Biology doi: 10.3390/biology15141156

Authors: Ares Alizade Nur Akman

Ciprofloxacin (CPX) has been associated with neuropsychiatric adverse effects; however, its contribution to depression-like behaviors and the underlying neurobiological mechanisms remain insufficiently characterized. Previous studies have indicated that cinnamic acid (CA) may exert protective actions in the nervous system by modulating oxidative and inflammatory pathways. Nevertheless, its effectiveness in preventing CPX-induced neurobehavioral impairments remains largely unknown. The present study aimed to investigate whether CA attenuates CPX-induced depression-like behaviors through modulation of neuroinflammation and oxidative stress. This study included 60 male Swiss albino mice distributed among six experimental groups (n = 10). Animals were assigned to receive a vehicle, CPX administered at 80 mg/kg, CPX combined with CA at doses of 50, 100, or 200 mg/kg, or CPX together with FLX (20 mg/kg) throughout the 14-day treatment period. Behavioral alterations were assessed using social interaction, forced swimming, tail suspension, and sucrose preference paradigms. In addition, hippocampal and prefrontal cortex tissues were examined for oxidative stress markers (MDA, GSH, and CAT), pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6), and neurotransmitters (serotonin, dopamine, and GABA) using ELISA-based assays. CPX administration induced significant depression-like behaviors, evidenced by reduced social interaction, increased immobility, and anhedonia (p < 0.05). These behavioral alterations were associated with increased lipid peroxidation, impaired antioxidant defense, elevated pro-inflammatory cytokine levels, and decreased monoaminergic and GABAergic neurotransmission in both HIP and PFC regions. CA treatment significantly improved CPX-induced behavioral and neurochemical alterations. Among the tested doses, the 100 mg/kg regimen produced the most consistent response, accompanied by reduced neuroinflammatory activity and restoration of neurotransmitter levels, particularly in the hippocampus. In conclusion, CA mitigated CPX-induced behavioral deficits and neurochemical alterations, an effect that may be attributed to its regulatory influence on oxidative stress, neuroinflammatory processes, and neurotransmitter balance within the HIP–PFC pathway. Collectively, the findings indicate that CA may have therapeutic relevance in reducing the neuropsychiatric consequences associated with CPX exposure.

Biology doi: 10.3390/biology15141155

Authors: Turki Turki Y.-H. Taguchi

Understanding gene expression requires integrating multiple regulatory layers, because transcript abundance does not necessarily correspond to translational activity or protein abundance. Ribosome profiling and proteomics help distinguish increased translation from ribosome stacking or translational buffering, but no de facto standard framework exists for unsupervised integration of transcriptome, translatome, and proteome profiles. Here, we propose a four-dimensional tensor decomposition-based unsupervised feature extraction approach for tri-omics integration. We applied higher-order singular value decomposition to transcriptome, Ribo-seq, and proteome profiles measured under branched-chain amino acid starvation. The resulting singular value vectors captured relationships among the three omics layers, including a component consistent with ribosome stacking, where transcriptome and translatome signals increased while proteome signals decreased, and another consistent with translational buffering, where proteome variation was suppressed despite transcriptome and translatome changes. Gene selection identified 1781 genes associated with ribosome stacking and 227 genes associated with translational buffering. Enrichment analyses linked the former to translation, post-translational protein modification, RNA polymerase II transcription, cell cycle regulation, endoplasmic reticulum protein processing, ubiquitin-mediated proteolysis, and stress-related pathways, and the latter to ribosome, translation elongation and termination, spliceosome, immune- and stress-related pathways, and ribosomopathy-associated diseases. Robustness analyses indicated that the results were not substantially affected by the duplicated proteome replicate or missing-value handling. Under the tested settings, comparison with MOFA+ and mixOmics suggested that our approach more directly extracted components interpretable as ribosome stacking and translational buffering. These results demonstrate that tensor decomposition-based unsupervised feature extraction is useful for identifying functionally relevant gene clusters from tri-omics data.

Biology doi: 10.3390/biology15141154

Authors: Luis Eduardo López-Vargas Diego Jesús Macías-Pinto Jhoy Fleming Córdoba-Calvo Jorge Hernan Patiño Rodriguez

Sub-Andean forests of the Colombian Central Cordillera are among the most biodiverse and threatened Neotropical ecosystems, yet their floristic composition, vegetation structure, and aboveground carbon storage remain poorly documented. We characterized the floristic diversity, vegetation structure, and aboveground carbon storage of the El Mangón sub-Andean forest remnant (24 ha; 1600–1700 m a.s.l., Cauca, Colombia) using general (non-systematic) collections across the total area and a structural inventory in five 50 × 4 m transects (498 individuals, 35 species). A total of 281 species, 209 genera, and 99 families were recorded; epiphytes represented 44.13% of species, exceeding typical values (25–35%) for this forest type. Diversity indices were intermediate (H′ = 2.55; DMg = 5.47; 1-D = 0.89). Palicourea crocea dominated structurally (IVI = 45.12), whereas aboveground carbon—re-estimated with the pantropical model (total = 72.85 Mg C ha−1)—was concentrated in a few large canopy trees (Alchornea latifolia, 32%; Myrsine guianensis, 16%), with P. crocea contributing only 3.6%. Three novel carbon indices (CVI, CCEI, CSI) integrate storage magnitude with capture efficiency and spatial stability; the CSI differed significantly among spatial-distribution groups (Kruskal–Wallis, p = 0.003), being higher in aggregated, large-stemmed species than in low-aggregation species. El Mangón ranks among the most diverse sub-Andean remnants documented to date in southwestern Colombia, underscoring its conservation priority in an increasingly fragmented landscape.

Biology doi: 10.3390/biology15141153

Authors: Zhanat Amanova Zhanna Sametova Sholpan Turyskeldy Alina Kurmasheva Ruslan Abitayev Abdurakhman Ussembay Zhanat Kondibayeva Dariya Toktyrova Dana Mazbayeva Sergazy Nurabayev Aslan Kerimbayev Yerbol Bulatov

Additional Affiliation [...]

Biology doi: 10.3390/biology15141152

Authors: Juan E. Dajil Carolina Block Laura E. Vega Pedro A. Garzo Oscar A. Stellatelli

The 21st century is defined by converging anthropogenic and biophysical stressors. This study assessed the vulnerability of the endemic specialist lizard Liolaemus multimaculatus and the habitat generalist L. wiegmannii to climate change and land-use/land-cover (LULC) transformation within the Pampean Eastern Dune Barrier up to 2050. Using satellite data, LULC spatial projections, and ecological niche models (ENMs), we quantified habitat dynamics and projected future climatic suitability. Historical analysis (1994–2022) revealed a 20% retraction of active dunes driven by exotic afforestation and urban growth. Projections for 2050 indicate an intensification of these trends, with urban areas accounting for nearly 26% of the regional territory, leading to an additional 17% loss of active dunes. Abundance modeling predicted a decline in L. multimaculatus within the remaining active dunes, while ENMs projected a near-total contraction of climatically suitable areas. Crucially, these correlative models may overlook potential physiological or behavioral adjustments; however, the limited dispersal capacity and physical landscape barriers inherent to this specialist likely preclude effective niche tracking. These findings confirm that ecological specialization heightens sensitivity to global change, creating a “double threat” for endemic species. Protecting remnant active dune patches is essential to mitigate the projected collapse of these range-restricted lineages.

Biology doi: 10.3390/biology15141151

Authors: Furkan Türkoğlu Ahmet Gedik Berk Koncalıoğlu Elif Nur Gencer Necip Gökhan Güner İlteriş Türk Batuhan Gencer Özgür Doğan

Objectives: Aging is associated with immunosenescence, which may alter the physiological response to trauma and influence long-term outcomes. This study aimed to compare clinical and laboratory parameters associated with in-hospital (iHM) and one-year mortality (OYM) between adult and geriatric patients with multisystem trauma and to explore laboratory findings consistent with immunosenescence in geriatric patients. Methods: In this retrospective study, 345 patients with multisystem trauma were categorized into adult (n = 255) and geriatric (n = 90) groups according to age. Clinical characteristics and laboratory parameters obtained at emergency department admission were analyzed in relation to iHM and OYM. Results: Although iHM did not differ significantly between groups (p = 0.764), OYM was significantly higher in the geriatric group (p < 0.001). In adults, iHM was associated with a higher Injury Severity Score (ISS), prolonged intensive care unit (ICU) stay, elevated white blood cell and monocyte counts, and hypoalbuminemia. OYM in adults was further associated with a higher ISS, longer hospital stays, and lower hemoglobin and hematocrit levels. In geriatric patients, iHM was associated with a higher ISS, male sex, high-energy trauma, elevated lymphocyte and creatinine levels, and lower hematological ratios. OYM in the geriatric group was additionally associated with advanced age, major surgical intervention, thrombocytopenia, elevated urea–creatinine levels, hypoalbuminemia, and lower hematological ratios. Conclusions: Despite comparable in-hospital mortality, geriatric patients with multisystem trauma demonstrated significantly higher one-year mortality. The reduced post-traumatic inflammatory response observed in geriatric patients may be indicative of underlying immunosenescence and diminished immune reserve, thus emphasizing the necessity for age-specific prognostic models in trauma care.

Biology doi: 10.3390/biology15141150

Authors: Pengcheng You Anye Chen Qiancheng Feng Junhong Hou Jiacheng Zheng Hao Chen

Hyperuricemia (HUA) is a common immunometabolic disorder associated with gout, renal dysfunction, and systemic inflammation, yet the molecular targets through which non-starch polysaccharides (NSPs) may modulate HUA-related inflammation remain unclear. Here, we applied an integrative bioinformatics and computational workflow combining public transcriptomic datasets, curated NSP-related targets, protein–protein interaction analysis, enrichment analysis, single-cell RNA sequencing, and Mendelian randomization. We further included GutMGene-based orthogonal support analysis, guided docking, structural dynamics analysis, exploratory ADMET profiling, and in silico TLR4 knockout to extend target prioritization. This approach prioritized a TLR4-centered inflammatory module, with TLR4, MSR1, TIRAP, and CXCL8 emerging as candidate genes. Enrichment analyses linked these genes to innate immune and NF-κB-related pathways, whereas single-cell analyses localized the prioritized signals mainly to myeloid compartments during gout flares. Mendelian randomization suggested positive associations between genetically predicted expression of TLR4-axis genes and serum uric acid levels. Under electrostatic-guided docking conditions, fucoidan and alginate yielded plausible interaction models with TLR4, and normal mode and RMSF analyses suggested altered flexibility in the MD-2 region. In silico Tlr4 knockout further perturbed urate-handling programs in renal proximal tubule-enriched cells. Together, these findings do not establish TLR4 as a newly discovered hyperuricemia gene or confirm direct receptor antagonism by NSPs, but they provide an NSP-oriented integrative framework that prioritizes the TLR4 axis, highlights myeloid-cell relevance, and nominates fucoidan and alginate for experimental follow-up.

Biology doi: 10.3390/biology15141149

Authors: Paweł Gordon Łukasz Szeleszczuk Małgorzata Lasota Dariusz Maciej Pisklak Marcin Gackowski

Factor Xa (FXa) remains an important target in the development of anticoagulant and antithrombotic agents. In this study, twenty isosteviol-derived oxime ether analogs previously reported as FXa inhibitors were used to develop a predictive QSAR model. The compounds were geometry-optimized at the B3LYP/6-311++G(d,p) level, and Dragon molecular descriptors were calculated from the optimized structures. After descriptor filtering, Random Forest-based supervised preselection and correlation-based pruning were applied. Several models of increasing complexity were evaluated, including multiple linear regression, additive MARSplines, and constrained second-order MARSplines models. The final model employed four active basis functions involving R6p+, C-025, ATSC7e, and Mor31p and demonstrated excellent calibration and cross-validated predictive ability (R2 = 0.929 and Q2_LOO = 0.865). Based on this model, twenty new isosteviol-derived analogs were designed and their activities were predicted after DFT optimization and descriptor calculation. Eight representative compounds were subsequently subjected to molecular docking against human factor Xa (PDB ID: 2P16), molecular dynamics simulations, MM/GBSA binding free energy calculations, and preliminary SwissADME/pkCSM profiling. Docking protocol validation yielded a redocking RMSD of 0.953 Å. Although ISV-M20 was the highest-ranked compound according to the QSAR model, subsequent receptor-based analyses identified ISV-M19, ISV-M04, and ISV-M06 as the derivatives with the most favorable combination of structural stability, persistent protein–ligand interactions, and binding free energies. The ADMET/toxicity screen further refined this prioritization: ISV-M19, ISV-M04, and ISV-M06 showed the most favorable preliminary toxicity balance among the prioritized derivatives, whereas ISV-M20 displayed additional developability liabilities, including very high lipophilicity, poor predicted solubility, P-gp substrate status, and a predicted hERG II alert. Overall, the results demonstrate that integrating interpretable QSAR modeling with receptor-based simulations and early ADMET/toxicity filtering provides a more balanced strategy for the rational design and prioritization of novel isosteviol-derived FXa inhibitors than any single computational approach alone.

Biology doi: 10.3390/biology15141148

Authors: Qiang Li Jianmei He

Selective hearing in multi-talker environments remains a central challenge for assistive listening technologies: conventional devices improve audibility but cannot infer which talker the listener intends to follow. This Perspective examines the emerging transition from auditory attention decoding to neuro-steered selective hearing. We argue that a recent real-time intracranial proof-of-principle study marks an important inflection point in this transition, because it shows, under high-fidelity recordings from neurosurgical patients and in controlled two-talker conditions, that decoded neural attention can be coupled online to relative-gain control, thereby improving speech perception and reducing listening effort within that experimental setting. Building on this proof of principle, we argue that the field should move beyond offline decoding accuracy as its primary benchmark and instead treat neuro-steered hearing as a closed-loop translational problem linking neural inference, acoustic scene analysis, and control policy. From this perspective, future benchmarks should integrate device-level control metrics, including latency, effective switch time, false-switch rate and recovery after erroneous updates, with listener-centered outcomes such as speech intelligibility, listening effort, user preference and everyday benefit. Accordingly, we outline a staged roadmap for electroencephalography-based systems, from controlled two-speaker paradigms to scene-aware control and ultimately wearable real-world implementations. We also discuss the complementary roles of magnetoencephalography, functional near-infrared spectroscopy, and functional magnetic resonance imaging in defining the neural mechanisms and design constraints of future systems. Overall, this Perspective frames neuro-steered selective hearing as a systems-level research pathway for evaluating whether neural attention signals can be translated into practical assistive listening technologies.

Biology doi: 10.3390/biology15141147

Authors: Cristóbal Garcés Carlos Vega Pablo Fierro

Chinook salmon Oncorhynchus tshawytscha (Walbaum, 1792) is a non-native species in southern South America, where self-sustaining populations are established. After spawning migrations, adults die and provide substantial subsidies to freshwater food webs. We report the first direct evidence of predation on spawning Chinook salmon by South American sea lions Otaria byronia (de Blainville, 1820) in a river of southern Chile, up to 160 km upstream from estuaries. Sea lions appear to be exploiting a novel prey resource, indicating behavioral plasticity with potential ecological consequences for native species and riverine trophic dynamics. We discuss the implications of this previously unreported predator–prey interaction for the ecology of invaded freshwater systems in South America.

Biology doi: 10.3390/biology15141146

Authors: Md. Zahorul Islam Mohammad Enamul Hoque Kayesh Michinori Kohara Kyoko Tsukiyama-Kohara Atsushi Miyamoto

The tree shrew (Tupaia belangeri) is increasingly recognized as an important experimental model for studying human diseases due to its close phylogenetic relationship with humans. Because the basilar artery’s response to endogenous vasoactive mediators varies among species, we investigated the effects of vasoactive substances on isolated tupaia basilar arteries to determine whether this species is suitable as a human model. 5-Hydroxytryptamine (5-HT) and histamine (His) induced contraction, while bradykinin (BK) and acetylcholine (ACh) produced concentration-dependent relaxation. Pharmacological analysis revealed that contractions triggered by 5-HT were regulated through 5-H1 and 5-HT2 receptors, while His-induced responses were mediated by H1 receptors. BK-induced relaxation was inhibited by the B2 antagonist HOE140 and Nω-nitro-L-arginine (L-NA), but not by B1 antagonists or indomethacin, suggesting a B2 receptor-mediated nitric oxide (NO) pathway. ACh-induced relaxation was markedly reduced in the presence of L-NA and the M3 antagonist pFHHSiD, indicating M3 receptor-mediated NO release. At basal tone, L-NA evoked a contractile response, while indomethacin led to relaxation, suggesting basal regulation by NO and prostanoids. These findings demonstrate that 5-HT1/5-HT2 and H1 receptors mediate contraction, while B2 and M3 receptors mediate relaxation in the tupaia basilar artery. This study highlights species-specific cerebrovascular regulation and supports the tupaia as a relevant model for investigating human cerebrovascular physiology and pathophysiology.

Biology doi: 10.3390/biology15141145

Authors: Mario García-Domínguez

Chronic pain represents a significant clinical challenge and is frequently associated with neuroinflammatory processes. The blood–brain barrier plays a central role in protecting the central nervous system by regulating the passage of molecules and immune cells from the periphery. Emerging evidence indicates that in chronic pain conditions, BBB integrity can be compromised, facilitating the infiltration of pro-inflammatory cytokines, immune cells, and neurotoxic mediators into the CNS. These changes contribute to microglial and astrocyte activation, enhancing central sensitization and the persistence of pain. Animal models and clinical studies suggest that mechanisms including tight junction disruption, oxidative stress, and matrix metalloproteinase release underlie this increased permeability. Understanding BBB modulation in chronic pain not only clarifies disease pathophysiology but also highlights potential therapeutic strategies aimed at preserving or restoring barrier integrity.

Biology doi: 10.3390/biology15141144

Authors: Le Wang Yuxiang Wang Hao Chen Zhiming He Yanping Long Lisha Yu Chuli Xiao Jiaxiu Zhou Xudong Yu Qingshan Long Xinhua Shu

Background: Depression-associated memory impairment is a clinically significant comorbidity that responds poorly to conventional antidepressants. Dihydromyricetin (DHM), a natural dihydroflavonoid, exhibits neuroprotective and antidepressant-like effects, but its impact on stress-induced memory deficits and the underlying mechanisms remain unclear. Methods: A chronic restraint stress (CRS) mouse model was employed. DHM was intraperitoneally administered daily (20 mg/kg bodyweight) for 8 consecutive days. Depression-like behavior and memory functions were assessed with the tail suspension test, the object recognition memory (ORM) task, and the Y-maze test. Network pharmacology, molecular docking, and molecular dynamics (MD) simulations were integrated to predict potential targets and associated signal pathways. Expression of hippocampal PKA, p-CREB, CREB, and BDNF was measured through Western blotting. Results: CRS significantly increased immobility time in the tail suspension test and impaired both recognition memory (ORM) and spatial working memory (Y-maze), without affecting locomotor activity. DHM treatment effectively reversed behavioral despair and memory deficits. Network pharmacology identified 47 intersecting targets between DHM and depression-related memory impairment, with CREB1, ESR1 and NOS1 as core hub nodes. KEGG enrichment particularly implicated the involvement of the cAMP signaling pathway and other signaling pathways, which are associated with depression and/or memory impairment. Molecular docking predicted strong binding affinities of DHM to CREB1 (−9.225 kcal/mol), NOS1 (−9.113 kcal/mol) and ESR1 (−7.903 kcal/mol). MD simulations confirmed the thermodynamic stability of DHM-ESR1 and DHM-NOS1 complexes. Western blot analysis demonstrated that DHM treatment significantly increased the levels of hippocampal PKA, p-CREB and BDNF, without altering total CREB expression in CRS mice. Conclusions: DHM alleviated CRS-induced depression-like behaviors and memory deficits, possibly through regulation of multiple signaling pathways, including the hippocampal PKA-CREB-BDNF signaling pathway. These findings highlight DHM as a promising natural therapeutic candidate for depression-associated cognitive impairment.

Biology doi: 10.3390/biology15141143

Authors: Magda Sochaczewska Waclaw Tworzydlo

Oocyte aging is a conserved biological process that limits reproductive success across animal taxa. While most research has focused on mammalian systems, particularly humans, comparative studies reveal both shared molecular mechanisms and lineage-specific adaptations that shape oocyte longevity. Here, we synthesise current knowledge on chromosomal instability, mitochondrial dysfunction, proteostasis collapse and epigenetic alterations, integrating insights from insects, nematodes and vertebrates. We argue that these phenomena should not be viewed as independent hallmarks of reproductive aging but rather as interconnected manifestations of a progressive decline in cellular quality control networks. By comparing taxa, we identify both conserved vulnerabilities, including cohesin loss, mitochondrial deterioration and genome instability, and lineage-specific adaptations that mitigate their effects. We further propose the hypothesis that biomolecular condensates, including the Balbiani body, nuage and recently described endolysosomal assemblies, may function as higher-order organizational hubs coordinating mitochondrial quality control, proteostasis and genome defence. This perspective provides a unifying framework for understanding oocyte aging as a systems-level process and highlights new directions for future studies of reproductive longevity.

Biology doi: 10.3390/biology15141142

Authors: Jian Chen Daomin Liu Peifeng Zhu Lu Liu

Background: The rising global prevalence of hyperlipidemia is closely linked to current dietary patterns, sparking interest in “medicine-food homology” (MFH) plants as natural resources that provide both nutritional benefits and therapeutic effects. This study reviews MFH plants used to treat hyperlipidemia, incorporating changes in regulatory mechanisms, the impact of processing on bioavailability, and evidence of their lipid-lowering effects. Methods: This narrative review, supported by a structured literature search, summarizes the practical applications of MFH plant species with both medicinal and edible properties and discusses their bioactive components and lipid-regulating mechanisms. Results: MFH plants not only contain anti-lipid active ingredients but also have improved bioavailability after processing through processing technology and function through lipid metabolism pathways and the gut-liver axis. Conclusions: The development and application of MFH plants face several challenges, including incomplete and inconsistent international regulatory frameworks, difficulties in quality control, and limited clinical evidence for lipid-lowering mechanisms. Nevertheless, MFH plants hold promise for development into functional foods or nutraceuticals aimed at supporting lipid regulation.

Biology doi: 10.3390/biology15141141

Authors: David Jiménez-De-Juan Félix Adanero-Jorge Carlos Alonso-Calleja Rosa Capita

The increasing prevalence of antibiotic resistance highlights the need to seek alternatives to currently used compounds. Minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) of nine ethanolic extracts of propolis (EEPs) from northwestern Spain and five phenolic compounds (carvacrol, eugenol, thymol, resveratrol, and trans-cinnamaldehyde) against Listeria spp. and Salmonella enterica strains were determined. All EEPs showed a strong antimicrobial effect against Listeria spp., with MICs (ppm) ranging between 78.00 ± 0.00 and 1041.67 ± 360.84 and MBCs (ppm) ranging between 312.50 ± 0.00 and 3333.33 ± 1443.38. The concentration of caffeic acid phenethyl ester (CAPE), isoprenyl caffeate (IPC), or total polyphenols did not influence the antimicrobial activity of EEPs. However, EEPs had only slight antimicrobial activity against S. enterica, with MICs ≥ 10,000 ppm and MBCs exceeding 10,000 ppm. MIC values (ppm) for phenolic compounds with respect to Listeria spp. strains ranged from 125.00 ± 0.00 to 2500.00 ± 0.00, and those for MBCs (ppm) ranged from 250.00 ± 0.00 to 5000.00 ± 0.00. For S. enterica, MICs (ppm) ranged from 250.00 ± 0.00 to 2500.00 ± 0.00 and MBCs (ppm) ranged from 416.67 ± 144.34 to 5000.00 ± 0.00. The results suggest that EEPs and phenolic compounds may offer natural alternatives to other antimicrobials in common use, with phenolic compounds being especially promising because of their antimicrobial activity against both Gram-positive and Gram-negative species.

Biology doi: 10.3390/biology15141140

Authors: Sun Kyeong Choi Seul Yi Samuel Praveen Young Baek Son Seonggil Go

Human-mediated species translocations are increasingly interacting with global climate change, yet empirical insights into how introduced populations achieve long-term demographic stability in new frontiers remain limited. This study systematically investigates the post-translocation establishment and multi-generational persistence of the endemic cyprinid Squalidus multimaculatus at its newly identified northern distribution limit in Goseong, Republic of Korea, following historical human-mediated introduction. Utilizing nationwide multi-decadal occurrence records, we mapped the species’ spatio-temporal dynamics across three temporal phases (T0, T1, and T2). Long-term biogeochemical water quality indices and thermal regimes were compared between the native baseline (Yeongdeok) and Goseong. Furthermore, demographic shifts and growth trajectories were evaluated using 676 field-sampled specimens through length–weight relationships, condition factor (KF) analysis, age structure mixture modeling, and the von Bertalanffy growth function (VBGF). Our results indicate that the Goseong habitat provides generally favorable biogeochemical conditions characterized by low nutrient loading and high dissolved oxygen stability. Crucial to this transition, a distinct winter warming shift expanded the available thermal window, reducing the frequency of extreme winter cold-stress events (≤2.0 °C) from 40.0% to 6.9%. Concurrently, the post-translocation population exhibited successful demographic stability, characterized by a self-sustaining age structure (ages 0+ to 4+), an inferred spawning window during June–July, and a growth trajectory (L∞ = 95.69 mm) broadly comparable to native benchmarks. These findings establish a reliable empirical baseline framework linking human-mediated introductions with long-term environmental transitions. Globally, this case study suggests that post-translocation success depends on the interplay between introduction pathways and climate suitability, offering key insights into population survival and ecosystem evolution under global change.

Biology doi: 10.3390/biology15141139

Authors: Rebecka Salwén Mehdi Amirhosseini Said Havarinasab

In the original publication [...]

Biology doi: 10.3390/biology15141138

Authors: Jae-Yong Park Wael Abdel-Fattah F. Marion Hulett

The PhoP–PhoR two-component system (TCS) controls transcription of the Pho regulon in response to inorganic phosphate limitation in Bacillus subtilis. In addition to its role in phosphate homeostasis, increasing evidence suggests that central metabolic pathways influence Pho regulon activity. Here, we investigated the mechanism underlying phosphate-independent activation of the Pho regulon in a ccpA mutant lacking the global regulator of CCR. Gene expression analyses demonstrated strong glucose-dependent induction of Pho regulon genes in the absence of both CcpA and the cognate histidine kinase PhoR. Using PhosTag gel electrophoresis analysis and a phoasphoablative mutation in phoP (D53A), we detected early PhoP phosphorylation and determined that Pho regulon activation requires a phosphorylatable form of PhoP, even when the cognate histidine kinase phoR gene was deleted. Because PhoR can phosphorylate non-cognate response regulator YycF, we examined whether the essential YycFG signaling system contributes to PhoP activation. Co-immunoprecipitation and in vitro phosphorylation assays confirmed a direct interaction between PhoP and YycG and demonstrated in vitro PhoP phosphorylation by YycG. Taken together, we propose a model in which CcpA limits excessive PhoP accumulation to preserve signaling specificity and prevent aberrant activation through non-cognate kinases. Furthermore, our study reveals a previously unrecognized link between carbon catabolite repression and phosphate starvation signaling and demonstrates another crosstalk between two-component signal transduction systems in the Gram-positive bacterium, B. subtilis.

Biology doi: 10.3390/biology15141137

Authors: Yong Chen Milana Frenkel-Morgenstern

Biological systems are inherently complex, dynamic, heterogeneous, and organized across multiple spatial and temporal scales [...]

Biology doi: 10.3390/biology15141136

Authors: Xinyi Huang Sichen Wei Wenkai Ding Yian Xiao Qitao Su

Ecological network resilience is an important indicator for evaluating whether regional ecosystems can maintain structural connectivity and functional stability under external disturbance. However, long-term changes in ecological network structure and robustness in the Poyang Lake Eco-economic Zone remain insufficiently understood. Based on land-use data from 1990, 2000, 2010, and 2020, this study integrated Morphological Spatial Pattern Analysis (MSPA), landscape connectivity assessment, the MCR model, complex network analysis, and robustness simulations to evaluate the spatio-temporal evolution of ecological network resilience in the Poyang Lake Eco-economic Zone. The results showed that the area of selected ecological sources in the study area decreased from 39.97% in 1990 to 33.14% in 2020, indicating continuous source-area shrinkage and habitat fragmentation. The ecological resistance surface showed increasing spatial heterogeneity, with relatively low resistance in mountain and lakeside wetland areas and high resistance in the central plain areas affected by agricultural and construction-land expansion. Topological analysis showed that network density increased from 0.10 to 0.15, average path length decreased from 3.04 to 2.53, and network efficiency increased from 0.34 to 0.45, suggesting enhanced local connectivity and transmission efficiency. However, the largest connected component decreased from 37 to 26, indicating a decline in regional-scale connectivity and an increasing risk of network fragmentation. Robustness simulations further showed that the network was relatively tolerant to random disturbance but highly sensitive to the priority failure of key nodes and corridors. Overall, the ecological network evolved from relatively continuous connectivity toward local clustering and residual trunk corridors. These findings suggest that ecological restoration in the Poyang Lake Eco-economic Zone should prioritize major ecological sources, cross-regional corridors, stepping-stone habitats, and critical linkage areas to improve network-level resilience.

Biology doi: 10.3390/biology15141135

Authors: Jianqing Zhao Wei Wang Jiayidaer Kamalibieke Yuanpan Mu Chenbo Shi Jun Luo

High-quality reference panels are important resources for genotype imputation and genomic selection in dairy goats; however, dairy-goat reference panels remain limited in sample size, population representation, and standardized workflow evaluation. In this study, 1092 dairy-goat samples from multiple populations, and public resequencing datasets, were integrated to construct and evaluate a dairy-goat reference panel for low-coverage whole-genome sequencing (lcWGS) and SNP-array data. Phasing and imputation strategies were compared using Beagle 5.4, SHAPEIT5, GLIMPSE2, and a BaseVar + Beagle pipeline, and the effects of reference-panel diversity, panel size, sequencing depth, and genotyping platform were evaluated using concordance, imputation quality score (IQS), and squared dosage correlation (r2). Beagle 5.4 phasing combined with GLIMPSE2 imputation reduced computational time by approximately 40% while maintaining high imputation accuracy. The largest evaluated panel (n = 1000) achieved concordance = 0.98, IQS = 0.94, and r2 = 0.91, while a practical population-size threshold of 600–800 individuals balanced accuracy gains and resource costs. Reference panels containing two to three genetically similar dairy-goat populations achieved stable performance, with concordance values above 0.90 and chromosome-level r2 values above 0.91. Low-coverage sequencing at 0.5× or above effectively reduced the loss of accuracy for low-frequency variants, whereas imputed SNP-array data increased marker density from 18 to 180 to 1850–18,500 SNPs per 1 Mb window in representative regions, corresponding to an approximately 103-fold increase, and produced more concentrated GWAS signal peaks on Chr5, Chr8, Chr17, and Chr19. These findings establish a technical framework and reference resource for genotype imputation, association analysis, and genomic selection in dairy goats.

Biology doi: 10.3390/biology15141134

Authors: Panpan Wang Xinxin Wang Meitong Pan Zhenzhen Li Lingyang Kong Wei Ma Xiubo Liu

Astragalus mongholicus is one of the original plant species of the medicinal herb Astragali Radix as recorded in the Chinese Pharmacopoeia, possessing significant medicinal value and being widely utilized worldwide. TCP transcription factors constitute a plant-specific transcription factor superfamily that plays essential regulatory roles in vegetative growth, organ development, and abiotic stress responses. However, the TCP gene family in A. mongholicus has not yet been systematically investigated, and its functional characteristics remain largely unknown. In this study, based on genome-wide data, a total of 25 AmTCP genes containing complete TCP domains were identified in A. mongholicus, and their protein properties, sequence alignment, gene structures, and phylogenetic relationships were systematically characterized using comprehensive bioinformatics tools. Promoter cis-element analysis revealed that the AmTCP promoter regions are enriched in cis-elements associated with hormones, light, and abiotic stresses (drought and salinity), suggesting their potential involvement in multiple signaling cascades. Furthermore, transcriptomic profiling combined with qRT-PCR validation demonstrated that AmTCP genes exhibit tissue-specific expression patterns and differential responses to salt stress and polyethylene glycol (PEG)-simulated drought stress. Notably, AmTCP3, AmTCP8, AmTCP11, AmTCP17, and AmTCP19 displayed tissue- and time-dependent alterations in expression under stress conditions, with AmTCP17 and AmTCP19 showing the most pronounced responsiveness. Collectively, our findings systematically elucidate the fundamental molecular characteristics of TCP transcription factors in A. mongholicus, providing a valuable reference for future investigations into the biological functions of this gene family during growth, development, and abiotic stress responses in this medicinal plant.

Biology doi: 10.3390/biology15141133

Authors: Ahmet Ali Berber Esra Yıldız Nurcan Berber Muammer Kurnaz Nihan Akıncı Kenanoğlu

Nanoplastics (NPs; ≤1 µm) have been detected in human placenta, blood, lung, atherosclerotic plaque, testis, semen, olfactory bulb, and brain, shifting the field from environmental description toward mechanistic interrogation of barrier crossing. This review synthesises current evidence on NP translocation across the intestinal epithelium, the blood–brain barrier (BBB) and the placental syncytiotrophoblast. We distinguish four evidence categories throughout the review: detection, association, mechanism, and causality. We also apply model-system labels (in silico, in vitro, ex vivo, animal, and human) to every mechanistic claim, so that the strength of each statement can be read off directly. Most current studies use pristine polystyrene nanoplastics at concentrations 3–6 orders of magnitude above plausible human exposure, so the mechanistic conclusions below are hypothesis-generating for human disease rather than definitive. We propose a working conceptual framework—corona-driven barrier selectivity (CDBS)—in which the particle–corona–surface complex, rather than the bare polymer, is hypothesised to dictate which receptor and transport machinery (TfR1, LRP1, FcRn, P-gp/BCRP, caveolae) each barrier engages. CDBS is offered as a hypothesis-stage organising tool requiring experimental validation, not as an established mechanism. We outline reported transport modes, including clathrin- and caveolin-mediated endocytosis, paracellular leakage via ROS-induced tight-junction disassembly, receptor-mediated transcytosis, and the candidate olfactory route. We emphasise that pristine polystyrene-bead doses commonly exceed plausible human exposure by 3–6 orders of magnitude, that detection methods underestimate sub-micrometre particles, and that causal links between NPs and human disease remain hypothesis-generating. A research agenda built on weathered reference materials, microphysiological systems, and integrative human biomarker science is proposed.

Biology doi: 10.3390/biology15141132

Authors: Dusanka Popovic Ivana Mirkov Dina Tucovic Aleksandra Popov Aleksandrov Anastasija Malesevic Stanislava Stanojevic Jasmina Glamoclija Maja Tolinacki Milica Zivkovic Jelena Kulas

Background: Antibiotic-associated gut dysbiosis affects lung health and contributes to disease progression, but the individual response to antibiotics, which leads to host-specific reactions to the same respiratory insult, is not fully understood. Methods: Before infection with Aspergillus fumigatus, Albino Oxford (AO) and Dark Agouti (DA) rats received a mixture of antibiotics with poor systemic absorption to induce microbial perturbation only in the gut, and lung and gut tissue and colonic contents were analyzed. Results: Treatment with antibiotics induced gut inflammation in both rat strains, which was more pronounced in AO rats, and a disturbance in lung immunity was observed only in DA rats. Antibiotic-associated gut microbiota disturbance revealed rat strain-specific bacterial profiles (increased Gammaproteobacteria in DA and decreased Coriobacteriia in AO rats). Although gut dysbiosis increased the risk of lung A. fumigatus infection in both rat strains, a higher fungal burden was detected in the lungs of AO rats, whereas lymph node cell activation and lung tissue inflammation were observed in DA rats. Conclusions: Rat strain differences in response to antibiotic- and/or infection-induced gut dysbiosis suggest that basal gut microbiota may influence the lung immune response during A. fumigatus disease, highlighting the importance of the interplay of genotype-specific host gut microbial community with the environmental constraints in shaping individual immune makeup.

Biology doi: 10.3390/biology15141131

Authors: Mehmet Emin Ayağ Mehmet Cudi Tuncer İlhan Özdemir

Experimental evidence has shown that gallic acid (GA), a naturally occurring polyphenolic compound, and docetaxel (DTX), a taxane chemotherapeutic agent, each possess antitumor activity against multiple cancer types. Although both compounds have been investigated individually, their combined effects in triple-negative breast cancer (TNBC) have received limited attention, and the molecular basis of their interaction remains unclear. The present study examined the in vitro effects of GA and DTX in MDA-MB-231 TNBC cells while simultaneously assessing their comparative cytotoxicity in HaCaT human keratinocytes. Evaluation of treatment efficacy included measurement of cell viability by the MTT assay and assessment of drug interactions using the Chou–Talalay combination index (CI) method. Apoptosis together with cell-cycle distribution was subsequently examined using both Annexin V/PI flow cytometry and TALI® image-based cytometry. Additional analyses included β-tubulin immunofluorescence (IF), caspase-9 immunocytochemistry, ELISA, wound-healing assays, quantitative real-time PCR, and bioinformatic analyses to investigate treatment-associated biological alterations. Combined exposure to GA and DTX produced a significant reduction in cell viability and exhibited synergistic activity in MDA-MB-231 cells. The coordinated biological response to the combined treatment was characterized by increased apoptotic cell death, arrest of the cell cycle at the G2/M phase, extensive disorganization of the β-tubulin network, and enhanced caspase-9 immunoreactivity. Beyond its effects on cell survival, the combined regimen substantially decreased the release of IL-6, IL-8, and TNF-α, limited wound-healing capacity, and reshaped the expression profile of the apoptosis- and cell cycle-related genes BCL2, BAX, CASP9, and CDKN1A. Bioinformatic analyses further revealed enrichment of apoptosis- and cell-cycle-associated pathways that were generally consistent with the experimental observations. The overall pattern of experimental responses indicates that combining GA with DTX enhances the in vitro antitumor efficacy of DTX in TNBC cells by simultaneously influencing apoptotic pathways, cell-cycle regulation, inflammatory cytokine secretion, and cellular migratory capacity. Although the bioinformatic findings provide supportive hypothesis-generating evidence, additional studies using three-dimensional models, in vivo experiments, and functional validation approaches are necessary to confirm the underlying molecular mechanisms and to further define the translational potential of this therapeutic combination.

Biology doi: 10.3390/biology15141130

Authors: Haidong Xu Hongyang Jing Jianni Sun Haifei Lu Rongjia Wang Qun Gao Guai Xie Yiming Wang Ling Peng

Coastal saline–alkaline land has considerable potential for soil carbon sequestration, but how different land-use types affect microbial resource limitation and carbon-use efficiency (CUE) in coastal saline–alkaline soils remains unclear. Four representative land-use types, namely bare land (BL), wetland (WL), grassland (GL), and forest land (FL), were investigated in the coastal saline–alkaline soils of the Yellow River Delta. Soil physicochemical properties, microbial biomass, and extracellular enzyme activities were measured, and ecoenzymatic stoichiometry, microbial resource limitation, and CUE were subsequently calculated. Compared with BL, vegetated land-use types decreased electrical conductivity by 52.1–95.8%, while soil water content, soil nutrient indicators, and microbial biomass indicators increased by 47.1–77.5%, 2.6–136.8%, and 2.2–274.4%, respectively. WL was mainly phosphorus-limited, whereas BL, GL, and FL were primarily nitrogen-limited. Despite relatively high soil organic carbon and nutrient availability, GL showed the strongest N limitation and was the only land-use type showing C limitation. Model-estimated CUE ranged from 0.544 to 0.579 and followed the order FL > BL > WL > GL. Random forest analysis showed that soil physicochemical properties contributed most to CUE variation (42.9%). Structural equation modeling further indicated that soil physicochemical properties were indirectly associated with CUE, mainly through stoichiometric characteristics and microbial resource limitation, showing positive and negative associations, respectively. These findings provide microbial evidence for optimizing land-use patterns, vegetation restoration, and carbon-oriented ecological restoration in coastal saline–alkaline land.

Biology doi: 10.3390/biology15141129

Authors: Gonçalo Jasmins Rosa Perestrelo Ricardo Luís Rodrigo Silva Pedro Sousa Carlos A. P. Andrade José Câmara

Marine macroalgae are now considered potential sources of renewable feedstocks to produce valuable bioactive compounds. However, the species-specific volatilomes and their correlation with antioxidant capacity remains largely unknown. This study aimed to investigate the volatilomic fingerprint, total phenolic content (TPC), total flavonoids content (TFC) and antioxidant capacity of four macroalgae belonging to distinct taxonomic groups: Rugulopteryx okamurae (brown algae), Asparagopsis taxiformis (red algae), Caulerpa webbiana (green algae), and coralline algae. To achieve this purpose, the volatilomic fingerprint was established using headspace solid-phase microextraction tandem gas chromatography–mass spectrometry (HS-SPME/GC-MS), and the TPC, TFC, and antioxidant capacity were evaluated using in chemico assays. A total of 59 volatile organic compounds (VOCs) were identified across the marine macroalgae, encompassing carbonyl compounds (on average, 40.7 ± 13.4% of total volatilomic fraction), hydrocarbons (17.0 ± 8.3%), organohalogens (23.0 ± 10.8%), terpenoids (6.5 ± 2.0%), alcohols (4.5 ± 2.0%), and the remaining chemical families showed a contribution lower than 5% to the total volatilomic fingerprint. Multivariate statistical analyses revealed significant differences (p < 0.05) in the volatilomic fingerprint among the macroalgae investigated, allowing clear discrimination between species. Organohalogen compounds emerged as key discriminant features for C. webbiana and A. taxiformis algae, while hydrocarbons were characteristic of the R. okamurae. Despite taxonomic differences, hexanal, benzaldehyde and β-ionone were VOCs found across all samples. Regarding bioactivity, R. okamurae exhibited the highest TPC (144 mgGAE/100 g DW), TFC (69 ± 6 mg QE/100 g DW), and antioxidant capacity. These findings confirm the large variability of the volatilomes of the different species of macroalgae and demonstrate the power of the HS-SPME/GC-MS, chemometric, and antioxidant analysis strategy for the differentiation of species and the identification of VOCs with valorization potential, helping to transform invasive or unused biomass of these species into new, sustainable bioproducts through emerging technological and biorefinery applications.

Biology doi: 10.3390/biology15141128

Authors: Sergio Madurga David López-Blanco Carles Foguet Sara Lahoz Helena Oliveres Reinaldo Moreno Teresa Gorria Leire Pedrosa Silvia Marin Mariam Rojas Jordi Camps Francesc Mas Joan Maurel Marta Cascante

The Consensus Molecular Subtype (CMS) classification provides a widely used transcriptomic framework for colorectal cancer (CRC) stratification with clear prognostic and therapeutic relevance. However, it does not fully capture the immune–metabolic heterogeneity underlying tumor–microenvironment interactions within each subtype. Here, we integrate a validated immune–metabolic gene signature as a functional layer to refine CMS classification and systematically characterize diversity across CMS1-4 tumors. Using transcriptomic data from 2918 CRC samples across three independent cohorts (GSE1, TCGA, and GSE2), we show that CMSs display robust yet distinct immune–metabolic distributions across datasets. CMS4 tumors exhibit glycolytic, stromal-dependent, and immunosuppressive profiles, whereas CMS2 and CMS3 are enriched in oxidative and metabolically flexible states. Importantly, CMS1 tumors segregate into two major immune–metabolic profiles, revealing marked heterogeneity within this immune-activated subtype. These patterns are preserved in metastatic samples, supporting their stability across disease stages. Overall, integrating immune–metabolic profiling into CMSs reveals previously unrecognized functional heterogeneity and provides a refined framework to interpret tumor–microenvironment states. This approach facilitates the identification of context-specific metabolic vulnerabilities with potential clinical relevance.

Biology doi: 10.3390/biology15141125

Authors: Sameena Nikhat Suman Bose Mohsen Khosravi-Maharlooei

Autoimmune diseases arise from a breakdown of immune tolerance and complex interplay of genetic susceptibility, environmental triggers, tissue-specific immune responses, microbiota, and regulatory pathways. Mouse models remain essential for dissecting these mechanisms, but no single model fully reproduces the heterogeneity, chronicity, and immune complexity of autoimmune disease in humans. This review summarizes classical murine and humanized mouse models used to study inflammatory bowel disease (IBD), multiple sclerosis (MS), type-1 diabetes (T1D), and rheumatoid arthritis (RA). We also highlight disease-specific scoring systems, including clinical indices, histopathology, imaging, cytokine profiling, autoantibody assessment, and human immune-cell readouts, as essential tools for standardized interpretation. Conventional murine models provide experimental control and mechanistic clarity, whereas humanized models improve assessment of human immune responses, patient-specific biology, and therapeutic translation. However, humanized systems remain limited by incomplete immune reconstitution, graft-versus-host disease, donor variability, cost, and incomplete tissue architecture. By providing a comparative framework spanning both conventional and humanized models, this review aims to guide informed model selection tailored to specific research questions in autoimmune disease biology and translational therapeutic development.

Biology doi: 10.3390/biology15141127

Authors: Limin Jia Liangwei Li Yaolei Zhang Jiahao Wang Zengbao Yuan Guangyi Fan Chengcheng Shi Man Zhang

In this study, we constructed a comparative genomic framework encompassing 57 genome sequences from four key taxonomic groups—Bacillariophyta, Parmales, choanoflagellates, and Bacillus—all of which possess either siliceous cell walls or silicon-transporting vesicle structures. By comparing these genomes with those of non-silicified species, including Chlorophyta, Streptophytes, Rhodophyta, and Dinoflagellates, we systematically analyzed the evolutionary distribution patterns of genes involved in silicon transport, silicification, and related processes across eukaryotes. Through orthogroup clustering and phylogenetic analysis, we identified 75 orthogroups universally conserved across all 57 species (including representing siliceous and non-siliceous groups), and an additional 105 orthogroups consistently present across the four silica-bearing lineages (Bacillariophyta, Parmales, choanoflagellates, and Bacillus), which were predominantly enriched in fundamental metabolic pathways. Furthermore, by integrating 120 known siliceous cell wall-related protein sequences, we identified three orthogroups broadly distributed across the four major lineages, suggesting an ancient evolutionary origin of certain silicon-related genetic components. Our findings provide genomic insights into the evolutionary trajectory of siliceous cell wall-associated genes and offer a valuable resource for future studies on biomineralization in eukaryotes.

Biology doi: 10.3390/biology15141126

Authors: Notsile H. Dlamini Serge L. Kameni Peixin Fan Seongbin Park Shengfa F. Liao Jean M. Feugang

Semen quality is a key determinant of reproductive performance in breeding boars, and emerging evidence suggests the seminal microbiome may influence sperm function. However, the composition of the seminal plasma microbiome and its relationship to sperm quality remain poorly characterized. This study aimed to investigate the microbial composition of boar seminal plasma and its association with sperm quality. Semen ejaculates collected from Duroc boars were analyzed and classified as Passed (≥70% normal morphology) or Failed (<70% normal morphology). Seminal plasma was isolated by centrifugation and analyzed using 16S/ITS rRNA gene sequencing. The dominant bacterial phyla were Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. The most abundant genera included Porphyromonas, Bacteroides, and Cladosporium. Only the Shannon diversity index was significantly higher in Failed samples for the bacterial microbiome (p = 0.038). Furthermore, correlation analysis showed a negative association between Tenericutes and sperm concentration (r = −0.90; p = 0.014). Linear discriminant analysis identified microbial biomarkers associated with sperm quality, including Rhodococcus, Sphingomonas, Lactobacillus, Streptococcus, and Empedobacter. The increased abundance of these genera in Failed samples suggests disruption of the normal seminal microbial community. In conclusion, boar seminal plasma harbors a distinct bacterial and fungal microbiome that is associated with sperm morphology.

Biology doi: 10.3390/biology15141124

Authors: Zhe Wang Zhenguo Liu Ge Zhang Hongfang Wang Xuepeng Chi Ying Wang Baohua Xu

Environmental stressors such as heavy metals and pesticides pose significant threats to honeybee health by inducing oxidative stress. Enhancing nutritional supply has emerged as a potential strategy for honeybees to enhance stress resistance. However, the underlying molecular mechanisms remain poorly understood. This study investigated the role of leucine (Leu) in regulating antioxidant responses in honeybees (Apis mellifera L.), with a focus on the involvement of sestrin and the Target of Rapamycin (TOR) signaling pathway. The results showed that Leu supplementation activated the TOR signaling pathway and upregulated sestrin expression, leading to enhanced antioxidant capacity and reduced reactive oxygen species (ROS) levels. Silencing sestrin disrupted antioxidant homeostasis, increased stress susceptibility, and caused midgut damage, confirming its essential role in oxidative stress resistance. Notably, inhibition of TOR did not prohibit the protective effects of Leu, suggesting that sestrin, rather than TOR, serves as a key mediator. Furthermore, Leu fine-tuned antioxidant responses under different stress conditions through sestrin. Overall, this study demonstrates that Leu and sestrin play a central role in maintaining antioxidant homeostasis and provide a theoretical basis for nutritional strategies to improve honeybee health and stress resilience.

Biology doi: 10.3390/biology15141123

Authors: Dan Hao Xiao Wang Guangqiang Shang Aysevil Pektas Stig Purup Bo Thomsen

Dextran sodium sulfate (DSS) was used to induce ulcerative colitis in a porcine model to investigate the transcriptional responses in inflamed colonic tissue. Eleven pigs were divided into two groups, of which five pigs were administered an oral dose of DSS daily for five days, whereas six non-treated pigs served as a control group. Differences in transcript expression between treated and control pigs identified 425 down-regulated and 780 up-regulated mRNAs in response to DSS treatment. Fifty-nine differentially expressed miRNAs were also identified, comprising 20 up-regulated and 39 down-regulated miRNAs. The top enrichment KEGG pathways for the up-regulated genes were breast cancer (ssc05224), gastric cancer (ssc05226), focal adhesion (ssc04510), and the PI3K-Akt signaling pathway (ssc04151). The top gene ontology terms for the up-regulated genes were blood vessel development (GO:0001568), extracellular matrix and external encapsulating structure (GO:0031012). Protein–protein interaction network analysis identified three hub genes, including LOXL1, MFAP2, and FSTL3. Seventeen high-confidence miRNA-mRNA pairs were recognized, and two genes (CD101 and AVL9) have been confirmed as targets for ssc-miR-24-3p by dual-luciferase reporter assay. Our study provides a better understanding of the key roles of mRNAs and miRNAs in regulating DSS-induced colitis in pigs and defines sets of coding and non-coding RNA transcripts, which may serve as intervention targets or biomarkers for ulcerative colitis.

Biology doi: 10.3390/biology15141122

Authors: Faris J. Tayeb Rashid Mir Sael Alatawi

Phenylketonuria (PKU) is an autosomal recessive inborn error of phenylalanine (Phe) metabolism caused by pathogenic variants in the phenylalanine hydroxylase (PAH) gene, resulting in toxic phenylalanine accumulation that, if untreated, causes profound intellectual disability and neurodevelopmental impairment. PKU is especially significant in the Kingdom of Saudi Arabia (KSA), where high consanguinity rates substantially elevate disease prevalence relative to Western populations, and the country’s expanding newborn screening programs have highlighted PKU as a persistent public health concern. This review provides a translational synthesis of the Saudi PKU literature, covering epidemiology, molecular pathophysiology, genetics, clinical presentation, diagnosis, treatment, prognosis, and future directions. We summarize global and regional incidence data and show that Saudi Arabia, driven by consanguinity, is among the countries with the highest reported PKU burden worldwide. We review the metabolic basis of phenylalanine neurotoxicity and the allelic heterogeneity of the PAH gene, with attention to variants enriched in Saudi and Arab cohorts, including the founder allele p.R252W. Diagnostic pathways anchored in newborn screening and tandem mass spectrometry are discussed alongside neurodevelopmental outcomes and gaps in Saudi PKU surveillance. We outline established and emerging therapies, including dietary management, sapropterin (BH4), pegvaliase, large neutral amino acids, and investigational gene and mRNA therapies. Throughout, we identify where genuine Saudi-specific evidence exists and where general PKU knowledge is extrapolated to the Saudi context because of limited local data, most notably the absence of a national PKU registry. This review is intended to serve as a translational reference for clinicians, metabolic dietitians, geneticists, and policymakers engaged in PKU care in Saudi Arabia and the wider Arab region.

Biology doi: 10.3390/biology15141121

Authors: Rancés Blanco Carmen Soto Juan P. Muñoz

Epstein–Barr virus (EBV) is a highly prevalent oncogenic virus that establishes persistent infection in most of the human population and is strongly associated with several lymphoid and epithelial malignancies, particularly nasopharyngeal carcinoma, gastric carcinoma, and lymphoepithelial carcinoma. This review summarizes current knowledge on the relationship between EBV infection and apoptosis regulation in epithelial cancers, with emphasis on how viral persistence may contribute to tumor cell survival and therapeutic resistance. The manuscript reviews evidence on EBV genome organization, latent and lytic infection programs, the epidemiology of EBV-associated epithelial tumors, and the main intrinsic and extrinsic apoptotic pathways. It then discusses how viral proteins, including latent membrane proteins, Epstein–Barr nuclear antigen 1 (EBNA1), BHRF1, and BARF1, as well as EBV-encoded microRNAs, modulate key apoptotic regulators such as p53, Bcl-2 family members, death receptor pathways, and caspases. Current evidence indicates that EBV can promote apoptosis resistance through coordinated effects on mitochondrial and death receptor-mediated cell death. Understanding these mechanisms may help clarify the contribution of EBV to epithelial oncogenesis and support therapeutic strategies aimed at restoring apoptotic sensitivity in EBV-associated tumors.

Biology doi: 10.3390/biology15141120

Authors: Yuhan Deng Yuqi Zhao Jiujiu Cao Tianyu Chen Ziyu Jiang Yamin Zhang Jiannan Chen

Tetrabromobisphenol A mono(2-hydroxyethyl) ether (TBBPA-MHEE) is an important byproduct during the production of tetrabromobisphenol A (TBBPA) and its related derivatives. Although it has been detected in aquatic environments, its in vivo developmental toxicity and underlying mechanisms remain poorly understood. In this study, zebrafish were used as a model organism to evaluate the early developmental toxicity, neurobehavioral toxicity, and candidate molecular responses associated with TBBPA-MHEE. The 96 h median lethal concentration (96 h-LC50) of TBBPA-MHEE for zebrafish embryos/larvae was 1.684 mg/L. Sublethal nominal exposure concentrations (2, 20, and 200 μg/L) caused developmental abnormalities, including reduced body length, pericardial edema, impaired swim bladder development, and significantly inhibited spontaneous motor activity as well as the response to light–dark transition and mechanical stimulation. Transgenic reporter assays further showed shortened motor neuron projections, reduced brain-region fluorescence in Tg(gad1b:mCherry) larvae, and downregulated the expression of neurodevelopment-related genes. Network toxicology analysis suggested that MTOR, SRC, MAPK3, and GSK3B were identified as candidate targets potentially associated with TBBPA-MHEE-induced neurotoxicity, with significant enrichment of the ErbB signaling pathway and possible perturbation of PI3K/Akt/mTOR-related responses. In addition, TBBPA-MHEE exposure increased the accumulation of reactive oxygen species (ROS) in the larval brain and induced inflammatory and apoptotic responses. Quercetin intervention partially alleviated ROS accumulation and inflammation and improved the developmental and motor phenotypes. Collectively, these findings indicate that TBBPA-MHEE induces neurodevelopmental toxicity in zebrafish, possibly associated with altered transcriptional responses related to ErbB signaling and the PI3K/Akt/mTOR axis, accompanied by oxidative stress, inflammatory responses, and apoptosis-related events. Because exposure concentrations were not analytically verified, all treatment levels are reported as nominal concentrations. This study provides experimental evidence for the toxicological assessment and environmental risk evaluation of TBBPA derivative pollutants.

Biology doi: 10.3390/biology15141117

Authors: Yuniel Méndez-Martínez Kerly Sánchez-Pacheco Alison Reyes-Caracundo Delia Olivares-Guadalupe Edilmar Cortés-Jacinto

Phytobiotics are promising dietary tools to improve metabolic stability and physiological resilience against chemical stressors in aquaculture. This study evaluated nrf2-linked antioxidant and metabolic modulation by dietary Origanum vulgare essential oil (OEO) in Nile tilapia (Oreochromis niloticus) under malathion-induced organophosphate stress. Fish, with an initial weight of 5.76 ± 0.56 g, were distributed in three tanks per treatment, with 15 fish per tank, and fed diets containing 0 (control), 0.75, 1.50, 2.25 and 3.00 g kg−1 OEO for eight weeks, followed by exposure to malathion (7.04 mg L−1) for 96 h. OEO enhanced (p < 0.05) growth performance, feed utilisation, and survival after exposure, with the greatest productive and survival outcomes at 3.00 g kg−1. Fish that received the supplement also had lower (p < 0.05) lipid peroxidation, better antioxidant enzyme activity and a more favourable modulation of nrf2, gpx and keap1 expression, together with biochemical and histological patterns that were consistent with a better condition of the liver and kidney. The heatmap and PCA supported a treatment-related separation, with 2.25 and 3.00 g kg−1 OEO showing the most favourable integrated physiological profiles. Dietary OEO was associated with antioxidant, metabolic and tissue-level resilience linked to modulation of nrf2-related transcriptional responses.

Biology doi: 10.3390/biology15141119

Authors: Ting Tang Wenguang Huang Huiping Zhong Ping Mo Yaxi Zheng Li Fu Kaiqin Li Jian Gao

Average nucleotide identity (ANI) values of 95–96% and digital DNA–DNA hybridization (dDDH) values of 70% are currently regarded as the gold standards for bacterial species delineation. However, the accuracy and applicability of ANI thresholds may vary among genera and depend on genome quality. In this study, three genome quality standards were applied to re-evaluate ANI classification thresholds for the genus Nocardiopsis: >90% completeness and <5% contamination (13 strains, 78 genome pairs), >90% completeness and <10% contamination (34 strains, 561 genome pairs), and >50% completeness and <10% contamination (40 strains, 780 genome pairs). Based on these analyses, we preliminarily estimated the species delineation thresholds for the genus Nocardiopsis as 96.68% for ANIm and 96.15% for ANIb, using the currently available genome datasets. Strain HUAS JQ3T was isolated from leaves of Camellia oleifera Abel collected in Taoyuan County, northwestern Hunan Province, China. Phylogenetic, genomic, morphological, cultural, and physiological analyses were conducted to determine its taxonomic status. Full-length 16S rRNA gene sequence analysis showed that strain HUAS JQ3T belongs to the genus Nocardiopsis and shares the highest sequence similarities with N. dassonvillei subsp. crassaminis D1T (100.00%), N. alborubida NBRC 13392T (99.86%), N. synnemataformans DSM 44143T (99.73%), and N. akebiae HDS 12T (99.73%). Phylogenetic analysis based on 16S rRNA gene sequences clustered strain HUAS JQ3T with N. alborubida, N. synnemataformans, and N. dassonvillei subsp. crassaminis. In contrast, whole-genome phylogenetic analysis indicated that strain HUAS JQ3T is most closely related to N. akebiae HDS 12T. Nevertheless, the ANIm/ANIb and dDDH values between strain HUAS JQ3T and N. akebiae HDS 12T were below the proposed species delineation thresholds of 70% dDDH and 96.68%/96.15% ANIm/b for the genus Nocardiopsis. In addition, strain HUAS JQ3T exhibited distinct morphological, cell culture, physiological, and biochemical characteristics compared with N. akebiae HDS 12T. The combined genotypic and phenotypic evidence gathered in this study demonstrates that strain HUAS JQ3T (= MCCC 1K08696T = JCM 36305T) represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis camelliae sp. nov. is proposed.

Biology doi: 10.3390/biology15141118

Authors: Elena V. Mitroshina Polina L. Strelkova Maria V. Korokozova Maria V. Vedunova

Alzheimer’s disease (AD) is one of the most prevalent neurodegenerative disorders worldwide and is characterized by progressive memory impairment, cognitive decline, and behavioral dysfunction. The brain’s high energy demand makes it vulnerable to hypoxia, which can trigger AD pathology. Hypoxia-inducible factor (HIF) is a transcription factor that mediates cellular and tissue adaptation to low oxygen levels. HIF-1 plays a dual role in AD: on the one hand, it is considered a potential neuroprotective target; on the other hand, its activation may exacerbate disease pathogenesis by promoting amyloid plaque formation. Given this ambiguity, further studies are needed. This study investigated the HIF prolyl hydroxylase inhibitor Roxadustat in 6-month-old male 5xFAD mice. Stabilization of the HIF-1 complex exerted a positive effect on learning ability and the retention of long-term spatial memory in 6-month-old male 5xFAD mice. Four-week treatment with Roxadustat significantly reduced pathological morphological alterations in cells of the prefrontal cortex. In addition, animals treated with Roxadustat exhibited significantly increased expression of the brain-derived neurotrophic factor (BDNF) in the cerebral cortex. Our findings suggest that stabilization of the HIF-1 complex through inhibition of HIF prolyl hydroxylase may represent a promising strategy for neuroprotection in AD.

Biology doi: 10.3390/biology15141114

Authors: Amelia Nanni Emma Elcombe Maverick Ho Ming Cheung Timothy Stait-Gardner Marina Gimeno Imke Tammen Marianne D. Keller

The neuronal ceroid lipofuscinoses are the most common group of human paediatric genetic neurodegenerative disorders and have also been reported in multiple animal species. This study explores sheep with the CLN6 disease subtype, which occurs in humans either as a late-infantile or as an adult-onset disease. This study characterised morphometric changes that occur in the brains of 15-month-old Merino sheep with CLN6 disease compared to healthy, adult Merino control brains using ultra-high field magnetic resonance imaging (MRI). The formalin-fixed brains of seven affected and three wild-type control sheep were scanned in a 9.4 T Bruker MRI scanner with a T1-weighted gradient echo. Bioimaging technology ‘Amira-Avizo’ was used to segment each region of interest to create a 3D reconstruction of each ovine brain. Volumetric and statistical analysis of each region of interest found that the thalamus, corpus callosum, occipital cortex, hippocampal region and striatum of affected sheep all experienced a significant loss of volume; 80%, 77%, 73%, 50%, 46% respectively, compared to the control brains. The left side of the affected brain showed a significant reduction of 44%, while the volume of the lateral ventricle non-significantly increased by 43%. However, the cerebellum and arbour vitae of affected sheep lost 15% and 8% of their volume, respectively, which was not significant. These findings are overall consistent with previous gross pathology, histopathology and traditional in vivo MRI findings of ovine CLN6 disease models, but suggest that postmortem ultra-high field MRI of formalin-fixed brains can be a complementary approach to in vivo studies. Volumetric analysis of affected brain regions, including the corpus callosum, thalamus, occipital cortex, striatum, and hippocampal region, can provide valuable biomarkers for assessing the effectiveness of therapeutic interventions in NCL.

Biology doi: 10.3390/biology15141116

Authors: Teerawech Promchiangsa Phatthanan Khiaokhoen Anupan Kongbangkerd Boworn Kunakhonnuruk

Bacopa monnieri (Brahmi), a valuable medicinal herb, faces challenges in consistent production and quality under natural cultivation. To overcome these limitations, this study investigated the impact of different light qualities (warm-white, red, blue, and green) on the in vitro growth, chlorophyll content, and accumulation of bacosides in B. monnieri using a temporary immersion system (TIS). The results revealed that green and blue light significantly enhanced biomass accumulation, with green light promoting the highest number of new shoots (24.2 shoots/clump) and blue light inducing the development of longer shoots with extended internodes (2.6 cm/internode). Interestingly, while green light resulted in the lowest chlorophyll content, it led to the highest accumulation of bacoside A3 (0.39% DW). In contrast, no significant differences were observed in bacopaside II content across all light treatments. However, bacopasaponin C production was significantly enhanced by warm-white and red light. These results demonstrate the potential of manipulating light quality within a TIS to optimize specific growth parameters and bioactive compound production in B. monnieri, offering valuable insights for enhancing the quality and yield of this important medicinal plant for industrial applications.

Biology doi: 10.3390/biology15141115

Authors: Ioanna Kotsiri Maria Prokou Charalampia Melangeli Domazinaki Eirini Papadakaki Emmanouil Magiorkinis

Obesity is a major global health problem and is closely associated with a broad range of metabolic disorders, including metabolic syndrome (MetS), dyslipidemia, hypertension, atherosclerosis, type 2 diabetes mellitus, and cardiovascular disease. The gut microbiota plays a central role in maintaining intestinal epithelial integrity, regulating glucose and lipid metabolism, and modulating immune function. Through the gut–brain axis, it also contributes to appetite regulation and energy homeostasis by influencing the release of anorexigenic hormones. Dysbiosis, including alterations in the relative abundance of major bacterial phyla such as Firmicutes and Bacteroidetes, has been associated with increased intestinal permeability, metabolic endotoxemia, and chronic low-grade inflammation, all of which may contribute to the development of obesity and insulin resistance. Diets rich in plant-derived fiber can beneficially shape gut microbiota composition. Bacterial fermentation of dietary fiber produces short-chain fatty acids (SCFAs), including butyrate, acetate, and propionate, which contribute to intestinal barrier integrity, inflammatory regulation, immune regulation, and metabolic homeostasis. Overall, the interaction between gut microbiota, diet, and host metabolic pathways represents a promising field for therapeutic and nutritional interventions aimed at preventing and managing MetS and metabolic diseases.

Biology doi: 10.3390/biology15141113

Authors: Jutamat Klinsoda Theera Thurakit Orawan La-Ongkham Pramuan Saithong Napassorn Peasura Wanida Pan-Utai Khemmapas Treesuwan Kanokwan Yodin Hataichanok Kantrong Jirawut Permpool Kanthida Wadeesirisak

Background: Incorporating probiotic bacteria such as BC, a spore-forming probiotic bacterium known for its resistance, into extruded snacks has emerged as an innovative approach to developing functional foods. Little is known about how the addition influences metabolomic changes during storage. Methods: The mung bean snacks were produced by extrusion, followed by BC fortification. The control snack without seasoning and the two BC treatments (0.1% and 0.5% w/w) were stored at room temperature for 3 months. Culture-based methods and qPCR were performed for microbial analysis. Metabolites were extracted, and metabolite profiles were evaluated using an LC-MS-based approach. Results: 0.5% BC was the most stable in the snack, with viable counts of 7.10 log CFU/g. The PCA plot demonstrated distinct clustering patterns among groups, despite no significant difference by PERMANOVA. In negative mode, L-tyrosine showed higher accumulation in the 0.1 BC group, whereas Threonine, L-histidine, and fatty acid metabolites were highly abundant in the 0.5 BC treatment. The positive mode showed discriminant metabolites, with L-glutamic acid, Isoleucine, and L-phenylalanine enriched in the 0.5 BC treatment. Overall, BC altered citrate and phenylalanine metabolism, and each treatment affected aminoacyl-tRNA biosynthesis. Conclusions: These findings demonstrate the maintenance of culturable B. coagulans in fortified extruded mung bean snacks during storage and provide exploratory insights into metabolite changes associated with amino acid metabolism, lipid oxidation, and flavor development that may be relevant to product quality and storage stability.

Biology doi: 10.3390/biology15141111

Authors: Yanwen Ma Lucia De Marchi Gianfranca Monni Joanna Giannessi Valentina Meucci Alessio Lenzi Marzia Vasarri Donatella Degl’Innocenti Carlo Pretti

Marine bivalves represent promising experimental models for the development of in vitro approaches in environmental biology, ecotoxicology, and bioactive compound screening. However, their application remains limited compared with that of more established vertebrate and mammalian cell systems, mainly due to the lack of standardized and reproducible protocols for maintaining primary cell cultures. This study aimed to establish and optimize a short-term primary cell culture protocol using gill and digestive gland tissues from the marine mussel Mytilus galloprovincialis. Primary cultures were prepared at four initial cell densities, ranging from 2.5 to 10 × 106 cells mL−1, and monitored over 72 h through cell density evaluation and metabolic activity assessment. Cells from both tissues were successfully maintained in short-term culture, predominantly showed rounded to spheroidal morphologies. Nevertheless, tissue-specific responses were observed. Gill-derived cultures displayed greater morphological homogeneity and stability across the tested densities, whereas digestive gland cultures showed greater cellular heterogeneity, aggregation, and stronger density-dependent responses. Metabolic activity remained stable during the first 24 h, while more evident differences among cell densities emerged after 48 and 72 h. Overall, intermediate cell densities, particularly 5 × 106 and 7.5 × 106 cells mL−1, provided the most suitable balance between cell maintenance and metabolic performance. This optimized methodological framework supports the further development of mussel primary cell cultures as reproducible and ecologically relevant in vitro models for studying early cellular responses and for preliminary environmental safety assessment.

Biology doi: 10.3390/biology15141112

Authors: Sarayu Bhogoju Parth Patel Neeraj Kapur Prashant D. Kunjadia Ajoy Aloysius Dave-Preston Esoe Jamie L. Sturgill Christine F. Brainson Luksana Chaiswing Patrick G. Sullivan Anthony N. Gerber Edward Castillo Stewart F. Graham Ishanu Chattopadhyay Girish Nair

Pulmonary fibrosis (PF) is a progressive lung condition characterized by irreversible scarring and high mortality, with limited effective treatments. Mitochondrial dysfunction has emerged as a critical factor in fibroblast activation in PF, although approaches to restore mitochondrial function remain underexplored. The present study investigated whether mitochondrial transfer from alveolar type II epithelial cells (A549) to patient-derived fibroblasts could restore mitochondrial function and bioenergetics. Histological analysis of fibrotic lungs reveals increased collagen deposition and elevated profibrotic markers, accompanied by reduced expression of mitochondrial biogenesis and respiratory proteins compared to non-fibrotic controls, indicating mitochondrial impairment. Freshly isolated donor mitochondria were functionally validated before mitoception using Seahorse analysis and patient-derived fibroblasts were confirmed by qRT-PCR using fibroblast-specific markers. In vitro transfer of mitochondria to diseased patient-derived fibroblasts exhibited a modest, dose and time-dependent increase in mitochondrial membrane potential compared to normal fibroblasts. Gene expression analysis revealed decreased fibrosis-associated markers and increased expression of mitochondrial and antioxidant genes following mitoception. Seahorse analysis after mitoception revealed enhanced ATP-linked respiration and improved selected mitochondrial bioenergetic parameters, whereas maximal respiration and spare respiratory capacity demonstrated variable responses. In contrast, normal fibroblasts displayed minimal changes. Collectively, these findings indicate that mitochondrial transfer modulates fibroblast bioenergetics and profibrotic signaling, supporting its potential as a therapeutic strategy for pulmonary fibrosis.

Biology doi: 10.3390/biology15141110

Authors: Godwin Sokpor Pauline Antonie Ulmke Hoang Duy Nguyen Linh Pham Princy Kakani Van Trung Chu Sebastian J. Arnold Beate Brand-Saberi Huu Phuc Nguyen Tran Tuoc

Factors regulating the genesis and expansion of basal progenitor cell sub-populations, including intermediate progenitor cells, are critical determinants of cortical neurogenesis and brain growth. Epigenetic (chromatin) marks have emerged as notable regulators of cortical development. However, it is unclear how these factors specifically interact in the epigenome to orchestrate brain development. Here, we combined in vivo electroporation and a CRISPR-dead (d)Cas9 system to probe the contribution of a specific histone modification mark, H3K9ac (H3K9 acetylation), in the epigenome of isolated intermediate progenitor cells in developing mouse cortices. CRISPR-dCas9-mediated addition of H3K9ac at the promoter region of lncRNA Sox1ot resulted in Sox1ot upregulation, with attendant increase in the intermediate progenitor pool and augmented neurogenesis. Thus, we found an interplay between H3K9ac and Sox1ot, which drives the amplification of cortical intermediate progenitor cell population. By targeting H3K9ac to the Sox1ot promoter, we were able to stimulate the proliferation of intermediate progenitor cells leading to enhanced cortical neurogenesis. In essence, we have identified H3K9ac as a key epigenetic regulator of Sox1ot expression, which may dynamically be involved in intermediate progenitor cell pool expansion during brain development and evolution.

Biology doi: 10.3390/biology15141109

Authors: Yuqiong Li Ya Qin Jie Shen Ru Chen Cuihong Yang Wenjing Liang Mengjin Tan Lisha Song Lijun Shi Lingjian Gui Shugen Wei Lingyun Wan

The size of the mitogenome varies greatly in angiosperms from different species, but the causes of expansion remain unclear. Species from the Zingiberaceae family often carry exceptionally large mitogenomes, where this phenomenon can be readily studied. C. kwangsiensis is a medicinal plant that is native to Guangxi, China, and it is traditionally used to treat blood stasis and gynecological conditions. We assembled its complete mitogenome by using the Illumina and Nanopore reads obtained from its analysis. The genome comprises 12 circular contigs with a multi-branched structure, totaling 7.76 Mb. It contains 39 protein-coding genes, 30 tRNAs (transfer RNAs), three rRNAs (ribosomal RNAs), and 652 C-to-U RNA edited sites. Repeated analysis revealed that the dispersed repeats are the major contributors to genome expansion. Comparisons with two other Zingiberaceae mitogenomes suggested that the large genome arose in a common ancestor rather than from a whole-genome duplication, with little contribution from DNA transfers from the chloroplasts and nuclei. Thus, the exceptionally large mitogenome of Curcuma appears to result largely from repeated accumulation in the non-coding regions, such as nuclear genome expansion in angiosperms. This finding also highlights the conservation of core mitochondrial genes. Our work provides new insights into mitogenomic size variations and gene conservation in plant species, including Zingiberaceae.

Biology doi: 10.3390/biology15141108

Authors: Elsayed Ibrahim Phyu P. Aung

Cutaneous metastases are an uncommon but clinically significant manifestation of internal malignancy, occurring in approximately 0.7–10.4% of patients with cancer. In some cases, they represent the first clinical manifestation of an otherwise occult malignancy, making accurate diagnosis critical for timely patient management. Distinguishing cutaneous metastases from primary cutaneous neoplasms, particularly malignant adnexal tumors, remains one of the most challenging problems in dermatopathology because of their substantial clinical, histopathologic, and immunophenotypic overlap. This review summarizes the epidemiology and biology of cutaneous metastasis and the clinical presentation of cutaneous metastases and emphasizes the central role of clinicopathologic correlation in diagnosis. Histologic features such as a purely dermal or subcutaneous location, intravascular tumor emboli, and a “bottom-heavy” growth pattern favor metastasis, whereas the presence of an in situ component or transition from a benign precursor lesion strongly supports a primary cutaneous neoplasm. We review the diagnostic utility of optimized immunohistochemical panels, highlighting the complementary roles of p63, cytokeratin 15, calretinin, and D2-40 (podoplanin) in establishing primary adnexal lineage, together with emerging markers including SOX10, androgen receptor, TRPS1, adipophilin, INSM1, SATB2, and BerEP4 for diagnostically challenging cases. We also discuss recent advances in molecular biology and comprehensive genomic profiling, including recurrent gene fusions (e.g., MYB::NFIB, CRTC1::MAML2, and YAP1 fusions) and characteristic mutational signatures that provide increasingly robust diagnostic evidence of tumor lineage. Finally, we provide a comprehensive, practical diagnostic algorithm for differentiating primary cutaneous adnexal carcinomas from cutaneous metastases of adenocarcinomas. By integrating traditional histopathologic techniques with modern immunohistochemical and molecular techniques, pathologists and clinicians can successfully navigate this complex differential diagnosis and thereby facilitate appropriate patient management and therapeutic intervention.

Biology doi: 10.3390/biology15141106

Authors: Emily Do Durga Puro Surajit Hansda

Inflammation is a critical protective response that maintains tissue homeostasis. However, persistent or dysregulated inflammation contributes significantly to the progression of cancer and neurodegenerative diseases. Recent advances in RNA biology have identified non-coding RNAs (ncRNAs), including microRNAs, long non-coding RNAs, and circular RNAs, as key modulators of inflammatory signaling networks. These RNA molecules regulate key pathways such as NF-κB, STAT3, MAPK, and PI3K/AKT, thereby influencing immune responses, tumor progression, neuronal survival, and cellular stress adaptation. In parallel, RNA-sensing receptors, including Toll-like receptors and RIG-I-like receptors, connect innate immune activation with chronic inflammatory pathology. Emerging evidence further demonstrates that inflammatory RNAs participate in epigenetic regulation, intercellular communication, and inter-organ crosstalk through extracellular vesicles and exosomes. In cancer, RNA-mediated feedback loops sustain tumor-promoting inflammation, metastasis, and immune evasion, whereas in neurodegenerative disorders, they contribute to glial activation, neuronal dysfunction, and progressive neuroinflammation. This review examines the mechanistic relationship between RNA dysregulation and inflammation across cancer and neurodegeneration, with particular emphasis on RNA signaling networks, exosomal communication, and targeted RNA-based therapeutics. Collectively, advances in understanding the RNA–inflammation axis may reveal new opportunities for precision diagnostics and next generation therapeutic interventions.

Biology doi: 10.3390/biology15141107

Authors: Lin Zhu Dan Zhang Zongping Li Hongxiao Sun Mengdi Cheng Jie Tang Liyuan Jia Xuli Liu Fulin Chen Hong Tan

Cynops orientalis, a member of the Salamandridae family, can regenerate severely injured limbs throughout its lifespan. The molecular mechanisms regulating limb regeneration in C. orientalis remain largely unknown. SERCA1 (sarcoplasmic/endoplasmic reticulum calcium ATPase 1) is a major sarco/endoplasmic reticulum calcium pump in skeletal muscle, and our previous transcriptomic sequencing results showed increased SERCA1 mRNA expression during the early stages of newt limb regeneration. In the present study, we investigated the role and regulatory mechanism of SERCA1 during newt limb regeneration by using a limb-amputation model, shRNA-mediated knockdown, Thapsigargin-mediated SERCA1 inhibition, miRNAomics analysis, dual-luciferase reporter assays and Agomir therapy. Knockdown of SERCA1 expression or suppression of SERCA1 activity impaired skeletal muscle cell dedifferentiation, disrupted AEC and blastema formation, reduced cell proliferation, and significantly delayed limb regeneration compared with control animals. Through miRNAomics analysis and in vitro dual-luciferase reporter assays, we identified miR-20487-5p as a negative regulator of SERCA1 expression in C. orientalis. In vivo treatment with miR-20487-5p Agomir down-regulated SERCA1 expression resulted in limb-regenerative defects. Mechanistically, shRNA-SERCA1 or miR-20487-5p Agomir treatment reduced ERK phosphorylation in regenerating limb tissue, suggesting an association between the miR-20487-5p/SERCA1 axis and MAPK/ERK activation. Taken together, our study supports the significant role of the miR-20487-5p/SERCA1/MAPK/ERK axis in early newt limb regeneration. This study expands the current understanding of molecular mechanisms initiating newt limb regeneration.

Biology doi: 10.3390/biology15141105

Authors: Sofia Balafouti George Zachos Eleni Petsalaki

During mitosis sister chromatids are accurately segregated into two daughter cells through a microtubule-based structure known as the mitotic spindle. Errors in mitotic spindle formation have been associated with human diseases and tumorigenesis. Chk1 has well established roles in DNA damage response and replication checkpoints. Recently, new roles have emerged in the onset of mitosis, chromosome segregation and cytokinesis. In this review, we recapitulate the known roles of Chk1 in cell division and highlight new roles of Chk1 in mitotic spindle assembly and its contribution to genome stability. Specifically, it was recently reported that, during the first stages of mitosis, ATRIP and its interacting partners, ATR and TopBP1, are recruited to centrosomes, where they activate Chk1. Then, Chk1 phosphorylates β-tubulin at Threonine 285 (T285), promoting microtubule nucleation and mitotic spindle formation. β-tubulin phosphorylation by Chk1 is required for proper mitotic progression, cytokinesis with equal-sized daughter cells and cell proliferation. This novel ATR-Chk1 signaling pathway reinforces the crosstalk between the cell cycle regulation and DNA damage response.

Biology doi: 10.3390/biology15141104

Authors: Gioacchin Iannolo Rosaria Tinnirello Valentina Lazzara Bruno Douradinha Vitale Miceli Giusy Daniela Albano

Chronic obstructive pulmonary disease (COPD) represents a major global health issue, characterized by persistent airflow limitation, chronic inflammation, and progressive tissue remodeling. Its clinical and molecular heterogeneity, combined with the lack of resolutive therapies, underscores the urgent need for advanced experimental tools to improve understanding and therapeutic development. Traditional 2D cell culture systems, though historically useful, fail to replicate the complexity of the human lung. In this review, we analyze the remarkable relevance of advanced 3D models for studying COPD pathophysiology, including epithelial injury and regeneration, extracellular matrix remodeling, and interactions with environmental triggers such as cigarette smoke and airborne pollutants. Three-dimensional in vitro models, such as ALI cultures, lung organoids, and lung-on-a-chip platforms, PCLS, and lung ECM-derived hydrogels offer more physiologically relevant environments to investigate epithelial dysfunction, immune responses, and host-pathogen interactions. We discuss the contribution of viral and bacterial infections to COPD exacerbations, and explore how 3D models have become essential tools for modeling these events. We also highlight recent advances in personalized medicine that use patient-derived organoids and ALI cultures for drug screening and biomarker discovery. Furthermore, we examine the therapeutic potential of probiotics and extracellular vesicle-associated microRNAs to modulate inflammation and epithelial repair. Collectively, these innovative systems represent powerful platforms to promote precision medicine in COPD.

Biology doi: 10.3390/biology15141103

Authors: Jun Luo Suhang Li Fuyuan Huang Qiong Yang Yangzhou Xiang Ying Liu

Epimedium sagittatum is an important understory shade-tolerant medicinal plant native to China. However, assessments of its responses to climate change under multiple scenarios and time periods remain insufficient, particularly regarding the mitigation of model overfitting and the quantitative disentanglement of hydrothermal constraints. In this study, based on 269 valid occurrence records and 24 initial environmental variables (reduced to 13 after collinearity screening), we employed a parameter-optimized MaxEnt 3.4.4 model (RM = 3.5, FC = QHP) coupled with the BCC-CSM2-MR climate model to project the dynamics of potential suitable habitats under current (1970–2000) and future (2050s, 2070s, 2090s) scenarios (SSP126, SSP370, SSP585). The results showed that the optimized model substantially reduced the risk of overfitting compared with the default parameters (ΔAICc dropped from 82.16 to 0) and achieved an AUC of 0.934. Precipitation of the Driest Quarter (Bio14, 53.4% contribution) and Minimum Temperature of the Coldest Month (Bio6, 20.5% contribution) were identified as the dominant factors governing the species’ distribution, with optimum conditions of ≥1.58 mm and −8.34 °C to 13.61 °C, respectively. Under future climate scenarios, the centroid of suitable habitats shifted progressively southwestward, with a cumulative displacement of approximately 127.47 km under SSP585, and water availability, rather than temperature, dominated the direction of this shift. Under the high-emission scenario, suitable areas exhibited a spatial reorganization characterized by westward expansion and eastward contraction. Based on these findings, this study proposes a three-tier planning framework comprising in situ conservation, climate-smart introduction, and assisted migration, providing a scientific basis for the conservation of germplasm resources and the spatial planning of artificial cultivation of E. sagittatum.

Biology doi: 10.3390/biology15141102

Authors: Xinliang Liu Tianqi Gao Meng Kou Mengjiao Lan Zhiyuan Gao Chen Li Xinru Yu Zongyun Li Qiang Li

Anthocyanins dictate the nutritional quality of purple-fleshed sweetpotato (PFSP), yet how the lignin pathway influences anthocyanin biosynthesis and phenylpropanoid metabolic flux allocation remains largely elusive. Through integrated transcriptomic and metabolomic analyses of a purple-fleshed sweetpotato cultivar (XZ13) and its natural mutant (XZ13M), we revealed that diminished anthocyanin accumulation correlated strongly with systemic transcriptional repression of the phenylpropanoid pathway. We subsequently identified a crucial methyltransferase gene, IbCCoAOMT7, with dual nucleocytoplasmic localization. Its overexpression in its storage roots was directly associated with reduced anthocyanin accumulation and increased lignin content. Further investigations suggested that IbCCoAOMT7 was putatively involved in modulating metabolic flux toward lignin biosynthesis that downregulates the transcriptional activity of core anthocyanin biosynthetic genes. Collectively, our study highlights that IbCCoAOMT7 represents a promising candidate gene that influences the balance between the lignin and anthocyanin pathways. These findings propose a tentative regulatory model, possibly involving substrate availability and transcriptional feedback inhibition, providing precise genetic targets for breeding anthocyanin-enriched sweetpotato.

Biology doi: 10.3390/biology15141101

Authors: Zhi Guo Xuyi Deng Sheng Lu Fenghao Liu Meijuan Zhou Yinghui Wang

Current approaches for preventing and suppressing the initiation and development of keratinocyte carcinoma remain limited, highlighting the urgent need to identify novel targets for tumor intervention. As major environmental pathogenic factor, chronic ultraviolet B (UVB) exposure promotes keratinocyte malignant transformation through epigenetic reprogramming, reshaping chromatin accessibility and gene expression program, which has not been fully elucidated. Here, we established a chronic UVB irradiation model to induce malignant transformation of keratinocytes and performed integrative analyses using ATAC-seq and RNA-seq. We identified 4903 differentially accessible regions (DARs), with increased accessibility at loci of tumor-promoting genes such as TP63, KRT13, KLF8, and EGFR, and enrichment of AP-1 family motifs. RNA-seq revealed 1136 differentially expressed genes (DEGs), predominantly enriched in inflammatory pathways. Integrative analysis highlighted concordant enrichment of inflammation-related genes within open chromatin regions. ATF3 was selected and its downregulated identified after UVB exposure. Functional assays confirmed that ATF3 represses chronic UVB-induced malignant transformation of keratinocytes. Notably, ChIP-qPCR validation verified GDA (Guanine deaminase) as the direct downstream target gene of ATF3. Reduced ATF3 binding elevates GDA promoter chromatin accessibility and upregulates GDA expression to drive malignant progression. In conclusion, our findings demonstrate that chronic UVB exposure remodels chromatin and transcriptomic landscapes and identify ATF3 and its direct target GDA as a critical tumor-suppressive regulatory module for UVB-induced keratinocyte carcinoma.

Biology doi: 10.3390/biology15141100

Authors: Christian Joseph N. Ong Jamil Allen G. Fortaleza Jowi Tsidkenu Pili Cruz Edison D. Ramos Joel G. Matamis Janice Kaylyn Lonogan Amelda C. Libres Carina M. Magtibay Jose Edwardo R. Mamaat Maylaine M. de Leon Carlos S. de Leon Jose Jurel M. Nuevo Rich Milton R. Dulay

Ganoderma lucidum (Lingzhi or Reishi) is among the most extensively studied medicinal mushrooms globally, owing to its diverse bioactive compounds and broad pharmacological properties. A scientometric analysis using the Scopus database was conducted to investigate global research trends on the bioactivity of G. lucidum. Bibliometric indicators, collaboration networks, keyword co-occurrence, thematic evolution, conceptual structure mapping, and life cycle modeling were assessed using Bibliometrix/Biblioshiny and VOSviewer version 1.6.20. A total of 2877 publications were included in the analysis. Scientific output increased markedly after 2010, peaking in 2025, indicating sustained growth in the field. China was identified as the leading contributor in terms of publication volume, influential authors, and prominent institutions, while international collaboration networks showed expanding global participation. Keyword and thematic analyses demonstrated a shift from early research focused on bioactivity screening, polysaccharides, and cultivation to mechanistic and translational investigations involving apoptosis, oxidative stress, immunomodulation, metabolomics, gut microbiota, network pharmacology, and disease-specific applications. Life cycle analysis suggested that the field is still in a rapid growth phase and has not yet reached saturation. Research on G. lucidum has evolved into a mature and highly interdisciplinary field, characterized by increasing scientific productivity, expanding international collaboration, and a growing emphasis on mechanistic and translational studies.

Biology doi: 10.3390/biology15141099

Authors: Carmen Morales-Luque Marta González-García Laura Carrillo-Franco Adriana Perales-Guerra Ana Redondo-Fernández Manuel Víctor López-González Marc Stefan Dawid-Milner

Ehlers–Danlos syndromes (EDSs) are heritable connective tissue disorders caused by defects in collagen and related extracellular matrix proteins. Because the vocal fold (VF) lamina propria is a collagen-dependent structure, the voice might be expected to be affected, yet voice and laryngeal involvement has received comparatively little attention. This scoping review, conducted according to the Joanna Briggs Institute framework and reported following the PRISMA extension for Scoping Reviews (PRISMA-ScR), mapped the available evidence on voice and laryngeal manifestations in adults with EDS. PubMed, Scopus, and Web of Science were searched to 11 March 2026, and thirteen studies were included: four questionnaire-based and nine clinical or instrumental. Self-reported voice complaints were common across EDS and hypermobility spectrum disorder populations, ranging from mild-to-moderate handicap in large cohorts to frequent, fluctuating difficulties in professional singers, although their prevalence varied with population and assessment method. Direct laryngeal examination revealed a recurring substrate of cricoarytenoid joint subluxation or fixation, arytenoid prolapse, and hyolaryngeal instability, together with microvascular and mucosal fragility, characteristically accompanied by preserved VF mobility. Muscle tension dysphonia was the most frequent diagnosis in high-vocal-demand cohorts. Reflux, vocal load, and autonomic comorbidities such as postural orthostatic tachycardia syndrome were frequently reported and may modulate the clinical picture. The evidence indicates that voice and laryngeal involvement is a plausible, multi-level manifestation of EDS that remains under-recognised. The current literature is limited by small, heterogeneous, and largely uncontrolled studies; prospective research using standardised multimodal assessment is needed to clarify its prevalence, mechanisms, and management.

Biology doi: 10.3390/biology15141098

Authors: Ergün Yukmel Rasit Raluca-Ioana Stefan-van Staden Damaris-Cristina Gheorghe

Vitamin B6 is a coenzyme involved in more than 150 biochemical reactions in the body. Its intake has favorable effects for many diseases like Parkinson’s disease, glaucoma, and endometriosis. Vitamin B6 can be obtained from tablets, aqua vitamin, and a variety of food sources, including meat, fish, and vegetables. There is a need for process analytical control for fast, ultrasensitive, and selective methods of determination of vitamin B6 in order to produce drugs of high pharmaceutical purity. Also, the on-site determination of vitamin B6 in vegetables can contribute to the fast, real-time control of the quality of vegetables. Therefore, a fast ultrasensitive sensing strip based on the immobilization of heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin on a matrix containing single-walled carbon nanotubes was constructed and used for on-site pharmaceutical process control of vitamin B6, as well as for on-site quality control of food. The sensing strip provided two linear concentration ranges: the first one between 1.69 × 10−15 and 1.69 × 10−5 g mL−1 with a sensitivity of 6.96 × 104 s−1 g−1 mL, and the second one between 1.69 × 10−5 and 1.69 × 10−3 g mL−1 with a sensitivity of 3.65 × 102 s−1 g−1 mL. The limit of quantification was 1.69 fg mL−1. A % recovery higher than 94.50% was determined for Vitamin B6 in tablets, aqua vitamin, and avocado, with % relative standard deviations lower than 1.00%. A lower determination limit was obtained when the sensing strip was used for the assay of vitamin B6 in different samples compared with other methods used to date for its assay. Also, the results of the analysis were obtained faster, in real time, compared with other methods for which a long sample processing time is needed before analysis.

Biology doi: 10.3390/biology15141097

Authors: Wenhui Ding Zhenhua Luo Yuanyan Xiong

Spatially resolved single-cell technologies can provide deep insights into cellular heterogeneity and tissue structural characteristics. However, the data obtained are purely observational and cannot reveal the specific mechanisms by which tissues respond to particular perturbations. Most computational models of single-cell perturbations either operate in a non-spatial latent space or fix tissue geometry within a static spatial structure, thereby limiting their ability to integrate molecular profiles with tissue topological remodeling. We propose SPAD-CFR (Spatial Point-cloud Attention-based Diffusion for CounterFactual Reprogramming). Each tissue is treated as a spatial point cloud containing cellular molecular profiles and physical coordinates. We implement Pearl’s three-step workflow for causal inference through deterministic diffusion inversion and sampling. This model can apply interventions to individual cells and generate counterfactual-style tissues in which molecular profiles and spatial coordinates change together. In validation across three datasets, SPAD-CFR reproduces the hierarchical structure of the mouse cerebral cortex, simulates phenotypic distribution differences across different histological grades of breast cancer, and reconstructs hypoxia-associated mesenchymal phenotypes at the invasion margins of triple-negative tumors. In melanoma, activation interventions targeting PD-1+ CD8+ T cells produce spatially confined, distance-dependent bystander cytotoxic effects. Based on these findings, we propose SPAD-CFR, a biologically informed generative framework for conducting counterfactual-style spatial simulations to validate hypotheses regarding microenvironment reprogramming.

Biology doi: 10.3390/biology15141096

Authors: Jiang Feng Ying Liu Hui Wang

Bats (order Chiroptera) are among the most diverse and ecologically vital mammals, defined by powered flight, remarkable echolocation, and exceptional physiological adaptations [...]

Biology doi: 10.3390/biology15141095

Authors: Xin Sun Zhuo Wang Rui Shu Yuli Qu Yongsheng Li Zhen Liu Ping Zhao Feng Chen Ran Zhang Cheng Cheng Peng Hu Yongjing Deng Jian Liu Junjun Dai

Bee pollination enhances the yield and fruit quality of loquats (Eriobotrya japonica Lindl.). However, the systemic effects of pollination on fruit metabolomics, particularly the metabolic differences among various cultivars following pollination, remain unclear. This study examined the metabolome of Baihua loquats following pollination by Apis cerana and compared it to that of unpollinated fruits. A total of 1964 metabolites were identified, including 334 differentially expressed metabolites. After analyzing ripe fruits of the white-fleshed loquat (Baihua, BH) and red-fleshed loquat (Dahongpao, DHP) following pollination, a total of 635 differentially expressed compounds were identified, with flavonoids, phenolic acids, and amino acids being the most abundant among the differentially expressed metabolites. This study further elucidated the biosynthetic pathways of phenylpropanoids, which account for the differences in the accumulation of BH and DHP in loquat following pollination. Consequently, these findings enhance our understanding of the overall metabolome of pollinated loquats, deepen our knowledge of polyphenolic metabolism in different loquat varieties, and provide new insights into the flavor differences between white-fleshed and red-fleshed loquats.

Biology doi: 10.3390/biology15131094

Authors: Jacob Warner-Palacio Hannah Hunsaker Amanda McKenna Brigita Budginas Levi Fridriksson Alexander Tam Christina Nelson David Sant Kyle B. Bills

Background: Glycemic control influences a wide range of psychiatric and physiological symptoms. Many psychiatric conditions are linked to poor glucose regulation. Anti-nuclear antibodies (ANAs), widely used to screen for autoimmune disease, may sometimes reflect transient metabolic immune activation rather than chronic pathology. Evidence suggests that glucose dysregulation, including glycemic variability, reactive hypoglycemia, and postprandial spikes, can trigger systemic inflammation, neuropsychiatric symptoms, and temporary autoantibody production. This review explores how these metabolic phenomena complicate diagnosis and may contribute to misclassification or overtreatment. Methods: We conducted a narrative literature review prioritizing studies on immune activation, psychiatric outcomes, metabolic measures (including continuous glucose monitoring), and therapeutic interventions. Articles from the last ten years were emphasized, with older foundational studies included when relevant. Results: Metabolic instability drives immune dysregulation through macrophage polarization, mitochondrial dysfunction, oxidative stress, and impaired clearance of apoptotic debris. Glycemic variability correlates with increased inflammatory cytokines, autonomic dysfunction, and psychiatric symptoms such as anxiety, depression, and cognitive impairment. Emerging evidence from small studies suggests that correcting glucose abnormalities may reduce metabolic dysfunction and improve neuropsychiatric symptoms. Conclusions: Recognizing glucose dysregulation as a contributor to autoimmune-like and psychiatric symptoms may refine diagnostic and therapeutic approaches. Incorporating a dynamic holistic approach, which in practice includes metabolic assessments, dietary interventions, use of continuous glucose monitoring, and history of blood sugar instability, into rheumatologic and psychiatric evaluations could improve diagnostic precision, reduce unnecessary immunosuppression, and enhance patient outcomes.

Biology doi: 10.3390/biology15131093

Authors: Fabio Conti Igino Chiuchiarelli Marinella Miglio Bruno Petriccione Bruno Santucci Fabrizio Bartolucci

We present the first vascular flora of Sirente-Velino Regional Park, a protected area located in central Apennine (Abruzzo, Central Italy), covering 550 km2. The floristic inventory was compiled based on extensive field surveys conducted from 1990 to 2025. Thanks to specific funding secured for the final three years (2023–2025), field trips became systematic, aimed at covering the entire territory of the park, including its diverse habitats across different seasons. Furthermore, an analysis of the relevant literature was performed, alongside a comprehensive review of herbarium specimens housed at APP, FI, NAP, and RO. The park’s flora comprises 2066 taxa (1370 species and 696 subspecies, including 11 hybrids), belonging to 117 families and 671 genera, with 122 classified as alien. Notably, 169 taxa are endemic to Italy. Our study reports 234 taxa for the first time within the park, while 52 remained unconfirmed in recent times and 22 are of doubtful occurrence. Five taxa are newly recorded for the Abruzzo region: Alchemilla alpinula, A. obtusa, A. vulgaris, Hyacinthoides non-scripta, and Salsola tragus. Additionally, the revision of APP herbarium specimens led to the exclusion of Euphorbia tommasiniana from the regional flora, reassigning the material to the alien E. saratoi. The species richness of the native flora exceeds expectations by 50.8%, a finding likely driven by the area’s significant geographical, geological, and microclimatic diversity, which results in high environmental heterogeneity. Conversely, alien taxa are 5.6% lower than expected, probably due to the high ecological integrity of the park, a predominantly mountainous territory with low population density and minimal anthropogenic disturbance. Representing 20.6% of the entire Italian flora, the Sirente-Velino Regional Park stands out as one of Europe’s protected areas with the greatest diversity of vascular plants.

Biology doi: 10.3390/biology15131092

Authors: Manman Zhao Tian Lin Ruiqiu Zhang Haodong Zhong Qianyi Niu Xiaobing Zhou Qingli Wang

Microphysiological Systems (MPS) have emerged as a transformative platform in biomedical research, enabling the investigation of disease mechanisms, drug screening, and toxicity prediction by closely simulating human physiological functions. However, the rapid advancement of MPS technology has raised a series of complex ethical challenges. These include the sourcing and application of human-derived stem cells, the protection of donors’ personal and genetic data, the potential for brain organoids to develop consciousness-like characteristics, and the challenges to species boundaries posed by human–animal chimera research. Meanwhile, although regulatory authorities encourage innovation, specialized certification standards and ethical review guidelines for MPS are yet to be fully established. The lack of technical standardization and a coherent ethical governance framework remain a major bottleneck hindering the broader application and industrialization of MPS. This review systematically outlines the key ethical issues facing MPS, compares the evolution and differences in international ethical regulatory frameworks, and discusses strategies for addressing these challenges—including the establishment of dynamic ethical governance mechanisms, harmonization of international standards, and the promotion of benefit-sharing and public engagement. Finally, we highlight the need to develop a scientific, unified, and actionable ethical governance system that balances technological innovation with responsible translation, supporting the sustainable development of MPS technology.

Biology doi: 10.3390/biology15131091

Authors: Chenyu Tang Lin Shi Shoukun Xu

Structural atrophy and metabolic dysfunction provide complementary biomarkers for Alzheimer’s disease (AD), and their joint modeling may support diagnostic assessment and cognitive score estimation. However, many multimodal methods rely on global fusion and insufficiently enhance cross-modal consistency before interaction, limiting the discriminative quality and clinical relevance of learned representations. We propose CGMF-Net, a cross-modal gated learning framework for joint AD classification and clinical score estimation using paired structural MRI (sMRI) and fluorodeoxyglucose PET (FDG-PET) data. CGMF-Net extracts multi-scale representations from both modalities, introduces a Cross-Modal Similarity Gate to strengthen consistent structural–metabolic responses before fusion, and employs bi-directional cross-attention to capture complementary interactions. The shared representation is optimized with classification supervision, MMSE-based auxiliary regression, and HSIC regularization to improve discriminability and reduce redundant coupling between directional representations. Experiments on ADNI demonstrate that CGMF-Net achieves the best overall classification performance among the compared methods, with 94.22% ACC and 97.74% AUC for AD vs. CN, and 86.67% ACC and 94.84% AUC for AD vs. MCI, while also showing favorable ADNI-2 to ADNI-1 generalization and competitive estimation of ADAS13, CDRSB, and MMSE. These results suggest that cross-modal gated learning provides clinically relevant multimodal representations for AD diagnosis and cognitive score estimation.

Biology doi: 10.3390/biology15131090

Authors: Nicholas R. Longrich Peter J. Makovicky Tim Tokaryk David M. L. Cooper Evan T. Saitta Gregory M. Erickson Tamas Szekely Eric Snively

Tyrannosaurs were giant predatory dinosaurs that occupied the apex of Late Cretaceous food chains. Little is known about the early life and reproductive ecology of tyrannosaurs due to the extreme rarity of hatchling and juvenile fossils. We report bones of hatchlings (<1 yr) for Tyrannosaurus rex and Gorgosaurus libratus, weighing ~2.5 kg and ~2.4 kg, respectively, i.e., <0.1% of adult mass. Clutches were likely large. We conservatively estimate ~20 eggs in a small adult T. rex versus ~30 eggs in the largest T. rex, and clutches of ~15 eggs in G. libratus; larger clutches of 50 or even 100 eggs are not impossible. This suggests an r-selected reproductive strategy. Synchrotron scans reveal Haversian bone remodeling, suggesting that tyrannosaurs moved soon after hatching. Hatchling tyrannosaurs’ small size and precociality suggest limited parental care; teeth of hatchlings show wear suggesting that they fed on relatively large vertebrates. Tyrannosaurs had proportionately larger offspring than most reptiles, but relatively smaller hatchlings than Eumaniraptora and birds, suggesting retention of a primitive reproductive strategy intermediate between that of basal diapsids and birds. Multiple dinosaur lineages evolved large eggs independently, suggesting an evolutionary trend towards increased parental investment.

Biology doi: 10.3390/biology15131089

Authors: Peng Tian Bengang Yao Wenjing Lin Maoting Yuan Shuran Li Yuzhu Qin Shuang Chen Tao Lai Zhenbiao Yang Wenwei Lin Xiang Zhou

CRISPR-associated protein 9 (Cas9)-mediated editing generates numerous mutations. Existing detection methods, such as ACT-PCR, T7EI endonuclease cleavage, HRM analysis, and high-throughput sequencing, often require stringent conditions, expensive reagents, or specialized instruments. Here, we introduce Mismatch-Enhanced Specific PCR (MES-PCR), a method that offers sensitivity for detecting mutations under non-stringent experimental conditions. Combined with quantitative PCR (MES-qPCR), it facilitates the calculation of sgRNA efficiency and enables screening for heterozygous mutations. We validated this method in soybean (Glycine max (L.) Merr.) and Arabidopsis thaliana, confirming its practicality. This approach significantly enhances the efficiency and reduces the cost of mutation screening, presenting a powerful tool to accelerate precision breeding and functional genomics research in crops.

Biology doi: 10.3390/biology15131088

Authors: Shanshan Guan Xiangchao Si Yongtao Tang Qiang Li Chuanjiang Zhou

Alternative splicing (AS) increases transcriptomic diversity; however, its role in teleost larval nutritional physiology remains undetermined. This study investigated alternative splicing (AS) dynamics associated with nutritional transition and the starvation-induced point of no return (PNR) in Leiocassis longirostris larvae. Using RNA sequencing and rMATS across eight developmental phases, differentially spliced events (DSEs) and differentially spliced genes (DSGs) were identified between the feeding and starvation trajectories. A total of 84,172 AS events were found, with 93.4% of which were skipped exons (SE). DSEs accumulated in a stage-dependent manner during feeding but increased suddenly under starvation, reaching peak levels at the PNR. DSGs were enriched in cell adhesion, energy sensing, and metabolic reprogramming pathways, with SE splicing most strongly correlated with the progression of starvation. The integration of DSGs with differential exon usage (DEU) revealed 47 PNR-core genes, including zak, lama2, mbpa, and nhsl2, which were validated by RT-PCR analysis. The results showed that AS dynamics are associated with stage-dependent regulatory coordination of developmental adaptation and starvation-induced PNR in L. longirostris larvae. This study identified molecular targets that may improve larval survival in aquaculture.

Biology doi: 10.3390/biology15131087

Authors: David Purec Vlad Iorgoni Ionica Iancu János Dégi Corina Pascu Luminița Costinar Corina Badea Alexandru Gligor Paula Nistor Alexandru Udrea Ioan Cristian Dreghiciu Viorel Herman

Feline panleukopenia virus (FPV) causes severe enteric and systemic disease in cats, with particular importance in shelter environments where susceptible kittens, high population turnover, environmental contamination, and variable vaccination histories increase infection pressure. Recent virome and microbiome studies suggest that FPV-associated enteritis may occur within a broader context of viral co-detection and intestinal microbial disturbance, but direct FPV-specific bacteriome evidence remains limited. This review aims to synthesize current evidence on FPV-associated enteritis in shelter cats by integrating viral pathogenesis, diagnostic interpretation, enteric virome co-detection, gut dysbiosis, recovery dynamics, and intervention-related ecological effects. The literature was organized using an evidence-tier framework that distinguishes direct FPV/feline panleukopenia evidence from feline enteric microbiome proxy evidence and broader comparative or mechanistic microbiome studies. This approach was used to define the limits of inference and to separate evidence-supported conclusions from hypothesis-generating ecological models. Feline panleukopenia in shelter cats should be interpreted not only as an individual viral infection, but also as an ecological process shaped by host susceptibility, shelter exposure, diagnostic complexity, viral co-detection, and microbial community disturbance. Current evidence supports a cautious framework in which virome co-detection and dysbiosis-associated patterns are not treated as direct proof of causation. Future longitudinal, context-controlled, and multi-layer studies integrating validated FPV diagnostics, virome and bacteriome profiling, clinical metadata, treatment records, and functional endpoints are needed to clarify the biological and clinical significance of gut ecosystem disruption in feline panleukopenia.

Biology doi: 10.3390/biology15131086

Authors: Amanda Guimarães de Araujo Eder Henrique Alves Pinto João Carlos Araújo de Oliveira Beatriz Guerra Pompermayer Stephany de Souza Valéria dos Santos Mônica Marques Telles Vanessa Vendramini

Açaí is considered a super fruit for its high concentration of flavonoid polyphenols, predominantly anthocyanins. The nutraceutical effect of açaí as an anti-inflammatory and antiapoptotic agent has been reported. This study aimed to investigate whether açaí protects paternal contribution against accelerated aging using the D-galactose model. Wistar rats (n = 24) were treated by voluntary consumption with vehicle paste (C) or a mixture with 200 mg/kg of D-galactose (DG) or 300 mg/kg of lyophilized açaí (A); D-galactose and açaí (DGA) were given separately. Fathers (F0) and offspring (F1) underwent Doppler ultrasound (aorta and kidney) and spermatic and immune cell analyses. In the F0 generation, the DG group showed altered epididymis weight, sperm quality, aortic diameter, neutrophil-to-lymphocyte ratio, systolic velocity and renal resistivity index. Açaí positively modulated sperm, neutrophil and vascular alterations in F0. The male F1 of the DG group showed lower body mass, as well as a greater number of abnormal spermatozoa and leukocyte DNA breaks; however, the DGA group had a significant increase in body mass and the NRL was positively correlated with leukocyte DNA breaks. Our data indicate that age acceleration, induced by D-galactose for 30 days, causes innate physiological dysfunction and compromises sperm contribution, which was positively modulated by açaí. The preconception use of lyophilized açaí also has some positive impact on intergenerational health, but the topic still deserves further investigation.

Biology doi: 10.3390/biology15131085

Authors: Min Wang Wei Zhou Zihui Zhang Lesheng Cao Lishan Wang Linan Xie Junwei Wu Haoce Xu Ning Jia

Background: Su(var)3-9 SET genes encode key histone methyltransferases that catalyze H3K9 methylation, a modification generally associated with heterochromatin formation and transcriptional repression. Methods: We identified 23 GmSu(var)3-9 SETs and systematically characterized their tissue-specific epigenetic modifications as well as their phylogenetic relationships, chromosomal distributions, conserved domains, gene structures, GO annotations, collinearity, cis-regulatory elements, and expression profiles across diverse tissues and under salt stress. Results: These genes were divided into seven groups, exhibiting diverse structures and uneven distribution on chromosomes. Gene structure and conserved motif analyses revealed high structural diversity among family members, with variations in intron–exon distribution, conserved motifs, and functional domains. Promoter analysis detected multiple cis elements responsive to light, hormones, and abiotic stresses. Most genes showed preferential expression in meristems, roots, and leaves, and responded to salt stress. Co-expression network analysis revealed that these genes were co-expressed with stress- and development-related genes. GmSUVH12 histone modifications exhibited obvious tissue specificity. Conclusions: Overall, these results provided insights into the evolutionary and functional roles of GmSu(var)3-9 SETs in soybean.

Biology doi: 10.3390/biology15131084

Authors: Ruobing Ying Ronglin Liu Yizhuo Feng Duo Yu Xinghao Tang Kehui Zheng Shijiang Cao

The COBRA gene family is crucial for plant cell wall formation and stress adaptation. Although COBRA/COBL genes have been characterized in several plant species, their potential contribution to cell wall-mediated responses in woody plants under combined heat–drought stress remains largely unclear. In this study, eight COBRA genes (PbCOBRA1–PbCOBRA8) were systematically identified in Phoebe bournei, a highly valued timber species, and their potential stress-associated roles were investigated by integrating comparative genomic analysis, tissue expression profiling, transcriptome-based WGCNA, physiological stress indicators, qRT-PCR validation, functional enrichment analysis, and three-dimensional structure prediction. Crucially, Weighted Gene Co-expression Network Analysis (WGCNA) discovered three modules that responded to different pressures, involving a total of four PbCOBRA genes (PbCOBRA1, PbCOBRA4, PbCOBRA6, and PbCOBRA8). PbCOBRA6 and PbCOBRA8, meanwhile, were assigned to the same module, which was uniquely associated with combined stress. With contrasting kME values, these two genes may play different roles within this module. The three-dimensional structure prediction further revealed the structural basis for PbCOBRA function under stress conditions. Taken together, these findings identify PbCOBRA members as promising stress-responsive candidate genes potentially associated with heat, drought, and combined stress responses in P. bournei. This study provides a theoretical basis for future functional validation and offers candidate genes for exploring cell wall-mediated stress adaptation in this valuable woody species.

Biology doi: 10.3390/biology15131081

Authors: Nemanja Radovanovic Jovan Pesovic Vanja Viric Nikola Andrejic Ivo Bozovic Goran Brajuskovic Dusanka Savic-Pavicevic Stojan Peric

Myotonic dystrophy type 1 (DM1) is caused by an expansion of CTG repeats in the DMPK gene. In a proportion of patients, the expanded allele contains variant repeats, which have been associated with later disease onset and different clinical presentation, although their full impact remains incompletely defined. We compared sociodemographic, neuromuscular, and multisystem clinical features between DM1 patients with pure CTG expansions (n = 66) and those with variant repeats (n = 9), who formed a consecutive cohort of unrelated index cases evaluated at the age of diagnosis in routine clinical practice. Patients with variant repeats were nine years older at diagnosis than patients with pure repeat expansions (p = 0.025), had more years of formal education (p = 0.024), and showed reduced muscle strength in proximal lower limbs (p = 0.049). No childhood or juvenile forms were observed among patients with variant repeats. Sex, disease duration, and most other clinical parameters, including multisystem involvement, did not differ between groups. The results of our exploratory study support variant repeats as disease modifiers in both age at onset and pattern of muscle involvement, and imply a two-sequential-component hypothesis in DM1 pathogenesis.

Biology doi: 10.3390/biology15131083

Authors: Yongbin Cai Jintao Gan Lirong Song Zhixin Lu Ye Qin Wanlu Ren Jianwen Wang Xinkui Yao Jun Meng Yaqi Zeng

The longissimus dorsi (LD) and biceps femoris (BF) muscles are important meat-producing regions in camels. Investigating differences in meat quality and proteomic profiles between the LD and BF muscles in Junggar Bactrian camels can provide a molecular basis for regulating camel meat quality and genetic improvement. In this study, 20 healthy adult male Junggar Bactrian camels were selected. Following slaughter, muscle samples were collected from the splenius (SP), triceps brachii (TB), LD, external oblique (EO), gluteus medius (GM), and BF. Meat quality parameters (pH, meat color, shear force, drip loss, and cooking loss) were measured. The LD exhibited the highest meat quality among the six cuts, in contrast to the BF, which showed the lowest. Proteomic analysis of LD and BF from 6 Junggar Bactrian camels was conducted to identify proteins associated with meat quality, yielding 81 differentially expressed proteins (DEPs). Gene Ontology (GO) enrichment analysis highlighted several significantly enriched terms among the DEPs (p < 0.05), including calcium-dependent phospholipid binding, zinc ion binding, and metal ion binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis (p < 0.05) further indicated notable enrichment in cytoskeletal organization, 2-oxocarboxylate metabolism, and the citric acid cycle. DEPs associated with meat quality were identified, including tubulin α-chain-like 3 and synaptic function regulator FMR1 isoform X15, which can serve as candidate DEPs for shear force. Protein phosphatase 1 regulatory subunit 14C isoform X1 can serve as a candidate differentially expressed protein for pH. Protein phosphatase 1 regulatory subunit 14C isoform X and anchoring protein repeat domain 1 can serve as candidate DEPs for cooking loss. Membrane-associated protein A4 and membrane-associated protein A7 isoform X1, as well as the transcriptional activator of cytochrome c oxidase 1, can serve as candidate DEPs for color a*. These data may serve as a reference for further studies on how different cuts affect meat quality and for practical efforts to improve camel meat quality.

Biology doi: 10.3390/biology15131082

Authors: Liliana León-López Carlos Daniel Martínez-Camacho Saraid Mora-Rochin Luis Martín Sánchez-Magaña Fabiola Araceli Guzmán-Ortiz Israel Benítez-García Edith Oliva Cuevas-Rodríguez Cuauhtémoc Reyes-Moreno

White corn (Zea mays L.) is a staple grain in the Mexican diet and an important source of carbohydrates, proteins, dietary fiber, vitamins, minerals, and bioactive compounds. This study evaluated the effects of H2O2 elicitation and germination time on germination performance, bioactive compounds, and antioxidant capacity of white corn sprouts. Response surface methodology, based on a rotatable central composite design (13 treatments) was used to optimize H2O2 concentration (0–50 mM) during 24 h soaking and germination times ranging from 0 to 96 h. Optimal conditions were 20 mM H2O2 and 92 h germination, yielding 94% germination, 236.94 mg GAE/100 g free phenolic content, 21.63 mg/100 g GABA, and 6311.06 µmol TE/100 g antioxidant capacity (ABTS). Under these conditions, protein, GABA, and gallic acid contents, as well as antioxidant activity, increased by 9.26%, 34.01%, 30.95%, and 27.24%, respectively, compared with germinated grains without elicitor treatment. These findings demonstrate that H2O2-assisted germination is an effective strategy for enhancing the nutritional and functional properties of white corn sprouts.

Biology doi: 10.3390/biology15131080

Authors: Guanxu Li Liu Yang Ziyi Yin Qihong Chen Haoze He Chengguo Wang

Ammonia nitrogen is one of the most common environmental stressors in aquaculture water environments, and its accumulation can induce physiological disturbance, altered ventilation regulation, and abnormal behavioral responses in fish. To achieve non-invasive quantitative characterization of rainbow trout responses to ammonia nitrogen stress, this study developed a computer-vision-based framework for the integrated analysis of locomotor behavior and ventilation activity. Rainbow trout were exposed to four ammonia nitrogen concentrations: 0, 15, 30, and 60 mg/L. A total of 16 rainbow trout were used in this study, with an average body length of 14.0 ± 1.0 cm and an average body weight of 38.65 ± 2.42 g. The fish were assigned to four experimental aquaria, with four fish maintained in one aquarium for each TAN treatment. Stereo videos for locomotor behavior analysis and monocular mouth-region videos for ventilation analysis were simultaneously collected, and the final 5 min of each recording was analyzed. YOLOv11n, multi-object tracking, and stereo vision were used to extract three-dimensional position sequences of rainbow trout and calculate the amount of exercise, average swimming speed, and spatial distribution. Meanwhile, optical-flow analysis was applied to quantify mouth opening–closing motion and estimate ventilation frequency. The results showed that with increasing ammonia nitrogen concentration, rainbow trout locomotor behavior tended to be suppressed, with average swimming speed showing the clearest decrease, whereas ventilation frequency continuously increased. Average swimming speed decreased from 3.83 cm/s in the 0 mg/L group to 1.03 cm/s in the 60 mg/L group, while ventilation frequency increased from 84.91 breaths/min to 133.43 breaths/min. Compared with locomotor indicators, ventilation frequency showed a more stable response to changes in ammonia nitrogen concentration. This study achieved the synchronous quantification of rainbow trout locomotor behavior and ventilation activity, revealing a differentiated response pattern characterized by enhanced ventilation and suppressed locomotor behavior under acute ammonia nitrogen stress. These findings provide a methodological reference for fish stress assessment and risk warning in aquaculture environments.

Biology doi: 10.3390/biology15131079

Authors: Zongyi Zhou Ruiqi Xiong Shunlian Fu Yang Su Qiang Ao Yong-Cong Chen Ping Ao

Schwann cells, the principal glial cells of the peripheral nervous system, play a central role in nerve repair following injury. Upon injury, mature Schwann cells dedifferentiate into repair Schwann cells. These processes are governed by complex gene regulatory networks, yet the quantitative dynamics of these processes remain unclear. Here, using a bottom-up systems biology approach, we constructed an endogenous regulatory network model based on experimentally validated interactions, without relying on high-throughput data as input. The model captures Schwann cell dedifferentiation dynamics and reveals a potential landscape composed of stable states and intermediate transition states. Simulations recapitulate post-injury trajectories and confirm the role of c-Jun upregulation in maintaining repair capacity. Furthermore, the model predicts multiple potential therapeutic targets, including tumor protein p53 (P53), c-Jun N-terminal kinase (JNK), and phosphatase and tensin homolog (PTEN), for sustaining repair competence. We also identify intrinsic heterogeneity within repair Schwann cells. Furthermore, we uncover key transition states that simultaneously connect repair-competent cells to both repair-deficient and apoptotic phenotypes. These intermediate states may represent critical regulatory bottlenecks and serve as key cellular targets for improving peripheral nerve regeneration. Overall, this work provides new insights into the precise regulation of Schwann cell fate and establishes a theoretical framework for regenerative medicine and clinical strategies in peripheral nerve repair.

Biology doi: 10.3390/biology15131078

Authors: Xinyang Zhang Jialin Luo Xiang Zhang Fang Yang Xiaojin Zhang Xujun Yu Liang Dong

Male infertility refers to the inability of a male partner to contribute to pregnancy after 12 months or more of regular unprotected intercourse. It is frequently associated with impaired spermatogenesis, and many cases cannot be completely explained by genetic, inflammatory, endocrine, or environmental factors. Trimethylamine N-oxide (TMAO) is generated when gut bacteria convert dietary choline, L-carnitine, and betaine into trimethylamine (TMA), which is oxidized in the liver mainly by flavin-containing monooxygenase 3 (FMO3). This focused review evaluates current evidence on TMAO and impaired spermatogenesis within the gut–testis axis. The rationale is biologically plausible because sperm motility depends on coordinated glycolytic and mitochondrial energy metabolism, whereas Leydig cell steroidogenesis depends on mitochondrial cholesterol transport and redox balance. Human observational studies associate TMAO with asthenozoospermia and Leydig cell-related markers, particularly insulin-like peptide 3 (INSL3), while mouse studies suggest testicular injury and reduced spermatogenesis after TMAO-related exposure. The Hippo/Yes-associated protein (YAP)–mitochondria–steroidogenic acute regulatory protein (StAR) axis has been proposed as one possible mechanism, but direct reproductive tract exposure, blood–testis barrier kinetics, and human validation remain unresolved. Overall, TMAO should be considered as a candidate metabolic mediator and not a proven causal factor or therapeutic target in male infertility.

Biology doi: 10.3390/biology15131077

Authors: Shaun Smith Judith Grisel

Individual differences in the sensitivity and response to drugs of abuse are reliably associated with later patterns of substance use and, for some, progression to a substance use disorder diagnosis. This review synthesizes human drug challenge, longitudinal, and translational animal evidence to characterize how early or initial sensitivity to drugs, shaped by heritable and developmental factors, may relate to subsequent risk. These initial responses, through associative learning, may influence how drug-paired cues acquire motivational significance over time. Ample evidence suggests that early response variability is a biologically grounded and measurable correlate of SUD vulnerability, detectable well before chronic neuroadaptation, with potential utility for targeted prevention and intervention efforts.

Biology doi: 10.3390/biology15131076

Authors: Ya Zhang Tianshu Zhou Yuting Zhang Hongyi Guo Xuguang Zhang

Seasonal hydrology reshapes large-river food webs by altering habitat connectivity and basal resource availability. Trophic baselines from before the 2021 Yangtze ten-year fishing ban are now valuable because monitoring has shifted from fish abundance alone toward food-web function and ecological recovery. We analysed carbon (δ13C) and nitrogen (δ15N) stable isotopes of fish and the baseline bivalve Corbicula fluminea collected in March (dry season) and August (wet season) 2016 from the Jingjiang section of the lower Yangtze River. In the dry season, 100 individuals of 27 species were analysed; species mean δ13C ranged from −30.52‰ (Micropercops swinhonis) to −21.19‰ (Aristichthys nobilis) and δ15N from 6.30‰ (Hypophthalmichthys molitrix) to 14.90‰ (Lophiogobius ocellicauda). In the wet season, 187 individuals of 47 species were analysed; species mean δ13C ranged from −32.07‰ (Pseudobrama simoni) to −20.84‰ (Salanx ariakensis) and δ15N from 6.27‰ (Misgurnus anguillicaudatus) to 14.87‰ (Saurogobio gymnocheilus). Among 24 shared species, δ13C differed significantly between seasons (paired t = 4.30, p < 0.001), but δ15N did not (t = 1.52, p = 0.143). Mean trophic level fell from 3.07 to 2.74 (t = 3.85, p < 0.001). This decline remained significant in a trophic-enrichment-factor sensitivity analysis using 2.5–4.0‰. Community-wide carbon range (CR), nitrogen range (NR), total convex-hull area (TA), mean nearest-neighbour distance (NND), and the standard deviation of nearest-neighbour distance (SDNND) showed larger wet-season CR (9.08 vs. 7.51), slightly larger NR, TA and NND, and lower SDNND. Seasonal hydrology thus mainly altered basal carbon pathways and relative trophic positions rather than reorganising feeding guilds. The dataset provides a pre-ban isotopic baseline for assessing whether post-ban recovery in the lower Yangtze includes restoration of trophic structure and energy-flow pathways.

Biology doi: 10.3390/biology15131075

Authors: Natalia Golub Boris Anokhin Desislava Stoianova Valentina Kuznetsova

(1) Background: Over the past few decades, the number and chromosomal arrangement of rDNA loci have been successfully used as cytogenetic markers in comparative studies of many insect taxa, including the hemipteran suborder Heteroptera (or true bugs). Of the seven generally accepted infraorders of true bugs, such data are available only for three: one of the early branching infraorders Nepomorpha and the sister infraorders Cimicomorpha and Pentatomomorpha. To address this gap, we obtained rDNA-FISH data for another “early” evolutionary lineage of true bugs, the infraorder Gerromorpha, in which we studied four species belonging to the families Gerridae and Mesoveliidae. (2) Methods: Standard karyotypes were studied using the Schiff–Giemsa method. To study the chromosomal distribution of the major rDNA (45S rDNA), the Fluorescence In Situ Hybridization (FISH) method was used with an 18S rDNA probe. (3) Results: Three variants of the chromosomal arrangement of 18S rDNA were identified in the studied species. The rDNA loci were located on one pair of autosomes in Aquarius paludum (n = 11AA + X) and Gerris lacustris (n = 10AA + X); on one pair of autosomes and on the X chromosome in Limnoporus rufoscutellatus (n = 10AA + X) (Gerridae); on one of the four X chromosomes and on the Y chromosome in Mesovelia furcata (n = 15AA + X1X2X3X4Y) (Mesoveliidae). The karyotype of L. rufoscutellatus was studied for the first time. (4) Conclusions: Our study provides the first data on the rDNA-FISH location for the infraorder Gerromorpha and expands current understanding of the chromosomal distribution of rDNA arrays in Heteroptera as a whole.

Biology doi: 10.3390/biology15131074

Authors: Tingting He Hongyu Wang Haoqi Ni Yuting Sun Xiang Gao Fan Zhou Jianmin Zhang Kedi Xu

Levodopa-induced dyskinesia (LID) is a severe motor complication associated with long-term levodopa (L-DOPA) treatment for Parkinson’s disease (PD). Its underlying mechanisms remain unclear, and candidate biomarkers lack consistency. To investigate cortico-striatal network alterations associated with LID, we simultaneously recorded single-neuron spikes and local field potentials (LFPs) from the dorsolateral striatum (DLS) and the primary motor cortex (M1) in LID rats. Our results showed that in the DLS, the LID group had a greater number of putative fast-spiking interneurons (FSIs) with lower firing rates, and fewer putative medium spiny neurons (MSNs) with higher firing rates. In M1, pyramidal neurons were fewer but fired faster, while interneurons were more numerous with no change in firing rate. Although gamma power increased and delta power decreased in both regions in LID rats, delta-gamma phase-amplitude coupling (PAC) was present in the DLS but absent in M1. Furthermore, cross-regional PAC analysis revealed significantly stronger coupling between the low-frequency phase of M1 and the high-frequency amplitude of the DLS than in the opposite direction, indicating an asymmetric pattern of cortico-striatal coupling in LID. These findings demonstrate region-specific alterations in neuronal activity and oscillatory coupling associated with LID and suggest that asymmetric cortico-striatal PAC may serve as a promising electrophysiological marker for characterizing abnormal network dynamics underlying dyskinesia.

Biology doi: 10.3390/biology15131072

Authors: Xiaxi Liuyang Jiayu Lu Yang Cao

Urban plant communities are widely regarded as important nature-based solutions for climate mitigation, yet their actual carbon benefits remain uncertain: vegetation growth is accompanied by carbon emissions from construction and long-term maintenance, and existing assessments rarely integrate community succession, interspecific competition, and maintenance-related emissions within a consistent life-cycle framework. To address these limitations, this study developed a dynamic succession-based life-cycle simulation model to project the 50-year carbon source–sink transitions of 150 typical urban plant communities in Tianjin, China. The model updates plant structural attributes—diameter at breast height, crown width, and tree height—iteratively by linking individual plant growth to environmental suitability and neighborhood competition through a Plant Health Index. Simulated structural trajectories were coupled with biomass equations and carbon content coefficients to estimate aboveground carbon sequestration, while construction and maintenance emissions were quantified using life cycle assessment, enabling evaluation of modeled net carbon balance rather than gross carbon sequestration alone. Under the modeled 50-year scenario, most communities were projected to act as carbon sources during the early stage but gradually shifted toward carbon sinks as biomass accumulated; 86.1% of the communities were projected to become net carbon sinks after 50 years (a scenario-based projection under specified growth, maintenance, and emission assumptions). The highest modeled net carbon balance reached 3186.08 kg·C·ha−1, whereas the weakest community remained a slight carbon source at −81.21 kg·C·ha−1. Vertical structural complexity and species richness were the strongest positive predictors of modeled net carbon balance, followed by three-dimensional green quantity and canopy closure. Among maintenance processes, fertilization was the dominant emission source, followed by pesticide application and irrigation; comparative scenario analysis showed that resource-saving maintenance consistently improved projected net carbon balance relative to high-maintenance management. These results suggest that low-carbon planting design should prioritize locally adapted species, multi-layered vertical structures, and adaptive maintenance over simply maximizing planting density or minimizing inputs. The results represent scenario-based projections of aboveground vegetation carbon balance; belowground biomass, soil carbon, litter carbon, dead organic matter, and parameter uncertainty were not fully incorporated, and future studies should address these limitations to improve the robustness and transferability of the proposed framework.

Biology doi: 10.3390/biology15131073

Authors: Henrique Silva

Post-occlusive reactive hyperemia (PORH) is a classical probe of microvascular function, yet its assessment remains largely based on amplitude-derived indices that do not capture the temporal organization of vascular regulation. Photoplethysmography (PPG), widely used in clinical and wearable technologies, offers a practical platform for nonlinear characterization of PORH. Twelve healthy adults underwent a standardized PORH protocol (10 min baseline, 5 min suprasystolic occlusion, 10 min reperfusion) with bilateral reflective green-light PPG. Pulse amplitude, detrended fluctuation analysis (global DFA α exponent), and multiscale entropy (Complexity Index, CI) were computed in 5 min epochs. Occlusion nearly abolished pulsatility in the test limb but produced only modest changes in fractal structure, as α decreased minimally despite near-zero flow. In contrast, CI showed a marked collapse, indicating loss of multiscale organization. During reperfusion, α exhibited a trend toward increased fractal persistence, whereas CI recovered only partially. Contralateral responses were small and detectable mainly through subtle reductions in α during occlusion and consistently higher CI compared with the test limb. These findings indicate that occlusion disrupts multiscale complexity without eliminating fractal persistence, whereas reperfusion restores correlation structure and only partially re-establishes dynamical richness. Overall, DFA and MSE reveal nonlinear features of PORH that are not captured by conventional amplitude-based metrics, extending the physiological interpretation of microvascular responses using widely available PPG technology.

Biology doi: 10.3390/biology15131071

Authors: Yixuan Yang Qiurui Li Shaoshi Luo Junming Sun Yiqiang Ouyang

Alzheimer’s disease (AD) is characterized by cognitive decline and amyloid-β (Aβ)-related pathology. Non-rodent models that capture selected aspects of human AD remain limited. We established and characterized a human APP-driven, Aβ-related AD-like tree shrew model following AAV-mediated delivery of triple-mutant human amyloid precursor protein (hAPP-SLA) carrying the Swedish, Austrian, and London mutations by bilateral stereotaxic injection directed at CA1 coordinates. Adult tree shrews received bilateral AAV-hAPP-SLA injections directed at CA1 coordinates and were evaluated by bioluminescence imaging, behavioral testing, PCR, RT-qPCR, Western blotting, ELISA, and histopathology. Vector-associated reporter signals remained detectable for 6 months. The experimental group showed exogenous hAPP expression and reduced endogenous tsAPP expression, increased relative hippocampal Aβ42 protein level, enhanced 4G8-reactive APP/Aβ-related signals, elevated total Aβ immunoreactivity, increased serum Aβ42/Aβ40 ratio, cytoarchitectural alterations, reduced Nissl staining, and Thioflavin S-reactive aggregate-associated signals. AT8 (Ser202/Thr205), GFAP, and Iba-1 immunoreactivity increased, whereas Synaptophysin and PSD-95 immunoreactivity was reduced. These changes were accompanied by reduced short-delay recognition-related performance and reduced social approach and social novelty preference. Aged tree shrews showed partly overlapping alterations. This model provides a non-rodent platform for studying human APP-driven Aβ-related pathology.

Biology doi: 10.3390/biology15131070

Authors: Wenyu Chen Yongjie Liu Minghao Sun Jiabao Cheng Xing Shen Zhongping Chai

Postharvest quality deterioration of Korla fragrant pear (Pyrus sinkiangensis Yu) severely constrains its market value, yet the regulatory role of preharvest soil management in shaping postharvest performance remains poorly understood. Although green manure is widely adopted to ameliorate orchard soil degradation, species-specific modulation of postharvest storage trajectories and the quantitative fidelity of soil-to-fruit nutrient transmission have rarely been resolved for climacteric pear species. This study investigated how green manure species modulate fruit quality at harvest and during postharvest storage life and their underlying soil–fruit linkages. Three preharvest treatments were imposed, as follows: control (CK), sweet clover (CM), and alfalfa (MX). Fruits were harvested and stored at 4 °C, with samplings at 1, 5, 10, 15, and 20 d. A critical quality transition was identified at 15 d, characterized by the concurrent peaking of soluble sugars, organic acids, vitamin C, and anthocyanins alongside an optimal sugar–acid ratio. Beyond this inflection point, CM and MX diverged markedly: CM enhanced soluble sugar accumulation, anthocyanin retention, and ester volatile production—most notably hexyl acetate, which increased over 14.4-fold—thereby generating a pronounced fruity aroma bouquet. Conversely, MX sustained higher amino acid and vitamin C levels and conferred superior late-storage stability, evidenced by a three-fold lower coefficient of variation in the sugar–acid ratio relative to CK. Partial-least-squares structural equation modeling (PLS–SEM) revealed soil fertility as the principal exploratory associative factor of fruit quality, but the fidelity of soil-to-fruit transmission was species-dependent. MX exhibited the highest observed associative strength (R2 = 0.971), whereas CM exhibited attenuated transmission fidelity (R2 = 0.777), with network analysis further indicating that CM exhibited divergent associative patterns of key soil–fruit correlations. These findings suggest that green manure identity is linked to postharvest quality through divergent soil–fruit coupling pathways: alfalfa shows nutrient transmission efficiency and stabilizes nutritional quality, whereas sweet clover promotes sugar-aroma accumulation at the cost of reduced soil–fruit conversion fidelity. Species-specific green manure selection thus offers a viable strategy for targeted modulation of postharvest traits in Korla fragrant pear.

Biology doi: 10.3390/biology15131069

Authors: Zhenjun Tian Lieyu Zhang Shengwang Gao Yimei Wei Yangwei Bai Shuping Wang

Rural greywater management is a critical global challenge due to the lack of centralized treatment in dispersed communities. This study aimed to characterize the pollution characteristics and bacterial community structure of samples from four greywater collection tanks in eastern China using high-throughput sequencing and absolute quantification of the 16S rRNA gene. Pollution characteristics showed spatial heterogeneity: chemical oxygen demand ranged from 19.8 to 272.5 mg/L, total nitrogen from 8.6 to 16.4 mg/L, and dissolved oxygen from 1.3 to 5.3 mg/L. Dissolved greenhouse gases also varied, with N2O reaching 103.6 ppmv and CH4 up to 50.4 ppmv. Based on the estimated absolute abundance of 16S rRNA gene copies, we found that the bacterial communities were dominated by Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota. Key genera such as Acinetobacter, Pseudomonas, and unclassified Enterobacteriaceae were positively correlated with nitrate, suggesting their potential association with denitrification and potential N2O production. The methanotrophic genus Methyloparacoccus was enriched in a tank with high dissolved organic carbon. Co-occurrence network analysis revealed that core taxa like unclassified Paracoccaceae and Limnohabitans function as module hubs, maintaining community stability. These findings reveal associations between bacterial taxa, pollutant transformation, and greenhouse gas emissions in rural greywater and provide fundamental insights to support the development of low-carbon, resource-oriented treatment technologies.

Biology doi: 10.3390/biology15131068

Authors: Marta S. Pimentel Catarina P. Santos Maria R. Pegado Eduardo Sampaio Pedro Pousão-Ferreira Vanessa M. Lopes David Abreu dos Santos João Caramelo Rui Rosa

The interaction between increased dissolved carbon dioxide, rising temperatures, and oxygen loss—the so-called “deadly trio”—is expected to strongly affect marine biota over the coming years, undermining ocean services and uses. Nonetheless, no study has so far scrutinized the cumulative impact of these three stressors on fish embryos and larvae. To fill this knowledge gap, we conducted a fully multi-factorial experiment to investigate the effects of warming (+4 °C: 22 °C), acidification (Δ − 0.4 pH units: 7.7 pH, pCO2 ~1000 μatm), and deoxygenation (Δ − 60% O2 saturation: 3 mg O2 L−1) on physiological and behavioral responses of the commercially important species Sparus aurata. Deoxygenation was the primary factor reducing hatching rates (64.25%), survival (46.71%), and heart rates (31.99%) of recently hatched larvae, being generally further exacerbated when combined with warming and acidification. No larvae exposed to the interaction of the three treatments reacted to the phototactic behavior test. However, acidification alone caused a 50% reduction in phototactic behavior. Our findings demonstrate that the deadly trio is detrimental to early fish development, impacting several key features at this critical life stage, and the need to assess the impacts of stressors’ interaction on marine taxa to better predict future ecosystem responses to ocean changes.

Biology doi: 10.3390/biology15131067

Authors: Sathita Areerat Attawit Kovitvadhi Koramit Jenjirawatn Surangkhalak Khamma Peeraya Chapanon Pipatpong Chundang Napat Praditrungwatana Nichaphon Pliantiangtam Preecha Patumcharoenpol Nattaphong Akrimajirachoote Massalin Nakphaichit Suvimol Charoensiddhi Tuchakorn Lertwanakarn Pornsucha Palaseweenun

The aquatic plant Wolffia globosa and the probiotic Limosilactobacillus reuteri KUB-AC5 have been proposed as candidate synbiotic components targeting gut microbiota modulation. In this study, we investigated the effects of W. globosa supplementation, alone or in combination with L. reuteri KUB-AC5, on the gut microbiota and health status in healthy adult dogs. For a 28-day feeding trial, 24 healthy dogs were randomly assigned to three dietary treatment groups: control, prebiotic (PRE; 3.5% W. globosa powder), and synbiotic (SYN, 3.5% W. globosa powder combined with L. reuteri KUB-AC5 at 1 × 108 CFU/day). No significant differences were observed in body weight, body condition score, fecal consistency, feed intake, or blood parameters among groups (p > 0.05). Although overall gut microbial diversity remained unchanged, linear discriminant analysis effect size analysis revealed the selective enrichment of specific bacterial taxa. The PRE group exhibited higher relative abundances of Parabacteroides merdae, Romboutsia lituseburensis, Subdoligranulum variabile, and Phocaeicola sartorii, whereas the SYN group showed increased levels of Escherichia coli and Terrisporobacter glycolicus and reduced levels of Anaerobiospirillum succiniciproducens and Campylobacter upsaliensis (p < 0.05). In conclusion, W. globosa, alone or combined with L. reuteri KUB-AC5, was safely used to modulate gut bacterial composition as a potential functional ingredient.

Biology doi: 10.3390/biology15131066

Authors: Zhongquan Jiang Jiale Chen Yuanhao Ren Tingting Lin Siping Li Fengyuan Shen Bo Qin Lei Li Changjian Li Na Ying Hanfeng Zheng

The gut microbiome of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) is increasingly recognized as a functional interface linking dietary inputs, epithelial barrier integrity, mucosal immunity, environmental stress, disease susceptibility, and antimicrobial-resistance risk in intensive aquaculture. Based on available salmonid studies and relevant evidence from broader fish and aquaculture systems, this review synthesizes current knowledge on salmonid gut microbial composition, nutritional modulation, microbiome–mucosal immune interactions, aquaculture stressors, antibiotic exposure, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metagenomics, multi-omics, and emerging microbiome-informed decision-support tools. Current evidence does not support a universally stable single-core microbiota in these species. Instead, community structure is shaped by developmental stage, freshwater–seawater transition, intestinal segment, digesta versus mucosa sampling, diet, temperature, stress, health status, and methodological workflow. Feed substitution and functional additives can remodel the gut microbiota, but these shifts should be interpreted alongside histology, barrier function, metabolic profiles, immune indicators, and disease-resistance phenotypes. Antibiotic exposure may reduce acute bacterial disease pressure while disturbing community structure and potentially enriching ARGs or ARG–MGE associations. Risk assessment should therefore move beyond ARG abundance toward host–ARG–MGE linkage using shotgun metagenomics, metagenome-assembled genomes, long-read sequencing, Hi-C, and externally validated multi-omics models. Machine learning and artificial intelligence approaches may support feature screening, risk stratification, and decision support, but their application in salmonid gut-health management remains at an early stage and requires external validation across sites, production stages, diets, and seasons.

Biology doi: 10.3390/biology15131065

Authors: Qianru Jia Jinghui Shi Rui Wang Xiaoqi He Binhui Guo Guanglong Zhu Li Song

Cyclin-dependent kinases (CDKs) and cyclins are master regulators of the cell cycle, playing critical roles in plant growth, development, and stress responses. While these gene families have been extensively studied in model plants, a comprehensive analysis in soybean remains underexplored. To address this gap, we performed a genome-wide identification and systematic analysis of these families in soybean using bioinformatic approaches. Expression profiles and protein interactions of selected GmCDK and GmCyclin candidates were tested by qRT-PCR and BiFC assays. A total of 28 GmCDK and 101 GmCyclin genes were identified, revealing a significant expansion compared to Arabidopsis, rice, and maize, primarily driven by whole-genome and segmental duplications. Phylogenetic analysis classified GmCDKs into seven conserved clades (CDKA-CDKG) and GmCyclins into ten distinct subfamilies. Expression profiling demonstrated dynamic, tissue-specific patterns, with distinct modules active during seed development and in tissues. Promoter analysis further linked these genes to hormonal and stress-responsive pathways. Crucially, BiFC assay identified specific interactions between GmCDKA2, GmCDKA3, GmCDKB1 and GmCYCA3-3, suggesting evolutionary divergence in soybean CDK-Cyclin regulatory networks. This study provides a foundational resource for the soybean cell cycle regulome, highlighting its evolutionary plasticity and implicating specific CDK-Cyclin pairs as potential targets for manipulating agronomic traits such as seed development and stress resilience.

Biology doi: 10.3390/biology15131064

Authors: Venhar Gurbuz Can Mehmet Demir Tansu Kusat Feyza Basak

In the original publication [...]

Biology doi: 10.3390/biology15131063

Authors: Bohan Yan Hexuan Li Dazhun Guan Yu Zhang Kexin Zhang Shuang Li Kangyu Wang

The Cysteine-rich Polycomb-like Protein (CPP) gene family is a class of transcription factors containing conserved CXC domains that are widely involved in the regulation of plant growth and development, cell division, and stress responses. Based on the ginseng genome and transcriptome database, all members of the PgCPP gene family in Panax ginseng were systematically identified, and comprehensive bioinformatics analyses, including phylogenetic, conserved domain, chromosomal localization and collinearity, cis-acting element, and expression pattern analyses, were conducted. In this study, we identified 44 PgCPP gene family members in ginseng, which were unevenly localized on multiple chromosomes. The phylogenetic tree divided them into three subfamilies, with members in the same subfamily being highly conserved. Conserved domain analysis revealed that all PgCPPs contain typical CXC motifs. Cis-acting elements were abundant in light response, hormone responses (abscisic acid, methyl jasmonate, salicylic acid), and stress response elements. Expression heatmaps demonstrated that different members have specific expression patterns across different ages, tissues, and species. After treatment with MeJA, transcriptional suppression of PgCPP03-4 and PgCPP03-13 was observed, and their expression levels demonstrated significant negative correlations with the contents of six protopanaxadiol-type ginsenosides. These findings suggest that PgCPP03-4 and PgCPP03-13 may act as negative regulators of protopanaxadiol-type ginsenoside biosynthesis within the MeJA signaling pathway. This systematic characterization and identification of the CPP gene family members in P. ginseng establishes a foundational framework for future functional validation and molecular breeding initiatives.

Biology doi: 10.3390/biology15131062

Authors: Mounia Chroho Eleftherios Touloupakis Cecilia Faraloni Latifa Bouissane

Chemical fertilizers are widely used to achieve rapid and high-yield crop production. However, their intensive use negatively impacts ecosystems by polluting air and groundwater, accelerating soil acidification and deterioration, and because they rely on energy-intensive production processes and excessive mining. Biofertilizers have emerged as a promising and sustainable solution. Among them, microalgae, particularly species of the genus Chlorella, have attracted significant attention. Chlorella microalgae are an eco-friendly and cost-effective biofertilizer option, with advantages such as ease of cultivation, fast growth and slow release of nutrients when applied to soil. In this context, this review summarizes the potential of Chlorella species as biofertilizers and highlights the important role of its phytohormones in this effect, in addition to its use in wastewater treatment, which results in biomass and water with biofertilizing potential.

Biology doi: 10.3390/biology15131061

Authors: Yanni Cao Kangcheng Xu Xiaohui Li Junyuan Zhang Wen Jin Yuxian Liu

Background/Objectives: While traditional transcriptomics and single-cell RNA sequencing can reveal differences in cell type and gene expression, they cannot provide spatial information within tissues. Spatial transcriptomics (ST), as an emerging technology in recent years, has achieved significant progress in resolving gene expression along the spatial dimension. This technology quantifies gene expression at defined spatial coordinates and describes the spatial distribution of transcripts and the co-localization patterns between cells within intact tissue, allowing for an integrated analysis of molecular and spatial information. This review aims to systematically trace the development of ST and highlight its application value in breast cancer research. Methods: We systematically reviewed the recent literature on ST platforms, on combined analyses of single-cell RNA sequencing (scRNA-seq) and ST, and on integrated spatial multi-omics in breast cancer. Key topics include tumor microenvironment organization, intra-tumor heterogeneity, the spatial distribution of immune cells, cancer-associated fibroblast function, treatment-response prediction, and personalized-treatment strategy development. Results: ST can characterize the spatial organization of interactions between breast cancer cells and the tumor microenvironment, describe the spatial dimensions of tumor heterogeneity, and provide multi-dimensional information that may support refined subtype classification and prognostic assessment. Existing studies indicate that ST shows significant potential to inform personalized treatment strategies, but the technology also faces bottlenecks in data integration, spatial resolution, standardization, and the need for functional validation. Conclusions: ST provides an important tool for an in-depth description of the complex spatial organization within breast cancer tumors. When integrated with functional perturbation, longitudinal cohorts, and orthogonal omics, it has the potential to ultimately improve clinical outcomes for breast cancer patients.

Biology doi: 10.3390/biology15131060

Authors: Ferah Bulut Muhammed Adam Munevver Gizem Hekim Mete Ozcan

Diabetes mellitus (DM) markedly increases the risk of cardiovascular complications through mechanisms involving hyperglycemia-induced oxidative stress, inflammation, and apoptosis. Humanin (HN), a mitochondria-derived peptide with established cytoprotective properties, has been reported to exert antioxidant and anti-apoptotic effects in several experimental models. However, its role in diabetic cardiac injury remains insufficiently understood. The present study investigated the protective effects of repeated HN treatment against diabetes-induced cardiac injury in a streptozotocin (STZ)-induced mouse model. Mice were divided into four groups: control, HN-treated, STZ-induced diabetic, and STZ + HN-treated groups (n = 10/group). HN (4 mg/kg) was administered daily for 15 consecutive days. Biochemical analyses were performed to evaluate oxidative stress, inflammatory cytokines, and apoptotic markers. STZ-induced diabetes significantly increased oxidative stress markers, pro-inflammatory cytokines, and apoptotic activity while reducing antioxidant defenses and anti-inflammatory cytokines compared with controls. Repeated HN treatment markedly attenuated these alterations and restored redox and inflammatory balance in diabetic cardiac tissue. These findings demonstrate that repeated HN treatment attenuates oxidative stress, inflammation, and apoptosis in the hearts of diabetic mice. The results further suggest that HN may represent a promising therapeutic candidate for limiting diabetes-associated cardiac complications.

Biology doi: 10.3390/biology15131059

Authors: Qinyao Wei Yeyu Chen Fubin Wang Wei Shao Yongshen Ru Huanchao Yang Jun Du Zhaobin Song Zhenming Lai Hua Li

Oocyte quality determines fertilization success during the reproductive period of fish and is affected by a key intrinsic factor: the level of lipid deposition in the yolk. In this study, lipidomics was used to characterize lipid profiles of adipose tissue, liver, serum and ovary to clarify divergent hepatic lipid allocation to fat depots versus ovary in Sichuan taimen (Hucho bleekeri). The results showed that glycerophospholipids (GPs) constituted the most diverse lipid class across all four tissues, with phosphatidylcholine (PC) being the most abundant in each tissue. Relative to adipose tissue, liver, and serum, the ovary exhibited significant enrichment of PC and phosphatidylethanolamine (PE) and higher accumulation of docosahexaenoic acid (DHA)- and arachidonic acid (ARA)-containing GPs and triacylglycerols (TGs), as well as enrichment in TGs, diacylglycerols (DGs), and cardiolipin (CL), compared to adipose tissue. The expression levels of fads6, elovl2, elovl5, dgat1b, dgat2, pparα, nfyb, and fabp7 were higher in the liver, while lpcat1 was highly expressed specifically in the ovary. The results of this study demonstrate that long-chain polyunsaturated fatty acids (LC-PUFAs) exhibited selective enrichment in the ovary, which facilitates yolk lipid deposition and provides structural and energetic support for oocyte development and early embryonic development. From a lipidomic perspective, this study reveals the regulatory characteristics underlying ovarian yolk deposition in H. bleekeri, providing important evidence for understanding the mechanisms of egg quality formation as well as a theoretical basis for broodstock management, artificial propagation, and the improvement of egg and larval quality.

Biology doi: 10.3390/biology15131058

Authors: Limin Jia Yinguang Hou Man Zhang Liangwei Li Yaolei Zhang Jiahao Wang Zengbao Yuan Guangyi Fan Chengcheng Shi Hansheng Zhao

Eukaryotic flagella are evolutionarily conserved organelles that mediate motility, sensory transduction, and environmental adaptation, yet their presence and gene composition vary considerably across algal lineages. Dinoflagellates, a lineage within the superphylum Alveolata, derived from secondary endosymbiosis, exhibit larger and more reorganized genomes than their red-algal relatives and possess a distinctive biflagellate morphology, making them an informative group for studying flagellar evolution. To systematically investigate flagellar gene distribution in this lineage, we performed comparative genomic analyses on 102 genomes spanning four algal groups—Chlorophyta, Rhodophyta, Alveolata (represented by dinoflagellates), and Bacillariophyta. Genomes were selected based on assembly completeness, retaining only those with BUSCO completeness > 50% to balance data quality with taxonomic coverage. Orthologous groups were identified using a reciprocal best BLAST v2.11.0(rBH) strategy, from which we curated 94 conserved flagellar gene families. Quantitative comparisons revealed significant lineage-specific expansions of flagellar gene families within dinoflagellates, including WDR35, TTLL5, and STK36, with fold enrichment values ranging from 3.6 to 5.8 (adjusted p < 0.01). Phylogenetic analyses further identified two axonemal components, BBS9 and C1A-18, as candidates acquired via horizontal gene transfer, with bootstrap support exceeding 80% and Alien Index values > 45. Collectively, these phylogenomic analyses suggest that lineage-specific expansion and horizontal gene transfer have jointly contributed to the evolution of flagellar systems in dinoflagellates, providing a framework for future functional studies.

Biology doi: 10.3390/biology15131057

Authors: Yiannis G. Zevgolis Panayiotis G. Dimitrakopoulos

Wildlife conservation and habitat management have entered a phase of irreducible complexity, in which the ecosystems where species must persist, populations must recover, and management must intervene are increasingly structured by interacting constellations of anthropogenic, biotic, and abiotic change [...]