Search Results (1,871)

This work introduces an approach to evolutionary analysis in which information encoded in amino-acid sequences is converted into a specific type of image, termed a genetic image. Genetic images derived from the amino-acid sequences of cytochrome b and cytochrome c oxidase subunit I are shown to be suitable for identifying evolutionary similarities between organisms. Furthermore, artificial neural networks are demonstrated to recognize these genetic images, enabling identification of species evolution. The results indicate the similarity of the genetic images of organisms belonging to species that emerged earlier during Earth’s evolutionary history to the genetic images of organisms belonging to species that emerged later. This finding indicates that genetic images are inherited and undergo gradual modification during evolutionary processes. The phenomenon of inheritance and modification of genetic images suggests that evolution tends to change the already existing functionalities of organisms, which allows for the ordering of organisms belonging to different species from ancient forms, through species that appeared successively during evolution, to those belonging to species that have developed more recently, up to Homo sapiens. Moreover, unlike analyses based on phylogenetic trees, the method presented in this article does not require computing hypothetical taxonomic units to study evolution. Combined with analyses of the inheritance of genetic images, it can support the interpretations of phylogenetic trees and evolutionary research. Full article

Saline–alkali stress severely limits crop production worldwide. Soybean [Glycine max (L.) Merr.] is particularly sensitive during seed germination, a stage critical for stand establishment. This complex stress environment encompasses two distinct yet equally critical dimensions: neutral salt stress and alkaline salt stress, each eliciting specialized physiological and metabolic responses. Here, a comparative assessment of four genotypes (tolerant: CN16, CN17; sensitive: Williams 82, K18) under 100 mmol/L Na⁺ revealed that alkaline salt stress exerts a significantly more potent inhibitory effect than neutral salt stress. Tolerant cultivars maintained 75–80% germination under alkaline conditions, whereas sensitive ones dropped below 15%, a divergence primarily driven by superior oxidative mitigation capacity. Integrated multi-omics analysis of the tolerant variety CN16 identified stage-specific regulatory shifts: early alkaline salt stress (60 h) triggers extensive transcriptional reprogramming focused on physical barrier reinforcement, including cell walls and lipid remodeling. By 96 h, regulatory modes between the two stress types diverged: neutral salt elicited a transcriptional surge, while alkaline salt transitioned to a metabolically dominant regulation, shifting flux from growth-related isoflavonoids to defense-related anthocyanins. Crucially, this study uncovers the distinct bioenergetic trade-offs governing these responses: whereas adaptation to neutral salt relies on low-energy galactose metabolism, tolerance to alkaline salt demands energy-intensive processes, specifically the active vacuolar compartmentalization of organic acids and anthocyanins for intracellular buffering. This obligatory energy expenditure restricts biomass accumulation, explaining the severe growth penalties observed in complex saline-alkali environments. Finally, the identification of a core regulatory module driven by key genes, including GmPHOT2b, GmLOG, and GmSHMT08, enriches the metabolic regulatory network under saline-alkali stress, providing core targets and a theoretical framework for precisely balancing metabolic expenditure with biomass accumulation in breeding practice. Full article

Fanconi anemia (FA) is a rare inherited disorder classically defined by defective DNA interstrand crosslink repair, leading to bone marrow failure and cancer predisposition. Increasing evidence indicates that FA pathophysiology extends beyond genomic instability to include mitochondrial dysfunction, oxidative stress, and impaired antioxidant responses. Across multiple cellular models and patient-derived samples, FA cells display altered mitochondrial bioenergetics, increased reactive oxygen species (ROS) production, and defective activation of redox-adaptive pathways, contributing to cumulative damage to DNA, lipids, and proteins. These alterations are particularly relevant in hematopoietic stem and progenitor cells, where metabolic stress and redox imbalance amplify stem cell exhaustion. Current data support a bidirectional interplay in which mitochondrial dysfunction and oxidative stress act mainly as secondary but amplifying factors of the primary DNA repair defect, establishing pathogenic feedback loops. Preclinical studies suggest that modulation of redox balance and mitochondrial function may improve cellular homeostasis, and early clinical investigations of antioxidant strategies indicate acceptable safety and measurable effects on oxidative biomarkers. However, clinical evidence remains limited and heterogeneous, with uncertain impact on long-term disease progression. Moreover, most mechanistic insights derive from in vitro or patient-derived models, while animal models and longitudinal clinical studies remain insufficient. Overall, a more integrated and translational framework is needed to clarify causality, validate biomarkers, and define the therapeutic potential of targeting metabolic and redox pathways in FA. Full article

Colorectal cancer (CRC) is a multifactorial disease influenced by genetic and environmental factors. The endothelial nitric oxide synthase (eNOS) gene, involved in nitric oxide (NO) production, is associated with carcinogenesis. This study aimed to evaluate the association between eNOS −786T>C and G894T polymorphisms and CRC susceptibility in an Algerian population. Genotype and allele frequencies were analyzed, and associations were assessed using odds ratios (ORs) and 95% confidence intervals (CIs). For −786T>C polymorphism, the CC genotype was significantly more frequent in patients than in controls (37.33% vs. 21.67%) and was associated with increased risk of CRC (OR = 2.15, 95% CI: 1.21–3.88, p = 0.004), whereas the TT genotype showed a protective effect (OR = 0.41, 95% CI: 0.20–0.81, p = 0.005). Regarding the G894T polymorphism, the TT genotype was significantly associated with increased susceptibility to CRC (44.67% vs. 8.33%; OR = 8.88, 95% CI: 4.19–15.40, p < 0.001), while the GG genotype was protective (OR = 0.18, 95% CI: 0.10–0.32, p < 0.001). Allelic analysis confirmed that the C and T alleles were risk factors. Furthermore, eNOS polymorphisms were significantly associated with tumor location. In conclusion, the eNOS −786T>C and G894T polymorphisms are significantly associated with CRC susceptibility in the Algerian population and could serve as potential genetic biomarkers. Full article

(1) Background: Mild traumatic brain injury (mTBI), the most prevalent form of traumatic brain injury, often results from repetitive impacts to the head and is associated with long-term neurological impairment. The pathophysiology of mTBI is multifactorial and involves alterations in mitochondrial bioenergetics, a key determinant of neuronal function and survival. Although mitochondrial dysfunction is recognized as a hallmark of mTBI, its long-term effects on bioenergetics and the roles of regulatory cytosolic and mitochondrial proteins remain poorly understood. We hypothesized that repeated mTBI (rmTBI) induces sustained deficits in mitochondrial bioenergetics that are associated with long-term changes in key bioenergetic and other regulatory proteins. (2) Methods: Using the repeated CHIMERA injury model in adult male rats, randomly assigned to sham or rmTBI groups, we assessed mitochondrial respiration in isolated mitochondria and whole cerebral cortex homogenates using a Clark O₂ electrode and an Oroboros O₂k respirometer at time points ranging from 1 day to 2 months post-injury. Western blotting was performed for expression of regulatory proteins HKI, DRP1, MFN2, VDAC1, and ANT2. (3) Results: At 2 months post-rmTBI, respiration was faster and uncoupled, while ATP synthesis was significantly slowed compared with sham rats. This was accompanied by decreased expression of mitochondrial MFN2 and ANT2, by increased mitochondrial expression of DRP1, and by decreased translocation of HKI to mitochondria. There was no significant difference in VDAC1 expression. Earlier time points showed no significant differences in bioenergetics or protein expression, but neuro-inflammatory markers (GFAP and Iba1) were significantly elevated at these earlier time points of post-injury. (4) Conclusions: These findings indicate that rmTBI leads to a delayed long-term impairment of mitochondrial bioenergetics associated with alterations in proteins critical for bioenergetic regulation and mitochondrial control. This suggests a pathophysiologic mechanism for the persistent cognitive and behavioral deficits observed following rmTBI. Full article

Background and Objectives: Tamoxifen, a cornerstone selective estrogen receptor modulator in breast cancer therapy, is increasingly recognized to be associated with retinal toxicity characterized by mitochondrial dysfunction, oxidative stress, lipid peroxidation, and oxidative DNA injury. By targeting mitochondrial bioenergetic dysfunction and redox disequilibrium, adenosine triphosphate (ATP) emerges as a biologically plausible candidate for retinal cytoprotection. This study aimed to evaluate the protective effect of ATP against tamoxifen-induced retinal toxicity in a rat model. Materials and Methods: Twenty-four male albino Wistar rats were randomly assigned to four groups: healthy control (HG), ATP-alone (ATPG, 4 mg/kg, intraperitoneally), tamoxifen-alone (TAMG, 5 mg/kg, orally), and tamoxifen plus ATP-treated (ATAG; ATP, 4 mg/kg, intraperitoneally; tamoxifen, 5 mg/kg, orally). Treatments were administered once daily for 30 days. Oxidative stress markers (malondialdehyde, total glutathione), antioxidant enzyme activities (superoxide dismutase, catalase), and oxidative DNA damage (8-hydroxy-2′-deoxyguanosine) were assessed in ocular tissues. Retinal histopathological evaluation included hematoxylin–eosin staining with semiquantitative assessment of edema, vascular congestion, polymorphonuclear leukocyte infiltration, and cytoplasmic vacuolization, together with quantitative measurements of retinal layer thicknesses and ganglion cell layer (GCL) cell counts. Results: Tamoxifen administration induced marked oxidative stress, antioxidant depletion, and increased oxidative DNA damage in ocular tissues, accompanied by significant thickening of retinal layers, reduced GCL cell counts, and pronounced disruption of retinal architecture. By comparison, ATP co-administration significantly suppressed lipid peroxidation and restored antioxidant defenses, thereby reducing oxidative DNA damage and preserving retinal structural integrity, as reflected by partial normalization of retinal layer thicknesses, preservation of GCL cell counts, and the presence of only mild residual edema. Conclusions: These findings indicate that ATP attenuates tamoxifen-induced retinal toxicity by supporting mitochondrial energy balance and redox homeostasis. Accordingly, ATP administration may represent a promising protective approach for reducing retinal injury associated with long-term tamoxifen therapy. Full article

Phospholipid transfer protein (PLTP) is a lipid transfer protein classically studied in the context of plasma lipoprotein metabolism, high-density lipoprotein (HDL) remodeling, and cardiovascular disease risk. PLTP facilitates phospholipid transfer between lipoproteins and regulates HDL particle size and composition through interactions with apolipoprotein A-I and apolipoprotein A-II. While its systemic roles in cholesterol handling, reverse cholesterol transport, and inflammatory signaling are well established, the cell-autonomous functions of PLTP within cardiomyocytes remain poorly defined, particularly in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). Extensive experimental and clinical studies demonstrate that PLTP enhances ABCA1-dependent cholesterol efflux primarily by stabilizing ABCA1 at the plasma membrane and by promoting the generation of lipid-poor apolipoprotein A-I and pre-β HDL particles, which serve as efficient cholesterol acceptors; the magnitude of these effects depends on cellular context, PLTP expression levels, and the availability of lipid acceptors. PLTP expression is metabolically regulated and widely distributed across tissues, including macrophages and other non-hepatic cells, supporting roles beyond circulating lipoprotein remodeling. Altered PLTP activity has been linked to atherosclerosis, cardiovascular disease, and inflammatory pathways, underscoring its relevance to cardiac pathophysiology. Emerging evidence further suggests that intracellular cholesterol distribution, rather than total cholesterol content alone, critically influences mitochondrial membrane composition, bioenergetics, and stress signaling in cardiomyocytes. These observations raise the possibility that PLTP-regulated lipid flux may indirectly shape mitochondrial function by modulating cellular cholesterol homeostasis. This review synthesizes current knowledge of PLTP biology, cholesterol metabolism, and lipoprotein remodeling, and integrates these concepts with emerging frameworks in cardiomyocyte lipid metabolism and mitochondrial physiology. We highlight human iPSC-derived cardiomyocytes as a strategic and translationally relevant platform to investigate PLTP’s non-canonical, cell-intrinsic roles, identify critical knowledge gaps, and propose future directions for elucidating how PLTP may influence mitochondrial function in human cardiac cells. Full article

Despite various technical measures, the soil is negatively affected by the passage of agricultural machinery. This study presents soil resistance measured by a horizontal on-the-go soil resistance force sensor and a vertical penetrologger on a medium-plasticity clay loam (41% particles < 0.01 mm, organic matter 5.43%) in Krakovany village (Western Slovakia). The field has been managed using a no-till system since 2013, with no seedbed preparation performed since 2017. In-track data after multiple passes of a tractor were compared with out-track data. The results indicate that the most significant increase in horizontal soil resistance force occurred after the first pass, with each subsequent increase being smaller than the previous one. The no-till field showed the smallest percentage increase in soil resistance force after one tractor pass compared to conventionally tilled fields previously studied using the same methodology in the same soil region. Out-track SRF reached values similar to those of the conventionally tilled field after harvest. Vertical penetration resistance showed the lowest increase at depths of 9 to 25 cm in the no-till field compared to tilled fields. The highest values were observed at a depth of 9 cm, whereas at 25 cm, the values approached their minimum in comparison with tilled fields. These findings suggest that long-term no-till management may contribute to reducing machinery-induced soil compaction compared to conventional tillage. Full article

Alzheimer’s disease is a complex neurodegenerative condition characterized by progressive cognitive decline, neuroinflammation, metabolic dysregulation, and abnormal protein deposition. While genetic factors and amyloid-beta-focused hypotheses have been extensively investigated, they fail to fully account for the prolonged prodromal phase or the early susceptibility of olfactory and limbic regions. Emerging evidence suggests chronic peripheral and mucosal infections may influence disease risk; however, mechanisms by which microbial activity outside the central nervous system contributes to persistent neuropathology remain poorly understood. This review explores the emerging concept that bacterial outer membrane vesicles act as mobile, lipid-rich vectors linking peripheral microbial reservoirs to neuroimmune and metabolic dysfunction in the aging brain. We discuss evidence suggesting vesicles originating from oral, olfactory, and upper airway niches can access the central nervous system via vascular routes and direct neural pathways, including olfactory and trigeminal nerves, where they influence glial and endothelial cell function. We also propose the Accumulative Vesicle Load Hypothesis, which describes how cumulative lifetime exposure to bacterial vesicles shapes disease onset, anatomical vulnerability, and progression, and incorporates components of other hypotheses proposed for Alzheimer’s disease. This offers a system-level perspective for early diagnosis and upstream therapeutic strategies, including minimally invasive vesicle profiling in nasal fluid, saliva, blood, and cerebrospinal fluid. This work is a conceptual review that summarizes current evidence in a hierarchically organized manner and proposes a testable model; it does not assert causality where direct human evidence is currently limited. Full article

Precise control of mitochondrial electron transport is essential to maintain mitochondrial coupling and efficiency in ATP production. Furthermore, disruptions to ETC complex function can drive increased oxidant production, resulting in oxidative damage to the mitochondrion and bioenergetic inefficiency. This is highly relevant in the aging heart, as increased cardiac oxidative stress and mitochondrial dysfunction are hallmarks of age-related cardiovascular disease. Lysine acetylation has recently been characterized as a novel regulator of mitochondrial metabolic and bioenergetic function in the aging heart. In the present study, we investigated how lysine acetylation regulates oxidant production and redox milieu through mitochondrial acetyltransferase GCN5L1. Using a cardiac-specific GCN5L1 knockout mouse model, we observed that age-associated lipid peroxidation and semiquinone radicals were decreased with GCN5L1 KO. RNA sequencing analysis identified mitochondrial bioenergetic and respiratory pathways revolving around the respiratory chain to be enriched in the old KO group. Further, we showed the old KO group to exhibit reduced acetylation of ETC complex and antioxidant proteins, improved ETC complex and antioxidant protein activity. Overall, GCN5L1 regulates redox homeostasis in the aged heart by regulating mitochondrial ETC complex activity, oxidative stress, and mitochondrial bioenergetics. These findings identify GCN5L1 and acetylation as potential therapeutic targets in aging and age-related diseases. Full article

Understanding the reproductive physiology of marine fish is critical for sustainable fisheries management, particularly under environmental variability. This study evaluated seasonal changes in body parameters (condition factor, Kn, and gonadosomatic index, GSI, as proxies for body condition and reproductive status, respectively) and biochemical composition (P, proteins; G, glucose; L, lipids; fatty acids; and bioenergetic ratios L/P, LG, all as proxy of integrated biochemical condition) of female gonads in Strangomera bentincki, a key pelagic species in the Humboldt Current System (HCS) off south-central Chile. Moreover, environmental factors (sea surface temperature and chlorophyll-a) were also analyzed to explore their influence on the FA profile of gonads. Female body parameters showed significant seasonal variations, with high values of Kn and GSI in autumn and spring, respectively. The biochemical composition also revealed significant seasonal variation in protein and glucose content, with the highest protein levels in winter and elevated glucose in autumn. While total lipid and energy content remained relatively stable across seasons, the L/P and L/G ratios presented seasonal variations. Similarly, the fatty acid composition showed pronounced seasonal differences, particularly with increased polyunsaturated fatty acids (e.g., DHA) in winter. The SST was the environmental factor with the greatest influence on the seasonal variations in the gonadal FA profile. Altogether, these findings suggest a partial capital breeding strategy in S. bentincki, where reproductive investment depends on both accumulated reserves and environmental conditions during reproduction. This study underscores the importance of incorporating reproductive biochemical indicators into ecosystem-based fisheries management models to improve assessments of stock health and reproductive potential. Full article

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease marked by progressive degeneration of motor neurons and skeletal muscle. Gene expression analysis of the spinal cord and gastrocnemius of the SOD1-G93A ALS mouse model revealed a strong increase in inflammatory pathways and, specifically in the ALS gastrocnemius, a decrease in mitochondrial transcription and an increase in ribosomal protein expression. Treatment of ALS mice with the polyamine spermidine (SPD), a promising molecule in combating neurodegeneration and muscle atrophy, is able to partially restore the expression of more than four thousand genes in gastrocnemius tissue, including the mitochondrial regulator Pgc1α, as well as all the mitochondrial encoded genes and a large class of ribosomal proteins. SPD enhanced mitochondrial bioenergetics, as evidenced by Seahorse experiments, and delayed muscle weakness in vivo, as shown by grip strength records. These findings suggest that SPD can act as a potential supplement in the therapeutic strategy for ALS, offering a foundation for further research to improve patient outcomes. Full article

A549 cells are widely used as an in vitro model of alveolar type II (ATII) epithelial cells; however, their phenotype and metabolic state are highly sensitive to culture conditions, cell density, and the duration of static, non-passaged cultivation. Here, we examined how prolonged static culture affects lipid metabolism, mitochondrial bioenergetics, and viability in A549 cells. A549 cultures were maintained without passaging for up to 25 days in DMEM or Ham’s F-12 and analyzed using lipid secretion assays, targeted lipidomics, [¹⁴C]-acetate incorporation, Seahorse bioenergetic profiling, and transcriptional analysis of stress-associated markers. Several surfactant-associated readouts were highest during early culture, peaking on day 7, as evidenced by elevated expression of ABCA3 and SP-A and maximal secretion of surfactant-associated phospholipids. With prolonged cultivation and increasing culture density, cellular phosphatidylglycerol levels declined progressively and became nearly undetectable by day 25, accompanied by reduced anabolic lipid metabolism, lower oxygen consumption, and impaired glycolytic activity. These changes coincided with increased reactive oxygen species, elevated intracellular Ca²⁺ levels, and increased expression of stress-associated transcripts, including CASP1, IL1B, and C3. Later stages were also associated with reduced mitochondrial respiration and decreased viability. Collectively, our findings show that prolonged static culture is associated with metabolic remodeling and reduced bioenergetic capacity in A549 cells. Full article

The Amazonian açaí waste is promising for producing charcoal through pyrolysis and bioenergy through combustion, but the property losses from its poor disposal in the environment remain unknown. Therefore, this work aimed to analyze how different storage conditions of the açaí waste over time, which mimic the reality throughout the Amazon, modify its bioenergetic properties. The samples were stored in a covered greenhouse for nine months in the following conditions: immersed in water, on the soil, and in open plastic bags. The biomass was analyzed by Fourier-transformed near-infrared spectroscopy, physical properties, stereomicroscopy, proximate composition, and thermogravimetry. The degraded waste showed endocarp attack and fungi proliferation. The chemical groups of primary cell wall components were concentrated, unlike water-soluble materials, raising the fixed carbon from 22% to 25% after 30 days. Consequently, higher heating values were kept (≈19 MJ/kg). However, water immersion storage sharply decreased the waste basic density from 0.81 g/cm³ to 0.56 g/cm³, dropping the energy density from 12 GJ/m³ to 8 GJ/m³. Moreover, storage raised ash content from 1.1% up to 1.9%. The storage hindered the start of the main phases of combustion and pyrolysis, which were later intensified, especially for soil-stored waste. Therefore, more stable combustion and pyrolysis require fresh waste. Besides natural drying, plastic bag storage over time kept the waste quality closer to that of the fresh waste. Full article

Background: Metabolic syndrome is associated with early impairments in cellular bioenergetics that are not fully captured by conventional body composition measures. Molecular hydrogen, produced endogenously through gut microbial fermentation and measurable in breath, has been implicated in redox and mitochondrial regulation. Whether breath hydrogen relates to preservation of intracellular, metabolically active tissue in metabolic syndrome remains unclear. Objectives: To examine the association between breath hydrogen concentration and an integrated cellular bioenergetic phenotype derived from intracellular body composition indices in sedentary adults with metabolic syndrome. Methods: Twenty-eight sedentary, middle-aged adults (51.2 ± 7.9 years, 19 females) with metabolic syndrome underwent fasting breath hydrogen assessment and multifrequency bioelectrical impedance analysis. A composite cellular bioenergetic phenotype was derived using principal component analysis of body cell mass, intracellular water, total body potassium, and glycogen. Associations between breath hydrogen and the composite phenotype were evaluated using Spearman correlation with bootstrapped confidence intervals, Theil-Sen regression, and Bayesian linear regression adjusted for age, sex, and waist circumference. Sensitivity analyses included fat-free mass. Results: A single principal component explained 98.6% of the variance across intracellular variables, indicating a highly coherent cellular bioenergetic phenotype. Breath hydrogen concentration was positively associated with this phenotype (ρ = 0.43, p = 0.021; BCa 95% CI 0.07–0.70). Theil-Sen regression confirmed a robust positive association (β = 0.017 per ppm hydrogen; 95% CI 0.002–0.046). Bayesian models showed posterior distributions centered on positive effect sizes, independent of central adiposity. In contrast, the association with fat-free mass alone was borderline. Conclusions: Breath hydrogen concentration reflects an integrated intracellular bioenergetic phenotype in sedentary adults with metabolic syndrome, tracking cellular quality rather than lean mass quantity. Breath hydrogen may serve as a non-invasive biomarker of cellular bioenergetic integrity and a potential tool for phenotype-guided metabolic interventions. Full article