Search for: All records

Among CRISPR-Cas genome editing systems,Streptococcus pyogenesCas9 (SpCas9), sourced from a human pathogen, is the most widely used. Here, through in silico data mining, we have established an efficient plant genome engineering system using CRISPR-Cas9 from probioticLactobacillus rhamnosus. We have confirmed the predicted 5’-NGAAA-3’ PAM via a bacterial PAM depletion assay and showcased its exceptional editing efficiency in rice, wheat, tomato, and Larix cells, surpassing LbCas12a, SpCas9-NG, and SpRY when targeting the identical sequences. In stable rice lines, LrCas9 facilitates multiplexed gene knockout through coding sequence editing and achieves gene knockdown via targeted promoter deletion, demonstrating high specificity. We have also developed LrCas9-derived cytosine and adenine base editors, expanding base editing capabilities. Finally, by harnessing LrCas9’s A/T-rich PAM targeting preference, we have created efficient CRISPR interference and activation systems in plants. Together, our work establishes CRISPR-LrCas9 as an efficient and user-friendly genome engineering tool for diverse applications in crops and beyond.

Hemoproteins have recently emerged as promising biocatalysts for new-to-nature carbene transfer reactions. However, mechanistic understanding of the interplay between productive and unproductive pathways in these processes is limited. Using spectroscopic, structural, and computational methods, we investigate the mechanism of a myoglobin-catalyzed cyclopropanation reaction with diazoketones. These studies shed light on the nature and kinetics of key catalytic steps in this reaction, including the formation of an early heme-bound diazo complex intermediate, the rate-determining nature of carbene formation, and the cyclopropanation mechanism. Our analyses further reveal the existence of a complex mechanistic manifold for this reaction that includes a competing pathway resulting in the formation of an N-bound carbene adduct of the heme cofactor, which was isolated and characterized by X-ray crystallography, UV-Vis, and Mössbauer spectroscopy. This species can regenerate the active biocatalyst, constituting a non-productive, yet non-destructive detour from the main catalytic cycle. These findings offer a valuable framework for both mechanistic analysis and design of hemoprotein-catalyzed carbene transfer reactions.

Understanding the relationship among elemental compositions, nanolamellar microstructures, and mechanical properties enables the rational design of high-entropy alloys (HEAs). Here, we construct nanolamellar Al_xCoCuFeNi HEAs with alternating high– and low–Al concentration layers and explore their mechanical properties using a combination of molecular dynamic simulation and density functional theory calculation. Our results show that the HEAs with nanolamellar structures exhibit ideal plastic behavior during uniaxial tensile loading, a feature not observed in homogeneous HEAs. This remarkable ideal plasticity is attributed to the unique deformation mechanisms of phase transformation coupled with dislocation nucleation and propagation in the high–Al concentration layers and the confinement and slip-blocking effect of the low–Al concentration layers. Unexpectedly, this ideal plasticity is fully reversible upon unloading, leading to a remarkable shape memory effect. Our work highlights the importance of nanolamellar structures in controlling the mechanical and functional properties of HEAs and presents a fascinating route for the design of HEAs for both functional and structural applications.

Soil water sustains life on Earth, and how to quantify water equilibrium and kinetics in soil remains a challenge for over a century despite significant efforts. For example, various models were proposed to interpret non‐Darcian flow in saturated soils, but none of them can capture the full range of non‐Darcian flow. To unify the different models into one overall framework and improve them if needed, this technical note proposes a theory based on the tempered stable density (TSD) assumption for the soil‐hydraulic property distribution, recognizing that the underlying hydrologic processes all occur in the same, albeit very complex and not measurable at all the relevant scales, soil‐water system. The TSD assumption forms a unified fractional‐derivative equation (FDE) using subordination. Preliminary applications show that simplified FDEs, with proposed hydrological interpretations and TSD distributed properties, effectively capture core equilibrium and kinetic water processes, spanning non‐Darcian flow, water retention, moisture movement, infiltration, and wetting/drying, in the soil‐water system with various degrees and scales of system heterogeneity. Model comparisons and evaluations suggest that the TSD may serve as a unified density for the properties of a broad range of soil‐water systems, driving multi‐rate mass, momentum, and energy equilibrium/kinetic processes often oversimplified by classical models as single‐rate processes.

A photochemical model of photosynthetic electron transport (PET) is needed to integrate photophysics, photochemistry, and biochemistry to determine redox conditions of electron carriers and enzymes for plant stress assessment and mechanistically link sun‐induced chlorophyll fluorescence to carbon assimilation for remotely sensing photosynthesis. Towards this goal, we derived photochemical equations governing the states and redox reactions of complexes and electron carriers along the PET chain. These equations allow the redox conditions of the mobile plastoquinone pool and the cytochrome b₆f complex (Cyt) to be inferred with typical fluorometry. The equations agreed well with fluorometry measurements from diverse C₃/C₄species across environments in the relationship between the PET rate and fraction of open photosystem II reaction centres. We found the oxidation of plastoquinol by Cyt is the bottleneck of PET, and genetically improving the oxidation of plastoquinol by Cyt may enhance the efficiency of PET and photosynthesis across species. Redox reactions and photochemical and biochemical interactions are highly redundant in their complex controls of PET. Although individual reaction rate constants cannot be resolved, they appear in parameter groups which can be collectively inferred with fluorometry measurements for broad applications. The new photochemical model developed enables advances in different fronts of photosynthesis research.

Hydrologically mediated hot moments (HM‐HMs) of transient anomalous diffusion (TAD) denote abrupt shifts in hydraulic conditions that can profoundly influence the dynamics of anomalous diffusion for pollutants within heterogeneous aquifers. How to efficiently model these complex dynamics remains a significant challenge. To bridge this knowledge gap, we propose an innovative model termed “the impulsive, tempered fractional advection‐dispersion equation” (IT‐fADE) to simulate HM‐HMs of TAD. The model is approximated using an L1‐based finite difference solver with unconditional stability and an efficient convergence rate. Application results demonstrate that the IT‐fADE model and its solver successfully capture TAD induced by hydrologically trigged hot phenomena (including hot moments and hot spots) across three distinct aquifers: (a) transient sub‐diffusion arising from sudden shifts in hydraulic gradient within a regional‐scale alluvial aquifer, (b) transient sub‐ or super‐diffusion due to convergent or push‐pull tracer experiments within a local‐scale fractured aquifer, and (c) transient sub‐diffusion likely attributed to multiple‐conduit flow within an intermediate‐scale karst aquifer. The impulsive terms and fractional differential operator integrated into the IT‐fADE aptly capture the ephemeral nature and evolving memory of HM‐HMs of TAD by incorporating multiple stress periods into the model. The sequential HM‐HM model also characterizes breakthrough curves of pollutants as they encounter hydrologically mediated, parallel hot spots. Furthermore, we delve into discussions concerning model parameters, extensions, and comparisons, as well as impulse signals and the propagation of memory within the context of employing IT‐fADE to capture hot phenomena of TAD in aquatic systems.