Biology doi: 10.3390/biology15212025

Authors: Ruji Peng Xiaoning Sun Cheng Luo Jianghan Du Yanhong Jiang Yanghu Sima Guang Wang Shiqing Xu

Silk spinning deficiency is often associated with developmental abnormalities and diminished vitality. In silkworm, the fat body functions as a crucial organ in nutrient metabolism and metamorphic development. However, the impact of silk spinning deficiency on fat body development and metabolic function during metamorphosis remains unclear. Here, using a silkworm model of silk spinning deficiency, we systematically analyzed its effects on fat body regeneration and metabolism during metamorphosis by integrating morphological observations, transcriptomics, untargeted metabolomics, histological staining, and biochemical and molecular assays. Silk spinning deficiency delayed the onset of fat body dissociation and impeded its subsequent remodeling, accompanied by extensive transcriptional reprogramming of metabolism-related genes in the fat body. Notably, the glucose metabolism pathway, a major energy source, shifted toward glycolysis and lactate production. Untargeted metabolomic analysis revealed marked perturbations in the metabolic networks of amino acids and lipids in the fat body. Lipid content analysis showed that silk spinning deficiency promoted the accumulation of lipid droplets and triglycerides in the fat body, potentially linked with the activation of the IIS/TOR signaling pathway. Collectively, these results demonstrate that silk spinning deficiency disrupts nutrient utilization and allocation during metamorphosis, thereby interfering with fat body dissociation and remodeling while promoting lipid accumulation.

Biology doi: 10.3390/biology15212024

Authors: Dominika Kołodziej-Sobczak Szymon Obertas Łukasz Sobczak Krzysztof Z. Łączkowski

In silico analyses, including absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling and drug-likeness evaluations, constitute powerful tools in modern drug discovery. These computational methods enable high-throughput screening of molecular libraries to assess therapeutic potential while identifying unfavourable pharmacokinetic and toxicological profiles early in the development process. To bridge the gap between computational models and empirical data, this study evaluates the reliability and limitations of predictive ADMET profiling by comparing in silico outputs across multiple platforms and referring them to available in vitro experimental data. The empirical dataset comprises recently published in vitro assays focusing on inhibitors of the protein tyrosine phosphatase 1B (PTP1B) enzyme. ADMET predictions were generated using three widely utilized, non-commercial platforms: SwissADME, ADMETlab 3.0, and admetSAR 3.0. The comparative analysis encompassed physicochemical parameters (MW, logP, TPSA), medicinal chemistry alerts (PAINS, ALARM NMR), absorption metrics (Caco-2, HIA), and multiple toxicity endpoints (Ames mutagenicity, DILI, hERG inhibition, nuclear receptor signaling, and mitochondrial toxicity). Significant differences observed in toxicity predictions across the platforms highlight the critical necessity of employing multi-tool predictive strategies to obtain a reliable and comprehensive outlook.

Biology doi: 10.3390/biology15212023

Authors: Qundong Liu Xuhong Song Tao Dou Gang Ding Longyun Li

Lonicera macranthoides is a traditional Chinese medicinal herb valued for its chlorogenic acid (CGA) and triterpenoid saponins. To elucidate the genetic basis of these medicinal properties, we generated a haplotype-resolved chromosome-scale genome assembly combining PacBio long-read sequencing and High-throughput Chromosome Conformation Capture (Hi-C) data. The assembly comprises two haplomes, LmacA (857.17 Mb, contig N50 = 31.19 Mb) and LmacB (824.65 Mb, contig N50 = 27.17 Mb), representing the most contiguous genomic resource for the genus to date. Comparative genomic analyses identified species-specific gene families enriched in triterpenoid biosynthesis, phenylpropanoid metabolism, and stress-response pathways. Integrated GWAS, transcriptomic, and metabolomic analyses identified key genes regulating CGA and triterpenoid saponin biosynthesis, including a UGT cluster, an HCT cluster, and MYB transcription factors. We further found evidence that jasmonic acid and isopentenyl adenine dynamically balance floral organ development and secondary metabolite accumulation via MYB/bHLH transcription factors and MAPK signaling. This study establishes the first biosynthetic pathways for CGA and saponins in L. macranthoides, reveals regulatory mechanisms driven by haplotype structural variations (notably a Chr7 inversion), and provides genomic resources for molecular breeding and bioactive compound exploitation.

Biology doi: 10.3390/biology15212022

Authors: Zhaowei Zhong Yizhen Lu Dingyuan Luo Zebin Chen Shengkai Shi Yangjie Xie Hongwei Liu Jincan Chen Yonghua Jiang

The Japanese eel (Anguilla japonica) is an economically important aquaculture species, and its reproductive development and artificial propagation have received considerable attention. However, the absence of a stable in vitro female germ cell culture system has hindered investigations into oogenesis, reproductive regulation, and germplasm conservation. In this study, cells isolated from immature Japanese eel ovaries were enriched through differential adhesion, Percoll density-gradient centrifugation, and single-cell cloning, followed by optimization of culture conditions. A stable oogonial stem cell-like cell line of A. japonica, designated AjOSCL, was established and characterized via morphological observation, proliferation assays, colony-forming assays, karyotyping, immunofluorescence staining, alkaline phosphatase detection, and transcriptomic sequencing. AjOSCL maintained stable growth and self-renewal capacity during continuous culture for over 35 passages in vitro, with a cumulative culture duration exceeding 12 months, and retained a predominant chromosome number of 2n = 38 (consistent with the chromosome number of A. japonica), suggesting chromosomal stability during long-term culture. AjOSCL exhibited strong alkaline phosphatase activity and expressed germline-related markers (e.g., Vasa and Nanos2), together with pluripotency-related genes or proteins such as Nanog and Oct4. Transcriptomic analysis further revealed that AjOSCL displayed a molecular profile compatible with a germline stem cell-like phenotype, with enrichment of pathways related to germ cell maintenance and oocyte development, including ECM–receptor interaction, TGF-β signaling, Wnt signaling, and oocyte meiosis. Collectively, these results indicate that AjOSCL may serve as a renewable in vitro model for studying oogonial maintenance, offering a foundation for future investigations into female germ cell biology and germplasm conservation in A. japonica.

Biology doi: 10.3390/biology15212021

Authors: Chatsuree Suksamai Thansita Bhunyakarnjanarat Kanthaporn Dityen Suwasin Udomkarnjananun Dhammika Leshan Wannigama Wiwat Chancharoenthana Asada Leelahavanichkul Patcharee Ritprajak

Current preclinical studies evaluating cGAS inhibition as a novel anti-inflammatory strategy rely predominantly on young murine models, leaving the impact of aging largely unexplored. At baseline, aged (56-week-old) female mice, in both WT and cGAS-/- mice, demonstrated more pronounced oxidative stress (malondialdehyde) and diminished antioxidant capacity (glutathione) relative to young (8-week-old) controls. Upon the induction of liver ischemia–reperfusion injury (IRI), the most severe hepatic damage was provoked exclusively in aged cGAS-/- mice. This exacerbated injury was confirmed by elevated liver enzymes, higher histological scores, widespread apoptosis (activated caspase-3), enhanced macrophage accumulation (F4/80+ cells), and increased serum cell-free DNA as a tissue damage marker. Additionally, aged cGAS-/- mice exhibited a significant surge in serum IL-6 and gut barrier dysfunction (FITC-dextran assay) at 6 h post-injury. Mechanistically, while cGAS-/- macrophages showed blunted inflammatory signaling upon lipopolysaccharide (LPS) stimulation, co-incubation with D-galactose, which induces intracellular peroxide accumulation, restored their pro-inflammatory responses to WT levels. Concurrently, starvation protocols revealed that cGAS-/- hepatocytes were more vulnerable to mitochondrial oxidative stress (MitoSOX) than WT cells. Ultimately, aging critically modifies the cGAS-deficient phenotype, warranting the careful re-evaluation of cGAS therapeutic models in aged populations.

Biology doi: 10.3390/biology15212020

Authors: Jing Hua Xiaowei Xu Jie Gu Yufeng Xie Anfei He Qi Yu Lei Wang Chang Liu

Engineered nano-metal oxides discharged into river–lake systems interact with water chemistry before reaching biota, yet the fraction of their acute toxicity that derives from the particles themselves, rather than from dissolved ions, remains unresolved in authentic natural waters. This study determined the acute toxic effects of CuO, ZnO, and SiO2 nanoparticles at a concentration of 100 mg/L dispersed in water samples from Taihu Lake and Suzhou River (two representative and polluted water bodies in eastern China) on Vibrio fischeri (V. fischeri), and partitioned each measured inhibition E(total) into an ion-attributed component E(ion) and a particle-attributed component E(particle) using paired assays of the whole suspension and of its 0.02 µm filtrate. Aggregation, surface charge, and dissolution kinetics were followed for 72 h (15 d for SiO2). CuO nanoparticles aggregated moderately in both natural waters and released at most 0.087 mg/L Cu2+, so that the persistent suspension inhibition of 0.09–0.64% coexisted with a mildly stimulatory ion fraction (−0.19% to 0.01%), leaving the particle component to account for 81.1–94.0% of the measured effect. ZnO nanoparticles released up to 7.15 mg/L Zn2+ in Suzhou River water, where inhibition rose in step with the dissolved fraction and the ion component contributed 56.8–95.6% of the effect; in Taihu Lake water, both the suspension and the ion fraction remained stimulatory. SiO2 nanoparticles and the released reactive silicate induced no acute inhibition over 15 d (mean −0.024% and −0.013% in the two waters, both significantly below zero) despite the net dissolution solubility reaching up to 32.4% of the nominal dose. The toxicity source therefore differs by material within the same water matrix, indicating that risk-management measures for CuO should target particle transport and settling, whereas measures for ZnO should suppress dissolution.

Biology doi: 10.3390/biology15212019

Authors: Guosheng Hu Yun Zhou Mengxi Wang Rong Huang Jikai Liu

Methicillin-resistant Staphylococcus aureus (MRSA) exhibits widespread multidrug resistance and frequently causes refractory wound infections, particularly in diabetic patients, creating an urgent need for new therapeutic options. Grifolin, a naturally occurring phenolic compound with antibacterial, anti-inflammatory, and antioxidant activities, represents a promising candidate for the comprehensive treatment of infected diabetic wounds. Herein, we systematically investigated the antibacterial activity and mechanism of grifolin against MRSA, as well as its therapeutic efficacy in a murine model of MRSA-infected diabetic wounds. In vitro, grifolin exhibited potent antibacterial activity against MRSA (MIC = 3 μg/mL, MBC = 4 μg/mL), effectively eliminated mature biofilms, and potentiated conventional antibiotics. Integrated transcriptomic and proteomic analyses, corroborated by qRT-PCR, revealed coordinated changes in membrane integrity, translation and metabolism, and quorum sensing and virulence. In vivo, grifolin significantly reduced the wound bacterial burden, suppressed the expression of pro-inflammatory cytokines IL-6 and TNF-α, promoted angiogenesis and tissue remodeling, and accelerated diabetic wound healing with favorable preliminary tolerability. This study highlights grifolin as a promising lead compound for combating MRSA infections and treating associated diabetic wound complications.

Biology doi: 10.3390/biology15212018

Authors: Ryan G. Gaudet Hamna Shahnawaz Dominic A. Ritacco

Interferons (IFNs) are synonymous with mobilizing cell-intrinsic defenses against microbial infection through the induction of interferon-stimulated genes (ISGs). Omics-based profiling has revealed that ISGs also dominate the transcriptional signature of a wide range of human disease conditions, including cancer, autoimmune and autoinflammatory disorders, and even normal aging. The ubiquity of the IFN signature means it is often interpreted as a biomarker for upstream inflammation, with little consideration given to how persistent ISG induction might influence downstream cellular and tissue physiology. However, the identification of endogenous targets for a growing number of ISG-encoded effectors has broadened our appreciation for the function of these genes—both in terms of how self-defense is achieved but also for the potential implications emanating from their prolonged induction. The same host-directed mechanisms that provide broad antimicrobial protection can, depending on context, either preserve tissue homeostasis or contribute to chronic inflammation and tissue dysfunction. In this perspective, we revisit the longstanding question of IFN causality in disease and argue that ISGs should be viewed as active participants in pathogenesis rather than passive markers of inflammatory activity. By examining disease-specific ISG expression patterns and synthesizing emerging evidence for the endogenous functions of ISGs, many of which converge on mitochondrial regulation, we propose a framework in which the composition of an IFN signature associated with a diseased tissue plays a major role in dictating whether inflammation is resolved or perpetuated.

Biology doi: 10.3390/biology15212017

Authors: Shuo Chen Yang He

The temporomandibular joint (TMJ) is one of the most complex and most frequently used synovial joints. The condylar surface is covered by a distinctive type of fibrocartilage that possesses a remarkable capacity for adaptive remodeling. In recent years, with rapid advances of single-cell transcriptomics and in vivo lineage-tracing technologies, fibrocartilage stem cells (FCSCs) residing in the superficial layer of the mandibular condyle have been demonstrated to play a decisive role in TMJ development, homeostasis, and the pathological progression of temporomandibular joint osteoarthritis (TMJOA). However, FCSCs do not constitute a single homogeneous population but rather exhibit substantial lineage heterogeneity. Under the spatiotemporal orchestration of distinct mechanical microenvironments and molecular signaling networks, different subpopulations of stem/progenitor cells adopt divergent fate trajectories toward chondrogenic or osteogenic differentiation. This review focuses on the cellular heterogeneity of FCSCs and the regulatory mechanisms governing their fate determination, summarizing recent advances in the field and discussing the translational potential of these findings for TMJ regenerative medicine and targeted therapeutic strategies.

Biology doi: 10.3390/biology15212016

Authors: Jiabing Yu Chao Li Mei Xiong Tiefeng Yu Weiyan Cheng Feng Hao Kai Gao

The effect of nitrogen (N) (0, 75, 150, 225 and 300 kg N ha−1, N0-N4) on the yield, photosynthetic properties and nitrogen-use efficiency of forage oat (Avena sativa L.) was studied in the Horqin Sandy Land in northern China. Mantel tests and chord diagrams were used to investigate the correlation of traits. Plant height, stem–leaf ratio, hay production, chlorophyll content and heading stage photosynthesis indices showed a unimodal response with highest values at N3 (225 kg N ha−1; p < 0.05). The dry matter yield at filling stage, net photosynthetic rate (Pn) at heading stage and total chlorophyll content (Total Chl) of N3 were 74.52%, 101.65%, and 62.18% higher than that of N0. The nitrogen contribution ratio (NFCR) of N3 reached 42.70%, which was 60.59% greater than that of N1. Nitrogen uptake efficiency (NUpE) was achieved at N3 that was 21.50% relative to N1.The N3 treatment showed the best comprehensive performance across agronomic, photosynthetic and nitrogen-use efficiency traits. In contrast, N3 achieved a favorable balance between yield and nitrogen use efficiency and can be regarded as a suitable nitrogen application rate for high-yield forage oat production in this region.

Biology doi: 10.3390/biology15212015

Authors: Yuna Zhang Tianjian Song Ye Chen Yuxin Huang Zexu Luo Yuxi Zhuang Jiang Chang

Illegal wildlife trade (IWT) is a major driver of biodiversity loss, and birds are among the most heavily trafficked taxa. Although China has one of the world’s largest wildlife markets, the spatial, temporal, and taxonomic structure of its domestic illegal bird trade remains poorly characterized. We retrieved and analyzed 1427 first-instance criminal verdicts issued between 2014 and 2021 from China Judgments Online, using descriptive and trade-network analyses to identify the key traded species, temporal patterns and major trading regions. The trade involved 19 orders, 48 families and 266 species, of which 37 were listed as threatened (CR, EN and VU) on the Red List of China’s Vertebrates and 24 were Class I nationally protected. Psittaciformes appeared in the greatest number of verdicts, and the recorded purposes indicate that they were traded mainly to meet experiential demand. Annual verdict counts rose steadily from 2014 to 2019 and then declined sharply, reaching 40 in 2021. Illegal bird trade was documented in 30 provincial-level regions and was concentrated in southwestern and southeastern China. Weighted by the number of verdicts, Guangdong was the leading province and Guangzhou the leading Chinese prefecture. Of the 1001 verdicts with a geolocatable origin and destination, 90.81% involved transactions over distances of less than 500 km. These findings improve understanding of China’s illegal bird trade and can inform law enforcement and public-awareness campaigns.

Biology doi: 10.3390/biology15212012

Authors: Pibiao Shi Runzhi Jiang Deling Wang Zhenmeng Ji Bin Li Minfeng Gu

The homeodomain-leucine zipper (HD-Zip) proteins are important transcription factors in the regulation of plant growth and development and abiotic stress responses. However, our understanding of the HD-Zip family is still limited in quinoa. In this study, 41 CqHD-Zip genes were identified in the quinoa genome and then phylogenetically classified into four subfamilies. Their characterizations, chromosomal locations, gene structures, conserved motifs, and phylogenetic relationships were comprehensively analyzed through genome-wide bioinformatics methods. Our RNA-Seq data showed that a subset of the 41 HD-Zip genes exhibited expression changes under salt stress, among which CqHDZ5, CqHDZ12, CqHDZ13, CqHDZ18, CqHDZ19, and CqHDZ21 responded positively to salt stress, and the results were confirmed by qRT-PCR analysis. Tissue expression revealed that CqHDZ5, CqHDZ13, CqHDZ18, and CqHDZ21 were significantly expressed in developing seeds, and CqHDZ12 and CqHDZ19 were highly expressed in roots. Additionally, the transcript levels of these six genes were significantly up-regulated in response to osmotic and low-temperature stress, indicating that they may participate in stress resistance against salt, osmosis, and low temperature. It is shown that HD-Zip is a multifunctional gene family, and the results will provide valuable information for further analysis of the potential role of HD-Zip genes in abiotic stress responses and genetic improvement of quinoa.

Biology doi: 10.3390/biology15212014

Authors: Diego Andrade Garcia Maria Eduarda Globa Masset Kauan Pinheiro da Silva Santos Maria Alice Guerreiro Gabriel Fidalgo Marcos Vinicius Colaço Liebert Parreiras Nogueira Adriana Bonomo Fabio Canto Ana Carolina Monteiro

Bone metastases are traditionally regarded as late manifestations of breast cancer progression. However, increasing evidence suggests that systemic skeletal alterations may emerge before overt tumor dissemination, raising the possibility that osteoimmune remodeling may contribute to the establishment of a permissive skeletal microenvironment. Pre-clinical studies from our group demonstrated that metastatic 4T1 breast cancer is associated with the expansion of RANKL-expressing adaptive immune populations and early skeletal alterations in BALB/c mice. Whether similar osteoimmune alterations occur in a distinct syngeneic immunocompetent breast cancer model remained unknown. Here, we generated an EO771-derived metastatic breast cancer population (EO771B) through serial multi-site in vivo selection under orthotopic, hematogenous and bone-associated pressures in immunocompetent C57BL/6 hosts. Compared with its parental counterpart, EO771B exhibited spontaneous dissemination to bone marrow, which was not detected for parental EO771 cells under the experimental conditions evaluated, while dissemination to tumor-draining lymph nodes (dLNs) and primary tumor growth did not differ significantly between the two populations. Microcomputed tomography revealed significant trabecular bone deterioration as early as day 11 following orthotopic inoculation, before bone-marrow dissemination became detectable by the clonogenic assay used in this study, with additional alterations in trabecular microarchitecture observed at later stages of tumor progression. These skeletal changes were accompanied by increased frequencies and/or numbers of RANKL-expressing CD4+ T cells and CD19+ B lymphocytes in the bone marrow, despite the absence of detectable tumor-derived colonies at the early time point. RANKL-expressing CD4+ T-cell populations also increased in tumor-dLNs and the primary tumor microenvironment during tumor progression. Adoptive transfer of tumor-educated leukocytes into lymphocyte-deficient Rag1−/− recipients reproduced trabecular bone deterioration, demonstrating that tumor-educated leukocytes can functionally promote skeletal remodeling, although the specific contribution of lymphocyte-derived RANKL was not directly tested. Collectively, these findings demonstrate that EO771B tumor progression is associated with osteoimmune alterations characterized by increased RANKL-expressing lymphocyte populations and trabecular bone deterioration before bone-marrow dissemination becomes detectable by clonogenic assay. Together with our previous findings in a distinct syngeneic breast cancer model, these results support the occurrence of tumor-associated osteoimmune remodeling across different tumor–host systems and establish the EO771B–C57BL/6 model as a platform for further mechanistic investigation.

Biology doi: 10.3390/biology15212013

Authors: Yu-Hao Zhou Xiao-Peng Ji Zhu-Hong You Lei Wang Chang-Qing Yu

Circular RNAs (circRNAs) have a covalently closed structure and high stability in complex biological samples, making them promising disease biomarkers. However, the sparsity and imbalance of known circRNA–disease associations (CDAs) necessitate computational approaches for CDA prediction. Competition among multiple circRNAs for shared miRNA pools gives rise to group-level ceRNA regulation, motivating the modeling of higher-order relationships among nodes. Three challenges remain in existing methods: insufficient modeling of higher-order cooperative relationships in similarity networks, incomplete integration of complementary predictive signals, and a lack of sample-level uncertainty awareness in fusion decisions. To address these challenges, we propose MHUCDA, a CDA prediction framework that integrates multi-view hypergraph contrastive learning with uncertainty-aware dual-branch fusion. Hypergraph convolution is used instead of conventional pairwise graph convolution to capture higher-order cooperative regulatory relationships in similarity networks. Cross-view contrastive learning enforces semantic consistency across multiple similarity views. A dual-branch architecture independently models candidate associations from two complementary perspectives, semantic propagation and local structural features, while a gating network dynamically assigns per-sample branch weights. Dual-branch prediction divergence is used as an empirical indicator of relative prediction risk, and predictions for high-divergence samples are adjusted toward a neutral reference value. On the CircR2Disease benchmark under five-fold cross-validation, MHUCDA achieves an AUC of 0.9687 and an AUPR of 0.9623, with consistent performance in separate within-dataset evaluations on three additional datasets. Uncertainty stratification analysis reveals an AUC gap of 0.1263 between the highest- and lowest-confidence groups, supporting the use of branch divergence for empirical risk stratification. Case analysis links selected high-confidence predictions to experimentally verified ceRNA regulatory axes, supporting further investigation of model scores for candidate prioritization.

Biology doi: 10.3390/biology15212011

Authors: Rasha K. Al-Akeel Ibrahim M. Ibrahim Abeer M. Alkhaibari Amr Mohamed Wei Zhang Makio Takeda Ahmed A. Ezat

The γ-aminobutyric acid (GABA)-gated chloride channel Resistance to Dieldrin (RDL) receptor is a major molecular target of insecticides, yet the structural basis by which resistance-associated mutations differentially influence chemically distinct ligands remains incompletely understood. Here, we investigated the effects of the classical A296S substitution on the interactions of the Anopheles gambiae RDL receptor with the phenylpyrazole fipronil and the isoxazoline fluralaner using homology modeling, molecular docking, 200 ns molecular dynamics simulations (apo receptors and three independent replicas of each ligand-bound complex), and MM/PBSA free-energy calculations that include an interaction-entropy (IE) term. Apo-state molecular dynamics simulations showed that A296S preserved the overall structural stability of the receptor while locally modifying the environment of the pore-lining M2 transmembrane helix. Although docking scored fluralaner more favorably than fipronil in both receptor variants, the replicated molecular dynamics simulations revealed ligand- and genotype-dependent behavior. In the wild-type receptor, fluralaner remained stably bound and had a favorable MM/PBSA free-energy estimate (−18.3 ± 4.2 kcal/mol), whereas the ligand RMSD of fipronil increased progressively and its estimate was close to zero (+1.2 ± 9.5 kcal/mol). In the A296S model, the fipronil estimate was similar (+1.6 ± 4.3 kcal/mol), but the fluralaner estimate became unfavorable (+10.0 ± 1.8 kcal/mol), and Ser296 itself contributed slightly unfavorably to both ligands. Together, these findings indicate that A296S does not act as a universal determinant of ligand recognition but is associated with ligand-specific changes in the modeled interaction landscape, with the larger predicted effect on fluralaner. These predictions derive from a homology model, were not tested by electrophysiology or binding assays, and do not measure functional resistance. They may nonetheless help inform the interpretation of cross-resistance patterns and structure-guided efforts targeting GABA receptor-based insecticides.

Biology doi: 10.3390/biology15212010

Authors: Antonio Leo Roberta Roberti Pio Francesco Vono Valentina Rajone Valeria Di Stefano Maria Pisano Maria Cristina Caroleo Emilio Russo

In genetic developmental and epileptic encephalopathies, disability results from both the molecular defect and epileptic activity. Antiseizure medications modulate pathways involved in seizure initiation and propagation but generally do not correct the disease-causing molecular alterations that contribute to epileptic susceptibility and neurodevelopmental dysfunction. Antisense oligonucleotides (ASOs) modify the splicing of ribonucleic acid (RNA) transcripts, promote RNA degradation, or reactivate silenced alleles. This narrative review examines variant-guided mechanisms, translational evidence, clinical outcomes, and barriers to implementation. ASO programs targeting SCN1A, SCN2A, SCN8A, KCNT1, GNAO1, and UBE3A range from individualized treatments to phase 3 trials. Published uncontrolled zorevunersen studies report preliminary clinical signals in Dravet syndrome, whereas sponsor-reported results from the randomized, sham-controlled EMBRAVE Part A study suggest seizure reduction with elsunersen in SCN2A-related disease. Conversely, sponsor-reported phase 3 Aspire topline results indicate that apazunersen did not meet its primary cognitive or key secondary multidomain endpoint in Angelman syndrome. These findings are not equivalent in evidentiary strength. Intrathecal delivery, heterogeneous central nervous system (CNS) exposure, target-dosage sensitivity, and compound-specific toxicity influence the therapeutic window. Disease modification requires controlled longitudinal demonstration of meaningful outcomes beyond target engagement or seizure reduction, considering development, adaptive functioning, survival, and treatment burden.

Biology doi: 10.3390/biology15212009

Authors: Sevda Hastaoğlu Örgen

Mitochondrial gene rearrangements provide useful characters for investigating genome evolution in Hymenoptera, but mitogenomic sampling within Cephidae remains limited. Here, the mitochondrial genome of Cephus nigrinus Thomson, 1871 was reconstructed from publicly available Illumina whole-genome sequencing data (SRA: SRR23907852) and compared with available cephid mitochondrial genomes. The assembled sequence is 16,782 bp long, has an A + T content of 81.38%, and contains 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. An A + T-rich region of 1295 bp was identified in the deposited annotation. Comparative gene-order analysis revealed a conserved rearrangement of the ancestral mitochondrial IQM cluster, characterized by the positioning of trnQ before trnI near nad2 and the relocation of trnM immediately downstream of rrnS. Phylogenetic analyses based on a concatenated dataset of 13 protein-coding genes, 22 tRNAs, and two rRNAs recovered C. nigrinus and C. pygmeus as sister taxa with strong support. However, the placement of this pair relative to C. cinctus received lower support in the maximum-likelihood analysis. The results expand available mitogenomic information for Cephinae and support conservation of the rearranged mitochondrial gene organization among the examined Cephus species. Further validation is needed to establish the complete structure of the repetitive control region.

Biology doi: 10.3390/biology15212008

Authors: Ruixiang Shi Xin Chen Yuheng Liang Yixin Huang Yixin Xie Huiyan Xie Bridgitta Bianca Goh Xiangmin Lin Lingli Lian

Aeromonas hydrophila poses a growing threat in aquaculture due to high mortality and increasing antibiotic resistance, highlighting an urgent need for novel antimicrobial agents. Artemisinin (ART), a natural bioactive compound, exhibits antibacterial activity against A. hydrophila, yet its underlying mechanism remains poorly understood. In this study, quantitative proteomics was employed to elucidate the antibacterial mechanism of ART against A. hydrophila LP-2 and to evaluate its combined inhibitory effect with gallic acid (GA). The results showed that ART inhibited A. hydrophila in a concentration-dependent manner. At concentrations of 400 μg/mL and above, ART reduced biofilm mass independently of planktonic growth and also induced cell membrane damage and intracellular reactive ROS accumulation. Proteomic analysis indicated that ART significantly perturbed multiple metabolic pathways, including amino acid metabolism, redox metabolism, ABC transporters, and quorum sensing. Furthermore, the combination of ART and GA exhibited a pronounced antibacterial effect, which was closely associated with massive accumulation of intracellular ROS. Mechanistically, oxidative stress-related genes (orf00650, orf00652) were significantly upregulated, whereas the efflux transporter gene (orf00659) was markedly downregulated, suggesting that the combined effect is jointly driven by enhanced oxidative damage and impaired drug efflux. Hemocompatibility test showed that ART caused no detectable hemolysis. This study reveals the multifaceted antibacterial mechanism of artemisinin against A. hydrophila LP-2 and demonstrates that gallic acid significantly enhances its antibacterial activity in this strain, providing a theoretical basis for the further development of artemisinin as a potential antibacterial agent against A. hydrophila.

Biology doi: 10.3390/biology15212007

Authors: Iain C. Wilkie

Propylene phenoxetol is the trade name of the chemical compound that has the systematic name 1-phenoxypropan-2-ol. Used as an anesthetic agent for aquatic animals—mainly invertebrates—for over 70 years, it has been employed most extensively for all five classes of the phylum Echinodermata both to narcotize whole animals—reversibly or terminally—and as a pharmacological agent for blocking neural conduction in isolated tissue preparations. Despite this long history, there is evidence that since the 1990s, there has been a sustained decline in propylene phenoxetol usage, which may be partly the result of an accumulation of misinformation about its chemical identity, physical properties, and physiological actions. This review surveys the use of propylene phenoxetol as an anesthetic for echinoderms and other animals, outlines the history of misinformation concerning its nature and qualities, and corrects that misinformation. Deficiencies in current knowledge are outlined, with the ultimate aim of encouraging further research to explore its potential as an option for the anesthetization of echinoderm subjects.

Biology doi: 10.3390/biology15212006

Authors: Qiang Li Jianmei He

Auditory cognitive neuroscience has moved from controlled sounds toward increasingly complex stimuli, but the choice of what sounds to test remains largely determined before neural responses are observed. A complementary experimental logic is emerging, in which neural responses are used not only to evaluate predefined stimuli but also to guide the generation and selection of subsequent stimuli. Here, we articulate a perspective on brain-guided generative auditory neuroscience, in which human neural responses are related to manipulable auditory representations to establish brain–sound relationships that guide which stimuli are generated or selected for subsequent testing. This framework enables the investigation of auditory structures that may not be specified in advance, including response-relevant stimulus organization, representational boundaries, contextual dependencies, and individual- or state-dependent brain–sound variation. We further discuss technical routes for establishing brain–sound relationships and using them to guide stimulus generation, as well as how iterative cycles of generation and human testing can progressively refine these relationships through recursive brain–sound inference. The value of this approach depends not on producing unusual sounds, but on whether brain-derived guidance yields reproducible insights beyond predefined or non-neural alternatives.

Biology doi: 10.3390/biology15212004

Authors: Pengzhe Sun Yonge Feng Zuwei Yan Qiang Zhang

Cervical cancer (CC) is characterized by widespread transcriptomic dysregulation, yet sequence matching patterns between mRNAs and their corresponding introns remain insufficiently characterized in differentially expressed genes (DEGs). This study aimed to describe computationally predicted intron–mRNA matching features in the reference sequences of CC DEGs. DEGs were identified using Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets, and the corresponding mRNA and intron sequences were retrieved from the Ensembl human reference genome. Reverse complementation combined with Smith–Waterman local alignment was used to analyze the positional distributions of predicted matching fragments across full-length mRNAs and within translation initiation and termination regions. Descriptive analyses were further stratified by the GC content of the matching fragments. On normalized full-length mRNA coordinates, high-GC fragments exhibited higher matching frequencies in certain segments near the 5′ end, whereas matching frequencies of low-GC fragments increased toward the 3′ end. Within the translation initiation region, predicted matching frequencies were generally higher upstream than downstream of the AUG codon, and the low-GC group exhibited a local peak near the initiation codon. Within the translation termination region, the low-GC group exhibited a pronounced peak downstream of the stop codon, whereas the high-GC group showed no similarly pronounced downstream peak and displayed greater positional fluctuations in matching frequency. Overall, the predicted matching distributions differed across the analyzed regions and GC groups. This study provides a sequence-level description of intron–mRNA matching patterns within this reference sequence collection of CC DEGs; their biological significance requires further validation.

Biology doi: 10.3390/biology15212005

Authors: Zesen Lai Jifen Yang Yuhong Rong Shen Xiong Yanyin Xu Zhaohao Zhang Jiang Xie Ziyu Li Huifang Yuan Xiangshuai Yan Hongjun Mu

Plant basic helix-loop-helix (bHLH) transcription factors constitute one of the largest and most functionally diverse transcription factor families in plants. Through a conserved bHLH domain, they bind E-box cis-elements or dimerize with partner proteins, coupling developmental and metabolic programs to environmental cues. However, a systematic synthesis of their multilayered stress responses remains lacking. Here, we review the structural features, genome-wide distribution, and evolutionary diversification of plant bHLH transcription factors, with emphasis on their regulatory functions under low-temperature, drought, salinity, and iron-deficiency conditions. We further integrate their roles in abscisic acid, jasmonic acid, and light signaling, as well as in anthocyanin and terpenoid biosynthesis, biotic stress, and immune responses. We also discuss emerging evidence linking bHLH factors to reproductive development, particularly anther and pollen formation under heat stress. Mechanistically, we summarize the multilayered regulatory network from four perspectives: transcriptional cascades, post-translational modifications, cooperative regulation by multiple transcription factors, and growth-defense trade-offs. Finally, we highlight current gaps, including limited functional validation in non-model/specialty economic crop species, underexplored combined-stress mechanisms, and lagging breeding translation, and propose future research directions. This review provides an integrated framework for plant stress biology and outlines evidence-based perspectives for future stress-tolerant crop improvement.

Biology doi: 10.3390/biology15212003

Authors: Xuebin Zhang Zhixuan Han Wenjie Hu Jiaonan Li Jingyi Yu Xinyu Hu Xinjun Liao

Plant pathogenic fungi pose a serious threat to agricultural and forestry production. Long- term reliance on chemical fungicides has led to rising pathogen resistance and ecological risks, making the discovery and development of novel, safe, and highly effective antifungal compounds of great practical significance. Three N-substituted-3-methylbut-2-enamide derivatives (compounds I–III) were synthesized and structurally characterized by single-crystal X-ray diffraction, infrared spectroscopy, and elemental analysis. The minimum inhibitory concentration (MIC) values of the three compounds were determined against six common plant pathogenic fungi, and the antifungal activity was found to be governed by the N-substituent structure. Compound III (3-methyl-N-(4-phenoxybenzyl) but-2-enamide) was the most active, with an MIC of 25–100 mg/mL, representing a 3-fold increase over the rigid fused-ring analogs I and II, which suggests that increased molecular flexibility favors antifungal activity. Preliminary mechanistic investigation of compound III revealed that it induces intracellular reactive oxygen species (ROS) accumulation, compensatory upregulation of reduced glutathione, and elevated malondialdehyde levels in fungi, thereby inhibiting fungal growth through oxidative stress-mediated damage. Zebrafish embryo toxicity assays showed that compound III exhibited concentration- and time-dependent developmental toxicity to zebrafish embryos. The median lethal concentration (LC50) was 1.032 mg/L under 72 hpf exposure conditions; sublethal exposure concentrations reduced embryo survival rate, caused developmental delay, and induced neurobehavioral abnormalities. This study revealed how structural features influence the antifungal activity of this class of enamide derivatives, preliminarily elucidated the oxidative stress-mediated antifungal effect, and completed the aquatic safety evaluation, providing an experimental basis for the further structural optimization of this lead scaffold.

Biology doi: 10.3390/biology15212002

Authors: Hailong Yan Yu Wang Lin Li Yufan He Jinxiang Han Kefei Zhu Yingchun Gong Nicola Fohrer Jianguang Qin Yuying Li

Freshwater ecosystems are highly vulnerable to biological invasions. The globally distributed invasive hydrozoan Craspedacusta sowerbii imposes strong top-down pressure on plankton communities owing to its distinct feeding selectivity. While prior studies have confirmed its preferential predation on zooplankton over phytoplankton, the integrated mechanisms underlying this prey discrimination remain poorly understood. Here, we integrated behavioral observations and comparative transcriptomics to investigate the prey preference strategy of adult C. sowerbii medusae. Behavioral assays demonstrated active predation exclusively on zooplankton, with no targeted hunting toward phytoplankton. Microscopic observations revealed efficient degradation of ingested zooplankton within 6 h, whereas phytoplankton cells were excreted with no apparent digestion. Transcriptomic analyses indicated that zooplankton feeding induces profound transcriptional reprogramming in C. sowerbii. Genes related to catalytic and hydrolase activities were significantly enriched, accompanied by substantial up-regulation of ribosome biogenesis and mitochondrial oxidative phosphorylation. In contrast, phytoplankton exposure triggered negligible metabolic perturbation. The coordinated activation of hydrolase, protein synthesis, energy metabolism, cytoskeletal movement, and mucus production forms the potential physiological basis for the feeding preference of C. sowerbii. Field observations further suggest that algicidal bacteria in the gastric cavity of medusae may assist auxiliary phytoplankton utilization. This study elucidates the regulatory mechanisms governing the trophic selectivity of C. sowerbii, fills key knowledge gaps in its feeding ecology, and offers new insights into the environmental adaptability and survival strategies of this species.

Biology doi: 10.3390/biology15212000

Authors: Xiaolong Wang Yue Wu Hua Chai Shasha Li Wei Li Zhao Yang

Medicago sativa is a high-yielding and high-protein forage crop with the largest cultivation area worldwide. However, winter freezing injury severely limits its growth in high-latitude regions of Northeast China, particularly affecting the root system, which acts as a vital functional tissue for cold resistance. To date, the physiological characteristics and metabolic responses of M. sativa roots to low temperatures remain unclear. In this study, roots of the cold-tolerant cultivar ‘Longmu801′ and the cold-sensitive cultivar ‘Sardi’ were compared during the overwintering period. Root physiological indicators were measured, and metabolomic profiling was performed. The results showed that the contents of glutathione (GSH), sucrose (SUC), soluble sugar (SS), and proline (Pro) in Longmu801 roots were markedly higher than those in Sardi, while peroxidase and superoxide dismutase activities and the contents of H2O2 and malondialdehyde (MDA) were significantly lower (p < 0.05). Metabolomic analysis identified 304 differentially accumulated metabolites (DAMs). Correlation analysis between DAMs and physiological indicators showed that DAMs in the MEblue module were positively and significantly correlated with glutathione, proline, and soluble sugar (p < 0.05). These DAMs were mainly associated with pathways including arginine and proline metabolism, glutathione metabolism, the tricarboxylic acid cycle, and pyruvate metabolism. Four candidate DAMs related to cold tolerance were further identified, namely spermidine, N-acetyl-L-glutamate 5-semialdehyde, citric acid, and malic acid. These findings provide a theoretical basis and candidate metabolic markers for breeding cold-tolerance M. sativa cultivars and improving overwintering production in high-latitude cold regions.

Biology doi: 10.3390/biology15212001

Authors: Yu-Hao Zhou Chang-Qing Yu Si-Qi Yao Lei Wang Zhu-Hong You

Circular RNAs (circRNAs) participate in gene regulation and disease-associated processes. Computational prediction of circRNA–disease associations (CDAs) can help prioritize candidates for biological investigation. Here, we propose a multi-view heterogeneous dual-stream graph autoencoder (MHDA) for CDA prediction. MHDA combines multi-view graph attention encoding, heterogeneous relation enhancement, dual-stream association reconstruction, and contrastive regularization. The encoder learns representations from complementary similarity views and adaptively fuses them. A heterogeneous attention module then integrates within-type and cross-type relationships. The decoder combines element-wise interactions with concatenated pair representations through gated fusion to score candidate associations. On the CircR2Disease dataset, MHDA achieves an AUC of 0.9633 and an AUPR of 0.9599 under five-fold cross-validation. Ablation analyses support the contributions of the main model components. Of the top 25 ranked candidate associations, 22 have supporting evidence in the published literature. These results suggest that MHDA is useful for prioritizing potential CDAs and provides promising candidates for subsequent experimental validation.

Biology doi: 10.3390/biology15211999

Authors: Veda B. Hacholli Marcin Gackowski Piotr Kośliński Abhishek Kumar Łukasz Szeleszczuk

This study retrospectively evaluates agreement between target-level molecular-modeling rankings from a previously published coumarin–pyrimidine library and an available cellular dataset for 14 experimentally evaluated compounds with documented structure assignments. Laboratory-reported MDA-MB-231 and MCF-10A IC50 values from multi-concentration MTT testing were compared with published AutoDock Vina scores using rank-based analyses. Compound 5e had the lowest laboratory-reported MDA-MB-231 IC50 (12.4 ± 0.2 µM; n = 2) and the largest descriptive selectivity index (7.75); this ratio is specific to the MDA-MB-231/MCF-10A comparison and is not interpreted as evidence of general tumor selectivity. Docking rankings showed weak correspondence with cellular potency, and no docking–phenotype association remained statistically significant after Benjamini–Hochberg adjustment. No basic 2D descriptor showed a compelling adjusted association. Complete 1H/13C NMR and validated HRMS documentation, quantitative purity measurements, and the complete full-series MTT raw export are not available; structure-dependent and potency claims are therefore interpreted cautiously. Overall, the analysis demonstrates limited cross-endpoint transferability between target-level docking rankings and whole-cell activity in the MDA-MB-231/MCF-10A dataset, without establishing a validated structure–activity relationship, generalized TNBC activity, apoptosis induction, a BCL-2 mechanism, or translational efficacy.

Biology doi: 10.3390/biology15211996

Authors: Mudassir Ahmad Bhat Neha Charak Harshdev Singh Sheikh Abdul Shakoor Renu Bhardwaj Ashok Kumar Deepak Pathania Fernanda Maria Policarpo Tonelli Khalid Rehman Hakeem

Grasses (Poaceae) are the foremost silicon (Si) accumulators among terrestrial plants. Plants take up Si as monosilicic acid, Si(OH)4, which polymerizes in cells and tissues such as the epidermis, xylem and phloem to form phytogenic (biogenic) silica, SiO2 · nH2O, deposited as phytoliths. This review, based on a documented literature search with explicit inclusion and exclusion criteria, evaluates evidence that phytoliths protect grasses against herbivores, fungal and bacterial pathogens and nematodes, and against drought, heat, salinity, metal toxicity, UV-B radiation and mechanical stress, and it examines combined stresses under climate change. We distinguish phytolith-specific evidence from studies that supplied soluble Si or Si nanoparticles, and we grade the evidence for each proposed mechanism. Physical mechanisms (abrasion, mechanical and apoplastic barriers, reduced non-stomatal water loss) are the best supported. Biochemical and hormonal mechanisms, including jasmonic acid, salicylic acid and ethylene signaling, remain hypotheses because Si(OH)4 is chemically inert and much of the evidence is correlative. Elevated CO2 can lower foliar Si concentration in some grasses, which may weaken protection, but effects on total Si accumulation and function are poorly known. Phytolith-occluded carbon is a potential but uncertain carbon sink. We identify research priorities and practical implications for crop, pasture and carbon management.

Biology doi: 10.3390/biology15211998

Authors: Yiyun Deng Xinyu Su Shiqi Wei Shuyue Yang Zuowei Pei

Background/Objectives: Elongation of very long chain fatty acids protein 6 (ELOVL6) is a key enzyme that catalyzes the conversion of palmitoyl-CoA (C16:0-CoA) to stearoyl-CoA (C18:0-CoA). Its product C18:0-CoA is further desaturated by stearoyl-CoA desaturase 1 (SCD1) to generate C18:1n-9-CoA. In this review, C18:0/C16:0 refers to the molar ratio of C18:0 to C16:0 within a specified lipid pool, such as acyl coenzyme A (acyl-CoA), total fatty acids, or phospholipids. It serves as a surrogate marker for ELOVL6 elongation flux under specific conditions. C18:1n-9/C18:0 refers to the oleic acid to stearic acid molar ratio. It serves as a surrogate marker for SCD1-related flux. C16:0/C18:1n-9 refers to the palmitic acid to oleic acid molar ratio. It is a composite readout influenced by both ELOVL6 and SCD1-related reactions. The “C16/C18 ratio” is used only as an umbrella term for C16/C18-related ratios. This review aims to explore how ELOVL6 modulates the balance of the C16/C18 ratio through molecular mechanisms. It also examines how this regulation contributes to glucose and lipid metabolism and to tissue-specific functions, and evaluates the potential of ELOVL6 as a therapeutic target for metabolic diseases. Methods: A structured literature search was conducted on recent advances regarding the enzymatic properties, transcriptional regulation, and animal model phenotypes of ELOVL6. A comprehensive synthesis was performed from molecular mechanisms to clinical translation. Results: In the liver, ELOVL6 mainly influences the direction of fatty acid storage and ceramide signaling. In adipose tissue, it influences insulin signal transduction by remodeling membrane phospholipid composition. In pancreatic β-cells, it affects insulin secretory function by contributing to the C16/C18 ratio. When the C16/C18 ratio becomes imbalanced, cells progress toward insulin resistance (IR), inflammation, and hepatic steatosis. Conclusions: Restoring the balance of the C16/C18 ratio is a potential therapeutic strategy for metabolic diseases. However, targeting ELOVL6 faces challenges such as structural biology bottlenecks and tissue-specific side effects. Future research should focus on the fine regulation of ELOVL6, combined with dietary interventions, to advance the translation of ELOVL6 from basic research to clinical intervention for metabolic diseases.

Biology doi: 10.3390/biology15211997

Authors: Emilia A. Bober Maya Natasha Thomas Małgorzata Woronkowicz Conor M. Ramsden

Diabetic retinopathy (DR) is a major cause of preventable blindness in working-age adults, yet the molecular mechanisms behind its vision-threatening complications remain not fully understood. Transcriptomics enables the study of these processes through active gene expression, providing a pathway to the discovery of new biomarkers and therapeutic targets. Vitreous humour is commonly affected in numerous retinal pathologies, including DR, and is accessible through pars plana vitrectomy, making it a good candidate for transcriptomics research. Following PubMed and Embase search, 18 articles on vitreous transcriptomics were included. They were subclassified into themes of non-coding RNA, RNA methylation, angiogenesis, inflammation and fibrosis. We concluded that vitreous transcriptomics has the potential to influence future DR diagnostics and therapeutics. However, current evidence is limited by underpowered studies and lack of standardised protocols.

Biology doi: 10.3390/biology15211995

Authors: Jing Wu Changdi Ke Yi Huang Hongwei Meng Lingyang Kong Min Wang Qifa Sun Caiming Shen

The Hengduan Mountains are a major hotspot for lake-sediment research, but regional vegetation responses to Holocene climate variability remain incompletely understood. Here, we analyzed pollen assemblages and concentrations from Dinggongniang Co (4633 m a.s.l.) to investigate regional vegetation-related changes over the past approximately 4.7 ka. Pollen percentage and concentration analyses were combined with ensemble empirical mode decomposition (EEMD) and Lomb–Scargle spectral analysis. Despite being located above the modern tree line, the lake sediments are dominated by arboreal pollen (89.5%), particularly Pinus, indicating substantial pollen input from lower-elevation forests. Total pollen concentrations were relatively low around 4.2 ka, increased markedly during the Roman Warm Period, and remained relatively elevated during the Medieval Climate Anomaly, suggesting changes in regional arboreal pollen input potentially associated with Asian summer monsoon-related hydroclimatic variability. Furthermore, time-series analyses identified a possible millennial-scale oscillation at approximately 1.3–1.4 ka, broadly consistent with variability documented in North Atlantic and Asian monsoon records. This finding highlights the value of high-altitude lake pollen records for tracing regional arboreal pollen input and suggests possible connections between Asian monsoon variability and broader Northern Hemisphere climate fluctuations. Although chronological uncertainties and multiple factors influencing pollen concentrations introduce some limitations, the observed patterns offer valuable insights into long-term vegetation-related environmental variability in the Hengduan Mountains.

Biology doi: 10.3390/biology15211994

Authors: Wenbin Fang Renxuan Huang Qing Fang Rongquan Zheng Shanjian Zheng

Acrossocheilus fasciatus is an economically important freshwater fish species in China, and infection with Citrobacter freundii poses a serious threat to the sustainable development of its aquaculture industry. In this study, histopathological examination, TUNEL staining, immune physiological assays, and whole-transcriptome sequencing were integrated to systematically characterize the expression profiles of lncRNAs, circRNAs, miRNAs, and mRNAs in the spleen of A. fasciatus following C. freundii infection. The results showed that infection caused marked tissue damage in the intestine, spleen, and kidney, significantly increased splenic cell apoptosis, and induced pronounced changes in immune physiological parameters. Whole-transcriptome analysis identified 88 differentially expressed lncRNAs, 193 differentially expressed circRNAs, 140 differentially expressed miRNAs, and 1935 differentially expressed mRNAs. KEGG enrichment analysis revealed that the differentially expressed mRNAs were mainly enriched in immune-related pathways, including neutrophil extracellular trap formation, complement and coagulation cascades, antigen processing and presentation, cytokine–cytokine receptor interaction, phagosome, chemokine signaling pathway, and IL-17 signaling pathway. Furthermore, a bioinformatically predicted lncRNA-miRNA-mRNA ceRNA network was constructed, comprising 10 mRNAs, 14 lncRNAs, and 22 miRNAs, which formed 44 putative regulatory interactions. In this network, miR-212-y may mediate the regulation of Il12rb2 and PIK3R1, whereas miR-8-y may be involved in the regulation of Ccr9 and PIK3R1. The qRT-PCR validation results were consistent with the RNA-seq expression trends. This study provides the first comprehensive characterization of non-coding RNA and mRNA expression profiles in the spleen of A. fasciatus after C. freundii infection and identifies potential ceRNA regulatory networks, providing a valuable reference for elucidating antibacterial immune mechanisms and screening candidate molecular markers for disease resistance research in A. fasciatus.

Biology doi: 10.3390/biology15211993

Authors: Francesco Cappello

This Special Issue, “Experimental Biology, Life Science and One Health: From Basic to Translational Research”, originated in the centenary of the Italian Society of Experimental Biology, founded in 1925 at Camillo Golgi’s Institute in Pavia [...]

Biology doi: 10.3390/biology15211992

Authors: Wenqi Liang Hang Zhang Zheming Ren Minghui Liu

Conjugated linoleic acid (CLA) exerts anti-inflammatory and antioxidant bioactivities, yet its optimal hepatic anti-inflammatory dosage under lipopolysaccharide (LPS) stimulation remains unclear. This study aimed to screen the effective dietary CLA dose against LPS-triggered liver inflammation in mice. Twenty-four male mice were divided into four groups (n = 6): normal diet (ND), ND+0.5% CLA, ND+1% CLA and ND+2% CLA. After 49 days of feeding, all mice received LPS injection and were sacrificed 24 h later. Serum and liver tissues were collected to detect pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), the oxidative stress marker malondialdehyde (MDA), antioxidant indices (superoxide dismutase, SOD and total antioxidant capacity, TAC), hepatic inflammatory gene mRNA and liver histopathology. The 1% CLA group exhibited lower serum and hepatic pro-inflammatory cytokines (TNF-α, IL-1β, IL-6) and the oxidative stress marker MDA, higher SOD and TAC (p < 0.01), and reduced hepatic inflammatory infiltration. All CLA treatments downregulated hepatic CXCL1 mRNA and upregulated peroxisome proliferator-activated receptor γ (PPARγ) mRNA (p < 0.05). In conclusion, 1% dietary CLA elicited optimal anti-inflammatory effects in this acute LPS-induced liver inflammation model, while 1% and 2% CLA showed comparable antioxidant effects. This study was a short-term acute inflammation mouse model. The tissue distribution and lipid metabolic profile of CLA were not examined, and the CLA mixed isomers were used. Moreover, the PPARγ pathway was inferred based solely on mRNA levels, and further in-depth verification is still needed.

Biology doi: 10.3390/biology15211991

Authors: Mingwei Sima Zhengyuan Fang Jiayu Liu Yan Cui Yongshi Liu Jingjing Liu Yan Bi Donghui Yue

Selective immune clearance could limit pulmonary fibrosis by removing disease-sustaining cells, but its value depends on preserving the capacity of the remaining tissue to repair. This narrative review examines PubMed literature searched through 10 October 2026, prioritizing studies published from 10 October 2024 to 10 October 2026 while retaining relevant earlier investigations. We compare human tissue profiling, immunopeptidomics, cell assays and animal interventions according to target recognition, effector-dependent elimination, treatment phase and retained repair capacity. Vaccination, checkpoint blockade and engineered immune cells provide different combinations of cytotoxicity, altered cell abundance and antifibrotic activity. However, repair-associated senescence and conflicting FAP-targeting outcomes show why marker expression alone cannot determine which cells should be removed. Epithelial proliferation and inferred cell trajectories are therefore assessed separately from lineage-supported differentiation, alveolar organization and sustained barrier, vascular and physiological recovery. The available studies do not yet establish that selective clearance produces lasting alveolar recovery, and clinical benefit in IPF remains unproven. Functional target validation, treatment after fibrosis is established, and follow-up after treatment withdrawal are priorities for translation.

Biology doi: 10.3390/biology15211990

Authors: Qin Wang Bao Wang Chenglong Zhu Huishan Yue Deqian Fan Wenjie Xu Jiangmin Zheng Jianzhong Ling Liulan Zhao Song Yang Xiaojing Song Ling Tan

Walking-associated locomotion has evolved independently in several fish lineages through distinct anatomical and biomechanical mechanisms. The spiny red gurnard (Chelidonichthys spinosus) provides an experimentally tractable model for dissecting the genetic basis of walking-associated locomotor specialization. We assembled a high-quality chromosome-level genome of the spiny red gurnard and performed a comparative genomic analysis across five walking-associated fish lineages. An integrated protein–protein interaction (PPI) network revealed high clustering coefficients and significant enrichment in fin development and locomotion pathways, indicating candidate functional similarity of lineage-specific genes at the protein interaction level. Shared positively selected genes (PSGs), including jph2, ccdc80, lrrc7, and ap3b2, were identified as candidate genes potentially associated with neuromuscular function. Specifically, in the spiny red gurnard, cdh23, showed lineage-specific positive-selection signals and amino acid changes, suggesting a potential contribution to mechanosensory adaptation. Furthermore, we identified changed conserved noncoding elements (CNEs) in each lineage, with some showing convergent changes near wnt3 and cyp26a1 in specific species pairs. A species-specific CNE deletion in the tax1bp1b intron was tested in HEK293T cells using sequences from zebrafish and spiny red gurnard; the two sequences showed different heterologous reporter activities. Overall, our analyses provide exploratory evidence for a dual pattern of genomic variation potentially underlying walking locomotor evolution: functional association at the protein network level coupled with predominantly lineage-specific yet occasionally convergent regulatory changes. This work also offers insights into environmental adaptation in fishes and a valuable genomic resource for studying convergent evolution.

Biology doi: 10.3390/biology15211989

Authors: Xuan Chen Jiadi Zhang Jiali Chen Di Wu Nufen Li Shangfeng Zhou Lifeng Wang Haona Yang

Echinochloa crus−galli is one of the world’s ten most pernicious weeds and is mainly controlled by chemical herbicides. However, the application of herbicides over long periods has escalated weed resistance, highlighting the need for eco−friendly alternatives. As a degradable natural allelochemical, dihydrocoumarin displays auxin−like activity and inhibits root growth in E. crus−galli in a manner dependent on concentration, phenotypically mimicking exogenous IAA. Previous studies have shown that dihydrocoumarin suppresses weed growth largely via auxin signaling. Here, we identified EcIAA9, a gene that responds to dihydrocoumarin and encodes a nuclear protein interacting with EcARF7. Heterologous rice assays showed that at 25 mg/L dihydrocoumarin, EcIAA9 overexpression increased primary−root inhibition from 30.81% (WT) to 54.44% and 52.00% (EcIAA9−OE). Conversely, OsIAA9 knockout lines consistently exhibited a milder root inhibition trend compared to the overexpression lines. These differential phenotypes collectively establish IAA9 as a key positive regulator in this pathway. Notably, EcIAA9 overexpression rice showed different responses to dihydrocoumarin and IAA, and combined treatments produced additive inhibitory effects. Knockout of OsARF7 failed to fully abolish dihydrocoumarin−triggered inhibition, indicating that ARF7 participates in this regulatory module, although functional compensation among ARF homologs may underlie this observation. In summary, the EcIAA9–EcARF7 regulatory module contributes to the repression of root growth triggered by dihydrocoumarin. These findings show that dihydrocoumarin phenotypically mimicked the inhibitory effect of IAA on barnyardgrass but acted through a somewhat different mechanism. This study provides new insights into the crosstalk between allelochemicals and auxin signaling.

Biology doi: 10.3390/biology15211988

Authors: Bodour S. Rajab Ahmed M. El-Sebaey Anmar A. Khan Talat A. Albukhari Bassem Refaat Hatem A. Sembawa Rehab M. Bagadood Eyad T. Albukhari Nani Nasreldin Mohamed E. El-Boshy

The present study investigated the protective effects of edaravone (EDA), metformin (Met), and their combined treatment against diabetic nephropathy (DN) in rats. Sixteen normal non-diabetic rats were allocated to the negative control (NC) and EDA-treated control (EDA10; 10 mg/kg/day) groups and received a standard diet throughout the study. Type 2 diabetes was induced by feeding male Wistar rats (n = 40) a high-fat diet (HFD) for four weeks followed by a single intraperitoneal injection of streptozotocin (STZ; 40 mg/kg). Of the 40 rats, 36 developed diabetes; 32 were subsequently maintained on the HFD for an additional four weeks to establish DN and were then randomly allocated into four equal diabetic groups (n = 8/group) for the 8-week therapeutic intervention as follows: untreated DN, DN treated with Met alone (300 mg/kg/day), and DN treated with Met combined with either 5 or 10 mg/kg/day EDA. The diabetic animals remained on the HFD throughout the intervention period. Blood, urine, and renal tissue were collected to assess glucose homeostasis along with renal function, histopathology, oxidative stress, antioxidant defense, inflammation, apoptosis, and selected molecular regulatory markers at both gene and protein levels. DN was associated with impaired glucose homeostasis together with marked renal dysfunction, histopathological injury, oxidative stress, inflammation, and apoptosis. While Met significantly ameliorated many of these abnormalities, co-administration of EDA produced additional improvements, with the greatest overall effects observed with the higher EDA dose. Correlation and Mantel network analyses showed stronger associations of Mapk1 expression with renal injury, inflammation, and oxidative stress markers in DN, whereas combined treatment was associated with stronger relationships between Akt1 and Hmox1 expression and the cytoprotective biomarkers. In conclusion, combined EDA and Met treatment produced greater overall renoprotective effects than Met monotherapy, with the higher EDA dose showing the strongest nephroprotection. Further studies are required to determine the mechanisms underlying EDA-associated renoprotection and their translational relevance in humans.

Biology doi: 10.3390/biology15211987

Authors: Alessandro Lo Giudice Martina Di Marco Giulia Maria Giorgia Lo Piano Francesca Chiara Cecala Claudia Campanella Francesco Cappello Celeste Caruso Bavisotto Giuseppa D’Amico Alessandra Maria Vitale

Glioblastoma (GBM) is one of the most aggressive primary brain tumors in adults, characterized by rapid growth, diffuse infiltration of surrounding brain parenchyma, and resistance to conventional therapies, resulting in poor prognosis. The diffuse infiltrative behavior of GBM represents a major therapeutic challenge, as cancer cells can disseminate beyond identifiable margins of the tumor, escaping complete eradication and contributing to recurrence. GBM cell migration is a heterogeneous process that can occur through distinct strategies, including single-cell and collective patterns, as well as through the formation of multicellular structures known as “oncostreams”. Understanding the mechanisms underlying these migratory modalities may help identify new targets for limiting local tumor dissemination and disease progression. In this context, a variety of in vitro models have been developed to investigate these processes. Among these, hydrogel-based scaffolds represent a promising platform to recapitulate some selected biochemical and biophysical properties of the brain extracellular matrix, enabling the investigation of how the extracellular environment cues influence GBM cell migration and invasion. In this review, we discuss the major cellular strategies of GBM cell migration and tissue invasion and critically examine hydrogel-based in vitro models used to investigate these processes, highlighting their design principles, biological relevance, and current limitations.

Biology doi: 10.3390/biology15211986

Authors: Guanghua Yang Heling Yu Zhiqiang Cai

SA/PVA/RNC/ZnONPs composite gel beads were prepared by calcium-mediated ionic cross-linking and freeze-drying, using sodium alginate (SA), poly(vinyl alcohol) (PVA), rape-straw-derived cellulose material (RNC) and zinc oxide particles (ZnONPs). SEM, FTIR, and XRD were used to examine the dried composite morphology, functional groups, and crystalline features. Swelling, water loss and antibacterial performance were evaluated. Among the tested formulations, 0.8 wt% PVA gave the highest reported equilibrium swelling ratio, and 1.0 wt% ZnONPs was selected on the basis of antibacterial screening. The antibacterial response against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus depended on material dosage and contact time. Antibacterial function was retained during repeated use and storage, and activity after pH preconditioning was lower at pH 1 than at pH 2–9. These observations do not establish nanoparticle immobilization, mechanical durability, or application safety. RNC loading and cross-linking conditions were fixed, so the selected formulation is not a globally optimized composition. Particle dimensions, colloidal behavior, hydrated-state mechanics, zinc release, ROS generation, and cytocompatibility require direct measurements. The material therefore represents a candidate for further investigation as an antibacterial composite, with proposed mechanisms and application suitability remaining to be validated.

Biology doi: 10.3390/biology15211985

Authors: Imran Khan Atif Ali Khan Khalil Anukul Taweechaipaisankul Suchinda Malaivijitnond Jittanun Srisutush Irene Aksoy Pierre Savatier Rangsun Parnpai

Somatic cell nuclear transfer (SCNT) can be used to propagate valuable cattle genotypes and to support genome editing, but its efficiency is still limited by incomplete epigenetic reprogramming. The donor nucleus maintains somatic chromatin and DNA methylation patterns that may interfere with embryonic genome activation, lineage specification and development. This review highlights key barriers to reprogramming and interventions used in donor cells, reconstructed embryos, or both, and discusses the strength and species specificity of the evidence. We propose a molecularly guided two-stage framework: donor cells are primed to overcome epigenetic resistance and then assessed after washout and recovery for viability, genomic integrity and target engagement. Only when a defined molecular defect persists is a transient embryo-stage intervention considered following nuclear transfer. Candidate targets include histone H3 lysine 9 trimethylation (H3K9me3), histone acetylation, DNA methylation, and abnormal X-inactive specific transcript (XIST) expression, although some approaches require further validation in cattle. Factorial experiments should separate the effects of each intervention and their interaction. Blastocyst yield is not the only measure of success; success must also be evaluated through molecular and developmental measures including placental function, pregnancy, live birth, and postnatal health. The integrated framework is not yet validated as a complete bovine protocol but provides testable criteria for improving SCNT efficacy and safety.

Biology doi: 10.3390/biology15211984

Authors: Ying Liu Wenyuan Chen Fangfang Kong Yueqin Leng Yan Yang Yangzhou Xiang

The geographical distribution of plant species is being fundamentally altered by ongoing global climate change. B. officinalis, an important medicinal and nectar plant native to South China, may experience uncertain alterations in its suitable habitat under projected climatic changes. To predict where B. officinalis may find suitable environments across China, this work drew upon 346 presence records alongside 24 predictor layers (climatic, topographic, vegetative, and anthropogenic) and employed an ENMeval-tuned MaxEnt framework. Habitat suitability was projected for the present day and three future time slices (2050s, 2070s, 2090s) under four Shared Socioeconomic Pathways (SSP126–SSP585). The main results are as follows. (1) Bio7 (temperature annual range), altitude, and Bio12 (annual precipitation) proved to be the three most influential predictors, with a combined relative importance exceeding 91%. Their optimal ranges were 16.05–29.88 °C for Bio7, 6.53–2513.17 m for altitude, and below approximately 1800 mm for Bio12, indicating a preference for subtropical mountain habitats with moderate seasonal temperature variation and well-drained conditions. (2) The present-day high-suitability zones lie predominantly within three provincial-level regions (Yunnan, Guizhou, and Sichuan) plus parts of southern Gansu and southeastern Fujian, spanning 61.16 × 104 km2. (3) Future projections reveal a clear emission-dependent divergence. Under the low-emission pathway (SSP126), suitable habitat fluctuates but partially recovers by the 2090s. Under the most extreme pathway (SSP585), suitable habitat shows persistent contraction, with the high-suitability extent declining to 7.91 × 104 km2 by the 2050s, a reduction of 87.07% relative to the present day, while the distributional core shifts more than 200 km northwestward. Across all scenarios, the centroid consistently migrates northwestward, though distances vary from 38.47 km (SSP245) to over 200 km (SSP585). Conservation priority should be given to retention zones in Yunnan, Guizhou, and Sichuan, whereas potential expansion areas in Shaanxi, Henan, and Shandong warrant close surveillance. These findings provide a quantitative basis for cultivation regionalization, wild resource conservation, and climate-adaptation strategies for B. officinalis.

Biology doi: 10.3390/biology15211983

Authors: Tianyi Er Chen Zhang Ziming Wang Sisi Ruan Jian Mao Hong Ma

As deep-space exploration advances, the health effects of the space environment have become a critical concern. Zebrafish (Danio rerio) have emerged as a valuable vertebrate model for space biology owing to their genetic tractability, optical transparency, and conserved organ systems. This review summarizes recent advances in using zebrafish to study spaceflight-associated health risks, focusing on ionizing radiation and altered gravity. We examine effects across the cardiovascular, nervous, musculoskeletal, sensory, reproductive, and other systems. Radiation induces cardiac dysfunction, neurobehavioral deficits, skeletal deformation, ocular damage, and reproductive toxicity, often through oxidative stress, apoptosis, and dysregulated signaling pathways. Microgravity and hypergravity primarily affect the musculoskeletal and vestibular systems, with microgravity reducing bone ossification and impairing otolith development. We also discuss current limitations, including the gap between ground-based simulations and actual space conditions, and the lack of combined-stressor studies. Finally, we highlight future directions, such as in-orbit live imaging, CRISPR/Cas9-based validation, and high-throughput countermeasure screening. This review aims to provide a theoretical framework for using zebrafish to assess space-environment-associated health risks and to inform research on health risks relevant to long-duration spaceflight.

Biology doi: 10.3390/biology15211982

Authors: Cong Wei Jianchuan Li Lifang Peng Shiyang Weng

Extreme altitudinal gradients are natural experiments for testing how environmental gradients shape genomic variation, yet remain poorly characterised in high-altitude reptiles. We analysed whole-genome resequencing data (~17×) from 44 rock agamas (Laudakia sacra and L. wui) from five populations spanning 2311–3758 m in the Yarlung Zangbo valley, Qinghai–Tibet Plateau. Variation within L. sacra formed a continuous altitudinal cline rather than four discrete units, with the first principal component (PC1) explaining 41.29% of the variance; diversity declined monotonically with altitude (π fell ~9-fold), linkage disequilibrium (LD) half-decay lengthened 27-fold and the inbreeding coefficient (FROH) reached 0.155 with effective population size lowest at the valley head. Redundancy analysis with permutation identified 593 altitude-associated SNPs, jointly supported by a rank-based cline screen (6.1-fold enrichment over independence), and selective sweep analysis detected 4573 candidate genes across the ten pairwise comparisons, with the extreme interspecific contrast (C1 vs. C5) spanning cytoskeletal, epigenetic, glycolytic and oxygen-sensing functions. Low diversity, high inbreeding, small effective size and large projected genetic offset coincided at the valley head, making it the most genetically depauperate and climate-vulnerable population. These results reveal genomic differentiation along the altitudinal–longitudinal gradient consistent with putative incipient local adaptation and identify conservation priorities for high-altitude reptiles.

Biology doi: 10.3390/biology15211981

Authors: Runlei Zhang Junkai Wang Shanfeng Wu Wenbo Mo Nan Yang

Landscape patterns along highways vary with the spatial extent examined, and similar responses may conceal differences in land cover and patch structure. We analyzed 14 nested cumulative buffer widths (0.05–10 km) across three sections of China’s Jinggang’ao Expressway from 2000 to 2020. Generalized additive models, block bootstrap resampling, annular land-cover comparisons, and temporal regressions were used to examine landscape structure and annual climate associations. Landscape Shape Index (LSI), Shannon’s Diversity Index (SHDI), and Largest Patch Index (LPI) showed nonlinear, section-specific patterns. Initial LSI minima occurred at 0.236, 0.288, and 0.343 km, respectively, and were consistently detected under temporal resampling, although their locations depended on model specification. Despite similar LSI patterns, land-cover composition differed among sections. From 250 to 500 m, cropland proportion (PLAND) decreased by 0.94–4.36 percentage points, while the share of cropland occupied by its largest patch increased by 5.14–11.69 percentage points. Climate associations were sensitive to temporal modeling; none of 36 coefficient tests passed false discovery rate correction under autoregressive models. Combining cumulative profiles, annular composition, and class-specific patch measures reveals structural differences that aggregate landscape metrics alone may obscure.

Biology doi: 10.3390/biology15211979

Authors: Anna Kharitonova Rainer Metcalf William Lawless Rekha S. Patel Bangmei Wang Wayne C. Guida Niketa A. Patel

Stimulator of Interferon Genes (STING) is a central mediator of innate immune signaling and a therapeutic target for inflammatory diseases. Previously, we identified Clonixeril (CXL) as a concentration-dependent inhibitory modulator of human STING (hSTING) signaling. Despite structural conservation, murine STING (mSTING) and hSTING differ in ligand recognition and activation. We posit that CXL may exhibit distinct activity in the murine system. Mice are used in biomedical research due to their genetic similarities to humans and their utility in evaluating systemic activity and safety of therapeutic compounds. We evaluated CXL effects on mSTING using computational modeling, as well as in vitro and in vivo studies. Molecular dynamics simulations and induced-fit docking predicted favorable CXL binding to mSTING. In 3T3-L1 cells, CXL enhanced DMXAA-induced STING, TBK1, and IRF3 phosphorylation and IFN-β mRNA expression, showing STING pathway activation. Acute CXL efficacy was evaluated in vivo in C57BL/6 mice. CXL increased IFN-β following DMXAA administration. Histopathology showed no treatment-associated abnormalities. HPLC detected CXL in serum and liver. The study identified species-specific responses, suggesting that mouse models may not accurately reflect the effects of CXL on hSTING signaling. Acute CXL treatment was well-tolerated, and CXL is a positive modulator of DMXAA-induced mSTING signaling in vivo.

Biology doi: 10.3390/biology15211976

Authors: Jiaqi Zhang Yuanyuan Dang Lin Wan Qiyan Liu Xinting Liu Linyan Hu Jing Wang Xiuyu Shi Hulin Zhao Guang Yang

Background: Tuberous sclerosis complex (TSC) frequently causes epilepsy, but cell-type-specific molecular alterations in human lesions remain incompletely understood. Methods: We performed single-nucleus RNA sequencing of cortical tissue from three TSC and three surgical control donors, with single-nucleus chromatin accessibility profiling in two donors per group from the same cohort. Donor-level pseudobulk differential analyses were combined with functional enrichment, inferred cell communication, and motif analyses. Results: Among the six cell types displayed in the main comparison, microglia had the most differentially expressed genes (872; 282 upregulated and 590 downregulated). Downregulated genes were enriched for lysosomal and lipid-storage processes. Inferred APP-CD74 input to microglia was higher for most source cell types, whereas APP-SORL1 changes varied by source. Chromatin analysis identified 9283 differentially accessible regions. Predicted regions linked to ABCA1, ATP6V0A1, and GPNMB showed decreased accessibility, concordant with lower RNA expression. Donor-averaged TFEB- and TFE3-associated chromatin variation across regions (chromVAR) scores were lower in TSC. Conclusions: These exploratory findings suggest microglial remodeling involving lysosomal and lipid-storage processes. It may provide a molecular basis for further investigation of microglia in epileptogenesis.

Biology doi: 10.3390/biology15211980

Authors: Teng Qin Xiaochen Wang Xingyao Shen Lei Ye Qingqing Dou Jinliang Liu

Pathogens present significant risks to public health and typically require detection in a hospital or clinic setting. The advancement of lateral flow assay (LFA) cassettes has made detection accessible to all, allowing individuals to perform tests from nearly any location. The extensive use of antigen rapid test (ART) kits for self-screening of COVID has reinforced the critical role of LFAs in accelerating diagnostic processes and subsequent disease prevention measures. This study delves into the realm of lateral flow assays, encompassing their fundamental design principles, interpretation of results, and the cutting-edge research focused on enhancing reporter materials and signal amplification techniques. Additionally, it emphasizes recent progress in employing LFAs for the effective identification of a diverse array of pathogenic microorganisms. This comprehensive overview has the potential to serve as a valuable reference for researchers in related disciplines.

Biology doi: 10.3390/biology15211978

Authors: Gang Zhang Chen Feng Helong Dai

Kidney transplantation is the optimal treatment for end-stage kidney disease (ESKD), but transplant-associated acute kidney injury (AKI), primarily driven by ischemia–reperfusion injury (IRI), contributes to delayed graft function (DGF) and inferior long-term graft outcomes. Rodent kidney transplantation models provide a clinically relevant platform. This review summarizes the establishment and application of rat and mouse kidney transplantation models for studying transplant-associated acute kidney injury. It highlights critical variables in model design, including surgical techniques, ischemic conditions, organ preservation, donor characteristics, and immunological settings that influence experimental outcomes. It further synthesizes current mechanistic evidence on oxidative stress, microvascular injury, immune activation, regulated cell death, tissue repair and fibrosis, molecular regulatory networks, multi-omics analyses, and remote organ injury. The review also examines interventions targeting donor conditioning, organ preservation and perfusion, reperfusion inflammation, recipient therapy, and regenerative repair, while considering their experimental limitations and translational relevance. Rodent kidney transplantation models can bridge conventional renal ischemia–reperfusion models and clinical transplantation. Future progress will depend on standardized surgical procedure, clinically relevant model selection, rigorous long-term outcome assessment, and the integration of emerging molecular technologies to enhance translational relevance.

Biology doi: 10.3390/biology15211977

Authors: Alexey Dorokhov Nikolay Sazonov Yulia Lyashchuk Vladimir Teterin Nikolay Panferov Alexey Ovchinnikov

This study is devoted to the quantitative assessment of the level of biological risk of the emergence and spread of infectious and parasitic potato diseases based on environmental stability parameters. The study examined the survival conditions of pathogens in soil, water systems, and on various environmental objects, classified according to the criterion of internal and external localization of pathogens. In this study, we conducted a scoring and rating analysis of the threats of potato infection by pathogens of bacterial, viral, helminth, and mycotic etiology, which pose a danger in terms of infection and death of plantings, significant yield losses, as well as deterioration of the quality of commercial and seed potato tubers. Particularly dangerous are species characterized by high survival in the external environment while retaining virulent properties. The developed system implied regular monitoring and updating of data on the emergence of pathogens with new forms of resistance. Phytosanitary control in the context of global trade requires systematization of available data on pathogens of infectious and parasitic potato diseases in order to promptly identify pathogens and prevent their further spread. The use of a scoring and rating approach increases the objectivity of phytosanitary risk assessment and can serve as a scientific basis for managerial decision-making aimed at reducing the epiphytotic potential of pathogens and ensuring stable potato production.

Biology doi: 10.3390/biology15211974

Authors: Taewan Kim Jaejoon Yoo Do-Hwan Lim

Cancer remains a leading cause of death worldwide, and drug resistance is a major obstacle to durable treatment responses. Recent advances in cancer genomics have highlighted extrachromosomal DNA, large circular DNA molecules outside chromosomes. Once dismissed as a cytogenetic curiosity, extrachromosomal DNA (ecDNA) is now recognized as a potent and mechanistically distinct contributor to cancer progression and therapeutic escape. It is present in many cancers and is associated with poor outcomes, particularly in aggressive tumors. Non-Mendelian segregation, open chromatin architecture, transcriptional hub formation, and structural plasticity enable copy-number plasticity, intratumoral heterogeneity, and reversible transitions between drug-sensitive and drug-resistant states. These properties can promote resistance through increased expression or loss of drug-targeted oncogenes and amplification of alternative signaling components that bypass the inhibited pathways. Clinical studies indicate that therapeutic pressure shapes the ecDNA landscape and that ecDNA is associated with treatment failure and differential therapeutic responses. Here, we synthesize understanding of ecDNA biology and its role in drug resistance, review clinical evidence linking ecDNA to treatment failure, summarize emerging approaches for ecDNA detection, and discuss strategies targeting ecDNA-specific vulnerabilities and challenges in clinical translation. These insights position ecDNA as a dynamic contributor to adaptive resistance and a potential biomarker of vulnerability in precision oncology.

Biology doi: 10.3390/biology15211975

Authors: Nana He Xinyi Li Lifeng Han Liming Wang Yidong Xu Shushen Sun Siqi Guo Yiwen Wang

Background: Type 2 diabetes mellitus (T2DM) is driven by insulin resistance and chronic inflammation, yet current single-target therapies inadequately address these interconnected pathologies. Xuanfei Baidu decoction (XFBD), originally developed for COVID-19, is known to inhibit JNK and JAK/STAT pathways and may offer a multi-target strategy. Methods: A high sugar diet (HSD) induced Drosophila T2DM model was treated with XFBD or its active component glycyrrhizic acid (GA). Phenotypic assays, metabolomics, 16S rRNA sequencing, qPCR, transgenic reporter flies, network pharmacology, and computational docking/dynamics simulations were performed. Results: XFBD dose-dependently alleviated HSD-induced developmental delay, hyperglycemia, insulin resistance (restored dilp2/3/5, InR, 4EBP expression and AKT phosphorylation), glycolipid disorders, and oxidative stress. Metabolomics identified 79 reversed metabolites enriched in T2DM-relevant pathways (D-amino acid, BCAA, TCA cycle). XFBD suppressed aberrant JNK and JAK/STAT activation, independent of gut microbiota modulation. GA recapitulated these effects in vivo. Conclusions: XFBD and GA ameliorate insulin resistance and metabolic dysregulation via JNK/JAK-STAT axis inhibition, providing a preclinical rationale for their therapeutic application in T2DM and related metabolic syndrome outcomes.

Biology doi: 10.3390/biology15211973

Authors: Pinpin Zhou Yanping Pan Ming Yang Yiyong Luo Huanhuan Chen Zichao Liu Fang Zhao Lizhou Tang Gonghua Lin

Leeches are classic animal-derived traditional Chinese medicines for activating blood circulation and eliminating blood stasis. The hematophagous Hirudinaria manillensis and the non-hematophagous Whitmania pigra are the two most widely used medicinal leeches, but their HMEI (H. manillensis elastase inhibitor) gene family, a gene family containing candidate elastase-inhibitor paralogs, has not been systematically compared across species and geographical populations. Here, we performed RNA-Seq on head tissues from five populations of each species and compared the expression of all HMEI paralogs. The 38 paralogs formed 9 descriptive sequence groups. Total HMEI expression showed no significant interspecies difference, yet the two species showed distinct transcriptional patterns in the sampled populations: expression in H. manillensis was concentrated in a few paralogs with ultra-high abundance, whereas expression in W. pigra was distributed across multiple moderately expressed paralogs. Total HMEI expression did not differ significantly among H. manillensis populations, whereas significant inter-population differences were detected in W. pigra. Four expression-based candidates for functional validation were identified: HMEI_Hman06 and HMEI_Hman15 from H. manillensis, and HMEI_Wpig01 and HMEI_Wpig17 from W. pigra. These results characterize interspecies and population-associated variation in HMEI expression, providing a transcriptomic resource for comparative biochemical and functional characterization of HMEI paralogs.

Biology doi: 10.3390/biology15211972

Authors: Deng Pan Yaqin Ding Yujun Chen Siteng Wu Ziang Su Juan Wang Zhipeng Zhu Yuxiang Liu Xiaoling Xu Weicong Fu

Urban residential areas are important habitats for birds and settings for residents’ daily contact with nature. Whether morphological functional-trait diversity and variation in species-level visual-attractiveness scores share environmental responses remains unclear. We surveyed 78 transects within 33 residential areas along the Min River in Fuzhou, China, over 12 months and integrated local vegetation, built-environment, and multi-scale landscape predictors. Grouped nested cross-validation, extreme gradient boosting (XGBoost), and out-of-fold (OOF) SHapley Additive exPlanations (SHAP) were used to compare predicted responses. Model performance was moderate for five metrics (OOF R2 = 0.250–0.404). (1) Total tree cover, mean tree height, and tree richness were the most consistent predictors of functional-trait and visual-attractiveness dispersion, while other effects were metric-specific. (2) Matched functional dispersion (FDis) and Rao’s quadratic entropy (Rao’s Q) metrics showed predicted responses that were predominantly concordant with those for tree-related variables, whereas local response divergence was concentrated in low-contribution understory variables. Most functional–visual associations and response-curve similarities did not consistently exceed null expectations from shared community composition. Model performance also declined under square-root and presence/absence weighting. (3) These findings support consideration of mature-tree retention, context-appropriate canopy structure, tree richness, and differentiated understory management, without treating higher-response intervals as causal targets. Concordance does not establish independent ecological synergy or measured aesthetic benefits.

Biology doi: 10.3390/biology15211971

Authors: Xijia Wang Wenpeng Li Xingbo Zhao

Aging disrupts communication between mitochondria and the nucleus, but compact molecular readouts of this interface remain limited. Here, we examined mitochondrial DNA light-strand promoter (LSP) methylation signals in skeletal muscle across natural-aging and mitochondrial-background models, and independently profiled candidate nuclear mitochondrial DNA insertion (NUMT) junction signals in brain and skeletal muscle across age groups. Natural aging was associated with reduced motor performance, altered skeletal-muscle mitochondrial status, and lower LSP methylation signals. Reciprocal F1 crosses and conplastic mice showed coordinated associations among mitochondrial background, LSP methylation signals, bioenergetic parameters, nuclear mitochondrial-gene expression, and physical performance. In parallel, short-read whole-genome sequencing revealed a non-monotonic candidate NUMT signal pattern, with the highest mean signal at 12 months. A Ptprc-associated candidate mitochondrial-nuclear junction was supported by split-read inference and junction-specific droplet digital PCR in a candidate-positive sample. Together, these findings identify LSP methylation signals and candidate NUMT junction signals as complementary but independently measured molecular features of mitonuclear aging.

Biology doi: 10.3390/biology15211970

Authors: Yujiao Lu Sagar Vyavahare Mayuri Gulhane Xinxin Dong Abbas Jarrahi Harminder D Singh Molly Braun Darrell W. Brann Krishnan M. Dhandapani

Alzheimer’s disease (AD) is increasingly recognized as a neurodegenerative disorder characterized by central insulin resistance and cerebral hypometabolism. The steroid hormone, 17β-estradiol (E2), interacts closely with insulin signaling pathways and is locally synthesized in the brain by the enzyme aromatase. However, the spatial and temporal dynamics of brain aromatase during AD progression and its relationship to central insulin resistance remain poorly understood. Using the 5xFAD mouse model, we examined whole-brain, regional, and neuron/astrocyte-specific alterations in aromatase expression along disease progression. Whole-brain aromatase expression remained unchanged at 2 months of age but progressively declined at 5 and 9 months, inversely correlating with amyloid-β plaque burden. Regional analysis of the cortex, hippocampal CA1, and hypothalamus revealed progressive aromatase loss in all regions; notably, the hypothalamus exhibited a significant decline at the earliest disease stage examined, preceding comparable changes in the cortex and hippocampus, while an age-related decline cannot be fully excluded, as only a single-aged wild-type (WT) control was used. Cell-level analysis revealed a progressive reduction in neuronal aromatase expression, whereas astrocytic aromatase displayed a biphasic response, increasing during early disease stages before declining at later stages. In parallel, neuronal insulin-resistance signaling increased progressively with disease advancement and was negatively correlated with neuronal aromatase expression across all regions examined (r = −0.82 to −0.87). Collectively, these findings demonstrate progressive regional and neuron/astrocyte-specific alterations in brain aromatase during the progression of amyloid pathology, identifying early hypothalamic vulnerability as a feature of AD-associated altered insulin signaling.

Biology doi: 10.3390/biology15211968

Authors: Xiaoyan Pan Yiqing Chen Yuanfeng Gao Xiaohua Chen Tingtian Wu Yuanling Li Guangyang Li Ziwei Lin Haofan Meng Zongzhu Chen

Soil microorganisms play essential roles in maintaining the function and stability of forest ecosystems. In this study, conducted in the Jianfengling Nature Reserve in Hainan, we performed Illumina high-throughput sequencing, in combination with principal coordinate analysis (PCoA), redundancy analysis, and other statistical methods, to compare the composition, community structure, and diversity of the soil microbiota in four types of forest vegetation, namely, monsoon forest, lowland rainforest, montane rainforest, and artificial forest (AF), and to identify the environmental variables associated with differences among the forest types. Different vegetation types differed significantly with respect to pH, total phosphorus content (TP), elevation, and concentrations of manganese (Mn) and iron (Fe). In contrast, no significant differences were observed in soil water content, bulk density, total nitrogen (TN), and total organic carbon (TOC) content. Compared to AF, natural forests were characterized by higher concentrations of TN, TOC, TP, Mn, and Fe, although the differences in TN and TOC were not statistically significant. For all four of the assessed vegetation types, Pseudomonadota, Actinomycetota, Acidobacteriota, and Verrucomicrobiota were identified as the dominant bacterial phyla, whereas Ascomycota, Basidiomycota, and Mucoromycota were predominant among the fungal phyla, indicating that these phyla are capable of surviving in different soil ecosystems. Although no significant differences in bacterial diversity were detected among vegetation types, PCoA revealed pronounced differentiation in bacterial community composition (PERMANOVA, p = 0.0001). Notably, within-group multivariate dispersion also differed significantly (PERMDISP, p = 0.0129), indicating that the observed compositional differences may be associated with the combined effects of centroid location effect and within-group multivariate dispersion. In contrast, significant differences were observed in fungal diversity, whereas differences in fungal community composition were not significant in the PCoA (PERMANOVA, p = 0.1777). These results suggest that vegetation type primarily influenced fungal diversity rather than fungal community structure. Mn concentration exhibited the highest marginal explanatory power for the variation in the bacterial community, with a significant effect; it was positively correlated with the ACE, Chao1, and Simpson indices, and negatively correlated with the Shannon index. TOC exhibited the highest marginal explanatory power within the fungal community, showing a negative correlation with the ACE, Chao1, and Shannon indices and a positive correlation with the Simpson index. Collectively, these findings provide insights into microbial differentiation within forest soils associated with different vegetation types and highlight distinct patterns in bacterial and fungal diversity, which will potentially serve as a basis for the development of conservation strategies.

Biology doi: 10.3390/biology15211969

Authors: Inés Baeza-Zaragoza Celia Llorente-Sáez Raquel Pérez-Sen Marina Arribas-Blázquez Luis Alcides Olivos-Oré Antonio R. Artalejo Rosa Gómez-Villafuertes Felipe Ortega

Oligodendrogliomas are diffuse low-grade gliomas of the adult central nervous system characterized by high recurrence rates and limited therapeutic options. Extracellular nucleotide signaling via purinergic receptors (P2X and P2Y) regulates pathophysiological processes in various brain tumors; however, its specific role in oligodendrogliomas remains unexplored. Here, we characterized the purinergic receptor profile in HOG cells, a human oligodendroglioma cell line, and evaluated the specific impact of P2Y1 receptor activation on tumor cell dynamics. Single-cell calcium imaging experiments demonstrated that extracellular ATP increases intracellular calcium concentration through both extracellular influx and internal store mobilization. Expression analyses at transcript and protein levels identified ionotropic P2X4 and P2X5 receptors, alongside metabotropic P2Y1, P2Y2, and P2Y4 receptors. Furthermore, the calcium responses induced by selective P2Y agonists confirmed functional responses for P2Y1 and P2Y2/P2Y4 receptors. Finally, long-term time-lapse videomicroscopy combined with single-cell lineage tracking revealed that P2Y1 activation reduced cell proliferation, prolonged cell cycle duration, tended to reduce migratory velocity, and triggered cell death. Pre-incubation with the selective P2Y1 antagonist MRS2179 completely abrogated these effects. Taken together, our findings provide the first evidence of a functional purinergic network in HOG human oligodendroglioma cell line and highlight the P2Y1 receptor as a tumor-suppressive candidate and potential therapeutic target for oligodendroglioma management.

Biology doi: 10.3390/biology15211967

Authors: Song Mi Lee Moon-Taek Park Sung Dae Kim

Ionizing radiation induces biological effects through direct energy deposition in biomolecules and indirect damage mediated by water radiolysis and reactive oxygen species. This review synthesizes the intracellular and intercellular events that connect these initial reactions to cell-fate determination. Following irradiation, cells coordinate DNA damage recognition, checkpoint control, and repair with oxidative stress and inflammatory signaling. Together, these responses connect the initial molecular damage with the intracellular and intercellular events that follow. The balance among damage severity, repair capacity, cell-cycle stage, genetic background, and microenvironmental signals shapes outcomes including recovery, transient or permanent arrest, senescence, mitotic catastrophe, apoptosis, regulated necrosis, and autophagy-associated survival or death. Irradiated cells further influence surrounding tissues through cytokines, chemokines, senescence-associated secretory factors, damage-associated molecular patterns, and cyclic GMP–AMP synthase–stimulator of interferon genes signaling. These integrated responses determine both therapeutic effects and normal-tissue injury, supporting investigation across molecular, cellular, immune, and tissue levels.

Biology doi: 10.3390/biology15211966

Authors: Burim N. Ametaj

Systems biology maps extensive networks but lacks a general principle identifying the minimum functional architecture of living organization. The Triadic Principle of Biology (TPB) proposes that stable, self-regulating biological systems require coordinated closure among three functionally distinguishable domains: Information, Energy/Material Transformation, and Interface/Boundary. These are categories of biological work rather than anatomical structures. This article states the claim, gives explicit rules for assigning a process to a domain and for fixing the system boundary, defines autonomy independently of the framework, and evaluates candidate manifestations in genetic coding, translation, cellular organization, epigenetics, development, physiology, evolution and disease against prospective admissibility criteria. The codon inequality provides one exact result, but it concerns code word length rather than functional domains and is not evidence for the TPB. The framework contributes a standardized functional vocabulary, criteria distinguishing genuine triads from arbitrary groupings, a taxonomy of failure modes, an operationalized closure index with explicit scoring functions and a worked example, and falsifiable predictions, including specified comparisons against rival decompositions such as sensing–regulation–action, supply–demand–control and Wicken’s exploitation–homeostasis dyad. Gánti’s chemoton is identified as the closest formal antecedent. Because these predictions remain untested, the article specifies the experiments and outcomes that would support, weaken or reject the principle.

Biology doi: 10.3390/biology15211965

Authors: Xinyu Ni Songle Fan Guojiao Lin Bingbing Guo Mingyang Liu Lifeng Wang

Natural rubber is synthesized in the laticifers of Hevea brasiliensis, but the transcriptional networks regulating latex-associated processes remain poorly understood. In particular, whether WRKY transcription factors participate in brassinosteroid (BR)-responsive regulation remains unclear. We identified the HbWRKY family using the haplotype A telomere-to-telomere reference genome of Hevea brasiliensis and integrated phylogeny, gene structure, duplication type, synteny, Ka/Ks, promoter cis-elements, tissue expression, and BR-treated transcriptomic data. The 109 HbWRKY proteins comprised 21 Group I, 72 Group II, and 14 Group III members, together with one atypical protein and one Group I-like protein. Whole-genome or segmental duplication accounted for 102 genes (93.6%), and Ka/Ks was below 1 for all 111 duplicated HbWRKY pairs, consistent with purifying selection. G-box elements occurred in 84 promoters (77.1%). Eighty-nine genes were expressed in bark and 37 in latex, with latex showing the highest value for nine genes. Seven HbWRKY genes were differentially expressed after BR treatment, and all were downregulated. HbWRKY7 (HbAchr10M0003572) and HbWRKY28 (HbAchr15M0012484) were prioritized because both combined differential expression following BR treatment, their highest recorded expression in bark among the seven tissues, and predicted promoter G-boxes. This updated family resource narrows the candidates for testing a BR-WRKY regulatory module in rubber tree.

Biology doi: 10.3390/biology15211964

Authors: Wan-Ting Huang Wen-Hui Liao Xiao-Yi Qin Jun-Jie Zhu

More than two billion years of photorespiratory evolution have shaped three sets of constraints: catalytic constraints associated with Rubisco oxygenase activity; compartmental topology constraints arising from compartmental organization, transport processes, and cofactor coupling; and physiological and ecological constraints arising from integration with metabolic and signaling networks. Photorespiratory engineering has emerged as a key strategy for improving photosynthetic efficiency in C3 crops, yet existing studies have not systematically assessed the practical implications of these constraints. Evaluation metrics remain inconsistent, the scope and depth of stability and risk assessments vary, and methodological heterogeneity hinders comparisons across studies. To address these issues, we synthesize the evolutionary history of photorespiration and findings from previous research to develop an evaluation and validation framework aligned with these constraints. This framework comprises eight assessment dimensions defining what to report, a context matrix specifying the conditions under which assessments should be conducted, and a five-tier validation pipeline defining the sequence of validation steps and the criteria for classifying outcomes. Retrospective application to five published case studies demonstrates that the framework enables consistent classification of outcomes and identifies distinct priorities for further improvement across studies involving different crop species, engineering strategies, and evaluation endpoints. By providing a practical evidence structure that can be updated as new findings emerge, this framework supports the transition from empirical exploration to systematic photorespiratory engineering and facilitates cross-study comparisons and the cumulative synthesis of evidence across assessment dimensions, experimental contexts, and outcomes.

Biology doi: 10.3390/biology15211962

Authors: Yangyang Ding Yutong Zhao Pengying Li Song Jiang Yundong Li Qibin Yang Ziyi Jiang Lishi Yang Jianhua Huang Jianzhi Shi Yafei Duan Falin Zhou

While female heterogamety in black tiger shrimp (Penaeus monodon) is consistent with a ZW/ZZ system, the sequence organization of its sex-associated region remains unclear. In this study, we examined the candidate sex-determining region on chromosome 19 (2.71–2.89 Mb) using PacBio HiFi reads from a marker-supported ZW female, genotypes from 200 full-sib offspring, local assembly, and public long reads. Three phase blocks overlapped this interval. Sex-associated SNPs assigned W-like and Z-like alleles in two blocks, while the central block remained unoriented. The first block contained gene24, a partial dmd-3-related gene model, and a 54 bp insertion in gene25 intron 1 (INS00000105; INS54). This insertion, supported by 17 W-like HiFi reads and two local assemblers, was called in 100/100 female offspring and 1/99 called males; one male was uncalled. Sanger reads confirmed the insertion and both flanks in three selected market-sourced females and the no-insertion junction in three selected males. Public reads from a Thai female reproduced the insertion-bearing structure, whereas Australian male reads supported the alternative structure. Separate Thai and Chinese long reads crossed the two phase gaps in their respective samples. Together, these results define local female-associated sequence differences and targets for functional investigation, rather than complete W and Z chromosome sequences.

Biology doi: 10.3390/biology15211963

Authors: Aleksandra Jaszczyńska Deniz Anıl Odabaşı Caner Aydinli Artur Osikowski Sebastian Hofman Andrzej Falniowski

The availability of freshly collected Pseudorientalia natonica (Küster, 1853) enabled a revision of the putative Pseudorientalia Radoman, 1983, species from the Aegean islands of Chios, Samos and Lesvos. It is worth noting that there is no single sequence of ‘real’ Pseudorientalia in GenBank. Phylogenetic relationships were studied using cytochrome c oxidase subunit I (COI) sequences, alongside morphological analyses of the shell, radula, female reproductive organs and penes. Molecular data revealed a well-supported Pseudorientalia clade that included populations from Chios and Samos. These populations were shown to represent two distinct species that are new to science. Unexpectedly, Tefennia tefennica Schütt and Yıldırım, 2003, was nested within this clade. As the observed morphological differences were slight and variable, Tefennia is regarded as a junior synonym of Pseudorientalia. In contrast, the putative Pseudorientalia populations from Lesvos formed a separate, well-supported lineage, being a sister to Grossuana Radoman, 1983, and Daphniola Radoman, 1973. Despite their close morphological resemblance to Pseudorientalia, these populations represent a new genus. A similar pattern was detected in ‘Pseudorientalia’ kanari D. A. Odabaşı, 2024, which also represents a distinct new genus, and an additional new species was recognised within this lineage. In Graecoanatolica Radoman, 1973, marked shell variation was found in a single, molecularly undifferentiated species.

Biology doi: 10.3390/biology15211961

Authors: Peikun Ma Haihua Ruan Hongyang Zhang

The skin is the largest organ of the human body and harbors a diverse microbial community that constitutes a complex ecosystem. Despite advances in next-generation sequencing (NGS) that have greatly facilitated the characterization of skin microbiota composition, a critical gap remains in understanding how intrinsic metabolites mediate host–microbe interactions and maintain microecological homeostasis. This review synthesizes current knowledge across interconnected layers of the skin ecosystem, including architecture, microbial communities, metabolites, and computational analytics. The skin’s structural features create spatially heterogeneous microenvironments that dictate microbial colonization patterns, while microbial communities have evolved adaptive strategies to exploit distinct metabolic niches. Intrinsic metabolites, encompassing lipids, proteins/peptides, ions, vitamins, and carbohydrates, constitute the chemical language through which host and microbes reciprocally communicate. The complexity of these interactions poses challenges for traditional analytical approaches, yet artificial intelligence is transforming the field by enabling progressive deepening of understanding, from predicting microbial functional potential to decoding the skin microbiome as a carrier of biological information. This multilevel framework provides a foundation for future investigations and may inform the development of personalized strategies for skin health management.

Biology doi: 10.3390/biology15211960

Authors: Bingqi Dang Abdugheni Abliz Jinting Liu Xinyu Shi Xu Li Jialin Li

In arid regions, water scarcity and limited vegetation regeneration capacity make the habitats of large herbivores particularly vulnerable to climate change and human activities. However, conventional habitat-suitability assessments may overlook potential environmental pressures associated with soil heavy-metal contamination. This study used the BIOMOD2 ensemble modeling framework to predict potential habitat suitability for the Mongolian wild ass under current environmental conditions and future climate scenarios. Current habitat-suitability predictions were further overlaid with soil heavy-metal contamination classes derived from the Nemerow integrated pollution index to examine their spatial correspondence. Under four-fold spatial block cross-validation, the EMca ensemble achieved an AUC of 0.893 ± 0.032 and a TSS of 0.610 ± 0.048. Distance to water sources was the most influential predictor, accounting for 43.76% of the total normalized variable importance. Highly suitable habitat was projected to decline from 0.4637 × 104 km2 under current conditions to 0–0.1180 × 104 km2 across future climate scenarios, with particularly pronounced reductions under SSP370 and SSP585 during the middle and late future periods. The spatial overlay analysis showed that 73.56% of current highly suitable habitat overlapped with light pollution, 24.31% with warning-level contamination, and 2.12% with moderate pollution. These findings indicate that high habitat suitability does not necessarily correspond to low soil-contamination levels. By integrating habitat suitability and soil-contamination patterns, this study provides a spatial basis for identifying conservation-priority habitats and areas requiring targeted environmental monitoring in Kalamaili National Park.

Biology doi: 10.3390/biology15211959

Authors: Jing He Jing Cai Xinyu Shi Jiaqi Chen Da Liu Nan Zhang Ye Jin

Background/Objectives: Osteoarthritis (OA) is the most prevalent degenerative joint disease worldwide, characterized by progressive cartilage degeneration, chronic synovial inflammation, and abnormal subchondral bone remodeling, with high disability rates and a substantial disease burden. The knee joint is the most commonly affected site in OA; therefore, this review focuses on knee OA. Traditionally, knee OA has been regarded as cartilage degeneration caused solely by mechanical wear; however, accumulating preclinical and translational evidence supports NLR family pyrin domain-containing protein 3 (NLRP3) inflammasome activation as an important contributing factor in specific inflammatory and metabolic knee OA phenotypes. This review aims to integrate the potential roles of the NLRP3 inflammasome and extracellular vesicles (EVs) in knee OA, and to explore their exploratory biomarker value and investigational therapeutic potential. Methods: This narrative review synthesizes the current published knowledge regarding NLRP3 inflammasome biology, knee OA pathogenesis, and translational research on extracellular-vesicle-based diagnostics and therapeutics. The relevant peer-reviewed literature was identified via literature searches in major biomedical databases up to September 2026. The authors assembled references based on thematic fit to the review scope, study quality, and maturity of available evidence. Original reports, clinical trials, meta-analyses, published systematic reviews, and clinical guidelines were considered; the non-peer-reviewed grey literature was not used as primary supporting evidence. Where conflicting study outcomes exist in the published literature, human clinical data and randomized controlled trial evidence were given greater interpretive weight relative to preclinical in vitro and animal-model findings. Results: This review proposes that the coupling among inflammatory responses, pyroptosis, and EVs-mediated signal transmission may constitute an important pathological link in knee OA progression. NLRP3 integrates mechanical, metabolic, and aging signals in chondrocytes, synovial macrophages, and subchondral bone cells, triggering pyroptosis and matrix degradation; it also mediates transcellular and trans-tissue cascade amplification of inflammatory signals via EVs and may drive the progression from focal injury to pan-articular degeneration. Small-molecule inhibitors targeting NLRP3 have evolved from the early experimental probe MCC950 to a new generation of tissue-selective clinical candidates; however, no NLRP3 inhibitor has yet entered dedicated clinical trials for knee OA. NLRP3-pathway molecules associated with EVs have exploratory potential as liquid biopsy biomarkers reflecting local joint inflammatory burden and may be investigated for early diagnosis and patient stratification in knee OA; engineered EVs may serve as targeted delivery vehicles, and preclinical studies have demonstrated inflammatory-microenvironment-responsive NLRP3 inhibition and cartilage-specific enrichment. Conclusions: NLRP3-targeted intervention is an investigational strategy with potential disease-modifying intent in knee OA, but it remains at the preclinical and early translational stages. To date, no clinical evidence demonstrates that selective NLRP3 inhibition improves pain, function, structural progression, or other patient-centered outcomes in knee OA; therefore, disease modification by NLRP3 inhibition remains unproven. Its early translational research faces core bottlenecks, including long-term local medication safety, intra-articular delivery efficiency, the high heterogeneity of knee OA, and standardized quality control of vesicle products. Future efforts should focus on vesicle-based multi-omics inflammatory subtyping, engineered vesicle systems that combine deep cartilage penetration with long-term joint retention, and multi-mechanism combination therapies. These approaches may generate hypotheses for future research into whether knee OA treatment can eventually move beyond symptomatic relief toward disease modification; however, this transition remains unproven and requires dedicated clinical trials with appropriate clinical endpoints. It should also be acknowledged that the available evidence is not entirely consistent: some studies have failed to demonstrate that stress-induced cartilage degradation is NLRP3-dependent, underscoring the importance of OA heterogeneity. Current evidence is largely derived from preclinical studies, and validation in human studies remains limited. It should be emphasized that, although NLRP3 inhibitors have reached clinical stages in other indications (such as neurodegenerative diseases, metabolic diseases, and cardiovascular diseases), these results primarily validate the druggability of the NLRP3 target itself and cannot be directly equated with clinical efficacy in knee OA. Dedicated clinical trials specifically designed for knee OA populations with appropriate clinical endpoints are required to establish therapeutic benefit.

Biology doi: 10.3390/biology15211958

Authors: Jeongwoo Yoo Jung-Hyun Lee

Snake electrocution on power distribution infrastructure remains poorly quantified. We analysed Korea Electric Power Corporation records from January 2024 to June 2025, including three additional records from early July 2025. Among 449 recorded incidents, photographs identified 324 individuals of 6 species from 323 incidents. The nationally endangered Amur ratsnake (Elaphe schrenckii) accounted for 202 individuals (62.3%). Spatial analyses used all 426 georeferenced records. Incidents peaked in June and occurred during daylight more often than expected from day length. The rate in Daegu–Gyeongbuk was 4.27 times that in the rest of the country (95% CI: 3.53–5.17). A case–control logistic model used 10 environmental variables, 189 case records, and 7341 control poles. Higher odds were associated with joint proximity to forest and farmland, sparse pole networks, and proximity to settlements and watercourses. External validation in an independent provincial case–control sample yielded an AUC of 0.683 (95% CI: 0.586–0.771). Across the full provincial inventory, the highest-ranked 30% of poles included 44.8% of incident poles (95% CI: 26.4–64.3%), compared with 30% expected under random selection. Predictive performance was modest and requires further evaluation before operational use.

Biology doi: 10.3390/biology15211957

Authors: Yingping Wu Jindong Ren Lizhi Lu Li Chen Xiaoyu Zhao

Chromosomal three-dimensional (3D) structural variations can mediate phenotypic differentiation in animals and plants by altering chromatin interaction patterns and regulating gene transcription. Eggshell color is an important economic trait of laying ducks, and the uterus (shell gland) of the oviduct is the core functional site for eggshell formation and pigment deposition. To reveal the 3D genomic regulatory mechanism underlying eggshell color differentiation in blue-shelled laying ducks, this study employed high-throughput chromosome conformation capture (Hi-C) technology to systematically compare chromosomal spatial conformation differences in the shell glands between blue-shelled and white-shelled laying ducks and to dissect the regulatory characteristics of chromatin architecture at different hierarchical levels. The results showed that both phenotypic groups possessed typical and conserved chromatin interaction patterns; however, their spatial folding characteristics differed significantly. Blue-shelled laying ducks (Q1) exhibited predominantly short-range loose chromatin interactions, whereas white-shelled laying ducks (B1) tended to have medium- and long-range large-scale DNA looping interactions. A/B compartment analysis revealed that chromosomal compartmentalization differed little between the two groups, with dynamic transitions occurring in both A and B compartments. Differentially compartmentalized genes were mainly enriched in pathways such as immune response, basal metabolism, reproductive development, calcium signaling, and estrogen signaling. TAD topological structure analysis revealed obvious TAD boundary remodeling on chromosome 4 in blue-shelled laying ducks and significant differences in TAD number, length, and boundary signal strength between the two groups. Changes in specific TAD boundaries also led to altered gene functions. Differentially expressed genes were mainly enriched in processes such as cell–cell adhesion, metabolism, and cell cycle, as well as regulatory pathways closely related to pigment deposition, including porphyrin and chlorophyll metabolism, melanin biosynthesis, riboflavin metabolism, and bile secretion. In summary, based on chromatin spatial conformation analysis, this study found that the eggshell color trait of laying ducks did not appear to depend primarily on macroscopic A/B compartment structural regulation; however, it was primarily associated with local specific TAD topological remodeling. This remodeling may be linked to gene expression in pigment deposition-related pathways by altering local chromatin interaction patterns. Given the limited sample size, these findings are preliminary and suggest a potential association between 3D chromatin architecture and eggshell color, which warrants further functional validation.

Biology doi: 10.3390/biology15211956

Authors: Tanyawat Kaewsalud Kamon Yakul Clemens Peterbauer Pornchai Rachtanapun Thanongsak Chaiyaso

Keratinase-I from T. vulgaris TK1-21 was engineered through computationally guided site-directed mutagenesis to enhance keratin hydrolysis and keratin waste valorization. Recombinant keratinase-I (rK-I) was expressed in Bacillus subtilis RIK1285, and molecular modeling suggested Leu214, Leu222, Ala270, and Ser280 as potential residues within the predicted substrate binding pocket. Among the engineered variants, S280L exhibited the highest catalytic performance, with 16.94% and 19.52% increases in apparent kinetic parameters toward α- and β-keratin, respectively, compared with rK-I. S280L also enhanced the hydrolysis of hydrothermally treated chicken feathers, producing higher protein (5.59 mg/mL) and peptide (1.38 mg/mL) concentrations than rK-I (4.73 and 1.08 mg/mL, respectively). The resulting keratin hydrolysate exhibited higher DPPH and ABTS radical scavenging activities, reaching 23.85 and 1100 μmol TE/g protein, respectively. LC-MS/MS identified three peptides detected only in the S280L-derived hydrolysate: SEEGVPISSGGF, EGVPISSGGF, and HLPGHQF. Bioinformatic analysis predicted potential bioactivities of these peptides. Subsequent in vitro evaluation of synthetic peptides showed that HLPGHQF exhibited 79 ± 2.5% ACE inhibitory and 17 ± 0.5% antioxidant activities, whereas EGVPISSGGF showed no detectable activity. These findings suggest that engineering the rK-I predicted substrate binding pocket could enhance keratin hydrolysis and facilitate the generation of value-added bioactive peptides.

Biology doi: 10.3390/biology15211955

Authors: Linqin Xu Xiaoyu Jiang Junjie Liu Lei Qi Chenxi Yang Haojun Li Yao Huang Lijun Zhou Shiling Feng Hongyu Yang Chunbang Ding Tao Chen

This study aimed to develop chloroplast sequence markers through comparative plastome analysis and evaluate their application in haplotype identification and genetic diversity assessment in sampled Camellia oleifera populations. Three newly assembled chloroplast genomes of Camellia sect. Oleifera ranged from 156,918 to 157,003 bp and retained the typical quadripartite structure. Comparative analyses of these genomes and 13 reference plastomes identified 605 long repeats and 3315 SSRs. The three new plastomes shared 29 preferred sense codons, 28 ending in A/U. Sliding-window nucleotide diversity highlighted eight candidate variable regions, with a maximum π of 0.01397. Among 324 individuals from 37 sampling populations, the 1772-bp concatenated alignment contained 38 variable sites and 55 haplotypes (Hd = 0.8052; π = 0.002183). Thirty-six haplotypes were singletons, while H003 occurred in 133 individuals across 35 populations. Sequence PCA and exploratory ADMIXTURE described broad variation. K = 2 had the lowest cross-validation error among the values shown for K = 2–10, and its two components were interpreted descriptively. These results document chloroplast sequence diversity and population structure in the sampled C. oleifera material and provide molecular resources for germplasm characterization and conservation sampling.

Biology doi: 10.3390/biology15211954

Authors: Wanjia Chen Luyang Zhou Rongpei Zhong Feng Tang Wenye Zhu Yinzhao Zhang Beiping Tan Junming Deng

Antarctic krill (Euphausia superba) meal is a valuable aquafeed ingredient, but its chitin-rich exoskeleton may limit nutrient utilization. A 12-week trial evaluated fishmeal-based diets containing 0, 1.5%, 3.0%, or 6.0% chitin in hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂). Dietary chitin did not significantly affect survival or growth. However, feeding rate and feed conversion ratio initially increased and then decreased, while protein efficiency ratio declined at all supplemented levels. At 1.5%, intestinal chitinase activity and IL-1β, TNF-α, and IL-6 were reduced. At ≥3.0%, serum T-BIL content, AST and ALT activities, AST/ALT ratio, plasma LPS content and DAO activity increased, whereas intestinal MPS, LZM, IgM, TGF-β1, IFN-γ, and IL-8 decreased. At 6.0%, lipase activity was further reduced. Some hepatic immune markers declined at 1.5% dietary chitin, while others decreased only at higher levels. In contrast, IL-10 increased at ≥3.0%, indicating altered hepatic immune homeostasis rather than generalized immunosuppression. Hepatic antioxidant capacity decreased at 6.0%. Dietary chitin ≥ 1.5% also reduced muscle hardness, gumminess, and chewiness. These findings indicate that even at the lowest tested inclusion level (1.5%), dietary chitin affected feed utilization and muscle texture, highlighting the need for further investigation of inclusion levels below 1.5%.

Biology doi: 10.3390/biology15211953

Authors: Linrong Wan Bowen Yin Rui Xi Yuanyuan Wen Lin Wang Mengyan Liu Xiaoling Tong Dingpei Long Fangyin Dai

Ribosomal protein S6 kinase (S6K) is a conserved effector of the mTOR signaling pathway that regulates cell growth and metabolism. The organism-level function of S6K in the silkworm Bombyx mori has not yet been examined by direct genetic manipulation. Here, we combined CRISPR/Cas9-mediated knockout, piggyBac-based transgenic re-expression and overexpression, and multi-tissue RNA-seq with weighted gene co-expression network analysis (WGCNA) to characterize the role of BmS6K in vivo. BmS6K-null mutants were viable but showed 26.5% and 28.6% reductions in pupal weight in males and females, respectively. Furthermore, mutant survival rates were 44.2% (males) and 28.5% (females) lower than those of controls, with mortality concentrated at the late fifth larval stage. Targeted transgenic re-expression rescued these phenotypic defects. Conversely, overexpressing BmS6K in a wild-type background increased the larval growth rate by 16.9% and significantly raised both whole cocoon weight and pupal weights. WGCNA of the three tissue types identified a core co-expression module (MEred) that was significantly enriched for genes involved in proton-transporting V-type ATPase activity and vacuolar complex assembly, mTOR signaling, and oxidative phosphorylation coupled to cellular redox homeostasis, including BmV1-ATPase, BmGabaT, and BmNadDac, whose orthologs represent core components or mediate critical cross-talk in the TOR-S6K pathway, a function conserved in Drosophila and mammals. Since the loss and gain of BmS6K produced opposite effects on growth and viability, it can be regarded as a candidate target for increasing cocoon yield in sericulture, as well as a target for RNAi-based control of lepidopteran pests through the suppression of its orthologs.

Biology doi: 10.3390/biology15211952

Authors: Mohammad S. Alawfi Dhafer A. Alzahrani Enas J. Albokhari Reem S. Aloufi

The Vachellia tortilis subsp. tortilis is a dryland tree included in the Fabaceae family. The genus Vachellia includes 164 species, 38 subspecies, and 25 varieties. The taxonomic placement of Vachellia has historically been unstable; the genus was only recently segregated from Acacia. In this study, we sequenced and characterized the chloroplast genome of V. tortilis subsp. tortilis and compared it with those of related species. The total chloroplast genome length of V. tortilis subsp. tortilis was 164,956 bp, and it contained 132 genes: 87 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. Simple repeat analysis showed that the chloroplast genome of V. tortilis subsp. tortilis contained 273 repeats. Codon usage bias analysis showed that the chloroplast genome of V. tortilis subsp. tortilis encoded 24,633 codons. The phylogenetic analysis revealed two distinct clades in the genus Vachellia: the first comprises V. tortilis subsp. tortilis and Vachellia tortilis subsp. raddiana, while the second includes Vachellia flava, Vachellia seyal, and Vachellia nilotica. This study improves knowledge of evolutionary relationships in the genus Vachellia and provides valuable genetic resources.

Biology doi: 10.3390/biology15211951

Authors: Sandra Chishimba Raffi Gugasyan Stephen J. Rogerson James G. Beeson

Background: Neutrophils play an essential role in pathogen clearance and can also contribute to pathogenesis and inflammation. Phenotypic changes of neutrophils during infection or inflammation may be associated with their functional activity. However, investigation of neutrophil phenotypes and functions in clinical studies is challenging because of their short viability ex vivo and difficulties in effectively cryopreserving neutrophils for subsequent analyses. Methods: We isolated neutrophils from human peripheral blood and evaluated different approaches for cryopreservation. We examined labelling of cell surface receptors of interest, including CD64, CD32, CD16, CD54, CD66b, CD62L and CD14, on fresh versus cryopreserved neutrophils by flow cytometry. Trypan blue staining was used to assess cell viability and membrane integrity. Results: We developed a neutrophil cryopreservation protocol that preserved cell immunophenotypes for downstream evaluation. All cell surface receptors tested could be labelled and quantified using flow cytometry. There were some differences in levels of surface staining for some receptors when comparing fresh and cryopreserved cells, but these differences did not interfere with the immunophenotypic evaluation of neutrophils. Discussion: Overall, the data suggest that our neutrophil cryopreserving and thawing protocols can preserve neutrophil surface receptors relevant to functions and phenotypes and are methods suitable for use in clinical studies.

Biology doi: 10.3390/biology15211950

Authors: Min Xu Hongmei Li Yong Liu Jiahao Wang Lijian Xue Jianzhong Ling Huiyu Li

Solenocera crassicornis (H. Milne Edwards, 1837) and Solenocera koelbeli De Man, 1911 are two commercially important shrimp species in the coastal waters of China; however, their inter-annual variation, seasonal spatial habitat use, and environmental niche differentiation remain poorly understood. Based on fishery-independent bottom-trawl surveys conducted over 21 cruises from November 2018 to January 2026 in the Southern Yellow Sea and East China Sea, we integrated Tweedie generalized additive models (GAMs) and boosted regression trees (BRTs) to generate habitat suitability index (HSI) model outputs and examine the observed spatiotemporal patterns and environmental niches of the two species. Model outputs yielded hold-out AUC-ROC values > 0.75; the models showed moderate to good temporal generalization but weaker spatial generalization, particularly for S. crassicornis. Field observations showed that S. crassicornis is a nearshore species whose distribution is primarily driven by sea surface temperature, sea bottom temperature and sea bottom salinity; it exhibited seasonal distributional shifts, with higher occurrence at northern latitudes (32–35° N) in summer and more southerly distribution in winter. S. koelbeli was a deep-water, high-salinity species mainly associated with sea bottom salinity and depth, found at 50–100 m and virtually absent from low-salinity estuarine waters, with high occurrence in autumn–winter and late spring. Both shrimp species shared core habitats (Zhoushan, Yushan and Wentai) but displayed temporal, spatial, and environmental niche partitioning according to our observations and model outputs. These findings provide scientific references for resource conservation and fishing ground management. Potential seasonal protection windows for broodstocks (June–September) and recruitment stocks (December–February) are proposed based on field observations and correlative model outputs, although these require further empirical validation.

Biology doi: 10.3390/biology15211949

Authors: Zhuo Bao Pengfei Diao Wei Shao Anar Bao Aminna Bai Hada Wuriyanghan Lele Li

Plant viral diseases cause severe yield losses in global crop production. SRC7, a novel soybean TIR-NBS-BSP-type resistance (R) protein, confers broad-spectrum antiviral immunity against multiple viruses including soybean mosaic virus (SMV), tobacco mosaic virus (TMV), potato virus Y (PVY), and plum pox virus (PPV). Its TIR-NBS domain (SRC7TN) mediates full antiviral resistance, making it an ideal bait for screening immune-related proximal candidate proteins. In this study, TurboID-based proximity labeling (PL) was applied to profile the SRC7TN proximal candidate proteins in N. benthamiana. We identified 262 high-confidence proximal candidate proteins, which were mainly enriched in plant immune signaling, redox regulation, protein modification and nuclear-related pathways. Among them, 21 candidates were functionally characterized, revealing multiple host factors contributing to SRC7-dependent antiviral immunity. Eleven interactions were confirmed via bimolecular fluorescence complementation (BiFC), and two nucleoside/nucleotide hydrolase-family proteins MZN14.5 and RIHA were subjected to further interaction-domain analysis. Collectively, this work constructs a high-confidence SRC7TN proximal-interaction network and highlights critical host factors in SRC7-mediated broad-spectrum antiviral immunity. It also validates TurboID’s utility for screening for NLR-proximal candidate proteins in heterologous plant systems and provides insights into R-protein-governed plant antiviral defense.

Biology doi: 10.3390/biology15211948

Authors: Chao Chen Mengli Cao Liyan Hu Xiaoyin Wang Ziqiang Ding Jiao Lin Shaoke Guo Jie Pei Xian Guo

INHA encodes the α-subunit of inhibin A and inhibin B and is involved in the regulation of male reproductive endocrinology; however, its cellular function in yak Sertoli cells remains poorly understood. In this study, primary yak Sertoli cells from 3-month-old donors were used to establish INHA overexpression and knockdown models, followed by RNA sequencing (RNA-Seq), directDIA quantitative proteomics, integrated transcriptome–proteome analysis, and functional assays. Donor-aware, false discovery rate (FDR)-controlled analyses identified 949 differentially expressed genes (DEGs) and 1388 differentially abundant proteins (DAPs) following overexpression, and 28 DEGs and 54 DAPs following knockdown. The two manipulations produced non-equivalent molecular responses under their respective experimental conditions. Functional enrichment analyses highlighted cytokine-related signaling, DNA replication and cell-cycle regulation, energy metabolism, and cell–matrix-related responses. TNF signaling was significantly enriched at both omics levels, whereas NF-κB signaling was significantly enriched at the transcriptomic level. Integrated analysis identified 98 molecules altered at both the mRNA and protein levels after INHA overexpression, of which 96 showed concordant changes. CCL2, CCL5, IL1RL1, LIF, CTSC, HK2, FN1, and ITGA11 were prioritized as representative INHA-responsive candidates, while quantitative reverse transcription PCR (qRT-PCR) supported selected transcript-level changes. Flow cytometry showed that INHA overexpression was associated with increased apoptosis and a lower proportion of viable cells, whereas knockdown produced the opposite pattern. β-Tubulin immunofluorescence revealed qualitative differences in microtubule staining patterns. These results characterize molecular and cellular responses associated with INHA perturbation and prioritize candidate pathways and molecules for further investigation in yak Sertoli cells.

Biology doi: 10.3390/biology15211947

Authors: Dan Wang Mengyang Pan Junxiang Mu Yanhong Ma Mengyuan Zhong Zerong Zhang Jiale Zhang Yao Chen Tuanrong Lin Yiqian Wang Longqiu Fan Xinlei Jiao Zhicheng Zhang

Potato (Solanum tuberosum L.) is the fourth largest food crop in the world, and drought stress seriously affects its yield and quality. Plant non-specific lipid transfer proteins (nsLTPs) play an important role in resisting biotic and abiotic stresses. Although the functions of nsLTPs have been reported in crops such as rice (Oryza sativa L.) and Arabidopsis thaliana, the systematic identification and functional analysis of nsLTPs in potato, a key food crop sensitive to drought, remain very scarce. In this study, the whole genome identification, drought stress expression analysis and potential function prediction of the potato StnsLTP gene family were carried out by bioinformatics and real-time quantitative polymerase chain reaction (RT-qPCR). A total of 123 potato StnsLTP genes were identified, which were unevenly distributed on 11 chromosomes. The encoded amino acid length was 88–390 aa, and 91.1% of StnsLTP proteins were hydrophobic. Conserved motif analysis showed that motif 4 was the most important conserved motif in this family. There were 0–4 introns and 1–4 exons. The family identified 45 pairs of tandem duplicated genes and 20 pairs of segmentally duplicated genes, and the nsLTP potato genes showed close phylogenetic relationships with tomato nsLTP genes. Combined with transcriptome data, three PEG-responsive candidate genes, StnsLTP.115, StnsLTP.117, and StnsLTP.118, were screened. After polyethylene glycol 6000 (PEG 6000) simulated drought treatment, the three genes showed different degrees of induced expression in the roots, stems and leaves of the three potato cultivars, and their expression differed markedly across cultivars, tissues and sampling time points. This study systematically elucidated the structure and evolutionary characteristics of the potato StnsLTP family, and identified three candidate genes responsive to PEG-simulated drought stress. This not only provides a basic reference for the functional study of the potato StnsLTP family, but also offers clues for analyzing potato drought response pathways and exploring candidate genes for potato stress response research.

Biology doi: 10.3390/biology15211946

Authors: Hongjun Zhou Luying Ye Yahong Xing Runsheng Zhang Haixia Lu Linting Zhang Rongli Liao Ruiyi Jiang Libin Zhuang Chuanyuan Deng

Urban park plant communities comprise cultivated and spontaneous species, but whether their beta-diversity drivers differ and whether urbanization homogenizes or differentiates composition remains unclear. We surveyed 102 plots in 21 parks along a coastal island-to-mainland gradient in Fuzhou, China. We partitioned taxonomic, functional and phylogenetic beta-diversity into turnover and nestedness, related them to environmental, anthropogenic and spatial predictors using Mantel tests, variation partitioning and db-RDA, and modeled local contributions (LCBD) using mixed models and structural equations. Turnover dominated both groups, with higher turnover and lower nestedness in cultivated plants. Cultivated functional and phylogenetic nestedness rose with distance (p < 0.01), whereas spontaneous nestedness fell across all dimensions (p < 0.05); the slopes differed significantly in all three dimensions. Taxonomic beta-diversity exceeded functional and phylogenetic, and LCBD synchronization was taxonomic only. Landscape configuration and anthropogenic factors drove cultivated beta-diversity, whereas spontaneous beta-diversity related to spatial structure, park area and elevation. Marine exposure lost significance for most responses once space was controlled. Composition varied among regions; island plots the most concentrated; LCBD depended on park area for spontaneous plants and on landscape configuration for cultivated ones. The two kinds of turnover reflect different processes, ecological replacement and planting decisions, and require parallel management.

Biology doi: 10.3390/biology15211944

Authors: Yue Qiao Ye Du Zhiheng Wang Huayong Shi Junjie Wang

Pyrabactin resistance-like (PYL) proteins are core abscisic acid (ABA) receptors, but their organization and stress-responsive functions remain poorly understood in broomcorn millet (Panicum miliaceum L.). Here, we identified PmPYL genes genome-wide and characterized their phylogeny, gene structure, conserved motifs, chromosomal distribution, synteny, selection pressure, promoter cis-elements, predicted regulatory networks, tissue expression, and responses to ABA, salinity, and osmotic stress. Fifteen PmPYL genes were identified, with eight located in the A subgenome and seven in the B subgenome. Phylogenetic analysis placed 11 PmPYL proteins in Group II and four in Group III, with none in Group I. Sequence and structural analyses revealed broad conservation of receptor features associated with ABA perception and PP2C interaction. Collinearity analysis identified seven synteny-supported A/B homoeologous pairs, while the examined duplicate pairs showed low Ka/Ks ratios. Promoter analyses revealed abundant hormone- and stress-responsive elements, while predicted protein interactions supported a conserved PYL–PP2C–SnRK2 signaling module. Pairwise promoter and tissue-expression comparisons indicated regulatory variation among retained homoeologs. qRT-PCR analysis of seedling leaves further showed distinct treatment- and time-dependent expression patterns, with PmPYL10, PmPYL8, and PmPYL12 showing pronounced changes under the examined conditions. These findings reveal a conserved ABA receptor framework with substantial regulatory diversification and identify candidate PmPYL genes for functional analysis of stress adaptation in broomcorn millet.

Biology doi: 10.3390/biology15211945

Authors: Meir Finkel Ariel Leib Leonid Friedman Gilad Ben Zvi Orr Comay

Insects are understudied in the Eastern Mediterranean, a region with heterogeneous biotas facing rapid regional warming and land-use changes. It is essential to establish a baseline for insect monitoring, including the extent of spatial, inter-annual, and seasonal variations in insect diversity and composition—all prominent in the Mediterranean. To assess these, we conducted an intensive three-year (2022–2024) sampling of ants and plant-dwelling beetles at three sites along Mt. Meron’s maquis-covered western slopes (Galilee, Israel, at 550, 850, and 1050 m above sea level), with similar tree, shrub, mammal, and bird communities. Results show high inter-annual variability of beetle species (~15% of species were collected in all three years; ~ 65% only in one of the study years), and a lesser but still significant spatial variation between sites (~50% in only one of the sites; 20% in all sites). In both respects, 30 collection events have not reached 90% of the total multi-annual detected species list. In ants, similar but less pronounced results were found. These findings underscore the need for a multi-year, multi-site intensive sampling effort to compile a complete species list as a baseline for trend monitoring of the Mediterranean maquis and warrant a discussion on its methodology.

Biology doi: 10.3390/biology15211943

Authors: Yanfang Lu Jie Wang Jian Ma Chunxi Zhang Na Li Xing Li Junping Mao Weiling Zhen

The desert–oasis ecotone is ecologically fragile, yet the profile-scale role of the Dry-Sand Layer (DSL) in regulating soil moisture stratification and plant community assembly remains poorly understood. We systematically investigated six representative sites across the middle Heihe River Basin (with soil types transitioning from silt loam to aeolian sandy soils), combining multi-depth soil hydro-physical profiling (0–120 cm) with comprehensive vegetation sampling (across 90 nested quadrats recording 37 vascular plant species). A distinct DSL commonly formed at 60–80 cm depth across sandy sites, characterized by a bulk density of 1.39 g. cm−3 and a distinct moisture trough (typically < 2.0%), decoupling shallow root zones from subsoil moisture pools (1.10% to 5.09%). This edaphic boundary filtered out deep-rooted species, restricting vegetation to shallow-rooted xerophytic shrubs and grasses (e.g., Reaumuria soongarica (Pall.) Maxim., Aristida adscensionis L.) exhibiting high interspecific niche overlap (>0.86) and clustered spatial patterns (C > 1). Structural equation modeling indicated that subsoil moisture regulated by the DSL directly drives plant community diversity (path coefficient β = +0.54) and coverage (β = +0.61). Overall, the DSL serves as an essential eco-hydrological buffer balancing shallow soil moisture retention and subsoil conservation, indicating that ecological restoration in hyper-arid ecotones should prioritize DSL preservation and native shallow-rooted vegetation.

Biology doi: 10.3390/biology15211942

Authors: Sergio Guzmán-Rodríguez Judith Nwaiwu Cristian D. Gutierrez-Reyes Carlos H. López-Lariz Ricardo Romero-Guevara Favour Chukwubueze Oluwatosin Daramola Tuli Bhattacharjee Yehia Mechref Bruno A. Marichal-Cancino

Cafeteria diet, rich in fat and sugar, rapidly induces metabolic dysfunction and alters central energy regulation. We examined behavior and hypothalamic protein abundance profiles in cafeteria-diet-fed rats classified into weight-gain quartiles (Q1–Q4) and compared with standard-chow-fed controls. Pre-adolescent male Sprague–Dawley rats (n = 39:10 controls; Q1–Q4, n = 7–8 each) received ad libitum access to standard chow or a palatable cafeteria diet and underwent open field testing followed by quantitative LC–MS/MS proteomics of the hypothalamus. Behavioral assessment showed no major differences in locomotion, anxiety-like parameters, or exploration, except for reduced grooming (p ≤ 0.05) in cafeteria-fed versus control animals. Global, threshold-independent analyses showed that the lower-weight-gain phenotype (Q1) was significantly more distant from controls than the higher-weight-gain phenotype (Q4) (multivariate distance to the control centroid; Mann–Whitney U, p = 0.006), a pattern also observed by principal component analysis and hierarchical clustering. Consistently, of 17 proteins that remained significant after false discovery rate correction, 16 differed between Q1 and control and only one between Q4 and control, despite both phenotypes having ad libitum access to the same cafeteria diet. These findings suggest that lower weight gain is associated with more extensive hypothalamic protein abundance changes, although a causal link remains to be established, and they highlight candidate pathways for future mechanistic studies.

Biology doi: 10.3390/biology15211941

Authors: Maria Pia Santacroce Adriana Lo Giudice Valeria Buonfrate Rosa Leone Marco Cordisco Claudia Castorani Nicola Zizzo Antonella Tinelli

In marine teleosts, neurotoxicity and neuropathology research is currently constrained by a lack of validated in vitro models. Although zebrafish embryonic cell cultures provide a well-established platform for investigating the cellular and biochemical mechanisms governing neuronal growth and differentiation, comparable models for marine species remain sparse. To address this methodological gap, the present study establishes a primary neuroglial cell culture system from the brain of the gilthead seabream (Sparus aurata) to investigate central nervous system (CNS) neurogenesis by characterizing the morphological, immunophenotypic, proliferative, and migratory properties of radial glial (RG) cells and their neuronal progeny. This in vitro model likely recapitulates native CNS tissue architecture, enabling the detailed examination of neural stem cell cleavage modes, stem cell niche dynamics, and radial glial scaffolding. Our findings demonstrate that seabream RG cells may act as multipotent neural stem cells, generating young neurons through asymmetric division and directing their migration along radial glial fibers. Cells actively undergoing neurogenesis within the central zones of RG colonies exhibited co-localization of PCNA and UCHL1 immunoreactivity, confirming their active proliferative state. After 3 weeks in vitro, the central core of the colonies retained proliferative stem cell niches driving ongoing neurogenesis, whereas the peripheral regions comprised differentiated GFAP-positive astrocytes interwoven with extended neuronal processes. Furthermore, time-lapse imaging of nuclear kinetics provided direct visual confirmation of neuroblast locomotion along RG scaffolding, during which migrating neuroblasts exhibited sequential nuclear dilation and elongation as structural hallmarks of active movement. These in vitro proliferative dynamics closely mirror the permanent neural plasticity of the teleost brain, constituting a valuable tool for comparative neurobiology and neurotoxicology, as well as a potentially useful resource for models of central nervous system repair.

Biology doi: 10.3390/biology15211940

Authors: Jianguo Liu Jiaxin Liu Chunfeng Chen Yukun Wang Bin Wang Huimin Feng Shiwei Song Yunna Zhu

DNA-binding with One Finger (DOF) transcription factors play crucial roles in modulating plant growth, development, and environmental stress responses. However, the DOF family in flowering Chinese cabbage (Brassica campestris) remains poorly characterized. Here, 67 BcDOF genes were identified in B. campestris, distributed nonuniformly across ten chromosomes and classified into nine subfamilies. Structural analyses revealed that all BcDOF proteins harbor a conserved zinc-finger DOF (zf-DOF) domain, with members within individual subfamilies generally sharing similar motif architectures and exon–intron structures. Evolutionary analyses indicated that whole-genome triplication and segmental duplication were the major drivers of BcDOF family expansion, while purifying selection contributed to the evolutionary conservation of duplicated gene pairs. Promoter analysis revealed abundant cis-acting elements related to hormone signaling and abiotic stress responses. Reverse transcription quantitative real-time PCR (RT-qPCR) further demonstrated that many BcDOF genes responded to heat and osmotic stresses. Among them, BcDOF56 was markedly induced by both heat and drought and localized to the nucleus. Heterologous overexpression of BcDOF56 in Arabidopsis significantly improved heat and drought tolerance, as indicated by reduced thiobarbituric acid reactive substances (TBARS) accumulation and elevated superoxide dismutase (SOD) activity relative to wild-type (WT) plants. Collectively, these findings advance our understanding of the evolutionary and functional divergence of the BcDOF family and highlight BcDOF56 as a potential target gene for improving abiotic stress tolerance in B. campestris.

Biology doi: 10.3390/biology15211939

Authors: Changan Chen Lingzhi Lei Yanfang Xu Zhimin Chen

Background: Autosomal dominant polycystic kidney disease (ADPKD) progression involves cyst expansion, interstitial remodeling, and progressive loss of renal function, but the cell-type-resolved programs linking cyst burden to tissue remodeling remain incompletely defined. Methods: We integrated the cyst-size-stratified human bulk transcriptomic dataset GSE7869 with the time-resolved Pkd1 single-cell dataset GSE268494. Differentially expressed genes were identified across small-, middle- and large-cyst groups, modeled by Mfuzz temporal clustering, prioritized by protein–protein interaction topology and functional enrichment, and further evaluated by immune deconvolution, single-cell mapping, AUCell pathway scoring and CellPhoneDB ligand–receptor inference. Results: We identified 3842 shared differentially expressed genes and two dominant monotonic modules. The progressively upregulated module was enriched for extracellular-matrix organization, adhesion, and fibrosis-associated genes, including COL1A1, COL5A2, FBN1, BGN, LAMC1, HSPG2, MMP2, LOX, and ITGA5. The progressively downregulated module highlighted tubular transport, proton transport, and mitochondrial/metabolic genes, including SLC12A3, AQP2, ATP5A1, ATP6V0C, ATP6V1B1, NDUFV1, REN, and AGT. Single-cell analyses localized the matrix module mainly to fibroblast/stromal compartments and the transport/metabolic module to segment-specific tubular epithelial populations. Immune deconvolution and ligand–receptor inference further implicated macrophage-associated remodeling and TGFB1-, CD47-, CD200-, PECAM1- and TNF-superfamily-related immune-parenchymal communication. Conclusions: ADPKD progression is associated with coordinated ECM/immune remodeling and tubular metabolic failure, providing candidate markers and communication axes for future spatial and functional validation.

Biology doi: 10.3390/biology15211938

Authors: Cheng Qiu Ziqing Guo Qin Zhou Qianwen Ge Xifeng Chen

YABBYs are transcription factors involved in fruit development, leaf polarity establishment, and adaptation to stresses in plants. Bitter gourd (Momordica charantia L.) is an important cucurbit crop, but YABBY genes have not been reported in this species. In this study, the YABBY gene family of bitter gourd was digitally identified using its T2T genome, and the sequence characteristics, phylogenetic relationships, and expression profiles of each gene member were analyzed through bioinformatic and experimental approaches. A total of eight YABBY homologous genes, designated McYABBY1 (Momordica charantia YABBY1) to McYABBY8, were identified and clustered into five clades in the phylogenetic tree, each showing a clear orthologous relationship to a corresponding Arabidopsis gene. RNA-seq data and RT-qPCR revealed distinct expression patterns among McYABBY genes across various organs and fruit developmental stages. Notably, McYABBY3 and McYABBY8 are actively and constitutively expressed during fruit ripening. Additionally, RT-qPCR showed that members of the McYABBY gene family exhibit differential expression in response to abiotic stress, with six up-regulated and two down-regulated under salt stress, and five up-regulated, two down-regulated, and one relatively unchanged under PEG-induced osmotic stress. These findings provide a basis for future functional studies and breeding applications of McYABBY genes in bitter gourd.

Biology doi: 10.3390/biology15211937

Authors: Shakta Mani Satyam Manasvi Udaya Kumar Ebrahim Safaii Shams Al-dawoodi Ilmia Shameer Rashmi Kumari Abdul Rehman Mohamed El-Tanani Afnan Afroz Anuradha Asokan Nair Karthik Nair Murk Jai Pal Paryani

Pantoprazole is widely used for the management of acid-related gastrointestinal disorders through inhibition of the gastric H+/K+-ATPase. Beyond its established acid-suppressive action, experimental studies have investigated its potential effects on cellular proton homeostasis, autophagy, oxidative and inflammatory signaling, cancer biology, antimicrobial resistance, glucose regulation, neurological responses, hepatic fibrosis, and iron-related outcomes. This narrative review critically examines these proposed biological effects and distinguishes established pharmacology from experimental mechanisms, preclinical findings, and human clinical evidence. Particular attention is given to the relationship between experimental concentrations and human exposure, the acid-dependent activation of pantoprazole, the distinction between direct molecular targets and downstream cellular responses, and the challenges of translating laboratory findings into clinical benefit. Pantoprazole also has a comparatively favorable CYP2C19-mediated drug-interaction profile relative to omeprazole and esomeprazole, although this advantage does not imply the absence of all clinically relevant interactions. The evidence across proposed repurposing indications remains heterogeneous, and biological activity in experimental models should not be interpreted as established therapeutic efficacy. Further exposure-informed mechanistic studies, pharmacokinetic and pharmacodynamic validation, and appropriately designed clinical trials are required to determine which proposed effects warrant clinical development. Pantoprazole should therefore be regarded as a candidate for mechanism-informed drug-repurposing research rather than an established treatment for the non-gastrointestinal indications discussed in this review.

Biology doi: 10.3390/biology15211936

Authors: Dongshun Fang Mengying Yang Qiyun Xie Zihan Zhang Mingjiang Wu Haibin Tong Binbin Chen

In the context of carbon peaking and carbon neutrality goals, large-scale macroalgal cultivation provides a sustainable source of marine biomass, whereas epiphytic algae, although often regarded as a constraint in seaweed farming, remain an underutilized resource. In this study, biomass of the epiphytic green alga U. lactuca was collected from the surface of cultivated S. fusiforme, processed into a concentrated aqueous extract, and applied to lettuce (Lactuca sativa var. longifolia) at dilution ratios of 1:600, 1:400, and 1:200. The results showed that the algal extract affected lettuce growth and quality in a concentration-dependent manner. The 1:600 treatment increased soluble sugar, soluble protein, and vitamin C contents by 134.25%, 31.65%, and 20.62%, respectively, while the 1:400 treatment produced the greatest increase in shoot biomass. The extract was also associated with changes in selected soil properties, including pH. High-throughput sequencing indicated that the treatment altered the composition of the rhizosphere-associated bacterial community, including shifts in the relative abundance of several taxa. Overall, these results suggest that appropriate application of epiphytic algal extract may serve as a promising improvement to lettuce growth and quality, with potential value for sustainable agricultural production.

Biology doi: 10.3390/biology15211935

Authors: Wenqing Jia Yukui Ma Xianchao Cheng Shuyu Luo

PIK3CA mutations drive tumorigenesis by activating phosphatidylinositol 3-kinase alpha (PI3Kα). The allosteric inhibitor STX-478 exhibits high selectivity toward PI3Kα and avoids adverse effects such as hyperglycemia. Hyperglycemia is the main reason for the limited clinical application of ATP-competitive PI3Kα inhibitors. To date, no allosteric PI3Kα inhibitors have been approved for clinical use. Consequently, developing novel allosteric PI3Kα inhibitors represents a promising therapeutic strategy for patients harboring PIK3CA mutations. This study establishes a workflow for discovering computationally prioritized allosteric PI3Kα inhibitor candidates, integrating virtual screening, multi-platform druggability evaluation, molecular dynamics simulations, metabolic pathways and metabolites analysis. We used virtual screening to identify computationally prioritized allosteric PI3Kα inhibitor candidates from a small molecule library based on the binding mode between STX-478 and PI3Kα, and further filtered compounds with favorable drug-like properties. Molecular dynamics simulations were carried out to assess the binding stability of these candidates with the protein. We also characterized the metabolic profile of the hit compound. Rosmarinic acid (an ester of caffeic acid and 3,4-dihydroxyphenyllactic acid compound) was screened out as a computationally prioritized allosteric PI3Kα inhibitor candidate. The CDOCKER energy of rosmarinic acid (−69.4529 kcal/mol) in complex with PI3Kα was lower than that of STX-478 (−66.7128 kcal/mol). Molecular dynamics simulations revealed that rosmarinic acid can stably bind to PI3Kα. ADMET prediction suggested that rosmarinic acid possesses favorable safety profiles and acceptable pharmacokinetic properties. This study lays a computational foundation for screening potential allosteric PI3Kα inhibitor candidates.

Biology doi: 10.3390/biology15211934

Authors: Marian Flis Krzysztof Łazowski Piotr Czyżowski Beata Hukowska-Szematowicz Natalia Brodalka Andrzej Fitzner

The long-term decline in European hare populations across Europe is linked to both environmental and anthropogenic factors. Among the factors influencing the population dynamics of lagomorphs, lagoviruses play a significant role. This study evaluated population indices and the presence of antibodies against EBHSV and RHDV2 in hares in Poland. A total of 109 individuals were examined from five regions where population density allowed for game management. Population indices were assessed, and the presence of antibodies was determined using ELISA tests with monoclonal antibodies. Body mass of hare was similar across all regions but differed significantly between juveniles and adults. Population growth rates were positive, while reproductive rates remained relatively low. Antibodies specific to EBHSV in hare were detected in all five regions—with an overall seroprevalence of 78.9%—indicating widespread prior exposure to this virus among the hares studied. RHDV2-reactive antibodies were found in 10.1% of the individuals. Given the risk of cross-reactivity and individual immune responses, results regarding RHDV2 should be regarded as serological evidence of possible exposure requiring further investigation. The findings provide serological evidence of lagovirus exposure in the examined hare populations even in areas with population densities sufficient for game management. These results underscore the importance of integrated hare population monitoring that combines traditional population metrics with serological surveillance, particularly regarding lagoviruses such as EBHSV and RHDV2.

Biology doi: 10.3390/biology15211933

Authors: Jin Li Qiaoxuan Li Hongcheng Li Xianmin Wang Tingting Duan

Rhizophora stylosa seedlings were grown at three initial NaCl levels (0, 100 and 400 mM), with individual or combined iron, manganese and zinc sulfate supplementation at the two saline levels. Eleven treatments comprised three independent pots each. Growth, root architecture, photosynthesis, tissue elements and biochemical responses were assessed after 90 days. Relative to SCK, the high-salt control receiving basal nutrients without supplemental micronutrients, combined Fe + Mn + Zn (SFeMnZn) increased the dry mass by 29.8%, net photosynthetic rate by 67.0% and total root length by 133.1% (all adjusted p < 0.01). Maximum photosystem II photochemical efficiency increased from 0.659 to 0.795 (adjusted p < 0.001). Zn produced the strongest overall growth response among individual supplements, although their dry-mass differences were not significant. Combined supplementation increased tissue micronutrient concentrations, reduced oxidative injury and altered antioxidant and osmolyte responses. Leaf RNA sequencing of SFeMnZn versus SCK identified 1024 differentially expressed transcript entries associated with photosynthetic, redox, carbon-metabolic and cation-exchange processes. The findings support evaluation of the tested sulfate supplementation regime for controlled nursery cultivation and identify molecular candidates for further investigation.

Biology doi: 10.3390/biology15211932

Authors: Laura Židek Jozefíková Anirban Jyoti Debnath Martina Gregorová Peter Nemeček Petra Ranušová Monika Šutáková Miroslava Sinčák Pavol Hauptvogel Ildikó Matušíková

Wheat cultivars differ markedly in their responses to cadmium (Cd), but it remains unclear how these differences are reflected across physiological and biochemical levels. This study investigated the physiological, enzymatic, and phenolic responses of three Slovak wheat cultivars representing different genomic backgrounds (tetraploid emmer wheat Zirnitra and hexaploid bread wheat Sunanka, and Ilona) exposed to 50 mg L−1 Cd2+ (as CdCl2) for 10 days, integrating growth and pigment responses with Cd accumulation, subcellular partitioning, pathogenesis-related (PR) enzyme activities, and targeted profiling of phenolic metabolites. Cd similarly reduced shoot fresh weight in all cultivars, while chlorophyll content declined significantly in Sunanka and Ilona but remained stable in Zirnitra. All cultivars strongly restricted root-to-shoot Cd translocation, with Cd predominantly recovered in the combined cytosolic/vacuolar fraction. The integrated analysis revealed particularly pronounced cultivar-specific differences in phenolic profiles. Sunanka shoots showed a reciprocal rutin (RUT)–quercetin (QUER) response, with RUT becoming undetectable and QUER strongly accumulating, whereas Ilona roots showed depletion of trans-ferulic acid and chlorogenic acid accompanied by marked protocatechuic acid accumulation. In Zirnitra roots, RUT increased markedly, and root RUT was positively associated with Cd accumulation after FDR correction. PR-enzyme activities also responded in a cultivar-, tissue-, and activity-band-specific manner. Overall, the findings demonstrate that similar growth inhibition and restricted Cd translocation can coexist with distinct biochemical responses in wheat cultivars of different genomic backgrounds, highlighting root rutin accumulation as a candidate for further investigation in relation to Cd exposure.

Biology doi: 10.3390/biology15211931

Authors: Cemal Turan Alen Soldo Ali Uyan

Mediterranean sharks, rays, and chimaeras face substantial conservation pressures, yet comparative regional assessments integrating life-history, ecological, and fisheries-related traits remain limited. We compiled and standardized 1634 species-specific data points for 80 species and applied a multi-criteria framework to estimate resilience (R) and vulnerability (V), followed by an Index of Resilience and Vulnerability (IRV) assessment. Based on the predefined trait framework, 46 shark, 32 ray, and 2 chimaera species were assessed. Mean R and V scores were 1.80 and 2.27 for sharks, 1.85 and 2.38 for rays, and 1.64 and 2.10 for chimaeras, respectively. Mean IRV was highest in sharks (0.17), followed by rays (0.16) and chimaeras (0.16). Across all species, R scores ranged from 1.29 to 2.57, V scores from 1.60 to 3.00, and IRV scores from 0.05 to 0.37. No species occurred in the comparatively high-resilience, low-vulnerability region of the R–V space. Several shark species exhibited particularly low IRV scores, while Dipturus nidarosiensis and D. batis showed the highest vulnerability among rays. IRV increased with R and decreased with V, as expected from the mathematical construction of the index. Comparisons with FishBase revealed broadly similar vulnerability patterns, whereas the IRV scores provided a complementary continuous perspective on species-level resilience and vulnerability. The IRV framework provides a comparative trait-based approach for regional prioritization of Mediterranean cartilaginous fishes.

Biology doi: 10.3390/biology15211930

Authors: Yangyang Cao Qian Gao Wendi Wang Zhiwei Fan Jun Wang Weibing Wu

Skeletal muscle dysfunction is the most common extrapulmonary complication of chronic obstructive pulmonary disease (COPD) and has a significant impact on patients’ exercise capacity, quality of life, and survival. Although previous studies have elucidated some of the mechanisms underlying COPD-associated skeletal muscle dysfunction, the specific pathways through which COPD causes skeletal muscle injury remain to be fully explored. In patients with COPD, pathological factors such as long-term smoking, chronic inflammation, oxidative stress (OS), and pyroptosis can stimulate the release of high-mobility group box 1 (HMGB1), a classical damage-associated molecular pattern (DAMP), into the extracellular space. HMGB1 then binds to relevant receptors, triggers downstream responses, and activates pyroptosis. Characterized by inflammasome activation, membrane pore formation, and the release of pro-inflammatory mediators, pyroptosis is thought to play an important effector mechanism linking persistent inflammation to skeletal muscle injury. An in-depth analysis of the relationship between aberrant activation of the HMGB1–pyroptosis pathway and COPD-associated skeletal muscle dysfunction may help identify urgently needed new therapeutic strategies. Therefore, this article explores the molecular mechanisms of the HMGB1–pyroptosis pathway, summarizes current research on its role in COPD-associated skeletal muscle dysfunction, and discusses relevant intervention strategies, providing a theoretical basis for targeting this pathway to treat COPD-associated skeletal muscle dysfunction.

Biology doi: 10.3390/biology15211929

Authors: Yanping Zhang Yulu Sun Xin Zhai Jie Zhou Li Liu

Marine heatwaves (MHWs) are escalating threats to coral reef ecosystems, yet the host transcriptomic mechanisms underlying acclimatization to repeated thermal stress remain poorly understood. Using de novo RNA sequencing, we tracked the temporal transcriptomic responses of the scleractinian coral Turbinaria peltata across two consecutive MHW-recovery cycles. The second heatwave elicited fewer differentially expressed genes (DEGs) than the first (279 vs. 379), whereas the second recovery phase showed the largest DEG set (399). Functionally, the first heatwave triggered acute stress defense and signal suppression, while the first recovery engaged extracellular matrix remodeling and calcium-mediated tissue repair, indicating incomplete restoration. The largest DEG set during the second recovery indicates that recurrent thermal stress imposes cumulative physiological costs demanding more extensive molecular reorganization—spanning metabolic reprogramming, mTOR and Wnt signaling, and sustained oxidative-stress management. Together with prior physiological and microbiome evidence in this species, our results support a model in which repeated heat exposure progressively shifts the coral host from acute shock defense responses toward compensatory metabolism and structural repair. Recovery thus emerges as an active but increasingly costly molecular adjustment under recurrent MHW regimes. These findings identify candidate molecular markers for evaluating coral resilience under intensifying MHW regimes.

Biology doi: 10.3390/biology15211928

Authors: Yanan Guo Wanru Li Yiyi Zhao Shoutao Zhang Weiyu Zhao

Background: Planarian neoblasts are pluripotent adult stem cells responsible for whole-body regeneration, yet antibody-based tools for their specific identification and isolation remain limited. This study aimed to generate a high-affinity single-chain variable fragment (scFv) targeting TSPAN-1, a neoblast surface marker, using phage display technology. Methods: A phage-displayed scFv library (3.86 × 107 CFU) was constructed from mice immunized with the recombinant large extracellular loop (LEL) of TSPAN-1 fused to maltose-binding protein (MBP). Four rounds of bio-panning were performed against immobilized His-LEL. Positive clones were screened by ELISA, colony PCR, and DNA sequencing. Among the characterized clones, scFv-16 showed the highest apparent affinity. This clone was subcloned for prokaryotic expression, and inclusion body proteins were refolded and purified. Results: Friguet analysis gave an apparent affinity constant (Kaff) of 4.20 × 108 M−1 for scFv-16 binding to His-TSPAN-1. This corresponds to a KD of 2.38 nM. Western blotting and immunofluorescence staining supported the specificity of scFv-16 for TSPAN-1. Conclusions: A high-affinity anti-TSPAN-1 scFv was successfully generated, providing a candidate molecular tool for neoblast identification and potential isolation in planarian regeneration studies.

Biology doi: 10.3390/biology15211927

Authors: Luciano Arellano-Arriagada Ayelen Antonella Baillo Leonardo Albarracin Solange Cisterna-Vergara Xi-Chen Bai Wenxiao Du Weichen Gong Yoshihito Suda Haruki Kitazawa Julio Villena

Respiratory viral infections remain a major health concern, highlighting the need for strategies that enhance host antiviral defenses. Lacticaseibacillus rhamnosus CRL1505 has demonstrated beneficial immunomodulatory effects in the respiratory tract; however, its direct effects on distinct respiratory cell populations remain incompletely characterized. Here, we evaluated the capacity of live and HK 1505 to modulate antiviral immunity in porcine bronchial epithelial (PBE) cells challenged with SIV and porcine alveolar macrophage (PAM) cells infected with PRRSV. Pretreatment with either live or HK 1505 significantly reduced infectious SIV titers in PBE cells and decreased PRRSV ORF5 expression and viral antigen detection in PAM cells, accompanied by enhanced expression of interferons and antiviral factors in both models. CRL1505 also differentially modulated inflammatory responses according to the cell type. In PAM cells, both treatments enhanced proinflammatory and regulatory cytokines, whereas in PBE cells they selectively increased IL-1β and IL-6 while reducing TNF-α, IL-8, and MCP-1. Negative regulators of innate immune signaling were also differentially modulated in both cell types. Importantly, HK 1505 retained significant antiviral and immunomodulatory activities, inducing responses that were generally similar to those observed with the viable preparation under the experimental conditions evaluated. These findings demonstrate that L. rhamnosus CRL1505 enhances antiviral responses in two distinct respiratory cell models, with differences in immunomodulatory profiles that may reflect the combined influence of cellular and viral contexts.

Biology doi: 10.3390/biology15211926

Authors: Qiaosen Shen Huaqing Lan Shasha Wei Jiahui Li Xiaoyan Lin Shujuan Li Feng Zhao

Zebrafish serve as a vertebrate model for assessing environmental neurotoxicity and exploring neurobehavioural phenotypes. However, rapid detection systems for larval zebrafish social preference are still lacking, which restricts efficient behavioural phenotyping and toxicological screening. Here, we developed and validated a 3D-printed three-chamber social preference assay for larval zebrafish that is fully compatible with the Noldus behavioural analysis platform. We confirmed that 14 days post fertilisation (dpf) zebrafish larvae display social preference toward conspecifics, whereas 7 dpf larvae have no significant social bias, defining the key developmental time window for larval social preference. The utility of this method was validated using multiple chemical and genetic models. Acute ethanol and developmental bisphenol A (BPA) exposure significantly disrupted larval social preference with altered locomotor activity, while equal-dose bisphenol AF (BPAF) exposure only impaired locomotion without affecting sociality, indicating distinct neurotoxic effects of BPA analogues. Additionally, two models with neurodevelopmental gene knockdown showed distinct alterations in larval social preference when assessed using this assay. Collectively, this study establishes an efficient larval social preference assay in zebrafish. It provides a feasible methodological tool for environmental neurotoxicity evaluation and phenotypic analysis of neurobehavioural phenotypes.