Background:Excessive use of inorganic trace minerals(ITMs)in swine production leads to high fecal mineral excretion and environmental risks,while most studies on organic trace minerals(OTMs)focus on single elements,wi...Background:Excessive use of inorganic trace minerals(ITMs)in swine production leads to high fecal mineral excretion and environmental risks,while most studies on organic trace minerals(OTMs)focus on single elements,with limited data on the synergistic effects and molecular mechanisms of combined OTMs(Fe,Cu,Mn,Zn)in growing-finishing pigs.Methods:This study aimed to investigate the effects of graded levels of micromineral proteinates(combined OTMs)on growth performance,mineral metabolism,and mRNA expression of mineral regulatory proteins.A total of 360 crossbred Duroc×Landrace×Large White pigs(initial body weight 47.1±4.8 kg)were randomly assigned to 6 dietary treatments:basal diet without microminerals(CON),basal diet with ITMs at commercially recommended levels(IT),and basal diets with 15%(OT 15%),25%(OT 25%),35%(OT 35%)commercially recommended levels(CRL)of combined micromineral proteinates.After a 70-day feeding trial,samples were analyzed using ICP-OES,ELISA,and RT-qPCR.Results:Results showed that reduced levels(15-35%CRL)of micromineral proteinates did not significantly affect average daily gain,average daily feed intake,or feed conversion ratio(gain-to-feed ratio)compared to IT(P>0.05),but significantly increased plasma Cu(1.73-1.83μg/mL)and Zn(1.72-1.97μg/mL)concentrations(P<0.05)and elevated activities of Cu/Zn-superoxide dismutase(32.9-35.9 U/L)and manganese superoxide dismutase(20.5-24.1 U/L)compared to CON(P<0.05),with no significant differences from IT(P>0.05).Fecal excretion of Fe,Cu,Mn,and Zn was significantly reduced by 35-50%in OT 15%-OT 35%groups compared to IT(P<0.05).OT 25%group exhibited the highest apparent absorptivity of Fe(38.5%),Cu(27.8%),and Zn(42.4%)(P<0.05),which was associated with significantly regulated mRNA expression of mineral regulatory proteins:upregulated DMT1,FPN1,ZIP4,and MT1A in the duodenum,and modulated HAMP,ATP7B,ZIP14,and ZnT1 in the liver(P<0.05).Conclusion:In conclusion,dietary supplementation with 25%CRL or less of combined micromineral proteinates can fully meet the nutritional needs of growing-finishing pigs,improve mineral absorptivity,and reduce fecal mineral excretion by regulating intestinal and hepatic mineral transport and homeostatic proteins,providing a sustainable alternative to high-dose ITMs.展开更多
Spinal cord injury is a severe neurological condition with limited neuronal regeneration and functional recovery.Currently,no effective treatments exist to improve spinal cord injury prognosis.Neuronal guidance protei...Spinal cord injury is a severe neurological condition with limited neuronal regeneration and functional recovery.Currently,no effective treatments exist to improve spinal cord injury prognosis.Neuronal guidance proteins are a diverse group of molecules that play crucial roles in axon and dendrite growth during nervous system development.Increasing evidence highlights their regulatory functions in spinal cord injury.This review provides a brief overview of the modulation patterns of key neuronal guidance proteins in neuronal axon growth during nervous system formation and subsequently focuses on their roles in neuronal regeneration and functional recovery following spinal cord injury.Neuronal guidance proteins include,but are not limited to,semaphorins and their receptors,plexins;netrins and their receptors,deleted in colorectal cancer and UNC5;Eph receptors and their ligands,ephrins;Slit and its receptor,Robo;repulsive guidance molecules and their receptor,neogenin;Wnt proteins and their receptor,Frizzled;and protocadherins.Localized Netrin-1 at the injury site inhibits motor axon regeneration after adult spinal cord injury while promoting oligodendrocyte growth.Slit2 enhances synapse formation in the injured spinal cord of rats.EphA7 regulates acute apoptosis in the early pathophysiological stages of spinal cord injury,while ephrinA1 plays a role in the nervous system’s injury response,with its reduced expression leading to impaired motor function in rats.EphA3 is upregulated following spinal cord injury,promoting an inhibitory environment for axonal regeneration.After spinal cord injury,bidirectional activation of ephrinB2 and EphB2 in astrocytes and fibroblasts results in the formation of a dense astrocyte-meningeal fibroblast scar.EphB1/ephrinB1 signaling mediates pain processing in spinal cord injury by regulating calpain-1 and caspase-3 in neurons.EphB3 expression increases in white matter after spinal cord injury,further inhibiting axon regeneration.Sema3A,expressed by neurons and fibroblasts in the scar surrounding the injury,inhibits motor neuron and sensory nerve growth after spinal cord injury.Sema4D suppresses neuronal axon myelination and axon regeneration,while its inhibition significantly enhances axon regeneration and motor recovery.Sema7A is involved in glial scar formation and may influence serotonin channel remodeling,thereby affecting motor coordination.Given these findings,the local or systemic application of neuronal guidance proteins represents a promising avenue for spinal cord injury treatment.展开更多
The study of target proteins is crucial for understanding molecular interactions and developing analytical platforms,therapeutic agents and functional tools.Herein,we present a novel nanoplatform activated by near-inf...The study of target proteins is crucial for understanding molecular interactions and developing analytical platforms,therapeutic agents and functional tools.Herein,we present a novel nanoplatform activated by near-infrared(NIR) light for triple-modal proteins study,which enabling target protein labeling,enrichment and visualization.Azido-naphthalimide-coated upconversion nanoparticles(UCNPs) serve as NIR light-responsive nanoplatforms,showing promising applications in studying interactions between various bioactive molecules and proteins in living systems.Under NIR light irradiation,azido-naphthalimides are activated by ultraviolet(UV) and blue light emitted from UCNPs and the resulting amino-naphthalimides intermediate not only crosslink nearby target proteins but also enable imaging performance.We demonstrate that this nanoplatform is capable of selective protein labeling and imaging in complex protein environments,achieving specific labeling and imaging of both intracellular and extracellular proteins in mammalian cells as well as bacteria.Furthermore,in vivo protein labeling has been achieved using this novel NIR light-activatable nanoplatform.This technique will open new avenues for discoveries and mechanistic interrogation in chemical biology.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
Meiotic resumption in mammalian oocytes involves nuclear and organelle structural changes,notably the chromatin configuration transition from a non-surrounding nucleolus(NSN)to surrounding nucleolus(SN)in germinal ves...Meiotic resumption in mammalian oocytes involves nuclear and organelle structural changes,notably the chromatin configuration transition from a non-surrounding nucleolus(NSN)to surrounding nucleolus(SN)in germinal vesicle oocytes.In the current study,we found that nuclear speckles(NSs),a subnuclear structure mainly composed of serine-arginine(SR)proteins,changed from a diffuse spotted distribution in mouse NSN oocytes to an aggregated pattern in SN oocytes.We also found that the SR protein-specific kinase 1(SRPK1),an enzyme that phosphorylates SR proteins,co-localized with NSs at the SN stage,and that NSN oocytes failed to transition to SN oocytes after the inhibition of SRPK1 activity.Furthermore,the typical structure of the chromatin ring around the nucleolus in SN oocytes collapsed after treatment with an SRPK1 inhibitor.Mechanistically,phosphorylated SR proteins were found to be related to chromatin as shown by a salt extraction experiment,and in situ DNaseⅠassay showed that the accessibility of chromatin was enhanced in SN oocytes when SRPK1 was inhibited,accompanied by a decreased repressive modification on histone and the abnormal recurrence of a transcriptional signal.In conclusion,our results indicated that SRPK1-regulated phosphorylation of SR proteins was involved in the NSN-SN transition and played an important role in maintaining the condensed nucleus of SN oocytes via interacting with chromatin.展开更多
Creutzfeldt-Jakob disease(CJD)is a rare neurodegenerative disorder characterized by abnormalities in the prion protein(PrP),the most common form of human prion disease.Although Genome-Wide Association Studies(GWAS)hav...Creutzfeldt-Jakob disease(CJD)is a rare neurodegenerative disorder characterized by abnormalities in the prion protein(PrP),the most common form of human prion disease.Although Genome-Wide Association Studies(GWAS)have identified numerous risk genes for CJD,the mechanisms underlying these risk loci remain poorly understood.This study aims to elucidate novel genetically prioritized candidate proteins associated with CJD in the human brain through an integrative analytical pipeline.Utilizing datasets from Protein Quantitative Trait Loci(pQTL)(NpQTL1=152,NpQTL2=376),expression QTL(eQTL)(N=452),and the CJD GWAS(NCJD=4110,NControls=13569),we implemented a systematic analytical pipeline.This pipeline included Proteome-Wide Association Study(PWAS),Mendelian randomization(MR),Bayesian colocalization,and Transcriptome-Wide Association Study(TWAS)to identify novel genetically prioritized candidate proteins implicated in CJD pathogenesis within the brain.Through PWAS,we identified that the altered abundance of six brain proteins was significantly associated with CJD.Two genes,STX6 and PDIA4,were established as lead causal genes for CJD,supported by robust evidence(False Discovery Rate<0.05 in MR analysis;PP4/(PP3+PP4)≥0.75 in Bayesian colocalization).Specifically,elevated levels of STX6 and PDIA4 were associated with an increased risk of CJD.Additionally,TWAS demonstrated that STX6 and PDIA4 were associated with CJD at the transcriptional level.展开更多
BACKGROUND Ovarian cancer(OC)is the most lethal gynecological cancer among females,and its early diagnosis could help for better outcomes of the patients.AIM To investigate the utility of serum insulin-like growth fac...BACKGROUND Ovarian cancer(OC)is the most lethal gynecological cancer among females,and its early diagnosis could help for better outcomes of the patients.AIM To investigate the utility of serum insulin-like growth factors-binding proteins 2(IGFBP2),secreted phosphoprotein 1(SPP1),thrombospondin 1 protein(TSP1)and D-dimer levels in addition to currently used biomarkers[cancer antigen 125(CA125)and human epididymis protein 4(HE4)]in the diagnosis of epithelial OC(EOC).METHODS This is a case-control study that included fifty females diagnosed with EOC,10 females with benign ovarian masses recruited from the Egyptian National Cancer Institute,and 30 healthy females as a control group.All subjects were assessed for serum HE4,CA125,IGFBP2,TSP1 and SPP1 measurement by enzyme-linkedimmunosorbent assay.RESULTS There was a statistically significant difference in serum levels between EOC,benign ovarian masses,and healthy control groups regarding CA125 and SPP1(P<0.001 for both markers),while HE4 and IGFBP2 increased significantly in EOC compared to healthy control groups(P<0.001 for all markers)with no significant difference between EOC and benign ovarian masses groups.However,there was no statistically significant difference among EOC,benign ovarian masses,and healthy control groups regarding the TSP1 serum levels(P=0.051).Receiver operating characteristic analysis revealed that combined assessment of SPP1 with CA125 or TSP1 increased the diagnosis of EOC patients to a sensitivity,specificity,and area under curve of(93.3%,100%,0.968;respectively,P<0.001).CONCLUSION SPP1 may be a potential marker for the differentiation between benign and malignant ovarian masses,while IGFBP2 can differentiate between healthy females and females with ovarian masses.Combining SPP1 with CA125 or TSP1 provides high sensitivity and specificity for the detection of EOC patients.展开更多
This article summarizes recent advances in the understanding of RNA-binding proteins(RBPs),with a focus on their roles in exercise-induced mRNA regulation and their implications for schizophrenia(SZ).RBPs are critical...This article summarizes recent advances in the understanding of RNA-binding proteins(RBPs),with a focus on their roles in exercise-induced mRNA regulation and their implications for schizophrenia(SZ).RBPs are critical regulators of mRNA stability,splicing,transport,translation,and degradation,directly influencing gene expression through sequence-and structure-specific binding.In the nervous system,RBPs sustain synaptic plasticity,neural development,and neuronal homeostasis.Emerging evidence shows that exercise modulates the expression and activity of RBPs,thereby influencing mRNA translation and neurotransmitter signaling,which may underlie its beneficial effects on brain function.Dysregulation of specific RBPs has been identified in SZ,implicating them in disrupted synaptic transmission,impaired plasticity,and neuroinflammation.RBPs involved in memory and emotional regulation show marked dysfunction in SZ patients.Some RBPs have been proposed as potential biomarkers for early diagnosis and treatment monitoring.Moreover,therapeutic modulation of RBPs,through pharmacological or behavioral interventions such as exercise,may restore neuronal function by targeting post-transcriptional gene regulation.Exercise,as a non-invasive modulator of RBP expression,holds promise as an adjunctive strategy in SZ treatment,particularly in early stages.Further research into RBP-mediated pathways may offer novel insights into SZ pathophysiology and inform the development of targeted interventions.展开更多
The awn can contribute to photosynthesis and carbohydrates,enhancing grain yield in wheat.We mapped QAwn.sxau-5A,a major QTL for awn development in wheat(Triticum aestivum).This QTL was delimited to a 994-kb interval ...The awn can contribute to photosynthesis and carbohydrates,enhancing grain yield in wheat.We mapped QAwn.sxau-5A,a major QTL for awn development in wheat(Triticum aestivum).This QTL was delimited to a 994-kb interval at the B1 locus on chromosome 5A,which included the candidate gene encoding a zinc finger protein(TraesCS5A01G542800)as an awn length inhibitor(ALI).The Ali-A1 allele for the awnless trait showed abundant sequence differences in the promoter regions compared to the ali-A1 allele for the long-awn trait.The results of the swap experiment on the promoters from the two ALI-A1 alleles showed that the two promoters caused a difference in the protein level,indicating the gene was regulated at the transcript level.However,the ali-A1 allele contained an SNP that caused a premature stop codon in its coding region,resulting in a truncated protein compared to the functional Ali-A1 protein.The Ali-A1 protein contained two ethylene-responsive element binding factor-associated amphiphilic repression(EAR)motifs,one at the N terminus(EAR-N)and the other at the C terminus(EAR-C),and they were involved in interactions with the wheat co-repressor protein TOPLESS(TPL1).The ali-A1 protein retained the EAR-N motif but lost the EAR-C motif,resulting in the attenuated ability to interact with TPL1.The tpl1 mutant produced a longer awn compared to the wild type.Ali-A1 repressed the transcription of two downstream genes,TaLRP-A1 and TaARF-B1,involved in endogenous auxin concentrations and auxin responses in wheat.We concluded that the awn length is regulated not only by the ALI-A1 gene at transcript levels but also by Ali-A1 and TPL1 at the protein level in wheat.展开更多
Recognizing essential proteins within bacteriophages is fundamental to uncovering their replication and survival mechanisms and contributes to advances in phage-based antibacterial therapies.Despite notable progress,e...Recognizing essential proteins within bacteriophages is fundamental to uncovering their replication and survival mechanisms and contributes to advances in phage-based antibacterial therapies.Despite notable progress,existing computational techniques struggle to represent the interplay between sequence-derived and structuredependent protein features.To overcome this limitation,we introduce GLM-EP,a unified framework that fuses protein language models with equivariant graph neural networks.Bymerging semantic embeddings extracted from amino acid sequences with geometry-aware graph representations,GLM-EP enables an in-depth depiction of phage proteins and enhances essential protein identification.Evaluation on diverse benchmark datasets confirms that GLM-EP surpasses conventional sequence-based and independent deep-learning methods,yielding higher F1 and AUROC outcomes.Component-wise analysis demonstrates that GCNII,EGNN,and the gated multi-head attention mechanism function in a complementary manner to encode complex molecular attributes.In summary,GLM-EP serves as a robust and efficient tool for bacteriophage genomic analysis and provides valuable methodological perspectives for the discovery of antibiotic-resistance therapeutic targets.The corresponding code repository is available at:https://github.com/MiJia-ID/GLM-EP(accessed on 01 November 2025).展开更多
Biomolecular condensates,also known as membraneless organelles,play a crucial role in cellular organization by concentrating or sequestering biomolecules.Despite their importance,synthetically mimicking these organell...Biomolecular condensates,also known as membraneless organelles,play a crucial role in cellular organization by concentrating or sequestering biomolecules.Despite their importance,synthetically mimicking these organelles using non-peptidic small organic molecules has posed a significant challenge.The present study reports the discovery of D008,a self-assembling small molecule that sequesters a unique subset of RNA-binding proteins.Analysis and screening of a comprehensive collection of approximately 1 million compounds in the Chinese National Compound Library(Shanghai)identified 44 self-assembling small molecules in aqueous solutions.Subsequent screening of the focused library,coupled with proteome analysis,led to the discovery of D008 as a small organic molecule with the ability to condensate a specific subset of RNA-binding proteins.In vitro experiments demonstrated that the D008-induced sequestration of RNA-binding proteins impeded mRNA translation.D008 may offer a unique opportunity for studying the condensations of RNA-binding proteins and for developing an unprecedented class of small molecules that control gene expression.展开更多
Objective Recent studies have overturned the traditional concept of the lung as a “sterile organ” revealing that pulmonary microbiota dysbiosis and abnormal surfactant proteins(SPs) expression are involved in the pr...Objective Recent studies have overturned the traditional concept of the lung as a “sterile organ” revealing that pulmonary microbiota dysbiosis and abnormal surfactant proteins(SPs) expression are involved in the progression of silicosis. This study aimed to investigate the relationship between abnormal SPs expression and dysbiosis of lung microbiota in silica-induced lung fibrosis, providing insights into mechanisms of silicosis.Methods Lung pathology, SPs expression, and microbiota composition were evaluated in silicaexposed mice. A mouse model of antibiotic-induced microbiota depletion was established, and alveolar structure and SPs expression were assessed. The roles of the lung microbiota and SPs in silicosis progression were further evaluated in mice with antibiotic-induced microbiota depletion, both with and without silica exposure.Results Silica exposure induced lung inflammation and fibrosis, along with increased expression of SPA expression. Antibiotics(Abx)-induced microbiota depletion elevated SP-A and SP-D expression.Furthermore, silica exposure altered lung microbiota composition, enriching potentially pathogenic taxa.However, antibiotic-induced microbiota depletion prior to silica exposure reduced silica-mediated lung fibrosis and inflammation.Conclusion Lung microbiota is associated with silica-induced lung injury. Overproduction of SP-A and SP-D, induced by Abx-induced microbiota depletion, may enhance the resistance of mouse lung tissue to silica-induced injury.展开更多
Identifying druggable proteins,which are capable of binding therapeutic compounds,remains a critical and resource-intensive challenge in drug discovery.To address this,we propose CEL-IDP(Comparison of Ensemble Learnin...Identifying druggable proteins,which are capable of binding therapeutic compounds,remains a critical and resource-intensive challenge in drug discovery.To address this,we propose CEL-IDP(Comparison of Ensemble Learning Methods for Identification of Druggable Proteins),a computational framework combining three feature extraction methods Dipeptide Deviation from Expected Mean(DDE),Enhanced Amino Acid Composition(EAAC),and Enhanced Grouped Amino Acid Composition(EGAAC)with ensemble learning strategies(Bagging,Boosting,Stacking)to classify druggable proteins from sequence data.DDE captures dipeptide frequency deviations,EAAC encodes positional amino acid information,and EGAAC groups residues by physicochemical properties to generate discriminative feature vectors.These features were analyzed using ensemble models to overcome the limitations of single classifiers.EGAAC outperformed DDE and EAAC,with Random Forest(Bagging)and XGBoost(Boosting)achieving the highest accuracy of 71.66%,demonstrating superior performance in capturing critical biochemical patterns.Stacking showed intermediate results(68.33%),while EAAC and DDE-based models yielded lower accuracies(56.66%–66.87%).CEL-IDP streamlines large-scale druggability prediction,reduces reliance on costly experimental screening,and aligns with global initiatives like Target 2035 to expand action-able drug targets.This work advances machine learning-driven drug discovery by systematizing feature engineering and ensemble model optimization,providing a scalable workflow to accelerate target identification and validation.展开更多
Tyrosine residues in proteins can be nitrated to form 3-nitrotyrosine(3-NT)under the influence of ozone(O_(3))and nitrogen dioxide(NO_(2))in the air,which may introduce health impacts.A selective and sensitive enzyme-...Tyrosine residues in proteins can be nitrated to form 3-nitrotyrosine(3-NT)under the influence of ozone(O_(3))and nitrogen dioxide(NO_(2))in the air,which may introduce health impacts.A selective and sensitive enzyme-linked-immunoassay(ELISA)method was developed to determine 3-NT in modified model protein(bovine serum albumin,BSA)and ambient aerosol samples.The nitration degrees(NDs)of BSA in the exposure experiments with different durations were detected by both the ELISA and spectrophotometric methods(i.e.,ND_(ELISA) and ND_(SEC-PDA)),which show good coincidence.The kinetic investigation by both ΔND_(ELISA) and ΔND_(SEC-PDA) in the exposure experiments shows that the rate coefficients(k)of the pseudo-first-order kinetic rate reactions of protein nitration were comparable.These results indicate that direct detection of 3-NT by the ELISA method can be applied for laboratory exposure samples analysis for kinetic studies.Based on the selective detection of 3-NT,ND_(ELISA) provides a promising measure for the assessment of ND in model proteins.3-NT was alsomeasured in PM_(2.5) samples in summer in Guangzhou,southern China,ranging from 10.1 to 404 pg/m^(3),providing clear evidence of protein nitration in ambient aerosols.We further proposed that 3-NT/protein can be used as a proxy to evaluate protein nitration in ambient aerosols.A significant correlationwas observed between 3-NT/protein and O_(3),confirming the crucial role of O_(3) in protein nitration.Our results show that the direct detection of 3-NT by the ELISA method can be more widely applied in the laboratory and field-based studies for understanding the mechanisms of protein nitration.展开更多
Bromodomain(BRD)-containing proteins are central mediators of gene regulation,serving as key components of chromatin remodeling complexes and histone recognition scaffolds.By specifically recognizing acetylated lysine...Bromodomain(BRD)-containing proteins are central mediators of gene regulation,serving as key components of chromatin remodeling complexes and histone recognition scaffolds.By specifically recognizing acetylated lysine residues on histones(Kac)via their conserved BRD,these proteins influence chromatin structure and gene expression.Although their overarching role is well-established,the precise molecular functions and mechanisms of individual BRD proteins remain incompletely characterized.The ciliate Tetrahymena thermophila,a unicellular eukaryote with a transcriptionally active macronucleus enriched in histone acetylation,is an excellent model for exploring the significance of BRD-containing proteins.In this comprehensive review,all BRD-containing proteins encoded in the T.thermophila genome are systematically examined,including their expression profiles,histone acetylation targets,interacting proteins,and potential roles.This review lays the groundwork for future investigations into the complex roles of BRD proteins in chromatin remodeling and transcription regulation,offering insights into basic eukaryotic biology and the molecular mechanisms underlying BRD-linked diseases.展开更多
Vesicles of lipid bilayer can adopt a variety of shapes due to different coating proteins.The ability of proteins to reshape membrane is typically characterized by inducing spontaneous curvature of the membrane at the...Vesicles of lipid bilayer can adopt a variety of shapes due to different coating proteins.The ability of proteins to reshape membrane is typically characterized by inducing spontaneous curvature of the membrane at the coated area.BAR family proteins are known to have a crescent shape and can induce membrane curvature along their concaved body axis but not in the perpendicular direction.We model this type of proteins as a rod-shaped molecule with an orientation and induce normal curvature along its orientation in the tangential plane of the membrane surface.We show how a ring of these proteins reshapes an axisymmetric vesicle when the protein curvature or orientation is varied.A discontinuous shape transformation from a protrusion shape without a neck to a one with a neck is found.Increasing the rigidity of the protein ring is able to smooth out the transition.Furthermore,we show that varying the protein orientation is able to induce an hourglass-shaped neck,which is significantly narrower than the reciprocal of the protein curvature.Our results offer a new angle to rationalize the helical structure formed by many proteins that carry out membrane fission functions.展开更多
The escalating global temperature,with 2024 as the hottest year,emphasizes the critical link between climate change and kidney health.Extreme heat,a conse-quence of global warming,causes multifaceted effects on human ...The escalating global temperature,with 2024 as the hottest year,emphasizes the critical link between climate change and kidney health.Extreme heat,a conse-quence of global warming,causes multifaceted effects on human physiology,including renal function alterations.This review investigates physiological and molecular mechanisms of heat stress-induced kidney injury,including acute kidney injury,chronic kidney disease(CKD),and urinary stone formation.It highlights how heat stress contributes to renal dysfunction via dehydration,electrolyte imbalances,and activation of the renin-angiotensin-aldosterone system and antidiuretic hormone pathways,particularly in vulnerable populations like outdoor workers,the elderly,and pregnant women.The review also emphasizes the roles of heat shock proteins(HSPs)-HSP27,HSP60,HSP70,and HSP90-in maintaining cellular integrity by preventing protein aggregation and repairing damaged proteins in renal tissues.Dysregulation of these proteins under prolonged heat stress is implicated in CKD progression.This review highlights the urgent need for targeted public health interventions:(1)Hydration;(2)Workplace cooling;(3)Community education;and(4)Developing pharmaco-logical therapies targeting HSPs.A multidisciplinary approach involving nephrology,environmental science,and public health is essential to mitigate the increasing burden of heat-related kidney disease in the era of global climate change.展开更多
Essential proteins are crucial for biological processes and can be identified through both experimental and computational methods.While experimental approaches are highly accurate,they often demand extensive time and ...Essential proteins are crucial for biological processes and can be identified through both experimental and computational methods.While experimental approaches are highly accurate,they often demand extensive time and resources.To address these challenges,we present a computational ensemble learning framework designed to identify essential proteins more efficiently.Our method begins by using node2vec to transform proteins in the protein–protein interaction(PPI)network into continuous,low-dimensional vectors.We also extract a range of features from protein sequences,including graph-theory-based,information-based,compositional,and physiochemical attributes.Additionally,we leverage deep learning techniques to analyze high-dimensional position-specific scoring matrices(PSSMs)and capture evolutionary information.We then combine these features for classification using various machine learning algorithms.To enhance performance,we integrate the outputs of these algorithms through ensemble methods such as voting,weighted averaging,and stacking.This approach effectively addresses data imbalances and improves both robustness and accuracy.Our ensemble learning framework achieves an AUC of 0.960 and an accuracy of 0.9252,outperforming other computational methods.These results demonstrate the effectiveness of our approach in accurately identifying essential proteins and highlight its superior feature extraction capabilities.展开更多
Bioactive peptides and proteins(BAPPs)are promising therapeutic agents for tissue repair with considerable advantages,including multifunctionality,specificity,biocompatibility,and biodegradability.However,the high com...Bioactive peptides and proteins(BAPPs)are promising therapeutic agents for tissue repair with considerable advantages,including multifunctionality,specificity,biocompatibility,and biodegradability.However,the high complexity of tissue microenvironments and their inherent deficiencies such as short half-live and susceptibility to enzymatic degradation,adversely affect their therapeutic efficacy and clinical applications.Investigating the fundamental mechanisms by which BAPPs modulate the microenvironment and developing rational delivery strategies are essential for optimizing their administration in distinct tissue repairs and facilitating clinical translation.This review initially focuses on the mechanisms through which BAPPs influence the microenvironment for tissue repair via reactive oxygen species,blood and lymphatic vessels,immune cells,and repair cells.Then,a variety of delivery platforms,including scaffolds and hydrogels,electrospun fibers,surface coatings,assisted particles,nanotubes,two-dimensional nanomaterials,and nanoparticles engineered cells,are summarized to incorporate BAPPs for effective tissue repair,modification strategies aimed at enhancing loading efficiencies and release kinetics are also reviewed.Additionally,the delivery of BAPPs can be precisely regulated by endogenous stimuli(glucose,reactive oxygen species,enzymes,pH)or exogenous stimuli(ultrasound,heat,light,magnetic field,and electric field)to achieve on-demand release tailored for specific tissue repair needs.Furthermore,this review focuses on the clinical potential of BAPPs in facilitating tissue repair across various types,including bone,cartilage,intervertebral discs,muscle,tendons,periodontal tissues,skin,myocardium,nervous system(encompassing brain,spinal cord,and peripheral nerve),endometrium,as well as ear and ocular tissue.Finally,current challenges and prospects are discussed.展开更多
Intrinsically disordered proteins(IDPs)and their regions(IDRs)play crucial roles in cellular func-tions despite their lack of stable three-dimensional structures.In this study,we investigate the interac-tions between ...Intrinsically disordered proteins(IDPs)and their regions(IDRs)play crucial roles in cellular func-tions despite their lack of stable three-dimensional structures.In this study,we investigate the interac-tions between the C-terminal do-main of protein 4.1G(4.1G CTD)and the nuclear mitotic apparatus protein(NuMA)under varying pH and salt ion conditions to under-stand the regulatory mechanisms affecting their binding.4.1G CTD and NuMA bind effec-tively under neutral and alkaline conditions,but their interaction is disrupted under acidic conditions(pH 3.6).The protonation of positively charged residues at the C-terminal of 4.1G CTD under acidic conditions leads to increased electrostatic repulsion,weakening the overall binding free energy.Secondary structure analysis shows that specific regions of 4.1G CTD re-main stable under both pH conditions,but the C-terminal region(aa 990−1000)and the N-terminal region of NuMA(aa 1800−1810)exhibit significant reductions in secondary struc-ture probability under acidic conditions.Contact map analysis and solvent-accessible surface area analysis further support these findings by showing a reduced contact probability be-tween these regions under pH 3.6.These results provide a comprehensive understanding of how pH and ionic strength regulate the binding dynamics of 4.1G CTD and NuMA,emphasiz-ing the regulatory role of electrostatic interactions.展开更多
基金financially supported by the Hainan Province Science and Technology Special Fund(Grant no:ZDYF2024XDNY187).
文摘Background:Excessive use of inorganic trace minerals(ITMs)in swine production leads to high fecal mineral excretion and environmental risks,while most studies on organic trace minerals(OTMs)focus on single elements,with limited data on the synergistic effects and molecular mechanisms of combined OTMs(Fe,Cu,Mn,Zn)in growing-finishing pigs.Methods:This study aimed to investigate the effects of graded levels of micromineral proteinates(combined OTMs)on growth performance,mineral metabolism,and mRNA expression of mineral regulatory proteins.A total of 360 crossbred Duroc×Landrace×Large White pigs(initial body weight 47.1±4.8 kg)were randomly assigned to 6 dietary treatments:basal diet without microminerals(CON),basal diet with ITMs at commercially recommended levels(IT),and basal diets with 15%(OT 15%),25%(OT 25%),35%(OT 35%)commercially recommended levels(CRL)of combined micromineral proteinates.After a 70-day feeding trial,samples were analyzed using ICP-OES,ELISA,and RT-qPCR.Results:Results showed that reduced levels(15-35%CRL)of micromineral proteinates did not significantly affect average daily gain,average daily feed intake,or feed conversion ratio(gain-to-feed ratio)compared to IT(P>0.05),but significantly increased plasma Cu(1.73-1.83μg/mL)and Zn(1.72-1.97μg/mL)concentrations(P<0.05)and elevated activities of Cu/Zn-superoxide dismutase(32.9-35.9 U/L)and manganese superoxide dismutase(20.5-24.1 U/L)compared to CON(P<0.05),with no significant differences from IT(P>0.05).Fecal excretion of Fe,Cu,Mn,and Zn was significantly reduced by 35-50%in OT 15%-OT 35%groups compared to IT(P<0.05).OT 25%group exhibited the highest apparent absorptivity of Fe(38.5%),Cu(27.8%),and Zn(42.4%)(P<0.05),which was associated with significantly regulated mRNA expression of mineral regulatory proteins:upregulated DMT1,FPN1,ZIP4,and MT1A in the duodenum,and modulated HAMP,ATP7B,ZIP14,and ZnT1 in the liver(P<0.05).Conclusion:In conclusion,dietary supplementation with 25%CRL or less of combined micromineral proteinates can fully meet the nutritional needs of growing-finishing pigs,improve mineral absorptivity,and reduce fecal mineral excretion by regulating intestinal and hepatic mineral transport and homeostatic proteins,providing a sustainable alternative to high-dose ITMs.
基金supported by Shenzhen University General Hospital Scientific Research Project,No.SUGH2019QD002Shenzhen Science and Technology Development Foundation,No.20220810173216001(both to ZS).
文摘Spinal cord injury is a severe neurological condition with limited neuronal regeneration and functional recovery.Currently,no effective treatments exist to improve spinal cord injury prognosis.Neuronal guidance proteins are a diverse group of molecules that play crucial roles in axon and dendrite growth during nervous system development.Increasing evidence highlights their regulatory functions in spinal cord injury.This review provides a brief overview of the modulation patterns of key neuronal guidance proteins in neuronal axon growth during nervous system formation and subsequently focuses on their roles in neuronal regeneration and functional recovery following spinal cord injury.Neuronal guidance proteins include,but are not limited to,semaphorins and their receptors,plexins;netrins and their receptors,deleted in colorectal cancer and UNC5;Eph receptors and their ligands,ephrins;Slit and its receptor,Robo;repulsive guidance molecules and their receptor,neogenin;Wnt proteins and their receptor,Frizzled;and protocadherins.Localized Netrin-1 at the injury site inhibits motor axon regeneration after adult spinal cord injury while promoting oligodendrocyte growth.Slit2 enhances synapse formation in the injured spinal cord of rats.EphA7 regulates acute apoptosis in the early pathophysiological stages of spinal cord injury,while ephrinA1 plays a role in the nervous system’s injury response,with its reduced expression leading to impaired motor function in rats.EphA3 is upregulated following spinal cord injury,promoting an inhibitory environment for axonal regeneration.After spinal cord injury,bidirectional activation of ephrinB2 and EphB2 in astrocytes and fibroblasts results in the formation of a dense astrocyte-meningeal fibroblast scar.EphB1/ephrinB1 signaling mediates pain processing in spinal cord injury by regulating calpain-1 and caspase-3 in neurons.EphB3 expression increases in white matter after spinal cord injury,further inhibiting axon regeneration.Sema3A,expressed by neurons and fibroblasts in the scar surrounding the injury,inhibits motor neuron and sensory nerve growth after spinal cord injury.Sema4D suppresses neuronal axon myelination and axon regeneration,while its inhibition significantly enhances axon regeneration and motor recovery.Sema7A is involved in glial scar formation and may influence serotonin channel remodeling,thereby affecting motor coordination.Given these findings,the local or systemic application of neuronal guidance proteins represents a promising avenue for spinal cord injury treatment.
基金supported by the National Natural Science Foundation of China (No.22007008)the LiaoNing Revitalization Talents Program (No.XLYC1907021)the Fundamental Research Funds for the Central Universities (Nos.DUT23YG120,DUT19RC(3)009)。
文摘The study of target proteins is crucial for understanding molecular interactions and developing analytical platforms,therapeutic agents and functional tools.Herein,we present a novel nanoplatform activated by near-infrared(NIR) light for triple-modal proteins study,which enabling target protein labeling,enrichment and visualization.Azido-naphthalimide-coated upconversion nanoparticles(UCNPs) serve as NIR light-responsive nanoplatforms,showing promising applications in studying interactions between various bioactive molecules and proteins in living systems.Under NIR light irradiation,azido-naphthalimides are activated by ultraviolet(UV) and blue light emitted from UCNPs and the resulting amino-naphthalimides intermediate not only crosslink nearby target proteins but also enable imaging performance.We demonstrate that this nanoplatform is capable of selective protein labeling and imaging in complex protein environments,achieving specific labeling and imaging of both intracellular and extracellular proteins in mammalian cells as well as bacteria.Furthermore,in vivo protein labeling has been achieved using this novel NIR light-activatable nanoplatform.This technique will open new avenues for discoveries and mechanistic interrogation in chemical biology.
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National Natural Science Foundation of China(Grant Nos.32070838 and 82301874)Open Fund of State Key Laboratory of Reproductive Medicine,Nanjing Medical University(Grant No.SKLRM K202102)。
文摘Meiotic resumption in mammalian oocytes involves nuclear and organelle structural changes,notably the chromatin configuration transition from a non-surrounding nucleolus(NSN)to surrounding nucleolus(SN)in germinal vesicle oocytes.In the current study,we found that nuclear speckles(NSs),a subnuclear structure mainly composed of serine-arginine(SR)proteins,changed from a diffuse spotted distribution in mouse NSN oocytes to an aggregated pattern in SN oocytes.We also found that the SR protein-specific kinase 1(SRPK1),an enzyme that phosphorylates SR proteins,co-localized with NSs at the SN stage,and that NSN oocytes failed to transition to SN oocytes after the inhibition of SRPK1 activity.Furthermore,the typical structure of the chromatin ring around the nucleolus in SN oocytes collapsed after treatment with an SRPK1 inhibitor.Mechanistically,phosphorylated SR proteins were found to be related to chromatin as shown by a salt extraction experiment,and in situ DNaseⅠassay showed that the accessibility of chromatin was enhanced in SN oocytes when SRPK1 was inhibited,accompanied by a decreased repressive modification on histone and the abnormal recurrence of a transcriptional signal.In conclusion,our results indicated that SRPK1-regulated phosphorylation of SR proteins was involved in the NSN-SN transition and played an important role in maintaining the condensed nucleus of SN oocytes via interacting with chromatin.
文摘Creutzfeldt-Jakob disease(CJD)is a rare neurodegenerative disorder characterized by abnormalities in the prion protein(PrP),the most common form of human prion disease.Although Genome-Wide Association Studies(GWAS)have identified numerous risk genes for CJD,the mechanisms underlying these risk loci remain poorly understood.This study aims to elucidate novel genetically prioritized candidate proteins associated with CJD in the human brain through an integrative analytical pipeline.Utilizing datasets from Protein Quantitative Trait Loci(pQTL)(NpQTL1=152,NpQTL2=376),expression QTL(eQTL)(N=452),and the CJD GWAS(NCJD=4110,NControls=13569),we implemented a systematic analytical pipeline.This pipeline included Proteome-Wide Association Study(PWAS),Mendelian randomization(MR),Bayesian colocalization,and Transcriptome-Wide Association Study(TWAS)to identify novel genetically prioritized candidate proteins implicated in CJD pathogenesis within the brain.Through PWAS,we identified that the altered abundance of six brain proteins was significantly associated with CJD.Two genes,STX6 and PDIA4,were established as lead causal genes for CJD,supported by robust evidence(False Discovery Rate<0.05 in MR analysis;PP4/(PP3+PP4)≥0.75 in Bayesian colocalization).Specifically,elevated levels of STX6 and PDIA4 were associated with an increased risk of CJD.Additionally,TWAS demonstrated that STX6 and PDIA4 were associated with CJD at the transcriptional level.
文摘BACKGROUND Ovarian cancer(OC)is the most lethal gynecological cancer among females,and its early diagnosis could help for better outcomes of the patients.AIM To investigate the utility of serum insulin-like growth factors-binding proteins 2(IGFBP2),secreted phosphoprotein 1(SPP1),thrombospondin 1 protein(TSP1)and D-dimer levels in addition to currently used biomarkers[cancer antigen 125(CA125)and human epididymis protein 4(HE4)]in the diagnosis of epithelial OC(EOC).METHODS This is a case-control study that included fifty females diagnosed with EOC,10 females with benign ovarian masses recruited from the Egyptian National Cancer Institute,and 30 healthy females as a control group.All subjects were assessed for serum HE4,CA125,IGFBP2,TSP1 and SPP1 measurement by enzyme-linkedimmunosorbent assay.RESULTS There was a statistically significant difference in serum levels between EOC,benign ovarian masses,and healthy control groups regarding CA125 and SPP1(P<0.001 for both markers),while HE4 and IGFBP2 increased significantly in EOC compared to healthy control groups(P<0.001 for all markers)with no significant difference between EOC and benign ovarian masses groups.However,there was no statistically significant difference among EOC,benign ovarian masses,and healthy control groups regarding the TSP1 serum levels(P=0.051).Receiver operating characteristic analysis revealed that combined assessment of SPP1 with CA125 or TSP1 increased the diagnosis of EOC patients to a sensitivity,specificity,and area under curve of(93.3%,100%,0.968;respectively,P<0.001).CONCLUSION SPP1 may be a potential marker for the differentiation between benign and malignant ovarian masses,while IGFBP2 can differentiate between healthy females and females with ovarian masses.Combining SPP1 with CA125 or TSP1 provides high sensitivity and specificity for the detection of EOC patients.
文摘This article summarizes recent advances in the understanding of RNA-binding proteins(RBPs),with a focus on their roles in exercise-induced mRNA regulation and their implications for schizophrenia(SZ).RBPs are critical regulators of mRNA stability,splicing,transport,translation,and degradation,directly influencing gene expression through sequence-and structure-specific binding.In the nervous system,RBPs sustain synaptic plasticity,neural development,and neuronal homeostasis.Emerging evidence shows that exercise modulates the expression and activity of RBPs,thereby influencing mRNA translation and neurotransmitter signaling,which may underlie its beneficial effects on brain function.Dysregulation of specific RBPs has been identified in SZ,implicating them in disrupted synaptic transmission,impaired plasticity,and neuroinflammation.RBPs involved in memory and emotional regulation show marked dysfunction in SZ patients.Some RBPs have been proposed as potential biomarkers for early diagnosis and treatment monitoring.Moreover,therapeutic modulation of RBPs,through pharmacological or behavioral interventions such as exercise,may restore neuronal function by targeting post-transcriptional gene regulation.Exercise,as a non-invasive modulator of RBP expression,holds promise as an adjunctive strategy in SZ treatment,particularly in early stages.Further research into RBP-mediated pathways may offer novel insights into SZ pathophysiology and inform the development of targeted interventions.
基金supported by the Grand Science and Technology Special Project in Shanxi Province(202201140601025-2)the National Natural Science Foundation of China(32201749)supported by the Agriculture and Food Research Initiative Competitive Grant 2022-68013-36439(WheatCAP)from the USDA National Institute of Food and Agriculture.
文摘The awn can contribute to photosynthesis and carbohydrates,enhancing grain yield in wheat.We mapped QAwn.sxau-5A,a major QTL for awn development in wheat(Triticum aestivum).This QTL was delimited to a 994-kb interval at the B1 locus on chromosome 5A,which included the candidate gene encoding a zinc finger protein(TraesCS5A01G542800)as an awn length inhibitor(ALI).The Ali-A1 allele for the awnless trait showed abundant sequence differences in the promoter regions compared to the ali-A1 allele for the long-awn trait.The results of the swap experiment on the promoters from the two ALI-A1 alleles showed that the two promoters caused a difference in the protein level,indicating the gene was regulated at the transcript level.However,the ali-A1 allele contained an SNP that caused a premature stop codon in its coding region,resulting in a truncated protein compared to the functional Ali-A1 protein.The Ali-A1 protein contained two ethylene-responsive element binding factor-associated amphiphilic repression(EAR)motifs,one at the N terminus(EAR-N)and the other at the C terminus(EAR-C),and they were involved in interactions with the wheat co-repressor protein TOPLESS(TPL1).The ali-A1 protein retained the EAR-N motif but lost the EAR-C motif,resulting in the attenuated ability to interact with TPL1.The tpl1 mutant produced a longer awn compared to the wild type.Ali-A1 repressed the transcription of two downstream genes,TaLRP-A1 and TaARF-B1,involved in endogenous auxin concentrations and auxin responses in wheat.We concluded that the awn length is regulated not only by the ALI-A1 gene at transcript levels but also by Ali-A1 and TPL1 at the protein level in wheat.
基金supported in part by funds from the Ministry of Science and Technology(2022FY101104).
文摘Recognizing essential proteins within bacteriophages is fundamental to uncovering their replication and survival mechanisms and contributes to advances in phage-based antibacterial therapies.Despite notable progress,existing computational techniques struggle to represent the interplay between sequence-derived and structuredependent protein features.To overcome this limitation,we introduce GLM-EP,a unified framework that fuses protein language models with equivariant graph neural networks.Bymerging semantic embeddings extracted from amino acid sequences with geometry-aware graph representations,GLM-EP enables an in-depth depiction of phage proteins and enhances essential protein identification.Evaluation on diverse benchmark datasets confirms that GLM-EP surpasses conventional sequence-based and independent deep-learning methods,yielding higher F1 and AUROC outcomes.Component-wise analysis demonstrates that GCNII,EGNN,and the gated multi-head attention mechanism function in a complementary manner to encode complex molecular attributes.In summary,GLM-EP serves as a robust and efficient tool for bacteriophage genomic analysis and provides valuable methodological perspectives for the discovery of antibiotic-resistance therapeutic targets.The corresponding code repository is available at:https://github.com/MiJia-ID/GLM-EP(accessed on 01 November 2025).
基金supported by JSPS(No.22H00350 to M.U.)Ministry of Health&Welfare,Republic of Korea(Korea Health Technology R&D Project through the Korea Health Industry Development Institute,No.HI19C1234 to H.K.)+3 种基金JST(the Establishment of University Fellowships towards the Creation of Science Technology Innovation,No.JPMJFS2123 to K.T.)supported and inspired by the International Collaborative Research Program of Institute for Chemical Research,Kyoto University(No.2024-84)Kyoto University On-Site Lab(Fudan-Kyoto Shanghai Lab)the international and interdisciplinary environments of JSPS CORE-to-CORE Program“Asian Chemical Biology Initiative”.
文摘Biomolecular condensates,also known as membraneless organelles,play a crucial role in cellular organization by concentrating or sequestering biomolecules.Despite their importance,synthetically mimicking these organelles using non-peptidic small organic molecules has posed a significant challenge.The present study reports the discovery of D008,a self-assembling small molecule that sequesters a unique subset of RNA-binding proteins.Analysis and screening of a comprehensive collection of approximately 1 million compounds in the Chinese National Compound Library(Shanghai)identified 44 self-assembling small molecules in aqueous solutions.Subsequent screening of the focused library,coupled with proteome analysis,led to the discovery of D008 as a small organic molecule with the ability to condensate a specific subset of RNA-binding proteins.In vitro experiments demonstrated that the D008-induced sequestration of RNA-binding proteins impeded mRNA translation.D008 may offer a unique opportunity for studying the condensations of RNA-binding proteins and for developing an unprecedented class of small molecules that control gene expression.
基金supported by the National Natural Science Foundation of China Joint Fund for Regional Innovation and Development(Grant numbers [U21A20334])the Postgraduate Innovation Funding Project of Hebei Province(Grant numbers [CXZZBS2022116])。
文摘Objective Recent studies have overturned the traditional concept of the lung as a “sterile organ” revealing that pulmonary microbiota dysbiosis and abnormal surfactant proteins(SPs) expression are involved in the progression of silicosis. This study aimed to investigate the relationship between abnormal SPs expression and dysbiosis of lung microbiota in silica-induced lung fibrosis, providing insights into mechanisms of silicosis.Methods Lung pathology, SPs expression, and microbiota composition were evaluated in silicaexposed mice. A mouse model of antibiotic-induced microbiota depletion was established, and alveolar structure and SPs expression were assessed. The roles of the lung microbiota and SPs in silicosis progression were further evaluated in mice with antibiotic-induced microbiota depletion, both with and without silica exposure.Results Silica exposure induced lung inflammation and fibrosis, along with increased expression of SPA expression. Antibiotics(Abx)-induced microbiota depletion elevated SP-A and SP-D expression.Furthermore, silica exposure altered lung microbiota composition, enriching potentially pathogenic taxa.However, antibiotic-induced microbiota depletion prior to silica exposure reduced silica-mediated lung fibrosis and inflammation.Conclusion Lung microbiota is associated with silica-induced lung injury. Overproduction of SP-A and SP-D, induced by Abx-induced microbiota depletion, may enhance the resistance of mouse lung tissue to silica-induced injury.
基金supported by the MSIT(Ministry of Science and ICT),Korea,under the ITRC(Information Technology Research Centre)support program(IITP-2024-RS-2024-00437191)supervised by the IITP(Institute for Information&Communications Technology Planning&Evaluation).
文摘Identifying druggable proteins,which are capable of binding therapeutic compounds,remains a critical and resource-intensive challenge in drug discovery.To address this,we propose CEL-IDP(Comparison of Ensemble Learning Methods for Identification of Druggable Proteins),a computational framework combining three feature extraction methods Dipeptide Deviation from Expected Mean(DDE),Enhanced Amino Acid Composition(EAAC),and Enhanced Grouped Amino Acid Composition(EGAAC)with ensemble learning strategies(Bagging,Boosting,Stacking)to classify druggable proteins from sequence data.DDE captures dipeptide frequency deviations,EAAC encodes positional amino acid information,and EGAAC groups residues by physicochemical properties to generate discriminative feature vectors.These features were analyzed using ensemble models to overcome the limitations of single classifiers.EGAAC outperformed DDE and EAAC,with Random Forest(Bagging)and XGBoost(Boosting)achieving the highest accuracy of 71.66%,demonstrating superior performance in capturing critical biochemical patterns.Stacking showed intermediate results(68.33%),while EAAC and DDE-based models yielded lower accuracies(56.66%–66.87%).CEL-IDP streamlines large-scale druggability prediction,reduces reliance on costly experimental screening,and aligns with global initiatives like Target 2035 to expand action-able drug targets.This work advances machine learning-driven drug discovery by systematizing feature engineering and ensemble model optimization,providing a scalable workflow to accelerate target identification and validation.
基金supported by the National Natural Science Foundation of China(No.41975156).
文摘Tyrosine residues in proteins can be nitrated to form 3-nitrotyrosine(3-NT)under the influence of ozone(O_(3))and nitrogen dioxide(NO_(2))in the air,which may introduce health impacts.A selective and sensitive enzyme-linked-immunoassay(ELISA)method was developed to determine 3-NT in modified model protein(bovine serum albumin,BSA)and ambient aerosol samples.The nitration degrees(NDs)of BSA in the exposure experiments with different durations were detected by both the ELISA and spectrophotometric methods(i.e.,ND_(ELISA) and ND_(SEC-PDA)),which show good coincidence.The kinetic investigation by both ΔND_(ELISA) and ΔND_(SEC-PDA) in the exposure experiments shows that the rate coefficients(k)of the pseudo-first-order kinetic rate reactions of protein nitration were comparable.These results indicate that direct detection of 3-NT by the ELISA method can be applied for laboratory exposure samples analysis for kinetic studies.Based on the selective detection of 3-NT,ND_(ELISA) provides a promising measure for the assessment of ND in model proteins.3-NT was alsomeasured in PM_(2.5) samples in summer in Guangzhou,southern China,ranging from 10.1 to 404 pg/m^(3),providing clear evidence of protein nitration in ambient aerosols.We further proposed that 3-NT/protein can be used as a proxy to evaluate protein nitration in ambient aerosols.A significant correlationwas observed between 3-NT/protein and O_(3),confirming the crucial role of O_(3) in protein nitration.Our results show that the direct detection of 3-NT by the ELISA method can be more widely applied in the laboratory and field-based studies for understanding the mechanisms of protein nitration.
基金supported by the National Natural Science Foundation of China(32200399 to Y.W.,32125006 to S.G.)Natural Science Foundation of Shandong Province(ZR2024ZD40 to S.G.,ZR2024MC112 to Y.W.)+4 种基金Young Talent of Lifting Engineering for Science and Technology in Shandong,China(SDAST2024QTA008 to Y.W.)Fundamental Research Funds for the Central Universities(202441014 to Y.W.)Postdoctoral Fellowship Program of the China Postdoctoral Science Foundation(CPSF)(GZC20232503 to Y.L.)China Postdoctoral Science Foundation(2024M753050 to Y.L.)Laoshan Laboratory(LSKJ202203203 to S.G.)。
文摘Bromodomain(BRD)-containing proteins are central mediators of gene regulation,serving as key components of chromatin remodeling complexes and histone recognition scaffolds.By specifically recognizing acetylated lysine residues on histones(Kac)via their conserved BRD,these proteins influence chromatin structure and gene expression.Although their overarching role is well-established,the precise molecular functions and mechanisms of individual BRD proteins remain incompletely characterized.The ciliate Tetrahymena thermophila,a unicellular eukaryote with a transcriptionally active macronucleus enriched in histone acetylation,is an excellent model for exploring the significance of BRD-containing proteins.In this comprehensive review,all BRD-containing proteins encoded in the T.thermophila genome are systematically examined,including their expression profiles,histone acetylation targets,interacting proteins,and potential roles.This review lays the groundwork for future investigations into the complex roles of BRD proteins in chromatin remodeling and transcription regulation,offering insights into basic eukaryotic biology and the molecular mechanisms underlying BRD-linked diseases.
基金support from the the National Natural Science Foundation of China(Grant Nos.12474199(RM)and 12374213(YC))Fundamental Research Funds for Central Universities of China(Grant No.20720240144(RM))111 Project(Grant No.B16029).
文摘Vesicles of lipid bilayer can adopt a variety of shapes due to different coating proteins.The ability of proteins to reshape membrane is typically characterized by inducing spontaneous curvature of the membrane at the coated area.BAR family proteins are known to have a crescent shape and can induce membrane curvature along their concaved body axis but not in the perpendicular direction.We model this type of proteins as a rod-shaped molecule with an orientation and induce normal curvature along its orientation in the tangential plane of the membrane surface.We show how a ring of these proteins reshapes an axisymmetric vesicle when the protein curvature or orientation is varied.A discontinuous shape transformation from a protrusion shape without a neck to a one with a neck is found.Increasing the rigidity of the protein ring is able to smooth out the transition.Furthermore,we show that varying the protein orientation is able to induce an hourglass-shaped neck,which is significantly narrower than the reciprocal of the protein curvature.Our results offer a new angle to rationalize the helical structure formed by many proteins that carry out membrane fission functions.
文摘The escalating global temperature,with 2024 as the hottest year,emphasizes the critical link between climate change and kidney health.Extreme heat,a conse-quence of global warming,causes multifaceted effects on human physiology,including renal function alterations.This review investigates physiological and molecular mechanisms of heat stress-induced kidney injury,including acute kidney injury,chronic kidney disease(CKD),and urinary stone formation.It highlights how heat stress contributes to renal dysfunction via dehydration,electrolyte imbalances,and activation of the renin-angiotensin-aldosterone system and antidiuretic hormone pathways,particularly in vulnerable populations like outdoor workers,the elderly,and pregnant women.The review also emphasizes the roles of heat shock proteins(HSPs)-HSP27,HSP60,HSP70,and HSP90-in maintaining cellular integrity by preventing protein aggregation and repairing damaged proteins in renal tissues.Dysregulation of these proteins under prolonged heat stress is implicated in CKD progression.This review highlights the urgent need for targeted public health interventions:(1)Hydration;(2)Workplace cooling;(3)Community education;and(4)Developing pharmaco-logical therapies targeting HSPs.A multidisciplinary approach involving nephrology,environmental science,and public health is essential to mitigate the increasing burden of heat-related kidney disease in the era of global climate change.
基金financially supported by the National Key R&D Program of China(Grant No.2022YFF1202600)the National Natural Science Foundation of China(Grant No.82301158)+4 种基金Science and Technology Innovation Action Plan of Shanghai Science and Technology Committee(Grant No.22015820100)Two-hundred Talent Support(Grant No.20152224)Translational Medicine Innovation Project of Shanghai Jiao Tong University School of Medicine(Grant No.TM201915)Clinical Research Project of Multi-Disciplinary Team,Shanghai Ninth People’s Hospital,Shanghai Jiao Tong University School of Medicine(Grant No.201914)China Postdoctoral Science Foundation(Grant No.2023M742332)。
文摘Essential proteins are crucial for biological processes and can be identified through both experimental and computational methods.While experimental approaches are highly accurate,they often demand extensive time and resources.To address these challenges,we present a computational ensemble learning framework designed to identify essential proteins more efficiently.Our method begins by using node2vec to transform proteins in the protein–protein interaction(PPI)network into continuous,low-dimensional vectors.We also extract a range of features from protein sequences,including graph-theory-based,information-based,compositional,and physiochemical attributes.Additionally,we leverage deep learning techniques to analyze high-dimensional position-specific scoring matrices(PSSMs)and capture evolutionary information.We then combine these features for classification using various machine learning algorithms.To enhance performance,we integrate the outputs of these algorithms through ensemble methods such as voting,weighted averaging,and stacking.This approach effectively addresses data imbalances and improves both robustness and accuracy.Our ensemble learning framework achieves an AUC of 0.960 and an accuracy of 0.9252,outperforming other computational methods.These results demonstrate the effectiveness of our approach in accurately identifying essential proteins and highlight its superior feature extraction capabilities.
基金supported by the National Natural Science Foundation of China(82372405,81871752)the Key Research and Development Program of Hubei Province(2022BCA052)+2 种基金the Key Research and Development Program of Wuhan City(2024020702030105)the Fundamental Research Funds for the Central Universities(2042023kf0199)the Translational Medicine and Interdisciplinary Research Joint Fund of Zhongnan Hospital of Wuhan University(ZNJC202014).
文摘Bioactive peptides and proteins(BAPPs)are promising therapeutic agents for tissue repair with considerable advantages,including multifunctionality,specificity,biocompatibility,and biodegradability.However,the high complexity of tissue microenvironments and their inherent deficiencies such as short half-live and susceptibility to enzymatic degradation,adversely affect their therapeutic efficacy and clinical applications.Investigating the fundamental mechanisms by which BAPPs modulate the microenvironment and developing rational delivery strategies are essential for optimizing their administration in distinct tissue repairs and facilitating clinical translation.This review initially focuses on the mechanisms through which BAPPs influence the microenvironment for tissue repair via reactive oxygen species,blood and lymphatic vessels,immune cells,and repair cells.Then,a variety of delivery platforms,including scaffolds and hydrogels,electrospun fibers,surface coatings,assisted particles,nanotubes,two-dimensional nanomaterials,and nanoparticles engineered cells,are summarized to incorporate BAPPs for effective tissue repair,modification strategies aimed at enhancing loading efficiencies and release kinetics are also reviewed.Additionally,the delivery of BAPPs can be precisely regulated by endogenous stimuli(glucose,reactive oxygen species,enzymes,pH)or exogenous stimuli(ultrasound,heat,light,magnetic field,and electric field)to achieve on-demand release tailored for specific tissue repair needs.Furthermore,this review focuses on the clinical potential of BAPPs in facilitating tissue repair across various types,including bone,cartilage,intervertebral discs,muscle,tendons,periodontal tissues,skin,myocardium,nervous system(encompassing brain,spinal cord,and peripheral nerve),endometrium,as well as ear and ocular tissue.Finally,current challenges and prospects are discussed.
基金supported by the National Natural Science Foundation of China(No.22073018,No.22377015).
文摘Intrinsically disordered proteins(IDPs)and their regions(IDRs)play crucial roles in cellular func-tions despite their lack of stable three-dimensional structures.In this study,we investigate the interac-tions between the C-terminal do-main of protein 4.1G(4.1G CTD)and the nuclear mitotic apparatus protein(NuMA)under varying pH and salt ion conditions to under-stand the regulatory mechanisms affecting their binding.4.1G CTD and NuMA bind effec-tively under neutral and alkaline conditions,but their interaction is disrupted under acidic conditions(pH 3.6).The protonation of positively charged residues at the C-terminal of 4.1G CTD under acidic conditions leads to increased electrostatic repulsion,weakening the overall binding free energy.Secondary structure analysis shows that specific regions of 4.1G CTD re-main stable under both pH conditions,but the C-terminal region(aa 990−1000)and the N-terminal region of NuMA(aa 1800−1810)exhibit significant reductions in secondary struc-ture probability under acidic conditions.Contact map analysis and solvent-accessible surface area analysis further support these findings by showing a reduced contact probability be-tween these regions under pH 3.6.These results provide a comprehensive understanding of how pH and ionic strength regulate the binding dynamics of 4.1G CTD and NuMA,emphasiz-ing the regulatory role of electrostatic interactions.
