Analysis of chloroplast genome characteristics and codon usage bias in 14 species of Annonaceae.

For the study of species evolution, chloroplast gene expression, and transformation, the chloroplast genome is an invaluable resource. Codon usage bias (CUB) analysis is a tool that is utilized to improve gene expression and investigate evolutionary connections in genetic transformation. In this study, we analysed chloroplast genome differences, codon usage patterns and the sources of variation on CUB in 14 Annonaceae species using bioinformatics tools. The study showed that there was a significant variation in both gene sizes and numbers between the 14 species, but conservation was still maintained. It's worth noting that there were noticeable differences in the IR/SC sector boundary and the types of SSRs among the 14 species. The mono-nucleotide repeat type was the most common, with A/T repeats being more prevalent than G/C repeats. Among the different types of repeats, forward and palindromic repeats were the most abundant, followed by reverse repeats, and complement repeats were relatively rare. Codon composition analysis revealed that all 14 species had a frequency of GC lower than 50%. Additionally, it was observed that the proteins in-coding sequences of chloroplast genes tend to end with A/T at the third codon position. Among these species, 21 codons exhibited bias (RSCU > 1), and there were 8 high-frequency (HF) codons and 5 optimal codons that were identical across the species. According to the ENC-plot and Neutrality plot analysis, natural selection had less impact on the CUB of A. muricate and A. reticulata. Based on the PR2-plot, it was evident that base G had a higher frequency than C, and T had a higher frequency A. The correspondence analysis (COA) revealed that codon usage patterns different in Annonaceae.

Momentum-Resolved Electronic Structures and Strong Electronic Correlations in Graphene-like Nitride Superconductors.

Although transition-metal nitrides have been widely applied for several decades, experimental investigations of their high-resolution electronic band structures are rare due to the lack of high-quality single-crystalline samples. Here, we report on the first momentum-resolved electronic band structures of titanium nitride (TiN) films, which are remarkable nitride superconductors. The measurements of the crystal structures and electrical transport properties confirmed the high quality of these films. More importantly, from a combination of high-resolution angle-resolved photoelectron spectroscopy and first-principles calculations, the extracted Coulomb interaction strength of TiN films can be as large as 8.5 eV, whereas resonant photoemission spectroscopy yields a value of 6.26 eV. These large values of Coulomb interaction strength indicate that superconducting TiN is a strongly correlated system. Our results uncover the unexpected electronic correlations in transition-metal nitrides, potentially providing a perspective not only to understand their emergent quantum states but also to develop their applications in quantum devices.

Inhibition of SAT1 alleviates chondrocyte inflammation and ferroptosis by repressing ALOX15 expression and activating the Nrf2 pathway.

Aims: Osteoarthritis (OA) is the most common chronic pathema of human joints. The pathogenesis is complex, involving physiological and mechanical factors. In previous studies, we found that ferroptosis is intimately related to OA, while the role of Sat1 in chondrocyte ferroptosis and OA, as well as the underlying mechanism, remains unclear. Methods: In this study, interleukin-1ß (IL-1ß) was used to simulate inflammation and Erastin was used to simulate ferroptosis in vitro. We used small interfering RNA (siRNA) to knock down the spermidine/spermine N1-acetyltransferase 1 (Sat1) and arachidonate 15-lipoxygenase (Alox15), and examined damage-associated events including inflammation, ferroptosis, and oxidative stress of chondrocytes. In addition, a destabilization of the medial meniscus (DMM) mouse model of OA induced by surgery was established to investigate the role of Sat1 inhibition in OA progression. Results: The results showed that inhibition of Sat1 expression can reduce inflammation, ferroptosis changes, reactive oxygen species (ROS) level, and lipid-ROS accumulation induced by IL-1ß and Erastin. Knockdown of Sat1 promotes nuclear factor-E2-related factor 2 (Nrf2) signalling. Additionally, knockdown Alox15 can alleviate the inflammation-related protein expression induced by IL-1ß and ferroptosis-related protein expression induced by Erastin. Furthermore, knockdown Nrf2 can reverse these protein expression alterations. Finally, intra-articular injection of diminazene aceturate (DA), an inhibitor of Sat1, enhanced type II collagen (collagen II) and increased Sat1 and Alox15 expression. Conclusion: Our results demonstrate that inhibition of Sat1 could alleviate chondrocyte ferroptosis and inflammation by downregulating Alox15 activating the Nrf2 system, and delaying the progression of OA. These findings suggest that Sat1 provides a new approach for studying and treating OA.

Erratum: Mitoquinone alleviates osteoarthritis progress by activating the NRF2-Parkin axis.

[This corrects the article DOI: 10.1016/j.isci.2023.107647.].

DMT1-mediated iron overload accelerates cartilage degeneration in Hemophilic Arthropathy through the mtDNA-cGAS-STING axis.

INTRODUCTION: Excess iron contributes to Hemophilic Arthropathy (HA) development. Divalent metal transporter 1 (DMT1) delivers iron into the cytoplasm, thus regulating iron homeostasis. OBJECTIVES: We aimed to investigate whether DMT1-mediated iron homeostasis is involved in bleeding-induced cartilage degeneration and the molecular mechanisms underlying iron overload-induced chondrocyte damage. METHODS: This study established an in vivo HA model by puncturing knee joints of coagulation factor VIII gene knockout mice with a needle, and mimicked iron overload conditions in vitro by treatment of Ferric ammonium citrate (FAC). RESULTS: We demonstrated that blood exposure caused iron overload and cartilage degeneration, as well as elevated expression of DMT1. Furthermore, DMT1 silencing alleviated blood-induced iron overload and cartilage degeneration. In hemophilic mice, articular cartilage degeneration was also suppressed by intro-articularly injection of DMT1 adeno-associated virus 9 (AAV9). Mechanistically, RNA-sequencing analysis indicated the association between iron overload and cGAS-STING pathway. Further, iron overload triggered mtDNA-cGAS-STING pathway activation, which could be effectively mitigated by DMT1 silencing. Additionally, we discovered that RU.521, a potent Cyclic GMP-AMP Synthase (cGAS) inhibitor, successfully suppressed the downward cascades of cGAS-STING, thereby protecting against chondrocyte damage. CONCLUSION: Taken together, DMT1-mediated iron overload promotes chondrocyte damage and murine HA development, and targeted DMT1 may provide therapeutic and preventive approaches in HA.

P21 resists ferroptosis in osteoarthritic chondrocytes by regulating GPX4 protein stability.

Ferroptosis is involved in the pathogenesis of osteoarthritis (OA) while suppression of chondrocyte ferroptosis has a beneficial effect on OA. However, the molecular mechanism of ferroptosis in OA remains to be elucidated. P21, an indicator of aging, has been reported to inhibit ferroptosis, but the relationship between P21 and ferroptosis in OA remains unclear. Here, we aimed to investigate the expression and function of P21 in OA chondrocytes, and the involvement of P21 in the regulation of ferroptosis in chondrocytes. First, we demonstrated that high P21 expression was observed in the cartilage from OA patients and destabilized medial meniscus (DMM) mice, and in osteoarthritic chondrocytes induced by IL-1ß, FAC and erastin. P21 knockdown exacerbated the reduction of Col2a1 and promoted the upregulation of MMP13 in osteoarthritic chondrocytes. Meanwhile, P21 knockdown exacerbated cartilage degradation in DMM-induced OA mouse models and decreased GPX4 expression in vivo. Furthermore, P21 knockdown sensitized chondrocytes to ferroptosis induced by erastin, which was closely associated with the accumulation of lipid peroxides. In mechanism, we demonstrated that P21 regulated the stability of GPX4 protein, and the regulation was independent of NRF2. Meanwhile, we found that P21 significantly affected the recruitment of GPX4 to linear ubiquitin chain assembly complex (LUBAC) and regulated the level of M1-linked ubiquitination of GPX4. Overall, our results suggest that P21 plays an essential anti-ferroptosis role in OA by regulating the stability of GPX4.

Design and first-round commissioning result of the SASE beamline at the Shanghai Soft X-ray FEL facility.

The Shanghai Soft X-ray Free-Electron Laser (SXFEL) is the first X-ray free-electron laser facility in China. The SASE beamline, which consists of a pink-beam branch and a mono-beam branch, is one of the two beamlines in the Phase-I construction. The pink-beam branch opened for users in 2023 after successful first-round beamline commissioning. In this paper, the design of the beamline is presented and the performance of the pink-beam branch is reported. The measured energy-resolving power of the online spectrometer is over 6000 @ 400 eV. The focusing spot size of the pink beam is less than 3 µm in both the horizontal and vertical at the endstation.

Highly efficient nonlinear vortex beam generation by using a compact nonlinear fork grating.

Vortex beams with an orbital angular momentum (OAM) are extremely important in optical trapping, optical micromachining, high-capacity optical communications, and quantum optics. Nonlinear generation of such a vortex beam enables vortex beams to be obtained at new wavelengths, which opens up new possibilities for all-optical switching and manipulation of vortex beams. However, previous nonlinear vortex beam generation suffers from either low efficiency or low-level integration. Here, we use the technique of ultraviolet photolithography-assisted inductively coupled plasma (ICP) etching to realize a compact nonlinear fork grating for high-efficiency nonlinear vortex beam generation. In our experiment, the depth of such a compact nonlinear fork-grating structure can be precisely controlled by etching time. The vortex beams with a topological charge of l = ±1, ± 2, ± 3 can be generated in the far field, and the normalized nonlinear conversion efficiency of such nonlinear vortex beam is 189% W-1cm-2. Our method not only provides an efficient and compact method for nonlinear vortex beam manipulation but also suits for timesaving and large-area nonlinear functional device fabrication.

Initial probe function construction in ptychography based on zone-plate optics.

X-ray ptychography is a popular variant of coherent diffraction imaging that offers ultrahigh resolution for extended samples. In x-ray ptychography instruments, the Fresnel zone-plate (FZP) is the most commonly used optical probe system for both soft x-ray and hard x-ray. In FZP-based ptychography with a highly curved defocus probe wavefront, the reconstructed image quality can be significantly impacted by the initial probe function form, necessitating the construction of a suitable initial probe for successful reconstruction. To investigate the effects of initial probe forms on FZP-based ptychography reconstruction, we constructed four single-mode initial probe models (IPMs) and three multi-mode IPMs in this study, and systematically compared their corresponding simulated and experimental reconstructions. The results show that the Fresnel IPM, spherical IPM, and Fresnel-based multi-mode IPMs can result in successful reconstructions for both near-focus and defocus cases, while random IPMs and constant IPMs work only for near-focus cases. Consequently, for FZP-based ptychography, the elaborately constructed IPMs that closely resemble real probes in wavefront phase form are more advantageous than natural IPMs such as the random or constant model. Furthermore, these IPMs with high phase similarity to the high-curvature large-sized probe adopted in experiments can help greatly improve ptychography experiment efficiency and decrease radiation damage to samples.

Mitoquinone alleviates osteoarthritis progress by activating the NRF2-Parkin axis.

Osteoarthritis (OA) is a prevalent degenerative disease of the elderly. The NRF2 antioxidant system plays a critical role in maintaining redox balance. Mitoquinone (MitoQ) is a mitochondria-targeted antioxidant. This research aimed to determine whether MitoQ alleviated OA and the role of the NRF2/Parkin axis in MitoQ-mediated protective effects. In interleukin (IL)-1ß-induced OA chondrocytes, MitoQ activated the NRF2 pathway, reducing extracellular matrix (ECM) degradation and inflammation. MitoQ also increased glutathione peroxidase 4 (GPX4) expression, leading to decreased levels of reactive oxygen species (ROS) and lipid ROS. Silencing NRF2 weakened MitoQ's protective effects, while knockdown of Parkin upregulated the NRF2 pathway, inhibiting OA progression. Intra-articular injection of MitoQ mitigated cartilage destruction in destabilized medial meniscus (DMM)-induced OA mice. Our study demonstrates that MitoQ maintains cartilage homeostasis in vivo and in vitro through the NRF2/Parkin axis. We supplemented the negative feedback regulation mechanism between NRF2 and Parkin. These findings highlight the therapeutic potential of MitoQ for OA treatment.

Near-infrared speckle wavemeter based on nonlinear frequency conversion.

The wavemeter is an important instrument for spectrum analysis, widely used in spectral calibration, remote sensing, atomic physics, and high-precision metrology. However, near-infrared (NIR) wavemeters require infrared-sensitive detectors that are expensive and less sensitive compared to silicon-based visible light detectors. To circumvent these limitations, we propose an NIR speckle wavemeter based on nonlinear frequency conversion. We combine a scattering medium and the deep learning technique to invert the nonlinear mapping of the NIR wavelength and speckles in the visible wave band. With the outstanding performance of deep learning, a high-precision wavelength resolution of 1 pm is achievable in our experiment. We further demonstrate the robustness of our system and show that the recognition of power parameters and multi-spectral lines is also feasible. The proposed method offers a convenient and flexible way to measure NIR light, and it offers the possibility of cost reduction in miniaturized wavemeter systems.

The roles of the Hippo-YAP signalling pathway in Cartilage and Osteoarthritis.

Osteoarthritis (OA) is an age-related disease, characterized by cartilage degeneration. The pathogenesis of OA is complicated and the current therapeutic approaches for OA are limited. Cartilage, an integral part of the skeletal system composed of chondrocytes, is essential for skeletal development, tissue patterning, and maintaining the normal activity of joints. The development, homeostasis and degeneration of cartilage are tightly associated with OA. Over the past decade, accumulating evidence indicates that Hippo/YAP is a vital biochemical signalling pathway that strictly governs tissue development and homeostasis. The joint tissues, especially for cartilage, are sensitive to changes of Hippo/YAP signalling. In this review, we summarize the role of Hippo/YAP signalling in cartilage and discuss its involvement in OA progression from points of cartilage degradation, subchondral bone remodeling, and synovial alteration. We also highlight the potential therapeutic implications of Hippo/YAP signalling and further discuss current limitations and controversy on Hippo/YAP-based application for OA treatment.

High-speed optical pulse shaping based on programmable lithium niobate spatial light modulators.

Pulse shaping plays a key role in various applications of ultrafast lasers, such as optical communications, laser micromachining, microscopy, and quantum coherent control. Conventional pulse shaping devices based on liquid crystal spatial light modulators (LCSLMs) or digital micromirror devices (DMDs) only have the shaping speed of several hertz to kilohertz, which is not suitable for applications requiring a high-speed response. Here, we demonstrate a high-speed programmable lithium niobate spatial light modulator (LNSLM) with 128 individual modulation channels and a modulation speed that can reach 1 MHz. Then we establish a high-speed LNSLM-based Fourier-transform (FT) pulse shaper to realize high-speed pulse shaping, and the update rate can reach 350 kHz, only limited by the electric circuit. The proposed high-speed pulse shaper scheme opens new avenues for future applications of ultrafast science, such as microscopic imaging, interaction between light and matter, and spectroscopy.

Completely Eradicating Singlet Oxygen in Li-O2 Battery via Cobalt(II)-Porphyrin Complex-Catalyzed LiOH Chemistry.

Li-O2 batteries have an extremely high theoretical specific energy; however, the large charge overpotential and highly reactive singlet oxygen (1O2) are two major obstacles. Porphyrin as a special kind of macrocyclic conjugated aromatic system exhibits excellent redox activity, which can be optimized by introducing a center metal atom. Herein, 5,10,15,20-tetrakis(4-aminophenyl)-porphyrin (TAPP) and 5,10,15,20-tetrakis(4-aminophenyl)-porphyrin-Co(II) (Co-TAP) are applied as effective redox mediators for Li-O2 batteries. The synergistic effects of a center metal atom and organic ligand make Co-TAP more favorable for oxygen reduction and evolution. To understand the fundamental reaction mechanisms with or without TAPP or Co-TAP, the discharge/charge processes and the parasitic reactions have been comprehensively studied. The results reveal that TAPP affects the formation mechanism of Li2O2, while Co-TAP transforms the main discharge product into LiOH without adding extra water. Co-TAP-containing batteries operated via LiOH chemistry completely eradicate 1O2 and significantly alleviate the parasitic reactions associated with 1O2.

Molecular Trade-Offs between Lattice Oxygen and Oxygen Vacancy Drive Organic Pollutant Degradation in Fungal Biomineralized Exoskeletons.

Fungal-mineral interactions can effectively alleviate cellular stress from organic pollutants, the production of which are expected to rapidly increase owing to the Earth moving into an unprecedented geological epoch, the Anthropocene. The underlying mechanisms that may enable fungi to combat organic pollution during fungal-mineral interactions remain unclear. Inspired by the natural fungal sporulation process, we demonstrate for the first time that fungal biomineralization triggers the formation of an ultrathin (hundreds of nanometers thick) exoskeleton, enriched in nanosized iron (oxyhydr)oxides and biomolecules, on the hyphae. Mapped biochemical composition of this coating at a subcellular scale via high spatial resolution (down to 50 nm) synchrotron radiation-based techniques confirmed aromatic C, C-N bonds, amide carbonyl, and iron (oxyhydr)oxides as the major components of the coatings. This nanobiohybrid system appeared to impart a strong (×2) biofunctionality for fungal degradation of bisphenol A through altering molecular-level trade-offs between lattice oxygen and oxygen vacancy. Together, fungal coatings could act as "artificial spores", which enable fungi to combat physical and chemical stresses in natural environments, providing crucial insights into fungal biomineralization and coevolution of the Earth's lithosphere and biosphere.

Highly efficient detection of near-infrared optical vortex modes with frequency upconversion.

Vortex beams carrying orbital angular momentum (OAM) have been widely applied in optical manipulations, optical micromachining, and high-capacity optical communications. Vortex mode detection is very important in various applications. However, the detection of near-infrared vortex modes is still difficult because of the wavelength limitations of the detection device. Here, we present a study on measuring optical near-infrared vortex modes with frequency upconversion, which can convert a near-infrared beam into a visible beam. In our experiment, the optical near-infrared vortex modes can be measured by the number and orientation of the fringes of the second harmonic intensity patterns. The proposed method is a convenient and flexible way to measure the different OAM of vortex beams, which may have potential applications in all kinds of circumstances that vortex modes involve.

Second-harmonic and sum-frequency generation based on birefringence phase matching of BaMgF4 crystal.

BaMgF4 is a ferroelectric nonlinear crystal with a very wide transparency window ranging from 125 nm to 13µm of the wavelength. Therefore, it is a candidate material to generate ultraviolet or deep ultraviolet laser, which is very important in lithography, semiconductor manufacturing, and advanced instrument development. Here, the second-order birefringence phase-matching processes of the BaMgF4 crystal were studied, including second-harmonic generation (SHG) and sum-frequency generation (SFG). In the experiments, we measured the phase-matching angle, nonlinear frequency conversion efficiency, and angle bandwidth of SHG and SFG processes of BaMgF4 crystal, which are in well agreement with the theoretical calculations. This study may promote the research of nonlinear optical process of BaMgF4 crystal and also the further development of all-solid-state vacuum ultraviolet lasers.

Non-line-of-sight optical communication based on orbital angular momentum.

Optical non-line-of-sight (NLOS) communication can exploit the indirect light path to provide free-space communications around obstacles that occlude the field of view. Here we propose and demonstrate an orbital angular momentum (OAM)-based NLOS communication scheme that can greatly improve its channel dimensionality. To verify the feasibility for extending the amount of multiplexed OAM channel dimensionality, the effects of bit accuracy versus the number of channels in measuring OAM modes are quantified. Moreover, to show the ability for broadcast NLOS tasks, we report a multi-receiver experiment where the transmitted information from scattered light can be robustly decoded by multiple neuron-network-based OAM decoders. Our results present a faithful verification of OAM-based NLOS communication for real-time applications in dynamic NLOS environments, regardless of the limit of wavelength, light intensity, or turbulence.

DOT1L O-GlcNAcylation promotes its protein stability and MLL-fusion leukemia cell proliferation.

Histone lysine methylation functions at the interface of the extracellular environment and intracellular gene expression. DOT1L is a versatile histone H3K79 methyltransferase with a prominent role in MLL-fusion leukemia, yet little is known about how DOT1L responds to extracellular stimuli. Here, we report that DOT1L protein stability is regulated by the extracellular glucose level through the hexosamine biosynthetic pathway (HBP). Mechanistically, DOT1L is O-GlcNAcylated at evolutionarily conserved S1511 in its C terminus. We identify UBE3C as a DOT1L E3 ubiquitin ligase promoting DOT1L degradation whose interaction with DOT1L is susceptible to O-GlcNAcylation. Consequently, HBP enhances H3K79 methylation and expression of critical DOT1L target genes such as HOXA9/MEIS1, promoting cell proliferation in MLL-fusion leukemia. Inhibiting HBP or O-GlcNAc transferase (OGT) increases cellular sensitivity to DOT1L inhibitor. Overall, our work uncovers O-GlcNAcylation and UBE3C as critical determinants of DOT1L protein abundance, revealing a mechanism by which glucose metabolism affects malignancy progression through histone methylation.

Structures and catalytic performances of Me/SAPO-34 (Me = Mn, Ni, Co) catalysts for low-tem perature SCR of NOx by ammonia.

Me/SAPO-34 (Me = Mn, Ni, Co) series of catalysts were prepared by a wetness impregnation method and investigated for the selective catalytic reduction of nitrogen oxides with ammonia (NH3-SCR). Among them, Mn/SAPO-34 catalyst was found as the most promising candidate based on its superior low-temperature activity. The catalysts were characterized by X-ray diffraction (XRD), transmission electron microscopy images (TEM), nuclear magnetic resonance (NMR), X-ray photoelectron spectroscopy (XPS), temperature programmed reduction and desorption (TPR and TPD), and diffuse reflectance infrared Fourier transformed spectroscopy (DRIFTS) of NH3/NOx adsorption. Mn/SAPO-34 is obviously different from Ni/SAPO-34 and Co/SAPO-34 in the active species state and distribution. Surface MnOx species which play an essential role in NO oxidation and NO2 adsorption, act as better active sites than nickel and cobalt mostly in the form of the aluminates and silicates.