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
The events of cell death and the expression of nuclear matrix protein (NMP) have been investigated in a promyelocytic leukemic cell line HL-60 induced with etoposide. By means of TUNEL assay, the nuclei displayed a ch...The events of cell death and the expression of nuclear matrix protein (NMP) have been investigated in a promyelocytic leukemic cell line HL-60 induced with etoposide. By means of TUNEL assay, the nuclei displayed a characteristic morphology change, and the amount of apoptotic cells increased early and reached maximun about 39% after treatment with etoposide for 2 h. Nucleosomal DNA fragmentation was observed after treatment for 4 h. The morphological change of HL-60 cells, thus, occurred earlier than the appearance of DNA ladder. Total nuclear matrix proteins were analyzed by 2-dimensional gel electrophoresis. Differential expression of 59 nuclear matrix proteins was found in 4 h etoposide treated cells. Western blotting was then performed on three nuclear matrix acssociated proteins, PML, HSC70 and NuMA. The expression of the suppressor PML protein and heat shock protein HSC70 were significantly upregulated after etoposide treatment, while NuMA, a nuclear mitotic apparatus protein, was down regulated. These results demonstrate that significant biochemical alterations in nuclear matrix proteins take place during the apoptotic process.展开更多
A variety of glycosylphosphatidylinositol （GPI）-linked proteins are acquired on spermatozoa from epididymal luminal fluids （ELF） during sperm maturation. These proteins serve roles in immunoprotection and in key s...A variety of glycosylphosphatidylinositol （GPI）-linked proteins are acquired on spermatozoa from epididymal luminal fluids （ELF） during sperm maturation. These proteins serve roles in immunoprotection and in key steps of fertilization such as capacitation, acrosomal exocytosis and sperm-egg interactions. Their acquisition on sperm cells is mediated both by membrane vesicles （epididymosomes, EP） which were first reported to dock on the sperm surface, and by lipid carriers which facilitate the transfer of proteins associated with the membrane-free fraction of ELF. While the nonvesicular fraction is more efficient, both pathways are dependent on hydrophobic interactions between the GPI-anchor and the external lipid layer of the sperm surface. More recently proteomic and hypothesis-driven studies have shown that EP from several mammals carry transmembrane （TM） proteins, including plasma membrane Ca^2＋-ATPase 4 （PMCA4）. Synthesized in the testis, PMCA4 is an essential protein and the major Ca^2＋ efflux pump in murine spermatozoa. Delivery of PMCA4 to spermatozoa from bovine and mouse EP during epididymal maturation and in vitro suggests that the docking of EP on the sperm surface precedes fusion, and experimental evidence supports a fusogenic mechanism for TM proteins. Fusion is facilitated by CD9, which generates fusion-competent sites on membranes. On the basis of knowledge of PMCA4＇s interacting partners a number of TM and membrane-associated proteins have been identified or are predicted to be present, in the epididymosomal cargo deliverable to spermatozoa. These Ca^2＋-dependent proteins, undetected in proteomic studies, play essential roles in sperm motility and fertility, and their detection highlights the usefulness of the hypothesis-driven approach.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
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
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
AIM:To explore the causal links among circulating inflammatory proteins(CIPs)and the varying severities of diabetic retinopathy(DR).METHODS:This research utilized a two sample Mendelian randomization(MR)approach to ex...AIM:To explore the causal links among circulating inflammatory proteins(CIPs)and the varying severities of diabetic retinopathy(DR).METHODS:This research utilized a two sample Mendelian randomization(MR)approach to explore the causal relationships between 91 CIPs and various severities of DR:background DR(BDR)or non-proliferative DR(NPDR),and proliferative DR(PDR).Single-nucleotide polymorphisms(SNPs)related to the 91 CIPs as exposure factors were identified.These SNPs were selected from an extensive genome-wide association study(GWAS)analyzing large genomic datasets.Genetic variation data of various DR phenotypes provided by the FinnGen collaboration were utilized as outcomes.Inverse-variance weighting(IVW)was used as the main MR analysis.Robustness of study results was evaluated through a series of sensitivity analyses,employing the MR-pleiotropy-test and mendelian randomization pleiotropy residual sum and outlier(MR-PRESSO)to confirm the absence of pleiotropy.RESULTS:In a bidirectional MR analysis,we uncovered a complex relationship between CIPs and DR.Elevated levels of tumor necrosis factor ligand superfamily member 14(TNFSF14),latency associated peptide transforming growth factors beta-1(LAP-TGF-beta1),interleukin-10(IL-10),and vascular endothelial growth factor A(VEGF-A)were associated with a reduced risk of NPDR.Conversely,elevated levels of fibroblast growth factor 23(FGF-23)were associated with an increased risk of NPDR.Concentrations of adenosine deaminase(ADA),matrix metalloproteinase-10(MMP-10),eotaxin,and IL-10 showed elevated levels and were linked to a reduced risk of NPDR.On the other hand,the levels of oncostatin-M,beta-nerve growth factor(β-NGF),and interleukin-7(IL-7)were elevated and associated with an increased risk of SNPDR.Elevated levels of ADA,MMP-10,and macrophage colony-stimulating factor 1(CSF1)were linked to a lower likelihood of PDR.Conversely,elevated levels of Caspase 8 and glial cell line-derived neurotrophic factor(GDNF)were associated with an increased risk of PDR.In reverse MR analysis,DR affected the expression of these factors.CONCLUSION:Our research demonstrates evidence supporting a potential causal link between key inflammatory factors and the risk and prognosis of various DR phenotypes.These findings emphasize the regulation of inflammatory factors responses as a strategic approach for preventing and managing DR.Altogether,our results validate the pathogenic role of inflammatory factors dysregulation in DR and support the rationale for exploring immunotherapeutic targets further.展开更多
Essential proteins are an indispensable part of cells and play an extremely significant role in genetic disease diagnosis and drug development.Therefore,the prediction of essential proteins has received extensive atte...Essential proteins are an indispensable part of cells and play an extremely significant role in genetic disease diagnosis and drug development.Therefore,the prediction of essential proteins has received extensive attention from researchers.Many centrality methods and machine learning algorithms have been proposed to predict essential proteins.Nevertheless,the topological characteristics learned by the centrality method are not comprehensive enough,resulting in low accuracy.In addition,machine learning algorithms need sufficient prior knowledge to select features,and the ability to solve imbalanced classification problems needs to be further strengthened.These two factors greatly affect the performance of predicting essential proteins.In this paper,we propose a deep learning framework based on temporal convolutional networks to predict essential proteins by integrating gene expression data and protein-protein interaction(PPI)network.We make use of the method of network embedding to automatically learn more abundant features of proteins in the PPI network.For gene expression data,we treat it as sequence data,and use temporal convolutional networks to extract sequence features.Finally,the two types of features are integrated and put into the multi-layer neural network to complete the final classification task.The performance of our method is evaluated by comparing with seven centrality methods,six machine learning algorithms,and two deep learning models.The results of the experiment show that our method is more effective than the comparison methods for predicting essential proteins.展开更多
Background The aim of this study was to determine whether and how Zn proteinate with moderate chelation strength(Zn-Prot M)can alleviate heat stress(HS)-induced intestinal barrier function damage of broilers.A complet...Background The aim of this study was to determine whether and how Zn proteinate with moderate chelation strength(Zn-Prot M)can alleviate heat stress(HS)-induced intestinal barrier function damage of broilers.A completely randomized design was used for comparatively testing the effects of Zn proteinate on HS and non-HS broilers.Under high temperature(HT),a 1(Control,HT-CON)+2(Zn source)×2(added Zn level)factorial arrangement of treatments was used.The 2 added Zn sources were Zn-Prot M and Zn sulfate(ZnS),and the 2 added Zn levels were 30 and 60 mg/kg.Under normal temperature(NT),a CON group(NT-CON)and pair-fed group(NT-PF)were included.Results The results showed that HS significantly reduced mRNA and protein expression levels of claudin-1,occludin,junctional adhesion molecule-A(JAMA),zonula occludens-1(ZO-1)and zinc finger protein A20(A20)in the jejunum,and HS also remarkably increased serum fluorescein isothiocyanate dextran(FITC-D),endotoxin and interleukin(IL)-1βcontents,serum diamine oxidase(DAO)and matrix metalloproteinase(MMP)-2 activities,nuclear factor kappa-B(NF-κB)p65 mRNA expression level,and protein expression levels of NF-κB p65 and MMP-2 in the jejunum.However,dietary supplementation with Zn,especially organic Zn as Zn-Prot M at 60 mg/kg,significantly decreased serum FITC-D,endotoxin and IL-1βcontents,serum DAO and MMP-2 activities,NF-κB p65 mRNA expression level,and protein expression levels of NF-κB p65 and MMP-2 in the jejunum of HS broilers,and notably promoted mRNA and protein expression levels of claudin-1,ZO-1 and A20.Conclusions Our results suggest that dietary Zn,especially 60 mg Zn/kg as Zn-Prot M,can alleviate HS-induced intestinal barrier function damage by promoting the expression of TJ proteins possibly via induction of A20-mediated suppression of the NF-κB p65/MMP-2 pathway in the jejunum of HS broilers.展开更多
AIM: To study the epitope distribution of hepatitis G virus (HGV) and to seek for the potential recombinant antigens for the development of HGV diagnostic reagents. METHODS: Fourteen clones encompassing HGV gene fragm...AIM: To study the epitope distribution of hepatitis G virus (HGV) and to seek for the potential recombinant antigens for the development of HGV diagnostic reagents. METHODS: Fourteen clones encompassing HGV gene fragments from core to NS3 and NS5 were constructed using prokaryotic expression vector pRSET and (or) pGEX, and expressed in E.coli. Western blotting and ELISA were used to detect the immunoreactivity of these recombinant proteins. RESULTS: One clone with HGV fragment from core to E1 (G1), one from E2 (G31), three from NS3 (G6, G61, G7), one from NS5B (G821) and one chimeric fragment from NS3 and NS5B (G61-821) could be expressed well and showed obvious immunoreactivity by Western blotting. One clone with HGV framment from NS5B (G82) was also well expressed, but could not show immunoreactivity by Western blotting. No obvious expression was found in the other six clones. All the expressed recombinant proteins were in inclusion body form, except the protein G61 which could be expressed in soluble form. Further purified recombinant proteins G1, G31, G61, G821 and G61-821 were detected in indirected ELISA as coating antigen respectively. Only recombinant G1 could still show immunoreactivity, and the other four recombinant proteins failed to react to the HGV antibody positive sera. Western blotting results indicated that the immunoactivity of these four recombinant proteins were lost during purification. CONCLUSION: Core to E1, E2, NS3 and NS5 fragment of HGV contain antigenic epitopes, which could be produced in prokaryotically expressed recombinant proteins. A high-yield recombinant protein (G1) located in HGV core to E1 could remain its epitope after purification, which showed the potential that G1 could be used as a coating antigen to develop an ELISA kit for HGV specific antibody diagnosis.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.
文摘The events of cell death and the expression of nuclear matrix protein (NMP) have been investigated in a promyelocytic leukemic cell line HL-60 induced with etoposide. By means of TUNEL assay, the nuclei displayed a characteristic morphology change, and the amount of apoptotic cells increased early and reached maximun about 39% after treatment with etoposide for 2 h. Nucleosomal DNA fragmentation was observed after treatment for 4 h. The morphological change of HL-60 cells, thus, occurred earlier than the appearance of DNA ladder. Total nuclear matrix proteins were analyzed by 2-dimensional gel electrophoresis. Differential expression of 59 nuclear matrix proteins was found in 4 h etoposide treated cells. Western blotting was then performed on three nuclear matrix acssociated proteins, PML, HSC70 and NuMA. The expression of the suppressor PML protein and heat shock protein HSC70 were significantly upregulated after etoposide treatment, while NuMA, a nuclear mitotic apparatus protein, was down regulated. These results demonstrate that significant biochemical alterations in nuclear matrix proteins take place during the apoptotic process.
文摘A variety of glycosylphosphatidylinositol （GPI）-linked proteins are acquired on spermatozoa from epididymal luminal fluids （ELF） during sperm maturation. These proteins serve roles in immunoprotection and in key steps of fertilization such as capacitation, acrosomal exocytosis and sperm-egg interactions. Their acquisition on sperm cells is mediated both by membrane vesicles （epididymosomes, EP） which were first reported to dock on the sperm surface, and by lipid carriers which facilitate the transfer of proteins associated with the membrane-free fraction of ELF. While the nonvesicular fraction is more efficient, both pathways are dependent on hydrophobic interactions between the GPI-anchor and the external lipid layer of the sperm surface. More recently proteomic and hypothesis-driven studies have shown that EP from several mammals carry transmembrane （TM） proteins, including plasma membrane Ca^2＋-ATPase 4 （PMCA4）. Synthesized in the testis, PMCA4 is an essential protein and the major Ca^2＋ efflux pump in murine spermatozoa. Delivery of PMCA4 to spermatozoa from bovine and mouse EP during epididymal maturation and in vitro suggests that the docking of EP on the sperm surface precedes fusion, and experimental evidence supports a fusogenic mechanism for TM proteins. Fusion is facilitated by CD9, which generates fusion-competent sites on membranes. On the basis of knowledge of PMCA4＇s interacting partners a number of TM and membrane-associated proteins have been identified or are predicted to be present, in the epididymosomal cargo deliverable to spermatozoa. These Ca^2＋-dependent proteins, undetected in proteomic studies, play essential roles in sperm motility and fertility, and their detection highlights the usefulness of the hypothesis-driven approach.
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.
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 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.
基金Supported by Natural Science Foundation of Hubei Province(No.2023AFC019,No.2020CFB240)Hubei Key Laboratories Opening Project(No.2023KFH019,No.2021KFY055)Fundamental Research Funds for Central Universities(No.2042020kf0065).
文摘AIM:To explore the causal links among circulating inflammatory proteins(CIPs)and the varying severities of diabetic retinopathy(DR).METHODS:This research utilized a two sample Mendelian randomization(MR)approach to explore the causal relationships between 91 CIPs and various severities of DR:background DR(BDR)or non-proliferative DR(NPDR),and proliferative DR(PDR).Single-nucleotide polymorphisms(SNPs)related to the 91 CIPs as exposure factors were identified.These SNPs were selected from an extensive genome-wide association study(GWAS)analyzing large genomic datasets.Genetic variation data of various DR phenotypes provided by the FinnGen collaboration were utilized as outcomes.Inverse-variance weighting(IVW)was used as the main MR analysis.Robustness of study results was evaluated through a series of sensitivity analyses,employing the MR-pleiotropy-test and mendelian randomization pleiotropy residual sum and outlier(MR-PRESSO)to confirm the absence of pleiotropy.RESULTS:In a bidirectional MR analysis,we uncovered a complex relationship between CIPs and DR.Elevated levels of tumor necrosis factor ligand superfamily member 14(TNFSF14),latency associated peptide transforming growth factors beta-1(LAP-TGF-beta1),interleukin-10(IL-10),and vascular endothelial growth factor A(VEGF-A)were associated with a reduced risk of NPDR.Conversely,elevated levels of fibroblast growth factor 23(FGF-23)were associated with an increased risk of NPDR.Concentrations of adenosine deaminase(ADA),matrix metalloproteinase-10(MMP-10),eotaxin,and IL-10 showed elevated levels and were linked to a reduced risk of NPDR.On the other hand,the levels of oncostatin-M,beta-nerve growth factor(β-NGF),and interleukin-7(IL-7)were elevated and associated with an increased risk of SNPDR.Elevated levels of ADA,MMP-10,and macrophage colony-stimulating factor 1(CSF1)were linked to a lower likelihood of PDR.Conversely,elevated levels of Caspase 8 and glial cell line-derived neurotrophic factor(GDNF)were associated with an increased risk of PDR.In reverse MR analysis,DR affected the expression of these factors.CONCLUSION:Our research demonstrates evidence supporting a potential causal link between key inflammatory factors and the risk and prognosis of various DR phenotypes.These findings emphasize the regulation of inflammatory factors responses as a strategic approach for preventing and managing DR.Altogether,our results validate the pathogenic role of inflammatory factors dysregulation in DR and support the rationale for exploring immunotherapeutic targets further.
基金the National Natural Science Foundation of China(Nos.11861045 and 62162040)。
文摘Essential proteins are an indispensable part of cells and play an extremely significant role in genetic disease diagnosis and drug development.Therefore,the prediction of essential proteins has received extensive attention from researchers.Many centrality methods and machine learning algorithms have been proposed to predict essential proteins.Nevertheless,the topological characteristics learned by the centrality method are not comprehensive enough,resulting in low accuracy.In addition,machine learning algorithms need sufficient prior knowledge to select features,and the ability to solve imbalanced classification problems needs to be further strengthened.These two factors greatly affect the performance of predicting essential proteins.In this paper,we propose a deep learning framework based on temporal convolutional networks to predict essential proteins by integrating gene expression data and protein-protein interaction(PPI)network.We make use of the method of network embedding to automatically learn more abundant features of proteins in the PPI network.For gene expression data,we treat it as sequence data,and use temporal convolutional networks to extract sequence features.Finally,the two types of features are integrated and put into the multi-layer neural network to complete the final classification task.The performance of our method is evaluated by comparing with seven centrality methods,six machine learning algorithms,and two deep learning models.The results of the experiment show that our method is more effective than the comparison methods for predicting essential proteins.
基金Key International Cooperation Program of the National Natural Science Foundation of China(32120103011)Jiangsu Shuang Chuang Tuan Dui program(JSSCTD202147)+1 种基金Jiangsu Shuang Chuang Ren Cai program(JSSCRC2021541)Initiation Funds of Yangzhou University for Distinguished Scientists.
文摘Background The aim of this study was to determine whether and how Zn proteinate with moderate chelation strength(Zn-Prot M)can alleviate heat stress(HS)-induced intestinal barrier function damage of broilers.A completely randomized design was used for comparatively testing the effects of Zn proteinate on HS and non-HS broilers.Under high temperature(HT),a 1(Control,HT-CON)+2(Zn source)×2(added Zn level)factorial arrangement of treatments was used.The 2 added Zn sources were Zn-Prot M and Zn sulfate(ZnS),and the 2 added Zn levels were 30 and 60 mg/kg.Under normal temperature(NT),a CON group(NT-CON)and pair-fed group(NT-PF)were included.Results The results showed that HS significantly reduced mRNA and protein expression levels of claudin-1,occludin,junctional adhesion molecule-A(JAMA),zonula occludens-1(ZO-1)and zinc finger protein A20(A20)in the jejunum,and HS also remarkably increased serum fluorescein isothiocyanate dextran(FITC-D),endotoxin and interleukin(IL)-1βcontents,serum diamine oxidase(DAO)and matrix metalloproteinase(MMP)-2 activities,nuclear factor kappa-B(NF-κB)p65 mRNA expression level,and protein expression levels of NF-κB p65 and MMP-2 in the jejunum.However,dietary supplementation with Zn,especially organic Zn as Zn-Prot M at 60 mg/kg,significantly decreased serum FITC-D,endotoxin and IL-1βcontents,serum DAO and MMP-2 activities,NF-κB p65 mRNA expression level,and protein expression levels of NF-κB p65 and MMP-2 in the jejunum of HS broilers,and notably promoted mRNA and protein expression levels of claudin-1,ZO-1 and A20.Conclusions Our results suggest that dietary Zn,especially 60 mg Zn/kg as Zn-Prot M,can alleviate HS-induced intestinal barrier function damage by promoting the expression of TJ proteins possibly via induction of A20-mediated suppression of the NF-κB p65/MMP-2 pathway in the jejunum of HS broilers.
基金Supported by National 863 Project,No.102-07-02-079th Five-Year Sci-Tech Plan,No.96-906A-03-08
文摘AIM: To study the epitope distribution of hepatitis G virus (HGV) and to seek for the potential recombinant antigens for the development of HGV diagnostic reagents. METHODS: Fourteen clones encompassing HGV gene fragments from core to NS3 and NS5 were constructed using prokaryotic expression vector pRSET and (or) pGEX, and expressed in E.coli. Western blotting and ELISA were used to detect the immunoreactivity of these recombinant proteins. RESULTS: One clone with HGV fragment from core to E1 (G1), one from E2 (G31), three from NS3 (G6, G61, G7), one from NS5B (G821) and one chimeric fragment from NS3 and NS5B (G61-821) could be expressed well and showed obvious immunoreactivity by Western blotting. One clone with HGV framment from NS5B (G82) was also well expressed, but could not show immunoreactivity by Western blotting. No obvious expression was found in the other six clones. All the expressed recombinant proteins were in inclusion body form, except the protein G61 which could be expressed in soluble form. Further purified recombinant proteins G1, G31, G61, G821 and G61-821 were detected in indirected ELISA as coating antigen respectively. Only recombinant G1 could still show immunoreactivity, and the other four recombinant proteins failed to react to the HGV antibody positive sera. Western blotting results indicated that the immunoactivity of these four recombinant proteins were lost during purification. CONCLUSION: Core to E1, E2, NS3 and NS5 fragment of HGV contain antigenic epitopes, which could be produced in prokaryotically expressed recombinant proteins. A high-yield recombinant protein (G1) located in HGV core to E1 could remain its epitope after purification, which showed the potential that G1 could be used as a coating antigen to develop an ELISA kit for HGV specific antibody diagnosis.
