Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors.

Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.

eYGFPuv-Assisted Transgenic Selection in Populus deltoides WV94 and Multiplex Genome Editing in Protoplasts of P. trichocarpa × P. deltoides Clone '52-225'.

Although CRISPR/Cas-based genome editing has been widely used for plant genetic engineering, its application in the genetic improvement of trees has been limited, partly because of challenges in Agrobacterium-mediated transformation. As an important model for poplar genomics and biotechnology research, eastern cottonwood (Populus deltoides) clone WV94 can be transformed by A. tumefaciens, but several challenges remain unresolved, including the relatively low transformation efficiency and the relatively high rate of false positives from antibiotic-based selection of transgenic events. Moreover, the efficacy of CRISPR-Cas system has not been explored in P. deltoides yet. Here, we first optimized the protocol for Agrobacterium-mediated stable transformation in P. deltoides WV94 and applied a UV-visible reporter called eYGFPuv in transformation. Our results showed that the transgenic events in the early stage of transformation could be easily recognized and counted in a non-invasive manner to narrow down the number of regenerated shoots for further molecular characterization (at the DNA or mRNA level) using PCR. We found that approximately 8.7% of explants regenerated transgenic shoots with green fluorescence within two months. Next, we examined the efficacy of multiplex CRISPR-based genome editing in the protoplasts derived from P. deltoides WV94 and hybrid poplar clone '52-225' (P. trichocarpa × P. deltoides clone '52-225'). The two constructs expressing the Trex2-Cas9 system resulted in mutation efficiency ranging from 31% to 57% in hybrid poplar clone 52-225, but no editing events were observed in P. deltoides WV94 transient assay. The eYGFPuv-assisted plant transformation and genome editing approach demonstrated in this study has great potential for accelerating the genome editing-based breeding process in poplar and other non-model plants species and point to the need for additional CRISPR work in P. deltoides.

Spike rates of frontal eye field neurons predict reaction times in a spatial attention task.

Which neuronal signal(s) predict reaction times when subjects respond to a target at covertly attended locations? Although recent studies showed that spike rates are not predictive, it remains a highly contested question. Therefore, we record single-unit activity from frontal eye field (FEF) neurons while macaques are performing a covert spatial attention task. We find that the attentional modulation of spike rates of FEF neurons is strongly correlated with behavioral reaction times. Moreover, this correlation already emerges 1 s before target dimming, which triggers the behavioral responses. This prediction of reaction times by spike rates is found in neurons showing attention-dependent enhanced and suppressed activity for targets and distractors, respectively, yet in varying degrees across subjects. Thus, spike rates of FEF neurons can predict reaction times persistently and well before the operant behavior during selective attention tasks. Such long prediction windows will be useful for developing spike-based brain-machine interfaces.

Lectin Receptor-like Kinase Signaling during Engineered Ectomycorrhiza Colonization.

Mutualistic association can improve a plant's health and productivity. G-type lectin receptor-like kinase (PtLecRLK1) is a susceptibility factor in Populus trichocarpa that permits root colonization by a beneficial fungus, Laccaria bicolor. Engineering PtLecRLK1 also permits L. bicolor root colonization in non-host plants similar to Populus trichocarpa. The intracellular signaling reprogramed by PtLecRLK1 upon recognition of L. bicolor to allow for the development and maintenance of symbiosis is yet to be determined. In this study, phosphoproteomics was utilized to identify phosphorylation-based relevant signaling pathways associated with PtLecRLK1 recognition of L. bicolor in transgenic switchgrass roots. Our finding shows that PtLecRLK1 in transgenic plants modifies the chitin-triggered plant defense and MAPK signaling along with a significant adjustment in phytohormone signaling, ROS balance, endocytosis, cytoskeleton movement, and proteasomal degradation in order to facilitate the establishment and maintenance of L. bicolor colonization. Moreover, protein-protein interaction data implicate a cGMP-dependent protein kinase as a potential substrate of PtLecRLK1.

Self-Optimized Ligand Effect of Single-Atom Modifier in Ternary Pt-Based Alloy for Efficient Hydrogen Oxidation.

Modifying the atomic and electronic structure of platinum-based alloy to enhance its activity and anti-CO poisoning ability is a vital issue in hydrogen oxidation reaction (HOR). However, the role of foreign modifier metal and the underlying ligand effect is not fully understood. Here, we propose that the ligand effect of single-atom Cu can dynamically modulate the d-band center of Pt-based alloy for boosting HOR performance. By in situ X-ray absorption spectroscopy, our research has identified that the potential-driven structural rearrangement into high-coordination Cu-Pt/Pd intensifies the ligand effect in Pt-Cu-Pd, leading to enhanced HOR performance. Thereby, modulating the d-band structure leads to near-optimal hydrogen/hydroxyl binding energies and reduced CO adsorption energies for promoting the HOR kinetics and the CO-tolerant capability. Accordingly, PtPdCu1/C exhibits excellent CO tolerance even at 1,000 ppm impurity.

A macropinocytosis-related gene signature predicts the prognosis and immune microenvironment in hepatocellular carcinoma.

Background: Available treatments for hepatocellular carcinoma (HCC), a common human malignancy with a low survival rate, remain unsatisfactory. Macropinocytosis (MPC), a type of endocytosis that involves the non-specific uptake of dissolved molecules, has been shown to contribute to HCC pathology; however, its biological mechanism remains unknown. Methods: The current study identified 27 macropinocytosis-related genes (MRGs) from 71 candidate genes using bioinformatics. The R software was used to create a prognostic signature model by filtering standardized mRNA expression data from HCC patients and using various methods to verify the reliability of the model and indicate immune activity. Results: The prognostic signature was constructed using seven MPC-related differentially expressed genes, GSK3B, AXIN1, RAC1, KEAP1, EHD1, GRB2, and SNX5, through LASSO Cox regression. The risk score was acquired from the expression of these genes and their corresponding coefficients. HCC patients in the discovery and validation cohorts were stratified, and the survival of low-risk score patients was improved in both cohorts. Time-dependent ROC analysis indicated that the model's prediction reliability was the highest in the short term. Subsequent immunologic analysis, including KEGG, located the immune action pathway of the differentially expressed genes in the direction of the cancer pathway, etc. Immune infiltration and immune checkpoint tests provided valuable guidance for future follow-up experiments. Conclusion: A risk model with MRGs was constructed to effectively predict HCC patient prognoses and suggest changes in the immune microenvironment during the disease process. The findings should benefit the development of a prognostic stratification and treatment strategy for HCC.

Promotion of healthy adipose tissue remodeling ameliorates muscle inflammation in a mouse model of sarcopenic obesity.

A large subset of elders is classified as having sarcopenic obesity, a prevalence of obesity in combination with sarcopenia which places an aging population at the risk of adverse health consequences from both conditions. However, its complex etiology has restrained the development of effective therapeutic strategies. Recent progress has highlighted that the mode by which adipose tissue (AT) remodels is a determinant of metabolic health in the context of obesity. Healthy AT remodeling confers metabolic protection including insulin-sensitizing and anti-inflammatory effects to non-adipose tissues including skeletal muscle. Here, we employed a doxycycline-inducible adipocyte Hif1a knockout system to evaluate the muscle-protective effects associated with HIF1α inactivation-induced healthy AT remodeling in a model of sarcopenic obesity. We found that adipocyte HIF1α inactivation leads to improved AT metabolic health, reduced serum levels of lipids and pro-inflammatory cytokines, and increase of circulating adipokine (APN) in ovariectomized obese mice fed with obesogenic high-fat diet (HFD). Concomitantly, muscle inflammation is evidently lower in obese OVX mice when adipocyte HIF1α is inactivated. Furthermore, these protective effects against muscle inflammation can be mimicked by the administration of adiponectin receptor agonist AdipoRon. Collectively, our findings underscore the importance of AT metabolic health in the context of concurrent sarcopenia and obesity, and promotion of healthy AT remodeling may represent a new therapeutic strategy to improve muscle health in sarcopenic obesity.

In situ constructing atomic interface in ruthenium-based amorphous hybrid-structure towards solar hydrogen evolution.

The rational steering and construction of efficient and stable atomic interfaces is highly desirable but rather challenging in solar energy conversion. Here, we report an in-situ oxygen impregnation strategy to build abundant atomic interfaces composed of homogeneous Ru and RuOx amorphous hybrid-mixture with ultrafast charge transfer, for solar hydrogen evolution with sacrificial agent free. Via in-situ synchrotron X-ray absorption and photoelectron spectroscopies, we can precisely track and identify the gradual formation of atomic interfaces towards homogeneous Ru-RuOx hybrid-structure at the atomic level. Benefiting from the abundant interfaces, the amorphous RuOx sites can intrinsically trap the photoexcited hole within an ultrafast process (<100 fs), and the amorphous Ru sites enable subsequent electron transfer (~1.73 ps). Hence, this hybrid-structure triggers long-lived charge-separated states, and results in a high hydrogen evolution rate of 60.8 µmol·h-1. This design integrating the two sites fulfilled each half-reaction in a single hybrid-structure suggests potential guidelines towards efficient artificial photosynthesis.

Ligand Assisted Thermal Atomization of Palladium Clusters: An Inspiring Approach for the Rational Design of Atomically Dispersed Metal Catalysts.

The transformation from metal nanocluster catalysts to metal single-atom catalysts is an important procedure in the rational design of atomically dispersed metal catalysts (ADCs). However, the conversion methods often involve high annealing temperature as well as reducing atmosphere. Herein, we reported a continuous and convenient approach to transfer Pd nanocluster into Pd single-atom in a ligand assisted annealing procedure, by which means we reduced its activating temperature low to 400 °C. Using ex-situ microscopy and spectroscopy, we comprehensively monitored the structural evolution of Pd species though the whole atomization process. Theoretical calculation revealed that the structural instability caused by remaining Cl ligands was the main reason for this low-temperature transformation. The present atomization strategy and mechanistic knowledge for the conversion from cluster to atomic dispersion provides guidelines for the rational design of ADCs.

General anesthesia vs. non-general anesthesia for vertebrobasilar stroke endovascular therapy.

Background: The optimal type of anesthesia for acute vertebrobasilar artery occlusion (VBAO) remains controversial. We aimed to assess the influence of anesthetic management on the outcomes in VBAO patients received endovascular treatment (EVT). Methods: Patients underwent EVT for acute VBAO at 21 stroke centers in China were retrospectively enrolled and compared between the general anesthesia (GA) group and non-GA group. The primary outcome was the favorable outcome, defined as a modified Rankin Scale (mRS) score 0-3 at 90 days. Secondary outcomes included functional independence (90-day mRS score 0-2), and the rate of successful reperfusion. The safety outcomes included all-cause mortality at 90 days, the occurrence of any procedural complication, and the rate of symptomatic intracranial hemorrhage (sICH). In addition, we performed analyses of the outcomes in subgroups that were defined by Glasgow Coma Scale (GCS) score (≤8 or >8). Results: In the propensity score matched cohort, there were no difference in the primary outcome, secondary outcomes and safety outcomes between the two groups. Among patients with a GCS score of 8 or less, the proportion of successful reperfusion was significantly higher in the GA group than the non-GA group (aOR, 3.57, 95% CI 1.06-12.50, p = 0.04). In the inverse probability of treatment weighting-propensity score-adjusted cohort, similar results were found. Conclusions: Patients placed under GA during EVT for VBAO appear to be as effective and safe as non-GA. Furthermore, GA might yield better successful reperfusion for worse presenting GCS score (≤8). Registration: URL: http://www.chictr.org.cn/; Unique identifier: ChiCTR2000033211.

Application of Time-Resolved Synchrotron X-ray Absorption Spectroscopy in an Energy Conversion Reaction.

The rational design of high-efficiency catalysts is hindered by the knowledge of active sites, which always experience dynamic transformations within different time scales. In this regard, tracking these time-dependent processes is essential to building the correlation between the active site and catalytic performance. Achieving this goal requires powerful characterization techniques to overcome the obstacle induced by the time mismatch. By virtue of the local structure sensitivity, synchrotron X-ray absorption spectroscopy (XAS) comprising step-scanning XAS, quick-scanning XAS, and energy-dispersive XAS has been widely applied to record structural evolution events. In this Perspective, we highlight the substantial accomplishments achieved by these time-resolved XAS techniques. Their principles, advantages, and limitations involved in monitoring energy-involving electrocatalysis were also introduced. Meanwhile, the key challenges that we are encountering and the further directions of time-resolved XAS are also provided. We sincerely hope that these insights could offer a reliable guideline for other researchers to design more efficient in situ experiments.

Understanding Synergistic Catalysis on Cu-Se Dual Atom Sites via Operando X-ray Absorption Spectroscopy in Oxygen Reduction Reaction.

The construction and understanding of synergy in well-defined dual-atom active sites is an available avenue to promote multistep tandem catalytic reactions. Herein, we construct a dual-hetero-atom catalyst that comprises adjacent Cu-N4 and Se-C3 active sites for efficient oxygen reduction reaction (ORR) activity. Operando X-ray absorption spectroscopy coupled with theoretical calculations provide in-depth insights into this dual-atom synergy mechanism for ORR under realistic device operation conditions. The heteroatom Se modulator can efficiently polarize the charge distribution around symmetrical Cu-N4 moieties, and serve as synergistic site to facilitate the second oxygen reduction step simultaneously, in which the key OOH*-(Cu1 -N4 ) transforms to O*-(Se1 -C2 ) intermediate on the dual-atom sites. Therefore, this designed catalyst achieves satisfied alkaline ORR activity with a half-wave potential of 0.905 V vs. RHE and a maximum power density of 206.5 mW cm-2 in Zn-air battery.

Virtual histology of morphometric similarity network after risperidone monotherapy and imaging-epigenetic biomarkers for treatment response in first-episode schizophrenia.

BACKGROUND: Antipsychotic treatment has been conceived to alter brain connectivity, but it is unclear how the changes of network phenotypes relate to the underlying transcriptomics. Given DNA methylation (DNAm) may alter transcriptional levels, we further integrated an imaging-transcriptomic-epigenetic analysis to explore multi-omics treatment response biomarkers. METHODS: Forty-two treatment-naive first-episode schizophrenia patients were scanned by TI weighted (T1W) imaging and DTI before and after 8-week risperidone monotherapy, and their peripheral blood genomic DNAm values were examined in parallel with MRI scanning. Morphometric similarity network (MSN) quantified with DTI and T1W data were used as a marker of treatment-related alterations in interareal cortical connectivity. We utilized partial least squares (PLS) to examine spatial associations between treatment-related MSN variations and cortical transcriptomic data obtained from the Allen Human Brain Atlas. RESULTS: Longitudinal MSN alterations were related to treatment response on cognitive function and general psychopathology symptoms, while DNAm values of 59 PLS1 genes were on negative and positive symptoms. Virtual-histology transcriptomic analysis linked the MSN alterations with the neurobiological, cellular and metabolic pathways or processes, and assigned MSN-related genes to multiple cell types, specifying neurons and glial cells as contributing most to the transcriptomic associations of longitudinal changes in MSN. CONCLUSIONS: We firstly reveal how brain-wide transcriptional levels and cell classes capture molecularly validated cortical connectivity alterations after antipsychotic treatment. Our findings represent a vital step towards the exploration of treatment response biomarkers on the basis of multiple omics rather than a single omics type as a strategy for advancing precise care.

Matching Bidentate Ligand Anchoring: an Accurate Control Strategy for Stable Single-Atom/ZIF Nanocatalysts.

Improving metal loading and controlling the coordination environment is nontrivial and challenging for single-atom catalysts (SACs), which have the greatest atomic efficiency and largest number of interface sites. In this study, a matching bidentate ligand (MBL) anchoring strategy is designed for the construction of CuN4 SACs with tunable coordination environments (Cu loading range from 0.4 to15.4 wt.%). The obtained Cu SA/ZIF and Cu SA/ZIF* (0.4 wt.%) (ZIF and ZIF* = Zeolitic imidazolate framework with Matching bidentate N-ligands) nanocomposites exhibit superior performance in homo-coupling of phenyl acetylene under light irradiation (TON = 580, selectivity > 99%), which is 22 times higher than that of Cu SA/NC-800 (NC = N-doped porous carbon). Experiments and density functional theory calculations confirmed that the specific Cu five-membered ring formed using the MBL anchoring strategy is the key to the immobilization of isolated Cu atoms. This strategy provides a basis for the construction of M SA/MOF, which has the potential to narrow the gap between experimental and theoretical catalysis, as further confirmed by the successful preparation of Fe SA/ZIF and Ni SA/ZIF.

FAIRE-MS reveals mitotic retention of transcriptional regulators on a proteome-wide scale.

Mitosis entails global and dramatic alterations, such as higher-order chromatin organization disruption, concomitant with global transcription downregulation. Cells reliably re-establishing gene expression patterns upon mitotic exit and maintaining cellular identities remain poorly understood. Previous studies indicated that certain transcription factors (TFs) remain associated with individual loci during mitosis and serve as mitotic bookmarkers. However, it is unclear which regulatory factors remain bound to the compacted mitotic chromosomes. We developed formaldehyde-assisted isolation of regulatory elements-coupled mass spectrometry (FAIRE-MS) that combines FAIRE-based open chromatin-associated protein pull-down and mass spectrometry (MS) to quantify the open chromatin-associated proteome during the interphase and mitosis. We identified 189 interphase and mitosis maintained (IM) regulatory factors using FAIRE-MS and found intrinsically disordered proteins and regions (IDP(R)s) are highly enriched, which plays a crucial role in liquid-liquid phase separation (LLPS) and chromatin organization during the cell cycle. Notably, in these IDP(R)s, we identified mitotic bookmarkers, such as CEBPB, HMGB1, and TFAP2A, and several factors, including MAX, HMGB3, hnRNP A2/B1, FUS, hnRNP D, and TIAL1, which are at least partially bound to the mitotic chromosome. Furthermore, it will be essential to study whether these IDP(R)s through LLPS helps cells transit from mitosis to the G1 phase during the cell cycle.

Controllable Itinerant Ferromagnetism in Weakly Correlated 5d SrIrO3.

The weakly correlated nature of 5d oxide SrIrO3 determines its rare ferromagnetism, and the control of its magnetic order is even less studied. Tailoring structure distortion is currently a main route to tune the magnetic order of 5d iridates, but only for the spatially confined insulating counterparts. Here, we have realized ferromagnetic order in metallic SrIrO3 by construction of SrIrO3/ferromagnetic-insulator (LaCoO3) superlattices, which reveal a giant coercivity of ∼10 T and saturation field of ∼25 T with strong perpendicular magnetic anisotropy. The Curie temperature of SrIrO3 can be controlled by engineering interface charge transfer, which is confirmed by Hall effect measurements collaborating with EELS and XAS. Besides, the noncoplanar spin texture is captured, which is caused by interfacial Dzyaloshinskii-Moriya interactions as well. These results indicate controllable itinerant ferromagnetism and an emergent topological magnetic state in strong spin-orbit coupled semimetal SrIrO3, showing great potential to develop efficient spintronic devices.

Actinide-uranium single-atom catalysis for electrochemical nitrogen fixation.

Actinide-based catalysts have been regarded as promising candidates for N2 fixation owing to their unique 5f orbital with flexible oxidation states. Herein, we report for the first time the dispersion of uranium (U) single atoms on TiO2 nanosheets via oxygen vacancy confinement for N2 electroreduction. The single-atom U catalyst exhibited a high NH3 yield of 40.57 µg h-1 mg-1, with a reasonably high Faraday efficiency of 25.77%, ranking first among the reported nitrogen-free catalysts. Isotope-labeling operando synchrotron infrared spectroscopy verifies that the key *N2Hy intermediate species was derived from the N2 gas of the feed. By using operando X-ray absorption spectroscopy, we found enhanced metal-support interaction between U single atoms and TiO2 lattice with more U-Olatt coordination under working conditions. Theoretical simulations suggest that the evolved 1Oads-U-4Olatt moieties act as a critical electron-feedback center, lowering the thermodynamic energy barrier for the N2 dissociation and the first hydrogenation step. This work provides the possibility of tailoring the interaction between metal active sites and supports for designing high-performance actinide-based single-atom catalysts.

[Tiaohe Yinyang acupotomy for knee osteoarthritis: a randomized controlled trial].

OBJECTIVE: To observe the clinical efficacy of Tiaohe Yinyang acupotomy (acupotomy for regulating and harmonizing yin and yang) for knee osteoarthritis (KOA). METHODS: A total of 88 patients with KOA were randomized into a acupotomy group and a sham-acupotomy group, 44 cases in each group. In the acupotomy group, acupotomy was applied at yin side (4-5 high stress points i.e. pes anserinus and terminal of popliteus) and yang side (1-2 high stress points i.e. stimulation point of infrapatellar ligament and suprapatellar bursa) of knee joint. In the sham-acupotomy group, sham-acupotomy was applied at the same points as the acupotomy group. The treatment was given once a week for 2 weeks in the two groups. Before and after treatment, the Western Ontario and McMaster Universities arthritis index (WOMAC) score, visual analogue scale (VAS) score, thickness of medial and lateral collateral ligaments of knee joint, motion range of knee joint and plantar pressure distribution were observed in the two groups. In the follow-up of 3 months after treatment, the WOMAC and VAS scores were recorded in the acupotomy group. RESULTS: After treatment, the sub item scores (pain, stiffness and function) and total scores of WOMAC and VAS scores were decreased in the both groups (P<0.05), pain score, function score and total score of WOMAC and VAS score in the acupotomy group were lower than those in the sham-acupotomy group (P<0.05). Before and after treatment, there were no statistical differences in thickness of medial and lateral collateral ligaments of knee joint and motion range of knee joint between the two groups (P>0.05). After treatment, the plantar medial pressure was increased while the plantar lateral pressure was decreased (P<0.05), and the plantar force line moved medially in the acupotomy group. In the follow-up, the sub item scores and total score of WOMAC and VAS score were lower than those before and after treatment in the acupotomy group (P<0.05). CONCLUSION: Tiaohe Yinyang acupotomy can improve the clinical symptoms of knee joint in patients with KOA by changing the local biological stress.

Universal and High-Speed Zeptomolar Protein Serum Assay with Unprecedented Sensitivity.

The accurate detection of trace protein biomarkers is critical for disease diagnosis, healthcare, and pathology research. Currently, the main predicaments of techniques are low sensitivity, prolonged procedures, and the need for specialized devices. Moreover, multistep handling and nonspecific biofouling can lead to high background noise and false positives. To overcome these barriers, a novel ultrasensitive electrochemical platform was developed by combining an electrochemistry approach with the silver mirror reaction to detect proteins at the zeptomolar level. This assay can be accomplished in about only 18 min. As a proof of the concept, human immunoglobulin G (h-IgG) as a model analyte exhibited an ultralow detection limit of 6.31 ag mL-1 (0.04 zeptomoles mL-1). This strategy can be exploited as a universal approach for the ultrasensitive detection of various proteins in clinical diagnostics and point-of-care testing.