A method is developed to predict the lateral load-carrying capacity of composite shear walls with double steel plates and filled concrete with binding bars(SCBs). Nonlinear finite element models of SCBs were establish...A method is developed to predict the lateral load-carrying capacity of composite shear walls with double steel plates and filled concrete with binding bars(SCBs). Nonlinear finite element models of SCBs were established by using the finite element tool, Abaqus. Tie constraints were used to connect the binding bars and the steel plates. Surface-to-surface contact provided by the Abaqus was used to simulate the interaction between the steel plate and the core concrete. The established models could predict the lateral load-carrying capacity of SCBs with a reasonable degree of accuracy. A calculation method was developed by superposition principle to predict the lateral load-carrying capacity of SCBs for the engineering application. The concrete confined by steel plates and binding bars is under multi-axial compression; therefore, its shear strength was calculated by using the Guo-Wang concrete failure criterion. The shear strength of the steel plates of SCBs was calculated by using the von Mises yielding criterion without considering buckling. Results of the developed method are in good agreement with the testing and finite element results.展开更多
RNA binding proteins(RBPs) are a crucial class of proteins that interact with RNA and play a key role in various biological process.Deficiencies or abnormalities of RBPs are closely linked to the occurrence and progre...RNA binding proteins(RBPs) are a crucial class of proteins that interact with RNA and play a key role in various biological process.Deficiencies or abnormalities of RBPs are closely linked to the occurrence and progression of numerous diseases,making RBPs potential therapeutic targets.However,the limited tissue penetration of 254 nm UV irradiation makes it difficult to efficiently crosslink weak and dynamic RNA-protein interactions in mammal tissues.Additionally,RNA degradation in metal catalyzed click reaction further hinders the enrichment of RNA-protein complexes(RPCs).Due to these inherent limitations,globally profiling the RNA binding proteome in mammal organs has long been a challenge.Herein,we proposed a novel method,which utilized a dual crosslinking with formaldehyde and 254 nm UV irradiation,metabolic labeling and metal-free thiol-yne click reaction to enable large-scale enrichment and identification of RBPs in mouse liver,called FTYc_UV.In this method,formaldehyde is first used to crosslink the crude RNA-protein complexes(cRPCs) in situ to address the problem of poor tissue penetration of 254 nm UV irradiation.Furthermore,this method integrates metabolic labeling with a metal-free thiol-yne click reaction to achieve non-destructive RNA tagging.After specifically RNA-RBPs crosslinking by 254 nm UV irradiation in tissue lysates,formaldehyde decrosslinking is employed to remove non-specific proteins,leading to effective enrichment of RPCs from mouse liver and thereby overcoming the poor specificity of formaldehyde crosslinking.Application of FTYc_UV in mouse liver successfully identified over 1600 RBPs covering approximately 75 % of previously reported RBPs.Furthermore,420 candidate RBPs,including 151metabolic enzymes,were also obtained,demonstrating the sensitivity of FTYc_UV and the potential of this method for in-depth exploration of RNA-protein interactions in biological and clinical research.展开更多
Lithium-sulfur batteries(LSBs)represent a next-generation energy storage technology,but widespread applications are restricted by the shuttle of lithium polysulfides(LiPSs).The rational design of separators has been d...Lithium-sulfur batteries(LSBs)represent a next-generation energy storage technology,but widespread applications are restricted by the shuttle of lithium polysulfides(LiPSs).The rational design of separators has been demonstrated to be one of the most efficient and cost-effective strategies to curb the shuttle effect,and tremendous research progress has been achieved.The efficiency of a separator depends on its interaction with LiPSs,which is governed by the surface energy and binding strength.Despite several review works that have been reported to advance the separators,most of them primarily focus on active material innovation and construction.The most crucial issues of surface binding energy have not been systematically reviewed,limiting the precise design of efficient separators.In this review,fundamentals related to surface energy and binding interactions with LiPSs are comprehensively analyzed and discussed.With surface binding and energy main lines,the advancements in separator engineering strategies are elaborately summarized and discussed.Moreover,techniques for evaluating affinity to LiPSs are thoroughly analyzed to avoid any ambiguities in measurement.Based on the research context,valuable research directions are suggested to construct efficient separators.This work provides guidelines to regulate the surface binding and energy of separators for high-performance LSBs.展开更多
Type 1 diabetes(T1D)is defined by autoimmune-mediated destruction of the insulin-producing pancreatic β-cells.Impaired insulin secretion due to β-cell apoptosis and islet massloss is the main feature of T1D[1].Curre...Type 1 diabetes(T1D)is defined by autoimmune-mediated destruction of the insulin-producing pancreatic β-cells.Impaired insulin secretion due to β-cell apoptosis and islet massloss is the main feature of T1D[1].Current therapeutic strategies for T1D are mainly through subcutaneous administration of insulin or islet/pancreas transplantation.展开更多
Ground state binding energies of donor impurities in a strained wurtzite GaN/AlxGal_xN heterojunction with a po- tential barrier of finite thickness are investigated using a variational approach combined with a numeri...Ground state binding energies of donor impurities in a strained wurtzite GaN/AlxGal_xN heterojunction with a po- tential barrier of finite thickness are investigated using a variational approach combined with a numerical computation. The built-in electric field due to the spontaneous and piezoelectric polarization, the strain modification due to the lattice mismatch near the interfaces, and the effects of ternary mixed crystals are all taken into account. It is found that the binding energies by using numerical wave functions are obviously greater than those by using variational wave functions when impurities are located in the channel near the interface of a heterojunction. Nevertheless, the binding energies using the former functions are obviously less than using the later functions when impurities are located in the channel far from an interface. The difference between our numerical method and the previous variational method is huge, showing that the former should be adopted in further work for the relevant problems. The binding energies each as a function of hydrostatic pressure are also calculated. But the change is unobvious in comparison with that obtained by the variational method.展开更多
In an earlier paper, the author employed the thesis that baryons are Yang-Mills magnetic monopoles and that proton and neutron binding energies are determined based on their up and down current quark masses to predict...In an earlier paper, the author employed the thesis that baryons are Yang-Mills magnetic monopoles and that proton and neutron binding energies are determined based on their up and down current quark masses to predict a relationship among the electron and up and down quark masses within experimental errors and to obtain a very accurate relationship for nuclear binding energies generally and for the binding of 56Fe in particular. The free proton and neutron were understood to each contain intrinsic binding energies which confine their quarks, wherein some or most (never all) of this energy is released for binding when they are fused into composite nuclides. The purpose of this paper is to further advance this thesis by seeing whether it can explain the specific empirical binding energies of the light 1s nuclides, namely, 2H, 3H, 3He and 4He, with high precision. As the method to achieve this, we show how these 1s binding energies are in fact the components of inner and outer tensor products of Yang-Mills matrices which are implicit in the expressions for these intrinsic binding energies. The result is that the binding energies for the 4He, 3He and 3H nucleons are respectively, independently, explained to less than four parts in one million, four parts in 100,000, and seven parts in one million, all in AMU. Further, we are able to exactly relate the neutron minus proton mass difference to a function of the up and down current quark masses, which in turn enables us to explain the 2H binding energy most precisely of all, to just over 8 parts in ten million. These energies have never before been theoretically explained with such accuracy, which leads to the conclusion that the underlying thesis provides the strongest theoretical explanation to date of what baryons are, and of how protons and neutrons confine their quarks and bind together into composite nuclides. As is also reviewed in Section 9, these results may lay the foundation for more easily catalyzing nuclear fusion energy release.展开更多
Background Post-weaning diarrhea(PWD)in piglets,often caused by F4^(+)enterotoxigenic Escherichia coli(ETEC),poses significant challenges in pig production.Traditional solutions like antibiotics and zinc oxide face in...Background Post-weaning diarrhea(PWD)in piglets,often caused by F4^(+)enterotoxigenic Escherichia coli(ETEC),poses significant challenges in pig production.Traditional solutions like antibiotics and zinc oxide face increasing restrictions due to growing concerns over antibiotic resistance and environmental sustainability.This study investigates the application of bivalent heavy chain variable domain(V_(H)H)constructs(BL1.2 and BL2.2)targeting ETEC virulence factors,administered in feed to mitigate ETEC-induced PWD in weaned piglets.Results The supplementation of BL1.2 and BL2.2 in both mash and pelleted feed significantly reduced the diarrhea incidence and fecal shedding of F4^(+)ETEC in challenged piglets.Pelleted feed containing V_(H)H constructs helped to preserve gut barrier integrity by maintaining levels of the tight junction protein occludin in the small intestine.Additionally,the constructs maintained blood granulocyte counts at a similar level to the non-challenged control group,including neutrophils,and ameliorated the acute phase protein response after challenge.Notably,even at low feed intake immediately after weaning,V_(H)H constructs helped maintain piglet health by mitigating ETEC-induced inflammation and the resulting diarrhea.Conclusions Our findings demonstrated that using V_(H)H constructs as feed additives could serve as an effective strategy to help manage ETEC-associated PWD,by reducing F4^(+)ETEC gut colonization and supporting gut barrier function of weaned piglets.The high stability of these V_(H)H constructs supports their incorporation into industrial feed manufacturing processes,offering a more sustainable preventive strategy compared to traditional antimicrobial interventions,which could contribute to sustainable farming practices.展开更多
Magnolol,a compound extracted from Magnolia officinalis,demonstrates potential efficacy in addressing metabolic dysfunction and cardiovascular diseases.Its biological activities encompass anti-inflammatory,antioxidant...Magnolol,a compound extracted from Magnolia officinalis,demonstrates potential efficacy in addressing metabolic dysfunction and cardiovascular diseases.Its biological activities encompass anti-inflammatory,antioxidant,anticoagulant,and anti-diabetic effects.Growth/differentiation factor-15(GDF-15),a member of the transforming growth factorβsuperfamily,is considered a potential therapeutic target for metabolic disorders.This study investigated the impact of magnolol on GDF-15 production and its underlying mechanism.The research examined the pharmacological effect of magnolol on GDF-15 expression in vitro and in vivo,and determined the involvement of endoplasmic reticulum(ER)stress signaling in this process.Luciferase reporter assays,chromatin immunoprecipitation,and in vitro DNA binding assays were employed to examine the regulation of GDF-15 by activating transcription factor 4(ATF4),CCAAT enhancer binding proteinγ(CEBPG),and CCCTC-binding factor(CTCF).The study also investigated the effect of magnolol and ATF4 on the activity of a putative enhancer located in the intron of the GDF-15 gene,as well as the influence of single nucleotide polymorphisms(SNPs)on magnolol and ATF4-induced transcription activity.Results demonstrated that magnolol triggers GDF-15 production in endothelial cells(ECs),hepatoma cell line G2(HepG2)and hepatoma cell line 3B(Hep3B)cell lines,and primary mouse hepatocytes.The cooperative binding of ATF4 and CEBPG upstream of the GDF-15 gene or the E1944285 enhancer located in the intron led to full-power transcription of the GDF-15 gene.SNP alleles were found to impact the magnolol and ATF4-induced transcription activity of GDF-15.In high-fat diet ApoE^(-/-)mice,administration of magnolol induced GDF-15 production and partially suppressed appetite through GDF-15.These findings suggest that magnolol regulates GDF-15 expression through priming of promoter and enhancer activity,indicating its potential as a drug for the treatment of metabolic disorders.展开更多
Chloride ions(Cl^(-))have been shown to impact the long-lasting nature of reinforced concrete.However,Cl^(-)that are already bound inside the concrete will not lead to the deterioration of the concrete’s characterist...Chloride ions(Cl^(-))have been shown to impact the long-lasting nature of reinforced concrete.However,Cl^(-)that are already bound inside the concrete will not lead to the deterioration of the concrete’s characteristics.The composition of the cement-based material,including the type of cement and auxiliary materials,greatly influences the ability of the material to bind Cl^(-),and varied components result in varying binding beha-vior of the Cl^(-).Simultaneously,the Cl^(-)binding process in concrete is influenced by both the internal and exterior surroundings,as well as the curing practices.These factors impact the hydration process of the cement and the internal pore structure of the concrete.Currently,mathematical theories and molecular dynamics simulations have increasingly been employed as the prevalent methods for examining the binding behaviors of Cl^(-)in concrete.These techniques are extensively utilized for predicting the lifespan and conducting microscopic studies of reinforced concrete in Cl^(-)settings.This work proposes recommendations for future research based on a summary of experimental and simulation investigations on Cl^(-)binding.Which will offer theoretical guidance for studying the binding of Cl^(-)in cement-based materials.展开更多
Objective Junctophilin-2(JPH2)is an essential structural protein that maintains junctional membrane complexes(JMCs)in cardiomyocytes by tethering the plasma membrane to the sarcoplasmic reticulum,thereby facilitating ...Objective Junctophilin-2(JPH2)is an essential structural protein that maintains junctional membrane complexes(JMCs)in cardiomyocytes by tethering the plasma membrane to the sarcoplasmic reticulum,thereby facilitating excitationcontraction(E-C)coupling.Mutations in JPH2 have been associated with hypertrophic cardiomyopathy(HCM),but the molecular mechanisms governing its membrane-binding properties and the functional relevance of its membrane occupation and recognition nexus(MORN)repeat motifs remain incompletely understood.This study aimed to elucidate the structural basis of JPH2 membrane association and its implications for HCM pathogenesis.Methods A recombinant N-terminal fragment of mouse JPH2(residues 1-440),encompassing the MORN repeats and an adjacent helical region,was purified under near-physiological buffer conditions.X-ray crystallography was employed to determine the structure of the JPH2 MORN-Helix domain.Sequence conservation analysis across species and junctophilin isoforms was performed to assess the evolutionary conservation of key structural features.Functional membrane-binding assays were conducted using liposome co-sedimentation and cell-based localization studies in COS7 and HeLa cells.In addition,site-directed mutagenesis targeting positively charged residues and known HCM-associated mutations,including R347C,was used to evaluate their effects on membrane interaction and subcellular localization.Results The crystal structure of the mouse JPH2 MORN-Helix domain was resolved at 2.6Å,revealing a compact,elongated architecture consisting of multiple tandem MORN motifs arranged in a curved configuration,forming a continuous hydrophobic core stabilized by alternating aromatic residues.A C-terminalα-helix further reinforced structural integrity.Conservation analysis identified the inner groove of the MORN array as a highly conserved surface,suggesting its role as a protein-binding interface.A flexible linker segment enriched in positively charged residues,located adjacent to the MORN motifs,was found to mediate direct electrostatic interactions with negatively charged phospholipid membranes.Functional assays demonstrated that mutation of these basic residues impaired membrane association,while the HCM-linked R347C mutation completely abolished membrane localization in cellular assays,despite preserving the overall MORN-Helix fold in structural modeling.Conclusion This study provides structural insight into the membrane-binding mechanism of the cardiomyocyte-specific protein JPH2,highlighting the dual roles of its MORN-Helix domain in membrane anchoring and protein interactions.The findings clarify the structural basis for membrane targeting via a positively charged linker and demonstrate that disruption of this interaction—such as that caused by the R347C mutation—likely contributes to HCM pathogenesis.These results not only enhance current understanding of JPH2 function in cardiac E-C coupling but also offer a structural framework for future investigations into the assembly and regulation of JMCs in both physiological and disease contexts.展开更多
Elucidation of ligand-protein interactions provides new insights into the physiological functions and mechanisms of ligand molecules,enabling new ideas for the treatment of diseases,and drug discovery and development....Elucidation of ligand-protein interactions provides new insights into the physiological functions and mechanisms of ligand molecules,enabling new ideas for the treatment of diseases,and drug discovery and development.Most ligand-protein binding occurs only in specific regions of proteins.The identification of protein targets and binding regions is crucial for drug discovery and development,as well as for the in-depth study of drug-protein conformational relationships[1].展开更多
Iron removal from zinc leachate in hydrometallurgy produces large volumes of low-grade,impurity-laden iron waste,posing significant environmental challenges.Magnetite precipitation offers a novel method for iron remov...Iron removal from zinc leachate in hydrometallurgy produces large volumes of low-grade,impurity-laden iron waste,posing significant environmental challenges.Magnetite precipitation offers a novel method for iron removal and resource recycling in zinc hydrometallurgy.However,the chemical similarity between ferrous and zinc ions,along with high zinc concentrations,causes zinc co-precipitation,challenging its application.To address this issue,this study utilized electron microscopy to observe key intermediate products in magnetite crystallization and employed EXAFS(extended X-ray absorption fine structure)to analyze their evolutionary mechanisms and zinc-binding configurations.The results indicate that the intermediate products during magnetite formation are sequentially green rust,feroxyhyte(δ-FeOOH),and weakly crystalline nanoparticles,and further analysis revealed that their transformation follows the dissolution-recrystallization mechanism.Furthermore,it was found that intermediate products such as green rust exhibit strong binding with zinc(via adsorption and lattice substitution),which was confirmed as a significant reason for the difficulty in separating zinc from magnetite.This study elucidates the transformation process of intermediate products during magnetite formation and,for the first time,reveals the binding configurations of zinc with these key intermediate products.This has significant implications for the development and optimization of new technologies for the efficient separation of iron and zinc during the magnetite precipitation process.展开更多
BACKGROUND Pancreatic surgery has markedly evolved during the past several years with the development of minimally invasive techniques such as laparoscopy.pancreaticojejunostomy(PJ),also known as pancreatoenterostomy,...BACKGROUND Pancreatic surgery has markedly evolved during the past several years with the development of minimally invasive techniques such as laparoscopy.pancreaticojejunostomy(PJ),also known as pancreatoenterostomy,is a critical step in surgical reconstruction after pancreatic resection.However,the laparoscopic performance of PJ presents additional technical challenges,especially in achieving a secure anastomosis while preserving the integrity of pancreatic tissue.AIM To evaluate the effectiveness and safety of binding and interlocking PJ(BIPJ)as a novel technique in laparoscopic pancreatic surgery.METHODS Data of patients who underwent laparoscopic pancreatic surgery from 2018 to 2023 were obtained from the hepatobiliary and pancreatic surgery database of the Second Affiliated Hospital of Zhejiang University School of Medicine and retrospectively analyzed.According to the different PJ methods used during surgery,the patients were divided into two groups:The BIPJ group and the ductto-mucosa PJ(DMPJ)group.RESULTS BIPJ was performed in 33 patients,and DMPJ was performed in 34 patients.The operative time was significantly shorter in the BIPJ group(median,340 minutes;interquartile range,310-350)than in the DMPJ group(median,388 minutes;interquartile range,341-464)(P=0.004).No significant differences were found between the DMPJ and BIPJ groups in terms of the rates of pancreatic fistula,intra-abdominal hemorrhage,intra-abdominal abscess,postoperative biliary fistula,reoperation,or postoperative hospital stay.CONCLUSION The suitability of laparoscopic PJ for all pancreatic textures,ability to perform full laparoscopy,shorter operation time,and comparable safety with traditional PJ make BIPJ a promising option for both surgeons and patients.展开更多
Dear Editor,The pandemic of coronavirus disease 2019(COVID-19)caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),continues despite extensive efforts to control viral transmission.Meanwhile,the emerg...Dear Editor,The pandemic of coronavirus disease 2019(COVID-19)caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),continues despite extensive efforts to control viral transmission.Meanwhile,the emergence of SARS-CoV-2 variants with antigenically divergence in viral protein dampens the efficacy of authorized vaccines,leading to the breakthrough infections in vaccinated population(Cao et al.,2021,2022;Tuekprakhon et al.,2022;Xiang et al.,2022).Moreover,diverse sarbecoviruses in bats and pangolins have been discovered and isolated(Ge et al.,2013;Xiao et al.,2020).Some of these viruses have exhibited efficient binding to human angiotensin-converting enzyme 2(hACE2)(Xiao et al.,2020;Liu et al.,2021;Temmam et al.,2022),highlighting the risk of spillover from wild animals to human.Thus,the development of pan-sarbecovirus vaccines is of high priority.展开更多
Genetic disruption of the RAS binding domain(RBD)of Phosphoinositide 3-kinase alpha(PI3Kα)impairs the growth of tumors driven by the small guanosine triphosphatase RAS in mice and does not impact PI3Kα's role in...Genetic disruption of the RAS binding domain(RBD)of Phosphoinositide 3-kinase alpha(PI3Kα)impairs the growth of tumors driven by the small guanosine triphosphatase RAS in mice and does not impact PI3Kα's role in insulin mediated control of glucose homeostasis.Selectively blocking the RAS-PI3Kαinteraction may represent a strategy for treating RAS-dependent cancers as it would avoid the toxicity associated with inhibitors of PI3Kαlipid kinase activity.We developed compounds that bind covalently to cysteine 242 in the RBD of PI3K p110αand block RAS activation of PI3Kαactivity.In mice,inhibitors slow the growth of RAS mutant tumors and Human Epidermal Growth Factor Receptor 2(HER2)overexpressing tumors,particularly when combined with other inhibitors of the RAS/Mitogen-activated protein kinase pathway,without causing hyperglycemia.Oncogenic mutations in the small guanosine triphosphatase RAS occur in 20%of human cancers,with RAS proteins activating both the mitogen-activated protein kinase(MAPK)and Phosphoinositide 3-kinase(PI3K)pathways(1-3).As each of these pathways has oncogenic potential,simultaneous activation,as occurs in mutant RAS driven cancers,generates aggressive disease.In RAS-driven cell and animal models,inhibition of both the MAPK and PI3K pathways is more efficacious than targeting the individual pathways(4);however,dose-limiting toxicities in humans prevent clinical success of this strategy.展开更多
BACKGROUND Aberrant microRNAs expression and associated pathways have been proved participate in regulation vast various physiologic and pathologic processed of different human cancers including liver cancer.While,the...BACKGROUND Aberrant microRNAs expression and associated pathways have been proved participate in regulation vast various physiologic and pathologic processed of different human cancers including liver cancer.While,the function of miR-451a in liver cancer still indistinct.AIM To study the effect of miR-451a in liver cancer development.METHODS GeneChip microarray analysis performed to detect miR-451a expression in liver cancer tissues and normal liver tissues.Reverse transcription-polymerase chain reaction was used to validate the expression of miR-451a in liver cancer cell and other tumor cell lines.Construction of liver cancer cell lines that stably overexpressed miR-451a by transfecting Lentivirus produced by Genechem company.Methylthiazolyldiphenyl-tetrazolium(MTT)bromide assay and colony formation assay to determine the effect of miR-451a in liver cancer cell proliferation.Flow cytometry used to investigate whether miR-451a involved in liver cancer cell apoptosis.Cell migration ability was measured via wound scratch assay.Target gene was explored by bioinformatic analysis,and downstream molecule of miR-451a in liver cancer identified by rescue experiments.RESULTS MiR-451a expression significantly downregulation in liver cancer tissues compared with that in normal liver tissue.MiR-451a also obviously low-expressed in liver cancer cell,colorectal carcinoma cell and esophageal carcinoma cell lines.Human hepatoblastoma G2(HepG2)and BEL-7404 cell lines that stably overexpressed miR-451a by transfecting lentivirus constructed successfully.MTT bromide assay and colony formation assay showed that the overexpressed miR-451a inhibit HepG2 cell proliferation viability,but not BEL-7404 cell.Flow cytometry determined that miR-451a regulating proliferation not through inducing apoptosis.Wound scratch assay revealed that miR-451a overexpression suppressed HepG2 cell migration.Furthermore,mex-3 RNA binding family member C was predicted as the target gene by bioinformatic analysis,and rescue experiments confirmed the hypothesis.CONCLUSION Therefore,miR-451a may be candidate miRNA for understanding molecular mechanisms of liver cancer development and novel target in liver cancer cell.展开更多
Accurate identification of RNA-ligand binding sites is essential for elucidating RNA function and advancing structurebased drug discovery.Here,we present RLsite,a novel deep learning framework that integrates energy-,...Accurate identification of RNA-ligand binding sites is essential for elucidating RNA function and advancing structurebased drug discovery.Here,we present RLsite,a novel deep learning framework that integrates energy-,structure-and sequence-based features to predict nucleotide-level binding sites with high accuracy.RLsite leverages energy-based threedimensional representations,obtained from atomic probe interactions using a pre-trained ITScore-NL potential,and models their contextual features through a 3D convolutional neural network(3D-CNN)augmented with self-attention.In parallel,structure-based features,including network properties,Laplacian norm,and solvent-accessible surface area,together with sequence-based evolutionary constraint scores,are mapped along the RNA sequence and used as sequential descriptors.These descriptors are modeled using a bidirectional long short-term memory(BiLSTM)network enhanced with multihead self-attention.By effectively fusing these complementary modalities,RLsite achieves robust and precise binding site prediction.Extensive evaluations across four diverse RNA-ligand benchmark datasets demonstrate that RLsite consistently outperforms state-of-the-art methods in terms of precision,recall,Matthews correlation coefficient(MCC),area under the curve(AUC),and overall robustness.Notably,on a particularly challenging test set composed of RNA structures containing junctions,RLsite surpasses the second-best method by 7.3%in precision,3.4%in recall,7.5%in MCC,and 10.8%in AUC,highlighting its potential as a powerful tool for RNA-targeted molecular design.展开更多
BACKGROUND The exact mechanisms underlying diabetic nephropathy(DN)remain incompletely elucidated,prompting researchers to explore new perspectives and identify novel intervention targets in this field.AIM To explore ...BACKGROUND The exact mechanisms underlying diabetic nephropathy(DN)remain incompletely elucidated,prompting researchers to explore new perspectives and identify novel intervention targets in this field.AIM To explore the role and underlying mechanisms of farnesoid X receptor(FXR)in the development of DN by regulating endoplasmic reticulum stress(ERS)molecular chaperone binding immunoglobulin protein(BiP)expression.METHODS Bioinformatics analyses identified potential FXR-binding elements in the BiP promoter.Dual-luciferase and chromatin immunoprecipitation(ChIP)assays confirmed FXR-BiP binding sites.In vitro studies used SV40 MES 13 cells under varying glucose conditions and treatments with FXR modulators[obeticholic acid(INT-747)and guggulsterones]or BiP small interfering RNA.The expression of BiP and ERS-related proteins[protein kinase R-like endoplasmic reticulum kinase(PERK),inositol-requiring enzyme 1(IRE1),activating transcription factor 6(ATF6)]was assessed alongside cell proliferation and extracellular matrix(ECM)synthesis.In vivo studies in DN mice(db/db)examined the effects of FXR activation on renal function and morphology.RESULTS FXR bound to the target sequence in the BiP promoter region,enhancing transcriptional activity,as confirmed by ChIP experiments.FXR expression decreased in SV40 MES 13 cells stimulated with high glucose and in renal tissues of DN mice compared with control.Treatment of SV40 MES 13 cells with the FXR agonist INT-747 significantly increased intracellular BiP expression,whereas silencing the FXR gene led to the downregulation of BiP levels.In vivo administration of INT-747 significantly elevated BiP levels in renal tissues,improved renal function and fibrosis in DN mice,while inhibiting the expression of ERS-related signaling proteins PERK,IRE1,and ATF6.CONCLUSION FXR promotes BiP expression by binding to its promoter,suppressing ERS pathways,and reducing mesangial cell proliferation and ECM synthesis.These findings highlight FXR as a potential therapeutic target for diabetic glomerulosclerosis.展开更多
Host-derived small RNAs are emerging as critical regulators in the dynamic interactions between host tissues and the microbiome,with implications for microbial pathogenesis and host defense.Among these,transfer RNA-de...Host-derived small RNAs are emerging as critical regulators in the dynamic interactions between host tissues and the microbiome,with implications for microbial pathogenesis and host defense.Among these,transfer RNA-derived small RNAs(tsRNAs)have garnered attention for their roles in modulating microbial behavior.However,the bacterial factors mediating tsRNA interaction and functionality remain poorly understood.In this study,using RNA affinity pull-down assay in combination with mass spectrometry,we identified a putative membrane-bound protein,annotated as P-type ATPase transporter(PtaT)in Fusobacterium nucleatum(Fn),which binds Fn-targeting tsRNAs in a sequence-specific manner.Through targeted mutagenesis and phenotypic characterization,we showed that in both the Fn type strain and a clinical tumor isolate,deletion of ptaT led to reduced tsRNA intake and enhanced resistance to tsRNA-induced growth inhibition.Global RNA sequencing and label-free Raman spectroscopy revealed the phenotypic differences between Fn wild type and PtaT-deficient mutant,highlighting the functional significance of PtaT in purine and pyrimidine metabolism.Furthermore,AlphaFold 3 prediction provides evidence supporting the specific binding between PtaT and Fn-targeting tsRNA.By uncovering the first RNA-binding protein in Fn implicated in growth modulation through interactions with host-derived small RNAs(sRNAs),our study offers new insights into sRNA-mediated host-pathogen interplay within the context of microbiome-host interactions.展开更多
基金Project(51178333)supported by the National Natural Science Foundation of ChinaProject(SLDRCE09-D-03)supported by the Ministry of Science and Technology of China
文摘A method is developed to predict the lateral load-carrying capacity of composite shear walls with double steel plates and filled concrete with binding bars(SCBs). Nonlinear finite element models of SCBs were established by using the finite element tool, Abaqus. Tie constraints were used to connect the binding bars and the steel plates. Surface-to-surface contact provided by the Abaqus was used to simulate the interaction between the steel plate and the core concrete. The established models could predict the lateral load-carrying capacity of SCBs with a reasonable degree of accuracy. A calculation method was developed by superposition principle to predict the lateral load-carrying capacity of SCBs for the engineering application. The concrete confined by steel plates and binding bars is under multi-axial compression; therefore, its shear strength was calculated by using the Guo-Wang concrete failure criterion. The shear strength of the steel plates of SCBs was calculated by using the von Mises yielding criterion without considering buckling. Results of the developed method are in good agreement with the testing and finite element results.
基金financial support from the National Key R&D Program of China (No.2021YFA1302604)Scientific and technological innovation project of China Academy of Chinese Medical Sciences (No.CI2021B017)China Postdoctoral Science Foundation (No.2023T160727)。
文摘RNA binding proteins(RBPs) are a crucial class of proteins that interact with RNA and play a key role in various biological process.Deficiencies or abnormalities of RBPs are closely linked to the occurrence and progression of numerous diseases,making RBPs potential therapeutic targets.However,the limited tissue penetration of 254 nm UV irradiation makes it difficult to efficiently crosslink weak and dynamic RNA-protein interactions in mammal tissues.Additionally,RNA degradation in metal catalyzed click reaction further hinders the enrichment of RNA-protein complexes(RPCs).Due to these inherent limitations,globally profiling the RNA binding proteome in mammal organs has long been a challenge.Herein,we proposed a novel method,which utilized a dual crosslinking with formaldehyde and 254 nm UV irradiation,metabolic labeling and metal-free thiol-yne click reaction to enable large-scale enrichment and identification of RBPs in mouse liver,called FTYc_UV.In this method,formaldehyde is first used to crosslink the crude RNA-protein complexes(cRPCs) in situ to address the problem of poor tissue penetration of 254 nm UV irradiation.Furthermore,this method integrates metabolic labeling with a metal-free thiol-yne click reaction to achieve non-destructive RNA tagging.After specifically RNA-RBPs crosslinking by 254 nm UV irradiation in tissue lysates,formaldehyde decrosslinking is employed to remove non-specific proteins,leading to effective enrichment of RPCs from mouse liver and thereby overcoming the poor specificity of formaldehyde crosslinking.Application of FTYc_UV in mouse liver successfully identified over 1600 RBPs covering approximately 75 % of previously reported RBPs.Furthermore,420 candidate RBPs,including 151metabolic enzymes,were also obtained,demonstrating the sensitivity of FTYc_UV and the potential of this method for in-depth exploration of RNA-protein interactions in biological and clinical research.
基金supported by the National Natural Science Foundation of China (52172228)the Natural Science Foundation of Fujian Province (2024J01475 and 2023J05127)
文摘Lithium-sulfur batteries(LSBs)represent a next-generation energy storage technology,but widespread applications are restricted by the shuttle of lithium polysulfides(LiPSs).The rational design of separators has been demonstrated to be one of the most efficient and cost-effective strategies to curb the shuttle effect,and tremendous research progress has been achieved.The efficiency of a separator depends on its interaction with LiPSs,which is governed by the surface energy and binding strength.Despite several review works that have been reported to advance the separators,most of them primarily focus on active material innovation and construction.The most crucial issues of surface binding energy have not been systematically reviewed,limiting the precise design of efficient separators.In this review,fundamentals related to surface energy and binding interactions with LiPSs are comprehensively analyzed and discussed.With surface binding and energy main lines,the advancements in separator engineering strategies are elaborately summarized and discussed.Moreover,techniques for evaluating affinity to LiPSs are thoroughly analyzed to avoid any ambiguities in measurement.Based on the research context,valuable research directions are suggested to construct efficient separators.This work provides guidelines to regulate the surface binding and energy of separators for high-performance LSBs.
基金supported by the National Natural Science Foundation of China(32325024,32400981,32222024,32271224,32471228,and 82270891)the National Key Research and Development Program of China(2023YFA1800400)+3 种基金the Shuguang Program of Shanghai Education Development Foundation and Shanghai Municipal Education Commission(23SG22)the Noncommunicable Chronic Diseases-National Science and Technology Major Project(2023ZD0507300)the ECNU public platform for Innovation(011)the instruments sharing platform of School of Life Sciences.
文摘Type 1 diabetes(T1D)is defined by autoimmune-mediated destruction of the insulin-producing pancreatic β-cells.Impaired insulin secretion due to β-cell apoptosis and islet massloss is the main feature of T1D[1].Current therapeutic strategies for T1D are mainly through subcutaneous administration of insulin or islet/pancreas transplantation.
基金supported by the National Natural Science Foundation of China(Grant No.60966001)the Key Project of the Natural Science Foundation of Inner Mongolia Autonomous Region,China(Grant Nos.20080404Zd02 and 2013ZD02)
文摘Ground state binding energies of donor impurities in a strained wurtzite GaN/AlxGal_xN heterojunction with a po- tential barrier of finite thickness are investigated using a variational approach combined with a numerical computation. The built-in electric field due to the spontaneous and piezoelectric polarization, the strain modification due to the lattice mismatch near the interfaces, and the effects of ternary mixed crystals are all taken into account. It is found that the binding energies by using numerical wave functions are obviously greater than those by using variational wave functions when impurities are located in the channel near the interface of a heterojunction. Nevertheless, the binding energies using the former functions are obviously less than using the later functions when impurities are located in the channel far from an interface. The difference between our numerical method and the previous variational method is huge, showing that the former should be adopted in further work for the relevant problems. The binding energies each as a function of hydrostatic pressure are also calculated. But the change is unobvious in comparison with that obtained by the variational method.
文摘In an earlier paper, the author employed the thesis that baryons are Yang-Mills magnetic monopoles and that proton and neutron binding energies are determined based on their up and down current quark masses to predict a relationship among the electron and up and down quark masses within experimental errors and to obtain a very accurate relationship for nuclear binding energies generally and for the binding of 56Fe in particular. The free proton and neutron were understood to each contain intrinsic binding energies which confine their quarks, wherein some or most (never all) of this energy is released for binding when they are fused into composite nuclides. The purpose of this paper is to further advance this thesis by seeing whether it can explain the specific empirical binding energies of the light 1s nuclides, namely, 2H, 3H, 3He and 4He, with high precision. As the method to achieve this, we show how these 1s binding energies are in fact the components of inner and outer tensor products of Yang-Mills matrices which are implicit in the expressions for these intrinsic binding energies. The result is that the binding energies for the 4He, 3He and 3H nucleons are respectively, independently, explained to less than four parts in one million, four parts in 100,000, and seven parts in one million, all in AMU. Further, we are able to exactly relate the neutron minus proton mass difference to a function of the up and down current quark masses, which in turn enables us to explain the 2H binding energy most precisely of all, to just over 8 parts in ten million. These energies have never before been theoretically explained with such accuracy, which leads to the conclusion that the underlying thesis provides the strongest theoretical explanation to date of what baryons are, and of how protons and neutrons confine their quarks and bind together into composite nuclides. As is also reviewed in Section 9, these results may lay the foundation for more easily catalyzing nuclear fusion energy release.
基金financially supported by the Green Development and Demonstration Programme(GUDP)(case number 34009-19-1585)。
文摘Background Post-weaning diarrhea(PWD)in piglets,often caused by F4^(+)enterotoxigenic Escherichia coli(ETEC),poses significant challenges in pig production.Traditional solutions like antibiotics and zinc oxide face increasing restrictions due to growing concerns over antibiotic resistance and environmental sustainability.This study investigates the application of bivalent heavy chain variable domain(V_(H)H)constructs(BL1.2 and BL2.2)targeting ETEC virulence factors,administered in feed to mitigate ETEC-induced PWD in weaned piglets.Results The supplementation of BL1.2 and BL2.2 in both mash and pelleted feed significantly reduced the diarrhea incidence and fecal shedding of F4^(+)ETEC in challenged piglets.Pelleted feed containing V_(H)H constructs helped to preserve gut barrier integrity by maintaining levels of the tight junction protein occludin in the small intestine.Additionally,the constructs maintained blood granulocyte counts at a similar level to the non-challenged control group,including neutrophils,and ameliorated the acute phase protein response after challenge.Notably,even at low feed intake immediately after weaning,V_(H)H constructs helped maintain piglet health by mitigating ETEC-induced inflammation and the resulting diarrhea.Conclusions Our findings demonstrated that using V_(H)H constructs as feed additives could serve as an effective strategy to help manage ETEC-associated PWD,by reducing F4^(+)ETEC gut colonization and supporting gut barrier function of weaned piglets.The high stability of these V_(H)H constructs supports their incorporation into industrial feed manufacturing processes,offering a more sustainable preventive strategy compared to traditional antimicrobial interventions,which could contribute to sustainable farming practices.
基金supported by the National Natural Science Foundation of China(Nos.82171552 and 82170479)the Natural Science Foundation of Shanghai Ctiy(No.21ZR1457500)the Science and Technology Bureau of Shanghai Putuo District(No.ptkwws202102).
文摘Magnolol,a compound extracted from Magnolia officinalis,demonstrates potential efficacy in addressing metabolic dysfunction and cardiovascular diseases.Its biological activities encompass anti-inflammatory,antioxidant,anticoagulant,and anti-diabetic effects.Growth/differentiation factor-15(GDF-15),a member of the transforming growth factorβsuperfamily,is considered a potential therapeutic target for metabolic disorders.This study investigated the impact of magnolol on GDF-15 production and its underlying mechanism.The research examined the pharmacological effect of magnolol on GDF-15 expression in vitro and in vivo,and determined the involvement of endoplasmic reticulum(ER)stress signaling in this process.Luciferase reporter assays,chromatin immunoprecipitation,and in vitro DNA binding assays were employed to examine the regulation of GDF-15 by activating transcription factor 4(ATF4),CCAAT enhancer binding proteinγ(CEBPG),and CCCTC-binding factor(CTCF).The study also investigated the effect of magnolol and ATF4 on the activity of a putative enhancer located in the intron of the GDF-15 gene,as well as the influence of single nucleotide polymorphisms(SNPs)on magnolol and ATF4-induced transcription activity.Results demonstrated that magnolol triggers GDF-15 production in endothelial cells(ECs),hepatoma cell line G2(HepG2)and hepatoma cell line 3B(Hep3B)cell lines,and primary mouse hepatocytes.The cooperative binding of ATF4 and CEBPG upstream of the GDF-15 gene or the E1944285 enhancer located in the intron led to full-power transcription of the GDF-15 gene.SNP alleles were found to impact the magnolol and ATF4-induced transcription activity of GDF-15.In high-fat diet ApoE^(-/-)mice,administration of magnolol induced GDF-15 production and partially suppressed appetite through GDF-15.These findings suggest that magnolol regulates GDF-15 expression through priming of promoter and enhancer activity,indicating its potential as a drug for the treatment of metabolic disorders.
文摘Chloride ions(Cl^(-))have been shown to impact the long-lasting nature of reinforced concrete.However,Cl^(-)that are already bound inside the concrete will not lead to the deterioration of the concrete’s characteristics.The composition of the cement-based material,including the type of cement and auxiliary materials,greatly influences the ability of the material to bind Cl^(-),and varied components result in varying binding beha-vior of the Cl^(-).Simultaneously,the Cl^(-)binding process in concrete is influenced by both the internal and exterior surroundings,as well as the curing practices.These factors impact the hydration process of the cement and the internal pore structure of the concrete.Currently,mathematical theories and molecular dynamics simulations have increasingly been employed as the prevalent methods for examining the binding behaviors of Cl^(-)in concrete.These techniques are extensively utilized for predicting the lifespan and conducting microscopic studies of reinforced concrete in Cl^(-)settings.This work proposes recommendations for future research based on a summary of experimental and simulation investigations on Cl^(-)binding.Which will offer theoretical guidance for studying the binding of Cl^(-)in cement-based materials.
文摘Objective Junctophilin-2(JPH2)is an essential structural protein that maintains junctional membrane complexes(JMCs)in cardiomyocytes by tethering the plasma membrane to the sarcoplasmic reticulum,thereby facilitating excitationcontraction(E-C)coupling.Mutations in JPH2 have been associated with hypertrophic cardiomyopathy(HCM),but the molecular mechanisms governing its membrane-binding properties and the functional relevance of its membrane occupation and recognition nexus(MORN)repeat motifs remain incompletely understood.This study aimed to elucidate the structural basis of JPH2 membrane association and its implications for HCM pathogenesis.Methods A recombinant N-terminal fragment of mouse JPH2(residues 1-440),encompassing the MORN repeats and an adjacent helical region,was purified under near-physiological buffer conditions.X-ray crystallography was employed to determine the structure of the JPH2 MORN-Helix domain.Sequence conservation analysis across species and junctophilin isoforms was performed to assess the evolutionary conservation of key structural features.Functional membrane-binding assays were conducted using liposome co-sedimentation and cell-based localization studies in COS7 and HeLa cells.In addition,site-directed mutagenesis targeting positively charged residues and known HCM-associated mutations,including R347C,was used to evaluate their effects on membrane interaction and subcellular localization.Results The crystal structure of the mouse JPH2 MORN-Helix domain was resolved at 2.6Å,revealing a compact,elongated architecture consisting of multiple tandem MORN motifs arranged in a curved configuration,forming a continuous hydrophobic core stabilized by alternating aromatic residues.A C-terminalα-helix further reinforced structural integrity.Conservation analysis identified the inner groove of the MORN array as a highly conserved surface,suggesting its role as a protein-binding interface.A flexible linker segment enriched in positively charged residues,located adjacent to the MORN motifs,was found to mediate direct electrostatic interactions with negatively charged phospholipid membranes.Functional assays demonstrated that mutation of these basic residues impaired membrane association,while the HCM-linked R347C mutation completely abolished membrane localization in cellular assays,despite preserving the overall MORN-Helix fold in structural modeling.Conclusion This study provides structural insight into the membrane-binding mechanism of the cardiomyocyte-specific protein JPH2,highlighting the dual roles of its MORN-Helix domain in membrane anchoring and protein interactions.The findings clarify the structural basis for membrane targeting via a positively charged linker and demonstrate that disruption of this interaction—such as that caused by the R347C mutation—likely contributes to HCM pathogenesis.These results not only enhance current understanding of JPH2 function in cardiac E-C coupling but also offer a structural framework for future investigations into the assembly and regulation of JMCs in both physiological and disease contexts.
文摘Elucidation of ligand-protein interactions provides new insights into the physiological functions and mechanisms of ligand molecules,enabling new ideas for the treatment of diseases,and drug discovery and development.Most ligand-protein binding occurs only in specific regions of proteins.The identification of protein targets and binding regions is crucial for drug discovery and development,as well as for the in-depth study of drug-protein conformational relationships[1].
基金Project(2022YFC3900200)supported by the Foundation for the National Key R&D Program of ChinaProjects(52404375,22276218)supported by the National Natural Science Foundation of ChinaProject(52121004)supported by the Innovative Research Groups of the National Natural Science Foundation of China。
文摘Iron removal from zinc leachate in hydrometallurgy produces large volumes of low-grade,impurity-laden iron waste,posing significant environmental challenges.Magnetite precipitation offers a novel method for iron removal and resource recycling in zinc hydrometallurgy.However,the chemical similarity between ferrous and zinc ions,along with high zinc concentrations,causes zinc co-precipitation,challenging its application.To address this issue,this study utilized electron microscopy to observe key intermediate products in magnetite crystallization and employed EXAFS(extended X-ray absorption fine structure)to analyze their evolutionary mechanisms and zinc-binding configurations.The results indicate that the intermediate products during magnetite formation are sequentially green rust,feroxyhyte(δ-FeOOH),and weakly crystalline nanoparticles,and further analysis revealed that their transformation follows the dissolution-recrystallization mechanism.Furthermore,it was found that intermediate products such as green rust exhibit strong binding with zinc(via adsorption and lattice substitution),which was confirmed as a significant reason for the difficulty in separating zinc from magnetite.This study elucidates the transformation process of intermediate products during magnetite formation and,for the first time,reveals the binding configurations of zinc with these key intermediate products.This has significant implications for the development and optimization of new technologies for the efficient separation of iron and zinc during the magnetite precipitation process.
基金Supported by National Natural Science Foundation of China,No.82272634 and No.62233016.
文摘BACKGROUND Pancreatic surgery has markedly evolved during the past several years with the development of minimally invasive techniques such as laparoscopy.pancreaticojejunostomy(PJ),also known as pancreatoenterostomy,is a critical step in surgical reconstruction after pancreatic resection.However,the laparoscopic performance of PJ presents additional technical challenges,especially in achieving a secure anastomosis while preserving the integrity of pancreatic tissue.AIM To evaluate the effectiveness and safety of binding and interlocking PJ(BIPJ)as a novel technique in laparoscopic pancreatic surgery.METHODS Data of patients who underwent laparoscopic pancreatic surgery from 2018 to 2023 were obtained from the hepatobiliary and pancreatic surgery database of the Second Affiliated Hospital of Zhejiang University School of Medicine and retrospectively analyzed.According to the different PJ methods used during surgery,the patients were divided into two groups:The BIPJ group and the ductto-mucosa PJ(DMPJ)group.RESULTS BIPJ was performed in 33 patients,and DMPJ was performed in 34 patients.The operative time was significantly shorter in the BIPJ group(median,340 minutes;interquartile range,310-350)than in the DMPJ group(median,388 minutes;interquartile range,341-464)(P=0.004).No significant differences were found between the DMPJ and BIPJ groups in terms of the rates of pancreatic fistula,intra-abdominal hemorrhage,intra-abdominal abscess,postoperative biliary fistula,reoperation,or postoperative hospital stay.CONCLUSION The suitability of laparoscopic PJ for all pancreatic textures,ability to perform full laparoscopy,shorter operation time,and comparable safety with traditional PJ make BIPJ a promising option for both surgeons and patients.
基金supported by the National Key Research and Development Program of China(2021YFC2302400)the National Natural Science Foundation of China(82241069 and 82350801)+2 种基金supported by the National Science Fund for Distinguished Young Scholar(81925025)the Innovation Fund for Medical Sciences(2019-I2M-5-049)from the Chinese Academy of Medical Sciencessponsored by Beijing Nova Program(20240484525).
文摘Dear Editor,The pandemic of coronavirus disease 2019(COVID-19)caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),continues despite extensive efforts to control viral transmission.Meanwhile,the emergence of SARS-CoV-2 variants with antigenically divergence in viral protein dampens the efficacy of authorized vaccines,leading to the breakthrough infections in vaccinated population(Cao et al.,2021,2022;Tuekprakhon et al.,2022;Xiang et al.,2022).Moreover,diverse sarbecoviruses in bats and pangolins have been discovered and isolated(Ge et al.,2013;Xiao et al.,2020).Some of these viruses have exhibited efficient binding to human angiotensin-converting enzyme 2(hACE2)(Xiao et al.,2020;Liu et al.,2021;Temmam et al.,2022),highlighting the risk of spillover from wild animals to human.Thus,the development of pan-sarbecovirus vaccines is of high priority.
文摘Genetic disruption of the RAS binding domain(RBD)of Phosphoinositide 3-kinase alpha(PI3Kα)impairs the growth of tumors driven by the small guanosine triphosphatase RAS in mice and does not impact PI3Kα's role in insulin mediated control of glucose homeostasis.Selectively blocking the RAS-PI3Kαinteraction may represent a strategy for treating RAS-dependent cancers as it would avoid the toxicity associated with inhibitors of PI3Kαlipid kinase activity.We developed compounds that bind covalently to cysteine 242 in the RBD of PI3K p110αand block RAS activation of PI3Kαactivity.In mice,inhibitors slow the growth of RAS mutant tumors and Human Epidermal Growth Factor Receptor 2(HER2)overexpressing tumors,particularly when combined with other inhibitors of the RAS/Mitogen-activated protein kinase pathway,without causing hyperglycemia.Oncogenic mutations in the small guanosine triphosphatase RAS occur in 20%of human cancers,with RAS proteins activating both the mitogen-activated protein kinase(MAPK)and Phosphoinositide 3-kinase(PI3K)pathways(1-3).As each of these pathways has oncogenic potential,simultaneous activation,as occurs in mutant RAS driven cancers,generates aggressive disease.In RAS-driven cell and animal models,inhibition of both the MAPK and PI3K pathways is more efficacious than targeting the individual pathways(4);however,dose-limiting toxicities in humans prevent clinical success of this strategy.
基金Supported by National Natural Science Foundation of China,No.31640052and Natural Science Foundation of Shandong Province,China,No.ZR2019BH031.
文摘BACKGROUND Aberrant microRNAs expression and associated pathways have been proved participate in regulation vast various physiologic and pathologic processed of different human cancers including liver cancer.While,the function of miR-451a in liver cancer still indistinct.AIM To study the effect of miR-451a in liver cancer development.METHODS GeneChip microarray analysis performed to detect miR-451a expression in liver cancer tissues and normal liver tissues.Reverse transcription-polymerase chain reaction was used to validate the expression of miR-451a in liver cancer cell and other tumor cell lines.Construction of liver cancer cell lines that stably overexpressed miR-451a by transfecting Lentivirus produced by Genechem company.Methylthiazolyldiphenyl-tetrazolium(MTT)bromide assay and colony formation assay to determine the effect of miR-451a in liver cancer cell proliferation.Flow cytometry used to investigate whether miR-451a involved in liver cancer cell apoptosis.Cell migration ability was measured via wound scratch assay.Target gene was explored by bioinformatic analysis,and downstream molecule of miR-451a in liver cancer identified by rescue experiments.RESULTS MiR-451a expression significantly downregulation in liver cancer tissues compared with that in normal liver tissue.MiR-451a also obviously low-expressed in liver cancer cell,colorectal carcinoma cell and esophageal carcinoma cell lines.Human hepatoblastoma G2(HepG2)and BEL-7404 cell lines that stably overexpressed miR-451a by transfecting lentivirus constructed successfully.MTT bromide assay and colony formation assay showed that the overexpressed miR-451a inhibit HepG2 cell proliferation viability,but not BEL-7404 cell.Flow cytometry determined that miR-451a regulating proliferation not through inducing apoptosis.Wound scratch assay revealed that miR-451a overexpression suppressed HepG2 cell migration.Furthermore,mex-3 RNA binding family member C was predicted as the target gene by bioinformatic analysis,and rescue experiments confirmed the hypothesis.CONCLUSION Therefore,miR-451a may be candidate miRNA for understanding molecular mechanisms of liver cancer development and novel target in liver cancer cell.
基金supported by the National Natural Science Foundation of China(Grant No.12204118)the Guizhou University Talent Fund(Grant No.[2022]30).
文摘Accurate identification of RNA-ligand binding sites is essential for elucidating RNA function and advancing structurebased drug discovery.Here,we present RLsite,a novel deep learning framework that integrates energy-,structure-and sequence-based features to predict nucleotide-level binding sites with high accuracy.RLsite leverages energy-based threedimensional representations,obtained from atomic probe interactions using a pre-trained ITScore-NL potential,and models their contextual features through a 3D convolutional neural network(3D-CNN)augmented with self-attention.In parallel,structure-based features,including network properties,Laplacian norm,and solvent-accessible surface area,together with sequence-based evolutionary constraint scores,are mapped along the RNA sequence and used as sequential descriptors.These descriptors are modeled using a bidirectional long short-term memory(BiLSTM)network enhanced with multihead self-attention.By effectively fusing these complementary modalities,RLsite achieves robust and precise binding site prediction.Extensive evaluations across four diverse RNA-ligand benchmark datasets demonstrate that RLsite consistently outperforms state-of-the-art methods in terms of precision,recall,Matthews correlation coefficient(MCC),area under the curve(AUC),and overall robustness.Notably,on a particularly challenging test set composed of RNA structures containing junctions,RLsite surpasses the second-best method by 7.3%in precision,3.4%in recall,7.5%in MCC,and 10.8%in AUC,highlighting its potential as a powerful tool for RNA-targeted molecular design.
基金Supported by the Talent Launch Fund of Chongqing Medical University Affiliated University City HospitalChongqing Medical University Affiliated University City Hospital Youth Program,No.2021ZD05.
文摘BACKGROUND The exact mechanisms underlying diabetic nephropathy(DN)remain incompletely elucidated,prompting researchers to explore new perspectives and identify novel intervention targets in this field.AIM To explore the role and underlying mechanisms of farnesoid X receptor(FXR)in the development of DN by regulating endoplasmic reticulum stress(ERS)molecular chaperone binding immunoglobulin protein(BiP)expression.METHODS Bioinformatics analyses identified potential FXR-binding elements in the BiP promoter.Dual-luciferase and chromatin immunoprecipitation(ChIP)assays confirmed FXR-BiP binding sites.In vitro studies used SV40 MES 13 cells under varying glucose conditions and treatments with FXR modulators[obeticholic acid(INT-747)and guggulsterones]or BiP small interfering RNA.The expression of BiP and ERS-related proteins[protein kinase R-like endoplasmic reticulum kinase(PERK),inositol-requiring enzyme 1(IRE1),activating transcription factor 6(ATF6)]was assessed alongside cell proliferation and extracellular matrix(ECM)synthesis.In vivo studies in DN mice(db/db)examined the effects of FXR activation on renal function and morphology.RESULTS FXR bound to the target sequence in the BiP promoter region,enhancing transcriptional activity,as confirmed by ChIP experiments.FXR expression decreased in SV40 MES 13 cells stimulated with high glucose and in renal tissues of DN mice compared with control.Treatment of SV40 MES 13 cells with the FXR agonist INT-747 significantly increased intracellular BiP expression,whereas silencing the FXR gene led to the downregulation of BiP levels.In vivo administration of INT-747 significantly elevated BiP levels in renal tissues,improved renal function and fibrosis in DN mice,while inhibiting the expression of ERS-related signaling proteins PERK,IRE1,and ATF6.CONCLUSION FXR promotes BiP expression by binding to its promoter,suppressing ERS pathways,and reducing mesangial cell proliferation and ECM synthesis.These findings highlight FXR as a potential therapeutic target for diabetic glomerulosclerosis.
基金supported by NSF 2333230 (J.L.),NIH National Institute of Dental and Craniofacial Research (NIDCR) awards,DE030943 (X.H.),DE023810 (X.H.) and DE031329 (J.L.),T90 DE026110,and K99 DE033794 (to P.-T.D.)
文摘Host-derived small RNAs are emerging as critical regulators in the dynamic interactions between host tissues and the microbiome,with implications for microbial pathogenesis and host defense.Among these,transfer RNA-derived small RNAs(tsRNAs)have garnered attention for their roles in modulating microbial behavior.However,the bacterial factors mediating tsRNA interaction and functionality remain poorly understood.In this study,using RNA affinity pull-down assay in combination with mass spectrometry,we identified a putative membrane-bound protein,annotated as P-type ATPase transporter(PtaT)in Fusobacterium nucleatum(Fn),which binds Fn-targeting tsRNAs in a sequence-specific manner.Through targeted mutagenesis and phenotypic characterization,we showed that in both the Fn type strain and a clinical tumor isolate,deletion of ptaT led to reduced tsRNA intake and enhanced resistance to tsRNA-induced growth inhibition.Global RNA sequencing and label-free Raman spectroscopy revealed the phenotypic differences between Fn wild type and PtaT-deficient mutant,highlighting the functional significance of PtaT in purine and pyrimidine metabolism.Furthermore,AlphaFold 3 prediction provides evidence supporting the specific binding between PtaT and Fn-targeting tsRNA.By uncovering the first RNA-binding protein in Fn implicated in growth modulation through interactions with host-derived small RNAs(sRNAs),our study offers new insights into sRNA-mediated host-pathogen interplay within the context of microbiome-host interactions.
