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25 pages, 2786 KiB  
Article
Xylem Functional Anatomy of Pure-Species and Interspecific Hybrid Clones of Eucalyptus Differing in Drought Resistance
by José Gándara, Matías Nión, Silvia Ross, Jaime González-Tálice, Paolo Tabeira and María Elena Fernández
Forests 2025, 16(8), 1267; https://doi.org/10.3390/f16081267 (registering DOI) - 2 Aug 2025
Abstract
Climate extremes threaten the resilience of Eucalyptus plantations, yet hybridization with drought-tolerant species may enhance stress tolerance. This study analyzed xylem anatomical and functional drought responses in commercial Eucalyptus grandis (GG) clones and hybrids: E. grandis × camaldulensis (GC), E. grandis × tereticornis [...] Read more.
Climate extremes threaten the resilience of Eucalyptus plantations, yet hybridization with drought-tolerant species may enhance stress tolerance. This study analyzed xylem anatomical and functional drought responses in commercial Eucalyptus grandis (GG) clones and hybrids: E. grandis × camaldulensis (GC), E. grandis × tereticornis (GT), and E. grandis × urophylla (GU1, GU2). We evaluated vessel traits (water transport), fibers (mechanical support), and wood density (D) in stems and branches. Theoretical stem hydraulic conductivity (kStheo), vessel lumen fraction (F), vessel composition (S), and associations with previous hydraulic and growth data were assessed. While general drought responses occurred, GC had the most distinct xylem profile. This may explain it having the highest performance in different irrigation conditions. Red gum hybrids (GC, GT) maintained kStheo under drought, with stable F and a narrower vessel size, especially in branches. Conversely, GG and GU2 reduced F and S; and stem kStheo declined for a similar F in these clones, indicating vascular reconfiguration aligning the stem with the branch xylem. Almost all clones increased D under drought in any organ, with the highest increase in red gum hybrids. These results reveal diverse anatomical adjustments to drought among clones, partially explaining their growth responses. Full article
(This article belongs to the Section Forest Ecophysiology and Biology)
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21 pages, 875 KiB  
Article
Comprehensive Analysis of Neural Network Inference on Embedded Systems: Response Time, Calibration, and Model Optimisation
by Patrick Huber, Ulrich Göhner, Mario Trapp, Jonathan Zender and Rabea Lichtenberg
Sensors 2025, 25(15), 4769; https://doi.org/10.3390/s25154769 (registering DOI) - 2 Aug 2025
Abstract
The response time of Artificial Neural Network (ANN) inference is critical in embedded systems processing sensor data close to the source. This is particularly important in applications such as predictive maintenance, which rely on timely state change predictions. This study enables estimation of [...] Read more.
The response time of Artificial Neural Network (ANN) inference is critical in embedded systems processing sensor data close to the source. This is particularly important in applications such as predictive maintenance, which rely on timely state change predictions. This study enables estimation of model response times based on the underlying platform, highlighting the importance of benchmarking generic ANN applications on edge devices. We analyze the impact of network parameters, activation functions, and single- versus multi-threading on response times. Additionally, potential hardware-related influences, such as clock rate variances, are discussed. The results underline the complexity of task partitioning and scheduling strategies, stressing the need for precise parameter coordination to optimise performance across platforms. This study shows that cutting-edge frameworks do not necessarily perform the required operations automatically for all configurations, which may negatively impact performance. This paper further investigates the influence of network structure on model calibration, quantified using the Expected Calibration Error (ECE), and the limits of potential optimisation opportunities. It also examines the effects of model conversion to Tensorflow Lite (TFLite), highlighting the necessity of considering both performance and calibration when deploying models on embedded systems. Full article
(This article belongs to the Section Fault Diagnosis & Sensors)
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34 pages, 1227 KiB  
Review
Beyond Cutting: CRISPR-Driven Synthetic Biology Toolkit for Next-Generation Microalgal Metabolic Engineering
by Limin Yang and Qian Lu
Int. J. Mol. Sci. 2025, 26(15), 7470; https://doi.org/10.3390/ijms26157470 (registering DOI) - 2 Aug 2025
Abstract
Microalgae, with their unparalleled capabilities for sunlight-driven growth, CO2 fixation, and synthesis of diverse high-value compounds, represent sustainable cell factories for a circular bioeconomy. However, industrial deployment has been hindered by biological constraints and the inadequacy of conventional genetic tools. The advent [...] Read more.
Microalgae, with their unparalleled capabilities for sunlight-driven growth, CO2 fixation, and synthesis of diverse high-value compounds, represent sustainable cell factories for a circular bioeconomy. However, industrial deployment has been hindered by biological constraints and the inadequacy of conventional genetic tools. The advent of CRISPR-Cas systems initially provided precise gene editing via targeted DNA cleavage. This review argues that the true transformative potential lies in moving decisively beyond cutting to harness CRISPR as a versatile synthetic biology “Swiss Army Knife”. We synthesize the rapid evolution of CRISPR-derived tools—including transcriptional modulators (CRISPRa/i), epigenome editors, base/prime editors, multiplexed systems, and biosensor-integrated logic gates—and their revolutionary applications in microalgal engineering. These tools enable tunable gene expression, stable epigenetic reprogramming, DSB-free nucleotide-level precision editing, coordinated rewiring of complex metabolic networks, and dynamic, autonomous control in response to environmental cues. We critically evaluate their deployment to enhance photosynthesis, boost lipid/biofuel production, engineer high-value compound pathways (carotenoids, PUFAs, proteins), improve stress resilience, and optimize carbon utilization. Persistent challenges—species-specific tool optimization, delivery efficiency, genetic stability, scalability, and biosafety—are analyzed, alongside emerging solutions and future directions integrating AI, automation, and multi-omics. The strategic integration of this CRISPR toolkit unlocks the potential to engineer robust, high-productivity microalgal cell factories, finally realizing their promise as sustainable platforms for next-generation biomanufacturing. Full article
(This article belongs to the Special Issue Developing Methods and Molecular Basis in Plant Biotechnology)
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29 pages, 5505 KiB  
Article
Triaxial Response and Elastoplastic Constitutive Model for Artificially Cemented Granular Materials
by Xiaochun Yu, Yuchen Ye, Anyu Yang and Jie Yang
Buildings 2025, 15(15), 2721; https://doi.org/10.3390/buildings15152721 (registering DOI) - 1 Aug 2025
Abstract
Because artificially cemented granular (ACG) materials employ diverse combinations of aggregates and binders—including cemented soil, low-cement-content cemented sand and gravel (LCSG), and concrete—their stress–strain responses vary widely. In LCSG, the binder dosage is typically limited to 40–80 kg/m3 and the sand–gravel skeleton [...] Read more.
Because artificially cemented granular (ACG) materials employ diverse combinations of aggregates and binders—including cemented soil, low-cement-content cemented sand and gravel (LCSG), and concrete—their stress–strain responses vary widely. In LCSG, the binder dosage is typically limited to 40–80 kg/m3 and the sand–gravel skeleton is often obtained directly from on-site or nearby excavation spoil, endowing the material with a markedly lower embodied carbon footprint and strong alignment with current low-carbon, green-construction objectives. Yet, such heterogeneity makes a single material-specific constitutive model inadequate for predicting the mechanical behavior of other ACG variants, thereby constraining broader applications in dam construction and foundation reinforcement. This study systematically summarizes and analyzes the stress–strain and volumetric strain–axial strain characteristics of ACG materials under conventional triaxial conditions. Generalized hyperbolic and parabolic equations are employed to describe these two families of curves, and closed-form expressions are proposed for key mechanical indices—peak strength, elastic modulus, and shear dilation behavior. Building on generalized plasticity theory, we derive the plastic flow direction vector, loading direction vector, and plastic modulus, and develop a concise, transferable elastoplastic model suitable for the full spectrum of ACG materials. Validation against triaxial data for rock-fill materials, LCSG, and cemented coal–gangue backfill shows that the model reproduces the stress and deformation paths of each material class with high accuracy. Quantitative evaluation of the peak values indicates that the proposed constitutive model predicts peak deviatoric stress with an error of 1.36% and peak volumetric strain with an error of 3.78%. The corresponding coefficients of determination R2 between the predicted and measured values are 0.997 for peak stress and 0.987 for peak volumetric strain, demonstrating the excellent engineering accuracy of the proposed model. The results provide a unified theoretical basis for deploying ACG—particularly its low-cement, locally sourced variants—in low-carbon dam construction, foundation rehabilitation, and other sustainable civil engineering projects. Full article
(This article belongs to the Special Issue Low Carbon and Green Materials in Construction—3rd Edition)
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22 pages, 3015 KiB  
Article
Determining Early Warning Thresholds to Detect Tree Mortality Risk in a Southeastern U.S. Bottomland Hardwood Wetland
by Maricar Aguilos, Jiayin Zhang, Miko Lorenzo Belgado, Ge Sun, Steve McNulty and John King
Forests 2025, 16(8), 1255; https://doi.org/10.3390/f16081255 (registering DOI) - 1 Aug 2025
Abstract
Prolonged inundations are altering coastal forest ecosystems of the southeastern US, causing extensive tree die-offs and the development of ghost forests. This hydrological stressor also alters carbon fluxes, threatening the stability of coastal carbon sinks. This study was conducted to investigate the interactions [...] Read more.
Prolonged inundations are altering coastal forest ecosystems of the southeastern US, causing extensive tree die-offs and the development of ghost forests. This hydrological stressor also alters carbon fluxes, threatening the stability of coastal carbon sinks. This study was conducted to investigate the interactions between hydrological drivers and ecosystem responses by analyzing daily eddy covariance flux data from a wetland forest in North Carolina, USA, spanning 2009–2019. We analyzed temporal patterns of net ecosystem exchange (NEE), gross primary productivity (GPP), and ecosystem respiration (RE) under both flooded and non-flooded conditions and evaluated their relationships with observed tree mortality. Generalized Additive Modeling (GAM) revealed that groundwater table depth (GWT), leaf area index (LAI), NEE, and net radiation (Rn) were key predictors of mortality transitions (R2 = 0.98). Elevated GWT induces root anoxia; declining LAI reduces productivity; elevated NEE signals physiological breakdown; and higher Rn may amplify evapotranspiration stress. Receiver Operating Characteristic (ROC) analysis revealed critical early warning thresholds for tree mortality: GWT = 2.23 cm, LAI = 2.99, NEE = 1.27 g C m−2 d−1, and Rn = 167.54 W m−2. These values offer a basis for forecasting forest mortality risk and guiding early warning systems. Our findings highlight the dominant role of hydrological variability in ecosystem degradation and offer a threshold-based framework for early detection of mortality risks. This approach provides insights into managing coastal forest resilience amid accelerating sea level rise. Full article
(This article belongs to the Special Issue Water and Carbon Cycles and Their Coupling in Forest)
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16 pages, 1258 KiB  
Article
Genome-Wide Association Analysis of Traits Related to Nitrogen Deficiency Stress in Potato
by Carmen Iribar, Alba Alvarez-Morezuelas, Leire Barandalla and Jose Ignacio Ruiz de Galarreta
Horticulturae 2025, 11(8), 889; https://doi.org/10.3390/horticulturae11080889 (registering DOI) - 1 Aug 2025
Abstract
Potato (Solanum tuberosum L.) crop yields may be reduced by nitrogen deficiency stress tolerance. An evaluation of 144 tetraploid potato genotypes was carried out during two consecutive seasons (2019 and 2020), with the objective of characterizing their variability in key physiological and [...] Read more.
Potato (Solanum tuberosum L.) crop yields may be reduced by nitrogen deficiency stress tolerance. An evaluation of 144 tetraploid potato genotypes was carried out during two consecutive seasons (2019 and 2020), with the objective of characterizing their variability in key physiological and agronomic parameters. Physiological parameters included chlorophyll content and fluorescence, stomatal conductance, NDVI, leaf area, and perimeter, while agronomic characteristics such as yield, tuber fresh weight, tuber number, starch content, dry matter, and reducing sugars were evaluated. To genotype the population, the GGP V3 Potato array was used, generating 18,259 high-quality SNP markers. Marker–trait association analysis was conducted using the GWASpoly package in R, applying Q + K linear mixed models to enhance precision. This methodology enabled the identification of 18 SNP markers that exhibited statistically significant associations with the traits analyzed in both trials and periods, relating them to genes whose functional implication has already been described. Genetic loci associated with chlorophyll content and tuber number were detected across non-stress and stress treatments, while markers linked to leaf area and leaf perimeter were identified specifically under nitrogen deficiency stress. The genomic distribution of these markers revealed that genetic markers or single-nucleotide polymorphisms (SNPs) correlated with phenotypic traits under non-stress conditions were predominantly located on chromosome 11, whereas SNPs linked to stress responses were mainly identified on chromosomes 2 and 3. These findings contribute to understanding the genetic mechanisms underlying potato tolerance to nitrogen deficiency stress, offering valuable insights for the development of future marker-assisted selection programs aimed at improving nitrogen use efficiency and stress resilience in potato breeding. Full article
(This article belongs to the Special Issue Genetics, Genomics and Breeding of Vegetable Crops)
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16 pages, 291 KiB  
Article
General and Specific Social Trust as Predictors of Depressive Symptoms: Evidence from Post-Crisis Iceland
by Haukur Freyr Gylfason
World 2025, 6(3), 107; https://doi.org/10.3390/world6030107 - 1 Aug 2025
Abstract
Social trust has been linked to the development and severity of depression, but trust is a complex, multidimensional construct. This study examines the extent to which two distinct forms of trust, general trust and specific trust, predict depressive symptoms. Drawing on longitudinal data [...] Read more.
Social trust has been linked to the development and severity of depression, but trust is a complex, multidimensional construct. This study examines the extent to which two distinct forms of trust, general trust and specific trust, predict depressive symptoms. Drawing on longitudinal data from the Directorate of Health’s national surveys conducted in 2007 and 2009, the analysis includes responses from 3211 Icelanders selected through a stratified random sample. Depressive symptoms were assessed using the Depression, Anxiety, and Stress Scale (DASS), while specific trust captured trust in close relationships, and general trust measured broader perceptions of trustworthiness in others. The two forms of trust together explained 7.6% of the variance in depressive symptoms, with specific trust contributing a substantially greater share. Both remained significant predictors after controlling for prior depression and physical health. These findings highlight the protective role of specific trust and suggest that general trust, an indicator of broader social capital, may also help buffer against depression. The results underscore the relevance of trust as a public health resource and support continued research into social determinants of mental health in Iceland. Full article
17 pages, 3817 KiB  
Article
The Distribution Characteristics of Frost Heaving Forces on Tunnels in Cold Regions Based on Thermo-Mechanical Coupling
by Yujia Sun, Lei Peng and Qionglin Li
Appl. Sci. 2025, 15(15), 8537; https://doi.org/10.3390/app15158537 (registering DOI) - 31 Jul 2025
Abstract
To address the freezing damage to tunnel lining caused by frost heaving of the surrounding rock in water-rich tunnels in cold regions, a numerical thermo-mechanical coupling model for tunnel-surrounding rock that considers the anisotropy of frost heave deformation was established by examining overall [...] Read more.
To address the freezing damage to tunnel lining caused by frost heaving of the surrounding rock in water-rich tunnels in cold regions, a numerical thermo-mechanical coupling model for tunnel-surrounding rock that considers the anisotropy of frost heave deformation was established by examining overall frost heaves in a freeze–thaw cycle. Using a COMSOL Multiphysics 6.0 platform and the sequential coupling method, the temperature field evolution of tunnel-surrounding rock, freezing cycle development, and distribution characteristics of the frost heaving force of a tunnel lining under different minimum temperatures, numbers of negative temperature days, frost heave ratios, and anisotropy coefficients of frost heave deformation were systematically simulated. The results revealed that the response of the temperature field of tunnel-surrounding rock to the external temperature varies spatially with time lags, the shallow surface temperatures and the area around the lining fluctuate with the climate, and the temperature of the deep surrounding rock is dominated by the geothermal gradient. The extent of the freezing cycle and the frost heaving force increase significantly when lowering the minimum temperature. The maximum frost heaving force usually occurs in the region of the side wall and the spring line, and tensile stress is prone to be generated at the spring line; the influence of slight fluctuations in the minimum temperature or the short shift in the coldest day on the frost heaving force is limited. A substantial increase in frost heaving force is observed with higher frost heave ratios; for example, an increase from 0.25% to 2.0% results in a 116% rise at the sidewall. Although the increase in the anisotropy coefficient of frost heave deformation does not change the overall distribution pattern of frost heaving force, it can exacerbate the directional concentration of frost heave strain, which can increase the frost heaving force at the periphery of the top arch of the lining. This study revealed the distribution pattern and key influencing factors of the freezing cycle and frost heaving force for tunnels, providing a theoretical basis and data reference for the frost resistance design of tunnels in cold regions. Full article
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33 pages, 2423 KiB  
Review
Chaperone-Mediated Responses and Mitochondrial–Endoplasmic Reticulum Coupling: Emerging Insight into Alzheimer’s Disease
by Manish Kumar Singh, Minghao Fu, Sunhee Han, Jyotsna S. Ranbhise, Wonchae Choe, Sung Soo Kim and Insug Kang
Cells 2025, 14(15), 1179; https://doi.org/10.3390/cells14151179 - 31 Jul 2025
Abstract
Alzheimer’s disease (AD) is increasingly recognized as a multifactorial disorder driven by a combination of disruptions in proteostasis and organelle communication. The 2020 Lancet commission reported that approximately 10 million people worldwide were affected by AD in the mid-20th century. AD is the [...] Read more.
Alzheimer’s disease (AD) is increasingly recognized as a multifactorial disorder driven by a combination of disruptions in proteostasis and organelle communication. The 2020 Lancet commission reported that approximately 10 million people worldwide were affected by AD in the mid-20th century. AD is the most prevalent cause of dementia. By early 2030, the global cost of dementia is projected to rise by USD 2 trillion per year, with up to 85% of that cost attributed to daily patient care. Several factors have been implicated in the progression of neurodegeneration, including increased oxidative stress, the accumulation of misfolded proteins, the formation of amyloid plaques and aggregates, the unfolded protein response (UPR), and mitochondrial–endoplasmic reticulum (ER) calcium homeostasis. However, the exact triggers that initiate these pathological processes remain unclear, in part because clinical symptoms often emerge gradually and subtly, complicating early diagnosis. Among the early hallmarks of neurodegeneration, elevated levels of reactive oxygen species (ROS) and the buildup of misfolded proteins are believed to play pivotal roles in disrupting proteostasis, leading to cognitive deficits and neuronal cell death. The accumulation of amyloid-β (Aβ) plaques and tau neurofibrillary tangles is a characteristic feature of AD. These features contribute to chronic neuroinflammation, which is marked by the release of pro-inflammatory cytokines and chemokines that exacerbate oxidative stress. Given these interconnected mechanisms, targeting stress-related signaling pathways, such as oxidative stress (ROS) generated in the mitochondria and ER, ER stress, UPR, and cytosolic chaperones, represents a promising strategy for therapeutic intervention. This review focuses on the relationship between stress chaperone responses and organelle function, particularly the interaction between mitochondria and the ER, in the development of new therapies for AD and related neurodegenerative disorders. Full article
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23 pages, 16311 KiB  
Article
Stratum Responses and Disaster Mitigation Strategies During Pressurized Pipe Bursts: Role of Geotextile Reinforcement
by Zhongjie Hao, Hui Chao, Yong Tan, Ziye Wang, Zekun Su and Xuecong Li
Buildings 2025, 15(15), 2696; https://doi.org/10.3390/buildings15152696 - 30 Jul 2025
Viewed by 129
Abstract
Urban subsurface pipeline bursts can induce catastrophic cascading effects, including ground collapse, infrastructure failure, and socioeconomic losses. However, stratum responses during the erosion cavity expansion phase and corresponding disaster mitigation strategies have rarely been researched. In this study, a numerical model validated through [...] Read more.
Urban subsurface pipeline bursts can induce catastrophic cascading effects, including ground collapse, infrastructure failure, and socioeconomic losses. However, stratum responses during the erosion cavity expansion phase and corresponding disaster mitigation strategies have rarely been researched. In this study, a numerical model validated through experimental tests was employed to investigate the effects of internal water pressures, burial depths, and different geotextile-based disaster mitigation strategies. It was revealed that a burial depth-dependent critical internal water pressure governed the erosion cavity expansion, and a predictive equation was derived based on the limit equilibrium theory. Higher internal water pressure accelerated the erosion cavity expansion and amplified the stratum stress within a range of twice the diameter D. Increased burial depth d reduced peak ground heave but linearly expanded the heave zone range, concurrently elevating the overall stratum stress level and generating larger stress reduction zones (i.e., when d/D = 3.0, the range of the stress reduction zone was 8.0D). All geotextile layout configurations exhibited different disaster mitigation effects (the peak ground heave was reduced by at least 15%). The semi-circular closely fitted configuration (SCCF) optimally restricted the expansion of the erosion cavity, reduced the stratum displacement (i.e., 39% reduction in the peak ground heave), and avoided stress concentration. Comprehensive analysis indicated that SCCF was suited for low-pressure pipelines in deformation-sensitive stratum and semi-circular configuration (SC) was suitable for deformation-insensitive pipeline sections. These findings provide actionable insights for tailoring mitigation strategies to specific operational risks. Full article
(This article belongs to the Section Building Energy, Physics, Environment, and Systems)
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25 pages, 9707 KiB  
Article
Mesoscale Mechanical Analysis of Concrete Based on a 3D Random Aggregate Model
by Shuaishuai Wei, Huan Zhang, Ding Wang, Xuchun Wang and Mengdi Cao
Coatings 2025, 15(8), 883; https://doi.org/10.3390/coatings15080883 - 29 Jul 2025
Viewed by 225
Abstract
The shape, size, and interfacial transition zone (ITZ) of aggregates significantly impact the nonlinear mechanical behavior of concrete. This study investigates concrete’s mechanical response and damage mechanisms by developing a three-dimensional, three-phase mesoscale model comprising coarse aggregates, mortar, and ITZ to explore the [...] Read more.
The shape, size, and interfacial transition zone (ITZ) of aggregates significantly impact the nonlinear mechanical behavior of concrete. This study investigates concrete’s mechanical response and damage mechanisms by developing a three-dimensional, three-phase mesoscale model comprising coarse aggregates, mortar, and ITZ to explore the compressive performance of concrete. A method for simulating the random distribution of aggregates based on three-dimensional grid partitioning is proposed, where the value of each grid point represents the maximum aggregate radius that can be accommodated if the point serves as the aggregate center. Aggregates are generated by randomly selecting grid points that meet specific conditions, avoiding overlapping distributions and significantly improving computational efficiency as the generation progresses. This model effectively enhances the precision and efficiency of aggregate distribution and provides a reliable tool for studying the random distribution characteristics of aggregates in concrete. Additionally, an efficient discrete element model (DEM) was established based on this mesoscale model to simulate the compressive behavior of concrete, including failure modes and stress–strain curves. The effects of aggregate shape and maximum aggregate size on the uniaxial compressive failure behavior of concrete specimens were investigated. Aggregate shape has a particular influence on the compressive strength of concrete, and the compressive strength decreases with an increase in maximum aggregate size. Combined with existing experimental results, the proposed mesoscale model demonstrates high reliability in analyzing the compressive performance of concrete, providing valuable insights for further research on the mechanical properties of concrete. Full article
(This article belongs to the Special Issue Advances in Pavement Materials and Civil Engineering)
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16 pages, 3286 KiB  
Article
Poxvirus K3 Orthologs Regulate NF-κB-Dependent Inflammatory Responses by Targeting the PKR–eIF2α Axis in Multiple Species
by Huibin Yu, Mary Eloise L. Fernandez, Chen Peng, Dewi Megawati, Greg Brennan, Loubna Tazi and Stefan Rothenburg
Vaccines 2025, 13(8), 800; https://doi.org/10.3390/vaccines13080800 - 28 Jul 2025
Viewed by 233
Abstract
Background: Protein kinase R (PKR) inhibits general mRNA translation by phosphorylating the alpha subunit of eukaryotic translation initiation factor 2 (eIF2). PKR also modulates NF-κB signaling during viral infections, but comparative studies of PKR-mediated NF-κB responses across mammalian species and their regulation by [...] Read more.
Background: Protein kinase R (PKR) inhibits general mRNA translation by phosphorylating the alpha subunit of eukaryotic translation initiation factor 2 (eIF2). PKR also modulates NF-κB signaling during viral infections, but comparative studies of PKR-mediated NF-κB responses across mammalian species and their regulation by viral inhibitors remain largely unexplored. This study aimed to characterize the conserved antiviral and inflammatory roles of mammalian PKR orthologs and investigate their modulation by poxviral inhibitors. Methods: Using reporter gene assays and quantitative RT-PCR, we assessed the impact of 17 mammalian PKR orthologs on general translation inhibition, stress-responsive translation, and NF-κB-dependent induction of target genes. Congenic human and rabbit cell lines infected with a myxoma virus strain lacking PKR inhibitors were used to compare the effects of human and rabbit PKR on viral replication and inflammatory responses. Site-directed mutagenesis was employed to determine key residues responsible for differential sensitivity to the viral inhibitor M156. Results: All 17 mammalian PKR orthologs significantly inhibited general translation, strongly activated stress-responsive ATF4 translation, and robustly induced NF-κB target genes. Inhibition of these responses was specifically mediated by poxviral K3 orthologs that effectively suppressed PKR activation. Comparative analyses showed human and rabbit PKRs similarly inhibited virus replication and induced cytokine transcripts. Amino acid swaps between rabbit PKRs reversed their sensitivity to viral inhibitor M156 and NF-κB activation. Conclusions: Our data show that the tested PKR orthologs exhibit conserved dual antiviral and inflammatory regulatory roles, which can be antagonized by poxviral K3 orthologs that exploit eIF2α mimicry to modulate the PKR-NF-κB axis. Full article
(This article belongs to the Special Issue Antiviral Immunity and Vaccine Development)
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20 pages, 2215 KiB  
Article
Acquired Radioresistance Through Adaptive Evolution with Gamma Radiation as Selection Pressure: Increased Expression and Induction of Anti-Stress Genes
by Takeshi Saito and Hiroaki Terato
Int. J. Mol. Sci. 2025, 26(15), 7275; https://doi.org/10.3390/ijms26157275 - 28 Jul 2025
Viewed by 141
Abstract
Elucidating the mechanisms of radioresistance in highly radiotolerant organisms can provide valuable insights into the adaptation and evolution of organisms. However, research has been limited on many naturally occurring radioresistant organisms due to a lack of information regarding their genetic and biochemical characteristics [...] Read more.
Elucidating the mechanisms of radioresistance in highly radiotolerant organisms can provide valuable insights into the adaptation and evolution of organisms. However, research has been limited on many naturally occurring radioresistant organisms due to a lack of information regarding their genetic and biochemical characteristics and the difficulty of handling them experimentally. To address this, we conducted an experiment on adaptive evolution using gamma radiation as the selection pressure to generate evolved Escherichia coli with gamma radiation resistance approximately one order of magnitude greater than that of wild-type E. coli. Gene expressions in all wild-type and evolved radioresistant E. coli in the presence or absence of gamma irradiation were analyzed and compared using RNA sequencing. Under steady-state conditions, the genes involved in survival, cell recovery, DNA repair, and response following stress exposure were upregulated in evolved E. coli compared with those in wild-type E. coli. Furthermore, the evolved E. coli induced these genes more efficiently following gamma irradiation and greater DNA repair activity than that in the wild-type E. coli. Our results indicate that an increased steady-state expression of various anti-stress genes, including DNA repair-related genes, and their highly efficient induction under irradiation are responsible for the remarkable radioresistance of evolved E. coli. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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17 pages, 1525 KiB  
Article
Clonidine Protects Endothelial Cells from Angiotensin II-Induced Injury via Anti-Inflammatory and Antioxidant Mechanisms
by Bekir Sıtkı Said Ulusoy, Mehmet Cudi Tuncer and İlhan Özdemir
Life 2025, 15(8), 1193; https://doi.org/10.3390/life15081193 - 27 Jul 2025
Viewed by 330
Abstract
Background: Cerebral aneurysm (CA) is a focal or diffuse pathological dilation of the cerebral arterial wall that arises due to various etiological factors. It represents a serious vascular condition, particularly affecting the elderly, and carries a high risk of rupture and neurological morbidity. [...] Read more.
Background: Cerebral aneurysm (CA) is a focal or diffuse pathological dilation of the cerebral arterial wall that arises due to various etiological factors. It represents a serious vascular condition, particularly affecting the elderly, and carries a high risk of rupture and neurological morbidity. Clonidine (CL), an α2-adrenergic receptor agonist, has been reported to suppress aneurysm progression; however, its underlying molecular mechanisms, especially in relation to cerebral endothelial dysfunction, remain unclear. This study aimed to investigate the potential of CL to mitigate CA development by modulating apoptosis, inflammation, and oxidative stress in an Angiotensin II (Ang II)-induced endothelial injury model. Methods: Human brain microvascular endothelial cells (HBMECs) were used to establish an in vitro model of endothelial dysfunction by treating cells with 1 µM Ang II for 48 h. CL was administered 2 h prior to Ang II exposure at concentrations of 0.1, 1, and 10 µM. Cell viability was assessed using the MTT assay. Oxidative stress markers, including reactive oxygen species (ROS) and Nitric Oxide (NO), were measured using 2′,7′–dichlorofluorescin diacetate (DCFDA). Gene expression levels of vascular endothelial growth factor (VEGF), matrix metalloproteinases (MMP-2 and MMP-9), high mobility group box 1 (HMGB1), and nuclear factor kappa B (NF-κB) were quantified using RT-qPCR. Levels of proinflammatory cytokines; tumor necrosis factor-alpha (TNF-α), Interleukin-6 (IL-6), and interferon-gamma (IFN-γ); were measured using commercial ELISA kits. Results: Ang II significantly increased ROS production and reduced NO levels, accompanied by heightened proinflammatory cytokine release and endothelial dysfunction. MTT assay revealed a marked decrease in cell viability following Ang II treatment (34.18%), whereas CL preserved cell viability in a concentration-dependent manner: 44.24% at 0.1 µM, 66.56% at 1 µM, and 81.74% at 10 µM. CL treatment also significantly attenuated ROS generation and inflammatory cytokine levels (p < 0.05). Furthermore, the expression of VEGF, HMGB1, NF-κB, MMP-2, and MMP-9 was significantly downregulated in response to CL. Conclusions: CL exerts a protective effect on endothelial cells by reducing oxidative stress and suppressing proinflammatory signaling pathways in Ang II-induced injury. These results support the potential of CL to mitigate endothelial injury in vitro, though further in vivo studies are required to confirm its translational relevance. Full article
(This article belongs to the Section Pharmaceutical Science)
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14 pages, 1333 KiB  
Article
Reliable RT-qPCR Normalization in Polypogon fugax: Reference Gene Selection for Multi-Stress Conditions and ACCase Expression Analysis in Herbicide Resistance
by Yufei Zhao, Xu Yang, Qiang Hu, Jie Zhang, Sumei Wan and Wen Chen
Agronomy 2025, 15(8), 1813; https://doi.org/10.3390/agronomy15081813 - 26 Jul 2025
Viewed by 203
Abstract
Asia minor bluegrass (Polypogon fugax), a widespread Poaceae weed, exhibits broad tolerance to abiotic stresses. Validated reference genes (RGs) for reliable RT-qPCR normalization in this ecologically and agriculturally significant species remain unidentified. This study identified eight candidate RGs using transcriptome data [...] Read more.
Asia minor bluegrass (Polypogon fugax), a widespread Poaceae weed, exhibits broad tolerance to abiotic stresses. Validated reference genes (RGs) for reliable RT-qPCR normalization in this ecologically and agriculturally significant species remain unidentified. This study identified eight candidate RGs using transcriptome data from seedling tissues. We assessed the expression stability of these eight RGs across various abiotic stresses and developmental stages using Delta Ct, BestKeeper, geNorm, and NormFinder algorithms. A comprehensive stability ranking was generated using RefFinder, with validation performed using the target genes COR413 and P5CS. Results identified EIF4A and TUB as the optimal RG combination for normalizing gene expression during heat stress, cold stress, and growth stages. EIF4A and ACT were most stable under drought stress, EIF4A and 28S under salt stress, and EIF4A and EF-1 under cadmium (Cd) stress. Furthermore, EIF4A and UBQ demonstrated optimal stability under herbicide stress. Additionally, application of validated RGs revealed higher acetyl-CoA carboxylase gene (ACCase) expression in one herbicide-resistant population, suggesting target-site gene overexpression contributes to resistance. This work presents the first systematic evaluation of RGs in P. fugax. The identified stable RGs provide essential tools for future gene expression studies on growth and abiotic stress responses in this species, facilitating deeper insights into the molecular basis of its weediness and adaptability. Full article
(This article belongs to the Special Issue Adaptive Evolution in Weeds: Molecular Basis and Management)
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