Structural insights into the catalytic mechanism of the AP endonuclease AtARP.

Base excision repair (BER) is a critical genome defense pathway that copes with a broad range of DNA lesions induced by endogenous or exogenous genotoxic agents. AP endonucleases in the BER pathway are responsible for removing the damaged bases and nicking the abasic sites. In plants, the BER pathway plays a critical role in the active demethylation of 5-methylcytosine (5mC) DNA modification. Here, we have determined the crystal structures of Arabidopsis AP endonuclease AtARP in complex with the double-stranded DNA containing tetrahydrofuran (THF) that mimics the abasic site. We identified the critical residues in AtARP for binding and removing the abasic site and the unique residues for interacting with the orphan base. Additionally, we investigated the differences among the three plant AP endonucleases and evaluated the general DNA repair capacity of AtARP in a mammalian cell line. Our studies provide further mechanistic insights into the BER pathway in plants.

FUS unveiled in mitochondrial DNA repair and targeted ligase-1 expression rescues repair-defects in FUS-linked motor neuron disease.

This study establishes the physiological role of Fused in Sarcoma (FUS) in mitochondrial DNA (mtDNA) repair and highlights its implications to the pathogenesis of FUS-associated neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). Endogenous FUS interacts with and recruits mtDNA Ligase IIIα (mtLig3) to DNA damage sites within mitochondria, a relationship essential for maintaining mtDNA repair and integrity in healthy cells. Using ALS patient-derived FUS mutant cell lines, a transgenic mouse model, and human autopsy samples, we discovered that compromised FUS functionality hinders mtLig3's repair role, resulting in increased mtDNA damage and mutations. These alterations cause various manifestations of mitochondrial dysfunction, particularly under stress conditions relevant to disease pathology. Importantly, rectifying FUS mutations in patient-derived induced pluripotent cells (iPSCs) preserves mtDNA integrity. Similarly, targeted introduction of human DNA Ligase 1 restores repair mechanisms and mitochondrial activity in FUS mutant cells, suggesting a potential therapeutic approach. Our findings unveil FUS's critical role in mitochondrial health and mtDNA repair, offering valuable insights into the mechanisms underlying mitochondrial dysfunction in FUS-associated motor neuron disease.

Physical activity modified association of urinary metals mixture and fasting blood glucose in children: From two panel studies.

There is unclear evidence available on the associations between multiple metals and fasting blood glucose (FBG) in children, and whether they could be beneficial from physical activity. We included 283 children aged 4-12 years from two panel studies with 4-consecutive morning urinary 13 essential metals and 10 non-essential metals repeated across 3 seasons. We employed multiple informant model, linear mixed-effect model, and quantile g-computation to evaluate associations of single metal and their mixture with FBG and interactions with extra-school activity. The results showed that positive relations of multiple essential metals (aluminum, chromium, copper, iron, molybdenum (Mo), nickel, selenium (Se), strontium, zinc) and non-essential metals (arsenic (As), cadmium (Cd), rubidium, titanium (Ti), thallium) with FBG were the strongest at lag 0 (the health examination day), especially in overweight & obesity children (FDR <0.05). The strongest effect presented 1-fold increment in As was related to FBG increased 1.66% (95%CI: 0.84%, 2.48%) in overweight & obesity children. Notably, modification of extra-school activity showed significant, and the effects of multiple metals on FBG were attenuated in children taking total extra-school activity ≥1 h/day, and only one type of which, low or moderate & high intensity extra-school activity reached 20 min/day (Pint <0.05). For instance, each 1-fold increased As was associated with 1.41% increased FBG in overall children taking total extra-school activity <1 h/day, while that of 0.13% in those ≥1 h/day. Meanwhile, mixture of all, essential and non-essential metals were associated with increased FBG, a trend that decreased and became nonsignificant in children having certain extra-school activity, which were dominated by Mo, Se, Ti, Cd. And such relations were substantially beneficial from extra-school activity in overweight & obesity children. Accordingly, multiple essential and non-essential metals, both individual and in mixture, were positively related to FBG in children, which might be attenuated by regular physical activity.

Risk stratification for radioactive iodine refractoriness using molecular alterations in distant metastatic differentiated thyroid cancer.

Objective: Patients with radioactive iodine-refractory differentiated thyroid cancer (RAIR-DTC) are often diagnosed with delay and constrained to limited treatment options. The correlation between RAI refractoriness and the underlying genetic characteristics has not been extensively studied. Methods: Adult patients with distant metastatic DTC were enrolled and assigned to undergo next-generation sequencing of a customized 26-gene panel (ThyroLead). Patients were classified into RAIR-DTC or non-RAIR groups to determine the differences in clinicopathological and molecular characteristics. Molecular risk stratification (MRS) was constructed based on the association between molecular alterations identified and RAI refractoriness, and the results were classified as high, intermediate or low MRS. Results: A total of 220 patients with distant metastases were included, 63.2% of whom were identified as RAIR-DTC. Genetic alterations were identified in 90% of all the patients, with BRAF (59.7% vs. 17.3%), TERT promoter (43.9% vs. 7.4%), and TP53 mutations (11.5% vs. 3.7%) being more prevalent in the RAIR-DTC group than in the non-RAIR group, except for RET fusions (15.8% vs. 39.5%), which had the opposite pattern. BRAF and TERT promoter are independent predictors of RAIR-DTC, accounting for 67.6% of patients with RAIR-DTC. MRS was strongly associated with RAI refractoriness (P<0.001), with an odds ratio (OR) of high to low MRS of 7.52 [95% confidence interval (95% CI), 3.96-14.28; P<0.001] and an OR of intermediate to low MRS of 3.20 (95% CI, 1.01-10.14; P=0.041). Conclusions: Molecular alterations were associated with RAI refractoriness, with BRAF and TERT promoter mutations being the predominant contributors, followed by TP53 and DICER1 mutations. MRS might serve as a valuable tool for both prognosticating clinical outcomes and directing precision-based therapeutic interventions.

Long term for patients with futile endovascular reperfusion after stroke.

AIMS: With the progress of thrombectomy technology, the vascular recanalization rate of patients with stroke has been continuously improved, but the proportion of futile recanalization (FR) is still quite a few. The long-term prognosis and survival of patients with FR and its influencing factors remain unclear. METHODS: Consecutive patients who received endovascular treatment (EVT) for ischemic stroke were enrolled between 2013 and 2021 from a single-center prospectively registry study. We evaluated the long-term outcome of these patients by Kaplan-Meier survival analysis, and the multivariable logistic regression curve was performed to analyze influencing factors. RESULTS: Among 458 patients with FR, 56.4% of patients survived at 1 year, and 50.4% at 2 years. In the multivariate regression analysis, age, premorbid modified Rankin Scale (mRS), National Institutes of Health Stroke Scale (NIHSS), posterior circulation infarct, general anesthesia, symptomatic intracerebral hemorrhage (sICH), and decompressive craniectomy were found to be related to unfavorable outcomes in long-term. Age, premorbid mRS, NIHSS, general anesthesia, and sICH were predictors of long-term mortality. CONCLUSIONS: Futile recanalization accounts for a large proportion of stroke patients after thrombectomy. This study on the long-term prognosis of such patients is beneficial to the formulation of treatment plans and the prediction of therapeutic effects.

Night shift work was associated with functional outcomes in acute ischemic stroke patients treated with endovascular thrombectomy.

Objective: This study aimed to explore the impact of late night shift work on the functional outcomes of patients with acute ischemic stroke (AIS) treated with endovascular thrombectomy (EVT). Methods: Consecutive AIS patients who underwent EVT between June 2019 and June 2021 were enrolled and divided into non-night shift work and night shift work groups based on their occupational histories. The primary outcome was the modified Rankin Scale score defined 3-month functional outcome. The secondary outcomes were 3-month mortality, symptomatic intracerebral hemorrhage (sICH), ICH and early recanalization. Results: A total of 285 patients were enrolled, 35 patients (12.3%) were night shift workers, who were younger (P < 0.001) and had a significantly higher prevalence of smoking (P < 0.001), hyperlipidemia (P = 0.002), coronary heart disease (P = 0.031), and atrial fibrillation (P < 0.001). The 3-month favorable outcomes were achieved in 44.8% and 25.7% of patients in the non-night shift work and night shift work groups, respectively (adjusted odds ratio [OR]: 0.24, 95% CI: 0.10-0.57; adjusted P = 0.001). No difference was found in 3-month mortality (adjusted OR: 0.43; 95% CI: 0.14-1.25, adjusted P = 0.121), rates of ICH (adjusted OR: 0.73; 95% CI: 0.33-1.60; adjusted P = 0.430), sICH (adjusted OR: 0.75; 95% CI: 0.34-1.67; adjusted P = 0.487), or early successful recanalization (adjusted OR: 0.42; 95% CI: 0.12-1.56; adjusted P = 0.197). These results were consistent after PSM analysis. Conclusion: Our findings suggest that late night shift work is significantly associated with unfavorable outcomes in patients with AIS after EVT.

Dual-signal readout sensing of ATP content in single dental pulp stem cells during differentiation via functionalized glass nanopipettes.

Adenosine triphosphate (ATP) is regarded as the "energy currency" in living cells, so real-time quantification of content variation of intracellular ATP is highly desired for understanding some important physiological processes. Due to its single-molecule readout ability, nanopipette sensing has emerged as a powerful technique for molecular sensing. In this study, based on the effect of targeting-aptamer binding on ionic current, and fluorescence resonance energy transfer (FRET), we reported a dual-signal readout nanopipette sensing system for monitoring ATP content variation at the subcellular level. In the presence of ATP, the complementary DNA-modified gold nanoparticles (cDNAs-AuNPs) were released from the inner wall of the nanopipette, which leads to sensitive response variations in ionic current rectification and fluorescence intensity. The developed nanopipette sensor was capable of detecting ATP in single cells, and the fluctuation of ATP content in the differentiation of dental pulp stem cells (DPSCs) was further quantified with this method. The study provides a more reliable nanopipette sensing platform due to the introduction of fluorescence readout signals. Significantly, the study of energy fluctuation during cell differentiation from the perspective of energy metabolism is helpful for differentiation regulation and cell therapy.

Loss of SHROOM3 affects neuroepithelial cell shape through regulating cytoskeleton proteins in cynomolgus monkey organoids.

Neural tube defects (NTDs) are severe congenital neurodevelopmental disorders arising from incomplete neural tube closure. Although folate supplementation has been shown to mitigate the incidence of NTDs, some cases, often attributable to genetic factors, remain unpreventable. The SHROOM3 gene has been implicated in NTD cases that are unresponsive to folate supplementation; at present, however, the underlying mechanism remains unclear. Neural tube morphogenesis is a complex process involving the folding of the planar epithelium of the neural plate. To determine the role of SHROOM3 in early developmental morphogenesis, we established a neuroepithelial organoid culture system derived from cynomolgus monkeys to closely mimic the in vivo neural plate phase. Loss of SHROOM3 resulted in shorter neuroepithelial cells and smaller nuclei. These morphological changes were attributed to the insufficient recruitment of cytoskeletal proteins, namely fibrous actin (F-actin), myosin II, and phospho-myosin light chain (PMLC), to the apical side of the neuroepithelial cells. Notably, these defects were not rescued by folate supplementation. RNA sequencing revealed that differentially expressed genes were enriched in biological processes associated with cellular and organ morphogenesis. In summary, we established an authentic in vitro system to study NTDs and identified a novel mechanism for NTDs that are unresponsive to folate supplementation.

Palladium-Catalyzed Dual C-H Carbonylation of Diarylamines Leading to Diversified Acridones under CO-Free Conditions.

A Pd-catalyzed dual C-H carbonylation of commercially available diarylamines using Co2(CO)8 as a safe CO source has been developed. This methodology provides a facile approach for the synthesis of diversified acridones in moderate to good yields. The protocol features good functional group compatibility, operational safety, easy scale-up, and versatile transformations.

ESRP1 controls biogenesis and function of a large abundant multiexon circRNA.

While the majority of circRNAs are formed from infrequent back-splicing of exons from protein coding genes, some can be produced at quite high level and in a regulated manner. We describe the regulation, biogenesis and function of circDOCK1(2-27), a large, abundant circular RNA that is highly regulated during epithelial-mesenchymal transition (EMT) and whose formation depends on the epithelial splicing regulator ESRP1. CircDOCK1(2-27) synthesis in epithelial cells represses cell motility both by diverting transcripts from DOCK1 mRNA production to circRNA formation and by direct inhibition of migration by the circRNA. HITS-CLIP analysis and CRISPR-mediated deletions indicate ESRP1 controls circDOCK1(2-27) biosynthesis by binding a GGU-containing repeat region in intron 1 and detaining its splicing until Pol II completes its 157 kb journey to exon 27. Proximity-dependent biotinylation (BioID) assay suggests ESRP1 may modify the RNP landscape of intron 1 in a way that disfavours communication of exon 1 with exon 2, rather than physically bridging exon 2 to exon 27. The X-ray crystal structure of RNA-bound ESRP1 qRRM2 domain reveals it binds to GGU motifs, with the guanines embedded in clamp-like aromatic pockets in the protein.

Enhanced activity of Co-Mo-S catalysts towards hydrodesulfurization and hydrogen evolution reaction via NaBH4 assisted formation.

Co-Mo-S based catalysts have promising applications in both the hydrogen evolution reaction (HER) and hydrodesulfurization (HDS). Herein, Co-Mo-S catalyst and Co-Mo-S catalyst with and without NaBH4 modification have been successfully synthesized by a simple hydrothermal synthesis method. Co-Mo-S catalysts with NaBH4 modification show better catalytic activity towards both HDS and the HER. The phase purity, morphology, crystal structures and electron valence distribution of the catalysts with and without NaBH4 modification were studied by experimental characterizations and theoretical calculations. The catalysts without NaBH4 modification are mostly 2H-MoS2, while the catalysts without NaBH4 modification have 1T-MoS2, and 1T-MoS2 is exposed to more active sites, which will be conducive to the results of HDS performance of the catalyst. DFT calculations investigated the required activation energies of 1T-MoS2 and 2H-MoS2 for HDS and HER, respectively. The activation energy required for both HDS and H2 generation of 1T-MoS2 is significantly lower than that for the 2H-MoS2 structure.

Predicting Futile Recanalization in Acute Ischemic Stroke Patients Undergoing Endovascular Thrombectomy: The Role of White Blood Cell Count to Mean Platelet Volume Ratio.

BACKGROUND: Approximately half of AIS patients have an unfavorable outcome even after complete reperfusion. White blood cell (WBC) count to mean platelet volume (MPV) ratio (WMR) may be a promising predictive factor for futile recanalization. This study aimed to determine the predictive value of WMR in identifying individuals at higher risk of futile recanalization. METHODS: In this retrospective cohort study, 296 patients who achieved complete reperfusion after endovascular treatment (EVT) were included in the analysis. WBC count and MPV were collected at admission. Multivariable logistic regression was used to examine the independent association of the WMR with functional outcomes at three months. Net reclassification improvement (NRI) and integrated discrimination improvement (IDI) analyses were used to compare the accuracy of WMR for predicting futile recanalization. RESULTS: The adjusted odds ratios for the fourth quartile of WMR were 3.142 (95% CI 1.405- 7.027, P = 0.005) for unfavorable outcomes at 3 months in comparison with the first quartile. The inclusion of WMR in the traditional model enabled a more accurate prediction of unfavorable outcomes (NRI 0.250, P = 0.031; IDI 0.022, P = 0.017). CONCLUSION: Elevated WMR at admission was independently associated with futile recanalization among AIS patients who received EVT and might be useful in identifying futile recanalization.

lncRNA Sequencing Reveals Neurodegeneration-Associated FUS Mutations Alter Transcriptional Landscape of iPS Cells That Persists in Motor Neurons.

Fused-in sarcoma (FUS) gene mutations have been implicated in amyotrophic lateral sclerosis (ALS). This study aimed to investigate the impact of FUS mutations (R521H and P525L) on the transcriptome of induced pluripotent stem cells (iPSCs) and iPSC-derived motor neurons (iMNs). Using RNA sequencing (RNA Seq), we characterized differentially expressed genes (DEGs) and differentially expressed lncRNAs (DELs) and subsequently predicted lncRNA-mRNA target pairs (TAR pairs). Our results show that FUS mutations significantly altered the expression profiles of mRNAs and lncRNAs in iPSCs. Using this large dataset, we identified and verified six key differentially regulated TAR pairs in iPSCs that were also altered in iMNs. These target transcripts included: GPR149, NR4A, LMO3, SLC15A4, ZNF404, and CRACD. These findings indicated that selected mutant FUS-induced transcriptional alterations persist from iPSCs into differentiated iMNs. Functional enrichment analyses of DEGs indicated pathways associated with neuronal development and carcinogenesis as likely altered by these FUS mutations. Furthermore, ingenuity pathway analysis (IPA) and GO network analysis of lncRNA-targeted mRNAs indicated associations between RNA metabolism, lncRNA regulation, and DNA damage repair. Our findings provide insights into potential molecular mechanisms underlying the pathophysiology of ALS-associated FUS mutations and suggest potential therapeutic targets for the treatment of ALS.

Structural characterization of an isocytosine-specific deaminase VCZ reveals its application potential in the anti-cancer therapy.

Non-natural nucleobase isocytosine (IC) is the isomer of cytosine; its chemical derivate 5-fluoroisocytosine (5-FIC) together with the isocytosine-specific deaminase (ICD) VCZ was suggested to be potential practical enzyme/prodrug pair for cancer therapy through gene-directed enzyme-prodrug therapy (GDEPT) method. In this study, we have determined the crystal structures of apo-VCZ and its complex with 5-FU. We identified the critical residues for substrate binding and catalytic reaction. We also captured the substrate-induced conformational changes of VCZ, then proposed the conjectural reaction procedures of VCZ for converting the IC into the uracil. Moreover, we evaluated the therapeutic effect of wildtype or the mutated VCZ protein in the colorectal cancer cell lines. Our studies will shed light on optimizing the ICD/5-FIC pairs by modifying either the enzyme or the prodrug based on the structural observations, thereby improving the possibility of applying the ICD/5-FIC pair in clinical trials.

Palladium-Catalyzed Carbonylative Dearomatization of Indoles to Achieve Carbonyl-Containing Spirocyclic Indolenines Bearing an All-Carbon Quaternary Center.

A Pd-catalyzed carbonylative dearomatization via an acyl Pd complex has been developed. Diversified carbonyl-containing spirocyclic indolenines with an all-carbon quaternary center were constructed in an efficient and straightforward way with good to excellent yields. The protocol features a simple catalytic system, operational simplicity, a broad substrate scope, easy scale-up, and versatile transformations. In addition, the asymmetric reaction was initially explored with moderate enantioselectivity.

lncRNA Sequencing Reveals Neurodegeneration-associated FUS Mutations Alter Transcriptional Landscape of iPS Cells That Persists In Motor Neurons.

Fused-in Sarcoma (FUS) gene mutations have been implicated in amyotrophic lateral sclerosis (ALS). This study aimed to investigate the impact of FUS mutations (R521H and P525L) on the transcriptome of induced pluripotent stem cells (iPSCs) and iPSC-derived motor neurons (iMNs). Using RNA sequencing (RNA Seq), we characterized differentially expressed genes (DEGs), differentially expressed lncRNAs (DELs), and subsequently predicted lncRNA-mRNA target pairs (TAR pairs). Our results show that FUS mutations significantly altered expression profiles of mRNAs and lncRNAs in iPSCs. We identified key differentially regulated TAR pairs, including LMO3, TMEM132D, ERMN, GPR149, CRACD, and ZNF404 in mutant FUS iPSCs. We performed reverse transcription PCR (RT-PCR) validation in iPSCs and iMNs. Validation confirmed RNA-Seq findings and suggested that mutant FUS-induced transcriptional alterations persisted from iPSCs into differentiated iMNs. Functional enrichment analyses of DEGs indicated pathways associated with neuronal development and carcinogenesis that were likely altered by FUS mutations. Ingenuity Pathway Analysis (IPA) and GO network analysis of lncRNA-targeted mRNAs indicated associations related to RNA metabolism, lncRNA regulation, and DNA damage repair. Our findings provide insights into the molecular mechanisms underlying the pathophysiology of ALS-associated FUS mutations and suggest potential therapeutic targets for the treatment of ALS.

Pressure-Transient Behavior of Vertical Wells Considering Dynamic Water Hammer and Dynamic Induced Fracture: Theory and Case Studies.

Water injection can result in the creation of induced fracture by connecting natural fractures. The induced fracture penetrates the entire reservoir, leading to the interconnection of injection and production wells and ultimately resulting in water breakthrough and the abandonment of production wells. During well work, the induced fracture exhibits dynamic behavior characterized by extension and closure, known as the dynamic-induced fracture phenomena. During the shut-in process, fracture closure phenomena are often accompanied by water hammer phenomena, which can be detected bottom hole pressure data. However, numerical simulation methods are difficult to describe their dynamic processes. Therefore, we urgently need a mathematical model to fill this gap. In this work, we developed a waterflooding-induced dynamic fracture (WIDF) model. Dynamic water hammer phenomena, multi-dynamic closure phenomena, and fracture storage phenomena are introduced into the WIDF model to describe the induced fracture dynamic behavior. Field cases demonstrate that the WIDF model can improve the accuracy of interpreted parameters and correct incorrect model selection. Green function and Newman product method are used to characterize single-phase water flows within tight reservoirs. Then, the induced fracture is discrete into N segments through the boundary element method. Discrete-induced fractures are divided into n parts. Based on the induced fracture bending property, conductivity variation is independent in each part. The feature line method is used to solve the pressure response of the dynamic water hammer. The Duhamel principle is applied to couple the storage effects and reservoir pressure response. The Laplace transform method transforms the model into Laplace space so that it can be solved easily, and the Stehfest numerical inversion method transforms the model into real space to obtain the final solution. Our results show that the dynamic water hammer flow (DWH) regime with an oscillation curve and the multi-dynamic closure flow (MDCF) regime with peaks exist on the type curve. Resistance coefficient (f) and inertia coefficient (I) control the DWH regime. Fracture storage coefficient (Cf), dynamic fracture closure rates (Delpatm), and induced fracture closure half-lengths (xdfm) control the MDCF regime. It is worth noting that the peak position can be adjusted by the Delpatm and xdfm parameters, achieving a more accurate match to the field cases. The Cf is identified, which corrected for the amplified wellbore storage coefficient. Obtained permeability is also in a reasonable range of permeability for tight reservoirs. In summary, a series of mathematical methods are used to develop and solve an injection well model to identify the dynamic behavior of the induced fracture. Numerical simulation methods are used to verify the accuracy of the WIDF model. Two field cases from X Oilfield demonstrate the practicability of the WIDF model. Dynamic identification of the induced fracture would help engineers develop appropriate injection schemes to prevent water breakthroughs.

FUS Unveiled in Mitochondrial DNA Repair and Targeted Ligase-1 Expression Rescues Repair-Defects in FUS-Linked Neurodegeneration.

This study establishes the physiological role of Fused in Sarcoma (FUS) in mitochondrial DNA (mtDNA) repair and highlights its implications to the pathogenesis of FUS-associated neurodegenerative diseases such as Amyotrophic lateral sclerosis (ALS). Endogenous FUS interacts with and recruits mtDNA Ligase IIIα (mtLig3) to DNA damage sites within mitochondria, a relationship essential for maintaining mtDNA repair and integrity in healthy cells. Using ALS patient-derived FUS mutant cell lines, a transgenic mouse model, and human autopsy samples, we discovered that compromised FUS functionality hinders mtLig3's repair role, resulting in increased mtDNA damage and mutations. These alterations cause various manifestations of mitochondrial dysfunction, particularly under stress conditions relevant to disease pathology. Importantly, rectifying FUS mutations in patient-derived induced pluripotent cells (iPSCs) preserves mtDNA integrity. Similarly, targeted introduction of human DNA Ligase 1 restores repair mechanisms and mitochondrial activity in FUS mutant cells, suggesting a potential therapeutic approach. Our findings unveil FUS's critical role in mitochondrial health and mtDNA repair, offering valuable insights into the mechanisms underlying mitochondrial dysfunction in FUS-associated neurodegeneration.