic peptide/guanylyl cyclase-B signaling prevents pulmonary arterial hypertension

Abstract C-type natriuretic peptide (CNP) is released from endothelial cells and acts as an autocrine/paracrine mediator, regulating systemic blood pressure and vascular remodeling via guanylyl cyclase-B (GC-B) and natriuretic peptide receptor-C. We investigate the impact of vascular CNP/GC-B signaling on the development of pulmonary arterial hypertension (PAH). Mice developing pulmonary hypertension (PH) show reduced pulmonary NPPC and NPR2 expression than mice without PH. S imilarly, endothelial cells (EC) from patients with idiopathic PAH exhibit lower NPPC and NPR2 expression than control EC. EC-specific CNP or GC-B conditional knockout (CNP ecKO or GC-B ecKO) mice, but not smooth muscle cell-specific GC-B conditional knockout (GC-B smcKO) mice, show more severe PH and greater expression of Edn1, Il6, Ccl2 and Tgfb1 mRNAs than their genetic controls in PAH models. CNP suppresses hypoxia-induced increases in expression of these mRNAs and restored SMAD2/3-SMAD1/5/9 balance in cultured human pulmonary arterial EC. Moreover, CNP administration prevents PH in genetic control and GC-B-smcKO mice but not in GC-B ecKO mice. CNP administration also has therapeutic effects against Sugen5416-hypoxia PAH models as well as additive benefits with established therapies. Endothelial CNP/GC-B signaling thus exerts pivotal preventative effects against development of PH, suggesting the therapeutic potential of CNP for PAH.

Early colonization before inundation consistent with northern glacial refugia in Southern Doggerland revealed by sedimentary ancient DNA

Prior to the formation of the present-day North Sea during the mid-Holocene, North-Western Europe was connected through the Doggerland landmass. While it has been known for the past century that Doggerland was forested, it has not been clear when the onset of forestation occurred or whether the environment was more habitable for humans than surrounding European areas. In this study, we reconstruct the paleoecology of a river system, the Southern River, from the late Late Pleistocene to the late Holocene using sedimentary ancient DNA (sedaDNA) from 252 sediment samples from 41 cores spanning the length of the river system and headwater area. We identify secure and insecure sedaDNA signals by integrating sedimentological and sedaDNA data into a taphonomic model. Secure sedaDNA signals are found in silty and fine sand deposits where 95 to 98% originates from local deposition, but coarse sands and gravels are insecure with 60 to 70% of the sedaDNA associated with mixed ecosystem signals from reworked and influxed sediments. Secure sediments reveal the presence of several temperate tree genera such as Quercus , Ulmus, and Corylus over 16,000 y ago in the Late Pleniglacial, and thermal indicator genus Tilia several thousand years earlier than has been recorded for surrounding European areas. In this area, we also detect an anomalous signal of the genus Pterocarya , considered extinct in the region since the Hoxnian Stage (~400 ka). These observations are consistent with colonization from nearby northern glacial refugia, suggesting a favorable environment in which the cultural Mesolithic could develop.

Value of hyperspectral data for wall to wall wetland vegetation mapping in heterogeneous landscapes

Abstract Remote sensing is increasingly employed today for the creation of wall-to-wall vegetation maps of protected areas. The main objective of this study was to evaluate whether it is feasible to develop a remote sensing-based wall-to-wall vegetation map of wetlands that is useful for nature conservation purposes without hyperspectral data. The research was conducted in the Narew National Park in north-eastern Poland. In 2020, three types of airborne data covering an area of 325 km 2 were acquired: hyperspectral, Light Detection and Ranging data (LiDAR), and from visible and near infrared range (RGBN) imagery. At the same time, botanists collected 1,921 reference polygons for training and validating the machine learning model. Then, classifications were conducted using the CatBoost algorithm with four different scenarios created from the mentioned datasets. The results indicate that, based on hyperspectral and LiDAR data, it is possible to produce a wall-to-wall vegetation map with an overall accuracy of 0.82. When hyperspectral data are replaced by less expensive and widely accessible RGBN data, accuracy declines by 0.10; this reduction decreases to 0.09 if textural features derived from the RGBN data are additionally incorporated into the classification. In scenarios where only LiDAR data are available, vegetation classification accuracy is much lower, reaching 0.63. Comparison of the remote sensing maps with a vegetation map created through field mapping methods indicates that, irrespective of whether hyperspectral or only RGBN and LiDAR data are available, remote sensing maps contribute substantial new knowledge regarding wetland vegetation in spatially heterogeneous landscapes and are highly useful for their conservation management.

Low thermal inertia of carbonaceous asteroid Bennu driven by cracks observed in returned samples

The <i>Mycobacterium smegmatis bd</i> -II terminal oxidase employs a carboxylate shift mechanism

Cytochrome bd is a terminal oxidase expressed under low oxygen conditions and central for the survival of many pathogens. Here, we characterize the cyt bd -II from Mycobacterium smegmatis , a member of a hitherto uncharacterized evolutionary group (qOR-2) of bd oxidases, by combining biochemical studies with cryo-electron microscopy (cryo-EM), and multiscale simulations. Overexpressing the appCB operon in its native host led to production of a highly active bd -II ( k obs = 30 e − s −1 ) that together with a high-resolution (2.8 Å) cryo-EM structure and multiscale simulations reveal unique proton pathways and oxygen channels responsible for its function. We propose that a pH-dependent molecular switch, involving coordination changes of heme d and surrounding bulky residues regulate substrate access into the active site. Taken together, our findings provide detailed mechanistic insight of qOR-2 type bd oxidases, and a basis for understanding the evolution of the superfamily.

Ground control strategies for longwall top-coal caving panel in extra-thick coal seams with thick-hard roof

An intralayer microcircuit in the temporal association cortex underlies sensory-induced escape in mice

Abstract A central goal in neuroscience is to clarify how neural circuits translate sensory input into adaptive behaviours. Although unisensory evoked escape circuits in mice are well defined, it remains unclear whether a single nucleus contains specialized sensory, sensory‒motor decision, and motor command neurons for escapes driven by distinct sensory cues, and how these neurons form functional microcircuits. Using multiple sensory stimuli in mice, we identified the temporal association cortex (TeA) as a critical escape hub. Combining in vivo electrophysiology, optogenetics and chemogenetics, we characterized three distinct neuron subtypes within TeA layer 5 (L5) CaMKII neurons that correspond to these three functional classes. Intratelencephalic (IT) neurons serve as sensory‒motor decision neurons, while layer matched pyramidal tract (PT) neurons projecting to the dorsal periaqueductal grey (dPAG) act as motor command neurons. We reveal a laminar IT–PT microcircuit that converts sensory input into sensory-motor decisions and commands for escape locomotion.

Mechanistic insights into lenacapavir-induced off-pathway HIV-1 capsid assembly

The HIV-1 capsid is a fullerene cone composed of hexameric and pentameric capsid proteins (CA) that packages the viral genome and mediates nuclear entry. Lenacapavir (LEN), a potent molecular long-acting inhibitor developed by Gilead, disrupts capsid morphogenesis by binding a phenylalanine–glycine (FG) pocket at the interface between adjacent CA subunits. Interestingly, cellular polyanion inositol hexakisphosphate (IP6) promotes conical capsid assembly by coordinating the central pore, which is allosterically coupled to the FG pocket. Because LEN and IP6 engage overlapping structural elements, they can compete to influence the capsid assembly pathway and outcomes. Using coarse-grained molecular simulations, we show that LEN accelerates hexamer formation while suppressing pentamer incorporation, yielding malformed, multilayered, and incomplete capsids. Simulations incorporating a ribonucleoprotein model further reveal that LEN-treated capsids often fail to encapsulate RNA, indicating impaired maturation. Our calculations confirm that LEN impairs the formation of high-curvature CA lattice regions necessary for closure, supporting a model of off-pathway assembly as a mechanism of viral inhibition. These findings define the core mechanism by which a small-molecule inhibitor disrupts the much larger-scale HIV-1 morphogenesis and underscore general principles for targeting self-assembling multi-protein complexes.

Zeptosecond electron pulse train via multiphoton inelastic Cherenkov diffraction