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At least 739 records · Page 41Linked to original sources

Ligand stabilization enables physiological GITR signaling and antitumor immunity

Agonistic antibodies targeting the costimulatory receptor GITR have failed in clinical trials despite a strong preclinical rationale, revealing fundamental limitations of receptor-targeted approaches to TNF superfamily agonism. Here, we demonstrate that pharmacological stabilization of the trimeric structure of human GITRL represents a mechanistically distinct strategy to overcome these limitations. Small-molecule stabilization of GITRL preserves its membrane residency. It enables bidirectional signaling between antigen-presenting cells and T cells, a physiological context that receptor-targeted antibodies bypass through non-physiological clustering of GITR. In humanized GITR/GITRL double-knock-in mice bearing syngeneic tumors, GITRL stabilization expands cytotoxic CD8 T cells, selectively depletes intratumoral regulatory T cells, activates APCs, and restructures the immune spatial architecture. In patient-derived tumor explants, GITRL stabilization reactivates suppressed CD8 T cells in an APC-dependent manner. Our findings establish ligand stabilization as a mechanistically distinct therapeutic strategy and provide a framework for engaging TNF receptor superfamily costimulatory pathways by modulating their native ligands.

cancer biology↗

Common nitrification inhibitors exhibit varied physiological mechanisms on an ammonia-oxidizing microorganism

Microbial ammonia oxidation, the first and rate-limiting step of nitrification, plays a central role in soil nitrogen cycling. It is most relevant in agricultural soils as nitrifiers compete with crops for ammonia-based fertilizers. Therefore, synthetic nitrification inhibitors are widely used alongside fertilizers to reduce the activities of dominant drivers of this process, i.e. ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the physiological responses of ammonia oxidizers remain poorly resolved. Here the response of the AOA Nitrososphaera viennensis to the nitrification inhibitors 3,4-dimethylpyrazole phosphate (DMPP) and allylthiourea (ATU) were investigated using a combination of functional genomics, physiological assays, and relief experiments. The results overturn earlier assumptions that DMPP and ATU act by chelating free copper. Both compounds affected ammonia oxidation and triggered broader shifts in energy metabolism and stress-response pathways, which diverged markedly between the two inhibitors. We propose a competitive inhibition of the ammonia monooxygenase complex with DMPP as it can be alleviated by additional ammonia and elicits activation of urea acquisition, while ATU acted as a non-competitive inhibitor generally inducing quiescence. Both modes of inhibition were associated with clear transcriptomic and proteomic signals that will be advantageous for the identification of mechanisms of other nitrification inhibitors in the future. Key word: Ammonia-oxidizing archaea, nitrification, nitrification inhibitors, archaea, nitrogen cycle

microbiology↗

Beyond ex vivo and in vivo CAR T: antigen-driven CAR T (adCAR-T) expansion method enables rapid, physiological CAR T cells programming.

Chimeric antigen receptor (CAR) T-cell therapy has demonstrated transformative efficacy in hematologic malignancies, but its broader use remains constrained by complex ex vivo manufacturing, prolonged production timelines, high cost, and dependence on lymphodepleting chemotherapy. Emerging in vivo CAR-T generation strategies aim to address these limitations, but they introduce additional safety concerns associated with systemic delivery of gene-modifying vectors, including off-target transduction and insertional mutagenesis. This paper describes a novel antigen-driven CAR T-cell expansion platform (adCAR-T) based on co-culture of CAR T cells with engineered target cells expressing defined antigen density and lacking the inhibitory checkpoint ligand PD-L1. This system induces immediate activation, rapid proliferation, and sustained cytotoxic differentiation of CAR T cells without reliance on artificial CD3/CD28 bead stimulation or exogenous cytokine-driven expansion. In contrast to conventional methods, the platform eliminates the lag phase of CAR T-cell expansion and enables rapid scaling to clinically relevant doses (108-109 cells) within several days, depending on the initial cell input. Mechanistically, antigen-driven CAR engagement and target-cell lysis trigger cytokine release and amplification of CAR T cells in a physiologically relevant manner. This process promotes coordinated expansion of both directly antigen-engaged and non-engaged CAR T cells. The platform preserves "functional fitness", minimizes exhaustion, and avoids systemic exposure to gene-delivery vectors. Taken together, this strategy defines a hybrid manufacturing paradigm that bridges the control of ex vivo production with the physiological logic of in vivo activation. Proposed method has a potential to reduce manufacturing complexity, improve safety, and possibly decrease or eliminate the need for lymphodepleting conditioning. This work presents a potential alternative to both standard ex vivo manufacturing and emerging in vivo CAR-T generation approaches, with important implications for improving the accessibility, safety, and cost-effectiveness of CAR T-cell therapies.

immunology↗

Physiological trade-offs drive the archaeal dominance and carbon turnover in deep subsurface

Marine sediments host a vast deep biosphere, yet how microorganisms persist under severe energy limitation and govern long-term organic carbon (OC) preservation remains poorly understood. Here we show that archaea, primarily Bathyarchaeia, systematically displace bacteria with depth and form net growth zones across East China Sea shelf deep sediments. Multi-omics analyses and bioenergetic modelling reveal that this transition is driven by sustained archaeal metabolism of diverse recalcitrant OC compounds, and a physiological trade-off that prioritizes cellular maintenance over growth, minimizing mortality in deep sediments. This strategy triggers a fundamental shift in sedimentary carbon turnover: from rapid bacterial degradation of labile OC near the surface to persistent archaea-driven turnover of recalcitrant OC at depth. We estimate that Bathyarchaeia mediate [~]77% of total OC degradation after 1,000 years of burial, corresponding to [~]18% ([~]11.4 Pg C) of millennial OC degradation in global shelf sediments. These findings identify subsurface archaea as key microbial regulators of long-term OC preservation and reveal how physiological trade-offs sustain life and carbon turnover in the energy-limited deep biosphere.

microbiology↗

DOC Release and Physiological Response of Zostera marina Under Light and Nutrient Gradients

The seagrass bed, known as an important blue carbon ecosystem, not only has robust carbon sequestration capacity, but also releases the fixed organic carbon into the water column in the form of dissolved organic carbon (DOC). Zostera marina is the main constructive species of the seagrass meadows of northern China, but the regulatory mechanism of its DOC release in response to environmental changes still remains unclear. Adult Z. marina was used as the experimental material in this research to investigate the effects of light intensity and nutrient concentration on its DOC release, and to observe its physiological responses. By using a total organic carbon (TOC) analyzer, dissolved oxygen monitoring, transmission electron microscopy (TEM), and transcriptome analysis, we explored how light and nutrients affect DOC release and the underlying physiological mechanisms in Z. marina. The results showed that both elevated light intensity and short-term nutrient enrichment promoted organic carbon release from Z. marina to the environment. Increased light enhanced the net primary productivity (NPP) of Z. marina, while the magnitude of DOC release increased more than NPP itself. Nutrient enrichment reduced NPP while raising the proportion of DOC released by Z. marina. Transcriptome analysis showed that nutrient enrichment significantly affected pathways, including flavonoid biosynthesis and fatty acid degradation. This study demonstrated that changes in light and nutrients can significantly influence DOC release and carbon allocation patterns in Z. marina, providing a theoretical basis for blue carbon accounting and ecological restoration evaluation in seagrass beds.

plant biology↗

Microinjection-based Single-Cell Toxicological Assessment Reveals How Physiological Levels of PFOS Impair Oocyte Maturation and Developmental Competence

Perfluorooctanesulfonic acid (PFOS) is a persistent environmental contaminant widely detected in human serum and follicular fluid and has been associated with reduced implantation rates and female fertility. However, its direct effects on mammalian oocyte maturation remain poorly understood. Here, we developed a microinjection-based single-oocyte toxicological assay to directly evaluate how physiologically relevant PFOS concentrations affect mouse oocyte maturation and early embryonic development. Microinjection of PFOS at follicular-fluid level (5.6 nM) and occupational exposure level (60 nM) significantly reduced germinal vesicle breakdown (GVBD) and polar body extrusion (PBE) rates compared with water-injected controls. Notably, all tested concentrations (2.4 nM serum level, 5.6 nM, and 60 nM) induced abnormal polar-body formation, disrupted meiotic spindle morphology, and increased the proportion of unhealthy oocytes. PFOS exposure also significantly elevated intracellular reactive oxygen species (ROS) levels and mitochondrial membrane potential at 5.6 nM, indicating oxidative stress and mitochondrial dysfunction. Cytological analyses revealed chromosome misalignment and widened metaphase I plates, suggesting chromosome missegregation and subsequent prometaphase II arrest with defective polar bodies. Single-cell RNA sequencing of PFOS-treated oocytes exhibiting abnormal small polar bodies identified distinct transcriptional signatures, including dysregulation of genes involved in mRNA processing, chromosome segregation, mitochondrial function, and cell division. Functionally, these oocytes failed to progress beyond the 2-cell stage following in vitro fertilization, indicating loss of developmental competence. Collectively, these findings demonstrate that PFOS directly disrupts meiotic progression through spindle defects, oxidative stress, and transcriptional dysregulation, ultimately compromising oocyte quality even at environmentally relevant exposure levels. Environmental ImplicationPFOS is a persistent environmental contaminant widely detected in human serum and follicular fluid. Our findings demonstrate that PFOS at physiologically relevant levels can impair oocyte maturation, disrupt meiotic chromosome segregation, and compromise early embryonic development. By using a single-oocyte toxicological assay, we reveal that even low-dose PFOS exposure can induce oxidative stress and transcriptional dysregulation. These results highlight the potential reproductive risks of chronic PFOS exposure and underscore the importance of stricter environmental monitoring and regulation to protect female reproductive health and fertility. This novel assay also has the potential to redefine safety thresholds for other environmental toxicants.

cell biology↗

Predictive metabolomics to decipher plant eco-evolutive tendencies and physiological traits

Plant ecological and evolutionary strategies are shaped by interactions between phylogenetic history and environmental constraints, resulting in leaf and stomatal traits. However, traditional trait-based and phylogenetic approaches often fail to fully explain biochemical mechanisms underlying ecological strategies, particularly for leaf and stomatal traits. Plant metabolomes integrate genetic, physiological, and environmental information and therefore represent a promising intermediate phenotype for investigating links between biochemical diversity, functional traits, and evolutionary patterns. We analysed metabolomic profiles from 74 plant species with various growth forms and ecological types. Using machine learning approaches, we explored whether metabolic variation could predict plant functional divisions, growth forms and phenological types, but also physiological traits related to drought resistance. Metabolomic data contained structured information associated with variation in plant functional traits, ecological strategies, and phylogenetic relationships. Machine learning models identified with high accuracy distinct metabolic signatures linked to differences among plant functional divisions, growth forms, phenology, and trait values. Our study demonstrates that predictive metabolomics provides a powerful and integrative framework to investigate plant ecological and evolutionary strategies. By linking biochemical diversity with plant phylogeny, and ecophysiological traits across multiple species, this approach offers new opportunities to explore the mechanistic basis of plant evolution.

plant biology↗

Passive Physiological Responses Fail to Predict Context-Dependent Action Selection in Bats

How social animals encode vocalizations, assign them value, and formulate behavioral responses remains largely unknown. We asked whether physiological signatures of social-call perception predict behavioral responses across contexts, using the Egyptian Fruit Bat (Rousettus aegyptiacus), an auditory specialist with a rich repertoire of social calls. Using heart rate monitoring during playback of conspecific vocalizations, we found that females showed larger heart rate responses than males to social calls (aggression and distress), whereas non-social echolocation calls evoked no sex difference. In vivo recordings from primary auditory cortex (A1) revealed call-selective units whose selectivity was independent of frequency tuning, with the largest selective fraction for distress calls. In a behavioral assay, female bats approached a distress-call playback only when a live conspecific was coupled with it. However, in isolation, the same calls elicited interest (grooming, pointing) but no approach. Together, the neural and autonomic signatures of social-call perception are present across contexts, whereas the behavioral response is not. Social context, therefore, does not modulate the behavioral readout of social calls; rather, it gates it. Significance StatementHow a social animal converts the perception of a vocalization into behavior remains poorly understood. Using the Egyptian Fruit Bat (Rousettus aegyptiacus), we show that physiological and neural responses to social calls are present in isolation, whereas approach behavior is not. We conclude that social context acts as a necessary gate between sensory representation and action, not a modulator that adjusts an existing response.

neuroscience↗

Synthetic expansion of non-coding DNA reveals physiological constraints on genome size

Genome size varies widely across eukaryotes, largely because of differences in non-coding DNA, but the physiological consequences of this variation remain unclear. To directly test how non-coding DNA abundance influences cellular physiology, we engineered a scalable genome-expansion system in the budding yeast S. cerevisiae that increases genome size while leaving the endogenous genome unchanged. By sequentially fusing yeast artificial chromosomes (YACs) carrying predominantly non-coding human DNA, we generated strains with up to 12.8 Mb of additional DNA, approximately doubling the native genome. Genome expansion reduced growth rate and increased cell size in proportion to the amount of non-coding DNA. Spike-in-normalized RNA-seq and ChIP-seq revealed that the non-coding DNA is pervasively transcribed, with a proportional amount of RNA polymerase II being redistributed from the endogenous genome to the added non-coding sequences. This resulted in a global decrease in the endogenous mRNA concentration. However, ribosome profiling and proteomics experiments revealed that there is little translation of YAC-associated transcripts. Our mathematical model shows that cellular growth rate decreases because non-coding DNA acts as a sink for transcriptional resources to lower the concentration of endogenous mRNA. Thus, our work links genome expansion to proliferative capacity and offers a mechanistic explanation for why the fastest-growing cells, such as yeast and bacteria, carry so little non-coding DNA.

Synthetic Biology↗

Shared Pain, Shared Decisions: How Empathy Shapes Social Conformity Through Physiology and Visual Attention

Empathy enables individuals to attune to others experiences through shared affective, sensorimotor, and neural representations, but its influence on higher-level decision-making and social alignment remains unknown. We examined whether empathy promotes social conformity and whether this effect depends on physiological arousal, visual attention, and socio-emotional traits. Seventy-three participants completed an empathy-for-pain task followed by a modified random-dot task in which they interacted with previously seen empathy targets, while physiological signals and eye movements were recorded. Drift-diffusion modeling showed that feedback from empathy targets increased conformity, reflected in stronger decision bias toward targets, faster evidence accumulation, and reduced decision conservatism. Visual attention to the eyes or mouth was linked to greater conformity depending on the context. Heart rate variability was unrelated to conformity, whereas phasic skin conductance was associated with smaller bias changes and greater conservatism. Alexithymia and autistic traits further shaped the empathy-conformity relationships. These findings suggest that empathic shared representation extends beyond affective resonance to influence social alignment in decision-making.

neuroscience↗

Bridging Gene Expression and Morphology: A Cell Size Score and Its Applications Across Multiple Diseases and Physiological Contexts

Cell size is a critical morphological parameter determining cellular functional homeostasis, yet existing large-scale transcriptomic databases lack direct cell size measurement data. By integrating high-resolution immunofluorescence images with transcriptomics, we identified 457 genes significantly correlated with cell area. Based on these findings, we developed an algorithm, Cell Size Score (CSS), to predict cell size from gene expression profiles. Validation across multiple independent datasets, including human cell lines, mouse models, and single-cell spatial transcriptomics, confirmed that CSS accurately predicts cell size. Furthermore, we observed a significant positive correlation between CSS and broad-spectrum chemotherapy drug resistance, suggesting that increased cell volume confers survival advantages to cancer cells. Moreover, CSS analysis of aging revealed sex-dependent, tissue-specific patterns of change, wherein male adipose and cardiac tissues exhibited progressive hypertrophy with age, while female reproductive organs showed significant atrophy. Additionally, CSS significantly increased in skeletal muscle after exercise, indicating that this metric can capture dynamic physiological adaptation processes. This study establishes a bridge between transcriptomics and cell morphology, providing novel insights into retrospectively analyzing the role of cell size in pathological and physiological processes such as cancer and aging using existing omics data, as well as understanding the molecular mechanisms underlying cell size regulation.

bioinformatics↗

Salt-induced osmotic stress remodels osmoadaptive gene expression and physiology in the polyhydroxyalkanoate-accumulating thermophilic bacterium Caldimonas thermodepolymerans

Caldimonas thermodepolymerans is a thermophilic polyhydroxyalkanoate (PHA)-producing bacterium with strong potential for sustainable bioplastic production. Besides serving as intracellular carbon and energy storage compounds, PHAs are increasingly associated with bacterial stress resistance and cellular robustness. This study aimed to investigate the physiological and transcriptomic response of C. thermodepolymerans to osmotic stress induced by elevated NaCl concentrations. Growth analysis demonstrated tolerance up to a supplementation of 2% NaCl, while moderate salt concentrations enhanced PHA accumulation, reaching 65% cell dry weight at 1.5% NaCl supplementation. To better understand the bacterial response to osmotic stress, RNA sequencing was performed under sublethal salt stress conditions. Differential expression analysis revealed major changes in genes related to osmoprotection, trehalose metabolism and type VI secretion systems, whereas motility and chemotaxis genes were strongly repressed. Phenotypic assays confirmed increased biofilm formation and reduced swarming motility under salt-induced osmotic stress. Although canonical PHA biosynthesis genes were not significantly differentially expressed, increased polymer accumulation suggests other underlying mechanisms linked to osmoadaptation. Together, these findings demonstrate that osmotic stress induces metabolic, physiological and regulatory responses in C. thermodepolymerans, highlighting the importance of PHA in stress adaptation besides its industrial applicability.

microbiology↗

Daylight, Daily Rhythms, and Downstream Physiology: A Translational Study in Diurnal Nile Grass Rats (Arvicanthis niloticus)

The circadian system evolved under natural light-dark cycles, while modern humans spend much of their time indoors under electric lighting that differs substantially from daylight in intensity, spectral composition, and temporal structure. How such lighting environments influence circadian system has not been systematically examined in a diurnal animal model under ecologically relevant conditions. In this study, we used the diurnal Nile grass rat (Arvicanthis niloticus) to assess daily locomotor rhythms across four lighting conditions designed to approximate common human exposure scenarios: rectangular daylight (D65-R; [~]5,600 lux), semi-sigmoidal daylight mimicking natural intensity dynamics (D65-S; matched peak intensity with [~]50% lower cumulative energy), fluorescent indoor light (F12; [~]150 lux), and fluorescent light supplemented with a one-hour midday daylight pulse (F12+D65-P). Using a within-subject design (n = 8), male grass rats were housed under each condition for two weeks. D65-R produced the highest daytime activity levels and the strongest day/night activity ratio, consistent with robust circadian entrainment. Despite matching peak intensity, D65-S did not yield comparable circadian outcomes, indicating that cumulative photon exposure, rather than peak intensity alone, contributes to entrainment strength. Notably, the addition of a one-hour midday daylight pulse (D65-P) partially increased circadian amplitude under otherwise fluorescent conditions, with higher periodogram amplitude relative to F12 alone. A separate cohort of males was exposed to D65-R or F12 for six weeks (n = 10/condition) to assess physiological outcomes, including metabolic and reproductive measures. Compared with the D65-R group, F12 group showed higher diabetic rate (10% vs. 40%) and reduced sperm mobility (45{+/-}6 vs. 19{+/-}1 %), consistent with potential downstream correlates of circadian rhythm disruption. Together, these findings demonstrate that lighting conditions characteristic of indoor environments produce weaker circadian organization than daylight-equivalent lighting in a diurnal rodent, which underscore the importance of light quality in shaping circadian rhythms and downstream physiological processes.

animal behavior and cognition↗

The Role of Photoperiod, Light Intensity, and Iron Concentration on Cellular Physiology Photophysiology, and Proteomics in Southern Ocean Phytoplankton.

Primary production in the Southern Ocean (SO) plays a critical role in regulating the global carbon cycle, yet the physiological mechanisms governing phytoplankton responses to iron (Fe) limitation and variable light remain poorly constrained. Using a custom made incubation system that simulated natural diel solar variability, we examined the interactive effects of Fe availability, light intensity, and photoperiod (continuous vs. variable) on three ecologically important SO phytoplankton: Fragilariopsis cylindrus, Phaeocystis antarctica, and Thalassiosira antarctica. Physiological, photophysiological, and proteomic measurements revealed that Fe availability was the dominant factor regulating growth, carbon production, photosynthetic performance and protein expression across all species. Distinct acclimation strategies emerged: F. cylindrus exhibited marked trade-offs between productivity and photoprotection under Fe stress, consistent with adaptation to stable, low-light, Fe-poor environments; P. antarctica maintained growth by flexibly modulating photoprotective and photosynthetic capacity, reflecting high plasticity suited to dynamic, open-ocean conditions; and T. antarctica expressed a balanced strategy, sustaining productivity and photoprotection simultaneously, characteristic of coastal bloom formers with higher Fe demand. Dynamic light regimes produced smaller, species-specific effects, influencing chlorophyll content and carbon storage primarily in T. antarctica. Correlation and z-score analyses demonstrated that Fe-rich photosynthetic proteins co-varied with biomass production, whereas photoprotective traits clustered independently, underscoring divergent energy-allocation strategies. Together, these results reveal how SO phytoplankton partition resources between productivity and photoprotection under shifting Fe-light regimes, providing mechanistic insight into their ecological niches.

ecology↗

Cell-type-specific ATF6α programs regulate epithelial mitochondrial homeostasis and pericyte remodeling during physiological and exposure-accelerated lung aging

Proteostasis declines with lung aging, while the role of the Unfolded Protein Response (UPR) in lung aging and age-associated pulmonary diseases remains understudied. We investigated how deficiency in the UPR sensor ATF6 affects physiological and smoke exposure-accelerated lung aging. ATF6 -deficient mice exhibited accelerated alveolar simplification, a sign of lung parenchymal aging, which was exacerbated by smoking. Nevertheless, small airway vascular fibrotic remodeling, a prominent smoking-induced pathology, was not evident in smoke-exposed ATF6 -deficient mice. Mechanistically, these divergent phenotypes arose from cell-type-specific ATF6 programs. In alveolar epithelial type 2 cells (AEC2s), the facultative progenitors of the lung parenchyma, ATF6 maintained mitochondrial bioenergetics and sustained efficient redifferentiation into alveolar epithelial type 1 cells (AEC1s). In lung pericytes, ATF6 promoted extravasation, redifferentiation into myofibroblast-like cells, and production of collagens 1 and 3. These findings identify ATF6 as a cell-type-specific regulator of differentiation programs during lung aging and highlight the need to study ATF6 under defined physiological and pathological contexts before therapeutically targeting this pathway.

cell biology↗

Physiological limits of localized hypothermia in the human cochlea: The role of vascular heat transport

PurposeMild therapeutic hypothermia (MTH) preserves cochlear function in animal models and is now entering early-phase human trials for hearing preservation. However, the extent to which the human cochlea can actually be cooled, and the mechanisms underlying MTH, remain unclear, in part because blood perfusion is expected to oppose localized cooling. In this study we evaluated the impact of blood flow on human cochlear temperature exposed to the MTH device using a combined experimental and computational approach. MethodsTemperature measurements were obtained from a human cadaver skull exposed to a commercial MTH device. These data were used to validate a three-dimensional bioheat transfer model incorporating realistic skull anatomy. The validated model was subsequently extended to include physiological blood perfusion in the internal carotid artery; a major heat source located near the cochlea. Finally, the in silico model was further expanded to incorporate the surrounding skin and brain tissues. ResultsIncorporating blood flow in internal carotid artery substantially altered predicted cochlear temperature distributions, highlighting the importance of localized vascular heat transport in the human cochlea during MTH. Although cochlear cooling was attenuated in the presence of perfusion, the therapeutic effects of MTH may not depend solely on the magnitude of local intracochlear temperature reduction. Additional mechanisms, such as reduced facial surface temperature, may also contribute to its efficacy. ConclusionThe validated in silico model provides a physiologically realistic framework for evaluating human cochlear thermal responses, investigating MTH mechanisms, and optimizing temperature-based strategies for hearing preservation.

bioengineering↗

Extracellular vesicle associated nucleic acids and proteins as a complementary fraction for fish biodiversity monitoring and physiological signal recovery

Monitoring the biodiversity and physiological condition of aquatic organisms under environmental stress is central to aquatic ecosystem management. Environmental nucleic acid methods (eDNA and eRNA) have transformed biomonitoring but face well-documented limitations, including susceptibility to degradation, difficulty distinguishing living from legacy or transported signals, and limited capacity to report organism condition. Extracellular vesicles (EVs) released from all kinds of species, are stable and widespread vesicles in environment, showing biomarker potential. Here we evaluate whether nucleic acids and proteins recovered from EVs provide a complementary capture fraction that helps address these limitations. All four targets (eDNA, eRNA, EV-DNA, EV-RNA) shared an identical 12S rRNA metabarcoding workflow and differed only in the pre-analytical capture step, filtration for bulk environmental nucleic acids versus sequential 0.22 {micro}m filtration, tangential flow filtration, and ultracentrifugation for the EV-encapsulated fraction. In a controlled aquarium, EV-DNA recovered all seven reference species (100% sensitivity) versus 85.7% for bulk methods, including a low-abundance detection of Anguilla japonica that warrants independent confirmation. In field sampling at Xinglinwan Reservoir, EV-RNA recovered 11 of 12 expected species (91.7% sensitivity) compared with 50-58% for bulk methods, including four reference taxa detected only by the EV fraction. EV-based methods also captured more even community representation, and EV-RNA showed lower human-read contamination than eDNA. Metaproteomic analysis of reservoir EVs recovered fish-derived proteins, dominated by Cyprinus carpio, including candidate stress-associated functions (chaperones, metallothioneins, oxidoreductases), independently corroborating the EV-based detection of C. carpio. Their abundance varied with seasons, suggesting their ability to respond to environmental changes. Together, these results indicate that EV-associated nucleic acids and proteins constitute an informative complementary fraction for integrated biodiversity and physiological-signal monitoring in impacted aquatic environments. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/735187v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@ee0e6borg.highwire.dtl.DTLVardef@f4d1daorg.highwire.dtl.DTLVardef@fd5123org.highwire.dtl.DTLVardef@da0ddc_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

Physiological Cross-Sectional Surfaces: A Method for Estimating Muscle Functional Capacity from 3D Digital Models of Fiber Architecture

Physiological cross-sectional area (PCSA) is defined as the summed cross-sectional area of all muscle fibers contracting in parallel and at optimal length. PCSA is widely used, yet the conventional equations used to compute PCSA were developed from two-dimensional (2D) interpretations of muscle architecture and may not accurately represent muscle fiber cross-sections in the case of real three-dimensional (3D) geometries of muscles. Related measures of functional cross-sectional area (FCSA) and geometric cross-sectional area (GCSA) were also developed and interpreted with simplified 2D representations. Using realistic 3D muscle architectures derived from medical imaging, we sought to investigate whether conventional definitions of PCSA, FCSA, and GCSA represent the summed cross-sectional areas of all parallel muscle fibers, the fundamental definition of PCSA. We found that none of these measures consistently represented this definition. Thus, we introduce the physiological cross-sectional surface (PCSS), a curved surface within a muscle volume that is everywhere perpendicular to the local fiber direction. We estimated PCSS in 3D muscle surface meshes reconstructed from MRI data, using fiber orientations derived from Laplacian fiber reconstruction. PCSS-derived estimates were compared with PCSA, FCSA, and GCSA across six muscles representing five architectural classes. PCSS differed from all conventional measures, with the magnitude and direction of disagreement depending on muscle architecture. PCSS-to-PCSA ratios ranged from 0.771 to 1.399, while GCSA underestimated PCSS by up to a factor of 2.256 in bi- and multipennate muscles and overestimated it in muscles with more uniform fiber arrangements. PCSS demonstrated high geometric fidelity (perpendicularity>0.987) and robustness to fiber density across a tenfold range (coefficients of variation 0.39-3.95%). These findings indicate that conventional cross-sectional area measures do not consistently account for all fiber cross-sections in parallel within realistic 3D muscle geometries. PCSS provides a geometrically rigorous alternative that may improve estimation of functional muscle capacity from subject-specific imaging data.

bioengineering↗