Search Results (347)

Autotrophic carbon-fixing microbes can assimilate atmospheric carbon dioxide into biomass via the Calvin–Benson–Bassham (CBB) cycle (their primary carbon fixation pathway), thereby reinforcing soil carbon sequestration in the plantation ecosystem; however, the succession of RubisCO-harboring microbial communities across stand ages remains poorly understood. Here, we investigated the community succession of microbes carrying the gene encoding RubisCO, a key enzyme in the CBB cycle, across a stand-age chronosequence in a Picea asperata plantation ecosystem. Our results revealed a progressive decrease in microbial α-diversity and a significant restructuring of community composition with increasing stand age, characterized by an enrichment of Proteobacteria and a concomitant depletion of Actinobacteria. While the Shannon–Wiener index was most strongly correlated with soil total nitrogen content, redundancy analysis identified soil pH as the predominant environmental driver of community turnover, a relationship that was found to be threshold-dependent, with substantial community shifts occurring in response to pH variations of 0.5 to 1.0 units. These findings suggest that sustaining the diversity of RubisCO-harboring microbes in older stands—a process potentially enhanced by soil nitrogen management—provides a viable strategy for augmenting the carbon sequestration capacity of managed forests through targeted microbiome regulation. Full article

Straw return improves paddy soil quality and nutrient cycling, but its combined effects with nitrogen application on extracellular enzyme activities and greenhouse gas emissions in cold-region paddies remain unclear. A field experiment was conducted in Northeast China under full straw return (8.8 t ha⁻¹) with six nitrogen rates (0, 110, 120, 130, 140, and 150 kg ha⁻¹); conventional nitrogen application without straw return (130 kg ha⁻¹) was the control (CK), while N0 distinguished straw input from nitrogen effects. Soil properties, extracellular enzyme activities, and CO₂, CH₄, and N₂O emissions were measured 20, 50, 80, 110, and 140 days after straw return. At 140 days, compared with CK, straw return increased the NH₄+-N and organic matter in the 0–15 cm soil layer by 41.75% and 28.69%, respectively, and reduced pH by 4.34%. Under N110–N150, straw return enhanced the carbon- and nitrogen-acquiring enzymes and oxidative enzymes by 15.88–162.23%. In particular, β-glucosidase, phenol oxidase, and peroxidase activities were significantly higher under N130–N140 than under CK. Compared with N150, N130–N140 maintained organic matter turnover without further increasing greenhouse gas emissions. Overall, under full straw incorporation in the Mollisol paddies of cool Northeast China, N130–N140 sustained high yield while balancing nutrient cycling, enzyme activity, and greenhouse gas mitigation. Full article

Corn dust is an abundant agro-industrial by-product with potential as an alternative energy source. Its use in animal feeding, however, is restricted by high fiber content and low digestibility. This study evaluated the effects of non-starch polysaccharide (NSP) enzymes and yeast (Candida tropicalis KKU20) on the chemical composition, fermentation characteristics, and microbial populations of fermented corn dust. The experiment was conducted using a completely randomized design with a 3 × 2 factorial arrangement plus an additional control treatment. Factor A consisted of three levels of enzyme supplementation (0.02%, 0.04%, and 0.06% of dry matter), and Factor B consisted of yeast supplementation (without yeast or with C. tropicalis KKU20, approximately 1 × 10¹³ cells/g of inoculum). The control treatment consisted of fermented corn dust without enzyme or yeast supplementation. Samples were fermented for 15 days prior to analysis. Yeast inoculation increased crude protein and non-fiber carbohydrate contents while reducing neutral detergent fiber, acid detergent fiber, and acid detergent lignin (p < 0.05). Significant enzyme × yeast interactions were observed for several components, particularly fiber fractions (p < 0.05). The reduction in fiber was more pronounced when enzymes were combined with yeast. Predicted energy values, including metabolizable and digestible energy, were increased following yeast supplementation (p < 0.05). Fermentation characteristics were mainly affected by yeast. Yeast-treated samples exhibited higher pH and ammonia–nitrogen concentrations, indicating increased nitrogen turnover during fermentation. In contrast, lactic and propionic acid concentrations were higher in treatments without yeast, while yeast inoculation was associated with lower acetic acid and slightly higher butyric acid levels. Microbial analysis indicated interactions between treatments for lactic acid bacteria populations, reflecting competition for available substrates. No coliform bacteria were detected, indicating acceptable hygienic quality. Overall, yeast inoculation modified the chemical composition of corn dust, particularly by increasing crude protein and reducing fiber fractions, while NSP enzymes contributed to fiber degradation, especially when combined with yeast. However, these changes reflect compositional modification rather than confirmed feeding value, and further evaluation under rumen or in vivo conditions is required. Full article

Drought stress significantly constrains crop productivity and yield stability. Sorghum (Sorghum bicolor L. Moench), a C4 cereal widely cultivated in arid and semi-arid regions, exhibits high water-use efficiency and remarkable drought tolerance. Understanding both the impacts of drought and the plant’s response mechanisms is essential for enhancing drought resilience in this crop. In this study, physiological changes and differential protein accumulation were analyzed in leaves of the sorghum inbred line BT × 623 under 10% PEG-6000-induced drought stress. The physiological adaptation to drought was characterized by improved water retention and mitigation of oxidative damage through the synergistic action of antioxidant enzymes. Using two-dimensional electrophoresis (2-DE) and MALDI-TOF-TOF mass spectrometry, 43 protein spots were successfully identified, corresponding to 38 unique proteins differentially expressed under osmotic stress. These proteins function in diverse biological processes, including protein synthesis, processing, and degradation; photosynthesis; carbohydrate and energy metabolism; transcriptional regulation; stress and defense; lipid and membrane metabolism; and amino acid metabolism. Proteomic profiling revealed that the coordinated modulation of multiple functional groups, such as those involved in photosynthesis, energy metabolism, transcriptional adjustment, ROS scavenging, and protein turnover, underpins sorghum’s osmotic stress adaptation. These findings provide key insights into the drought resistance mechanisms of sorghum at both physiological and proteomic levels. Full article

Intensive nitrogen (N) fertilization in Phyllostachys edulis (Carrière) J.Houz. forests increases productivity but also accelerates nitrous oxide (N₂O) emissions, posing a challenge to balancing forest yield with environmental sustainability. Silicon (Si), a beneficial element for bamboo, has emerged as a potential regulator of soil nitrogen (N) cycling, but its role in controlling N₂O emissions in forest ecosystems is not fully understood. In this study, we conducted a factorial pot experiment using P. edulis forest soil, with data collected over two years, but only the second-year results were analyzed, with controlled N (0, 80, and 160 mg kg⁻¹) and Si (0, 25, and 50 mg kg⁻¹) additions. The experiment lasted two years, but only the second-year data were used for analysis. We investigated how Si affected soil inorganic N dynamics, enzyme activities, plant growth, and cumulative N₂O emissions. Si addition significantly reduced N-induced N₂O emissions by up to 53%, with the strongest mitigation observed under moderate N input (p < 0.05, two-way ANOVA). This effect was associated with lower activities of AMO, NaR, and NiR, together with reduced availability of oxidized N substrates, indicating that Si mitigated N₂O emissions mainly by constraining upstream N transformation processes rather than by directly suppressing N₂O fluxes. Si addition also tended to promote plant biomass accumulation. These findings suggest that integrating Si fertilization into bamboo forest management may help improve nutrient use efficiency while mitigating greenhouse gas emissions. Full article

Ubiquitination is a reversible post-translational modification crucial for cellular homeostasis and protein degradation. It is orchestrated by a cascade of ubiquitin-activating enzymes (E1), conjugating enzymes (E2), and ligases (E3) that tag proteins with ubiquitin, and deubiquitinating enzymes (DUBs) that remove these tags. Through this tightly regulated ubiquitination/deubiquitination system, cells control protein turnover, localization, and activity, thereby governing processes ranging from cell cycle progression and DNA repair to immune and stress responses. Here, we review the structural and functional mechanisms of each class of enzymes in the ubiquitin–proteasome system, including E1, E2, E3, and DUBs, and highlight their roles in key signaling pathways and physiological processes. We further discuss how the dysregulation of these enzymes leads to diseases such as cancer, neurodegenerative disorders, and immune diseases, underlining the potential of targeting ubiquitination pathways for therapeutic intervention. Full article

Irreversible covalent enzyme inhibitors, including targeted covalent inhibitors (TCIs) and mechanism-based enzyme inhibitors (MBEIs), play an increasingly important role in drug discovery. Their pharmacological behavior is governed by intrinsic inactivation parameters, typically described by the inactivation constant K_I, the maximal inactivation rate constant k_inact, and their ratio k_inact/K_I. However, no consensus exists regarding how these parameters should be experimentally determined and interpreted, particularly in high-throughput screening environments where IC₅₀ values are often used as primary descriptors. This article presents a critical survey of the kinetic methodologies employed to characterize irreversible enzyme inhibition. Continuous progress-curve analysis, discontinuous end-point assays, IC₅₀-based estimation strategies, direct mass-spectrometric monitoring of covalent modification, and numerical approaches required by pre-incubation protocols are examined and compared. Attention is given to the statistical robustness of parameter estimation under realistic experimental error, including bootstrap-based uncertainty analysis. For mechanism-based enzyme inhibitors, the kinetic consequences of branching between productive turnover and irreversible inactivation are analyzed, and limitations of classical half-life-based linearization methods are discussed. Intrinsic inactivation parameters are distinguished from protocol-dependent observables, and experimental conditions that may compromise reliable parameter extraction are identified. The objective is to clarify how irreversible inhibitors should be kinetically characterized when the goal is mechanistic understanding and rational drug design. By bridging classical enzymology with current discovery practices, this review provides practical guidance on what experimental data can legitimately support and where caution is required. Full article

Background and Objectives: This study aimed to evaluate associations between dental caries, periodontal pockets, and radiologically detected periapical lesions in relation to serum levels of Dickkopf-1 (Dkk-1) and tartrate-resistant acid phosphatase 5B (TRAP-5B) in oncologic patients with ear, nose, and throat (ENT) cancer compared with healthy controls. Materials and Methods: The study included 63 subjects divided into a study group of 33 patients diagnosed with ENT cancer and a control group of 30 healthy individuals. Blood samples were collected to assess serum Dkk-1 levels using a sandwich enzyme immunoassay and TRAP-5B levels. Radiological dental evaluation included orthopantomography (OPT) and cone beam computed tomography (CBCT) to assess the number and depth of dental caries and the presence of periapical lesions. Periodontal pockets were recorded through clinical examination. Results: Serum biomarker analysis demonstrated significant differences between groups: TRAP-5B levels were significantly higher in patients with ENT cancer, whereas Dkk-1 concentrations were significantly lower compared with healthy controls (p < 0.001). OPT revealed up to eight carious lesions in both groups. The mean number of carious lesions was higher in healthy subjects (2.97 ± 2.48) than in patients with ENT cancer (2.06 ± 2.29). CBCT evaluation revealed 0–8 carious lesions in healthy individuals and 0–6 lesions in patients with ENT cancer, with a significantly higher mean number of lesions in the control group (2.97 ± 2.48 vs. 1.85 ± 1.89). Periodontal pockets were more frequent in patients with ENT cancer (0.67 ± 1.32) than in controls (0.37 ± 0.81). OPT evaluation also showed a higher mean number of periapical lesions in patients with ENT cancer (0.82 ± 1.29) compared with controls (0.37 ± 0.67). CBCT examination demonstrated that the mean number of periapical lesions in patients with ENT cancer was more than twice that of the control group, although this difference did not reach statistical significance. Conclusions: Patients with ENT cancer exhibited significantly altered systemic bone turnover biomarker profiles, characterized by increased TRAP-5B and decreased Dkk-1 levels. Clinically, these patients also presented a higher prevalence of periodontal pockets and periapical lesions, whereas carious lesions were more frequently detected in healthy individuals. The combined radiological and biochemical findings contribute to a better understanding of oral–systemic interactions in oncologic patients and highlight the importance of comprehensive dental evaluation prior to oncologic therapy. Full article

Montane forests are commonly limited by phosphorus (P) scarcity, yet Rhododendron species persist via specialized P-acquisition strategies. However, the microbial processes governing P utilization among wild Rhododendron species remain unclear. We collected soil and root samples from three wild Rhododendron species—Rhododendron latoucheae Franch. (R. latoucheae), Rhododendron fortunei Lindl. (R. fortunei) and Rhododendron simsii Planch. (R. simsii)—in a montane forest and analyzed soil P fractions, acid phosphatase activity, and fungal community traits to investigate their relationships with P cycling. The results showed significant differences in P fraction contents between non-rhizosphere and rhizosphere soils among the three species. In R. fortunei, rhizospheric NaOH-Po decreased tenfold while H₂O-Pi increased by 9.13 mg/kg, indicating a shift toward labile P. In contrast, R. latoucheae and R. simsii showed increases in moderately labile P by 32.54% and 22.09%, respectively. R. latoucheae exhibited the lowest acid phosphatase activity in non-rhizosphere soil (4.810 ± 0.560 μmol/d/g), which increased significantly in the rhizosphere. Fungal community analysis revealed a significant enrichment of Podila in the rhizosphere of R. latoucheae (10.84%) and R. simsii (9.17%), while Penicillium (6.80%), Trichoderma (3.65%) and Mortierella (5.83%) were dominant in the R. fortunei rhizosphere. R. latoucheae mineralized organic P through acid phosphatase hydrolysis driven by nutrient scarcity. R. fortunei likely mobilizes inorganic P through ericoid mycorrhizal-associated secretion of organic acids and the activity of specialized phosphate-solubilizing fungi facilitated by high substrate availability. Soil nutrients (SOC, TN, $\mathrm{N}{\mathrm{O}}_3^{-}$-N) influenced fungal abundances and indirectly shaped soil P fractions, whereas fungal taxa abundance in the rhizosphere directly drove P turnover. Our results confirm that different wild Rhododendron species employ distinct P-acquisition strategies mediated by rhizosphere fungi and enzyme activities, and provide new insights into microbial-driven P cycling in montane forests. Full article

Anthocyanins are widespread specialized metabolites that provide pigmentation and antioxidant capacity, contributing to pollinator and seed-disperser attraction and to plant resistance to diverse environmental stresses. In human diets, anthocyanins are valued for their antioxidant and health-promoting properties. The biosynthetic pathway of anthocyanins is relatively conserved across plant species and is controlled by structural genes that encode the enzymes of the pathway along with regulatory genes, particularly transcription factors. This network integrates developmental and environmental signals, with light serving as a dominant cue: anthocyanins typically accumulate in light-exposed tissues and are repressed in darkness. A key node in this light-dependent switch is CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase that, in the dark, promotes polyubiquitination and proteasome-mediated turnover of positive regulators of anthocyanin production. Although ELONGATED HYPOCOTYL 5 (HY5) is a canonical COP1 target and major activator of anthocyanin biosynthesis, COP1 control of this pathway extends well beyond HY5. Evidence from Arabidopsis and multiple horticultural crops, including apple, pear, eggplant, and tomato, indicates that COP1 also regulates anthocyanin accumulation through interactions with additional transcription factors and regulatory modules. Here, we synthesize recent advances in COP1-centered regulation of anthocyanin biosynthesis, with an emphasis on post-translational mechanisms and COP1 targets beyond HY5. We also discuss emerging opportunities to leverage this regulatory axis for nutritional improvement in horticultural species. Full article

Protein phosphorylation and dephosphorylation reactions of intracellular molecules catalyzed by enzymes such as kinases and phosphatases are essential reactions in a lot of cellular functions such as intracellular signal transduction in living systems. The design and synthesis of artificial enzyme mimics are important research topics in bioorganic and bioinorganic chemistry. In this paper, we report on the construction of artificial phosphatases via the supramolecular self-assembly of compounds such as an amphiphilic bis(Zn²⁺-cyclen) (cyclen = 1,4,7,10-tetraazacyclododecane) complex, barbital derivatives modified with benzocrown ethers and boronophenyl groups, and a copper(II) ion in a two-phase solvent system. We have developed a hypothesis whereby a mono(4-nitrophenyl)phosphate (MNP) substrate coordinates to the Cu₂(µ-OH)₂ core in supramolecular complexes and is activated either by Lewis acidic units such as alkali metal (Li⁺, Na⁺ and K⁺)-benzocrown ether complexes or by boronophenyl moieties. The findings suggest that supramolecular phosphatase functionalized with a benzo-12-crown-4-Li⁺ complex shows a higher level of activity in the MNP hydrolysis of a two-phase solvent system compared with that of our previous supramolecular phosphatases in terms of hydrolysis activity and catalytic turnover. Full article

Enzyme performance parameters, including the turnover number and specificity constant, exhibit remarkable diversity due to biological evolution and natural selection. In some bacterial and human enzymes, catalytic efficiencies approach fundamental physical limits, underscoring the importance of physical constraints on enzymatic function. A deeper understanding of these constraints, particularly in far-from-equilibrium irreversible processes, is therefore essential for rational enzyme engineering. Such constraints are most naturally addressed within the frameworks of nanothermodynamics and stochastic thermodynamics, which remain relatively unfamiliar to much of the molecular biology community. Recent theoretical and experimental advances indicate that classical enzyme kinetic parameters are not independent, but are systematically linked to energetic dissipation. In particular, enzymes appear to occupy a characteristic dissipation plane defined by entropy production, reflecting the coupled influence of thermodynamic principles and evolutionary selection. In this review, we synthesize evidence across diverse enzyme families demonstrating correlated increases in housekeeping dissipation, evolutionary divergence, and enzymatic performance. Together, these findings support dissipation as a physically grounded parameter that connects enzyme kinetics, biological evolution, and nonequilibrium thermodynamics. Full article

The growing demand for sustainable fertilization practices has stimulated interest in circular fertilizers derived from agro-industrial and agricultural wastes. This study assessed the agronomic and biological performance of several waste-based fertilizers—produced through composting, vermicomposting, and sulfur–bentonite enrichment—on chemical and microbiological soil properties. Composts and vermicomposts were prepared from olive pomace, citrus residues, wood sawdust, and straw, with or without elemental sulfur obtained from petroleum gas desulfurization. Field trials were conducted on a sandy loam soil (Motta San Giovanni, Italy) to compare the different formulations. After six months, soils amended with waste-based fertilizers exhibited significant improvements in key parameters relative to both the control and mineral fertilizer treatment. Vermicompost applications (SV1, SV2) increased total organic carbon by 20–30% (up to 2.1%), total nitrogen by 35–45% (0.22–0.23%), microbial biomass carbon by ~25% (≈1090 µg C g⁻¹), and dehydrogenase and fluorescein diacetate activities by 10–20% compared with compost or sulfur–bentonite treatments. Compost amendments (SC1, SC2) raised soil pH (8.2–8.3) and organic matter content (≈3.3–3.6%), while sulfur–bentonite formulations lowered pH to 7.1–7.3 and increased water-soluble phenols (up to 40 µg TAE g⁻¹ d.s). The highest cation exchange capacity (22–23 cmol (+) kg⁻¹) was observed in vermicompost-amended soils. Microbial community analysis revealed greater fungal abundance under sulfur–bentonite treatments, whereas bacteria and actinomycetes predominated in compost-amended soils. Principal Component Analysis (explaining 76% of variance) identified two main functional pathways: vermicompost treatments clustered with indicators of high biological activity (TOC, TN, MBC, and enzyme activities), while compost and sulfur–bentonite treatments were associated with pH, phenolic compounds, and fungal biomass, reflecting slower but more stable organic matter turnover. Overall, vermicompost-based fertilizers proved most effective in enhancing short-term nutrient availability and microbial activation, whereas composts favored long-term soil carbon accumulation and stability. These results highlight the potential of circular fertilizers derived from agro-industrial wastes to restore soil health, close nutrient cycles, and reduce dependence on synthetic fertilizers—thereby advancing sustainable and circular agriculture. Full article

Osteoarthritis (OA) is a degenerative joint disease characterized by cartilage degradation, synovial inflammation, osteophyte formation, joint space narrowing, and persistent pain. During OA progression, synovial inflammation triggers the release of pro-inflammatory cytokines, including IL-1β, TNF-α, and IL-6, which activate matrix metalloproteinases (MMPs) and aggrecanases, driving extracellular matrix (ECM) degradation. Emerging evidence indicates that transient receptor potential (TRP) channels, via calcium (Ca²⁺) signaling, function as molecular sensors in joint tissues, including chondrocytes, synoviocytes, sensory neurons, and regulate cartilage homeostasis, synovial inflammation, and OA pain. In cartilage, TRP channels govern chondrocyte survival, mechanotransduction, autophagy, oxidative stress, and ECM turnover, thereby modulating cartilage homeostasis. In synovial tissue, TRP channels regulate inflammatory signaling and cytokine, chemokine, and matrix-degrading enzyme production, leading to synovitis and joint destruction. In sensory neurons innervating the joint, TRP channels respond to mechanical and inflammatory stimuli, increasing nociceptor excitability, neuropeptide release, and pain sensitization, driving OA pain. TRP channel signaling also modulates immune cell infiltration and macrophage-driven inflammation, sustaining chronic pain and tissue damage in OA. This review summarizes emerging evidence on TRP channel functions in OA pathogenesis and highlights their potential as therapeutic targets to alleviate inflammation, protect cartilage, and reduce OA-associated pain. Full article

Age-related osteoporosis is driven in part by senescence-associated rewiring of bone marrow mesenchymal stem cells (MSCs) from osteogenic toward adipogenic fates. Accumulating evidence indicates that epigenetic drift and reduced autophagy are not isolated lesions but are mechanistically coupled through a bidirectional DNA methylation and autophagy axis. Here, we summarize how promoter hypermethylation of genes involved in autophagy and osteogenesis suppresses autophagic flux and osteoblast lineage transcriptional programs. Conversely, autophagy insufficiency reshapes the methylome by limiting methyl donor availability, most notably S-adenosylmethionine (SAM), and by reducing the turnover of key epigenetic regulators, including DNA methyltransferases (DNMTs), ten-eleven translocation (TET) dioxygenases, and histone deacetylases (HDACs). This self-reinforcing circuitry exacerbates mitochondrial dysfunction, oxidative stress, and inflammation driven by the senescence-associated secretory phenotype (SASP), thereby stabilizing adipogenic bias and progressively impairing marrow niche homeostasis and bone remodeling. We further discuss therapeutic strategies to restore balance within this axis, including selective modulation of epigenetic enzymes; activation of AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin (mTOR) signaling with downstream engagement of Unc-51-like autophagy-activating kinase 1 (ULK1) and transcription factor EB (TFEB); targeting sirtuin pathways; mitochondria- and autophagy-supportive natural compounds; and bone-targeted delivery approaches or rational combination regimens. Full article