A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response.

Fragile X syndrome, a common form of inherited intellectual disability, is caused by loss of the fragile X mental retardation protein FMRP. FMRP is present predominantly in the cytoplasm, where it regulates translation of proteins that are important for synaptic function. We identify FMRP as a chromatin-binding protein that functions in the DNA damage response (DDR). Specifically, we show that FMRP binds chromatin through its tandem Tudor (Agenet) domain in vitro and associates with chromatin in vivo. We also demonstrate that FMRP participates in the DDR in a chromatin-binding-dependent manner. The DDR machinery is known to play important roles in developmental processes such as gametogenesis. We show that FMRP occupies meiotic chromosomes and regulates the dynamics of the DDR machinery during mouse spermatogenesis. These findings suggest that nuclear FMRP regulates genomic stability at the chromatin interface and may impact gametogenesis and some developmental aspects of fragile X syndrome.

Ultrafiltration separation of Am(VI)-polyoxometalate from lanthanides.

Partitioning of americium from lanthanides (Ln) present in used nuclear fuel plays a key role in the sustainable development of nuclear energy1-3. This task is extremely challenging because thermodynamically stable Am(III) and Ln(III) ions have nearly identical ionic radii and coordination chemistry. Oxidization of Am(III) to Am(VI) produces AmO22+ ions distinct with Ln(III) ions, which has the potential to facilitate separations in principle. However, the rapid reduction of Am(VI) back to Am(III) by radiolysis products and organic reagents required for the traditional separation protocols including solvent and solid extractions hampers practical redox-based separations. Herein, we report a nanoscale polyoxometalate (POM) cluster with a vacancy site compatible with the selective coordination of hexavalent actinides (238U, 237Np, 242Pu and 243Am) over trivalent lanthanides in nitric acid media. To our knowledge, this cluster is the most stable Am(VI) species in aqueous media observed so far. Ultrafiltration-based separation of nanoscale Am(VI)-POM clusters from hydrated lanthanide ions by commercially available, fine-pored membranes enables the development of a once-through americium/lanthanide separation strategy that is highly efficient and rapid, does not involve any organic components and requires minimal energy input.

Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development.

Ten-Eleven Translocation (Tet) family of dioxygenases dynamically regulates DNA methylation and has been implicated in cell lineage differentiation and oncogenesis. Yet their functions and mechanisms of action in gene regulation and embryonic development are largely unknown. Here, we report that Xenopus Tet3 plays an essential role in early eye and neural development by directly regulating a set of key developmental genes. Tet3 is an active 5mC hydroxylase regulating the 5mC/5hmC status at target gene promoters. Biochemical and structural studies further demonstrate that the Tet3 CXXC domain is critical for specific Tet3 targeting. Finally, we show that the enzymatic activity and CXXC domain are both crucial for Tet3's biological function. Together, these findings define Tet3 as a transcription regulator and reveal a molecular mechanism by which the 5mC hydroxylase and DNA binding activities of Tet3 cooperate to control target gene expression and embryonic development.

The AAA-ATPase Yta4/ATAD1 interacts with the mitochondrial divisome to inhibit mitochondrial fission.

Mitochondria are in a constant balance of fusion and fission. Excessive fission or deficient fusion leads to mitochondrial fragmentation, causing mitochondrial dysfunction and physiological disorders. How the cell prevents excessive fission of mitochondria is not well understood. Here, we report that the fission yeast AAA-ATPase Yta4, which is the homolog of budding yeast Msp1 responsible for clearing mistargeted tail-anchored (TA) proteins on mitochondria, plays a critical role in preventing excessive mitochondrial fission. The absence of Yta4 leads to mild mitochondrial fragmentation in a Dnm1-dependent manner but severe mitochondrial fragmentation upon induction of mitochondrial depolarization. Overexpression of Yta4 delocalizes the receptor proteins of Dnm1, i.e., Fis1 (a TA protein) and Mdv1 (the bridging protein between Fis1 and Dnm1), from mitochondria and reduces the localization of Dnm1 to mitochondria. The effect of Yta4 overexpression on Fis1 and Mdv1, but not Dnm1, depends on the ATPase and translocase activities of Yta4. Moreover, Yta4 interacts with Dnm1, Mdv1, and Fis1. In addition, Yta4 competes with Dnm1 for binding Mdv1 and decreases the affinity of Dnm1 for GTP and inhibits Dnm1 assembly in vitro. These findings suggest a model, in which Yta4 inhibits mitochondrial fission by inhibiting the function of the mitochondrial divisome composed of Fis1, Mdv1, and Dnm1. Therefore, the present work reveals an uncharacterized molecular mechanism underlying the inhibition of mitochondrial fission.

Molecular basis for C-degron recognition by CRL2APPBP2 ubiquitin ligase.

E3 ubiquitin ligases determine the specificity of eukaryotic protein degradation by selective binding to destabilizing protein motifs, termed degrons, in substrates for ubiquitin-mediated proteolysis. The exposed C-terminal residues of proteins can act as C-degrons that are recognized by distinct substrate receptors (SRs) as part of dedicated cullin-RING E3 ubiquitin ligase (CRL) complexes. APPBP2, an SR of Cullin 2-RING ligase (CRL2), has been shown to recognize R-x-x-G/C-degron; however, the molecular mechanism of recognition remains elusive. By solving several cryogenic electron microscopy structures of active CRL2APPBP2 bound with different R-x-x-G/C-degrons, we unveiled the molecular mechanisms underlying the assembly of the CRL2APPBP2 dimer and tetramer, as well as C-degron recognition. The structural study, complemented by binding experiments and cell-based assays, demonstrates that APPBP2 specifically recognizes the R-x-x-G/C-degron via a bipartite mechanism; arginine and glycine, which play critical roles in C-degron recognition, accommodate distinct pockets that are spaced by two residues. In addition, the binding pocket is deep enough to enable the interaction of APPBP2 with the motif placed at or up to three residues upstream of the C-end. Overall, our study not only provides structural insight into CRL2APPBP2-mediated protein turnover but also serves as the basis for future structure-based chemical probe design.

Signatures of Adaptation and Purifying Selection in Highland Populations of Dasiphora fruticosa.

High mountains harbor a considerable proportion of biodiversity, but we know little about how diverse plants adapt to the harsh environment. Here we finished a high-quality genome assembly for Dasiphora fruticosa, an ecologically important plant distributed in the Qinghai-Tibetan Plateau and lowland of the Northern Hemisphere, and resequenced 592 natural individuals to address how this horticulture plant adapts to highland. Demographic analysis revealed D. fruticosa underwent a bottleneck after Naynayxungla Glaciation. Selective sweep analysis of two pairs of lowland and highland populations identified 63 shared genes related to cell wall organization or biogenesis, cellular component organization, and dwarfism, suggesting parallel adaptation to highland habitats. Most importantly, we found that stronger purging of estimated genetic load due to inbreeding in highland populations apparently contributed to their adaptation to the highest mountain. Our results revealed how plants could tolerate the extreme plateau, which could provide potential insights for species conservation and crop breeding.

3D-SMGE: a pipeline for scaffold-based molecular generation and evaluation.

In the process of drug discovery, one of the key problems is how to improve the biological activity and ADMET properties starting from a specific structure, which is also called structural optimization. Based on a starting scaffold, the use of deep generative model to generate molecules with desired drug-like properties will provide a powerful tool to accelerate the structural optimization process. However, the existing generative models remain challenging in extracting molecular features efficiently in 3D space to generate drug-like 3D molecules. Moreover, most of the existing ADMET prediction models made predictions of different properties through a single model, which can result in reduced prediction accuracy on some datasets. To effectively generate molecules from a specific scaffold and provide basis for the structural optimization, the 3D-SMGE (3-Dimensional Scaffold-based Molecular Generation and Evaluation) work consisting of molecular generation and prediction of ADMET properties is presented. For the molecular generation, we proposed 3D-SMG, a novel deep generative model for the end-to-end design of 3D molecules. In the 3D-SMG model, we designed the cross-aggregated continuous-filter convolution (ca-cfconv), which is used to achieve efficient and low-cost 3D spatial feature extraction while ensuring the invariance of atomic space rotation. 3D-SMG was proved to generate valid, unique and novel molecules with high drug-likeness. Besides, the proposed data-adaptive multi-model ADMET prediction method outperformed or maintained the best evaluation metrics on 24 out of 27 ADMET benchmark datasets. 3D-SMGE is anticipated to emerge as a powerful tool for hit-to-lead structural optimizations and accelerate the drug discovery process.

MDM2 E3 ligase activity is essential for p53 regulation and cell cycle integrity.

MDM2 and MDM4 are key regulators of p53 and function as oncogenes when aberrantly expressed. MDM2 and MDM4 partner to suppress p53 transcriptional transactivation and polyubiquitinate p53 for degradation. The importance of MDM2 E3-ligase-mediated p53 regulation remains controversial. To resolve this, we generated mice with an Mdm2 L466A mutation that specifically compromises E2 interaction, abolishing MDM2 E3 ligase activity while preserving its ability to bind MDM4 and suppress p53 transactivation. Mdm2L466A/L466A mice exhibit p53-dependent embryonic lethality, demonstrating MDM2 E3 ligase activity is essential for p53 regulation in vivo. Unexpectedly, cells expressing Mdm2L466A manifest cell cycle G2-M transition defects and increased aneuploidy even in the absence of p53, suggesting MDM2 E3 ligase plays a p53-independent role in cell cycle regulation and genome integrity. Furthermore, cells bearing the E3-dead MDM2 mutant show aberrant cell cycle regulation in response to DNA damage. This study uncovers an uncharacterized role for MDM2's E3 ligase activity in cell cycle beyond its essential role in regulating p53's stability in vivo.

Correction: MDM2 E3 ligase activity is essential for p53 regulation and cell cycle integrity.

[This corrects the article DOI: 10.1371/journal.pgen.1010171.].

Microstructures of layered Ni-rich cathodes for lithium-ion batteries.

Millions of electric vehicles (EVs) on the road are powered by lithium-ion batteries (LIBs) based on nickel-rich layered oxide (NRLO) cathodes, and they suffer from a limited driving range and safety concerns. Increasing the Ni content is a key way to boost the energy densities of LIBs and alleviate the EV range anxiety, which are, however, compromised by the rapid performance fading. One unique challenge lies in the worsening of the microstructural stability with a rising Ni-content in the cathode. In this review, we focus on the latest advances in the understanding of NLRO microstructures, particularly the microstructural degradation mechanisms, state-of-the-art stabilization strategies, and advanced characterization methods. We first elaborate on the fundamental mechanisms underlying the microstructural failures of NRLOs, including anisotropic lattice evolution, microcracking, and surface degradation, as a result of which other degradation processes, such as electrolyte decomposition and transition metal dissolution, can be severely aggravated. Afterwards, we discuss representative stabilization strategies, including the surface treatment and construction of radial concentration gradients in polycrystalline secondary particles, the fabrication of rod-shaped primary particles, and the development of single-crystal NRLO cathodes. We then introduce emerging microstructural characterization techniques, especially for identification of the particle orientation, dynamic changes, and elemental distributions in NRLO microstructures. Finally, we provide perspectives on the remaining challenges and opportunities for the development of stable NRLO cathodes for the zero-carbon future.

Characteristic Plasmon Energies for 2D In2Se3 Phase Identification at Nanoscale.

Two-dimensional (2D) materials with competing polymorphs offer remarkable potential to switch the associated 2D functionalities for novel device applications. Probing their phase transition and competition mechanisms requires nanoscale characterization techniques that can sensitively detect the nucleation of secondary phases down to single-layer thickness. Here we demonstrate nanoscale phase identification on 2D In2Se3 polymorphs, utilizing their distinct plasmon energies that can be distinguished by electron energy-loss spectroscopy (EELS). The characteristic plasmon energies of In2Se3 polymorphs have been validated by first-principles calculations, and also been successfully applied to reveal phase transitions using in situ EELS. Correlating with in situ X-ray diffraction, we further derive a subtle difference in the valence electron density of In2Se3 polymorphs, consistent with their disparate electronic properties. The nanometer resolution and independence of orientation make plasmon-energy mapping a versatile technique for nanoscale phase identification on 2D materials.

Integrated Metabolomic and transcriptomic analyses reveal deoxycholic acid promotes transmissible gastroenteritis virus infection by inhibiting phosphorylation of NF-κB and STAT3.

BACKGROUND: Acute diarrhea, dehydration and death in piglets are all symptoms of transmissible gastroenteritis virus (TGEV), which results in significant financial losses in the pig industry. It is important to understand the pathogenesis and identify new antiviral targets by revealing the metabolic interactions between TGEV and host cells. RESULTS: We performed metabolomic and transcriptomic analyses of swine testicular cells infected with TGEV. A total of 1339 differential metabolites and 206 differentially expressed genes were detected post TEGV infection. The differentially expressed genes were significantly enriched in the HIF-1 signaling pathway and PI3K-Akt signaling. Integrated analysis of differentially expressed genes and differential metabolites indicated that they were significantly enriched in the metabolic processes such as nucleotide metabolism, biosynthesis of cofactors and purine metabolism. In addition, the results showed that most of the detected metabolites involved in the bile secretion was downregulated during TGEV infection. Furthermore, exogenous addition of key metabolite deoxycholic acid (DCA) significantly enhanced TGEV replication by NF-κB and STAT3 signal pathways. CONCLUSIONS: We identified a significant metabolite, DCA, related to TGEV replication. It added TGEV replication in host cells by inhibiting phosphorylation of NF-κB and STAT3. This study provided novel insights into the metabolomic and transcriptomic alterations related to TGEV infection and revealed potential molecular and metabolic targets for the regulation of TGEV infection.

Ambient Aqueous Synthesis of Imine-Linked Covalent Organic Frameworks (COFs) and Fabrication of Freestanding Cellulose Nanofiber@COF Nanopapers.

Covalent organic frameworks (COFs) are usually synthesized under solvothermal conditions that require the use of toxic organic solvents, high reaction temperatures, and complicated procedures. Additionally, their insolubility and infusibility present substantial challenges in the processing of COFs. Herein, we report a facile, green approach for the synthesis of imine-linked COFs in an aqueous solution at room temperature. The key behind the synthesis is the regulation of the reaction rate. The preactivation of aldehyde monomers using acetic acid significantly enhances their reactivity in aqueous solutions. Meanwhile, the still somewhat lower imine formation rate and higher imine breaking rates in aqueous solution, in contrast to conventional solvothermal synthesis, allow for the modulation of the reaction equilibrium and the crystallization of the products. As a result, highly crystalline COFs with large surface areas can be formed in relatively high yields in a few minutes. In total, 16 COFs are successfully synthesized from monomers with different molecular sizes, geometries, pendant groups, and core structures, demonstrating the versatility of this approach. Notably, this method works well on the gram scale synthesis of COFs. Furthermore, the aqueous synthesis facilitates the interfacial growth of COF nanolayers on the surface of cellulose nanofibers (CNFs). The resulting CNF@COF hybrid nanofibers can be easily processed into freestanding nanopapers, demonstrating high efficiency in removing trace amounts of antibiotics from wastewater. This study provides a route to the green synthesis and processing of various COFs, paving the way for practical applications in diverse fields.

Customizable Organic Charge-Transfer Cocrystals for the Dual-Mode Optoelectronics in the NIR (II) Window.

Organic molecules have been regarded as ideal candidates for near-infrared (NIR) optoelectronic active materials due to their customizability and ease of large-scale production. However, constrained by the intricate molecular design and severe energy gap law, the realization of optoelectronic devices in the second near-infrared (NIR (II)) region with required narrow band gaps presents more challenges. Herein, we have originally proposed a cocrystal strategy that utilizes intermolecular charge-transfer interaction to drive the redshift of absorption and emission spectra of a series BFXTQ (X = 0, 1, 2, 4) cocrystals, resulting in the spectra located at NIR (II) window and reducing the optical bandgap to ∼0.98 eV. Significantly, these BFXTQ-based optoelectronic devices can exhibit dual-mode optoelectronic characteristics. An investigation of a series of BFXTQ-based photodetectors exhibits detectivity (D*) surpassing 1013 Jones at 375 to 1064 nm with a maximum of 1.76 × 1014 Jones at 1064 nm. Moreover, the radiative transition of CT excitons within the cocrystals triggers NIR emission over 1000 nm with a photoluminescence quantum yield (PLQY) of ∼4.6% as well as optical waveguide behavior with a low optical-loss coefficient of 0.0097 dB/µm at 950 nm. These results promote the advancement of an emerging cocrystal approach in micro/nanoscale NIR multifunctional optoelectronics.

Asymmetric Transfer Hydrogenation of Cyclobutenediones.

Four-membered carbocycles are fundamental substructures in bioactive molecules and approved drugs and serve as irreplaceable building blocks in organic synthesis. However, developing efficient protocols furnishing diversified four-membered ring compounds in a highly regio-, diastereo-, and enantioselective fashion remains challenging but very desirable. Here, we report the unprecedented asymmetric transfer hydrogenation of cyclobutenediones. The reaction can selectively afford three types of four-membered products in high yields with high stereoselectivities, and the highly functionalized products enable a series of further transformations to form more diversified four-membered compounds. Asymmetric synthesis of di-, tri-, and tetrasubstituted bioactive molecules has also been achieved. Systematic mechanistic studies and theoretical calculations have revealed the origin of the regioselectivity, the key hydrogenation transition state models, and the sequence of the double and triple hydrogenation processes. The work provides a new choice for the catalytic asymmetric synthesis of cyclobutanes and related structures and demonstrates the robustness of asymmetric transfer hydrogenation in the accurate selectivity control of highly functionalized substrates.

Facet-Dependent Surface Restructuring on Nickel (Oxy)hydroxides: A Self-Activation Process for Enhanced Oxygen Evolution Reaction.

Unraveling the catalyst surface structure and behavior during reactions is essential for both mechanistic understanding and performance optimization. Here we report a phenomenon of facet-dependent surface restructuring intrinsic to ß-Ni(OH)2 catalysts during oxygen evolution reaction (OER), discovered by the correlative ex situ and operando characterization. The ex situ study after OER reveals ß-Ni(OH)2 restructuring at the edge facets to form nanoporous Ni1-xO, which is Ni deficient containing Ni3+ species. Operando liquid transmission electron microscopy (TEM) and Raman spectroscopy further identify the active role of the intermediate ß-NiOOH phase in both the OER catalysis and Ni1-xO formation, pinpointing the complete surface restructuring pathway. Such surface restructuring is shown to effectively increase the exposed active sites, accelerate Ni oxidation kinetics, and optimize *OH intermediate bonding energy toward fast OER kinetics, which leads to an extraordinary activity enhancement of ∼16-fold. Facilitated by such a self-activation process, the specially prepared ß-Ni(OH)2 with larger edge facets exhibits a 470-fold current enhancement than that of the benchmark IrO2, demonstrating a promising way to optimize metal-(oxy)hydroxide-based catalysts.

Isotope Effect-Enabled Crystal Enlargement in Metal-Organic Frameworks.

Synthesizing large metal-organic framework (MOF) single crystals has garnered significant research interest, although it is hindered by the fast nucleation kinetics that gives rise to numerous small nuclei. Given the different chemical origins inherent in various types of MOFs, the development of a general approach to enhancing their crystal sizes presents a formidable challenge. Here, we propose a simple isotopic substitution strategy to promote size growth in MOFs by inhibiting nucleation, resulting in a substantial increase in the crystal volume ranging from 1.7- to 165-fold. Impressively, the crystals prepared under optimized conditions by normal approaches can be further enlarged by the isotope effect, yielding the largest MOF single crystal (2.9 cm × 0.48 cm × 0.23 cm) among the one-pot synthesis method. Detailed in situ characterizations reveal that the isotope effect can retard crystallization kinetics, establish a higher nucleation energy barrier, and consequently generate fewer nuclei that eventually grow larger. Compared with the smaller crystals, the isotope effect-enlarged crystal shows 33% improvement in the X-ray dose rate detection limit. This work enriches the understanding of the isotope effect on regulating the crystallization process and provides inspiration for exploring potential applications of large MOF single crystals.

Structure of GDP-bound Rab7 Q67L in complex with ORP1L.

Molecular processes are orchestrated by various proteins that promote early endosomes to become late endosomes and eventually fuse with lysosomes, guaranteeing the degradation of the content. Rab7, which is localized to late endosomes, is one of the most well-known GTPases. ORP1L is recruited by Rab7 to facilitate the fusion of late endosomes and lysosomes. Here, we present the structure of GDP-bound Rab7 Q67L with ORP1L. Structural analysis, supported by biochemical and ITC binding experiments, not only provides structural insight into the interactions between the ORP1L ANK domain and Rab7 but also suggests that the GTPase activity of Rab7 does not interfere with its ORP1L-binding capacity.

A Dual Encapsulation Strategy for High-Temperature Micro PCM Particles with High Cyclic Durability.

Addressing critical issues such as high-temperature corrosion,  leakage, degradation, and subpar cyclic performance is imperative for phase change materials (PCMs), prompting the development of appropriate encapsulation techniques to surmount these challenges. In this study, a dual encapsulation strategy is proposed for high-temperature micro PCM particles. Al-Si core is microencapsulated via the "solvent evaporation-heating curing" method. Subsequently, TiO2 is employed as the skeleton material for form-stable encapsulation of PCM microcapsules by "cold pressed sintering". Detailed analysis of the crystalline phase transformation mechanism in the sintering synthesis pathway of TiO2 underscore its potential as a robust structural material with exceptional thermal stability. Furthermore, the incorporation of hexagonal boron nitride (hBN) results in a substantial enhancement of the thermal conductivity of the composites, increasing by 121.1-131.3%. The prepared form-stable phase change microcapsules (FSPCMs) are subjected to 5000 thermal cycles in the air atmosphere. There is no observed PCM leakage or composite ruptures in the FSPCM. Moreover, the oxidized mass gain is merely 3.3%, signifying exceptional oxidation resistance. Thermophysical analysis indicates that FSPCM can retain 91.3% of the enthalpy after 2000 cycles, with over 80% preservation after 5000 cycles, underscoring its remarkable cyclic thermal durability.

Injectable Hydrogel System Incorporating Black Phosphorus Nanosheets and Tazarotene Drug for Enhanced Vascular and Nerve Regeneration in Spinal Cord Injury Repair.

Spinal cord injury (SCI) often leads to cell death, vascular disruption, axonal signal interruption, and permanent functional damage. Currently, there are no clearly effective therapeutic options available for SCI. Considering the inhospitable SCI milieu typified by ischemia, hypoxia, and restricted neural regeneration, a novel injectable hydrogel system containing conductive black phosphorus (BP) nanosheets within a lipoic acid-modified chitosan hydrogel matrix (LAMC) is explored. The incorporation of tannic acid (TA)-modified BP nanosheets (BP@TA) into the LAMC hydrogel matrix significantly improved its conductivity. Further, by embedding a bicyclodextrin-conjugated tazarotene drug, the hydrogel showcased amplified angiogenic potential in vitro. In a rat model of complete SCI, implantation of LAMC/BP@TA hydrogel markedly improved the recovery of motor function. Immunofluorescence evaluations confirmed that the composite hydrogel facilitated endogenous angiogenesis and neurogenesis at the injury site. Collectively, this work elucidates an innovative drug-incorporated hydrogel system enriched with BP, underscoring its potential to foster vascular and neural regeneration.