Radix Rehmanniae Praeparata promoted zebrafish fin regeneration through aryl hydrocarbon receptor-dependent autophagy.

HEADINGS ETHNOPHARMACOLOGICAL RELEVANCE: Rehmanniae Radix Praeparata (RRP), a staple in traditional Chinese medicine, is derived from Rehmannia glutinosa Libosch and is renowned for its wound-healing properties. Despite its clinical prevalence, the molecular mechanisms underlying RRP's wound-healing effects have not been fully elucidated. AIM OF THE STUDY: This research endeavored to delineate the molecular and cellular mechanisms underlying the beneficial effects of RRP on wound healing, utilizing a zebrafish model. MATERIALS AND METHODS: Zebrafish larvae at 3 days post-fertilization were amputated at the fin and subsequently treated with RRP. The pro-wound healing and regenerative effects of RRP were evaluated through morphological analysis, assessment of cell proliferation and apoptosis, Additionally, mechanistic insights were gained through a comprehensive approach encompassing network pharmacology analysis, cell tracing, RNA-sequencing, CRISPR/Cas9 gene editing, and pharmacological inhibition. RESULTS: Our findings demonstrate that RRP significantly accelerates caudal fin regeneration in zebrafish following injury by suppressing cell apoptosis, promoting cell proliferation, and upregulating the expression of regenerative-related genes. Furthermore, RRP triggers autophagy signals during the regenerative process, which is attenuated by the autophagy inhibitor chloroquine (CQ). Notably, the administration of RRP enhances the expression of ahr1 and ahr2 in the regenerating fin. Genetic knockout of ahr1a, ahr1b, or ahr2 using CRISPR/Cas9, or pharmacological blockade of AHR signals with the antagonist CH-223191, diminishes the regenerative potential of RRP. Remarkably, zebrafish lacking ahr2 completely lose their fin regeneration ability. Additionally, inhibition of AHR signaling suppresses autophagy signaling during fin regeneration. CONCLUSIONS: This study uncovers that RRP stimulates fin regeneration in zebrafish by inducing AHR signals and, at least partially, activating the autophagy process. These findings provide novel insights into the molecular mechanisms underlying the wound-healing effects of RRP and may pave the way for the development of novel therapeutic strategies.

Unraveling the Nature of Spin Coupling in a Metal-Free Diradical: Theoretical Distinction of Ferromagnetic and Antiferromagnetic Interactions.

Metal-free diradicals based on polycyclic aromatic hydrocarbons are promising candidates for organic spintronics due to their stable magnetism and tunable spin coupling. However, distinguishing and elucidating the origins of ferromagnetic and antiferromagnetic interactions in these systems remain challenging. Here, we investigate the 2-OS diradical molecule sandwiched between gold electrodes using a combined density functional theory and hierarchical equations of motion approach. We find that the dihedral angle between the radical moieties controls the nature and strength of the intramolecular spin coupling, transitioning smoothly from antiferromagnetic to ferromagnetic as the angle increases. Distinct features in the inelastic electron tunneling spectra are identified that can discern the two coupling regimes, including spin excitation steps whose energies directly reveal the exchange coupling constant. Mechanical stretching of the junction is predicted to modulate the spectral line shapes by adjusting the hybridization of the molecular radicals with the electrodes. Our work elucidates the electronic origin of tunable spin interactions in 2-OS and provides spectroscopic fingerprints for characterizing magnetism in metal-free diradicals.

Crosstalk between intestinal flora and human iron metabolism: the role in metabolic syndrome-related comorbidities and its potential clinical application.

The interaction of iron and intestinal flora, both of which play crucial roles in many physiologic processes, is involved in the development of Metabolic syndrome (MetS). MetS is a pathologic condition represented by insulin resistance, obesity, dyslipidemia, and hypertension. MetS-related comorbidities including type 2 diabetes mellitus (T2DM), obesity, metabolism-related fatty liver (MAFLD), hypertension polycystic ovary syndrome (PCOS), and so forth. In this review, we examine the interplay between intestinal flora and human iron metabolism and its underlying mechanism in the pathogenesis of MetS-related comorbidities. The composition and metabolites of intestinal flora regulate the level of human iron by modulating intestinal iron absorption, the factors associated with iron metabolism. On the other hand, the iron level also affects the abundance, composition, and metabolism of intestinal flora. The crosstalk between these factors is of significant importance in human metabolism and exerts varying degrees of influence on the manifestation and progression of MetS-related comorbidities. The findings derived from these studies can enhance our comprehension of the interplay between intestinal flora and iron metabolism, and open up novel potential therapeutic approaches toward MetS-related comorbidities.

Generalized system-bath entanglement theorem for Gaussian environments.

The entanglement between system and bath often plays a pivotal role in complex systems spanning multiple orders of magnitude. A system-bath entanglement theorem was previously established for Gaussian environments in J. Chem. Phys. 152, 034102 (2020) regarding linear response functions. This theorem connects the entangled responses to the local system and bare bath properties. In this work, we generalize it to correlation functions. Key steps in derivations involve using the generalized Langevin dynamics for hybridizing bath modes and the Bogoliubov transformation that maps the original finite-temperature reservoir to an effective zero-temperature vacuum by employing an auxiliary bath. The generalized theorem allows us to evaluate the system-bath entangled correlations and the bath mode correlations in the total composite space, as long as we know the bare-bath statistical properties and obtain the reduced system correlations. To demonstrate the cross-scale entanglements, we utilize the generalized theorem to calculate the solvation free energy of an electron transfer system with intramolecular vibrational modes.

The γδ T cells dual function and crosstalk with intestinal flora in treating colorectal cancer is a promising area of study.

The occurrence of colorectal cancer (CRC) is highly prevalent and severely affects human health, with the third-greatest occurrence and the second-greatest rate of death globally. Current CRC treatments, including surgery, radiotherapy, and chemotherapy, do not significantly improve CRC patients' survival rate and quality of life, so it is essential to develop new treatment strategies. Adoptive cell therapy and other immunotherapy came into being. Currently, there has been an especially significant emphasis on γδ T cells as being the primary recipient of adoptive cell therapy. The present investigation found that γδ T cells possess the capability to trigger cytotoxicity in CRC cells, secrete cytokines, recruit immune cells for the purpose of destroying cancer cells, and inhibit the progress of CRC indirectly. Nevertheless, It is possible for γδ T cells to initiate a storm of inflammatory factors and inhibit the immune response to promote the advancement of CRC. This review demonstrates a close association between the γδ T cell initiation pathway and their close association with the intestinal flora. It has been observed that the intestinal flora performs a vital function in facilitating the stimulation and functioning of γδ T cells. The tumor-fighting effect is mainly regulated by desulphurizing Vibrio and lactic acid bacteria. In contrast, the regulation of tumor-promoting impact is closely related to Clostridia and ETBF. This review systematically combs γδ T cell dual function and their relationship to intestinal flora, which offers a conceptual framework for the γδ T cell application for CRC therapies.

Multimode Brownian oscillators: Exact solutions to heat transport.

In this work, we investigate the multimode Brownian oscillators in nonequilibrium scenarios with multiple reservoirs at different temperatures. For this purpose, an algebraic method is proposed. This approach gives the exact time-local equation of motion for the reduced density operator, from which we can easily extract not only the reduced system but also hybrid bath dynamical information. The resulting steady-state heat current is found to be numerically consistent with another discrete imaginary-frequency method followed by Meir-Wingreen's formula. It is anticipated that the development in this work would constitute an indispensable component of nonequilibrium statistical mechanics for open quantum systems.

Extended dissipaton equation of motion for electronic open quantum systems: Application to the Kondo impurity model.

In this paper, we present an extended dissipaton equation of motion for studying the dynamics of electronic impurity systems. Compared with the original theoretical formalism, the quadratic couplings are introduced into the Hamiltonian accounting for the interaction between the impurity and its surrounding environment. By exploiting the quadratic fermionic dissipaton algebra, the proposed extended dissipaton equation of motion offers a powerful tool for studying the dynamical behaviors of electronic impurity systems, particularly in situations where nonequilibrium and strongly correlated effects play significant roles. Numerical demonstrations are carried out to investigate the temperature dependence of the Kondo resonance in the Kondo impurity model.

Dissipatons as generalized Brownian particles for open quantum systems: Dissipaton-embedded quantum master equation.

Dissipaton theory had been proposed as an exact, nonperturbative approach to deal with open quantum system dynamics, where the influence of the Gaussian environment is characterized by statistical quasi-particles, named dissipatons. In this work, we revisit the dissipaton equation of motion theory and establish an equivalent dissipaton-embedded quantum master equation (DQME) that gives rise to dissipatons as generalized Brownian particles. As explained in this work, the DQME supplies a direct approach to investigate the statistical characteristics of dissipatons and, thus, the physically supporting hybrid bath modes. Numerical demonstrations are carried out on the electron transfer model, exhibiting the transient statistical properties of the solvation coordinate.

Ultrafast laser induced charge migration with de- and re-coherences in polyatomic molecules: A general method with application to pyrene.

We develop a general method to study ultrafast laser induced charge migration in molecules, which includes both electronic and nuclear dynamics. The method can be applied to relatively large systems. A detailed analysis of charge migration in pyrene is performed. Decoherences and recoherences of charge migration in pyrene are found and explained in terms of nuclear motions.

Open quantum systems with nonlinear environmental backactions: Extended dissipaton theory vs core-system hierarchy construction.

In this paper, we present a comprehensive account of quantum dissipation theories with the quadratic environment couplings. The theoretical development includes the Brownian solvation mode embedded hierarchical quantum master equations, a core-system hierarchy construction that verifies the extended dissipaton equation of motion (DEOM) formalism [R. X. Xu et al., J. Chem. Phys. 148, 114103 (2018)]. Developed are also the quadratic imaginary-time DEOM for equilibrium and the λ(t)-DEOM for nonequilibrium thermodynamics problems. Both the celebrated Jarzynski equality and Crooks relation are accurately reproduced, which, in turn, confirms the rigorousness of the extended DEOM theories. While the extended DEOM is more numerically efficient, the core-system hierarchy quantum master equation is favorable for "visualizing" the correlated solvation dynamics.

Hierarchical equations of motion approach for accurate characterization of spin excitations in quantum impurity systems.

Recent technological advancement in scanning tunneling microscopes has enabled the measurement of spin-field and spin-spin interactions in single atomic or molecular junctions with an unprecedentedly high resolution. Theoretically, although the fermionic hierarchical equations of motion (HEOM) method has been widely applied to investigate the strongly correlated Kondo states in these junctions, the existence of low-energy spin excitations presents new challenges to numerical simulations. These include the quest for a more accurate and efficient decomposition for the non-Markovian memory of low-temperature environments and a more careful handling of errors caused by the truncation of the hierarchy. In this work, we propose several new algorithms, which significantly enhance the performance of the HEOM method, as exemplified by the calculations on systems involving various types of low-energy spin excitations. Being able to characterize both the Kondo effect and spin excitation accurately, the HEOM method offers a sophisticated and versatile theoretical tool, which is valuable for the understanding and even prediction of the fascinating quantum phenomena explored in cutting-edge experiments.

Knocking out central metabolism genes to identify new targets and alternating substrates to improve lipid synthesis in Y. lipolytica.

Introduction: Systematic gene knockout studies may offer us novel insights on cell metabolism and physiology. Specifically, the lipid accumulation mechanism at the molecular or cellular level is yet to be determined in the oleaginous yeast Y. lipolytica. Methods: Herein, we established ten engineered strains with the knockout of important genes involving in central carbon metabolism, NADPH generation, and fatty acid biosynthetic pathways. Results: Our result showed that NADPH sources for lipogenesis include the OxPP pathway, POM cycle, and a trans-mitochondrial isocitrate-α-oxoglutarate NADPH shuttle in Y. lipolytica. Moreover, we found that knockout of mitochondrial NAD+ isocitrate dehydrogenase IDH2 and overexpression of cytosolic NADP+ isocitrate dehydrogenase IDP2 could facilitate lipid synthesis. Besides, we also demonstrated that acetate is a more favorable carbon source for lipid synthesis when glycolysis step is impaired, indicating the evolutionary robustness of Y. lipolytica. Discussion: This systematic investigation of gene deletions and overexpression across various lipogenic pathways would help us better understand lipogenesis and engineer yeast factories to upgrade the lipid biomanufacturing platform.

On the practical truncation tier of fermionic hierarchical equations of motion.

The fermionic hierarchical equations of motion (HEOM) approach has found wide application in the exploration of open quantum systems, and extensive efforts have been committed to improving its efficiency and accuracy in practical calculations. In this work, by scrutinizing the stationary-state and dynamic properties of Kondo-correlated quantum impurity systems, we show that the strength of Kondo correlation induced by the system-environment entanglement primarily determines the converged hierarchical truncation tier of the HEOM method. This complements the rule of thumb regarding the positive correlation between the height of hierarchy and system-environment coupling strength. These insights will provide useful guidelines for developing a more sophisticated fermionic HEOM method for the investigation of many-body open quantum systems.

Effects of Landscape Features on Bird Community in Winter Urban Parks.

Urban parks, as critical components of the urban green space, have practical significance in studying the influence of landscape characteristics on birds. Nine urban parks in Fuzhou, China, were used as study objects to explore the influence of landscape features (patch, landscape, and surrounding environment indices) on bird communities. The results showed that (1) from December 2021 to February 2022, we found a total of 2874 individuals belonging to 61 species of 9 orders, 32 families, which were dominated by the birds of Passeriformes (37 species of 24 families, accounting for 89.91% of the total number of individuals) and resident birds in Fuzhou urban parks (n = 30; 85.46%); (2) The park area, park perimeter, woodland area, grassland area, and the park shape index increased as the distance to the city center increases; (3) Bird diversity responds differently to different landscape features. The total abundance of birds, the abundance of winter migrant birds, and the richness of winter migrant birds increased with the park area. And the park shape index affects positively for the the α-diversity of birds and the abundance of resident birds. Woodland proportion and waterbody shape index affected positively on the richness and α-diversity of resident birds. To promote the diversity of regional birds, it is recommended that the construction and planning of urban parks should enlarge the park area as much as possible, increase the proportion of woodland, and make shorelines more irregular. Our study could serve as a reference for the construction of biodiversity enhancements in core green areas of urban parks.

Unveiling the Decisive Factor for the Sharp Transition in the Scanning Tunneling Spectroscopy of a Single Nickelocene Molecule.

Scanning tunneling microscopy (STM) has been utilized to realize the precise measurement and control of local spin states. Experiments have demonstrated that when a nickelocene (Nc) molecule is attached to the apex of an STM tip, the dI/dV spectra exhibit a sharp or a smooth transition when the tip is displaced toward the substrate. However, what leads to the two distinct types of transitions remains unclear, and more intriguingly, the physical origin of the abrupt change in the line shape of dI/dV spectra remains unclear. To clarify these intriguing issues, we perform first-principles-based simulations on the STM tip control process for the Cu tip/Nc/Cu(100) junction. In particular, we find that the suddenly enhanced hybridization between the d orbitals on the Ni ion and the metallic bands in the substrate leads to Kondo correlation overwhelming spin excitation, which is the main cause of the sharp transition in the dI/dV spectra observed experimentally.

Quantum mechanics of open systems: Dissipaton theories.

This Perspective presents a comprehensive account of the dissipaton theories developed in our group since 2014, including the physical picture of dissipatons and the phase-space dissipaton algebra. The dissipaton-equation-of-motion-space (DEOM-space) formulations cover the Schrödinger picture, the Heisenberg picture, and further the imaginary-time DEOM. Recently developed are the dissipaton theories for studying equilibrium and nonequilibrium thermodynamic mixing processes. The Jarzynski equality and Crooks relation are accurately reproduced numerically. It is anticipated that dissipaton theories would remain essential toward a maturation of quantum mechanics of open systems.

Coherent excitation energy transfer in model photosynthetic reaction center: Effects of non-Markovian quantum environment.

Excitation energy transfer (EET) and electron transfer (ET) are crucially involved in photosynthetic processes. In reality, the photosynthetic reaction center constitutes an open quantum system of EET and ET, which manifests interplay of pigments, solar light, and phonon baths. So far, theoretical studies have been mainly based on master equation approaches in the Markovian condition. The non-Markovian environmental effect, which may play a crucial role, has not been sufficiently considered. In this work, we propose a mixed dynamic approach to investigate this open system. The influence of phonon bath is treated via the exact dissipaton equation of motion (DEOM), while that of photon bath is via the Lindblad master equation. Specifically, we explore the effect of non-Markovian quantum phonon bath on the coherent transfer dynamics and its manipulation on the current-voltage behavior. Distinguished from the results of the completely Markovian-Lindblad equation and those adopting the classical environment description, the mixed DEOM-Lindblad simulations exhibit transfer coherence up to a few hundred femtoseconds and the related environmental manipulation effect on the current. These non-Markovian quantum coherent effects may be extended to more complex and realistic systems and be helpful in the design of organic photovoltaic devices.

A statistical quasi-particles thermofield theory with Gaussian environments: System-bath entanglement theorem for nonequilibrium correlation functions.

For open quantum systems, the Gaussian environmental dissipative effect can be represented by statistical quasi-particles, namely, dissipatons. We exploit this fact to establish the dissipaton thermofield theory. The resulting generalized Langevin dynamics of absorptive and emissive thermofield operators are effectively noise-resolved. The system-bath entanglement theorem is then readily followed between an important class of nonequilibrium steady-state correlation functions. All these relations are validated numerically. A simple corollary is the transport current expression, which exactly recovers the result obtained from the nonequilibrium Green's function formalism.

Nonequilibrium work distributions in quantum impurity system-bath mixing processes.

The fluctuation theorem, where the central quantity is the work distribution, is an important characterization of nonequilibrium thermodynamics. In this work, based on the dissipaton-equation-of-motion theory, we develop an exact method to evaluate the work distributions in quantum impurity system-bath mixing processes in the presence of non-Markovian and strong couplings. Our results not only precisely reproduce the Jarzynski equality and Crooks relation but also reveal rich information on large deviation. The numerical demonstrations are carried out with a spin-boson model system.

Electron Transfer under the Floquet Modulation in Donor-Bridge-Acceptor Systems.

Electron transfer (ET) processes are of broad interest in modern chemistry. With the advancements of experimental techniques, one may modulate the ET via such events as light-matter interactions. In this work, we study the ET under a Floquet modulation occurring in the donor-bridge-acceptor systems, with the rate kernels projected out from the exact dissipaton equation of motion formalism. This together with the Floquet theorem enables us to investigate the interplay between the intrinsic non-Markovianity and the driving periodicity. The observed rate kernel exhibits a Herzberg-Teller-like mechanism induced by the bridge fluctuation subject to effective modulation.