Chemistry & Biology[JOURNAL]
Sun
200 papers
BF- and PO-Chealted Oxasmaragdyrins - Excited state properties, singlet oxygen generation, and imaging potential in mice bearing colon tumor.
Patel N, Dukh M, Pandey RK … +5 more , Tripathi N, Ravikanth M, Jang Y, Gobeze HB, D'Souza F
J Photochem Photobiol B · 2026 May · PMID 41985213 · Publisher ↗
Free-base oxasmaragdyrin (SmFb), a 22-π electron aromatic macrocycles containing four pyrroles and a furan ring connected via three methine bridges and two direct bonds, and its BF- (SmBF) and PO-chealted (SmPO) derivati...
Free-base oxasmaragdyrin (SmFb), a 22-π electron aromatic macrocycles containing four pyrroles and a furan ring connected via three methine bridges and two direct bonds, and its BF- (SmBF) and PO-chealted (SmPO) derivatives, peripherally modified at the meso-aryl rings with polar and nonpolar groups, have been evaluated for their singlet oxygen producing ability and fluorescence imaging potential in mice bearing colon cancer. The oxasmaragdyrin derivatives investigated in this study exhibited absorption into the visible/near-IR region, fluorescence between 700 and 750 nm, and phosphorescence in the range of 875-1000 nm. The measured fluorescence lifetimes and quantum yields were close to those of the tetrapyrrole analogs. Using both femtosecond and nanosecond transient absorption spectral studies, the excited state properties of representative SmBF and SmPO were investigated in toluene. The triplet lifetimes of SmBF and SmPO were found to be 72 and 38 ns, respectively. Both SmBF and SmPO derivatives showed singlet oxygen-producing ability with quantum yields comparable to the free-base tetraphenylporphyrin. An energy-level diagram was prepared to illustrate the generation of singlet oxygen from the Sm derivatives. The tumor-specificity and fluorescence imaging capabilities and biodistribution of these analogs were compared in mice bearing Colon26 tumors using the 'In Vivo Imaging System' (IVIS) spectrum. Such studies revealed the significant potential for tumor imaging of BF-Sm among the investigated Sm compounds.
Local Lung HIF-1α and VEGF Activation to Reverse Emphysema by a Sulfated Caffeic Acid Dehydropolymer.
Truong TM, Thompson ML, Desai UR … +1 more , Sakagami M
Biology (Basel) · 2026 Apr · PMID 41972567 · Full text
In emphysema, the alveolar septal structure is progressively destroyed, which is believed to be irreversible. However, as it has recently been linked to vascular endothelial growth factor (VEGF) deficiency, we hypothesiz...
In emphysema, the alveolar septal structure is progressively destroyed, which is believed to be irreversible. However, as it has recently been linked to vascular endothelial growth factor (VEGF) deficiency, we hypothesized that VEGF stimulation can promote lung cell proliferation/migration to reverse emphysema. Our sulfated caffeic acid dehydropolymer, CDSO3, was thus examined in vitro and in vivo, given its VEGF-stimulating activity via ferrous ion (Fe) chelation-mediated stabilization of hypoxia-inducible factor-1α (HIF-1α). In lung epithelial/endothelial cells, CDSO3 promoted proliferation and wound closure by 1.6-3.0-fold at 10 μM; however, these effects were negated by excess FeSO or an HIF-1α inhibitor, indicating an Fe- and HIF-1α-dependent mechanism. In rat models of emphysema induced by cigarette smoke extract or the VEGF receptor antagonist SU5416, two-week lung administration of CDSO3 at 60 μg/kg from day 21 enabled: 68-79% recovery of exercise endurance and airspace enlargement/destruction; a 1.8-fold increase in proliferating cell nuclear antigen above healthy levels; normalization of cleaved caspase-3; restoration of HIF-1α; and a 1.3-fold increase in VEGF above healthy levels. In contrast, CDSO3 pre-chelated with Fe was ineffective. In conclusion, Fe chelation-mediated HIF-1α stabilization and VEGF stimulation via local lung delivery of CDSO3 can reverse emphysema by promoting cell growth and survival.
Repeated low-level red light modulates retinal metabolic alterations in lens-induced myopic chicks.
He C, Huang Y, Zhang S … +7 more , Li J, Liang J, Peng J, Wu Y, Hong Y, Zheng YF, He M
J Photochem Photobiol B · 2026 May · PMID 41967278 · Publisher ↗
BACKGROUND: Repeated low-level red-light (RLRL) therapy effectively controls myopia, yet its retinal metabolic mechanisms remain elusive. This study aimed to elucidate RLRL-induced metabolic alterations in a lens-induced...
BACKGROUND: Repeated low-level red-light (RLRL) therapy effectively controls myopia, yet its retinal metabolic mechanisms remain elusive. This study aimed to elucidate RLRL-induced metabolic alterations in a lens-induced myopia (LIM) chick model. METHODS: Seven-day-old chicks were randomized into three groups (n = 7 each): normal control (NC), LIM (monocular -10 D lens wear), and LIM + RL (LIM with red-light intervention). The LIM + RL group received 650 nm red light (5 mW cm, 3 min twice daily) for 7 days. Ocular biometry, choroidal thickness, and retinal safety were assessed. Retinal tissues were harvested for untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics, followed by multivariate analysis, pathway enrichment, validation of selected metabolites, and qPCR analysis of pathway-related genes. RESULTS: Red light (RL) reduced myopic shift (-3.82 ± 0.8 D vs -7.75 ± 1.2 D, p = 0.0003) and axial elongation (0.508 ± 0.04 mm vs 0.644 ± 0.03 mm, p = 0.0022), corresponding to 50.6% and 43.3% reduction, respectively. Structurally, RLRL inhibited myopia-associated choroidal thinning without detectable structural retinal damage. Metabolomic profiling revealed that RLRL reversed widespread LIM-induced dysregulation in amino acid and lipid metabolism. Specifically, RLRL upregulated metabolites associated with neuroprotection (N-acetylaspartylglutamate) and visual function (retinene), while downregulating markers linked to inflammation (arachidonic acid) and vascular dysregulation (asymmetric dimethylarginine). qPCR validation further showed that PTGS2 and IL-6 were increased in LIM retinas and reduced after RLRL treatment, whereas NOS3 showed the opposite trend. CONCLUSIONS: RLRL effectively retards myopia progression in chicks by modulating specific retinal metabolic profiles. The protective mechanism involves enhancing mitochondrial energy metabolism, suppressing pro-inflammation lipid pathways, and restoring nitric oxide signaling to preserve choroidal thickness, providing a metabolic basis for RLRL's safety and efficacy.
Structural insights into subtype-specific agonist recognition by sphingosine-1-phosphate receptors.
Yu L, Jiao H, Pang B … +7 more , Ti R, Gan B, Qin Z, Wang J, Zhu L, Hu H, Ren R
PLoS Biol · 2026 Apr · PMID 41961881 · Full text
Sphingosine-1-phosphate (S1P), a key metabolite of sphingolipids, plays crucial roles in a wide range of physiological and pathological processes. S1P primarily exerts its functions by binding to G protein-coupled sphing...
Sphingosine-1-phosphate (S1P), a key metabolite of sphingolipids, plays crucial roles in a wide range of physiological and pathological processes. S1P primarily exerts its functions by binding to G protein-coupled sphingosine-1-phosphate receptors (S1PRs), which comprise five subtypes (S1PR1-5) in humans, thereby activating these receptors and their downstream signaling pathways. Understanding the molecular determinants that govern agonist selectivity among different S1PR subtypes is vital for the rational and precise development of targeted therapeutic agents. Here, four cryo-electron microscopy structures of agonist-bound S1PR1-Gi1 complexes are reported. Through an integrated approach combining structural analysis, molecular dynamics simulations, and pharmacological assays, the molecular basis for the selectivity of CYM5442, HY-X-1011, Ponesimod, and SAR247799 toward S1PR1 over S1PR2-S1PR5 is uncovered. Nonconserved residues within the ligand-binding pocket and at the Gi1-protein interface contribute to S1PR1 selectivity by these agonists. A distinct agonist binding orientation toward transmembrane helices 5-7, combined with branched substituents that increase the agonist's molecular width, results in steric clashes with residues in S1PR3. Additionally, branched moieties located at the tail portions of the agonist restrict its deep insertion into the binding pocket of both S1PR3 and S1PR5. These structural features collectively enhance its selectivity for S1PR1 over S1PR3 and S1PR5. Furthermore, polar interactions with conserved polar residues in the top region of the binding pocket also influence agonist selectivity. Besides, the relatively broad molecular width of the agonist sterically hinders its binding into S1PR2 and S1PR4 pocket by nonconserved residue pairs bearing bulky side chains. These findings establish a structural framework for the rational design of next-generation S1PR1 highly selective agonists with improved therapeutic potential.
αβ integrin-targeted IR-820 dye-based small molecule probe for fluorescence imaging of tumor.
Yuan X, Zhang Y, Xuan J … +2 more , Yu S, Huang C
J Photochem Photobiol B · 2026 May · PMID 41955688 · Publisher ↗
Owing to its advantages of high sensitivity, high specificity, and real-time detection capabilities, fluorescence molecular imaging techniques, such as near-infrared (NIR) fluorescence imaging, have been used to real-tim...
Owing to its advantages of high sensitivity, high specificity, and real-time detection capabilities, fluorescence molecular imaging techniques, such as near-infrared (NIR) fluorescence imaging, have been used to real-time intraoperative navigation in oncological surgery. Despite a variety of NIR fluorescent probes have been developed for tumor detection in biological field, just limited amount of these probes including the 5-aminolevulinic acid, fluoresceine, methylene blue and pafolacianine were approved by FDA for clinical use. And only pafolacianine has the tumor target property. Herein, we developed a near-infrared fluorescent probe IR-820-cRGD for in vivo tumor imaging. This probe integrates the near-infrared dye IR-820 with a cyclic peptide cRGD that can bind to the integrin αβ receptor overexpressed on the surface of tumor cells, thus enabling the probe specifically accumulate at the tumor site. The results suggested that both the MDA-MB-231 cell line and tumor regions of nude mouse tumor models exhibited significantly higher fluorescence intensity compared to the normal cells or tissues. This demonstrates the probe's capability for precise tumor localization with low background signal, offering potential for early tumor diagnosis and therapeutic applications such as fluorescence-guided surgery.
Photodynamic inactivation for the control of disease-transmitting vectors: Mechanisms, photosensitizers, and biological targets - A review.
Garbuio M, Silva KJS, Dias LD … +2 more , Bagnato VS, Lima AR
J Photochem Photobiol B · 2026 May · PMID 41955687 · Publisher ↗
Climate change has expanded the geographic distribution and increased the prevalence of vector-borne infectious diseases worldwide. Rising temperatures, altered precipitation patterns, and the intensification of extreme...
Climate change has expanded the geographic distribution and increased the prevalence of vector-borne infectious diseases worldwide. Rising temperatures, altered precipitation patterns, and the intensification of extreme weather events favor vector survival, reproduction, and dispersal, undermining the effectiveness of conventional control strategies. Chemical and biological insecticides face increasing limitations due to resistance development, reduced environmental stability, and ecological concerns. Photodynamic inactivation (PDI) has emerged as a promising alternative for sustainable vector control due to its multi-target oxidative mechanism and intrinsically limited environmental persistence. The technique relies on the activation of photosensitizers by light in the presence of molecular oxygen (O), leading to the generation of reactive oxygen species (ROS) capable of inducing oxidative damage in essential biomolecules and resulting in vector inactivation. Unlike conventional insecticides, photosensitizers (PS) may undergo photodegradation after activation, minimizing environmental persistence, bioaccumulation, and non-target effects, while reducing the likelihood of resistance development. This review synthesizes current evidence on the application of PDI against vectors relevant to human and animal health, including insects and arachnids, with emphasis on mechanisms of action, classes of PS, light sources, and experimental conditions reported in laboratory and semi-field studies. Additionally, we examine how environmental variables influenced by climate change, such as temperature, solar radiation, precipitation patterns, and water turbidity, may affect photodynamic efficiency under field conditions. A literature analysis was conducted using Web of Science, PubMed, and Scopus databases (2021-2025). In sum, we identify key research gaps, methodological challenges, and future perspectives for integrating PDI into climate-resilient integrated vector management strategies.
Dietary restriction shapes intergenerational ribosome abundance and early growth of Caenorhabditis elegans offspring.
Pradhan S, Stojanovski K, Dellemann F … +4 more , Psalmon S, Tuomaala J, Stroustrup NE, Towbin BD
PLoS Biol · 2026 Apr · PMID 41955178 · Full text
Cells adjust their proteome to their environment. Most prominently, ribosome expression often scales near linearly with the cellular growth rate to provide sufficient translational capacity while preventing metabolically...
Cells adjust their proteome to their environment. Most prominently, ribosome expression often scales near linearly with the cellular growth rate to provide sufficient translational capacity while preventing metabolically wasteful ribosomal excess. In microbes, such proteome adjustments can passively perpetuate through symmetric cell division. However, in animals, a passive propagation is hindered by the separation between soma and germline. This separation raises the question whether the proteome of animals is reset at every generation or can be propagated from parent to offspring across this barrier. We addressed this question for the intergenerational effects of dietary restriction in Caenorhabditis elegans, combining proteomics and live imaging. Under ad libitum feeding, the offspring of dietarily restricted mothers grew more slowly than progeny of well-fed mothers. However, this growth disparity was attenuated when mTORC1 signaling in the progeny was inhibited, creating conditions in which the protein-synthesis capacity at hatching is less limiting. Maternal inhibition of mTORC1 signaling, either ubiquitously or specifically in the pharynx, similarly reduced growth and ribosomal protein levels in offspring, whereas other growth-reducing perturbations, such as reduced insulin signaling or mTORC1 inhibition in the epidermis, did not reduce progeny ribosomal protein levels. We conclude that maternal physiology shapes ribosomal protein provisioning across the soma-germline boundary, thereby modulating early offspring growth in accordance with post-hatching ribosome demand.
Specificity and recognition of the ADP-ribosyl-ubiquitin modification in the DNA damage response.
Chatrin C, Zhu K, Simmons MDR … +12 more , Maginn L, Schützenhofer K, Lu Y, Đukić N, Wijngaarden S, Kloet MS, Kliza KW, Heden van Noort GJV, Filippov DV, Ahel D, Smith R, Ahel I
PLoS Biol · 2026 Apr · PMID 41926452 · Full text
ADP-ribosylation (ADPr) is a post-translational modification that has regulatory roles in multiple cellular pathways including the DNA damage response and in innate immunity. Recently, it has been uncovered that ADP-ribo...
ADP-ribosylation (ADPr) is a post-translational modification that has regulatory roles in multiple cellular pathways including the DNA damage response and in innate immunity. Recently, it has been uncovered that ADP-ribose can be further modified by a family of ubiquitin E3 ligases, the DELTEXES, which catalyze ubiquitin transfer directly onto ADP-ribose, creating a hybrid ADPr-Ub modification which can be recognized by proteins with dedicated ADPr-Ub binding domains. With this hybrid modification recently been identified in cellular systems, we use a series of in vitro and cellular assays in human cells to investigate the amino acid preference for ADPr-Ub production as well as conditions required for reversal of the modification. We show that ADPr on both serine and glutamate-linked peptides can be ubiquitinated by the RING-DTC domains of DTX2 and DTX3L in vitro and that this can be recognized by RNF114, RNF138 and RNF166 for ubiquitin chain elongation. Finally, we demonstrate that DTX2 rather than DTX3L plays a role in ADPr-Ub production at sites of DNA damage to promote the recruitment of RNF114, RNF138, and RNF166 in an HPF1-independent manner.
Targeting TNF-SDH axis in macrophages reverses abnormal succinate metabolism and M1 polarization to alleviate UVB-induced skin damage.
Li M, Guo Y, Sun X … +6 more , Chen S, Zhang R, Chen Y, Gu H, Chen X, Lian N
J Photochem Photobiol B · 2026 May · PMID 41921367 · Publisher ↗
Ultraviolet B (UVB) radiation is a major environmental factor causing skin damage, yet the actual role of macrophages in UVB-induced inflammatory remains incompletely understood. This study aimed to investigate the funct...
Ultraviolet B (UVB) radiation is a major environmental factor causing skin damage, yet the actual role of macrophages in UVB-induced inflammatory remains incompletely understood. This study aimed to investigate the function and metabolic regulation of macrophages in UVB-induced skin injury. Clinical specimens from sun-exposed and non-sun-exposed human skin, murine models of acute and chronic UVB-induced damage, ex vivo skin co-culture system, and in vitro keratinocyte-macrophage co-culture systems were employed in our study. We found that depletion of macrophages by clodronate liposome significantly alleviated UVB-induced mouse skin damage. Further analysis revealed that UVB radiation promoted M1 polarization and induced metabolic dysregulation of macrophages. Pharmacological inhibition of TNF signaling using R7050 suppressed M1 polarization and ameliorated skin damage, while also rescuing UVB-induced metabolic alterations in macrophages. Importantly, restoration of succinate dehydrogenase (SDH) in macrophages reversed M1 polarization. These results demonstrated that macrophages contributed to UVB-induced skin injury via metabolic alterations and M1 polarization, processes orchestrated by the TNF-SDH axis. Targeting this pathway may represent a promising therapeutic strategy for UVB-induced skin pathologies.
A novel method for drug-target affinity prediction by integrating predicted evolutionary information and multi-scale protein graphs.
Jiang M, Hang H, Cui Z … +8 more , Feng J, Pang W, Ma T, Zhang Z, Fan Y, Pang S, Zhou W, Zhang Y
BMC Biol · 2026 Mar · PMID 41913214 · Full text
BACKGROUND: Drug-target affinity (DTA) prediction is crucial for drug discovery. While protein evolutionary features are vital for identifying conserved regions, current methods rely on computationally expensive multiple...
BACKGROUND: Drug-target affinity (DTA) prediction is crucial for drug discovery. While protein evolutionary features are vital for identifying conserved regions, current methods rely on computationally expensive multiple sequence alignment (MSA), creating a significant bottleneck. To address this, we propose MAFI-DTA, a novel model that circumvents the computational burden of MSA by deriving evolutionary context directly from sequences using the advanced protein language model, ESM-3. Furthermore, we introduced a multi-scale protein graph construction strategy based on varying numbers of residues, enabling the effective extraction of structural information across different scales through a neural network integrating graph neural networks, BiLSTM, and transformer modules. RESULTS: Experimental validation on multiple benchmark datasets demonstrates that MAFI-DTA achieves significantly better performance compared to existing approaches. This improved accuracy is attributed to the effective incorporation of both the predicted evolutionary information and the multi-scale graph representations. The source code is available at https://github.com/aliveadult/MAFI . CONCLUSIONS: MAFI-DTA successfully captures crucial evolutionary and multi-scale structural context efficiently, overcoming the limitations of traditional MSA methods. This approach provides a high-performing tool that facilitates the study of drug-target interactions and accelerates the drug discovery process.
Structures of the human glucose-6-phosphate transporter provide insights into its transport cycle and substrate recognition.
Zhang W, Jiao H, Xue J … +7 more , Zhou J, Wang Y, Pan Q, Guo Y, Zhang G, Hu H, Guo X
PLoS Biol · 2026 Mar · PMID 41911224 · Full text
The human glucose-6-phosphate transporter (G6PT/SLC37A4) mediates the translocation of glucose-6-phosphate (G6P) from the cytoplasm into the endoplasmic reticulum, a process essential for glucose production and the maint...
The human glucose-6-phosphate transporter (G6PT/SLC37A4) mediates the translocation of glucose-6-phosphate (G6P) from the cytoplasm into the endoplasmic reticulum, a process essential for glucose production and the maintenance of blood glucose homeostasis between meals. Dysfunction of G6PT causes glycogen storage disease type Ib (GSD-Ib), a severe metabolic disorder characterized by hypoglycemia, hepatomegaly, and neutropenia. Despite its physiological and clinical significance, the structural basis of G6P recognition and the molecular mechanisms underlying GSD-Ib have remained elusive. Here, we present cryo-electron microscopy structures of human G6PT, revealing a monomer in an outward-open state at 3.1 Å and a homodimeric assembly in a face-to-face topology at 3.3 Å. By combining computational modeling of the G6P-G6PT complexes with functional characterization, we have uncovered the key molecular elements that govern the alternating-access mechanism: an electropositive substrate-binding pocket tailored for phosphorylated sugars; conserved aromatic residues that seal the cytosolic gate; and a dynamic inter-domain salt bridge that regulates the conformational transition. Our work provides fundamental insights into the transport cycle of the organophosphate:phosphate antiporter (OPA) family, offers a framework for interpreting GSD-Ib pathology at the molecular level, and establishes a foundation for advancing the mechanistic understanding of the human SLC37 family.
Subcellular photoprotection through precision nutraceuticals: Divergent actions of rutin and punicalagin on redox and mitochondrial homeostasis in human dermal fibroblasts.
Riente A, Di Giacinto F, De Giulio MM … +5 more , Niccolini B, Tabolacci E, Clementi ME, De Spirito M, Maulucci G
J Photochem Photobiol B · 2026 May · PMID 41895055 · Publisher ↗
Excessive ultraviolet A (UVA) exposure is a major environmental factor contributing to skin photoaging and oxidative damage. Identifying natural compounds that can counteract these effects is increasingly relevant for pr...
Excessive ultraviolet A (UVA) exposure is a major environmental factor contributing to skin photoaging and oxidative damage. Identifying natural compounds that can counteract these effects is increasingly relevant for preventive and personalized healthcare. Precision nutrition uses diet-derived bioactives to modulate molecular pathways in defined cellular contexts. Polyphenols are promising for sustaining redox and metabolic balance under stress. This study examined the photoprotective actions of rutin (buckwheat, citrus peel) and punicalagin (pomegranate) in human dermal fibroblasts exposed to UVA radiation. Phasor-based fluorescence lifetime imaging microscopy (FLIM) quantified lipid peroxidation-related oxidative stress (F) and oxidative phosphorylation activity (F). Mitochondrial morphology was assessed via fission (Fis1) and fusion (MFN2) markers. Though UVA exposure tended to increase oxidative stress, the observed variation is not significant. Rutin provided superior antioxidant protection under UVA stress, substantially reducing F to 0.129 ± 0.02 with a near-significant trend, while punicalagin demonstrated stronger baseline antioxidant activity. Both compounds enhanced oxidative phosphorylation under stress: punicalagin increased F to 0.823 ± 0.02 (p = 0.004 vs UVA) and rutin to 0.789 ± 0.02 (p = 0.023 vs UVA). UVA disrupted mitochondrial networks, elevating fission and reducing fusion. Rutin reversed these effects, restoring fusion and reducing fission, whereas punicalagin provided partial recovery. In summary, rutin offered broader cytoprotection by mitigating oxidative stress and preserving mitochondrial integrity, while punicalagin mainly supported metabolic activity. These distinct responses highlight polyphenol-based nutraceuticals as precision tools for targeted skin photoprotection, suggesting their potential use in dietary or topical formulations to counteract everyday UVA exposure and photoaging.
Agronomic Performance, Mineral Composition, and Biochemical Characteristics of Basil ( L.) Grown in Trout () Aquaponic Systems.
Elakrouch M, Mohaddab M, Elmoussaoui S … +3 more , Libault A, Rachid A, Jijakli MH
Biology (Basel) · 2026 Mar · PMID 41892271 · Full text
Aquaponic systems are among the sustainable approaches for combining fish farming and plant cultivation and have been proposed as potentially economically viable food production technologies. Their performance depends on...
Aquaponic systems are among the sustainable approaches for combining fish farming and plant cultivation and have been proposed as potentially economically viable food production technologies. Their performance depends on the balanced environmental conditions shared by fish, nitrifying bacteria, and plants. This study assessed the performance of a trout-based () decoupled aquaponic system for basil ( L.) growth and essential oil composition. Two cultivation strategies were compared over 60 days: a non-supplemented system relying exclusively on trout rearing water, and a system supplemented with mineral nutrients formulated according to the recommendations of the Hoagland nutrient solution. Basil grown without mineral supplementation maintained a healthy appearance and stable physiological status, with satisfactory growth, although it remained lower than in supplemented plants. The mineral profile of the plants showed similar nitrate and phosphorus concentrations between non-supplemented and supplemented plants, with nitrate levels of 5.40 ± 0.29 mg g and 5.52 ± 0.29 mg g, respectively, and phosphorus levels of 5.46 ± 0.23 mg g and 6.14 ± 0.91 mg g, respectively. In contrast, potassium concentration was lower in non-supplemented plants (36.89 ± 3.31 mg g) compared to supplemented plants (55.56 ± 7.16 mg g). Essential oil yield expressed per cultivated surface area remained comparable between systems, reaching 2.96 and 3.09 mL m in the supplemented and non-supplemented systems, respectively. GC-MS analysis revealed that linalool (≈24%) was the predominant compound in both systems. Notably, estragole content was higher in non-supplemented plants (21.35 ± 1.46%) compared to supplemented plants (5.24 ± 0.68%). Overall, trout-based aquaponic systems not only support satisfactory basil growth but also enhance the production of essential oils with desirable aromatic characteristics, representing a sustainable and efficient strategy for aromatic plant cultivation.
Organizational Principles of Biological Systems.
Navarro-Quiroz RC, Navarro Quiroz K, Navarro Quiroz V … +14 more , Gabucio A, Fernández-Cisnal R, Geribaldi-Doldán N, Fernandez-Ponce C, Gomar IS, Bello Lemus Y, Zárate Peñata E, Pacheco-Lugo LA, Londoño-Pacheco LC, Rebolledo Cobos M, Acosta Hoyos A, Pava Garzon D, Camacho JLV, Navarro Quiroz E
Biology (Basel) · 2026 Mar · PMID 41892259 · Full text
How does the complex, adaptive, and autonomous organization of life emerge from the laws of physics and information? This review argues that the answer lies in a convergent set of universal organizational principles that...
How does the complex, adaptive, and autonomous organization of life emerge from the laws of physics and information? This review argues that the answer lies in a convergent set of universal organizational principles that constitute a physical and informational grammar of the living. Living systems are dissipative structures that achieve organizational closure-materially and energetically open, yet causally closed-thereby attaining genuine autonomy and agency. Their architecture exhibits fractal and modular scaling laws that maximize energy flow, robustness, and evolvability under universal physical constraints. Critically, organisms operate at critical transitions-zones of controlled instability where fluctuations amplify information processing, transforming noise into adaptive signal. This self-organized criticality enables functional degeneracy, relational redundancy, and evolutionary antifragility. Cognition emerges as a distributed process of active inference, operating through a predictive-corrective cycle that integrates perception, action, and learning under the Free Energy Principle. From molecular networks to ecosystems, the same physico-informational grammars unfold recursively, revealing a deep organizational holography: the principles of organization are replicated across scales. Evolution under the Law of Increasing Functional Information is not random drift, but a directional expansion of functional complexity-a thermodynamic gradient towards greater agency. This synthesis challenges biological exceptionalism: the trajectory from thermodynamics to cognition is continuous, physically constrained, and potentially inevitable. Life does not violate physical laws-it fulfills them in regimes of high informational complexity, instantiating fundamental principles in self-organized architectures capable of prediction, memory, and purpose. The objective of this work is to articulate how the synthesis of these principles not only unifies physics and biology, but also illuminates the profound continuity between thermodynamics, chemistry, informational constraints, organization, and the mind.
Pan-Cancer Analysis of Gene Reveals Tumor-Specific Prognostic Effects.
Alfadul SM, Omama K, Potapova AY … +9 more , Ivanov-Rostovtsev PA, Fanian M, Mubarak R, Gasimelseed HA, Balla MM, Bakhiet AMA, Berma K, Alfaki M, Babak MV
Biology (Basel) · 2026 Mar · PMID 41892220 · Full text
Pregnancy-associated plasma protein A () is a metalloproteinase that regulates insulin-like growth factor availability via cleavage of IGF-binding proteins, yet its role in cancer remains incompletely understood. Using i...
Pregnancy-associated plasma protein A () is a metalloproteinase that regulates insulin-like growth factor availability via cleavage of IGF-binding proteins, yet its role in cancer remains incompletely understood. Using integrated public datasets, we systematically examined expression, prognostic relevance, cellular localization, and stromal associations across multiple tumor types. was reduced in several cancers and primarily localized to stromal cells, whereas in cholangiocarcinoma and thyroid carcinoma it was elevated and also detected in malignant cells. High expression was associated with poorer overall survival in bladder, cervical, lung squamous, mesothelioma, pancreatic, and gastric cancers, but exhibited a protective effect in lower-grade glioma. In tumors with adverse prognosis, strongly correlated with cancer-associated fibroblast (CAF) infiltration and CAF marker genes; however, multivariable Cox analyses indicated that generally retained an independent prognostic factor, whereas CAF infiltration was mostly not independently associated with overall survival. Interestingly, in LGG, despite negative -CAF correlations, multivariable analysis showed that remained protective while CAF infiltration was associated with worse survival. Pathway analyses linked -associated genes to proteoglycans in cancer and PI3K-AKT and RAS signaling. Collectively, these findings establish as an independent prognostic factor across most cancers, while its expression frequently coincides with high CAF infiltration in select tumor types, highlighting the need for further investigation.
Earthworm Powder Mitigates Soybean Meal-Induced Growth Inhibition in Rice Field Eel () by Regulating Appetite and Improving Intestinal Health.
Hou K, Wang H, Zhang L … +7 more , Wang X, Zhang H, Wang F, Deng Q, Yang X, Zhang J, Hu Y
Biology (Basel) · 2026 Mar · PMID 41892216 · Full text
The substitution of fish meal with soybean meal (SBM) in aquafeeds aligns with sustainable development but often leads to depressed feed intake and growth in fish. This study aimed to investigate the mitigating effect of...
The substitution of fish meal with soybean meal (SBM) in aquafeeds aligns with sustainable development but often leads to depressed feed intake and growth in fish. This study aimed to investigate the mitigating effect of earthworm powder (EP) on these negative impacts in rice field eels (), focusing on appetite regulation, intestinal health, and gut microbiota. Three isonitrogenous (~41% crude protein) and isolipidic (~6.4% crude lipid) diets (control [CON], high-SBM [SBM], and SBM + 2.5% EP [EP]) were tested in a 56-day trial. Juveniles (initial weight 18.00 ± 0.01 g) were stocked at 40 fish per net (0.5 m × 0.5 m× 0.5 m) and fed to visual satiety once daily. The results indicated that EP improved growth performance through a dual mechanism. Firstly, it was associated with significantly increased feed intake, correlated with the upregulated expression of orexigenic genes (, ) in the brain, and associated with reduced levels of anorexigenic hormones (Cholecystokinin, Leptin). Secondly, it correlated with enhanced intestinal health, evidenced by improved morphology (villus height, goblet cells), improved digestive enzyme activity, enhanced antioxidant capacity (increased Catalase and Superoxide Dismutase activities), repaired intestinal barrier function (upregulated , ), and alleviated intestinal inflammation (downregulated , ). Furthermore, EP supplementation was associated with a shift in gut microbiota, including the suppression of the potential pathogen and promotion of the beneficial bacterium , alongside increased concentrations of major short-chain fatty acids (acetate, propionate, and butyrate). These correlative observations suggest that EP may help mitigate the growth-inhibiting effects of SBM in , offering a potential functional strategy for high-SBM aquafeeds.
Structural insights into photo-state-specific binding of affibody Aff6 to the photosensory core module of DrBphP.
Zhu L, Wang R, Jin M … +4 more , Dong Y, Zhao H, Wang J, Zhu L
J Photochem Photobiol B · 2026 May · PMID 41887156 · Publisher ↗
Light-inducible heterodimerization systems offer precise, reversible control of protein interactions in living cells. Leveraging the high tissue-penetration of red/far-red light, the MagRed system, composed of a bacterio...
Light-inducible heterodimerization systems offer precise, reversible control of protein interactions in living cells. Leveraging the high tissue-penetration of red/far-red light, the MagRed system, composed of a bacteriophytochrome Deinococcus radiodurans BphP (DrBphP) and its engineered affibody binder Aff6, achieves robust photoswitchable dimerization. This makes MagRed well-suited for in vivo and deep-tissue optogenetic application. However, the structural mechanism underlying Aff6's photo-state-specific recognition of DrBphP remains elusive. Here, we combine solution NMR spectroscopy, surface plasmon resonance (SPR), molecular docking and mutational analysis to elucidate the light-dependent interaction between a monomeric photosensory core module of DrBphP (DrBphP-PCM) and Aff6. We show that DrBphP-PCM alone is sufficient for light-inducible heterodimerization with Aff6, exhibiting a ∼ 23-fold affinity difference between the Pfr and Pr states. NMR titration reveals that Aff6 binds primarily to the PHY domain and the C-terminal region of the helical spine. Furthermore, docking and mutagenesis identify a key aromatic interaction (involving F327/H334 of DrBphP and F18 of Aff6) as the molecular basis for this conformational selectivity. Additionally, Aff6 binding stabilizes the Pfr state and retards the Pfr-to-Pr reversion of DrBphP-PCM. These findings not only provide critical structural insight into MagRed function but also establish a foundation for rationally engineering next-generation phytochrome-based optogenetic tools.
Proteome dynamics during establishment of California grunion (Leuresthes tenuis) cell lines.
Corona MM, Li J, Kültz D
BMC Biol · 2026 Mar · PMID 41882687 · Full text
BACKGROUND: Establishing continuous cell lines is hindered by limited molecular resolution of culture establishment and the transition to sustained proliferation. Here, proteome changes across passages were quantified in...
BACKGROUND: Establishing continuous cell lines is hindered by limited molecular resolution of culture establishment and the transition to sustained proliferation. Here, proteome changes across passages were quantified in two independently derived California grunion (Leuresthes tenuis) embryonic-derived cell cultures, alongside morphology and growth metrics, to identify proteome dynamics associated with early establishment and subsequent stabilization of continuous proliferation under the standard conditions. RESULTS: Morphological analysis identified a reproducible transition window centered on passage 4 (P4), coincident with changes in growth trajectories and consolidation toward epithelial-like morphology in three replicate cell lines LtE-1, LtE-2, and LtE3. Two of these replicate lines (LtE1 and LtE2) were analyzed by quantitative cell population proteomics confirming this transition, consistent with establishment-associated selection and/or cell-state change in a mixed early culture. Marker proteins associated with epithelial identity increased in abundance while fibroblast-associated markers declined. Across the transition window and subsequent passages, LtE-1 and LtE-2 shared broad remodeling of biosynthetic, proteostatic, adhesion/ECM, and lipid-related functions, and recurrence-filtered interaction networks highlighted passage-linked module consolidation. However, LtE-1 and LtE-2 differed in their temporal trajectories (transient surges in LtE-1 versus sustained reinforcement in LtE-2). Because early cultures contained mixed morphologies and cell population proteomics integrates across subpopulations, these patterns are presented as proteome dynamics of establishment and candidate biosignatures rather than definitive cell-intrinsic mechanisms. CONCLUSIONS: Passage-resolved cell population proteomics in two replicate California grunion embryonic-derived cell cultures define a baseline of establishment-associated remodeling and identifies candidate biosignatures linked to a reproducible transition window and subsequent stabilization of proliferation. The resulting passage-resolved baseline motivates lineage-resolved validation to distinguish the relative contributions of selection, cell-state transitions, and media adaptation to the observed establishment trajectory.
Zr-modified TiO₂ nanocomposites with enhanced visible-light photocatalytic and photobiological performance.
Karthikeyan B, Jenefa T, Ramya KS … +4 more , Vanitha U, Rajaraman D, Sakthivel M, Nagaraj K
J Photochem Photobiol B · 2026 May · PMID 41865704 · Publisher ↗
A green sol-gel method was utilized to produce a Zr-decorated TiO₂ nanocomposite exhibiting improved photocatalytic and biological activity under visible light irradiation. X-ray diffraction (XRD), scanning electron micr...
A green sol-gel method was utilized to produce a Zr-decorated TiO₂ nanocomposite exhibiting improved photocatalytic and biological activity under visible light irradiation. X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy-dispersive X-ray spectroscopy (EDX) provided structural and morphological characterisation, confirming the coexistence of anatase and rutile phases, with acidic conditions (pH 2) promoting rutile production. Diffuse reflectance spectroscopy (DRS) demonstrated altered optical properties due to Zr inclusion and nanoscale phenomena. The photocatalytic efficacy was assessed via the degradation of Brilliant Green dye, revealing that the Zr-TiO₂ nanocomposite demonstrated much superior performance compared to pristine TiO₂, especially under solar illumination, due to enhanced visible-light absorption and charge separation. Operational parameters, such as solution pH, were tuned to improve degrading efficiency. In addition to photocatalysis, the nanocomposite exhibited significant antibacterial and antifungal properties, an elevated antioxidant capacity of 89.4%, and remarkable anti-inflammatory benefits. In vitro cytotoxicity investigations demonstrated selective anticancer efficacy against MCF-7, KB, and HepG2 cell lines, while displaying no harm towards normal NHDF B cells. These results underscore the promise of Zr-TiO₂ nanocomposites for combined environmental remediation and photobiological applications.
Generative AI in structure-based drug discovery.
Zhong Z, Durrant JD
BMC Biol · 2026 Mar · PMID 41864943 · Full text
Generative artificial intelligence is reshaping how researchers discover protein-binding compounds and develop them into drug candidates. Unlike traditional methods that screen existing molecules, structure-based generat...
Generative artificial intelligence is reshaping how researchers discover protein-binding compounds and develop them into drug candidates. Unlike traditional methods that screen existing molecules, structure-based generative AI designs novel compounds tailored to a protein's three-dimensional binding pocket. This review outlines how these approaches are applied in early drug discovery, focusing on general principles. We categorize methods according to their generative modeling paradigms and their strategies for using structural data to guide molecular design, distinguishing de novo incremental builders from models that generate full structures. We also survey lead-optimization techniques, highlighting a recent shift toward generation-driven medicinal chemistry.
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