Umami is a fundamental taste sensation, often described as a delicious and pleasant flavor perception. To enhance or complement the original flavor and meet the tastes of diverse regions, umami dipeptides have been extensively utilized in global food manufacturing. Currently, the application and purification techniques of dipeptides are relatively mature, while their umami mechanisms and molecular modification are both scarce. In this work, the 3D structure of the umami dipeptide target T1R1/T1R3 was first obtained through sequence alignment and homology modeling, then followed by the successful construction of a database containing 400 samples of dipeptides. Subsequently, the complex models of T1R1/T1R3, respectively, with DG (Asp-Gly) and EK (Glu-Lys) (i.e., T1R1_DG/T1R3, T1R1/T1R3_DG, T1R1_EK/T1R3, and T1R1/T1R3_EK) were obtained via molecular docking and virtual screening. Finally, based on comparative molecular dynamics (MD) simulation trajectories, the binding free energy was calculated to investigate receptor–ligand recognition and conformational changes, providing some implications for potential modifications of umami dipeptides. T1R1 tends to bind relatively small umami dipeptides, whereas T1R3 does the opposite, both of which favor the recognition of acidic and hydrophilic dipeptides. By comparing strategies such as hydroxyl introduction and chain length alteration, electrostatic effects may be more important than non-polar effects in molecular design. This work not only explores the recognition mechanism of umami dipeptides with the receptor T1R1/T1R3 showing certain theoretical significance, but also provides feasible suggestions for dipeptide screening and modification having certain application value.

MRNA vaccines have shown great potential in responding to emerging infectious diseases, with their efficacy and stability largely dependent on the delivery vehicles—lipid nanoparticles (LNPs). This study aims to explore the mechanisms by which LNPs encapsulate mRNA, as well as the effects of different N/P ratios and acid types in nucleic acid solutions on the structure and properties of LNPs, using the ethanol solvent injection method as the encapsulation technique. Six systems were designed, based on the composition and proportions of the existing mRNA vaccine mRNA-1273, and molecular dynamics (MD) simulations were employed to investigate the self-assembly process of LNPs. Ethanol was used as a solvent instead of pure water to better mimic experimental conditions. The results indicate that lipid components self-assemble into nanoparticles under neutral conditions, with the ionizable lipid SM-102 predominantly concentrating in the core of the particles. Upon mixing with nucleic acids in acidic conditions, LNPs undergo disassembly, during which protonated SM-102 encapsulates mRNA through electrostatic interactions, forming stable hydrogen bonds. Cluster structure analysis revealed that the four lipid components of LNPs are distributed sequentially from the outside inwards as DMG-PEG 2000, DSPC, cholesterol, and protonated SM-102. Moreover, LNPs constructed under low pH or low N/P ratios using citric acid exhibited larger volumes and more uniform distribution. These findings provide a scientific basis for further designing and optimizing LNP components to enhance the efficacy of mRNA vaccine encapsulation.

Understory vegetation is a critical component of forest ecosystems. Its removal can substantially alter litter decomposition processes, with cascading effects on carbon (C) and nutrient cycling in terrestrial ecosystems. However, the global response patterns of litter decomposition to understory removal and underlying controlling factors remain unclear. We conducted a meta-analysis of 330 observations from 29 peer-reviewed field litterbag studies to assess the effects of understory removal on litter decomposition. We evaluated the changes in decomposition rate, mass loss, and nutrient dynamics to quantify the impacts of understory removal on litter decomposition. We assessed the associated shifts in soil microbial communities, measured using phospholipid fatty acids (PLFAs), to examine how microbial responses mediate decomposition during understory removal. We examined whether canopy type moderated these responses and explored the key predictors of decomposition for understory removal. Understory removal significantly reduced litter decomposition rate and mass loss by an average of 29.6% and 14.8%, respectively, while increasing lignin remaining by 30.1%. Soil microbial biomass also declined, with total, fungal, and actinomycete PLFAs decreasing by 12.0%, 30.8%, and 27.5%, respectively. Across canopy types, understory removal decreased litter mass loss in both broadleaved and coniferous forests. However, the remaining N and P increased significantly in broadleaved forests but changed only marginally in coniferous forests. Random forest analysis showed that initial litter quality and variations in fungal biomass were the primary predictors of decomposition responses. Understory vegetation removal significantly suppresses litter decomposition by reducing fungal biomass, and interacting with litter quality constraints and canopy type strongly moderates these effects. This highlights the essential role of understory vegetation in sustaining nutrient cycling and microbial functioning in forest ecosystems and underscores its critical role in guiding sustainable forest management.

Poplar is a deciduous tree belonging to the willow family, whose wood has the characteristics of light texture and toughness. It can be used to produce pulp, and is one of the main raw materials in the paper industry. A large amount of lignin is produced during pulping and papermaking process, where the generated waste liquid and pollutants are one of the main sources of industrial pollution. Regulating lignin content not only enables factories to process more pulp, but also greatly reduces the use of chemical reagents and the production of pollutants. Caffeoyl coenzyme A O-methyltransferase (CCoAOMT) is a class of S-adenosyl methionine (SAM) methyltransferases, which can effectively regulate the total amount of lignin biosynthesis. At present, molecular recognition mechanism of CCoAoMT with the substrate caffeoyl coenzyme A (CCoA) and corresponding conformational change both remain unclear, significantly restricting the design of weakly active enzymes. In this work, the overall conformational changes of CCoAOMT after binding CCoA were firstly explored by comparative molecular dynamics (MD) simulations. The results show that the four regions of α1, α2, α6 and α8 located outside binding pocket show greater flexibility, which is conducive to substrate binding. Through free energy landscape (FEL) and conformation cluster analyses, the representative functional motion modes were investigated, with the regions involved being β5, α2 and α8. According to adaptive steered molecular dynamics (ASMD) simulations, the complete recognition process of the receptor by SAM and CCoA, and allostery in the transport channel of substrates both were observed. With the binding of substrates, the structure of CCoAOMT gradually becomes more compact, accompanied by its transport channel from open to closed state. By binding free energy prediction and energy decomposition, a series of key residues favoring the receptor-substrate mutual recognition were proposed. Specifically, CCoA exhibits H-bonds with N170, D218, T42, Y188, N39, R186, N174 and R30, as well as hydrophobic interactions with K1 and I40. In particular, Y188 and D218 both anchor CCoA caffeoyl group to the Ca²⁺ active site by forming stable H-bonds. Based on exhaustive single mutation and folding entropy calculation, six mutants (K1L, N39G, I40P, T42N, N174D and D218V) may be candidates for low-activity CCoAOMT.

The influence of forest type on soil aggregates distribution, stability, and the contribution of aggregate-associated carbon (C) to bulk soil organic carbon (SOC) remains poorly understood. This may be crucial for the accumulation and persistence of SOC in subtropical ecosystems. In this study, we examined soil aggregate distribution and stability at two depths (0–15 and 15–30 cm) in 10-, 20-, and 30-year-old Cryptomeria japonica (Japanese cedar) and Chimonobambusa quadrangularis (square bamboo) plantations. We further assessed the contribution of carbon (C) associated with distinct aggregate fractions to bulk SOC. Across all stand ages and soil depths, macroaggregates accounted for 19%–56% of total soil aggregates in Japanese cedar plantations, whereas their proportion was 30%–337% higher in square bamboo plantations. In contrast, fine aggregates constituted 3%–67% of total aggregates in Japanese cedar plantations, but were 29%–94% lower in square bamboo plantations than in Japanese cedar plantations. Compared with Japanese cedar plantations, aggregate mean weight diameter (MWD) and geometric mean diameter (GMD) increased by 17%–88% and 35%–152%, respectively, in square bamboo plantations. In Japanese cedar soils, C and nitrogen (N) were primarily concentrated in coarse macroaggregates and fine macroaggregates, whereas in square bamboo plantations, C and N were mainly associated with coarse macroaggregates only. Both aggregate-associated soil C and N varied significantly with aggregate size and forest type, and Japanese cedar soils exhibited higher aggregate C/N ratios, particularly in older stands. Bulk SOC was positively correlated with macroaggregate-associated C in both forest types and with the silt and clay fractions in Japanese cedar plantations. MWD increased with higher macroaggregate C content and declined as the proportion of C in smaller aggregate fractions increased. These findings indicate that forest type plays a critical role in regulating soil aggregation and SOC stabilization pathways, with square bamboo plantations enhancing C sequestration by promoting macroaggregate formation and stability.