Browse Articles

Ratio-based indicators for cytosolic Ca ²⁺ with visible light excitation

Calcium ions (Ca 2+ ) play central roles in cellular physiology. Fluorescent indicators for Ca 2+ ions revolutionized our ability to make rapid, accurate, and highly parallel measurement of Ca 2+ concentrations in living cells. The use of ratio-based imaging with one particular indicator, fura-2, allowed practitioners to correct for a number of experimental confounds, including dye bleaching, variations in sample thickness, and fluctuations in illumination intensity. Ratio-based imaging with fura-2 was the most accurate and reliable method for measuring Ca 2+ concentrations. Two drawbacks to fura-2 exist. First, it requires ultraviolet (UV) excitation, which is more toxic to living cells than visible light. Second, our ability to use fura-2 for accurate, stable, ratio-based determinations of Ca 2+ concentration in living cells is fast becoming a method of the past. This is due, in part, because modern microscopes are phasing out the use of mercury arc lamps that provide the UV excitation needed for fura-2 imaging. To address this problem, we describe the design, synthesis, and cellular application of benzo[ b ]phosphole-based fluorescent Ca 2+ indicators for ratio-based imaging of Ca 2+ in living cells that can be used with modern light emitting diode (LED)-equipped fluorescence microscopes. We report isoCaRed-1Me, a Ca 2+ indicator that enables ratio-based imaging in immortalized cell lines, primary mammalian hippocampal neurons, and human-induced pluripotent stem cell–derived cardiomyocytes. These data show that isoCaRed-1Me will be useful for ratio-based Ca 2+ imaging using modern microscopes.

Development and clinical validation of a novel platelet count-based nomogram for predicting microvascular invasion in HCC

Downscaling mutualistic networks from species to individuals reveals consistent interaction niches and roles within plant populations

Species-level networks emerge as the combination of interactions spanning multiple individuals, and their study has received considerable attention over the past 30 y. However, less is known about the structure of interaction configurations within species, even though individuals are the actual interacting units in nature. We compiled 46 empirical, individual-based, interaction networks on plant-animal seed dispersal mutualisms, comprising 1,037 plant individuals across 29 species from various regions. We compared the structure of individual-based networks to that of species-based networks and, by extending the niche concept to interaction assemblages, we explored individual plant specialization. Using a Bayesian framework to account for uncertainty derived from sampling, we examined how plant individuals “explore” the interaction niche of their populations. Both individual-based and species-based networks exhibited high variability in network properties, lacking remarkable structural and topological differences between them. Within populations, frugivores’ interaction allocation among plant individuals was highly heterogeneous, with one to three frugivore species dominating interactions. Regardless of species or bioregion, plant individuals displayed a variety of interaction profiles across populations, with a consistently-small percentage of individuals playing a central role and exhibiting high diversity in their interaction assemblage. Plant populations showed variable mid to low levels of niche specialization; and individuals’ interaction niche “breadth” accounted for 70% of the population interaction diversity, on average. Our results highlight how downscaling from species to individual-based networks helps understanding the structuring of interactions within ecological communities and provide an empirical basis for the extension of niche theory to complex mutualistic networks.

Spatiotemporal dynamics of suspended sediment in coastal Mekong Delta: a hydrodynamic modelling approach under tropical monsoon climate

Abstract Suspended sediment concentration (SSC) plays a pivotal role in shaping coastal dynamics, impacting terrestrial and marine ecosystems. This study employed the hydrodynamic model MIKE21 to simulate hydrological runoff and sediment transport within the Mekong River’s fluvial-marine continuum, the longest river in Southeast Asia currently challenged with escalating anthropogenic pressures and sea-level rise. By strategically selecting hourly observed data from various locations (river channel, coastal estuary) and periods (dry and rainy seasons) for model calibration and validation, we demonstrated the robust performance of the model simulation of both water levels (RMSE: 0.343 m) and SSC (RMSE: 0.006 kg.m−3). Spatiotemporal analysis of 2019–2023 revealed the pronounced sensitivity of water level, velocity, and flow direction under tropical monsoon regime. SSC time series decomposition further extracted seasonal amplitudes, while spatial patterns showed distinctly the lowest concentrations occurring in April and the highest in September annually. Furthermore, SSC upward trends were observed during low-flow periods, while downward trends predominated during high-flow periods. Our quantitative analysis offers a comprehensive understanding of hydrological processes within tropical monsoon coastal regions. These findings support the establishment of long-term monitoring frameworks to inform nature-based strategies for sustainable coastal development.

Clear cell renal carcinoma essentially requires CDKL3 for oncogenesis

Clear cell renal cell carcinoma (ccRCC) is the predominant human renal cancer with surging incidence and fatality lately. Hyperactivation of hypoxia-inducible factor (HIF) and mammalian target of rapamycin (mTOR) signaling are the common signatures in ccRCC. Herein, we employed spontaneous ccRCC model to demonstrate the indispensability of an underappreciated Ser/Thr kinase, CDKL3, in the initiation and progression of ccRCC. Ablation of CDKL3 does not affect normal kidney, but abrogates Akt-mTOR hyperactivity and thoroughly prevents the formation and growth of the HIF-agitated ccRCC in vivo. Remarkable clinical correlations also supported the oncogenic role of CDKL3. Mechanism-wise, cytosolic CDKL3 unexpectedly behaves as the adaptor to physically potentiate mTORC2-dependent Akt activation without functioning through kinase activity. And mTORC2 can phosphorylate and stabilize CDKL3 to form a positive feedback loop to sustain the cancer-favored Akt-mTOR overactivation. Together, we revealed the pathological importance and molecular mechanism of CDKL3-mediated Akt-mTOR axis in ccRCC initiation and progression.

Lactobacillus lysates protect oral epithelial cells from pathogen-associated damage, increase secretion of pro-inflammatory cytokines and enhance barrier integrity

Abstract Periodontitis is a chronic gum disease characterised by inflammation and the loss of bone. We have explored the potential prophylactic effects of lysates from four Lactobacillus strains against the toxic effects of three periodontal pathogens (Porphyromonas gingivalis, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans). TR146 oral epithelial cells were pre-treated with Lactobacillus lysates (L. rhamnosus - GG, L. rhamnosus - SD11, L. reuteri and L. plantarum) and then challenged with pathogenic material (live cells, lysates, or supernatants). Cytokine analysis was performed on supernatants of cells treated with probiotic lysates from 1.5 h to 24 h. Effects of probiotic lysates on re-epithelialisation were determined using keratinocyte scratch assays, monitoring both migration and proliferation. Epithelial barrier function was observed after lysate addition by trans-epithelial electrical resistance (TEER) and by quantifying claudin-1 expression. Treatment of host cells with Lactobacillus lysates before pathogen exposure conferred significant protection against viability loss. Although extended pre-treatment did not generally increase protection, against live Aggregatibacter actinomycetemcomitans, significant increases in viability were seen after 24 h of pre-treatment for GG, SD11 and L. plantarum. Pro-inflammatory cytokines TNF-α, IP-10, IL-6, and IL-8 increased significantly with extended probiotic treatment, while IL-1β and IL-1α secretion significantly increased but remained constant over time. Secretion of the growth-promoting cytokine TGF-β increased after 3 h of treatment, however no increases in the regulatory cytokine IL-10 were recorded. Only exposure to SD11 significantly enhanced re-epithelialisation, TEER and claudin-1 expression while GG increased TEER but decreased claudin-1 expression. L. plantarum significantly inhibited re-epithelialisation but did not impact TEER or claudin-1 expression. All lysates significantly improved TEER in the presence of pathogenic material, demonstrating a protective effect on barrier function.

Structural basis of disease mutation and substrate recognition by the human SLC2A9 transporter

Urate provides ~50% of the reducing potential in human and primate plasma which is key to detoxifying reactive oxygen by-products of cellular metabolism. Urate is the endpoint of purine metabolism in primates, and its concentration in plasma is a balance between excretion from kidney and intestine, and subsequent reabsorption in and through cells of kidney proximal tubules to maintain a regulated concentration in plasma. SLC2A9 is the primary transporter that returns urate from the basolateral side of kidney tubule cells back to plasma. A shorter splice variant of SLC2A9 is directed to the apical surface where several transporters recapture urate from the tubule back into cells. Too high a concentration in plasma causes hyperuricemia, is linked to gout, and favors kidney stone formation. To understand the molecular basis of uric acid transport and the role of disease-causing mutations in SLC2A9, we determined structures of human SLC2A9 in its apo form, and its urate-bound form by cryo-EM, at resolution of 3.3 Å and 4.1 Å respectively. Both structures are captured in an inward open conformation. Using the inward-facing structure as a template we modeled the outward-facing conformation to understand the alternating access mechanism. Alternative salt bridge pairs on the cytoplasmic side suggest a mechanism that can balance the energetics of the inward open and outward open states. The location of disease-causing mutants suggests their role in impacting function. Our structures elucidate the molecular basis for urate selectivity and transport and provide a platform for future structure-based drug discovery aimed at reducing plasma urate levels in diseases of hyperuricemia and gout.

Real-time update algorithms for digital twin models of distribution network equipment under internet of things and optical imaging technology

Mapping of the full polarization switching pathways for HfO ₂ and its implications

The discovery of ferroelectric phases in HfO 2 offers insights into ferroelectricity. Its unique fluorite structure and complex polarization switching pathways exhibit distinct characteristics, challenging conventional analysis methods. Combining group theory and first-principles calculations, we identify numerous unconventional electric polarization switching pathways in HfO 2 with energy barriers of 0.32 to 0.57 eV as a function of the different shift in the suboxygen lattices. In total, we identify 47 switching pathways for the orthorhombic phase, corresponding to the left cosets of the F m 3 ¯ m group with P c a 2 1 group. Contrary to the conception that the tetracoordinated oxygen (O IV ) layers are inactive, our result demonstrates that both the tricoordinated oxygen (O III ) and O IV can be displaced, leading to polarization switching along any axial direction. The multiple switching pathways in HfO 2 result in both 180° polarization reversal and the formation of 90° domains observed experimentally. Calculations show that specific switching pathways depend on the orientation of the applied electric field relative to the HfO 2 growth surface. This allows HfO 2 to automatically adjust the in-plane polarization direction under an out-of-plane electric field, thereby maximizing the out-of-plane component and contributing to the wake-up process. These findings redefine the roles of O III and O IV layers, clarify unconventional switching pathways, and enhance our understanding of electric field response mechanisms, wake-up, and fatigue in ferroelectrics.

Enhancing solar power efficiency with hybrid GEP ANFIS MPPT under dynamic weather conditions

Engineered immunological niche directs therapeutic development in models of progressive multiple sclerosis

Primary progressive multiple sclerosis (MS) is a demyelinating autoimmune disease with only a single class of FDA-approved treatment, B cell depletion. Novel treatments could emerge from a deeper understanding of the interplay between multiple cell types within diseased tissue throughout progression. We initially describe an engineered biomaterial–based immunological niche (IN) as a surrogate for diseased tissue to investigate immune cell function and phenotype dynamics throughout a chronic progressive mouse model of MS. Using these niches, we identify an array of dysregulated CC chemokine signaling as potential targets. We then develop antigen-loaded nanoparticles that reduce CC chemokine signaling, while delivering antigen. These nanoparticles serve as an antigen-specific treatment, and a single injection reduces disease burden, even if administered after symptomatic disease onset. This report demonstrates proof of principle of a biomaterial scaffold as a diseased tissue surrogate that can monitor immune function, identify potential drug targets, and guide the development of a therapeutic.

Survival and data-driven phenotypes in head and neck cancer

Peer income exposure across the income distribution

Children from families across the income distribution attend public schools, making schools and classrooms potential sites for interaction between more- and less-affluent children. However, limited information exists regarding the extent of economic integration in these contexts. We merge educational administrative data from Oregon with measures of family income derived from IRS records to document student exposure to economically diverse school and classroom peers. Our findings indicate that affluent children in public schools are relatively isolated from their less affluent peers, while low- and middle-income students experience relatively even peer income distributions. Students from families in the top percentile of the income distribution attend schools where 20 percent of their peers, on average, come from the top five income percentiles. A large majority of the differences in peer exposure that we observe arise from the sorting of students across schools; sorting across classrooms within schools plays a substantially smaller role.

Investigating the failure mechanisms of cascade landslide dams under overtopping conditions: an experimental approach

Mycorrhiza increases plant diversity and soil carbon storage in grasslands

Experimental studies have shown that symbiotic relationships between arbuscular mycorrhizal (AM) fungi and host plants can regulate soil organic carbon (SOC) storage. Although the impacts of mycorrhiza are highly context-dependent, it remains unclear how these effects vary across broad spatial scales. Based on data from 2296 field sites across grassland ecosystems of China, here we show that mycorrhizal fungi symbiosis enhances SOC storage in the topsoil and subsoil through increasing plant diversity and elevating biomass allocation to belowground. SOC storage is significantly higher in both the topsoil and subsoil in systems dominated by obligate mycorrhizal (OM) and facultative mycorrhizal (FM) plants than those dominated by nonmycorrhizal (NM) plants. Also, the relative abundance of OM plants increases at the expense of FM plants as temperature and precipitation increase. These findings provide valuable insights into the potential mechanisms by which mycorrhizal fungi may influence grassland plant diversity and SOC storage in the context of global change.

Research on the positioning of buried polyethylene pipelines considering the acoustic attenuation characteristics

Persistence selection between simulated biogeochemical cycle variants for their distinct effects on the Earth system

The average long-term impact of Darwinian evolution on Earth’s habitability remains extremely uncertain. Recent attempts to reconcile this uncertainty by “Darwinizing” nonreplicating biogeochemical processes subject to persistence-based selection conform with the historicity of the geochemical record but lack mechanistic clarity. Here, we present a theoretical framework showing how: 1) A biogeochemical “cycle-biota-variant” (CBV) can be defined non-arbitrarily as one biologically facilitated pathway for net recycling of an essential element, plus the genotypes driving the relevant interconversion reactions. 2) Distinct CBVs can be individuated if they have climatic or geochemical side effects that feed-back on relative persistence. 3) The separation of spatial/temporal scales between the dynamics of such effects and those of conventional Darwinian evolution can introduce a degree of randomness into the relationship between CBVs and their Earth system impact properties, loosely analogous to that between the biochemical causes and evolutionary effects of genetic mutation. 4) Threshold behavior in climate feedback can accentuate biotic impacts and lead to CBV-level “competitive exclusion”. 5) CBV-level persistence selection is observationally distinguishable from genotype-level selection by strong covariance between “internal” CBV properties (genotypes and reactions) and “external” climatic effects, which we argue is analogous to the covariance between fitness and traits under conventional Darwinian selection. These factors cannot circumvent the basic fact that local natural selection will often favor phenotypes that ultimately destabilize large-scale geochemical/climatic properties. However, we claim that our results nevertheless demonstrate the theoretical coherence of persistence-selection between non-replicating life–environment interaction patterns and therefore have broad biogeochemical applicability.

Myocardial metabolic flexibility following ketone infusion demonstrated by hyperpolarized [2-13C]pyruvate MRS in pigs

Substance P receptor signaling contributes to host maladaptive responses during enteric bacterial infection

Immune responses in the intestine are intricately balanced to prevent pathogen entry without inducing immunopathology. The nervous system is well established to interface with the immune system to fine-tune immunity in various organ systems including the gastrointestinal tract. Specialized sensory neurons can detect bacteria, bacterial products, and the resulting inflammation, to coordinate the immune response in the gastrointestinal tract. These sensory neurons release peptide neurotransmitters such as Substance P (SP), to induce both neuronal signaling and localized responses in nonneuronal cells. With this in mind, we assessed the immunoregulatory roles of SP receptor signaling during enteric bacterial infection with the noninvasive pathogen Citrobacter rodentium . Pharmacological antagonism of the SP receptor significantly reduced bacterial burden and prevented colonic crypt hyperplasia. Mice with SP receptor signaling blockade had significantly reduced inflammation and recruitment of T cells in the colon. Reduced colonic T cell recruitment is due to reduced expression of adhesion molecules on colonic endothelial cells in SP receptor antagonist-treated mice. Using SP receptor T cell conditional knockout mice, we further confirmed SP receptor signaling enhanced select aspects of T cell responses. Our data demonstrate that SP receptor signaling can significantly reduce inflammation and prevent host-maladaptive responses without impinging upon host protection.

Measuring social mobility in temporal networks

Abstract In complex networks, the “rich-get-richer” effect (nodes with high degree at one point in time gain more degree in their future) is commonly observed. In practice this is often studied on a static network snapshot, for example, a preferential attachment model assumed to explain the more highly connected nodes or a rich-club effect that analyses the most highly connected nodes. In this paper, we consider temporal measures of how success (measured here as node degree) propagates across time. By analogy with social mobility (a measure of people moving within a social hierarchy through their life) we define hierarchical mobility to measure how a node’s propensity to gain degree changes over time. We introduce an associated taxonomy of temporal correlation statistics including mobility, philanthropy and community. Mobility measures the extent to which a node’s degree gain in one time period predicts its degree gain in the next. Philanthropy and community measure similar properties related to node neighbourhood. We apply these statistics both to artificial models and to 26 real temporal networks. We find that most of our networks show a tendency for individual nodes and their neighbourhoods to remain in similar hierarchical positions over time, while most networks show low correlative effects between individuals and their neighbourhoods. Moreover, we show that the mobility taxonomy can discriminate between networks from different fields. We also generate artificial network models to gain intuition about the behaviour and expected range of the statistics. The artificial models show that the opposite of the “rich-get-richer” effect requires the existence of inequality of degree in a network. Overall, we show that measuring the hierarchical mobility of a temporal network is an invaluable resource for discovering its underlying structural dynamics.