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This is ongoing work towards developing and integrating a Bayesian Neural Network (BNN) model for Particle-in-Cell (PIC) stress in MFiX legacy code.
Lithium is extensively utilized in industrial energy production, particularly in lithium-ion batteries, and in pharmaceuticals for the treating clinical mood disorders. Consequently, lithium is frequently detected in various environmental matrices. It has been reported to cause a range of toxic effects on aquatic organisms including oxidative stress, neurological disorders, and reproductive suppression. Water acidification is a global issue with numerous negative impacts on aquatic organisms. It can alter the physio-chemical properties and bioavailability of metal ions. The acidic leaching process during lithium battery treatment and global water acidification both suggest that lithium contamination often occurs in acidic environments. In the present study, Daphnia magna neonates were exposed to four treatments (control, lithium alone, low pH, and combined) to investigate whether an acidic environment exacerbates the toxic effects of lithium on aquatic organisms and to explore potential toxic action mechanisms. The results indicated that low pH posed a significant threat to the growth and reproduction of D. magna. When exposed to both lithium and low pH, there was increased lithium accumulation and an energy trade-off response, leading to increased energy allocation to reproduction and reduced energy for growth. Lithium exposure stimulated D. magna activity, while low pH inhibited it, suggesting that an imbalance in energy consumption and supply. Combined exposure to lithium and low pH resulted in severe oxidative stress due to mitochondrial dysfunction, under-utilization of energy substances, and increased ionic homeostasis disturbances. Consequently, the exposed organism altered apoptosis and autophagy processes to maintain homeostasis. In conclusion, the present study demonstrated that lithium and water acidification posed a population-level threat to D. magna, and their combined exposure significantly largely exacerbated the toxic effects.
Uniaxial stress has proven to be a powerful experimental tuning parameter for effectively controlling lattice, charge, orbital, and spin degrees of freedom in quantum materials. In addition, its ability to manipulate the symmetry of materials has garnered significant attention. Recent technical progress to combine uniaxial stress cells with quantum oscillation and angle-resolved photoemission techniques allowed to study the electronic structure as function of uniaxial stress. This review provides an overview on experimental advancements in methods and examines studies on diverse quantum materials, encompassing the semimetal WTe2, the unconventional superconductor Sr2RuO4, Fe-based superconductors, and topological materials.
Over 75% percent of ovarian cancer patients are diagnosed with advanced-stage disease characterized by unresectable intraperitoneal dissemination and the presence of ascites, or excessive fluid build-up within the abdomen. Conventional treatments include cytoreductive surgery followed by multi-line platinum and taxane chemotherapy regimens. Despite an initial response to treatment, over 75% of patients with advanced-stage ovarian cancer will relapse and succumb to platinum-resistant disease. Recent evidence suggests that fluid shear stress (FSS), which results from the movement of fluid such as ascites, induces epithelial-to-mesenchymal transition and confers resistance to carboplatin in ovarian cancer cells. This study demonstrates, for the first time, that FSS-induced platinum resistance correlates with increased cellular protoporphyrin IX (PpIX), the penultimate downstream product of heme biosynthesis, the production of which can be enhanced using the clinically approved pro-drug aminolevulinic acid (ALA). These data suggest that, with further investigation, PpIX could serve as a fluorescence-based biomarker of FSS-induced platinum resistance. Additionally, this study investigates the efficacy of PpIX-enabled photodynamic therapy (PDT) and the secretion of extracellular vesicles under static and FSS conditions in Caov-3 and NIH:OVCAR-3 cells, two representative cell lines for high-grade serous ovarian carcinoma (HGSOC), the most lethal form of the disease. FSS induces resistance to ALA-PpIX-mediated PDT, along with a significant increase in the number of EVs. Finally, the ability of PpIX-mediated photodynamic priming (PDP) to enhance carboplatin efficacy under FSS conditions is quantified. These preliminary findings in monolayer cultures necessitate additional studies to determine the feasibility of PpIX as a fluorescence-based indicator, and mediator of PDP, to target chemoresistance in the context of FSS.
Chloroplasts (photosynthetic plastids) are semiautonomous organelles that contain their own small genomes. The proteomes of chloroplasts, however, are a mixture of plastid and nuclear-encoded proteins. Chloroplasts perform photosynthesis, which is prone to damaging the organelles, leading to the production of reactive oxygen species (ROS) that damage the cell under environmental stresses. Thus, for the cell to maintain proper chloroplast function, efficient photosynthesis, and avoid ROS damage, it relies on complex crosstalk between the chloroplast, the nucleus, other organelles within the cell, and the cytoplasm in between. This communication involves retrograde signals from chloroplasts to control nuclear gene expression, programmed cell death (PCD), and chloroplast degradation. Here we review these signals with an emphasis on the roles of the ROS singlet oxygen ( 1 O 2 ) and plastid gene expression. We cover (1) recent work on understanding how multiple 1 O 2 signaling pathways can be initiated within stressed chloroplasts, (2) how individualized post-translational regulatory systems allow chloroplasts to control their proteomes and degradation, and (3) how chloroplast signals ultimately control cell fate decisions, such as PCD, senescence, and vacuole-mediated degradation of chloroplasts (chloroplast quality control). Overall, this chapter discusses how chloroplasts can act as environmental sensors for the cell and allow plants to acclimate to stress and thrive in dynamic environments.
Persistent drought affects global crop production and is becoming more severe in many parts of the world in recent decades. Deciphering how plants respond to drought will facilitate the development of flexible mitigation strategies. Sorghum bicolor L. Moench (sorghum), a major cereal crop and an emerging bioenergy crop, exhibits remarkable resilience to drought. To better understand the molecular traits that underlie sorghum's remarkable drought tolerance, we undertook a large-scale sorghum gene expression profiling effort, totaling nearly 1500 transcriptome profiles, across a 3-year field study with replicated plots in California's Central Valley. This study included time-resolved gene expression data from roots and leaves of two sorghum genotypes, BTx642 and RTx430, with different pre-flowering and post-flowering drought-tolerance adaptations under control and drought conditions. Quantification of genotype-specific drought tolerance effects was enabled by de novo sequencing, assembly, and annotation of both BTx642 and RTx430 genomes. These reference-quality genomes were used to construct a pangene set for characterizing conserved and genotype-specific expression. By integrating time-resolved transcriptomic responses to drought in the field across three consecutive years, we identified a set of 726 drought-responsive genes that responded similarly in all 3 years of our field study. Functional enrichment analysis identified abiotic stress, secondary cell wall-related processes and metabolism as particularly affected under both types of drought stress. We also found that some glyoxylate cycle pathway genes, including malate synthase and isocitrate lyase, are differentially regulated particularly during post-flowering drought stress, implicating this pathway as potentially important for drought responsiveness. This expansive dataset represents a unique resource for sorghum and drought research communities and provides a methodological framework for the integration of multi-faceted time-resolved transcriptomic datasets.
ABSTRACT Fusarium oxysporumis a cross-kingdom pathogen. While some strains cause disseminated fusariosis and blinding corneal infections in humans, others are responsible for devastating vascular wilt diseases in plants. To better understand the distinct adaptations ofF. oxysporumto animal or plant hosts, we conducted a comparative phenotypic and genetic analysis of two strains: MRL8996 (isolated from a keratitis patient) and Fol4287 (isolated from a wilted tomato [Solanum lycopersicum]). Infection of mouse corneas and tomato plants revealed that, while both strains cause symptoms in both hosts, MRL8996 caused more severe corneal disease in mice, whereas Fol4287 induced more pronounced wilting symptoms in tomato plants.In vitroassays using abiotic stress treatments revealed that the human pathogen MRL8996 was better adapted to elevated temperatures, whereas the plant pathogen Fol4287 was more tolerant to osmotic and cell wall stresses. Both strains displayed broad resistance to antifungal treatment, with MRL8996 exhibiting the paradoxical effect of increased tolerance to higher concentrations of the antifungal caspofungin. We identified a set of accessory chromosomes (ACs) that encode genes with different functions and have distinct transposon profiles between MRL8996 and Fol4287. Interestingly, ACs from both genomes also encode proteins with shared functions, such as chromatin remodeling and post-translational protein modifications. Our phenotypic assays and comparative genomics analyses lay the foundation for future studies correlating genotypes with phenotype and for developing targeted antifungals for agricultural and clinical uses. IMPORTANCE Fusarium oxysporumis a cross-kingdom fungal pathogen that infects both plants and animals. In addition to causing many devastating wilt diseases, this group of organisms was recently recognized by the World Health Organization as a high-priority threat to human health. Climate change has increased the risk ofFusariuminfections, asFusariumstrains are highly adaptable to changing environments. Deciphering fungal adaptation mechanisms is crucial to developing appropriate control strategies. We performed a comparative analysis ofFusariumstrains using an animal (mouse) and plant (tomato) host andin vitroconditions that mimic abiotic stress. We also performed comparative genomics analyses to highlight the genetic differences between human and plant pathogens and correlate their phenotypic and genotypic variations. We uncovered important functional hubs shared by plant and human pathogens, such as chromatin modification, transcriptional regulation, and signal transduction, which could be used to identify novel antifungal targets.
Cellular noise, the non-genetic variability observed among isogenic cells, arises from factors such as growth conditions, aging, and stochastic gene expression, influencing cell stress-response, metabolism, morphology, and size. Here, such plasticity, while critical for adaptation, often goes unnoticed with traditional population-averaging biotechnologies that inevitably mask cell-specific variations and prompting the question, "What else might we be missing". However, recent breakthroughs in optical imaging, microfluidics, and omics, are beginning to uncover the complexity of cellular plasticity. This special is-sue highlights some of these breakthroughs, with key contributions including innovations in multimodal chemical imaging, label-free microscopy, spatial and temporal omics, and droplet-based microfluidics. Collectively, these cutting-edge tools provide unprecedent-ed insights into non-genetic cell-to-cell variability, enhancing our understanding of cellu-lar plasticity and its implications for health, energy, and ecology.
Escherichia coli employs diverse strategies to adapt to acidic environments that disrupt enzyme activity and the thermodynamic feasibility of essential reactions. To understand the impact of pH stress on cell metabolism, we present the PET-FBA (pH-, Enzyme protein allocation-, and Thermodynamics-constrained Flux Balance Analysis) framework. PET-FBA extends genome-scale modeling by integrating enzyme protein costs and reaction Gibbs free energy changes. Additionally, by incorporating pH-dependent enzyme kinetics in response to intracellular acidification, this framework enables the simulation of E. coli's metabolic adjustments across varying external pH levels. The model's accuracy is validated by comparing in silico growth simulations with experimental measurements under both anaerobic and aerobic conditions, as well as in silico gene knockouts of essential genes. By explicitly incorporating pH effects, our model accurately replicates the metabolic shift towards lactate production as the primary fermentation product at low pH in anaerobic conditions. This shift is only predicted when enzyme kinetics are dynamically adjusted as a function of pH. Further analysis revealed that this shift can be attributed to the reduced protein efficiency of the acetyl-CoA branch compared to lactate dehydrogenase under acidic stress, which then becomes crucial for maintaining NAD regeneration and cell growth at low pH. Furthermore, we identified strategies for enhancing cell growth under acidic anaerobic conditions by improving the enzyme activity of lactate dehydrogenase and pyruvate formate lyase, which increases NAD production efficiency and reduces enzyme protein allocation costs. Designed as a lightweight yet versatile framework, PET-FBA enables efficient genome-scale metabolic analysis. Using E. coli as a model system, our framework provides a systematic approach to understanding metabolic responses to environmental stress, pinpointing key metabolic bottlenecks, and identifying potential targets for strain optimization.
Abstract Transcription poses a major challenge for genome stability. The RECQL5 helicase helps safeguard genome integrity and is the only member of the human RecQ helicase family that directly binds to RNA polymerase II (Pol II) and affects its progression. While RECQL5 mitigates transcription stress in cells, the molecular mechanism underlying this phenomenon is unclear. Here, we use cryo-electron microscopy to determine the structures of stalled human Pol II elongation complexes (ECs) bound to RECQL5. Our structures reveal the molecular interactions stabilizing RECQL5 binding to the Pol II EC and highlight its role as a transcriptional roadblock. Additionally, we find that, in its nucleotide-free state, RECQL5 twists the downstream DNA in the EC and, upon nucleotide binding, undergoes a conformational change that allosterically induces Pol II toward a post-translocation state. We propose that this mechanism may help restart Pol II elongation and, therefore, contribute to reducing transcription stress.
Metal halide perovskite (MHP) solar cells exhibit a metastable response to bias governed by coupled ionic–electronic processes, complicating the conventional reciprocity relation between luminescence intensity and device open-circuit voltage (V oc ). This limits the use of luminescence as a diagnostic for device screening or accelerated stress testing, motivating new approaches that can interpret photoluminescence (PL) signals under nonequilibrium conditions. From the artificial intelligence perspective, we develop an explainable deep learning framework that integrates convolutional neural networks (CNN), long short-term memory (LSTM) layers, and an attention mechanism to learn spatiotemporal features from operando photoluminescence PL image sequences. The model achieves a mean absolute error of ±0.027 V in predicting open-circuit voltage transients and reduces extreme-tail errors by up to 78% compared to physics-based reciprocity calculations. Gradient-weighted Class Activation Mapping (Grad-CAM) provides interpretability by highlighting physically meaningful regions such as electrode edges and emergent defect features. From the engineering application perspective, this framework enables accurate, contactless prediction of device V oc and identification of degradation-relevant features during accelerated aging of perovskite solar cells. This approach demonstrates how explainable AI can enhance operando diagnostics and reliability analysis in photovoltaic devices under nonequilibrium conditions.
Applying external pressure to a pouch cell results in improved performance, implicating systems-level design of batteries. Here, different formats and amounts of external pressure to Li-Li x Ni 0.8 Mn 0.1 Co 0.1 O 2 (Li-NMC811) pouch cells were studied under lean electrolyte conditions. Due to the more uniform lithium plating/stripping, a constant gap fixture that retains the distance of the frame during cycling performed greater than a constant pressure fixture that retains applied pressure to the cell. In addition, the use of flexible foam in a constant gap fixture revealed enhanced cycle life at 10 psi; however, at 30 psi, the use of a rigid plate extended cycle life to over 250 cycles, while the foam severely shortened cycle life. This discrepancy with pressure was proven to be driven by stress distribution on cell components. The failure mechanisms and the effects of pressure fixture design on cell components were unveiled, shedding light on improving high-energy battery performance through at-scale fixture design.
Abstract This study on severe malarial anemia (SMA: Hb < 6.0 g/dL), a leading global cause of childhood morbidity and mortality, compares the entire expressed whole blood host transcriptome between Kenyan children (3-48 mos.) with non-SMA (Hb ≥ 6.0 g/dL, n = 39) and SMA ( n = 18). Differential expression analyses reveal 1403 up-regulated and 279 down-regulated transcripts in SMA, signifying impairments in host inflammasome activation, cell death, and innate immune and cellular stress responses. Immune cell profiling shows decreased memory responses, antigen presentation, and immediate pathogen clearance, suggesting an immature/improperly regulated immune response in SMA. Module repertoire analysis of blood-specific gene signatures identifies up-regulation of erythroid genes, enhanced neutrophil activation, and impaired inflammatory responses in SMA. Enrichment analyses converge on disruptions in cellular homeostasis and regulatory pathways for the ubiquitin-proteasome system, autophagy, and heme metabolism. Pathway analyses highlight activation in response to hypoxic conditions [Hypoxia Inducible Factor (HIF)−1 target and Reactive Oxygen Species (ROS) signaling] as a central theme in SMA. These signaling pathways are also top-ranking in protein abundance measures and a Ugandan SMA cohort with available transcriptomic data. Targeted RNA-Seq validation shows strong concordance with our entire expressed transcriptome data. These findings identify key molecular themes in SMA pathogenesis, offering potential targets for new malaria therapies.
Corrosion of the antireflective coating on a photovoltaic cell ("ARc corrosion") has previously been observed in studies using hot-humid test conditions with external high-voltage (HV) bias. This study primarily focuses on known vulnerable, legacy aluminum back surface field (Al-BSF) cells in mini-modules (MiMos) put through comparative stepped stress tests. Each cell type had MiMos at +1500 V, -1500 V, or unbiased ("Voc") potential, which were sequentially subjected to test conditions of 60deg C/60% relative humidity (RH) for 96 h, as in International Electrotechnical Commission (IEC) Technical Specification 62804-1; 70 deg C/70% RH for 200 h; and 85 deg C/85% RH for 200 h. Characterizations at each step included visual camera and electroluminescence (EL) imaging, colorimetry, and current-voltage (I-V) curve tracing. Final characterizations included: Suns-Voc; spatial mapping of external quantum efficiency (EQE); high-resolution photoluminescence (PL), EL, and dark lock-in thermography (DLIT) imaging. Forensics were performed on extracted cores, including scanning electron microscopy (SEM) with energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), and scanning Auger microscopy (SAM). Forensics were also conducted on MiMos from previous studies that underwent stepped HV aging and separate outdoor aged full-sized modules. ARc corrosion was specifically seen for the glass/encapsulant/cell side of the +1500V (HV+) stressed MiMos and modules. Appearance, color, and reflectance were the most distinguishing characteristics relative to glass corrosion, gridline-corrosion and -delamination as well as other concurrent degradation modes. SEM/EDS and SAM identified conversion of silicon nitride to hydrated silica, hydrous silica, or hydrated amorphous silica, which preferentially occurred at the edges and tips of the pyramidal textured cell surface.
Corrosion of the antireflective coating on a photovoltaic cell ("ARc corrosion") has previously been observed in studies using hot-humid test conditions with external high-voltage (HV) bias. This study primarily focuses on known vulnerable legacy aluminum back surface field cells in mini-modules (MiMos) put through comparative stepped stress tests. Each cell type had MiMos at +1500 V, -1500 V, or unbiased ("Voc") potential, which were sequentially subjected to test conditions of 60 degrees C/60% relative humidity (RH) for 96 h, as in International Electrotechnical Commission Technical Specification 62804-1; 70 degrees C/70% RH for 200 h; and 85 degrees C/85% RH for 200 h. Characterizations at each step included visual camera and electroluminescence (EL) imaging, colorimetry, and current-voltage curve tracing. Final characterizations included: Suns-Voc, spatial mapping of external quantum efficiency, high-resolution photoluminescence, EL, and dark lock-in thermography imaging. Forensics were performed on extracted cores, including scanning electron microscopy (SEM) with energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy, and scanning Auger microscopy (SAM). Forensics were also conducted on MiMos from previous studies that underwent stepped HV aging and separate outdoor aged full-sized modules. ARc corrosion was specifically seen for the glass/encapsulant/cell side of the +1500 V (HV+) stressed MiMos and modules. Appearance, color, and reflectance were the most distinguishing characteristics relative to glass corrosion, gridline corrosion and delamination, and other concurrent degradation modes. SEM/EDS and SAM identified the conversion of silicon nitride to hydrated silica, hydrous silica, or hydrated amorphous silica, which preferentially occurred at the edges and tips of the pyramidal textured cell surface.
Rechargeable batteries that incorporate shaped three-dimensional electrodes have been shown to have increased power and energy densities when compared to a conventional geometry, i.e. a planar cathode and anode that sandwich an electrolyte. Electrodes can be shaped to enable a higher active material loading, while keeping ion transport distances small. However, the relationship between electrical and mechanical performance of shaped electrodes remains poorly understood. Many electrode designs have been explored, where the electrodes are individually shaped or intertwined, and advances in manufacturing and shape/topology optimization have made such designs a reality. Here, we explore sinusoidal half cells and interdigitated full cells. First, we use a simple electrostatics model to understand the cell resistance as a function of shape. Here we focus on low-temperature conditions, where the electrolyte conductivity decreases relative to that of the electrode; here, LiPF 6 EC:DMC electrolyte and MnO 2 electrode are considered. Next, we use a chemo-mechanics model to examine the stress that arises due to intercalation-driven volume expansion. We show that shaped electrodes provide a significant reduction in resistance in low-temperature conditions, however, they exhibit unfavorable stress concentrations. Overall, we find that the fully interdigitated electrodes may provide the best balance with respect to this resistance-stress trade-off.
Background The application of single-cell omics tools to biological systems can provide unique insights into diverse cellular populations and their heterogeneous responses to internal and external perturbations. Thus far, most single-cell studies in plant systems have been limited to RNA-sequencing approaches, which only provide indirect readouts of cellular functions. Results Here, we present a single-cell proteomics workflow for plant cells that integrates tape-sandwich protoplasting, piezoelectric cell sorting, nanoPOTS sample preparation, and ion mobility-based MS data acquisition method for label-free single-cell proteomics analysis of Arabidopsis leaf mesophyll cells. From a single leaf protoplast, over 3,000 proteins were quantified with high precision. The workflow is demonstrated to identify stress associated changes in protein abundance by analyzing 117 protoplasts from well-watered and water-deficit stressed plants. Additionally, we describe a new approach for constructing covarying protein networks at the single-cell level and demonstrate how single-cell protein covariation analysis can reveal previously unrecognized protein functions while also capturing stress-induced changes in protein–protein dynamics. Conclusions The label-free scProteomic approach presented here represents a significant advance through the demonstration of a facile protoplast isolation method combined with deep and precise proteomic coverage of Arabidopsis leaf mesophyll cell types. We believe this study will serve as an informative reference to future plant scProteomic investigations.
Here, this study develops a thermal stress model of solid-oxide electrolysis cells (SOECs) including a model for creep strain and failure probability that is integrated with a dynamic plant-wide model of a hydrogen production process. Uncertainties in key material properties of the cell are quantified to assess their impact on stress profile variability. The oxygen electrode is found to have about 10 times higher failure probability compared to the fuel electrode. The study shows that if the stack operation is not optimized, cycling operation would lead to stress build-up eventually leading to catastrophic failure. A dynamic optimization problem is set up for obtaining the optimal operational profile considering a variable hydrogen production rate. Due to the tradeoff between the efficiency and stress build-up, the dynamic optimization problem is multi-objective. It is observed that the optimizer can considerably reduce the stress build-up (i.e., can increase the stack life) albeit at the cost of a lower efficiency thus exhibiting strong tradeoffs between capital and operating costs. For example, if the stack would be replaced in 0.5 yr, specific energy requirement would be 48.5 kWh/kg H 2 while for a stack replacement time of about 6 yr, the specific energy requirement rises by about 4.2 %.