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17 pages, 2957 KB  
Article
Characterizing Ethnomedicinal Tetrastigma hemsleyanum Diels et Gilg Grown Under Different Cultivation Methods Using Stable Isotopes and Elemental Analyses
by Chunan Wang, Xianbo Wang, Hanyi Mei, Yongzhi Zhang, Chunlin Li, Karyne M. Rogers, Zuguang Li, Yuwei Yuan and Jing Nie
Plants 2026, 15(10), 1589; https://doi.org/10.3390/plants15101589 - 21 May 2026
Abstract
Tetrastigma hemsleyanum Diels et Gilg is a high-value edible and medicinal homologous plant, routinely grown under conventional field or greenhouse production systems across Asia. However, mislabeling of conventional products as the rarer (and more expensive) wild version may occur for financial gain. In [...] Read more.
Tetrastigma hemsleyanum Diels et Gilg is a high-value edible and medicinal homologous plant, routinely grown under conventional field or greenhouse production systems across Asia. However, mislabeling of conventional products as the rarer (and more expensive) wild version may occur for financial gain. In this study, stable isotopes (δ13C, δ15N, δ2H, and δ18O) and metal contents (Cr, Cu, Ni, As, Cd, Pb) were used to characterize plant tissues (tuber root, stem, leaf) and corresponding soils originating from simulated-wild-cultivated (WC) and greenhouse-cultivated (GC) pot trials using the same soil. Carbon and nitrogen isotopes served as key indicators for distinguishing GC and WC products. Specifically, δ13C values of GC plant tissues were 1.4 to 2.4‰ more positive than those of WC plant tissues (p < 0.05), and δ15N values in GC tissues were 2.7 to 4.6‰ more positive than δ15N in WC tissues (p < 0.01). Lower δ15N values observed in WC products indicate slower nitrogen turnover compared with GC products. Soil metal concentrations had significant differences between the two cultivation systems, but only limited effects on metal bioconcentration factors (BCFs) and translocation factors (TFs) in T. hemsleyanum tissues. Pb and Cd concentrations in root tissues had large differences between cultivation systems, and carbon dynamics in GC plants were more negatively affected by Pb levels in soils. These findings provide the first investigation of T. hemsleyanum grown under different cultivation practices and establish a scientific basis for distinguishing other wild or simulated-wild labeled food and medicinal plant products from conventionally grown products in future studies. Full article
(This article belongs to the Section Plant Response to Abiotic Stress and Climate Change)
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21 pages, 3555 KB  
Article
Biodegradation of Polystyrene by Hafnia paralvei: A Novel Isolate from the Gastrointestinal Tract of Common Carp
by Mina Popovic, Luka Dragacevic, Milan Kojic, Daria Tsibulskaia and Neveka Rajic
Microplastics 2026, 5(2), 98; https://doi.org/10.3390/microplastics5020098 (registering DOI) - 21 May 2026
Abstract
This study highlights the strong ability of a new bacterial strain, Hafnia paralvei UUNT_MP29, isolated from the gastrointestinal tract (GIT) of common carp (Cyprinus carpio), to break down polystyrene (PS). As an omnivorous bottom feeder, C. carpio is constantly exposed to [...] Read more.
This study highlights the strong ability of a new bacterial strain, Hafnia paralvei UUNT_MP29, isolated from the gastrointestinal tract (GIT) of common carp (Cyprinus carpio), to break down polystyrene (PS). As an omnivorous bottom feeder, C. carpio is constantly exposed to microplastics, creating a unique environment that favors the evolution of specialized microbiota capable of degrading polymers. Genomic analysis of the isolate identified key homologs involved in xenobiotic breakdown, including alcohol dehydrogenase (Adh), 3-hydroxybutyrate dehydrogenase (HDH), and a small glutamine-rich tetratricopeptide repeat-containing protein (SGTA), showing a strong metabolic system for processing long-chain hydrocarbons. Growth experiments showed the strain quickly adapted, reaching maximum cell density and forming mature biofilms by Day 16. Gravimetric analysis confirmed that H. paralvei UUNT_MP29 uses PS as its primary carbon source, with a significant weight loss of 16.76% over 16 days. Kinetic modeling indicated the degradation follows first-order kinetics (R2 = 0.9243) with a high degradation rate constant (k) of 0.2078 day−1. Surface analyses using FTIR and SEM confirmed extensive oxidative changes, as evidenced by the rising Carbonyl Index and surface erosion. TGA also showed reduced thermal stability of the treated polymer, suggesting microbial chain scission. These findings demonstrate the strong degradative ability of H. paralvei UUNT_MP29 and highlight the GIT of plastic-exposed aquatic animals as a promising area for discovering powerful biocatalysts for microplastic cleanup. Full article
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19 pages, 16207 KB  
Article
Isolation and Functional Characterization of a Gene Encoding Squalene Synthase from Amaranthus tricolor
by Yuanfeng Lv, Xiaoyang Lin, Zaifeng Du, Guihong Qi, Yinan Yang, Yufeng Luo and Hongbo Zhang
Agronomy 2026, 16(10), 1014; https://doi.org/10.3390/agronomy16101014 - 21 May 2026
Abstract
Squalene, a high-value triterpenoid precursor widely used in pharmaceuticals and vaccine adjuvants, is primarily sourced from shark liver oil—an unsustainable practice that has driven interest in developing plant-based production alternatives. The first committed reaction in triterpenoid biosynthesis is catalyzed by squalene synthase (SQS), [...] Read more.
Squalene, a high-value triterpenoid precursor widely used in pharmaceuticals and vaccine adjuvants, is primarily sourced from shark liver oil—an unsustainable practice that has driven interest in developing plant-based production alternatives. The first committed reaction in triterpenoid biosynthesis is catalyzed by squalene synthase (SQS), yet no SQS gene has been characterized in Amaranthus tricolor, a species recognized for its high squalene content. Here, we cloned and functionally characterized AtrSQS, a novel squalene synthase gene isolated from A. tricolor for the first time. Sequence analysis revealed that AtrSQS contains conserved domains and six characteristic motifs shared among plant SQSs, with high homology to orthologs from dicotyledonous species. To investigate its functional role in squalene biosynthesis, AtrSQS was overexpressed in Nicotiana tabacum under the CaMV 35S promoter. Transgenic lines exhibited significantly increased AtrSQS expression and accumulated squalene up to 6.81 μg/g dry weight, a 4.76-fold increase over wild-type plants. Additionally, the content of downstream product 2,3-oxidosqualene was also significantly elevated in the transgenic lines. Integrated transcriptomic and metabolomic analyses revealed that AtrSQS overexpression upregulated key mevalonate pathway genes (AACT, HMGS, MVD) and FPPS. Meanwhile, it suppressed competitive carotenoid biosynthesis and the production of an SQS-specific inhibitor, indicating a successful redirection of metabolic flux toward squalene production. These findings demonstrate that AtrSQS is crucial for squalene biosynthesis and provide both a valuable genetic resource and mechanistic insights for engineering plant-based squalene production systems. Full article
25 pages, 852 KB  
Review
Genomic Biomarkers for First-Line Treatment Selection in Metastatic Pancreatic Ductal Adenocarcinoma: A Narrative Review
by Anushareddy Muddasani, Ahmed Abdelnoor and Ashish Manne
Cancers 2026, 18(10), 1664; https://doi.org/10.3390/cancers18101664 - 21 May 2026
Abstract
Metastatic pancreatic ductal adenocarcinoma (PDAC) is typically treated with fluorouracil, leucovorin, irinotecan, and oxaliplatin (FOLFIRINOX) or gemcitabine plus nab-paclitaxel (GnP), but the choice between regimens remains largely empirical. This narrative review summarizes biomarkers with potential to inform first-line selection in metastatic PDAC, emphasizing [...] Read more.
Metastatic pancreatic ductal adenocarcinoma (PDAC) is typically treated with fluorouracil, leucovorin, irinotecan, and oxaliplatin (FOLFIRINOX) or gemcitabine plus nab-paclitaxel (GnP), but the choice between regimens remains largely empirical. This narrative review summarizes biomarkers with potential to inform first-line selection in metastatic PDAC, emphasizing genomic and transcriptomic correlates of differential benefit. Recent head-to-head trials, particularly Pancreatic Adenocarcinoma Signature Stratification for Treatment (PASS-01) and GENERATE (Japan Clinical Oncology Group [JCOG] 1611), indicate that modified FOLFIRINOX (mFOLFIRINOX) is not uniformly superior to GnP, strengthening the rationale for biomarker-guided selection. The strongest evidence favoring platinum-based/FOLFIRINOX strategies involves homologous recombination repair deficiency (HRD), especially alterations in germline breast cancer gene 1/2 (BRCA1/2) or partner and localizer of BRCA2 (PALB2), as well as broader genomic scar signatures. Transcriptomic subtype and GATA-binding protein 6 (GATA6) expression are promising but remain unsettled because retrospective data favor classical/GATA6-high disease for FOLFIRINOX, whereas PASS-01 suggested better outcomes with GnP in classical tumors. Candidate biomarkers favoring GnP include high human equilibrative nucleoside transporter 1 (hENT1), low class III β-tubulin (TUBB3) expression, and exploratory phosphatidylinositol 3-kinase (PI3K)/KIT/NOTCH pathway mutation signals. Comprehensive molecular profiling also identifies actionable alterations that may redirect patients to targeted therapy or clinical trials rather than standard chemotherapy alone. Importantly, no biomarker has yet been prospectively validated in a biomarker-stratified randomized trial with regimen selection as the primary endpoint; all biomarker-regimen associations described in this review should therefore be considered hypothesis-generating rather than practice-defining. Nevertheless, the convergence of genomic, transcriptomic, and organoid-based approaches makes biologically informed first-line selection increasingly feasible in metastatic PDAC. Full article
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12 pages, 1048 KB  
Article
Prognostic Significance of Cdc42 Expression in Colorectal Cancer and Its Concordance Between Primary Tumors and Matched Metastases: A Retrospective Observational Study
by Oktay Halit Aktepe, Osman Butun, Olcay Kurtulan, Aziz Karaoglu and Suayib Yalcin
J. Clin. Med. 2026, 15(10), 3848; https://doi.org/10.3390/jcm15103848 - 16 May 2026
Viewed by 202
Abstract
Background and Objectives: Aberrant activation or overexpression of cell division cycle 42 (Cdc42) has been demonstrated in various tumors; however, its prognostic relevance in colorectal cancer (CRC) remains insufficiently defined. Thus, we evaluated the prognostic impact of Cdc42 expression in patients with CRC. [...] Read more.
Background and Objectives: Aberrant activation or overexpression of cell division cycle 42 (Cdc42) has been demonstrated in various tumors; however, its prognostic relevance in colorectal cancer (CRC) remains insufficiently defined. Thus, we evaluated the prognostic impact of Cdc42 expression in patients with CRC. In a paired primary–metastasis subset, we also assessed the concordance of Cdc42 expression between primary tumors and matched metastatic tissues. Materials and Methods: Cdc42 expression was assessed by immunohistochemistry in patients with colorectal cancer who underwent colectomy for curative or palliative purposes between January 2009 and January 2019. Cdc42 expression was quantified as a staining index and then dichotomized into low- and high-Cdc42 groups using a median cutoff value of six. Overall survival (OS) was analyzed by Kaplan–Meier curves with log-rank testing, and independent prognostic factors were assessed using Cox proportional hazard models. Results: The study included 94 patients (median age, 60 years) with a median follow-up of 88.4 months. High Cdc42 expression was significantly associated with Kirsten rat sarcoma viral oncogene homolog (KRAS) wild-type status (p = 0.001), lymph node metastasis (p = 0.039), and perineural invasion (p = 0.021). Patients with high Cdc42 expression had significantly poorer OS than those with low expression (median OS: 48.5 months, 95% confidence interval [CI]: 33.3–63.7 vs. 114.4 months, 95% CI: 24.0–204.9; p = 0.003). In multivariable Cox regression, high Cdc42 expression remained an independent predictor of worse OS (hazard ratio [HR]: 2.365, 95% CI: 1.336–4.184; p = 0.003), together with advanced stage and moderate-to-poor differentiation. In the paired primary–metastasis subset, Cdc42 expression in primary tumors correlated positively with that in matched metastases (Spearman ρ = 0.416, p = 0.016), whereas no overall directional shift between paired primary and metastatic samples was observed (Wilcoxon signed-rank test: Z = 0.423, p = 0.672). Conclusions: High Cdc42 expression may serve as an adverse prognostic marker in CRC. Cdc42 shows moderate concordance between primary tumors and matched metastases without a consistent directional shift. Full article
(This article belongs to the Section Oncology)
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14 pages, 3343 KB  
Article
Identification of Macrophage Migration Inhibitory Factor in Mytilus coruscus and Its Role in Methylation During Antibacterial Immunity
by Xuechun Wang, Chentenghong Yuan, Xirui Si, Pengzhi Qi and Bin Shen
Fishes 2026, 11(5), 296; https://doi.org/10.3390/fishes11050296 - 15 May 2026
Viewed by 98
Abstract
Macrophage migration inhibitory factor (MIF) is broadly acknowledged as a central pro-inflammatory regulator, owing to its multifaceted functions including immune cell recruitment, initiation and amplification of pro-inflammatory cytokine cascades, enhancement of macrophage viability, facilitation of macrophage polarization toward a pro-inflammatory state, and attenuation [...] Read more.
Macrophage migration inhibitory factor (MIF) is broadly acknowledged as a central pro-inflammatory regulator, owing to its multifaceted functions including immune cell recruitment, initiation and amplification of pro-inflammatory cytokine cascades, enhancement of macrophage viability, facilitation of macrophage polarization toward a pro-inflammatory state, and attenuation of glucocorticoid-mediated immunosuppression. However, functional investigations of MIF in Mytilus coruscus remain limited. In this study, we identified the MIF gene in M. coruscus, and bioinformatic analyses revealed that the gene encodes a 115-amino-acid polypeptide that exhibits close phylogenetic affinity with MIF homologs from other mollusks. McMIF was predominantly expressed in immune-related tissues, with notably high expression levels in the digestive gland. Upon Vibrio alginolyticus infection, both the mRNA and protein levels of McMIF were significantly upregulated, suggesting that McMIF is involved in the antibacterial immune response of M. coruscus. Meanwhile, the m6A modification level of McMIF was markedly reduced following infection, suggesting a potential relationship between m6A modification and the antibacterial immune function of MIF. Furthermore, knockdown of McMIF followed by LPS stimulation led to an increased level of apoptosis in digestive gland cells, suggesting that McMIF is involved in the inhibition of apoptosis induced by immune stimulation. Collectively, these findings provide insights into the immunological characteristics of McMIF in M. coruscus. Full article
(This article belongs to the Special Issue Advances in the Immunology of Aquatic Animals)
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21 pages, 3412 KB  
Article
EZH2-Associated Hypermethylated Gene Signature Predicts Immunotherapy Response and Implicates DUSP5 in Tumor-Immune Regulation in Triple-Negative Breast Cancer
by Mingzhan Xue, Sujitha Jeya, Reem Elasad, Sarra Mestiri, Fares Al Ejeh and Mariam Al-Muftah
Cancers 2026, 18(10), 1606; https://doi.org/10.3390/cancers18101606 - 15 May 2026
Viewed by 244
Abstract
Background/Objectives: Triple-negative breast cancer (TNBC) is a candidate for immune checkpoint blockade; however, current biomarkers remain insufficient to predict therapeutic response or capture tumor-intrinsic mechanisms. Enhancer of Zeste Homolog 2 (EZH2)-mediated epigenetic repression has been implicated in immune evasion, yet the contribution of [...] Read more.
Background/Objectives: Triple-negative breast cancer (TNBC) is a candidate for immune checkpoint blockade; however, current biomarkers remain insufficient to predict therapeutic response or capture tumor-intrinsic mechanisms. Enhancer of Zeste Homolog 2 (EZH2)-mediated epigenetic repression has been implicated in immune evasion, yet the contribution of EZH2-repressed genes to anti-tumor immunity and clinical outcomes in TNBC remains unclear. We aimed to identify EZH2-associated epigenetically repressed genes in TNBC and evaluate their relevance as tumor-intrinsic regulators and potential predictors of immunotherapy outcome. Methods: We performed integrative in silico analyses of The Cancer Genome Atlas (TCGA) breast cancer cohorts to identify EZH2-associated hypermethylated genes in TNBC. A composite 30-gene signature (30GS) was defined based on transcriptional repression and promoter hypermethylation. Associations with clinical outcomes, tumor- and immune-related programs, and therapeutic response were evaluated, with validation in the I-SPY2 cohort and an independent TNBC patient cohort. Results: The 30GS was significantly reduced in TNBC and basal-like tumors and associated with improved clinical outcomes and enrichment of tumor- and immune-related signatures. In the I-SPY2 cohort, the 30GS predicted pathological complete response in patients receiving chemo-immunotherapy (AUC = 0.7377, p = 0.0007). Gene-level analysis identified Dual Specificity Phosphatase 5 (DUSP5) as the gene most consistently associated with immune-related parameters. In an independent TNBC cohort, DUSP5-high tumors demonstrated transcriptional programs enriched for inflammatory, immune-related, and signaling pathways within the NanoString Breast Cancer 360 panel. Conclusions: This study defines an EZH2-associated epigenetic program linked to tumor-intrinsic immune programs in TNBC and identifies DUSP5 as a candidate gene associated with immune-related transcriptional states. Full article
(This article belongs to the Section Cancer Biomarkers)
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17 pages, 5705 KB  
Article
Identification and Functional Analysis of ZmMAPKKKA-Interacting Proteins Involved in Cold Stress Response in Maize (Zea mays L.)
by Tao Yu, Jianguo Zhang, Xuena Ma, Shiliang Cao, Wenyue Li and Gengbin Yang
Agronomy 2026, 16(10), 978; https://doi.org/10.3390/agronomy16100978 (registering DOI) - 14 May 2026
Viewed by 117
Abstract
Maize (Zea mays L.), a typical thermophilic crop originating from tropical regions, exhibits an inherent sensitivity to low-temperature stress. Cold stress severely restricts maize seed germination, seedling growth, the physiological metabolism, and the final grain yield, which greatly limits its geographical cultivation [...] Read more.
Maize (Zea mays L.), a typical thermophilic crop originating from tropical regions, exhibits an inherent sensitivity to low-temperature stress. Cold stress severely restricts maize seed germination, seedling growth, the physiological metabolism, and the final grain yield, which greatly limits its geographical cultivation range and sustainable industrial development. Elucidating the molecular regulatory mechanisms underlying maize cold tolerance and excavating cold-resistant functional genes are essential for the molecular breeding of cold-tolerant maize varieties and expanding maize planting areas in high-latitude and low-temperature-prone regions. In this study, using the strongly cold-tolerant maize inbred line B144 as the experimental material, we cloned the ZmMAPKKKA gene (NCBI accession: LOC103651289) and systematically screened and verified its cold-stress-specific interacting proteins via multiple molecular biological assays. The full-length coding sequence (CDS) of ZmMAPKKKA is 1134 bp, encoding a 377-amino-acid protein with a predicted molecular weight of 40.37 kDa. The quantitative real-time PCR (qRT-PCR) results demonstrated that the ZmMAPKKKA expression was significantly upregulated by 16.56-fold in maize roots after 12 h of low-temperature treatment, indicating a tissue-specific and robust cold response in root tissues. A total of 25 interacting proteins were identified through yeast two-hybrid screening, among which three stress-responsive proteins, including a protein kinase (LOC100286253), a protein phosphatase 2C (PP2C) (LOC542176), and a NAC transcription factor (LOC118474710), were selected for subsequent verification. The Pull-Down, Co-immunoprecipitation (Co-IP), and bimolecular fluorescence complementation (BiFC) assays consistently confirmed that ZmMAPKKKA specifically interacts with these three proteins both in vitro and in vivo under cold stress conditions. This study is the first to construct a ZmMAPKKKA-centered protein interaction module in the maize mitogen-activated protein kinase (MAPK) cascade under cold stress, establishing a novel kinase–phosphatase–transcription factor regulatory cascade that improves the current understanding of cold signal transduction mechanisms in maize. Homologous genes of ZmMAPKKKA in gramineous crops including rice (Oryza sativa) and sorghum (Sorghum bicolor) have been proven to participate in diverse abiotic stress responses, suggesting the conserved functional roles of MAPKKK family genes across gramineous species. Collectively, our findings provide comprehensive insights into the molecular mechanism of the maize MAPK signaling pathway mediating cold stress adaptation and supply valuable functional gene resources for cold-tolerant maize germplasm innovation and molecular breeding. Full article
(This article belongs to the Special Issue Plant Stress Tolerance: From Genetic Mechanism to Cultivation Methods)
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29 pages, 2400 KB  
Article
YBX1 Expression Marks Proliferative Tumour States with Context-Dependent Genomic Instability: A Pan-Cancer Analysis
by Selena Wang, Zahra Shafaei Pishabad, Debina Sarkar, Apeksha Arun Bhandarkar, Makhdoom Sarwar, Aaron Jeffs, Glen Reid, Antony Braithwaite and Sunali Mehta
Int. J. Mol. Sci. 2026, 27(10), 4340; https://doi.org/10.3390/ijms27104340 - 13 May 2026
Viewed by 237
Abstract
Y-box binding protein 1 (YB-1; encoded by YBX1) is a multifunctional DNA- and RNA-binding protein implicated in cell cycle regulation, DNA repair, stress adaptation, and therapy resistance. Elevated YBX1 expression has been associated with aggressive disease across multiple cancer types; however, its [...] Read more.
Y-box binding protein 1 (YB-1; encoded by YBX1) is a multifunctional DNA- and RNA-binding protein implicated in cell cycle regulation, DNA repair, stress adaptation, and therapy resistance. Elevated YBX1 expression has been associated with aggressive disease across multiple cancer types; however, its pan-cancer genomic and clinical correlates, and the extent to which these reflect proliferative activity versus genomic instability, remain incompletely defined. Here, we performed an integrative pan-cancer analysis across 53 independent datasets spanning 33 tumour types, incorporating transcriptomic (YBX1 mRNA), proteomic (RPPA), genomic, and clinical data. We found that YBX1 is rarely altered at the genomic level, whereas its mRNA expression is highly variable within tumour cohorts. Tumours with high YBX1 mRNA expression consistently exhibited conserved transcriptional programmes enriched for cell cycle, mitotic, RNA processing, and signalling pathways, patterns that were also reflected at the protein level by concordant pathway associations with elevated YB-1 abundance. These molecular features co-occurred with clinicopathological characteristics indicative of aggressive disease. High YBX1 mRNA expression was associated with increased mutation burden, chromosomal alteration burden, hypoxia, and homologous recombination deficiency at the pan-cancer level, with similar molecular associations observed in tumours stratified by elevated YB-1 protein levels. The association between YBX1 expression and chromosomal alteration burden was largely attenuated after accounting for proliferative activity, particularly G2/M-associated transcriptional programmes used as a proxy for mitotic activity. While the relationship with mutation burden was heterogeneous across tumour types, this pattern suggests that links between YBX1 expression and chromosomal instability primarily reflect shared proliferative and mitotic tumour biology rather than an independent genomic instability programme. Clinically, high YBX1 mRNA expression was associated with advanced disease stage, higher histologic grade, reduced progression-free survival, and poorer overall survival. Elevated YB-1 protein levels were also associated with advanced disease stage and poorer survival outcomes and demonstrated a similar, although non-significant, directional trend with histologic grade. Collectively, these findings demonstrate that elevated YBX1 expression marks proliferative and clinically aggressive tumour states within which genomic instability-related features arise in a context-dependent manner, providing a clarified pan-cancer framework for interpreting YB-1-associated tumour biology. Full article
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13 pages, 2742 KB  
Article
High-Affinity Nanobody Against the LEDGF PWWP Domain Inhibits Chromatin Binding In Vitro
by Thibault Vantieghem, Sofie Jansen, Thatcher Zinabu Akele, Pieterjan Van Maele, Sam Noppen, Dominique Schols, Maarten Dewilde, Zeger Debyser and Sergei V. Strelkov
Biomolecules 2026, 16(5), 716; https://doi.org/10.3390/biom16050716 - 13 May 2026
Viewed by 209
Abstract
Background and objectives: The PWWP domain of lens epithelium-derived growth factor p75 (LEDGF/p75) mediates chromatin engagement through recognition of histone H3 lysine 36 di- and trimethylation (H3K36me2/3) and nucleosomal DNA. LEDGF/p75 plays a role in multiple human diseases. In particular, its interaction with [...] Read more.
Background and objectives: The PWWP domain of lens epithelium-derived growth factor p75 (LEDGF/p75) mediates chromatin engagement through recognition of histone H3 lysine 36 di- and trimethylation (H3K36me2/3) and nucleosomal DNA. LEDGF/p75 plays a role in multiple human diseases. In particular, its interaction with HIV-1 integrase enables viral genome integration. However, the LEDGF PWWP domain remains difficult to target with small molecules as it lacks optimally shaped binding pockets. Here, we report the generation of high-affinity nanobodies (Nbs) to investigate the structure and function of this domain. Methods: Camelids were immunized with recombinant LEDGF PWWP domain, and immune phage display libraries were screened for affinity. Selected Nbs were recombinantly expressed in E. coli and purified. Their interaction with the PWWP domain of LEDGF and its close homolog HRP-2 was characterized using size-exclusion chromatography and surface plasmon resonance. Structural characterization of the Nbs was performed using X-ray crystallography. Functional effects on chromatin engagement were evaluated using an AlphaScreen assay. Results: Nine sequence-distinct Nbs were identified, seven of which were confirmed to bind the LEDGF PWWP domain with nanomolar affinities. Five Nbs also bound the HRP-2 domain, consistent with conserved functional surfaces, while two showed reduced affinity. The crystal structures of two Nbs (NbC03 and NbH10) confirmed there were canonical immunoglobulin folds, while the latter additionally revealed a domain-swapped dimer. Moreover, NbH10 dose-dependently inhibited the interaction between full-length LEDGF/p75 and H3K36me3-modified nucleosomes in vitro. Conclusions: This work establishes a validated panel of Nbs targeting the LEDGF PWWP domain and identifies one Nb capable of functionally disrupting the LEDGF–chromatin interaction. These Nbs serve as valuable tools for functional studies and structure-based drug design. Full article
(This article belongs to the Section Molecular Biology)
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20 pages, 1457 KB  
Article
Resilience of Deforestation Reduction Policies Across Land Tenure Regimes: Evidence from the Post-2019 Policy Shock in the Brazilian Amazon
by Roxana Juliá
Land 2026, 15(5), 819; https://doi.org/10.3390/land15050819 (registering DOI) - 12 May 2026
Viewed by 197
Abstract
This paper examines the resilience of deforestation control policies across land tenure regimes in the Brazilian Legal Amazon, using Brazil’s post-2019 shift in environmental governance policies as a quasi-natural experiment. Combining high-resolution deforestation data with detailed tenure classifications, the analysis evaluates how land [...] Read more.
This paper examines the resilience of deforestation control policies across land tenure regimes in the Brazilian Legal Amazon, using Brazil’s post-2019 shift in environmental governance policies as a quasi-natural experiment. Combining high-resolution deforestation data with detailed tenure classifications, the analysis evaluates how land governance mediates deforestation outcomes under weakened enforcement and regulatory rollback. Using a difference-in-differences framework with spatial panel data and event-study specifications, the results reveal substantial heterogeneity across tenure regimes. Areas characterized by strong legal recognition—particularly homologated Indigenous territories and strictly protected conservation units—remain comparatively resilient, exhibiting stable or declining deforestation. In contrast, lands with weaker or incomplete property rights, including non-homologated Indigenous territories, agrarian settlements, and untitled public lands, experience significant increases in deforestation. The findings also highlight important within-land category variation, underscoring the role of formal recognition and cadastral validation in shaping environmental outcomes. Overall, the results demonstrate that the durability of deforestation reductions depends critically on the strength of land tenure institutions in the face of changing policy regimes. Full article
(This article belongs to the Special Issue Sustainable Land Management Practices in the Face of Climate Change)
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18 pages, 6042 KB  
Article
Temperature-Dependent Conformational Dynamics of Substrate Entrance Loops in β-Glucosidase: Insights from Molecular Dynamics Simulations
by Ki Hyun Nam
Int. J. Mol. Sci. 2026, 27(10), 4279; https://doi.org/10.3390/ijms27104279 - 11 May 2026
Viewed by 190
Abstract
β-Glucosidase (BGL) is widely used in biofuel production, industrial value-added chemicals, and food industry applications. The substrate entrance loops of BGL play a role in substrate specificity and accessibility. To better understand the substrate entrance loops of BGL, a high-resolution crystal structure of [...] Read more.
β-Glucosidase (BGL) is widely used in biofuel production, industrial value-added chemicals, and food industry applications. The substrate entrance loops of BGL play a role in substrate specificity and accessibility. To better understand the substrate entrance loops of BGL, a high-resolution crystal structure of BGL from Thermoanaerobacterium saccharolyticum (TsaBGL) was determined at 1.65 Å, and all-atom molecular dynamics (MD) simulations were performed. The crystal structure of TsaBGL exhibited both folded and straight conformations of the flexible L3 loop, along with rigid conformations of L1, L2, and L4 loops. MD simulations revealed that the folded L3 loop transitioned to a straight conformation, indicating the preference for the straight conformation. At the optimal temperature for enzyme activity, the flexibility of the L3 loop of TsaBGL decreased, whereas that of the L1 loop increased. Moreover, the positions of L1 and L2 loops shifted in a direction opposite to the substrate entrance, resulting in an expanded substrate-binding entrance and increased substrate accessibility to the active site. MD simulations of three homologous BGLs showed that, despite sequence variability, a conserved dynamic trend exists in which the L1 loop exhibits higher flexibility, whereas the L3–L4 loops maintain structural rigidity under optimal conditions. These results provide both an understanding of the loop dynamics involved in substrate accessibility in BGLs and insights into enzyme engineering to improve catalytic performance. Full article
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26 pages, 73675 KB  
Article
The Biocolonization Control Mechanism of Traditional Raw Earth–Rubble Walls in Fuzhou
by Muye Guan, Rui Zhu, Yuhong Ding, Li Chen, Jingwei Liang, Qingnian Deng and Ruiming Guan
Coatings 2026, 16(5), 576; https://doi.org/10.3390/coatings16050576 - 11 May 2026
Viewed by 322
Abstract
Focusing on the R&D demand for green earthen building materials in coastal high-temperature and high-humidity areas, this study explores the biocolonization control mechanism of raw earth–rubble walls, taking the traditional raw earth–rubble walls of ancient buildings in Sanfang Qixiang, Fuzhou, as the research [...] Read more.
Focusing on the R&D demand for green earthen building materials in coastal high-temperature and high-humidity areas, this study explores the biocolonization control mechanism of raw earth–rubble walls, taking the traditional raw earth–rubble walls of ancient buildings in Sanfang Qixiang, Fuzhou, as the research subject. FTIR, XRD, Raman, and SEM-EDS combined technologies were employed for characterization. The results show that the raw earth is rich in proteins, amino acids, and other nutrients, which provide the nutritional basis for plant growth. The raw earth and rubble share homologous mineral components. The rubble is fired from raw earth mixed with iron minerals such as hematite, with carbonaceous substances generated during the firing process. Iron, carbon, and potassium released from the weathered rubble may inhibit the growth of plant roots. The raw earth is relatively looser than the rubble, and the two form a dense–loose alternating structure. Combined with the secondary calcification mechanism in the raw earth, this structure resists the expansion and cracking of the wall and improves the viscosity and hardness of the wall. It is concluded that in a high-temperature and high-humidity environment, the raw earth first releases nutrients to promote plant growth. As time progresses, the relevant substances released by the rubble continuously inhibit root growth. Combined with the structural characteristics of the wall with high firmness and crack resistance, plants growing on the wall will not damage the wall structure. This finding provides a theoretical basis for the biocolonization control mechanism of raw earth–rubble walls and also offers practical references for the protection and sustainable reuse of raw earth buildings in similar areas. Full article
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20 pages, 13159 KB  
Article
Flavobacterium psychrophilum as an Important Pathogen Associated with Overwintering Mortality Syndrome in Grass Carp (Ctenopharyngodon idella): Isolation, Characterization, and Pathogenicity
by Hongyang Song, Mingyang Xue, Yong Zhou, Wenzhi Liu, Wei Liu, Nan Jiang, Yiqun Li, Yan Meng, Xin Ren and Yuding Fan
Animals 2026, 16(10), 1465; https://doi.org/10.3390/ani16101465 - 10 May 2026
Viewed by 290
Abstract
Grass carp (Ctenopharyngodon idella), a key species in China’s freshwater aquaculture, faces hindered industrial development due to overwintering mortality disease outbreaks. A Gram-negative bacterial strain, designated Hbh25210, was isolated from overwintering mortality-diseased grass carp in a Hubei Province farm. It was [...] Read more.
Grass carp (Ctenopharyngodon idella), a key species in China’s freshwater aquaculture, faces hindered industrial development due to overwintering mortality disease outbreaks. A Gram-negative bacterial strain, designated Hbh25210, was isolated from overwintering mortality-diseased grass carp in a Hubei Province farm. It was identified as Flavobacterium psychrophilum by 16S rRNA gene sequencing, showing 100% homology to reference strains in GenBank. The strain can be successfully cultured at 15 °C within 3 to 5 days. Multilocus sequence typing (MLST) classified it as ST-51 (CC-ST56), while serotyping assigned it to the 0 type, indicating phylogenetic affinity to Japanese cyprinid isolates. Artificial infection experiments confirmed its pathogenicity: muscle injection resulted in 15–75% mortality in grass carp, with clinical symptoms consistent with natural infections. Histopathological changes included hepatic necrosis, splenic congestion, glomerular swelling, and muscle fiber dissolution; intestinal lesions were particularly prominent in infected fish. 16S rRNA gene sequencing of diseased tissues showed Flavobacterium psychrophilum constituted over 60% of the microbial community in most ulcerative lesions samples and reached as high as 98.8% in certain cases. Strain Hbh25210 exhibited high-level resistance to multiple antibiotics, including ciprofloxacin, cefadroxil, neomycin, florfenicol, sulfamethoxazole, doxycycline, trimethoprim–sulfamethoxazole, and flumequine. Conversely, it was relatively sensitive to enrofloxacin, gentamicin, and amikacin. Quantitative PCR showed the bacterial load in muscle remained the highest, followed by the intestine and spleen, which peaked at 96 h post-injection. In conclusion, this study indicates that Flavobacterium psychrophilum is an important pathogen associated with overwintering mortality syndrome in grass carp. Our research findings can provide a basis for the effective prevention and control of overwintering mortality syndrome in major freshwater fish species. Full article
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15 pages, 2064 KB  
Review
UTY (KDM6C) in Cancer: Epigenetic Regulation, Tumour Suppressor Functions, and Clinical Implications
by Chitrakshi Chopra, Chandra Prakash Prasad and Manish Kumar
Epigenomes 2026, 10(2), 31; https://doi.org/10.3390/epigenomes10020031 - 9 May 2026
Viewed by 270
Abstract
The ubiquitously transcribed tetratricopeptide repeat Y-linked gene (UTY/KDM6C), a catalytically impaired histone demethylase encoded on the Y chromosome, has garnered increasing attention for its emerging roles in tumorigenesis and cancer progression. Despite high sequence homology with its X-linked paralog UTX/KDM6A, UTY exhibits markedly [...] Read more.
The ubiquitously transcribed tetratricopeptide repeat Y-linked gene (UTY/KDM6C), a catalytically impaired histone demethylase encoded on the Y chromosome, has garnered increasing attention for its emerging roles in tumorigenesis and cancer progression. Despite high sequence homology with its X-linked paralog UTX/KDM6A, UTY exhibits markedly reduced or absent H3K27me3 demethylase activity due to critical amino acid substitutions in its Jumonji C domain. Consequently, UTY primarily functions through non-enzymatic mechanisms, acting as a scaffold in chromatin-remodelling complexes like COMPASS and SWI/SNF, or mediating protein–protein interactions that regulate transcriptional programs independent of demethylation. This aligns with epigenetic dysregulation in cancers, where imbalances in repressive H3K27me3 and active H3K4me either drive tumour suppressor silencing or oncogene activation. Unlike frequently mutated UTX in cancers such as breast, renal cell carcinoma, and acute myeloid leukaemia, UTY’s contributions in cancer are less defined, constrained by male-specific expression. Emerging evidence suggests UTY as a context-dependent tumour suppressor in AML and squamous-like pancreatic ductal adenocarcinoma. While direct functional validation remains limited in several cancer types, UTY is increasingly implicated as a potential tumour suppressor in haematological malignancies and prostate cancer. Therapeutically targeting UTY’s scaffold functions shows promise for male-specific cancers and merits future investigation. Full article
(This article belongs to the Special Issue Epigenetic Signatures in Metabolic Health and Cancer)
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