FEBS Open Bio最新文献

The family Thymelaeaceae Juss., includes numerous botanically and medicinally important species, yet its taxonomy, particularly within the genus Daphne Tourn. ex L., remains unresolved. In the present study, we sequenced and de novo assembled the chloroplast (cp) genome of Daphne mucronata Royle from Pakistan and assembled cp genomes of four additional Daphne species, one Dirca L. species and two Thymelaea Mill. species using public raw data. Comparative analyses across 14 genera, including 17 Daphne species, revealed substantial structural variation in cp genomes. The cp genomes contained 111-112 unique genes, including 77-78 protein-coding genes, 30 tRNA genes and four rRNA genes. When considering duplicated copies in the inverted repeat regions, the total gene count ranged from 128 to 142 (83-96 protein-coding genes, 37-38 tRNA genes and eight rRNA genes). Variability in total gene number was primarily driven by inverted repeat contraction and expansion and pseudogenization of some genes. ndhF was pseudogenized in seven Daphne species, whereas ndhI and ndhG were pseudogenized in one species each. Two large inversion events were detected, involving 19 and 40 genes, respectively; the first inversion was synapomorphic and provided significant phylogenetic signal. Phylogenetic analysis of shared protein-coding sequences from 74 species (87 individuals) recovered Daphne as a strongly supported monophyletic clade when taxa previously proposed for exclusion from the genus were omitted, whereas Wikstroemia Endl. and Gyrinops Gaertn. exhibited paraphyly. This study expands the cp genome resources for Thymelaeaceae and provides new insights into the structural evolution of cp genome.

Health and safety knowledge is critical in a laboratory setting but is often taught passively. As passive learning approaches are associated with lower student engagement and subsequent attainment, higher education institutions are increasingly focussed on active learning methodologies. One such approach is the use of card-based games to gamify learning. Based on this, this study designed and evaluated three health and safety card games focussing on personal protective equipment, hazard symbols and laboratory equipment identification. Students' health and safety knowledge was evaluated using a 10-point scale before and after completion of all three games. Wider pedagogical impact on factors such as student experience, transferable skill development and gamified learning value was also evaluated using open-answer questions or a 5-point Likert scale. A total of 91 foundation year students participated in the study. Most students reported positive responses regarding their enjoyment (89.9 %) and learning (74.7 %) from the games. Students liked their design (80.1 – 91.1%) and visual appeal (82.3 – 91.1 %), considering them a valuable addition to their laboratory induction (89.9 %). Pre- and postevaluation revealed a significant increase in self-perceived knowledge of health and safety (6.4 ± 2.1 to 8.4 ± 1.5, P < 0.001), PPE (7.6 ± 2.0 to 8.7 ± 1.5, P < 0.001), laboratory hazards (6.8 ± 1.9 to 8.2 ± 1.5, P < 0.001) and laboratory equipment (6.3 ± 2.1 to 8.2 ± 1.8, P < 0.001). Stratification of participants based on socio-economic factors and university entry qualifications revealed no significant differences. These findings highlight the wide benefits of card games as active learning tools to enhance health and safety education while providing a positive and equitable student experience.

Excess extracellular inorganic phosphate ions (Pi) and calcium ions (Ca²⁺) cause apoptosis and subsequent mineralization of chondrocytes. Here, we investigated the mechanism underlying the effect of these minerals. The chondrogenic cell line ATDC5 was treated with 2 mm Pi and/or Ca²⁺, and apoptosis, mineralization, and intracellular Pi concentrations were determined. Further, Pi- and Ca²⁺-treated cells were incubated with the Pi transporter (Pit-1) blocker phosphonoformic acid (PFA), the calcium-sensing receptor (CaSR) antagonist NPS-2143, and the CaSR agonist GdCl₃. Individual addition of Pi and Ca²⁺ did not induce apoptosis and mineralization, while combined addition of the minerals induced both. The Pit-1 blocker and the CaSR antagonist completely inhibited the apoptosis induced by combined addition of Pi and Ca²⁺. Intracellular Pi concentration was remarkably increased by combined addition of Pi and Ca²⁺ as compared to the findings for individual addition. The Pit-1 blocker and CaSR antagonist completely inhibited the increase in intracellular Pi concentration induced by the combined addition of Pi and Ca²⁺. The CaSR agonist considerably increased the intracellular Pi concentration. Our results indicate that excess extracellular Ca²⁺ activates CaSR, which induces the intake of excess extracellular Pi through Pit-1 into ATDC5 cells. The resulting increase in intracellular Pi concentration induces apoptosis.

The predominant cause of death among diabetic patients comes from cardiovascular complications, including vascular calcification. The objectives of this study were to improve the understanding of the molecular mechanisms involved in diabetes-related calcification and to test potential preventive therapies. We found that levels of plasma pyrophosphate-a potent inhibitor of calcification-were decreased in type 1 and type 2 diabetic patients with cardiovascular symptoms. To further investigate vascular calcification, we developed a diabetic mouse model that showed increased aorta and renal calcification compared to control. Alkaline phosphatase activity was also increased in the circulation of diabetic mice, which resulted in a significant decrease in plasma pyrophosphate. Oral treatment with pyrophosphate prevented diabetes-induced calcification in mice, providing a direct translational value for clinical applications.

Cancer-associated fibroblasts (CAFs) contribute to immunosuppression in the ovarian cancer microenvironment, partly through upregulation of indoleamine 2,3-dioxygenase 1 (IDO1). This study examined CAF-mediated suppression of T-cell function and the potential of IDO1 inhibition to reverse these effects. CAFs from high-grade serous ovarian cancer (HGSOC) patients exhibited increased IDO1, COX2, and PD-L1 expression upon interaction with activated T cells, along with elevated immunosuppressive cytokines. CAFs suppressed T-cell proliferation and induced PD-1 expression in CD4+ and CD8+ T cells, effects reversed by epacadostat. IDO1 inhibition enhanced T-cell proliferation via AKT signaling, restored T-cell cytotoxicity, and increased ovarian cancer cell apoptosis. These findings suggest that targeting IDO1 may help counteract CAF-mediated immunosuppression and enhance antitumor immunity in HGSOC.

Mitochondria-associated membranes (MAMs) are specialized contact sites between the endoplasmic reticulum (ER) and mitochondria that maintain cellular homeostasis through precisely orchestrated molecular mechanisms. These dynamic interfaces are maintained at 10–50 nm distances by complex tethering proteins, including the core IP3R–GRP7 5–VDAC1 complex and regulatory proteins, such as the sigma-1 receptor. MAMs coordinate multiple essential cellular processes: lipid synthesis and transfer, calcium signaling, metabolic regulation, and quality control through autophagy and mitophagy. Recent advances in super-resolution microscopy and proteomics have revealed that MAM dysfunction drives pathogenesis across various diseases. In Alzheimer's disease, disrupted MAM spacing directly affects Aβ production and mitochondrial function, while in Parkinson's disease, α-synuclein accumulation at MAMs impairs phosphatidylserine metabolism and mitochondrial dynamics. Beyond neurodegeneration, MAMs play crucial roles in metabolic disorders, cancer progression, and viral infections. This review provides mechanistic insights into MAM biology, from molecular organization to disease pathogenesis, integrating structural analyses with dynamic visualization approaches. We examine emerging therapeutic strategies targeting MAM-associated pathways and highlight their potential in treating complex diseases.

The complex interplay of metabolic signaling networks is critical to the pathophysiology of lung cancer. The anabolic mTORC1 kinase and catabolic process of autophagy are key among these regulatory pathways. While their relationship has long been viewed as a matter of simple inhibition, with mTORC1 as a negative regulator of autophagy, new evidence suggests that this relationship may be more nuanced than previously described. Here, we demonstrate that an autophagy-related, ATG4B, is required for mTORC1 activity and is associated with negative clinical outcomes in non-small cell lung cancer (NSCLC). Targeting ATG4B in vitro suppresses cell proliferation, protein synthesis rates, and mTORC1 signaling in NSCLC cell lines. In contrast, overexpressing the ATG4B protease in healthy models of lung tissue increased mTORC1 kinase activity in healthy lung cell models, indicating that an increase in ATG4B is sufficient to drive cellular anabolic signaling. Finally, we found that ATG4B expression is high in NSCLC patient tumors, is elevated in early-stage cancer, and predicts survival in lung adenocarcinoma patients. Taken together, our results demonstrate that ATG4B is required for anabolic behavior in NSCLC, indicating that the autophagic cascade may be a required input for mTORC1 activity and cellular anabolism in lung cancer. These results have implications for the field of cancer biology more broadly, as they indicate that the far from being a simple target of mTORC1, the autophagic cascade may serve as a requisite input for anabolic signaling, casting new light on the relationship between these processes in cancer pathophysiology.

Ecological interactions in the soil are often mediated by small molecules, which can later become valuable drugs. The cellular slime mould Dictyostelium discoideum is a soil microbe with a life cycle consisting of unicellular (amoeba) and multicellular phases (fruiting bodies). After Dictyostelium amoebae have consumed all available bacteria, they form stalked fruiting bodies to aid dispersal of the spores. The dying stalk cells repurpose a hybrid polyketide synthase to make abundant chlorinated metabolites, which persist in their fruiting bodies. The most abundant of the chlorinated metabolites, CDF-1, is a chlorinated dibenzofuran, which was shown to be an effective antimicrobial, being roughly as potent as ampicillin. Here, we identify CDF-2 and -3 by purification, followed by MS and NMR, after increasing their yields by using producer species and growth condition optimisation. Similar to CDF-1, CDF-2 and -3 are chlorinated dibenzofurans and exhibit more potent antibacterial activity against Gram-positive bacteria than ampicillin. We propose that the ecological function of CDF-2 and -3 is to protect the dormant spores from degradative bacteria.

Tropomyosin receptor kinase (Trk) receptors are essential regulators of neuronal development, survival, and plasticity through their interactions with neurotrophins. This review examines the structural and molecular mechanisms connecting ligand binding to the diverse signaling outcomes of Trk receptors. We analyze how neurotrophin binding and allosteric interactions trigger conformational changes that activate distinct signaling pathways. Our discussion explores how allosteric modulation—binding of ligands to sites distinct from the primary receptor site—and ligand bias—where different neurotrophins binding the same receptor preferentially activate certain downstream pathways—may together shape receptor function, focusing on structural and conformational mechanisms. Despite recent advances, important structural details remain unresolved. Further insights into Trk receptor structure and dynamics could significantly enhance therapeutic development by enabling the design of drugs that selectively target-specific signaling pathways.

The accurate detection of cellular senescence is of paramount importance given its involvement in aging and age-related pathologies. Over the years, a variety of markers and methodologies have been developed to address this issue. Initially, wet-lab assays, dealing with single morphological traits and molecular markers, were implemented, though exhibiting technical challenges and ineffectiveness in identifying the inherently complex senescence phenotype. Recent developments led to the adoption of combinatorial approaches in the form of multimarker guideline algorithms, effectively bypassing these obstacles. Moreover, technological advances have facilitated the emergence of molecular signatures that exploit the large amount of data generated in the last decades to increase our awareness of this phenomenon and its consequences. Due to the overwhelming expansion of these signatures, we performed an analysis of their advantages and disadvantages, and here, we discuss future improvements.